Download IB104 - Lecture 7 - Molecules of life

IB104 - Lecture 7 - Molecules of life
Reading - Chapter 3 (but not individual amino acid structures)
Buckminster Fuller was a famous American architect who designed
domes. Soccer balls used to use the same C60 architecture. Fullerenes are
now major players in nanotechnology. Life involves organic molecules that are based on carbon. You are
familiar with inorganic carbon, like graphite, diamonds, and hopefully
Buckminsterfullerenes or buckyballs (handout).
Jan 10 1964
graphite
diamond
Buckminsterfullerene C60
Carbon can make four covalent bonds. Carbon has the atomic number
6, and atomic weight 12. Thus six each of protons, neutrons, and
electrons. These electrons occupy the inner orbital completely with two,
and then one each in the four second level orbitals. This means there are
four electrons available to form four stable covalent bonds by “pairing”
with electrons from other atoms.
If we simply add hydrogens to carbon we have hydrocarbons, e.g.
methane.
Keep doing this with multiple carbons and you get propane, etc. Long
hydrocarbon chains are the stuff of natural gas and oil. Also rings, e.g.
benzene.
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1. Carbohydrates are the simplest of the four major kinds of
biochemicals (a subset of organic molecules) involved in life.
Carbohydrates are the basic energy sources and stores for all
organisms, and are also commonly structural. The simplest carbohydrates are the monomers called sugars, known
technically as monosaccharides (from the same root as the word
saccharin for the artificial sweetener). Glucose and fructose are two
major ones. These are six carbon sugars, in the form of a ring with
hydroxyl (-OH) groups on most of the carbons and a double-bond
ketone or aldehyde group somewhere (C=O and H-C=O).
Disaccharides consist of two such monomers. Famous examples are:
Sucrose (common sugar) formed from glucose and fructose.
Maltose (e.g. for beer) is two glucose monomers together.
Lactose (e.g. in mammalian milk) is glucose and galactose.
While fructose is a normal sugar we consume all the time in foods, it is
metabolized somewhat differently from glucose, hence some believe that
high-fructose drinks and other foods are part of the obesity problem. Sucrose
Linear
OR
“weird” ring
Polysaccharides are many sugar monomers joined together. This joining
chemical reaction involves loss of a water molecule from two hydroxyls
leaving an ester bond, so is variously called condensation or synthesis
or dehydration. The opposite reaction is hydrolysis (splitting or lysis
with water). These two reactions mediate every example of monomers to
polymers we will consider today.
condensation
hydrolysis
Plus H2O
Polysaccharides fill both energy storage and structural roles.
Glycogen is the animal storage
form and has many branching
chains of glucose monomers. This
is your first energy source after
using free glucose in the blood
stream. Exchange between
glycogen and glucose is regulated
by hormones like insulin and
glucagon. Diabetes results from
mis-regulation of this exchange.
Starch is the plant storage form
and has linear stiff chains. It is
therefore useful for making collars
on shirts stiff. Animals eat starch in
plants like corn and potatoes, etc.,
hydrolyse it to glucose, and then
store it as glycogen.
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Chitin is the animal structural form
making the exoskeletons of arthropods
and nematodes (and cell walls of fungi).
Most animals cannot digest it.
Cellulose is the plant structural form
and constitutes the outer walls of plant
cells. Wood is dried out cellulose - it
consists of cross-linked polysaccharides.
Again, most animals cannot digest it.
2. Lipids are primarily involved
in energy storage and
membrane structure, but there
are also waxes for protection
against desiccation, and unusual
lipids that function as hormones.
Most lipids are made up of
monomers called fatty acids.
These are long hydrocarbon
chains, e.g. 20 carbons, with a
carboxyl or acid group (HOC=O) on the end (acid because
they easily release a H+ ion in
solution in water). Linoleic acid
is one example. These are the
monomeric building blocks that
are put together in various ways.
Triglycerides are the major polymer of fatty acids, consisting of a threecarbon alcohol (glycerol) linked to three fatty acids by condensation
reactions and the loss of three water molecules. This is the form in which
fatty acids are stored in our bodies as fat to provide energy when needed.
The fatty acid chains can be saturated, or unsaturated, meaning that at
least one carbon-carbon bond is a double bond - which causes the fatty
acid to kink. “bad”
“good”
Triglycerides with saturated fatty acids can be packed more tightly and
typically are solid at room temperature, e.g. animal fats like butter and
lard. Those with at least one unsaturated fatty acid are usually liquid at
room temperatures, generally plant oils like olive and coconut oil.
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Phospholipids are triglycerides with one of the fatty acids replaced by a
phosphate group, which gives it an ambivalent character, with one side
being polar and the other nonpolar, and they make up membranes.
Waxes involve various combinations of long fatty acids; they are
nonpolar and hydrophobic. They commonly function to protect plants
from water loss, form the combs in honey bee nests, protect our outer
ear passage, and are employed by us in innumerable ways (e.g. skiing).
polar
nonpolar
Finally, there is a group of lipids that do not have fatty acids. These can
be long chains too, or rings, the most famous being the steroids, which
are all based on a backbone provided by cholesterol. These are some of
the lipid hormones such as testosterone and oestrogen.
3. Proteins bring us to another level of complexity, where the building
blocks are rather varied, and the final polymers are essentially infinitely
varied. Proteins are both the building blocks of cells and the enzymes
that facilitate all cellular activities. They also do almost everything else,
from being hormones to energy reserves of last resort, and we will have
occasion to learn about several of them during this course. Generic structure of the monomer, an amino acid.
Amino group
(basic)
Carboxyl
group
(acidic)
R group
(20 kinds with distinct
properties in the 20 amino
acids found in proteins)
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8 of the 20 amino acids showing the range of R groups possible. Note
that glycine is the most simple with a single hydrogen R group.
tyrosine (tyr)
lysine (lys)
glutamate (glu)
UNCHARGED,
POLAR AMINO ACID
POSITIVELY CHARGED,
POLAR AMINO ACID
NEGATIVELY CHARGED,
POLAR AMINO ACID
valine (val)
phenylalanine (phe)
methionine (met)
glycine (gly)
Note the very different sizes of the R groups. I only require memorizing
the names of two of these amino acids. Both have sulfur atoms in their R
groups. They are cysteine, and methionine (shown below; cysteine is
similar to methionine but doesn’t have the methyl or CH3 group attached
to the sulfur on the end of the R group).
proline (pro)
alanine
(ala)
valine
(val)
tryptophan
(trp)
methionine
(met)
proline
(pro)
Polypeptide chains are formed by condensation reactions between AAs.
All 20 amino acids
Take biochemistry if you
want to learn them all.
newly
forming
polypeptide
chain
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A. The primary or 1D structure of proteins is the linear arrangement of
covalently linked amino acids. Note that there is a polarity to proteins;
they always start with an amino group and end with a carboxy group.
These are sometimes abbreviated as the N- and C-termini of proteins.
B. The secondary or 2D structure of proteins is maintained by
hydrogen bonds, between the carboxy group of one amino acid and the
amino group of another.
disulfide bridges
Amino acid sequence of two linked polypeptides that make up the
protein hormone insulin. Note that the two are linked via disulfide
bonds between cysteines. This is common for extra-cellular proteins and
these disulfide bonds help maintain the protein structure.
Linus Pauling first proposed the alpha
helical structure for proteins. He was
the greatest American chemist,
responsible for much of theoretical
chemistry. He proposed the alpha
helical secondary structure for proteins
in the early 1950s, and received the
Nobel Prize in Chemistry in 1954.
Later he became a peace activist
opposing the US and Russian atom
bomb programs and won the Nobel
Peace prize in 1962. He is the only
person ever to win two unshared
Nobel prizes. He spent the last part of
his life promoting the usefulness of
megadoses of vitamin C, but
nevertheless died 18 years ago in his long-time home of California.
Alpha helix
Hydrogen
bonds within
a strand
Beta pleated sheet
Hydrogen bonds between strands
C. The tertiary or 3D structure of proteins is maintained by a
combination of hydrogen bonds and weaker Van der Waals forces. This
final structure is also known as the conformation of the protein and this
shape determines its properties and abilities, e.g. globular enzymes, long
rigid structural proteins, ion channels that span membranes, etc.
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D. Some proteins are only functional when several individual proteins
join together in a quaternary structure. The most famous example is
hemoglobin with four subunits (2 alpha chains and 2 beta chains), each
with its own heme group carrying an oxygen molecule. The alpha and
beta chains differ slightly.
beta
chain
beta
chain
heme
group
twists and
coils in the
polypeptide
chain of a
globin
molecule
alpha
chain
4. The nucleic acids - monomers carry energy and signals, while
polymers are the medium of inheritance and protein synthesis.
Monomer is a nucleotide, made up of three parts, a 5-carbon ribose
sugar ring, a ringed base that includes nitrogens, and 1-3 phosphates.
The best known of these monomers is ATP or adenosine adenine
triphosphate, the universal carrier of energy in biology,
pictured here.
alpha
chain
Dinucleotides: Nucleotides can be connected together by condensation
reactions to give dinucleotides, e.g. NAD or nicotinamide adenine
dinucleotide that also carries energy in the form of an attached
hydrogen as NADH.
The nucleic acid polymers are the single-stranded RNA and doublestranded DNA, and we will consider their structure and synthesis in
more detail later - as we will protein synthesis.
nicotinamide
RNA
DNA
adenine
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