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• ACID
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ACID
In computer science, ACID (Atomicity,
Consistency, Isolation, Durability) is a set of
properties that guarantee that database
transactions are processed reliably. In the
context of databases, a single logical
operation on the data is called a transaction.
For example, a transfer of funds from one
bank account to another, even involving
multiple changes such as debiting one
account and crediting another, is a single
transaction. The chosen initials refer to the
acid test.
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ACID
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Jim Gray defined these properties of a
reliable transaction system in the late
1970s and developed technologies to
achieve them automatically.
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ACID
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In 1983, Andreas Reuter and Theo Härder coined
the acronym ACID to describe them.
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ACID Atomicity
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Atomicity requires that each transaction is
"all or nothing": if one part of the
transaction fails, the entire transaction
fails, and the database state is left
unchanged. An atomic system must
guarantee atomicity in each and every
situation, including power failures, errors,
and crashes. To the outside world, a
committed transaction appears (by its
effects on the database) to be indivisible
("atomic"), and an aborted transaction
does not happen.
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ACID Consistency
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The consistency property ensures that any
transaction will bring the database from
one valid state to another
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ACID Isolation
The isolation property ensures that the
concurrent execution of transactions
results in a system state that would be
obtained if transactions were executed
serially, i.e. one after the other. Providing
isolation is the main goal of concurrency
control. Depending on concurrency control
method, the effects of an incomplete
transaction might not even be visible to
another transaction.
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ACID Durability
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Durability means that once a transaction
has been committed, it will remain so,
even in the event of power loss, crashes,
or errors. In a relational database, for
instance, once a group of SQL statements
execute, the results need to be stored
permanently (even if the database crashes
immediately thereafter). To defend against
power loss, transactions (or their effects)
must be recorded in a non-volatile
memory.
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ACID Examples
The following examples further
illustrate the ACID properties. In
these examples, the database table
has two columns, A and B. An integrity
constraint requires that the value in A
and the value in B must sum to 100.
The following SQL code creates a
table as described above:
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ACID Atomicity failure
Assume that a transaction attempts to
subtract 10 from A and add 10 to B. This is
a valid transaction, since the data continue
to satisfy the constraint after it has
executed. However, assume that after
removing 10 from A, the transaction is
unable to modify B. If the database
retained A's new value, atomicity and the
constraint would both be violated.
Atomicity requires that both parts of this
transaction, or neither, be complete.
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ACID Consistency failure
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Consistency is a very general term
which demands that the data must
meet all validation rules. In the
previous example, the validation is a
requirement that A + B = 100. Also, it
may be inferred that both A and B
must be integers. A valid range for A
and B may also be inferred. All
validation rules must be checked to
ensure consistency.
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ACID Consistency failure
Assume that a
transaction attempts
to subtract 10 from A
without altering B
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ACID Isolation failure
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To demonstrate isolation, we assume
two transactions execute at the same
time, each attempting to modify the
same data. One of the two must wait
until the other completes in order to
maintain isolation.
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ACID Isolation failure
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Consider two transactions. T1 transfers
10 from A to B. T2 transfers 10 from B
to A. Combined, there are four actions:
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ACID Isolation failure
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If these operations are performed in
order, isolation is maintained,
although T2 must wait. Consider what
happens if T1 fails half-way through.
The database eliminates T1's effects,
and T2 sees only valid data.
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ACID Isolation failure
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By interleaving the
transactions, the
actual order of
actions might be:
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ACID Isolation failure
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Again, consider what happens if
T1 fails halfway through
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ACID Durability failure
Assume that a transaction transfers 10
from A to B. It removes 10 from A. It then
adds 10 to B. At this point, a "success"
message is sent to the user. However, the
changes are still queued in the disk buffer
waiting to be committed to the disk. Power
fails and the changes are lost. The user
assumes (understandably) that the
changes have been made.
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ACID Implementation
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Processing a transaction often requires a
sequence of operations that is subject to
failure for a number of reasons. For
instance, the system may have no room
left on its disk drives, or it may have used
up its allocated CPU time.
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ACID Implementation
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There are two popular families of techniques:
write ahead logging and shadow paging. In
both cases, locks must be acquired on all
information that is updated, and depending
on the level of isolation, possibly on all data
that is read as well. In write ahead logging,
atomicity is guaranteed by copying the
original (unchanged) data to a log before
changing the database.[dubious – discuss]
That allows the database to return to a
consistent state in the event of a crash.
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ACID Implementation
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In shadowing, updates are applied to a
partial copy of the database, and the new
copy is activated when the transaction
commits.
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ACID Locking vs multiversioning
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Many databases rely
upon locking to
provide ACID
capabilities
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ACID Locking vs multiversioning
An alternative to locking is multiversion
concurrency control, in which the database
provides each reading transaction the
prior, unmodified version of data that is
being modified by another active
transaction
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ACID Distributed transactions
Guaranteeing ACID properties in a
distributed transaction across a distributed
database where no single node is
responsible for all data affecting a
transaction presents additional
complications
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Concurrency control Database transaction and the ACID rules
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The concept of a database transaction (or
atomic transaction) has evolved in order to
enable both a well understood database
system behavior in a faulty environment
where crashes can happen any time, and
recovery from a crash to a well understood
database state
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Concurrency control Database transaction and the ACID rules
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Atomicity - Either the effects of all or none
of its operations remain ("all or nothing"
semantics) when a transaction is
completed (committed or aborted
respectively). In other words, to the
outside world a committed transaction
appears (by its effects on the database) to
be indivisible, atomic, and an aborted
transaction does not leave effects on the
database at all, as if never existed.
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Concurrency control Database transaction and the ACID rules
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Consistency - Every transaction must
leave the database in a consistent
(correct) state, i.e., maintain the
predetermined integrity rules of the
database (constraints upon and among
the database's objects)
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Concurrency control Database transaction and the ACID rules
Isolation - Transactions cannot interfere
with each other (as an end result of their
executions). Moreover, usually (depending
on concurrency control method) the effects
of an incomplete transaction are not even
visible to another transaction. Providing
isolation is the main goal of concurrency
control.
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Concurrency control Database transaction and the ACID rules
Durability - Effects of successful
(committed) transactions must persist
through crashes (typically by
recording the transaction's effects and
its commit event in a non-volatile
memory).
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Concurrency control Database transaction and the ACID rules
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The concept of atomic transaction has
been extended during the years to what
has become Business transactions
which actually implement types of
Workflow and are not atomic. However
also such enhanced transactions
typically utilize atomic transactions as
components.
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Polylactic acid
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Solubility in water
Insoluble in Water
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Polylactic acid
Polylactic acid or polylactide (PLA) is a
thermoplastic aliphatic polyester derived
from renewable resources, such as corn
starch (in the United States), tapioca roots,
chips or starch (mostly in Asia), or
sugarcane (in the rest of the world). In
2010, PLA was the second most important
bioplastic of the world in regard to
consumption volume.
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Polylactic acid
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The name "polylactic acid" does not
comply with IUPAC standard
nomenclature, and is potentially
ambiguous or confusing, because PLA
is not a polyacid (polyelectrolyte), but
rather a polyester.
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Polylactic acid - Production
There are several industrial routes to
usable (i.e. high molecular weight) PLA.
Two main monomers are used: lactic
acid, and the cyclic di-ester, lactide. The
most common route to PLA is the ringopening polymerization of lactide with
various metal catalysts (typically tin
octoate) in solution, in the melt, or as a
suspension. The metal-catalyzed
reaction tends to cause racemization of
the PLA, reducing its stereoregularity
compared to the starting material.
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Polylactic acid - Production
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Carboxylic acid and alcohol end groups
are thus concentrated in the amorphous
region of the solid polymer, and so they
can react
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Polylactic acid - Production
This compound is more reactive than
lactide, because its polymerization is
driven by the loss of one equivalent of
carbon dioxide per equivalent of lactic acid
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Polylactic acid - Manufacturers
Galactic and Total Petrochemicals
operate a joint venture, Futerro, which
is developing a second generation
polylactic acid product
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Polylactic acid - Manufacturers
Since 2009, PURAC has been
producing lactides D and L monomers for PLA production - at a
plant in Spain with a production
capacity of several thousand tons
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Polylactic acid - Chemical and physical properties
Due to the chiral nature of lactic acid,
several distinct forms of polylactide exist:
poly-L-lactide (PLLA) is the product
resulting from polymerization of L,L-lactide
(also known as L-lactide)
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Polylactic acid - Chemical and physical properties
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PLA has similar mechanical properties to
PETE polymer, but has a significantly
lower maximum continuous use
temperature.
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Polylactic acid - Chemical and physical properties
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Polylactic acid can be processed like
most thermoplastics into fiber (for
example using conventional melt
spinning processes) and film
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Polylactic acid - Chemical and physical properties
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There is also poly(L-lactide-co-D,Llactide) (PLDLLA) – used as
PLDLLA/TCP scaffolds for bone
engineering.
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Polylactic acid - Applications
Poly(lactic acid) can be processed by
extrusion, injection molding, film & sheet
casting, and spinning, providing access to
a wide range of materials.
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Polylactic acid - Applications
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Being able to degrade into innocuous
lactic acid, PLA is used as medical
implants in the form of screws, pins,
rods, and as a mesh. Depending on the
exact type used, it breaks down within
the body within 6 months to 2 years.
This gradual degradation is desirable
for a support structure, because it
gradually transfers the load to the
body (e.g. the bone) as that area heals.
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Polylactic acid - Applications
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PLA can also be used as a compostable
packaging material, either cast, injection
molded, or spun
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Polylactic acid - Applications
Pure poly-L-lactic acid (PLLA), on the
other hand, is the main ingredient in
Sculptra, a long lasting facial volume
enhancer, primarily used for lipoatrophy of
cheeks
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Polylactic acid - Applications
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PLA is also used as a feedstock material in 3D
printers such as Reprap and Makerbot.
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Polylactic acid - Recycling
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Currently, the SPI resin identification code 7
("others") is applicable for PLA. In Belgium,
Galactic started the first pilot unit to
chemically recycle PLA (Loopla). Unlike
mechanical recycling, waste material can
hold various contaminants. Polylactic acid
can be recycled to monomer by thermal
depolymerization, or hydrolysis. When
purified, the monomer can be used for the
manufacture of virgin PLA with no loss of
original properties (cradle-to-cradle
recycling).
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DNA nanotechnology - Properties of nucleic acids
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These qualities make the assembly of
nucleic acid structures easy to control
through nucleic acid design
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DNA nanotechnology - Properties of nucleic acids
Because the formation of correctly
matched base pairs is energetically
favorable, nucleic acid strands are
expected in most cases to bind to each
other in the conformation that maximizes
the number of correctly paired bases
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Food microbiology - Poly-γ-glutamic acid
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Poly-γ-glutamic acid (γ-PGA) produced by
various strains of Bacillus has potential
applications as a thickener in the food
industry.
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Nutrition - Essential fatty acids
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In industrialized societies, people typically
consume large amounts of processed
vegetable oils, which have reduced
amounts of the essential fatty acids along
with too much of omega-6 fatty acids
relative to omega-3 fatty acids.
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Nutrition - Essential fatty acids
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The amount and type of carbohydrates
consumed, along with some types of
amino acid, can influence processes
involving insulin, glucagon, and other
hormones; therefore the ratio of omega-3
versus omega-6 has wide effects on
general health, and specific effects on
immune function and inflammation, and
mitosis (i.e
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Transaction processing - ACID criteria
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Jim Gray defined properties of a reliable
transaction system in the late 1970s under
the acronym ACID — atomicity,
consistency, isolation, and durability.
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Catalytic triad - Acid
The second histidine is not as
effective an acid is the more common
aspartate or glutamate, leading to a
lower catalytic efficiency.
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Adenosine triphosphate - Amino acid activation in protein synthesis
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Aminoacyl-tRNA synthetase enzymes
utilise ATP as an energy source to
attach a tRNA molecule to its specific
amino acid, forming an aminoacyltRNA complex, ready for translation at
ribosomes. The energy is made
available by ATP hydrolysis to
adenosine monophosphate (AMP) as
two phosphate groups are removed.
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Collagen - Amino acids
Collagen has an unusual
amino acid composition and
sequence:
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Collagen - Amino acids
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Glycine is found at almost every
third residue.
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Collagen - Amino acids
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Proline makes up about 17% of
collagen.
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Collagen - Amino acids
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Collagen contains two uncommon
derivative amino acids not directly
inserted during translation. These
amino acids are found at specific
locations relative to glycine and are
modified post-translationally by
different enzymes, both of which
require vitamin C as a cofactor.
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Collagen - Amino acids
Hydroxylysine derived from lysine depending on the type of collagen, varying
numbers of hydroxylysines are
glycosylated (mostly having disaccharides
attached).
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Collagen - Amino acids
Cortisol stimulates
degradation of (skin)
collagen into amino acids.
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Biological database - Nucleic Acids Research Database Issue
An important resource for finding
biological databases is a special yearly
issue of the journal Nucleic Acids
Research (NAR). The Database Issue of
NAR is freely available, and categorizes
many of the publicly available on line
databases related to biology and
bioinformatics. A companion database to
the issue called the Online Molecular
Biology Database Collection lists 1,380
online databases. Other collections of
databases exist such as MetaBase and
the Bioinformatics Links Collection.
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Nafion - Superacid catalyst for fine chemical production
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Nafion, as a superacid, has potential
as a catalyst for organic synthesis.
Studies have demonstrated catalytic
properties in alkylation,
isomerization, oligomerization,
acylation, ketalization, esterification,
hydrolysis of sugars and ethers, and
oxidation. New applications are
constantly being discovered. These
processes, however, have not yet
found strong commercial use. Several
examples are shown below:
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Nafion - Superacid catalyst for fine chemical production
The amount of Nafion-H needed to
catalyze the acylation of benzene with
aroyl chloride is 10–30% less than the
Friedel-Crafts catalyst:
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Nafion - Superacid catalyst for fine chemical production
Catalysis of
protection groups
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Nafion - Superacid catalyst for fine chemical production
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It is possible to immobilize enzymes
within the Nafion by enlarging pores
with lipophilic salts. Nafion maintains
a structure and pH to provide a stable
environment for the enzymes.
Applications include catalytic
oxidation of adenine dinucleotides.
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Electrochemistry - Acidic medium
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In acid medium H+ ions and water are
added to half-reactions to balance the
overall reaction. For example, when
manganese reacts with sodium
bismuthate.
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Electrochemistry - Acidic medium
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Unbalanced reaction: Mn2+(aq) +
NaBiO3(s) → Bi3+(aq) + MnO4–
(aq)
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Electrochemistry - Acidic medium
Reduction: 2 e– + 6 H+(aq) +
BiO3–(s) → Bi3+(aq) + 3 H2O(l)
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Electrochemistry - Acidic medium
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Finally, the reaction is balanced by
multiplying the number of electrons
from the reduction half reaction to
oxidation half reaction and vice versa
and adding both half reactions, thus
solving the equation.
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Metabolism - Amino acids and proteins
Amino acids also contribute to cellular
energy metabolism by providing a carbon
source for entry into the citric acid cycle
(tricarboxylic acid cycle), especially when
a primary source of energy, such as
glucose, is scarce, or when cells undergo
metabolic stress.
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Metabolism - Fatty acids, isoprenoids and steroids
1
The enzymes of fatty acid biosynthesis are
divided into two groups, in animals and
fungi all these fatty acid synthase
reactions are carried out by a single
multifunctional type I protein, while in plant
plastids and bacteria separate type II
enzymes perform each step in the
pathway.
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Metabolism - Fatty acids, isoprenoids and steroids
Terpenes and isoprenoids are a large
class of lipids that include the carotenoids
and form the largest class of plant natural
products
1
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Omega-3 fatty acid
1
Omega-3 fatty acids (also called ω-3
fatty acids or n-3 fatty acids) refer to a
group of three fats called ALA (found
in plant oils), EPA, and DHA (both
commonly found in marine oils).
Common sources of animal omega-3
EPA and DHA fatty acids include fish
oils, egg oil, squid oils, krill oil, while
some plant oils contain the omega 3
ALA fatty acid such as seabuckthorn
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Omega-3 fatty acid
Fish are much more efficient than
mammals at converting the ALA to the
EPA and DHA omega-3 fatty acids.
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Omega-3 fatty acid
The fatty acids have two ends, the
carboxylic acid (-COOH) end, which is
considered the beginning of the chain,
thus "alpha", and the methyl (CH3) end,
which is considered the "tail" of the chain,
thus "omega." The nomenclature of the
fatty acid is taken from the location of the
first double bond, counted from the methyl
end, that is, the omega (ω-) or the n- end.
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Omega-3 fatty acid - Health effects
1
Supplementation does not appear to be
associated with a lower risk of all-cause
mortality.
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Omega-3 fatty acid - Cancer
1
The evidence linking the consumption of
fish to the risk of cancer is poor.
Supplementation with omega-3 fatty acids
does not appear to affect this either.
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Omega-3 fatty acid - Cancer
1
There is tentative evidence that marine
omega-3 polyunsaturated fatty acids
reduce the risk of breast cancer but this is
not conclusive.
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Omega-3 fatty acid - Cancer
The effect of consumption on prostate
cancer is not conclusive. There is a
decreased risk with higher blood levels of
DPA, but an increased risk of more
aggressive prostate cancer with higher
blood levels of combined EPA and DHA
(found in fatty fish oil).
1
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Omega-3 fatty acid - Cardiovascular disease
Evidence does not support a
beneficial role for omega-3 fatty acid
supplementation in preventing
cardiovascular disease (including
myocardial infarction and sudden
cardiac death) or stroke. Fish oil
supplementation has not been shown
to benefit revascularization or
arrythmia and has no effect on heart
failure admission rates. Eating a diet
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Omega-3 fatty acid - Cardiovascular disease
1
Large amounts may increase low-density
lipoproteins (LDL) , up to 46%, although
LDL changes from small to larger,
buoyant, less atherogenic particles.
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Omega-3 fatty acid - Cardiovascular disease
Omega-3 fatty acids also have mild
antihypertensive effects. When
subjects consumed omega-3 fatty
acids from oily fish on a regular basis,
their systolic blood pressure was
lowered by about 3.5–5.5 mmHg. The
18 carbon α-linolenic acid (ALA) has
not been shown to have the same
cardiovascular benefits that DHA or
EPA may have.
1
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Omega-3 fatty acid - Cardiovascular disease
Evidently, omega-3 fatty acids reduce
blood triglyceride levels, and regular intake
may reduce the risk of secondary and
primary heart attack
1
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Omega-3 fatty acid - Cardiovascular disease
1
Large amounts may increase the risk of
hemorrhagic stroke ; lower amounts are
not related to this risk; 3 grams of total
EPA/DHA daily are generally recognized
as safe (GRAS) with no increased risk of
bleeding involved and many studies used
substantially higher doses without major
side effects (for example: 4.4 grams
EPA/2.2 grams DHA in 2003 study).
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Omega-3 fatty acid - Inflammation
Although not confirmed as an approved
health claim, current research suggests
that the anti-inflammatory activity of longchain omega-3 fatty acids may translate
into clinical effects. For example, there is
evidence that rheumatoid arthritis sufferers
taking long-chain omega-3 fatty acids from
sources such as fish have reduced pain
compared to those receiving standard
NSAIDs. Some potential benefits have
1
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Omega-3 fatty acid - Developmental disorders
Although not supported by current
scientific evidence as a primary
treatment for ADHD, autism spectrum
disorders, and other developmental
differences, omega-3 fatty acids have
gained popularity for children with
these conditions.
1
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Omega-3 fatty acid - Developmental disorders
Omega-3 fatty acids offer a promising
complementary approach to standard
treatments for ADHD and developmental
coordination disorder. Fish oils appear to
reduce ADHD-related symptoms in some
children. A randomized, controlled trial has
suggested that "fatty acid supplementation
may offer a safe efficacious treatment
option for educational and behavioral
problems among children with DCD" .
1
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Omega-3 fatty acid - Developmental disorders
There is not enough scientific
evidence to support the effectiveness
of omega-3 fatty acids for autism
spectrum disorders.
1
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Omega-3 fatty acid - The brain and cognitive abilities
The DHA obtained through the
consumption of polyunsaturated fatty
acids has not been found to be
positively associated with cognitive
performance.[not in citation given] In
addition, DHA is vital for the grey
matter structure of the human brain, as
well as retinal stimulation and
neurotransmission.
1
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Omega-3 fatty acid - Psychiatric disorders
Though there is some evidence that
omega-3 fatty acids are related to a variety
of mental disorders, they may tentatively
be useful as an add-on for the treatment of
depression associated with bipolar
disorder and there is preliminary evidence
that EPA supplementation is helpful in
cases of depression. There is, however, a
significant difficulty in interpreting the
literature due to participant recall and
1
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Omega-3 fatty acid - Cognitive aging
Epidemiological studies suggest that
consumption of omega-3 fatty acids can
reduce the risk of dementia, but evidence
of a treatment effect in dementia patients
is inconclusive. However, clinical evidence
suggests benefits of treatment specifically
in patients who show signs of cognitive
decline but who are not sufficiently
impaired to meet criteria for dementia.
1
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Omega-3 fatty acid - Adverse effects
In a letter published October 31,
2000,[dated info] the United States
Food and Drug Administration Center
for Food Safety and Applied Nutrition,
Office of Nutritional Products,
Labeling, and Dietary Supplements
noted that known or suspected risks of
EPA and DHA consumed in excess of 3
grams per day may include the
possibility of:
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Omega-3 fatty acid - Adverse effects
1
Oxidation of omega-3 fatty acids, forming
biologically active oxidation products
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Omega-3 fatty acid - Adverse effects
Reduced glycemic
control among diabetics
1
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Omega-3 fatty acid - Chemistry
1
Chemical structure of alpha-linolenic
acid (ALA), an essential omega-3 fatty
acid, (18:3Δ9c,12c,15c, which means a
chain of 18 carbons with 3 double
bonds on carbons numbered 9, 12, and
15)
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Omega-3 fatty acid - Chemistry
As with most naturally-produced fatty
acids, all double bonds are in the cisconfiguration, in other words, the two
hydrogen atoms are on the same side of
the double bond; and the double bonds
are interrupted by methylene bridges (-CH
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Omega-3 fatty acid - Chemistry
1
2-), so that there are two single bonds between
each pair of adjacent double bonds.
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Omega-3 fatty acid - List of omega-3 fatty acids
1
This table lists several different names for the
most common omega-3 fatty acids found in
nature.
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Omega-3 fatty acid - List of omega-3 fatty acids
1
Clupanodonic acid 22:5 (n3)all-cis-7,10,13,16,19docosapentaenoic acid
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Omega-3 fatty acid - Mechanism of action
The 'essential' fatty acids were given
their name when researchers found
that they are essential to normal growth
in young children and animals, though
the modern definition of 'essential' is
more strict. A small amount of omega-3
in the diet (~1% of total calories)
enabled normal growth, and increasing
the amount had little to no additional
effect on growth.
1
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Omega-3 fatty acid - Mechanism of action
1
Likewise, researchers found that omega-6
fatty acids (such as γ-linolenic acid and
arachidonic acid) play a similar role in
normal growth. However, they also found
that omega-6 was "better" at supporting
dermal integrity, renal function, and
parturition. These preliminary findings led
researchers to concentrate their studies on
omega-6, and it is only in recent decades
that omega-3 has become of interest.
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Omega-3 fatty acid - Mechanism of action
If both omega-3 and omega-6 fatty
acids are present, they will "compete"
to be transformed, so the ratio of longchain omega-3:omega-6 fatty acids
directly affects the type of eicosanoids
that are produced.
1
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Omega-3 fatty acid - Mechanism of action
1
The simplest way would be by consuming more
omega-3 and fewer omega-6 fatty acids.
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Omega-3 fatty acid - Mechanism of action
They are required during the prenatal
period for the formation of synapses and
cell membranes. These processes are
also essential in postnatal human
development for injury response of the
central nervous system and retinal
stimulation.
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Omega-3 fatty acid - Conversion efficiency of ALA to EPA and DHA
1
Men's bodies convert short-chain omega-3
fatty acids to long-chain forms (EPA, DHA)
with an efficiency below 5%. The omega-3
conversion efficiency is greater in women,
but less well-studied.
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Omega-3 fatty acid - Conversion efficiency of ALA to EPA and DHA
Thus, accumulation of long-chain
omega-3 fatty acids in tissues is more
effective when they are obtained
directly from food or when competing
amounts of omega-6 analogs do not
greatly exceed the amounts of omega3.
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Omega-3 fatty acid - Conversion efficiency of ALA to EPA and DHA
1
argue that it is the absolute amount of
ALA, rather than the ratio of omega-3
and omega-6 fatty acids, that controls
the conversion efficiency.
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Omega-3 fatty acid - The omega-6 to omega-3 ratio
1
Some older clinical studies indicate
that the ingested ratio of omega-6 to
omega-3 (especially linoleic vs alphalinolenic) fatty acids is important to
maintaining cardiovascular health.
However, three studies published in
2005, 2007 and 2008, including a
randomized controlled trial, found
that while omega-3 polyunsaturated
fatty acids are extremely beneficial in
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Omega-3 fatty acid - The omega-6 to omega-3 ratio
1
arachidonic acid) than
those of omega-3
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Omega-3 fatty acid - The omega-6 to omega-3 ratio
Typical Western diets provide ratios of
between 10:1 and 30:1 (i.e., dramatically
higher levels of omega-6 than omega-3).
The ratios of omega-6 to omega-3 fatty
acids in some common vegetable oils are:
canola 2:1, hemp 2-3:1, soybean 7:1, olive
3–13:1, sunflower (no omega-3), flax 1:3,
cottonseed (almost no omega-3), peanut
(no omega-3), grapeseed oil (almost no
omega-3) and corn oil 46:1 ratio of omega1
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Omega-3 fatty acid - History
Although omega-3 fatty acids have
been known as essential to normal
growth and health since the 1930s,
awareness of their health benefits has
dramatically increased since the
1980s.
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Omega-3 fatty acid - History
Food and Drug Administration gave
"qualified health claim" status to EPA and
DHA omega-3 fatty acids, stating,
"supportive but not conclusive research
shows that consumption of EPA and DHA
[omega-3] fatty acids may reduce the risk
of coronary heart disease." This updated
and modified their health risk advice letter
of 2001
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Omega-3 fatty acid - History
The Canadian Government has
recognized the importance of DHA omega3 and permits the following biological role
claim for DHA: "DHA, an omega-3 fatty
acid, supports the normal development of
the brain, eyes and nerves."
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Omega-3 fatty acid - Dietary sources
1
Hoki (blue grenadier) 0.41
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Omega-3 fatty acid - Dietary sources
Strawberry or
Kiwifruit0.10-0.20
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Omega-3 fatty acid - Daily values
1
As macronutrients, fats are not assigned
Dietary Reference Intakes. Macronutrients
have acceptable intake (AI) levels and
acceptable macronutrient distribution
ranges (AMDRs) instead of RDAs. The AI
for omega-3 is 1.6 grams/day for men and
1.1 grams/day for women, while the AMDR
is 0.6% to 1.2% of total energy.
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Omega-3 fatty acid - Daily values
Approximately 10 percent of the
AMDR can be consumed as EPA
and/or DHA." There was insufficient
evidence as of 2005 to set an upper
tolerable limit for omega-3 fatty acids.
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Omega-3 fatty acid - Daily values
1
Heavy metal poisoning by the body's
accumulation of traces of heavy
metals, in particular mercury, lead,
nickel, arsenic, and cadmium, is a
possible risk from consuming fish oil
supplements.[medical citation
needed] Also, other contaminants
(PCBs, furans, dioxins, and PBDEs)
might be found, especially in lessrefined fish oil supplements
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Omega-3 fatty acid - Daily values
The FDA has advised that adults can
safely consume a total of 3 grams per day
of combined DHA and EPA, with no more
than 2 g per day coming from dietary
supplements.
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Omega-3 fatty acid - Daily values
Throughout their history, the Council for
Responsible Nutrition and the World
Health Organization have published
acceptable standards regarding
contaminants in fish oil. The most stringent
current standard is the International Fish
Oils Standard.[non-primary source
needed] Fish oils that are molecularly
distilled under vacuum typically make this
highest-grade, and have measurable
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Omega-3 fatty acid - Daily values
1
A recent trend has been to fortify food
with omega-3 fatty acid supplements.
Global food companies have launched
omega-3 fatty acid fortified bread,
mayonnaise, pizza, yogurt, orange
juice, children's pasta, milk, eggs,
popcorn, confections, and infant
formula.
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Omega-3 fatty acid - Daily values
1
The American Heart Association has
set up dietary recommendations for
EPA and DHA due to their
cardiovascular benefits: Individuals
with no history of coronary heart
disease or myocardial infarction
should consume oily fish or fish oils
two times per week; those having been
diagnosed with coronary heart
disease after infarction should
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Omega-3 fatty acid - Fish
Although fish are a dietary source of
omega-3 fatty acids, fish do not synthesize
them; they obtain them from the algae
(microalgae in particular) or plankton in
their diets.
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Omega-3 fatty acid - Fish oil
1
Marine and freshwater fish oil vary in content
of arachidonic acid, EPA and DHA
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Omega-3 fatty acid - Krill
1
Krill oil is a newly discovered source of
omega-3 fatty acids. Various claims are
made in support of krill oil as a superior
source of omega-3 fatty acids. The effect
of krill oil, at a lower dose of EPA + DHA
(62.8%), was demonstrated to be similar
to that of fish oil.
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Omega-3 fatty acid - Plant sources
Flaxseed (or linseed) (Linum
usitatissimum) and its oil are perhaps
the most widely available botanical
source of the omega-3 fatty acid ALA.
Flaxseed oil consists of approximately
55% ALA, which makes it six times
richer than most fish oils in omega-3
fatty acids. A portion of this is
converted by the body to EPA and
DHA, though the actual converted
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Omega-3 fatty acid - Plant sources
100 g of the leaves of
Purslane contains 300–
400 mg ALA.
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Omega-3 fatty acid - Eggs
Eggs produced by hens fed a diet of
greens and insects contain higher
levels of omega-3 fatty acids than
those produced by chickens fed corn
or soybeans. In addition to feeding
chickens insects and greens, fish oils
may be added to their diets to increase
the omega-3 fatty acid concentrations
in eggs.
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Omega-3 fatty acid - Eggs
1
The addition of flax and canola seeds to
the diets of chickens, both good sources of
alpha-linolenic acid, increases the omega3 content of the eggs, predominantly DHA.
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Omega-3 fatty acid - Eggs
1
The addition of green algae or seaweed to
the diets boosts the content of DHA and
EPA content, which are the forms of
omega-3 approved by the FDA for medical
claims. A common consumer complaint is
"Omega-3 eggs can sometimes have a
fishy taste if the hens are fed marine oils."
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Omega-3 fatty acid - Meat
1
Each day that an animal spends in the
feedlot, the amount of omega 3 fatty
acids in its meat is diminished.
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Omega-3 fatty acid - Meat
1
The omega-6 to omega-3 ratio of grassfed beef is about 2:1, making it a more
useful source of omega-3 than grain-fed
beef, which usually has a ratio of 4:1.
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Omega-3 fatty acid - Meat
The researchers found that grassfinished beef is higher in moisture
content, 42.5% lower total lipid
content, 54% lower in total fatty acids,
54% higher in beta-carotene, 288%
higher in vitamin E (alphatocopherol), higher in the B-vitamins
thiamin and riboflavin, higher in the
minerals calcium, magnesium, and
potassium, 193% higher in total
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Omega-3 fatty acid - Meat
In most countries, commercially
available lamb is typically grass-fed,
and thus higher in omega-3 than other
grain-fed or grain-finished meat
sources. In the United States, lamb is
often finished (i.e., fattened before
slaughter) with grain, resulting in
lower omega-3.
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Omega-3 fatty acid - Meat
1
The omega-3 content of chicken meat may
be enhanced by increasing the animals'
dietary intake of grains high in omega-3,
such as flax, chia, and canola.
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Omega-3 fatty acid - Meat
1
Kangaroo meat is also a source of
omega-3, with fillet and steak
containing 74 mg per 100 g of raw
meat.
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Omega-3 fatty acid - Mammalian brains and eyes
1
The brains and eyes of mammals are
extremely rich in DHA as well as other
omega-3 fatty acids. DHA is a major
structural component of the
mammalian brain, and is in fact the
most abundant omega-3 fatty acid in
the brain.
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Omega-3 fatty acid - Seal oil
Seal oil is a source of EPA, DPA, and
DHA. According to Health Canada, it helps
to support the development of the brain,
eyes and nerves in children up to 12 years
of age. However, like all seal products, it is
not allowed for import into the European
Union.
1
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Omega-3 fatty acid - Other sources
The microalgae Crypthecodinium
cohnii and Schizochytrium are rich
sources of DHA, but not EPA, and can
be produced commercially in
bioreactors.
1
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Omega-3 fatty acid - Other sources
1
Oil from brown algae (kelp) is a
source of EPA.
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Omega-3 fatty acid - Other sources
1
The study found that butter made from
the milk of grass fed cows contains
substantially more CLA, vitamin E,
beta-carotene, and omega-3 fatty
acids than butter made from the milk
of cows that have limited access to
pasture
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Redox - Acidic media
For instance, when
manganese(II) reacts
with sodium
bismuthate:
1
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Redox - Acidic media
1
The reaction is balanced by scaling
the two half-cell reactions to involve
the same number of electrons
(multiplying the oxidation reaction by
the number of electrons in the
reduction step and vice versa):
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Carbon fixation - Reductive citric acid cycle
The reductive citric acid cycle is the
oxidative citric acid cycle run in reverse. It
has been found in anaerobic and
microaerobic bacteria. It was proposed in
1966 by Evans, Buchanan and Arnon who
were working with the anoxygenic
photosynthetic green sulfur bacterium that
they called Chlorobium thiosulfatophilum.
The reductive citric acid cycle is
sometimes called the Arnon-Buchanan
1
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Fuel cell - Phosphoric acid fuel cell (PAFC)
1
This increases the corrosion or oxidation of
components exposed to phosphoric acid.
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Ellen Swallow Richards - The Lake Placid Conference
They sent out many invitations for the Lake
Placid Conference scheduled to take place Sept
1
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Techno - Acid house
Acid house party fever escalated in
London and Manchester, and it quickly
became a cultural phenomenon
1
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Techno - Acid house
The success of house and acid house
paved the way for wider acceptance of the
Detroit sound, and vice-versa: techno was
initially supported by a handful of house
music clubs in Chicago, New York, and
Northern England, with Detroit clubs
catching up later;Brewster 2006:398–443
but in 1987, it was Strings of Life which
eased London club-goers into acceptance
of house, according to DJ Mark
1
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Polysaccharide - Acidic polysaccharides
Acidic polysaccharides are
polysaccharides that contain carboxyl
groups, phosphate groups and/or
sulfuric ester groups.
1
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Polysaccharide - Periodic acid-Schiff stain (PAS)
Polysaccharides with unprotected
Diol#Vicinal_diols|vicinal diols or
amino sugars (i.e. some OH groups
replaced with amine) give a positive
Periodic acid-Schiff stain (PAS). The list
of polysaccharides that stain with PAS
is long. Although mucins of epithelial
origins stain with PAS, mucins of
connective tissue origin have so many
acidic substitutions that they do not
have enough glycol or amino-alcohol
groups left to react with PAS.
1
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Protein folding - Relationship between folding and amino acid sequence
1
The amino-acid sequence of a protein
determines its native conformation. A
protein molecule folds spontaneously
during or after Protein
biosynthesis|biosynthesis. While these
macromolecules may be regarded as
Self-assembly|folding themselves, the
process also depends on the solvent
(water or lipid bilayer), the
concentration of Salt (chemistry)|salts,
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Protein folding - Relationship between folding and amino acid sequence
1
Minimizing the number of hydrophobic
side-chains exposed to water is an
important driving force behind the
folding process. Formation of
intramolecular hydrogen bonds
provides another important
contribution to protein stability. The
strength of hydrogen bonds depends
on their environment, thus H-bonds
enveloped in a hydrophobic core
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Protein folding - Relationship between folding and amino acid sequence
The process of folding often begins
translation (genetics)|co-translationally, so
that the N-terminus of the protein begins to
fold while the C-terminus|C-terminal
portion of the protein is still being protein
biosynthesis|synthesized by the ribosome
1
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Protein folding - Relationship between folding and amino acid sequence
1
There are two models of protein folding that are
currently being confirmed:
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Protein folding - Relationship between folding and amino acid sequence
1
'The first:' The diffusion collision model, in
which a nucleus is formed, then the
secondary structure is formed, and finally
these secondary structures are collided
together and pack tightly together.
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Protein folding - Relationship between folding and amino acid sequence
1
'The second:' The nucleation-condensation
model, in which the secondary and tertiary
structures of the protein are made at the
same time.
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Protein folding - Relationship between folding and amino acid sequence
Recent studies have shown that some proteins
show characteristics of both of these folding models.
1
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Protein folding - Relationship between folding and amino acid sequence
1
At the coarsest level, it appears that in
transitioning to the native state, a
given amino acid sequence takes on
roughly the same route and proceeds
through roughly the same
intermediates and transition states
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Protein folding - Relationship between folding and amino acid sequence
1
This is not to say that nearly identical amino acid
sequences always fold similarly
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Bacteriophage - Synthesis of proteins and nucleic acid
The host’s normal synthesis of
proteins and nucleic acids is
disrupted, and it is forced to
manufacture viral products, instead
1
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Nucleic acid double helix
1
The double helical structure of a nucleic
acid complex arises as a consequence of
its Nucleic acid secondary
structure|secondary structure, and is a
fundamental component in determining its
Nucleic acid tertiary structure|tertiary
structure
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Nucleic acid double helix
The DNA double helix polymer of
nucleic acids, held together by
nucleotides which base pairing|base
pair together
1
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Nucleic acid double helix - History
1
The double-helix model of DNA structure
was first published in the journal Nature
(journal)|Nature by James D
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Nucleic acid double helix - History
1
The realization that the structure of DNA is
that of a double-helix elucidated the
mechanism of base pairing by which
genetic information is stored and copied in
living organisms and is widely considered
one of the most important scientific
discoveries of the 20th century
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Nucleic acid double helix - Nucleic acid hybridization
1
Melting occurs preferentially at
certain points in the nucleic acid
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Nucleic acid double helix - Nucleic acid hybridization
1
Strand separation by gentle heating,
as used in PCR, is simple providing
the molecules have fewer than about
10,000 base pairs (10 kilobase pairs,
or 10 kbp)
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Nucleic acid double helix - Base pair geometry
These values precisely define the
location and orientation in space of
every base or base pair in a nucleic
acid molecule relative to its
predecessor along the axis of the helix
1
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Nucleic acid double helix - Base pair geometry
1
*'Shift': displacement along an axis in the
base-pair plane perpendicular to the first,
directed from the minor to the major
groove.
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Nucleic acid double helix - Base pair geometry
*'Tilt': rotation
around the shift axis.
1
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Nucleic acid double helix - Base pair geometry
1
*'Roll': rotation around the slide
axis.
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Nucleic acid double helix - Base pair geometry
1
*'Twist': rotation around
the rise axis.
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Nucleic acid double helix - Base pair geometry
1
*'pitch': the number of base pairs
per complete turn of the helix.
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Nucleic acid double helix - Base pair geometry
Rise and twist determine the
handedness and pitch of the helix. The
other coordinates, by contrast, can be
zero. Slide and shift are typically small
in B-DNA, but are substantial in A- and
Z-DNA. Roll and tilt make successive
base pairs less parallel, and are
typically small. A
[http://rutchem.rutgers.edu/~xiangjun/3
DNA/images/bp_step_hel.gif diagram]
1
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Nucleic acid double helix - Base pair geometry
Note that tilt has often been used
differently in the scientific literature,
referring to the deviation of the first,
inter-strand base-pair axis from
perpendicularity to the helix axis. This
corresponds to slide between a
succession of base pairs, and in helixbased coordinates is properly termed
inclination.
1
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Nucleic acid double helix - Helix geometries
1
At least three DNA conformations are believed
to be found in nature, A-DNA, B-DNA, and ZDNA
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Nucleic acid double helix - Helix geometries
1
A-DNA and Z-DNA differ significantly
in their geometry and dimensions to
B-DNA, although still form helical
structures
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Nucleic acid double helix - Helix geometries
1
Other conformations are possible; A-DNA,
B-DNA, C-DNA, E-DNA, L-DNA (the
enantiomeric form of D-DNA), P-DNA, SDNA, Z-DNA, etc
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Nucleic acid double helix - Grooves
1
Twin helical strands
form the DNA
backbone
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Nucleic acid double helix - Non-double helical forms
1
Alternative Non-helical models of
DNA structure|non-helical models
were briefly considered in the late
1970s as a potential solution to
problems in the DNA
replication|replication of DNA in
plasmids and chromatin
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Nucleic acid double helix - Non-double helical forms
1
ssDNA|Single-stranded nucleic acids do
not adopt a helical formation, and are
described by models such as the random
coil or worm-like chain.
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Nucleic acid double helix - Bending
1
DNA is a relatively rigid
polymer, typically
modelled as a wormlike chain
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Nucleic acid double helix - Persistence length/axial stiffness
1
DNA in solution does not take a rigid
structure but is continually changing
conformation due to thermal vibration
and collisions with water molecules,
which makes classical measures of
rigidity impossible. Hence, the
bending stiffness of DNA is measured
by the persistence length, defined as:
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Nucleic acid double helix - Persistence length/axial stiffness
1
:The length of DNA over which the
time-averaged orientation of the
polymer becomes uncorrelated by a
factor of e.
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Nucleic acid double helix - Persistence length/axial stiffness
1
This value may be directly measured
using an atomic force microscope to
directly image DNA molecules of
various lengths. In an aqueous
solution, the average persistence
length is 46-50nm or 140-150 base
pairs (the diameter of DNA is 2nm),
although can vary significantly. This
makes DNA a moderately stiff
molecule.
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Nucleic acid double helix - Persistence length/axial stiffness
1
The persistence length of a section of
DNA is somewhat dependent on its
sequence, and this can cause
significant variation. The variation is
largely due to base stacking energies
and the residues which extend into the
minor groove|minor and major
grooves.
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Nucleic acid double helix - Models for DNA bending
1
The entropic flexibility of DNA is remarkably
consistent with standard polymer physics
models, such as the Kratky-Porod worm-like
chain model. Consistent with the worm-like
chain model is the observation that bending
DNA is also described by Hooke's law at very
small (sub-Newton (unit)|piconewton) forces.
However, for DNA segments less than the
persistence length, the bending force is
approximately constant and behaviour
deviates from the worm-like chain
predictions.
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Nucleic acid double helix - Models for DNA bending
1
This effect results in unusual ease in
circularising small DNA molecules
and a higher probability of finding
highly bent sections of DNA.
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Nucleic acid double helix - Bending preference
1
DNA molecules often have a preferred
direction to bend, i.e. anisotropic
bending. This is, again, due to the
properties of the bases which make up
the DNA sequence - a random
sequence will have no preferred bend
direction, i.e. isotropic bending.
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Nucleic acid double helix - Bending preference
Preferred DNA bend direction is
determined by the stability of stacking
each base on top of the next
1
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Nucleic acid double helix - Bending preference
DNA molecules with exceptional
bending preference can become
intrinsically bent. This was first
observed in trypanosomatid
kinetoplast DNA. Typical sequences
which cause this contain stretches of
4-6 'T' and 'A' residues separated by
'G' and 'C' rich sections which keep
the A and T residues in phase with the
minor groove on one side of the
1
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Nucleic acid double helix - Bending preference
The intrinsically bent structure is
induced by the 'propeller twist' of
base pairs relative to each other
allowing unusual bifurcated
Hydrogen-bonds between base steps.
At higher temperatures this structure,
and so the intrinsic bend, is lost.
1
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Nucleic acid double helix - Bending preference
1
All DNA which bends anisotropically has,
on average, a longer persistence length
and greater axial stiffness. This increased
rigidity is required to prevent random
bending which would make the molecule
act isotropically.
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Nucleic acid double helix - Circularization
1
DNA circularization depends on both the
axial (bending) stiffness and torsional
(rotational) stiffness of the molecule
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Nucleic acid double helix - Stretching
Longer stretches of
DNA are entropically
elastic under tension
1
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Nucleic acid double helix - Stretching
Under sufficient tension and positive
torque, DNA is thought to undergo a phase
transition with the bases splaying
outwards and the phosphates moving to
the middle. This proposed structure for
overstretched DNA has been called P-form
DNA, in honor of Linus Pauling who
originally presented it as a possible
structure of DNA.
1
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Nucleic acid double helix - Stretching
1
The mechanical properties of DNA under
compression have not been characterized
due to experimental difficulties in
preventing the polymer from bending
under the compressive force.
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Nucleic acid double helix - Supercoiling and topology
1
The B form of the DNA helix twists 360°
per 10.4-10.5 bp in the absence of
torsional strain. But many molecular
biological processes can induce
torsional strain. A DNA segment with
excess or insufficient helical twisting is
referred to, respectively, as positively
or negatively supercoiled. DNA in vivo
is typically negatively supercoiled,
which facilitates the unwinding
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Nucleic acid double helix - Supercoiling and topology
1
Within the cell most DNA is topologically
restricted. DNA is typically found in closed
loops (such as plasmids in prokaryotes)
which are topologically closed, or as very
long molecules whose diffusion
coefficients produce effectively
topologically closed domains. Linear
sections of DNA are also commonly bound
to proteins or physical structures (such as
membranes) to form closed topological
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Nucleic acid double helix - Supercoiling and topology
Francis Crick was one of the first to
propose the importance of linking numbers
when considering DNA supercoils. In a
paper published in 1976, Crick outlined the
problem as follows:
1
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Nucleic acid double helix - Supercoiling and topology
1
In considering supercoils formed by closed
double-stranded molecules of DNA certain
mathematical concepts, such as the
linking number and the twist, are needed.
The meaning of these for a closed ribbon
is explained and also that of the writhing
number of a closed curve. Some simple
examples are given, some of which may
be relevant to the structure of chromatin.
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Nucleic acid double helix - Supercoiling and topology
1
Analysis of DNA topology uses
three values:
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Nucleic acid double helix - Supercoiling and topology
1
:L = linking number - the number of
times one DNA strand wraps around
the other. It is an integer for a closed
loop and constant for a closed
topological domain.
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Nucleic acid double helix - Supercoiling and topology
:T = twist - total number of turns in the
double stranded DNA helix. This will
normally tend to approach the number of
turns that a topologically open double
stranded DNA helix makes free in solution:
number of bases/10.5, assuming there are
no intercalating agents (e.g., ethidium
bromide) or other elements modifying the
stiffness of the DNA.
1
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Nucleic acid double helix - Supercoiling and topology
1
:W = writhe - number of turns of the double stranded
DNA helix around the superhelical axis
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Nucleic acid double helix - Supercoiling and topology
Any change of T in a closed topological
domain must be balanced by a change in
W, and vice versa. This results in higher
order structure of DNA. A circular DNA
molecule with a writhe of 0 will be circular.
If the twist of this molecule is subsequently
increased or decreased by supercoiling
then the writhe will be appropriately
altered, making the molecule undergo
plectonemic or toroidal superhelical
1
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Nucleic acid double helix - Supercoiling and topology
When the ends of a piece of double
stranded helical DNA are joined so that
it forms a circle the strands are knot
theory|topologically knotted
1
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Nucleic acid double helix - The linking number paradox
1
For many years, the origin of residual
supercoiling in eukaryotic genomes
remained unclear. This topological
puzzle was referred to by some as the
linking number paradox. However,
when experimentally determined
structures of the nucleosome
displayed an over-twisted left-handed
wrap of DNA around the histone
octamer, this paradox was considered
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Nucleic acid
'Nucleic acids' are polymeric
macromolecules, or large
biomolecule|biological molecules,
essential for all known forms of life.
Nucleic acids, which include DNA
(deoxyribonucleic acid) and RNA
(ribonucleic acid), are made from
monomers known as nucleotides. Each
nucleotide has three components: a
pentose|5-carbon sugar, a
1
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Nucleic acid
1
Together with proteins, nucleic acids are
the most important biological
macromolecules; each is found in
abundance in all living things, where they
function in encoding, transmitting and
expressing genetic information—in other
words, information is conveyed through
the nucleic acid sequence, or the order of
nucleotides within a DNA or RNA molecule
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Nucleic acid
Nucleic acids were discovered by
Friedrich Miescher in 1869.
Experimental studies of nucleic acids
constitute a major part of modern
Biological research|biological and
medical research, and form a
foundation for Genomics|genome and
forensic science, as well as the
biotechnology and pharmaceutical
industry|pharmaceutical industries.
1
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Nucleic acid - Occurrence and nomenclature
Although first discovered within the Cell
nucleus|nucleus of Eukaryote|eukaryotic
cells, nucleic acids are now known to be
found in all life forms as well as some
nonliving entities, including within bacteria,
archaea, Mitochondrion|mitochondria,
chloroplasts, viruses and viroids
1
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Nucleic acid - Occurrence and nomenclature
1
The basic component of biological
nucleic acids is the nucleotide, each
of which contains a pentose sugar
(ribose or deoxyribose), a phosphate
group, and a nucleobase.
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Nucleic acid - Occurrence and nomenclature
Nucleic acids are also generated within
the laboratory, through the use of
enzymesMullis, Kary B. The Polymerase
Chain Reaction (Nobel Lecture). 1993.
(retrieved December 1, 2010)
http://nobelprize.org/nobel_prizes/chemistr
y/laureates/1993/mullis-lecture.html (DNA
and RNA polymerases) and by Solidphase synthesis|solid-phase chemical
synthesis. The chemical methods also
1
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Nucleic acid - Molecular composition and size
1
Nucleic acids are generally very large
molecules. Indeed, DNA molecules
are probably the largest individual
molecules known. Well-studied
biological nucleic acid molecules
range in size from 21 nucleotides
(small interfering RNA) to large
chromosomes (Chromosome
1|human chromosome 1 is a single
molecule that contains 247 million
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Nucleic acid - Molecular composition and size
1
In most cases, naturally occurring DNA
molecules are double-stranded and
RNA molecules are single-stranded.
There are numerous exceptions,
however—some viruses have genomes
made of Reoviridae|double-stranded
RNA and other viruses have M13
bacteriophage|single-stranded DNA
genomes, and, in some circumstances,
nucleic acid structures with Triplehttps://store.theartofservice.com/itil-2011-foundation-complete-certification-kit-fourth-edition-study-guide-ebook-and-online-course.html
Nucleic acid - Molecular composition and size
1
Also, the nucleobases found in the two
nucleic acid types are different: adenine,
cytosine, and guanine are found in both
RNA and DNA, while thymine occurs in
DNA and uracil occurs in RNA.
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Nucleic acid - Molecular composition and size
1
This gives nucleic acids Directionality
(molecular biology)|directionality,
and the ends of nucleic acid
molecules are referred to as 5'-end
and 3'-end
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Nucleic acid - Molecular composition and size
Non-standard nucleosides are also
found in both RNA and DNA and
usually arise from modification of the
standard nucleosides within the DNA
molecule or the primary (initial) RNA
transcript. Transfer RNA (tRNA)
molecules contain a particularly large
number of modified nucleosides.
1
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Nucleic acid - Topology
1
In contrast, single-stranded RNA and
DNA molecules are not constrained to
a regular double helix, and can adopt
Nucleic acid tertiary structure|highly
complex three-dimensional structures
that are based on short stretches of
intramolecular base-paired
sequences that include both WatsonCrick and noncanonical base pairs, as
well as a wide range of complex
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Nucleic acid - Topology
Nucleic acid molecules are usually
unbranched, and may occur as linear and
circular molecules. For example, bacterial
chromosomes, plasmids, mitochondrial
DNA and chloroplast DNA are usually
circular double-stranded DNA molecules,
while chromosomes of the eukaryotic
nucleus are usually linear double-stranded
DNA molecules. Most RNA molecules are
linear, single-stranded molecules, but both
1
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Nucleic acid - Nucleic acid sequences
One DNA or RNA molecule differs
from another primarily in the Nucleic
acid sequence|sequence of
nucleotides
1
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Nucleic acid - Deoxyribonucleic acid
1
Deoxyribonucleic acid (DNA) is a nucleic
acid containing the genetic instructions
used in the development and functioning
of all known living organisms (with the
exception of RNA viruses)
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Nucleic acid - Deoxyribonucleic acid
1
The code is read by copying stretches of
DNA into the related nucleic acid RNA in a
process called transcription.
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Nucleic acid - Deoxyribonucleic acid
1
Within cells DNA is organized
into long structures called
chromosomes
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Nucleic acid - Ribonucleic acid
Transfer RNA serves as the carrier
molecule for amino acids to be used in
protein synthesis, and is responsible for
decoding the mRNA
1
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Nucleic acid - Artificial nucleic acid analogs
nucleic acid analogues|Artificial nucleic
acid analogs have been designed and
synthesized by chemists, and include
peptide nucleic acid, morpholino- and
locked nucleic acid, as well as GNA
(nucleic acid)|glycol nucleic acid and TNA
(nucleic acid)|threose nucleic acid. Each of
these is distinguished from naturally
occurring DNA or RNA by changes to the
backbone of the molecule.
1
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Calcium carbonate - Solubility in a strong or weak acid solution
Solutions of strong acid|strong
(hydrochloric acid|HCl), moderately strong
(sulfamic acid|sulfamic) or weak acid|weak
(acetic acid|acetic, citric acid|citric, sorbic
acid|sorbic, lactic acid|lactic, phosphoric
acid|phosphoric) acids are commercially
available. They are commonly used as
descaling agents to remove limescale
deposits. The maximum amount of CaCO3
that can be dissolved by one liter of an
1
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Calcium carbonate - Solubility in a strong or weak acid solution
1
For vanishing acid concentrations, one
can recover the final pH and the solubility
of CaCO3 in pure water.
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Calcium carbonate - Solubility in a strong or weak acid solution
1
For the same total acid concentration, the
initial pH of the weak acid is less acid than
the one of the strong acid; however, the
maximum amount of CaCO3 which can be
dissolved is approximately the same. This
is because in the final state, the pH is
larger than the pKA, so that the weak acid
is almost completely dissociated, yielding
in the end as many H+ ions as the strong
acid to dissolve the calcium carbonate.
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Calcium carbonate - Solubility in a strong or weak acid solution
*The calculation in the case of
phosphoric acid (which is the most
widely used for domestic applications)
is more complicated since the
concentrations of the four dissociation
states corresponding to this acid must
be calculated together with [HCO3−],
[CO32−], [Ca2+], [H+] and [OH−]. The
system may be reduced to a seventh
degree equation for [H+] the numerical
1
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Calcium carbonate - Solubility in a strong or weak acid solution
where [A] = [H3PO4] + [H2PO4−] +
[HPO42−] + [PO43−] is the total acid
concentration. Thus phosphoric acid is
more efficient than a monoacid since at
the final almost neutral pH, the second
dissociated state concentration
[HPO42−] is not negligible (see
phosphoric acid#pH and composition
of a phosphoric acid aqueous
solution|phosphoric acid).
1
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Acid rain
1
The chemicals in acid rain can cause
paint to peel, corrosion of steel
structures such as bridges, and
erosion of stone statues.
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Acid rain - Definition
1
Clean or unpolluted rain has an acidic pH,
but usually no lower than 5.7, because
carbon dioxide and water in the air react
together to form carbonic acid, a weak
acid according to the following reaction:
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Acid rain - Definition
1
Carbonic acid then can ionize in water forming low
concentrations of hydronium and carbonate ions:
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Acid rain - Definition
1
However, unpolluted rain can also contain
other chemicals which affect its pH (acidity
level). A common example is nitric acid
produced by electric discharge in the
atmosphere such as lightning. Acid
deposition as an environmental issue
(discussed later in the article) would
include additional acids to .
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Acid rain - History
1
The corrosive effect of polluted, acidic city
air on limestone and marble was noted in
the 17th century by John Evelyn, who
remarked upon the poor condition of the
Arundel marbles.E. S. de Beer, ed. The
Diary of John Evelyn, III, 1955 (19
September 1667) p. 495.
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Acid rain - History
1
In 1852, Robert Angus Smith was the first
to show the relationship between acid rain
and atmospheric pollution in Manchester,
England.Seinfeld, John H.; Pandis, Spyros
N (1998)
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Acid rain - History
Public awareness of acid rain in the
U.S increased in the 1970s after The
New York Times published reports
from the Hubbard Brook Experimental
Forest in New Hampshire of the
myriad deleterious environmental
effects shown to result from it.
1
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Acid rain - History
1
Occasional pH readings in rain and fog
water of well below 2.4 have been
reported in industrialized areas. Industrial
acid rain is a substantial problem in China
and Russia and areas downwind from
them. These areas all burn sulfurcontaining coal to generate heat and
electricity.
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Acid rain - History
The use of tall smokestacks to reduce
local pollution has contributed to the
spread of acid rain by releasing gases into
regional atmospheric circulation
1
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Acid rain - History of acid rain in the United States
1
It looked at the effects of acid rain and
funded research on the effects of acid
precipitation on freshwater and terrestrial
ecosystems, historical buildings,
monuments, and building materials
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Acid rain - History of acid rain in the United States
1
From the start, policy advocates from
all sides attempted to influence
NAPAP activities to support their
particular policy advocacy efforts, or
to disparage those of their opponents.
For the U.S. Government's scientific
enterprise, a significant impact of
NAPAP were lessons learned in the
assessment process and in
environmental research management
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Acid rain - History of acid rain in the United States
1
Subsequent Reports to Congress have
documented chemical changes in soil and
freshwater ecosystems, nitrogen
saturation, decreases in amounts of
nutrients in soil, episodic acidification,
regional haze, and damage to historical
monuments.
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Acid rain - History of acid rain in the United States
1
Title IV of these amendments established
the Acid Rain Program, a cap and trade
system designed to control emissions of
sulfur dioxide and nitrogen oxides
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Acid rain - History of acid rain in the United States
1
During the 1990s, research continued. On
March 10, 2005, EPA issued the Clean Air
Interstate Rule (CAIR). This rule provides
states with a solution to the problem of
power plant pollution that drifts from one
state to another. CAIR will permanently
cap emissions of SO2 and NOx in the
eastern United States. When fully
implemented, CAIR will reduce SO2
emissions in 28 eastern states and the
District of Columbia by over 70% and NOx
emissions by over 60% from 2003 levels.
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Acid rain - History of acid rain in the United States
Since the 1990s, SO2 emissions have
dropped 40%, and according to the Pacific
Research Institute, acid rain levels have
dropped 65% since
1976.[http://www.sfgate.com/cgibin/article.cgi?f=/c/a/2007/12/03/MNMMTJ
US1.DTLhw=Cap+trade+Acid+Rainsn=00
1sc=1000 'Cap-and-trade' model eyed for
cutting greenhouse gases], San Francisco
Chronicle, December 3, 2007
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Acid rain - History of acid rain in the United States
In 2007, total SO2 emissions were 8.9
million tons, achieving the program's long
term goal ahead of the 2010 statutory
deadline.[http://www.epa.gov/airmarkt/prog
ress/arp07.html Acid Rain Program 2007
Progress Report], United States
Environmental Protection Agency, January
2009.
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Acid rain - History of acid rain in the United States
1
The EPA estimates that by 2010, the
overall costs of complying with the
program for businesses and
consumers will be $1 billion to $2
billion a year, only one fourth of what
was originally predicted.
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Acid rain - Emissions of chemicals leading to acidification
1
Emissions of nitrogen oxides which are
oxidized to form nitric acid are of
increasing importance due to stricter
controls on emissions of sulfur containing
compounds
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Acid rain - Natural phenomena
1
The principal natural phenomena that
contribute acid-producing gases to the
Earth's atmosphere|atmosphere are
emissions from volcanoes. Thus, for
example, fumaroles from the Laguna
Caliente crater of Poás Volcano create
extremely high amounts of acid rain and
fog, with acidity as high as a pH of 2,
clearing an area of any vegetation and
frequently causing irritation to the eyes
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Acid rain - Natural phenomena
1
Acid-producing gasses are also created by
biology|biological processes that occur on
the land, in wetlands, and in the oceans.
The major biological source of sulfur
containing compounds is dimethyl sulfide.
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Acid rain - Natural phenomena
Nitric acid in rainwater is an important
source of fixed nitrogen for plant life, and
is also produced by electrical activity in the
atmosphere such as lightning.
1
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Acid rain - Natural phenomena
1
Acidic deposits have been detected in
glacier|glacial ice thousands of years
old in remote parts of the globe.
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Acid rain - Natural phenomena
Soils of coniferous forests are naturally
very acidic due to the shedding of needles,
and the results of this phenomenon should
not be confused with acid rain.
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Acid rain - Human activity
1
The gases can be carried hundreds of
kilometers in the atmosphere before they
are converted to acids and deposited
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Acid rain - Chemical processes
Combustion of fuels produces sulfur
dioxide and nitric oxides. They are
converted into sulfuric acid and nitric
acid.[http://www.sciencedaily.com/releases
/1998/09/980928072644.htm Clean Air Act
Reduces Acid Rain In Eastern United
States], ScienceDaily, September 28,
1998
1
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Acid rain - Gas phase chemistry
In the gas phase sulfur dioxide is
oxidized by reaction with the hydroxyl
radical via an intermolecular reaction:
1
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Acid rain - Gas phase chemistry
1
In the presence of water, sulfur trioxide (SO3) is
converted rapidly to sulfuric acid:
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Acid rain - Chemistry in cloud droplets
1
When clouds are present, the loss rate of
SO2 is faster than can be explained by
gas phase chemistry alone. This is due to
reactions in the liquid water droplets.
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Acid rain - Chemistry in cloud droplets
1
Sulfur dioxide dissolves in water and
then, like carbon dioxide,
hydrolysis|hydrolyses in a series of
Chemical equilibrium|equilibrium
reactions:
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Acid rain - Chemistry in cloud droplets
1
There are a large number of aqueous
reactions that redox|oxidize sulfur from
S(oxidation state|IV) to S(VI), leading to
the formation of sulfuric acid. The most
important oxidation reactions are with
ozone, hydrogen peroxide and oxygen
(reactions with oxygen are catalyzed by
iron and manganese in the cloud
droplets).
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Acid rain - Wet deposition
1
Wet deposition of acids occurs when
any form of precipitation (rain, snow,
and so on.) removes acids from the
atmosphere and delivers it to the
Earth's surface. This can result from
the deposition of acids produced in the
raindrops (see aqueous phase
chemistry above) or by the
precipitation removing the acids
either in clouds or below clouds. Wet
removal of both gases and aerosols
are both of importance for wet
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Acid rain - Dry deposition
Acid deposition also occurs via dry
deposition in the absence of precipitation.
This can be responsible for as much as 20
to 60% of total acid deposition. This
occurs when particles and gases stick to
the ground, plants or other surfaces.
1
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Acid rain - Adverse effects
1
Acid rain has been shown to have
adverse impacts on forests,
freshwaters and soils, killing insect
and aquatic life-forms as well as
causing damage to buildings and
having impacts on human health.
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Acid rain - Surface waters and aquatic animals
The United States Environmental
Protection Agency's (EPA) website
states: Of the lakes and streams
surveyed, acid rain caused acidity in
75% of the acidic lakes and about 50%
of the acidic streams.
1
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Acid rain - Soils
The hydronium ions of acid rain also
mobilize toxins such as aluminium, and
leach away essential nutrients and
minerals such as magnesium.US EPA:
[http://www.epa.gov/acidrain/effects/forest
s.html Effects of Acid Rain – Forests]
1
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Acid rain - Soils
Soil chemistry can be dramatically
changed when base cations, such as
calcium and magnesium, are leached
by acid rain thereby affecting sensitive
species, such as sugar maple (Acer
saccharum).
1
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Acid rain - Forests and other vegetation
Adverse effects may be indirectly
related to acid rain, like the acid's
effects on soil (see above) or high
concentration of gaseous precursors
to acid rain. High altitude forests are
especially vulnerable as they are often
surrounded by clouds and fog which
are more acidic than rain.
1
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Acid rain - Forests and other vegetation
1
Other plants can also be damaged by acid
rain, but the effect on food crops is
minimized by the application of lime and
fertilizers to replace lost nutrients
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Acid rain - Ocean acidification
1
Coral's limestone skeletal is sensitive
to pH drop, because the calcium
carbonate, core component of the
limestone dissolves in acidic (low pH)
solutions.
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Acid rain - Human health effects
1
Acid rain does not directly affect human
health. The acid in the rainwater is too
dilute to have direct adverse effects.
However, the particulates responsible for
acid rain (sulfur dioxide and nitrogen
oxides) do have an adverse effect.
Increased amounts of fine particulate
matter in the air do contribute to heart and
lung problems including asthma and
bronchitis.[http://www.epa.gov/acidrain/eff
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Acid rain - Other adverse effects
Acid rain can damage buildings,
historic monuments, and statues,
especially those made of rocks, such
as limestone and marble, that contain
large amounts of calcium carbonate.
Acids in the rain react with the
calcium compounds in the stones to
create gypsum, which then flakes off.
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Acid rain - Other adverse effects
1
The effects of this are commonly seen
on old gravestones, where acid rain
can cause the inscriptions to become
completely illegible. Acid rain also
increases the corrosion rate of metals,
in particular iron, steel, copper and
bronze.
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Acid rain - Affected areas
1
Places significantly impacted by acid rain
around the globe include most of eastern
Europe from Poland northward into
Scandinavia, the eastern third of the
United States, and southeastern Canada.
Other affected areas include the
southeastern coast of China and Taiwan.
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Acid rain - Technical solutions
1
Many coal-firing power stations use
flue-gas desulfurization (FGD) to
remove sulfur-containing gases from
their stack gases
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Acid rain - Technical solutions
1
In some areas the sulfates are sold to
chemical companies as gypsum when
the purity of calcium sulfate is high.
In others, they are placed in landfill.
However, the effects of acid rain can
last for generations, as the effects of
pH level change can stimulate the
continued leaching of undesirable
chemicals into otherwise pristine
water sources, killing off vulnerable
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Acid rain - Technical solutions
1
Fluidized bed combustion also reduces the amount
of sulfur emitted by power production.
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Acid rain - International treaties
1
A number of international treaties on the
long range transport of atmospheric
pollutants have been agreed for example,
1985 Helsinki Protocol on the Reduction of
Sulphur Emissions|Sulphur Emissions
Reduction Protocol under the Convention
on Long-Range Transboundary Air
Pollution. Canada and the US signed the
Air Quality Agreement in 1991. Most
European countries and Canada have
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Acid rain - Emissions trading
1
In this regulatory scheme, every current
polluting facility is given or may purchase
on an open market an emissions
allowance for each unit of a designated
pollutant it emits. Operators can then
install pollution control equipment, and sell
portions of their emissions allowances
they no longer need for their own
operations, thereby recovering some of
the capital cost of their investment in such
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Acid rain - Emissions trading
Code 7651 is to achieve significant
environmental and public health benefits
through reductions in emissions of sulfur
dioxide (SO2) and nitrogen oxides (NOx),
the primary causes of acid rain
1
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Kidney - Acid-base homeostasis
Two organ systems, the kidneys and
lungs, maintain acid-base homeostasis,
which is the maintenance of pH around a
relatively stable value. The lungs
contribute to acid-base homeostasis by
regulating carbon dioxide (CO2)
concentration.
1
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Kidney - Acid-base homeostasis
1
The kidneys have two very important roles
in maintaining the acid-base balance: to
reabsorb bicarbonate from urine, and to
excrete hydrogen ions into urine
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Biomolecule - Amino acids
Amino acids contain both amino and
carboxylic acid functional groups. (In
biochemistry, the term amino acid is used
when referring to those amino acids in
which the amino and carboxylate
functionalities are attached to the same
carbon, plus proline which is not actually
an amino acid).
1
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Biomolecule - Amino acids
Modified amino acids are sometimes
observed in proteins; this is usually the
result of enzymatic modification after
translation (biology)|translation (protein
synthesis). For example, phosphorylation
of serine by kinases and
dephosphorylation by phosphatases is an
important control mechanism in the cell
cycle. Only two amino acids other than the
standard twenty are known to be
1
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Biomolecule - Amino acids
1
* Selenocysteine is incorporated into some
proteins at a UGA codon, which is normally a
stop codon.
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Biomolecule - Amino acids
1
* Pyrrolysine is incorporated into some
proteins at a UAG codon. For instance, in
some methanogens in enzymes that are
used to produce methane.
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Biomolecule - Amino acids
1
Besides those used in protein synthesis,
other biologically important amino acids
include carnitine (used in lipid transport
within a cell), ornithine, GABA and taurine.
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Biochemistry - Nucleic acids
1
Nucleic acids are the molecules that make
up DNA, an extremely important
substance that all cellular organisms use
to store their genetic information. The
most common nucleic acids are
deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA). Their monomers
are called nucleotides. The most common
nucleotides are adenine, cytosine,
guanine, thymine, and uracil. Adenine
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Biochemistry - Nucleic acids
1
Aside from the genetic material of the
cell, nucleic acids often play a role as
second messengers, as well as forming
the base molecule for adenosine
triphosphate (ATP), the primary energycarrier molecule found in all living
organisms.
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Biochemistry - Nucleic acids
1
Also, the nitrogenous bases possible
in the two nucleic acids are different:
adenine, cytosine, and guanine occur
in both RNA and DNA, while thymine
occurs only in DNA and uracil occurs
in RNA.Tropp (2012), pp
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Boric acid - Pyrotechnics
1
Boron is used in pyrotechnics to prevent
the amide-forming reaction between
aluminum and nitrates. A small amount of
boric acid is added to the composition to
neutralize alkaline amides that can react
with the aluminum.
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Boric acid - Pyrotechnics
1
Boric acid can be used as a colorant to
make fire green. For example, when
dissolved in methanol it is popularly used
by torch (juggling)|fire jugglers and fire
spinners to create a deep green flame.
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Tooth enamel - Acid-etching techniques
Invented in 1955, acid-etching
employs dental etchants and is used
frequently when bonding dental
restoration to teeth.Summitt et al., p
1
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Tooth enamel - Acid-etching techniques
1
The effects of acid-etching on enamel
can vary. Important variables are the
amount of time the etchant is applied,
the type of etchant used, and the
current condition of the enamel.
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Tooth enamel - Acid-etching techniques
1
There are three types of patterns
formed by acid-etching
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Neurovirology - CSF nucleic acid amplification using Polymerase Chain Reaction (PCR)
PCR is frequently used to for rapid
identification of specific DNA viruses from
the CSF, while Reverse transcriptase PCR
is commonly used to identify RNA viruses
in the CSF.Irani, D (2008)
1
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Nucleic acid design
1
In addition, there are many Nucleic acid
tertiary structure|tertiary structure
considerations which affect the choice of a
secondary structure for a given design.
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Nucleic acid design
1
However, nucleic acid structures are less versatile
than proteins in their functionality.
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Nucleic acid design
1
Nucleic acid design can be considered
the inverse of nucleic acid structure
prediction. In structure prediction,
the structure is determined from a
known sequence, while in nucleic
acid design, a sequence is generated
which will form a desired structure.
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Nucleic acid design - Fundamental concepts
1
Thus, in nucleic acids the sequence
determines the pattern of binding and
thus the overall structure.
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Nucleic acid design - Fundamental concepts
1
Nucleic acid design is the process by
which, given a desired target
structure or functionality, sequences
are generated for nucleic acid strands
which will self-assemble into that
target structure. Nucleic acid design
encompasses all levels of DNA
structure|nucleic acid structure:
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Nucleic acid design - Fundamental concepts
1
* Nucleic acid primary structure|Primary
structuremdash;the raw sequence of
nucleobases of each of the component
nucleic acid strands;
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Nucleic acid design - Fundamental concepts
* Nucleic acid secondary
structure|Secondary
structuremdash;the set of interactions
between bases, i.e., which parts of
which strands are bound to each other;
and
1
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Nucleic acid design - Fundamental concepts
* Nucleic acid tertiary
structure|Tertiary
structuremdash;the locations of the
atoms in three-dimensional space,
taking into consideration geometrical
and Steric effects|steric constraints.
1
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Nucleic acid design - Fundamental concepts
One of the greatest concerns in nucleic
acid design is ensuring that the target
structure has the lowest free energy (i.e. is
the most thermodynamically favorable)
whereas misformed structures have higher
values of free energy and are thus
unfavored.
1
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Nucleic acid design - Fundamental concepts
1
These goals can be achieved through
the use of a number of approaches,
including heuristic, thermodynamic,
and geometrical ones. Almost all
nucleic acid design tasks are aided by
computers, and a number of software
packages are available for many of
these tasks.
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Nucleic acid design - Fundamental concepts
Two considerations in nucleic acid
design are that desired hybridizations
should have melting temperatures in a
narrow range, and any spurious
interactions should have very low
melting temperatures (i.e
1
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Nucleic acid design - Heuristic methods
Heuristic methods use simple criteria
which can be quickly evaluated to judge
the suitability of different sequences for a
given secondary structure. They have the
advantage of being much less
computationally expensive than the energy
minimization algorithms needed for
thermodynamic or geometrical modeling,
and being easier to implement, but at the
cost of being less rigorous than these
1
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Nucleic acid design - Heuristic methods
1
Sequence symmetry minimization divides
the nucleic acid sequence into overlapping
subsequences of a fixed length, called the
criterion length
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Nucleic acid design - Heuristic methods
1
Another related but more involved
approach is to use methods from
coding theory to Coding theory
approaches to nucleic acid
design|construct nucleic acid
sequences with desired properties.
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Nucleic acid design - Thermodynamic models
Information about the Nucleic acid
secondary structure|secondary structure of
a nucleic acid complex along with its
sequence can be used to predict the
Thermodynamics|thermodynamic
properties of the complex.
1
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Nucleic acid design - Thermodynamic models
1
GC-content alone can also be used to
estimate the free energy and melting
temperature of a nucleic acid duplex
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Nucleic acid design - Thermodynamic models
1
Software for thermodynamic modeling of nucleic
acids includes [http://nupack.org/ Nupack],
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Nucleic acid design - Thermodynamic models
[http://mfold.rna.albany.edu//
mfold/UNAFold], and
[http://www.tbi.univie.ac.at/~ivo/RNA/
Vienna].
1
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Nucleic acid design - Thermodynamic models
1
A related approach, inverse secondary
structure prediction, uses stochastic
local search which improves a nucleic
acid sequence by running a Nucleic
acid structure prediction|structure
prediction algorithm and the modifying
the sequence to eliminate unwanted
features.
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Nucleic acid design - Geometrical models
--ref name=Sherman06ref
name=Birac06/ref name=Birac06/ref
name=Birac06!--* mdash;An annotated
comparison of nucleic acid design
software.
1
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Nucleic acid design - Geometrical models
--Nanotech
footer|state=autocollapseBi
omolecular structure
1
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Lead-acid batteries
The 'Lead–acid battery' was invented in
1859 by French physicist Gaston Planté
and is the oldest type of rechargeable
battery. Despite having a very low energyto-weight ratio and a low energy-to-volume
ratio, its ability to supply high surge
currents means that the cells have a
relatively large power-to-weight ratio.
These features, along with their low cost,
makes it attractive for use in motor
1
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Lead-acid batteries
1
'Gel-cells' and 'absorbed glass-mat'
batteries are common in these roles,
collectively known as VRLA
battery|VRLA (valve-regulated leadacid) batteries.
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Lead-acid batteries
1
Lead-acid battery sales account for 40–
45% of the value from batteries sold
worldwide (1999, not including China and
Russia), a manufacturing market value of
about US$15 billion.
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Lead-acid batteries - History
1
In 1859, Gaston Planté's lead-acid battery
was the first battery that could be
recharged by passing a reverse current
through it
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Lead-acid batteries - History
1
In the 1970s the VRLA battery|valveregulated lead acid battery (often
called sealed) was developed; it uses a
gel electrolyte instead of a liquid,
allowing the battery to be used in
different positions without leakage.
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Lead-acid batteries - Discharge
In the discharged state both the
positive and negative plates become
lead(II) sulfate (), and the electrolyte
loses much of its dissolved sulfuric
acid and becomes primarily water.
1
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Lead-acid batteries - Discharge
1
The discharge process is driven by the
conduction of electrons from the
negative plate back into the cell at the
positive plate in the external circuit.
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Lead-acid batteries - Discharge
1
The sum of the molecular masses of the
reactants is 642.6 g/mol, so theoretically a
cell can produce two Faraday
(unit)|faradays of charge (192,971
coulombs) from 642.6 g of reactants, or
83.4 ampere-hours per kilogram (or 13.9
ampere-hours per kilogram for a 12-volt
battery). At 2 volts per cell, this comes to
167 watt-hours per kilogram, but lead-acid
batteries in fact give only 30–40 watthttps://store.theartofservice.com/itil-2011-foundation-complete-certification-kit-fourth-edition-study-guide-ebook-and-online-course.html
Lead-acid batteries - Charging
In the charged state, each cell contains
negative plates of elemental lead (Pb) and
positive plates of lead(IV) oxide () in an
electrolyte of approximately 33.5% v/v (4.2
mol/l) sulfuric acid ().
1
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Lead-acid batteries - Charging
The charging process is driven by the
forcible removal of electrons from the
positive plate and the forcible introduction
of them to the negative plate by the
charging source.
1
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Lead-acid batteries - Charging
1
Some vendors append a suffix, indicating
the terminal types, terminal locations, and
battery dimensions. Batteries for
passenger motor vehicles usually use BCI
sizing nomenclature.
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7-Chlorokynurenic acid
1
'7-Chlorokynurenic acid' (7-CTKA) is
a NMDA receptor antagonist with
antidepressant activity in rats.
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Ocean acidification
'Ocean acidification' is the ongoing
decrease in the PH#Seawater|pH of the
Earth's oceans, caused by the uptake of
carbon dioxide () from the Earth's
atmosphere|atmosphere.
1
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Ocean acidification
1
Between 1751 and 1994 surface ocean
pH is estimated to have decreased from
approximately 8.25 to 8.14,
representing an increase of almost 30%
in Hydron (chemistry)|H+ ion
concentration in the world's
oceans.[http://www.scorint.org/OBO2009/AO_Report.pdf Report
of the Ocean Acidification and Oxygen
Working Group, International Council
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Ocean acidification
Increasing acidity is thought to have a
range of consequences, such as
depressing metabolic rates in jumbo squid,
depressing the immune responses of blue
mussels, and coral bleaching.
1
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Ocean acidification
As members of the InterAcademy
Panel, 105 academy of
sciences|science academies have
issued a statement on ocean
acidification recommending that by
2050, global emissions be reduced by
at least 50%, compared to the 1990
level., Secretariat: TWAS (the Academy
of Sciences for the Developing World),
Trieste, Italy.
1
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Ocean acidification
Ocean acidification has occurred
previously in Earth's history. The most
notable example is the PaleoceneEocene Thermal Maximum (PETM),
which occurred approximately
56million years ago. For reasons that
are currently uncertain, massive
amounts of carbon entered the ocean
and atmosphere, and led to the
dissolution of carbonate sediments in
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Ocean acidification - Carbon cycle
1
The carbon cycle describes the fluxes of
carbon dioxide () between the oceans,
Earth|terrestrial biosphere, lithosphere,
and the atmosphere. Human activities
such as the combustion of fossil fuels and
land use changes have led to a new flux of
into the atmosphere. About 45% has
remained in the atmosphere; most of the
rest has been taken up by the oceans,
with some taken up by terrestrial plants.
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Ocean acidification - Carbon cycle
The carbon cycle involves both
organic compounds such as cellulose
and inorganic carbon compounds
such as carbon dioxide and the
carbonates. The inorganic compounds
are particularly relevant when
discussing ocean acidification for it
includes many forms of dissolved
present in the Earth's oceans.
1
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Ocean acidification - Carbon cycle
1
When dissolves, it reacts with water
to form a balance of ionic and nonionic chemical species: dissolved free
carbon dioxide (), carbonic acid (),
bicarbonate () and carbonate (). The
ratio of these species depends on
factors such as seawater temperature
and alkalinity (as shown in a Bjerrum
plot). These different forms of Total
inorganic carbon|dissolved inorganic
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Ocean acidification - Acidification
Dissolving in seawater increases the
hydrogen ion () concentration in the
ocean, and thus decreases ocean pH, as
follows:
1
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Ocean acidification - Acidification
1
Ken Caldeira|Caldeira and Wickett (2003)
placed the rate and magnitude of modern
ocean acidification changes in the context
of probable historical changes during the
last 300million years.
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Ocean acidification - Acidification
1
Since the industrial revolution began, it is
estimated that surface ocean pH has
dropped by slightly more than 0.1 units on
the logarithmic scale of pH, representing
about a 29% increase in
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Ocean acidification - Rate
This rate is 100 times faster than any
changes in ocean acidity in the last
20million years, making it unlikely that
marine life can somehow adapt to the
changes.[http://blogs.nationalgeographic.c
om/blogs/news/chiefeditor/2009/12/acidific
ation.html UN: Oceans are 30 percent
more acidic than before fossil fuels] It is
predicted that, by the year 2100, the level
of acidity in the ocean will reach the levels
1
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Ocean acidification - Rate
1
The researchers determined that the
current rate of ocean acidification is
faster than at any time in the past
300million years
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Ocean acidification - Rate
A review by climate scientists at the
RealClimate blog, of a 2005 report by the
Royal Society of the UK similarly
highlighted the centrality of the rates of
change in the present anthropogenic
acidification process,
writing:[http://www.realclimate.org/index.ph
p/archives/2005/07/the-acid-ocean-theother-problem-with-cosub2sub-emission/
The Acid Ocean – the Other Problem with
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Ocean acidification - Rate
The [present] fossil fuel acidification is
much faster than natural changes, and so
the acid spike will be more intense than
the earth has seen in at least
800,000years.
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Ocean acidification - Rate
It's yet another reason to be very
seriously concerned about the amount
of carbon dioxide that is in the
atmosphere now and the additional
amount we continue to put
out.Huffington Post, 9 July 2012,
Ocean Acidification Is Climate
Change's 'Equally Evil Twin,' NOAA
Chief Says,
http://www.huffingtonpost.com/2012/
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Ocean acidification - Rate
A 2013 study claimed acidity was
increasing at a rate 10 times faster
than in any of the evolutionary crises
in the earth's history.
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Bioconversion of biomass to mixed alcohol fuels - Carboxylic acids
1
Conversion of carboxylate salts to carboxylic acids
via reactive distillation
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Bioconversion of biomass to mixed alcohol fuels - Acetic acid versus ethanol
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Cellulosic-ethanol -manufacturing plants
are bound to be net exporters of electricity
because a large portion of the
lignocellulosic biomass, namely lignin,
remains undigested and it must be burned,
thus producing electricity for the plant and
excess electricity for the grid. As the
market grows and this technology
becomes more widespread, coupling the
liquid fuel and the electricity markets will
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Bioconversion of biomass to mixed alcohol fuels - Acetic acid versus ethanol
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Acetic acid, unlike ethanol, is biologically
produced from simple sugars without the
production of carbon dioxide:
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Bioconversion of biomass to mixed alcohol fuels - Acetic acid versus ethanol
C6H12O6 → 2
CH3CH2OH + 2 CO2
(Biological production of
ethanol)
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Bioconversion of biomass to mixed alcohol fuels - Acetic acid versus ethanol
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C6H12O6 → 3 CH3COOH
(Biological production of acetic
acid)
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Bioconversion of biomass to mixed alcohol fuels - Acetic acid versus ethanol
Because of this, on a mass basis, the
yields will be higher than in ethanol
fermentation. If then, the undigested
residue (mostly lignin) is used to produce
hydrogen by gasification, it is ensured that
more energy from the biomass will end up
as liquid fuels rather than excess
heat/electricity.[http://www.osti.gov/bridge/
servlets/purl/841137-u4bFGI/841137.PDF
Eggeman, T., Verser, D., and Weber, E.
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Bioconversion of biomass to mixed alcohol fuels - Acetic acid versus ethanol
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C6H12O6 (from cellulose) + 6 H2 (from lignin)
→ 3 CH3CH2OH + 3 H2O (Overall reaction)
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Bioconversion of biomass to mixed alcohol fuels - Acetic acid versus ethanol
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A more comprehensive description of the
economics of each of the fuels is given on
the pages alcohol fuel and ethanol fuel,
more information about the economics of
various systems can be found on the
central page biofuel.
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Lactose intolerance - Stool acidity test
If the stools are acidic,
the infant is intolerant to
lactose.
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Soybean - Alpha-linolenic acid
For more information on the health
benefits of omega-3 and omega-6 fatty
acids, see Essential fatty acids.
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Soybean - Phytic acid
Soybeans contain a high level of phytic
acid, which has many effects including
acting as an antioxidant and a chelating
agent. The beneficial claims for phytic acid
include reducing cancer, minimizing
diabetes, and reducing inflammation.
However, phytic acid is also criticized for
reducing vital minerals due to its chelating
effect, especially for diets already low in
minerals.
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Ibotenic acid
Cite pmid|10435405Cite
pmid|6482962 and has shown to be
highly neurotoxic when injected
directly into the brains of mice and
rats.[http://www.erowid.org/plants/a
manitas/amanitas_info6.shtml Erowid
-- Amanitas]
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Ibotenic acid - Psychopharmacology
Unlike muscimol, the main
psychoactive drug|psychoactive
constituent of Amanita muscaria, which
produces sedative|sedative-hypnotic
effects and dissociative hallucinations,
ibotenic acid's psychoactivity is not
completely established and does not
contribute in any known way to the
effects of Amanita muscaria other than
serving as a prodrug to
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Ibotenic acid - Use in research
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When injected intracranially, ibotenic acid
causes the development of excitotoxic
lesions of the brain
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Ibotenic acid - Name
1
Ibotenic comes from the Japanese name
for the Amanita strobiliformis mushroom,
iboten(gutake), from which it was first
isolated.
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Helicobacter pylori - Adaptation to the stomach’s acidic environment
1
pylori is able to sense the pH gradient
in the mucus and move towards the
less acidic region (a process called
chemotaxis)
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Helicobacter pylori - Adaptation to the stomach’s acidic environment
1
H. pylori is found in the mucus, on the
inner surface of the epithelium, and
occasionally inside the epithelial cells
themselves. It adheres to the
epithelial cells by producing
adhesins, which bind to lipids and
carbohydrates in the epithelial cell
membrane. One such adhesion is
BabA, which binds to the Lewis
antigen system|Lewis b antigen
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Helicobacter pylori - Adaptation to the stomach’s acidic environment
In addition to using chemotaxis to
avoid areas of low pH, H. pylori also
neutralizes the acid in its
environment. It does this by
producing large amounts of urease,
which breaks down the urea present in
the stomach to carbon dioxide and
ammonia. The ammonia, which is
basic, then neutralizes stomach acid.
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Denaturation (biochemistry) - Nucleic acid denaturation
The denaturation of nucleic acids such as
DNA due to high temperatures is the
separation of a double strand into two single
strands, which occurs when the hydrogen
bonds between the strands are broken. This
may occur during polymerase chain reaction.
Nucleic acid strands realign when normal
conditions are restored during annealing
(biology)|annealing. If the conditions are
restored too quickly, the nucleic acid strands
may realign imperfectly.
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Denaturation (biochemistry) - Acids
Acidic protein
denaturants include:
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Domoic acid - Toxicology
Considerable recent research has
been carried out by the Marine
Mammal Center and other scientific
centers on the association of domoic
acid-producing harmful algal blooms
and neurological damage in marine
mammals of the Pacific Ocean.
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Domoic acid - Toxicology
Domoic acid can
bioaccumulation|bioaccumulate in
ocean|marine organisms such as shellfish,
anchovy|anchovies, and sardines that feed
on the phytoplankton known to produce
this toxin. DA can accumulate in high
concentrations in the tissues of these
plankton feeders when the toxic
phytoplankton itself is high in
concentration in the surrounding waters.
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Domoic acid - Toxicology
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In the brain, domoic acid especially damages the
hippocampus and amygdaloid nucleus
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Lipoic acid - Pharmacology and medical uses of free lipoic acid
1
Because lipoic acid is not an essential
nutrient, no Recommended Daily
Allowance (RDA) has been established
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Lipoic acid - Pharmacology and medical uses of free lipoic acid
For use in dietary supplement
materials and compounding
pharmacies, the United States
Pharmacopeia|USP has established
an official monograph for racemic
R/SLA.[http://www.drugfuture.com/Phar
macopoeia/USP32/pub/data/v32270/u
sp32nf27s0_m45550.html Alpha Lipoic
Acid C8H14O2S2 206.33]
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Lipoic acid - Possible beneficial effects
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Lipoic acid has been the subject of numerous
research studies and clinical trials:
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Lipoic acid - Possible beneficial effects
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* Prevent organ
dysfunction
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Lipoic acid - Possible beneficial effects
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* Reduce endothelial dysfunction
and improve albuminuria
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Lipoic acid - Possible beneficial effects
* Treat or prevent
cardiovascular disease
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Lipoic acid - Possible beneficial effects
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* Accelerate chronic
wound healing
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Lipoic acid - Possible beneficial effects
* Reduce levels of Asymmetric
dimethylarginine|ADMA in diabetic endstage renal disease patients on
hemodialysis
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Lipoic acid - Possible beneficial effects
* Management of
burning mouth syndrome
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Lipoic acid - Possible beneficial effects
1
* Reduce iron overload
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Lipoic acid - Possible beneficial effects
* Improve or prevent agerelated cognitive dysfunction
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Lipoic acid - Possible beneficial effects
* Prevent erectile
dysfunction (animal models)
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Lipoic acid - Possible beneficial effects
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* Treat multiple sclerosis
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Lipoic acid - Possible beneficial effects
* Inhibit Advanced glycation endproduct|advanced glycation end products
(AGE)
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Lipoic acid - Possible beneficial effects
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Borbe; Ulrich (Hrsg.) Verfasser: Reschke,
Barbara ; Borbe, Harald [Hrsg.]Verleger:
[Frankfurt (Main)] : pmi (1991) The original
rationale for using (R/S)-lipoic acid as a
nutritional supplement was that
endogenous RLA was known to have
biochemical properties like a B-vitamin
(acting as a substrate or cofactor essential
for enzyme function)
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Lipoic acid - Possible beneficial effects
1
Several papers found RLA and acetyl
carnitine reversed age-related
markers in old rats to youthful levels.
Erratum in: Proc Natl Acad Sci U S A
2002 May 14;99(10):7184-5
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Lipoic acid - Possible beneficial effects
1
RLA may function in vivo like a B-vitamin
and at higher doses like plant-derived
nutrients, such as curcumin,
sulphoraphane, resveratrol, and other
nutritional substances that induce phase II
detoxification enzymes, thus acting as
cytoprotective agents. This stress
response indirectly improves the
antioxidant capacity of the cell.
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Lipoic acid - Possible beneficial effects
1
A recent human pharmacokinetic study of
RLA demonstrated the maximum
concentration in plasma and bioavailability
are significantly greater than the free acid
form, and rivals plasma levels achieved by
intravenous administration of the free acid
form. Additionally, high plasma levels
comparable to those in animal models
where Nrf2 was activated were achieved.
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Lipoic acid - Adverse effects
1
The safety of alpha lipoic acid in pregnant
or nursing women, children, or people with
kidney or liver disease is unknown
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Lipoic acid - Antioxidant and prooxidant effects of lipoic acid
1
Dihydrolipoic acid (DHLA) can also form
intracellularly and extracellularly via nonenzymatic, thiol-disulfide exchange
reactions.
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Lipoic acid - Antioxidant and prooxidant effects of lipoic acid
The cytosolic and mitochondrial redox
state is maintained in a reduced state
relative to the extracellular matrix and
plasma due to high concentrations of
glutathione. Despite the strongly reducing
milieu, LA has been detected intracellularly
in both oxidized and reduced forms. Free
LA is rapidly metabolized to a variety of
shorter chain metabolites (via β-oxidation
and either mono or bis-methylation) that
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Lipoic acid - Antioxidant and prooxidant effects of lipoic acid
1
In cells, LA is reduced to dihydrolipoic
acid, which is generally regarded as the
more bioactive form of LA and the form
responsible for most of the antioxidant
effects
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Lipoic acid - Metal chelation
1
Alpha Lipoic Acid (ALA) has a half life of 3
hours. Lipoic acid administration can
significantly enhance biliary excretion of
inorganic mercury in rat experiments,
although it is not known if this is caused by
chelation by lipoic acid or some other
mechanism. Lipoic acid has the potential to
cross the blood–brain barrier in humans,
unlike DMSA and 2,3-Dimercapto-1propanesulfonic acid|DMPS; its
effectiveness, however, is heavily dependent
on the dosage and frequency of application.
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Lipoic acid - Medicinal differences between (R)-lipoic acid and (S)-lipoic acid
1
Preparation and use of salts of the
pure enantiomers of alpha-lipoic
acid
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Lipoic acid - Medicinal differences between (R)-lipoic acid and (S)-lipoic acid
1
Pharmaceutical compositions containing
R-alpha-lipoic acid or S-alpha.-lipoic acid
as active ingredient
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Lipoic acid - Medicinal differences between (R)-lipoic acid and (S)-lipoic acid
Lipoic acid in vivo seems primarily to
induce the oxidative stress response
rather than directly scavenge free radicals
(see above). This effect is specific for RLA.
Very few studies compare individual
enantiomers with racemic lipoic acid. It is
unclear if twice as much racemic lipoic
acid can replace RLA.
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Lipoic acid - Clinical trials and approved uses
RLA is being used in a federally funded
clinical trial for multiple sclerosis at Oregon
Health and Science University. (R)-Lipoic
acid is currently being used in two
federally funded clinical trials at Oregon
State University to test its effects in
preventing heart disease and
atherosclerosis. Alpha-lipoic acid is
approved in Germany as a drug for the
treatment of
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Lipoic acid - Intravenous Delivery
In the 1970s the first human clinical
studies using alpha-lipoic acid (ALA) in the
United States were carried out by Fredrick
C. Bartter MD, Burton M. Berkson MD
PhD, and associates from the National
Institutes of Health. They administered
intravenous ALA (racemic) to 79 people
with acute and severe liver damage at
various medical centers across the United
States and 75 recovered full liver function
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Lipoic acid - Intravenous Delivery
Dr.'s Bartter and Berkson were
subsequently appointed the FDA chief
investigators for this therapeutic
agent and Dr. Berkson went on to use
it successfully for the treatment of
chronic liver disease (viral hepatitis,
autoimmune hepatitis, etc.)
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Lipoic acid - Intravenous Delivery
1
Because of ALA's ability to modify gene
expression by stabilizing NF kappa B
transcription, Berkson started using
intravenous ALA for the treatment of
various cancers for which no effective
treatments exist. In a 2006 publication, he
and co-authors described the long term
survival of a patient with metastatic
pancreatic cancer using ALA and various
oral antioxidants
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Lipoic acid - Intravenous Delivery
Berkson, B. M., Rubin, D. M., and
Berkson, A. J. (2006) The long-term
survival of a patient with pancreatic
cancer with metastases to the liver
after treatment with the intravenous
alpha-lipoic acid/low-dose naltrexone
protocol. Integr Cancer Ther 5, 83-9..
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Calorie restriction - Insufficient calories and amino acids for exercise
1
Calorie restriction comes into conflict with
the high caloric needs of
sportsperson|athletes, and may not
provide them sufficient energy levels or
amino acids for repair, although this is not
a criticism of CR per se, since it is
certainly possible to be an unhealthy
athlete or an athlete destined to die at a
young age due to poor diet, stresses, etc
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Antioxidant - Uric acid
1
The antioxidant effects of uric acid have
led researchers to suggest this mutation
was beneficial to early primates and
humans
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Antioxidant - Uric acid
With respect to multiple sclerosis,
Gwen Scott explains the significance of
uric acid as an antioxidant by
proposing that Serum UA levels are
inversely associated with the incidence
of multiple sclerosis|MS in humans
because MS patients have low serum
UA levels and individuals with
hyperuricemia (gout) rarely develop the
disease
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Antioxidant - Uric acid
1
Uric acid's antioxidant activities are also
complex, given that it does not react with
some oxidants, such as superoxide, but
does act against peroxynitrite, peroxides,
and hypochlorous acid
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Antioxidant - Ascorbic acid (vitamin C)
1
Ascorbic acid is present at high levels
in all parts of plants and can reach
concentrations of 20millimolar in
chloroplasts.
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Carbon nanotube chemistry - Covalent reactivity via acid-oxidation
Studies in 2007 revealed that the acidoxidation of SWCNTs generated
carbonaceous fragments, resulting from
the acid-oxidation of the SWCNT
structure, which are immobilised to the
outer surface of the SWCNT. After
purification and removal of these
fragments indicated that the final SWCNT
structure bore no acidic groups and that
these carbonaceous fragments may be the
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Alginic acid - Potassium alginate
1
Potassium alginate is widely used in foods
as a Stabilizer (food)|stabilizer, thickener,
and emulsifier.
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Alginic acid - Potassium alginate
1
Its use as a pharmaceutical excipient is
currently limited to experimental
hydrogel systems. The viscosity,
adhesiveness, Elasticity
(physics)|elasticity, stiffness, and
cohesiveness of potassium alginate
hydrogels have been determined and
compared with values from a range of
other hydrogel-forming materials. The
effect of calcium ions on the
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Excitatory amino acid antagonist
1
An 'excitatory amino acid antagonist' is a
pharmacological agent which acts to
decrease the stimulation of receptors for
excitatory amino acids (primarily
glutamate).
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Industrial wastewater treatment - Treatment of acids and alkalis
Acids and alkalis can usually be
Neutralization (chemistry)|neutralised
under controlled conditions. Neutralisation
frequently produces a Precipitation
(chemistry)|precipitate that will require
treatment as a solid residue that may also
be toxic. In some cases, gasses may be
evolved requiring treatment for the gas
stream. Some other forms of treatment are
usually required following neutralisation.
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Industrial wastewater treatment - Treatment of acids and alkalis
Waste streams rich in hard
water|hardness ions as from deionisation processes can readily lose
the hardness ions in a buildup of
precipitated calcium and magnesium
salts
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Digestate - Acidogenic digestate
1
Acidogenic digestate is fibrous and
consists of structural plant matter
including lignin and cellulose.
Acidogenic digestate has high
moisture retention properties. The
digestate may also contain minerals
and remnants of bacteria.
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Fatty acid methyl ester
1
'Fatty acid methyl esters' ('FAME') are a
type of fatty acid ester that can be
produced by an alkali-catalyzed reaction
between fats or fatty acids and methanol.
The molecules in biodiesel are primarily
FAMEs, usually obtained from vegetable
oils by transesterification.
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Fatty acid methyl ester
1
Since every microorganism has its specific
FAME profile (microbial fingerprinting), it
can be used as a tool for microbial source
tracking (MST). The types and
proportions of fatty acids present in
cytoplasm membrane and outer
membrance (gram negative) lipids of cells
are major phenotypic traits.
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Fatty acid methyl ester
Clinical analysis can determine the
lengths, bonds, rings and branches of the
FAME. To perform this analysis, a
bacterial culture is taken, and the fatty
acids extracted and used to form methyl
esters. The volatile derivatives are then
introduced into a gas chromatography|gas
chromatagraph, and the patterns of the
peaks help identify the organism. This is
widely used in characterizing new species
1
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Fertilizers - Soil acidification
1
The use of such acidulated fertilizers in the
tropical and semi-tropical regions of
Indonesia and Malaysia has contributed to
soil degradation on a large scale from
aluminium toxicity, which can only be
countered by applications of limestone or
preferably magnesian dolomite, which
neutralises acid soil pH and also provides
essential magnesium.
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Fertilizers - Soil acidification
1
Nitrogen-containing inorganic and organic
fertilizers can cause soil acidification when
added.http://www.sciencemag.org/cgi/cont
ent/full/324/5928/721b#R1http://soil.scijournals.org/cgi/content/f
ull/72/1/238 This may lead to decreases in
nutrient availability which may be offset by
liming (soil)|liming.
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Kainic acid - Applications
1
* neuroscience
research
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Kainic acid - Applications
1
** neurodegenerative agent
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Amino acid
Structurally they can be classified
according to the functional groups'
locations as Alpha and beta carbon|alpha(α-), beta- (β-), gamma- (γ-) or delta- (δ-)
amino acids; other categories relate to
Chemical polarity|polarity, pH level, and
side chain group type (aliphatic, Openchain compound|acyclic, aromatic,
containing hydroxyl or sulfur, etc.) In the
form of proteins, amino acids comprise the
1
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Amino acid
They include the 22 Proteinogenic amino
acid|proteinogenic (protein-building) amino acids
1
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Amino acid
1
Atta-Ur-Rahman others, p.299 Codon–
transfer RNA|tRNA combinations not
found in nature can also be used to
Expanded genetic code|expand the
genetic code and create novel proteins
known as alloproteins incorporating nonproteinogenic amino acids.
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Amino acid
For example: in the human brain,
glutamate (standard glutamic acid) and
gamma-amino-butyric acid (GABA, nonstandard gamma-amino acid) are
respectively the main
Neurotransmitter#Excitatory and
inhibitory|excitatory and inhibitory
neurotransmitters; hydroxyproline (a major
component of the connective tissue
collagen) is synthesised from proline; the
1
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Amino acid
Essential amino acids may also differ
between species.For example, ruminants
such as cows obtain a number of amino
acids via microbes in the
reticulorumen|first two stomach chambers.
1
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Amino acid
1
Because of their biological significance,
amino acids are important in nutrition and
are commonly used in nutritional
supplements, fertilizers, and food
technology. Industrial uses include the
production of drugs, biodegradable
plastics and asymmetric catalysis|chiral
catalysts.
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Amino acid - History
1
In 1902, Hermann Emil Fischer|Emil
Fischer and Franz Hofmeister
proposed that proteins are the result of
the formation of bonds between the
amino group of one amino acid with
the carboxyl group of another, in a
linear structure which Fischer termed
peptide.
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Amino acid - General structure
1
In some amino acids, the amine group is
attached to the β or γ-carbon, and these
are therefore referred to as beta or gamma
amino acids.
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Amino acid - General structure
1
Amino acids are usually classified by
the chemical property|properties of
their side-chain into four groups. The
side-chain can make an amino acid a
weak acid or a weak base|weak basic
(chemistry)|base, and a hydrophile if
the side-chain is polar
molecule|polar or a hydrophobe if it
is nonpolar. The chemical structures
of the 22 standard amino acids, along
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Amino acid - General structure
In chemical terms, proline is,
therefore, an imino acid, since it lacks
a amine|primary amino group,
although it is still classed as an amino
acid in the current biochemical
nomenclature, and may also be called
an N-alkylated alpha-amino acid.
1
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Amino acid - Isomerism
The L and D convention for amino
acid configuration refers not to the
optical activity of the amino acid
itself, but rather to the optical activity
of the isomer of glyceraldehyde from
which that amino acid can, in theory,
be synthesized (D-glyceraldehyde is
dextrorotary; L-glyceraldehyde is
levorotatory).
1
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Amino acid - Isomerism
Cysteine is unusual since it has a
sulfur atom at the second position in
its side-chain, which has a larger
atomic mass than the groups attached
to the first carbon, which is attached
to the α-carbon in the other standard
amino acids, thus the (R) instead of
(S).
1
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Amino acid - Zwitterions
1
Amino acids also exist as zwitterions
in the solid phase, and crystallize with
salt-like properties unlike typical
organic acids or amines.
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Amino acid - Isoelectric point
Zwitterions have minimum solubility at
their isolectric point and some amino acids
(in particular, with non-polar side-chains)
can be isolated by precipitation from water
by adjusting the pH to the required
isoelectric point.
1
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Amino acid - Standard amino acids
1
The order in which the amino acids are
added is read through the genetic code
from an Messenger RNA|mRNA template,
which is a RNA copy of one of the
organism's genes.
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Amino acid - Standard amino acids
1
Twenty-two amino acids are naturally
incorporated into polypeptides and
are called proteinogenic or natural
amino acids
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Amino acid - Non-standard amino acids
1
Aside from the 22 standard amino acids,
there are many other amino acids that are
called non-proteinogenic or non-standard.
Those either are not found in proteins (for
example carnitine, Gamma-aminobutyric
acid|GABA), or are not produced directly
and in isolation by standard cellular
machinery (for example, hydroxyproline
and selenomethionine).
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Amino acid - Non-standard amino acids
1
Non-standard amino acids that are found
in proteins are formed by post-translational
modification, which is modification after
translation during protein synthesis
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Amino acid - Non-standard amino acids
1
A rare exception to the dominance of
α-amino acids in biology is the βamino acid beta alanine (3aminopropanoic acid), which is used
in plants and microorganisms in the
synthesis of pantothenic acid (vitamin
B5), a component of coenzyme A.
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Amino acid - In human nutrition
1
Glucogenic amino acids can also be converted into
glucose, through gluconeogenesis.
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Amino acid - In human nutrition
1
The amounts required also depend on
the age and health of the individual,
so it is hard to make general
statements about the dietary
requirement for some amino acids.
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Lipids - Fatty acids
1
Most naturally occurring fatty acids
are of the cis configuration, although
the trans form does exist in some
natural and partially hydrogenated
fats and oils.
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Lipids - Fatty acids
Fatty esters include important
biochemical intermediates such as
wax esters, fatty acid thioester
coenzyme A derivatives, fatty acid
thioester Acyl carrier protein|ACP
derivatives and fatty acid carnitines
1
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Lesch-Nyhan syndrome - Overproduction of uric acid
One of the first symptoms of the
disease is the presence of sand-like
crystals of uric acid in the diapers of
the affected infant. Overproduction of
uric acid may lead to the development
of uric acid crystals or stones in the
kidneys, ureters, or Urinary
bladder|bladder. Such crystals
deposited in joints later in the disease
may produce gout-like arthritis, with
1
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Lesch-Nyhan syndrome - Overproduction of uric acid
1
The serum uric acid concentration is often
normal, as the excess purines are
promptly eliminated in the urine
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Antifreeze - Organic acid technology
Certain cars are built with organic acid
technology (OAT) antifreeze (e.g., DEXCOOL[http://www.havoline.com/products/n
a/antifreeze_01.html Products: North
America: Anti Freeze/Coolants].
Havoline.com (2003-01-31). Retrieved on
2011-01-01.), or with a hybrid organic acid
technology (HOAT) formulation (e.g.,
Zerex G-05), both of which are claimed to
have an extended service life of five years
1
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Antifreeze - Organic acid technology
One of the anti-corrosion components
presented as Sodium or Potassium 2ethylhexanoate and Ethylhexanoic acid is
incompatible with Nylon 6,6 and Silicone
rubber, and is known as Plasticizer
1
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Antifreeze - Organic acid technology
DEX-COOL antifreeze uses two
inhibitors: sebacate and 2-EHA (2ethylhexanoic acid), the latter which
works well with the hard water found in
the US, but is a plasticizer which can
cause gaskets to leak.
1
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Antifreeze - Organic acid technology
1
According to internal GM documents,
the ultimate culprit appears to be
operating vehicles for long periods of
time with low coolant levels
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Antifreeze - Organic acid technology
Honda and Toyota's new extended life
coolant use OAT with sebacate but without
the 2-EHA. Some added phosphates
provide protection while the OAT builds up.
Honda specifically excludes 2-EHA from
their formulas.
1
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Antifreeze - Hybrid organic acid technology
1
HOAT coolants typically mix an OAT with a
traditional inhibitor, such as silicates or
phosphates.
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Antifreeze - Hybrid organic acid technology
1
G05 is a low-silicate, phosphate free formula that
includes the benzoate inhibitor.
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Excitatory amino acid agonist
1
A 'excitatory amino acid agonist' is a
pharmacological agent which acts to
increase the stimulation of receptors
for excitatory amino acids (primarily
glutamate).
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Nuclear magnetic resonance spectroscopy - Nucleic acids
Nucleic acid NMR is the use of NMR
spectroscopy to obtain information about
the structure and dynamics of polynucleic
acids, such as DNA or RNA. , nearly half
of all known RNA structures had been
determined by NMR spectroscopy.
1
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Nuclear magnetic resonance spectroscopy - Nucleic acids
The types of NMR usually done with
nucleic acids are Proton NMR|1H or
proton NMR, Carbon-13 NMR|13C NMR,
Nitrogen-15 NMR|15N NMR, and
Phosphorus-31 NMR|31P NMR
1
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Nuclear magnetic resonance spectroscopy - Nucleic acids
1
NMR is also useful for probing the binding
of nucleic acid molecules to other
molecules, such as proteins or drugs, by
seeing which resonances are shifted upon
binding of the other molecule.
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Albumin human - Amino acid sequence
The approximate sequence of human serum
albumin is:http://www.uniprot.org/uniprot/P02768
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Albumin human - Amino acid sequence
1
The italicized first 24 amino acids are
signal and propeptide portions not
observed in the transcribed, translated,
and transported protein but present in
the gene. There are 609 amino acids in
this sequence with only 585 amino
acids in the final product observed in
the blood.
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Rennet - Acid coagulation
1
Milk can also be coagulated by
adding an acid, such as citric
acid.
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Rennet - Acid coagulation
1
The acidification can also come from bacterial
fermentation such as in cultured milk.
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Benzoic acid - Carboxyl group
1
* Benzoic acid esters are the product of the
acid catalysed reaction with alcohols.
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Benzoic acid - Carboxyl group
1
* Benzoic acid amides are more easily
available by using activated acid
derivatives (such as benzoyl chloride) or
by coupling reagents used in peptide
synthesis like
Dicyclohexylcarbodiimide|DCC and 4Dimethylaminopyridine|DMAP.
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Benzoic acid - Carboxyl group
* The more active benzoic acid
anhydride|anhydride is formed by
dehydration using acetic anhydride or
phosphorus pentoxide.
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Benzoic acid - Carboxyl group
* Highly reactive acid derivatives
such as Acyl halide|acid halides are
easily obtained by mixing with
halogenation agents like phosphorus
chlorides or thionyl chloride.
1
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Benzoic acid - Carboxyl group
1
* Orthoesters can be obtained by the
reaction of alcohols under acidic
water free conditions with
benzonitrile.
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Benzoic acid - Carboxyl group
1
* Reduction to benzaldehyde and
benzyl alcohol is possible using
DIBAL-H, lithium aluminium
hydride|LiAlH4 or sodium
borohydride.
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Benzoic acid - Carboxyl group
* The copper catalysed
decarboxylation of benzoate to
benzene may be effected by heating in
quinoline. Also, Hunsdiecker
decarboxylation can be achieved by
forming the silver salt and heating.
Benzoic acid can also be
decarboxylated by heating with an
alkali hydroxide or calcium
hydroxide.
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Anticonvulsant - Fatty acids
1
* The valproic acid|valproates mdash;
valproic acid, sodium valproate, and
divalproex sodium (1967).
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Biosynthesis - Amino acids
The other amino acids, valine,
methionine, leucine, isoleucine,
phenylalanine, lysine, threonine and
tryptophan for adults and histidine,
and arginine for babies are obtained
through diet.
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Biosynthesis - The glutamate family of amino acids
The glutamate family of amino acids
includes the amino acids that derive from
the amino acid glutamate. This family
includes: glutamate, glutamine, proline,
and arginine. This family also includes the
amino acid lysine, which is derived from αketoglutarate.
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Biosynthesis - The glutamate family of amino acids
The biosynthesis of glutamate and
glutamine is a key step in the nitrogen
assimilation discussed above. The
enzymes GOGAT and Glutamate
dehydrogenase|GDH catalyze the
nitrogen assimilation reactions.
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Biosynthesis - The glutamate family of amino acids
Pyrroline-5-carboxylate is further
reduced by the enzyme pyrroline-5carboxylate reductase (P5CR) to yield
a proline amino acid.
1
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Biosynthesis - The glutamate family of amino acids
1
In the first step of arginine biosynthesis in
bacteria, glutamate is acetylated by
transferring the acetyl group from acetylCoA at the N-α position; this prevents
spontaneous cyclization
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Biosynthesis - The glutamate family of amino acids
1
There are two distinct lysine biosynthetic
pathways: the diaminopimelic acid
pathway, and the Alpha-aminoadipate
pathway|α-amionoadipate pathway, which
is not present in prokaryotes. The most
common of the two synthetic pathways is
the diaminopimelic acid pathway; it
consists of several enzymatic reactions
that add carbon groups to aspartate to
yield lysine:
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Biosynthesis - The glutamate family of amino acids
# Aspartate kinase initiates the
diaminopimelic acid pathway by
phosphorylating aspartate and producing
aspartyl phosphate.
1
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Biosynthesis - The glutamate family of amino acids
# Aspartate-semialdehyde
dehydrogenase|Aspartate semialdehyde
dehydrogenase catalyzes the NADPHdependent reduction of aspartyl phosphate
to yield aspartate semialdehyde.
1
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Biosynthesis - The glutamate family of amino acids
1
# Dihydrodipicolinate synthase catalyzes
the condensation reaction of pyruvate with
aspartate semialdehyde to yield 2,3dihydrodipicolinate.
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Biosynthesis - The glutamate family of amino acids
1
# Dihydrodipicolinate reductase
catalyzes the reduction of 2,3dihydrodipicolinate by NADPH to
yield Δ’-piperideine-2,6dicarboxylate.
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Biosynthesis - The glutamate family of amino acids
# Tetrahydrodipicolinate Nacetyltransferase|Tetrahydrodipicolinate
acyltransferase catalyzes the acetylation
reaction that results in ring opening and
yields N-acetyl α-amion-ε-ketopimelate.
1
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Biosynthesis - The glutamate family of amino acids
# Succinyldiaminopimelate
transaminase|N-succinyl-α-amion-εketopimelate-glutamate
aminotransaminase catalyzes the
transamination reaction that removes
the keto group of N-acetyl α-amion-εketopimelate and replaces it with an
amino group to yield N-succinyl-Ldiaminopimelate.
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Biosynthesis - The glutamate family of amino acids
# succinyl-diaminopimelate
desuccinylase|N-acyldiaminopimelate
deacylase catalyzes the deacylation of
N-succinyl-L-diaminopimelate to yield
L,L-diaminopimelate.
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Biosynthesis - The glutamate family of amino acids
# Diaminopimelate
decarboxylase|DAP decarboxylase
catalyzes the removal of the carboxyl
group, yielding L-lysine.
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Biosynthesis - The serine family of amino acids
The serine family of amino acid
includes: serine, cysteine, and glycine.
Most microorganisms and plants obtain
the sulfur for synthesizing methionine
from the amino acid cysteine.
Furthermore, the conversion of serine
to glycine provides the carbons needed
for the biosynthesis of the methionine
and histidine.
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Biosynthesis - The serine family of amino acids
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During serine biosynthesis, the enzyme
phosphoglycerate dehydrogenase
catalyzes the initial reaction that
oxidizes 3-phospho-D-glycerate to yield
Phosphohydroxypyruvic acid|3phosphonooxypyruvate
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Biosynthesis - The serine family of amino acids
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There are two known pathways
for the biosynthesis of glycine
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Biosynthesis - The serine family of amino acids
Cysteine biosynthesis is a two-step
reaction that involves the
incorporation of inorganic sulfur. In
microorganisms and plants, the
enzyme Serine Oacetyltransferase|serine
acetyltransferase catalyzes the
transfer of acetyl group from acetylCoA onto L-serine to yield O-acetyl-Lserine. The following reaction step,
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Biosynthesis - The aspartate family of amino acids
The aspartate family of amino acids
includes: threonine, lysine, methionine,
isoleucine, and aspartate. Lysine and
isoleucine are considered part of the
aspartate family even though part of their
carbon skeleton is derived from pyruvate.
In the case of methionine, the methyl
carbon is derived from serine and the
sulfur group, but in most organisms, it is
derived from cysteine.
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Biosynthesis - The aspartate family of amino acids
# Aspartate kinase catalyzes the
initial step in the diaminopimelic acid
pathway by transferring a phosphoryl
from ATP onto the carboxylate group
of aspartate, which yields aspartyl-βphosphate.
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Biosynthesis - The aspartate family of amino acids
# Aspartate-semialdehyde
dehydrogenase catalyzes the
reduction reaction by
dephosphorylation of aspartyl-βphosphate to yield aspartate-βsemialdehyde.
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Biosynthesis - The aspartate family of amino acids
# 4-hydroxy-tetrahydrodipicolinate
synthase|Dihydrodipicolinate synthase
catalyzes the Condensation
reaction|condensation reaction of
aspartate-β-semialdehyde with pyruvate to
yield dihydrodipicolinic acid.
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Biosynthesis - The aspartate family of amino acids
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# Dihydrodipicolinate reductase|4hydroxy-tetrahydrodipicolinate
reductase catalyzes the reduction of
dihydrodipicolinic acid to yield
tetrahydrodipicolinic acid.
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Biosynthesis - The aspartate family of amino acids
# 2,3,4,5-tetrahydropyridine-2,6dicarboxylate Nsuccinyltransferase|Tetrahydrodipico
linate N-succinyltransferase catalyzes
the transfer of a succinyl group from
succinyl-CoA on to
tetrahydrodipicolinic acid to yield Nsuccinyl-L-2,6-diaminoheptanedioate.
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Biosynthesis - The aspartate family of amino acids
# N-succinyldiaminopimelate
aminotransferase catalyzes the transfer of
an amino group from glutamate onto Nsuccinyl-L-2,6-diaminoheptanedioate to
yield N-succinyl-L,L-diaminopimelic acid.
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Biosynthesis - The aspartate family of amino acids
# Succinyldiaminopimelate
transaminase|Succinyl-diaminopimelate
desuccinylase catalyzes the removal of
acyl group from N-succinyl-L,Ldiaminopimelic acid to yield L,Ldiaminopimelic acid.
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Biosynthesis - The aspartate family of amino acids
# Siaminopimelate decarboxylase
catalyzes the final step in lysine
biosynthesis that removes the carbon
dioxide group from meso-diaminopimelic
acid to yield L-lysine.
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Gel electrophoresis - Nucleic acids
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In the case of nucleic acids, the direction
of migration, from negative to positive
electrodes, is due to the naturally
occurring negative charge carried by their
sugar-phosphate backbone.
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Gel electrophoresis - Nucleic acids
Therefore, agents that disrupt the
hydrogen bonds, such as sodium
hydroxide or formamide, are used to
denature the nucleic acids and cause
them to behave as long rods
again.Troubleshooting DNA agarose
gel electrophoresis
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Gel electrophoresis - Nucleic acids
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Gel electrophoresis of large DNA or
RNA is usually done by agarose gel
electrophoresis. See the Chain
termination method page for an
example of a polyacrylamide DNA
sequencing gel. Characterization
through ligand interaction of nucleic
acids or fragments may be performed
by mobility shift affinity
electrophoresis.
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Gel electrophoresis - Nucleic acids
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Electrophoresis of RNA samples can
be used to check for genomic DNA
contamination and also for RNA
degradation. RNA from eukaryotic
organisms shows distinct bands of 28s
and 18s rRNA, the 28s band being
approximately twice as intense as the
18s band. Degraded RNA has less
sharpely defined bands, has a
smeared appearance, and intensity
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Canola - Erucic acid issues
Although wild rapeseed oil contains
significant amounts of erucic acid, a
known toxin, the cultivar used to produce
commercial, food-grade canola oil was
plant breeding|bred to contain less than
2% erucic acid, levels that are not believed
to cause harm in humans, and no health
effects have been associated with
consumption by humans of the genetically
modified oil
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Canola - Erucic acid issues
The Chinese and Indians have used
rapeseed oils for thousands of years, but
the form used was unrefined (natural),
which may make a difference in effect on
health.
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Multiplex (assay) - Nucleic acid-based multiplex techniques
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* DNA microarray used for gene expression or
Single nucleotide polymorphism|SNP detection
assays
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Multiplex (assay) - Nucleic acid-based multiplex techniques
* DNA sequencing#High-throughput
sequencing|High-throughput
sequencing which can produce millions
of short DNA sequences in parallel
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Multiplex (assay) - Nucleic acid-based multiplex techniques
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* Multiplex PCR for applications requiring the
amplification or sequencing of DNA or RNA
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Multiplex (assay) - Nucleic acid-based multiplex techniques
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* Multiplex Ligation-dependent
Probe Amplification (MLPA)
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Multiplex (assay) - Nucleic acid-based multiplex techniques
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* Sequencing by ligation|DNA
sequencing by ligation
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Multiplex (assay) - Nucleic acid-based multiplex techniques
* Luminex/XMAP is bead based
multiplexing, where beads are
internally dyed with fluorescent dyes to
produce a specific spectral address
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