Download PPT - Hss-1.us

The Chemistry of Life
:
• Text: BJ Chap 2, AP Chap 5
• Reading Assignments
– BJ Chap 2 pp 38 – 69, AP pp129 - 166
• Homework Assignment
– Chap 2 Review Questions pp 40-41
2A. Basic Chemistry (BJ – pp 38
-54, AP pp 129 – 143)
•
•
BJ: 2A1 – Matter (AP p 129)
Matter – anything that occupies space and has mass. In ordinarily chemical reactions
matter can neither be created or destroyed, so it is said to conserve.
•
Energy - Energy is the quality or dimension that describes the amount of work that can be
performed by a force, an attribute of objects and systems that is subject to a conservation
law. Different forms of energy include kinetic, potential, thermal, gravitational, sound, light,
elastic, and electromagnetic energy. The forms of energy are often named after a related
force.
•
Any form of energy can be transformed into another form, but the total energy always
remains the same. This principle, the conservation of energy.
•
Chemical energy is that part of the energy in a substance that can be released by a
chemical reaction.
•
For non-nuclear related reactions, matter and energy can be thought of as different having
following three own conservation laws. But with Einstein’s theory of relativity showing the
equivalence of matter and energy through the relationship of E = mc2, we now often refer
to the conservation of matter and energy or mass and energy.
Element and Atoms – (AP pp
129-134)
• An element: is a pure substance that cannot be broken down into
simpler substance by ordinary chemical means.
– Pure substance that from form one type of atom that is defined by its
atomic number; that is, by the number of protons in its nucleus. The
term is also used to refer to a pure chemical substance composed of
atoms with the same number of protons.
– There are 92 - 94 naturally occurring elements and several manmade
elements
– As of 2007 117 elements have been observed as of 2007, 94 occur
naturally on Earth New elements are discovered from time to time
through artificial nuclear reactions.
– All chemical matter consists of these elements
– Elements with atomic numbers greater than 82 (i.e,. bismuth and those
above), are inherently unstable and undergo radioactive decay. In
addition, elements 43 and 61 (technetium and promethium) have no
stable isotopes, and also decay.
Types of Elements
•
•
•
•
-- Monatomic
-- Diatomic
-- Polyatomic
Element Symbols - - Most common See
periodic Chart. Must know the most common.
• -- H, He, O, C, Na, Cl, N,
• to life:
• Most abundant in human body O, C, H, N, Ca
–P, K, S, Cl, Na, Mg, Cu, F, Fe, I, Zn
Atoms
•
•
An atom: the smallest component of an element having the chemical properties of
the element
Periodic Table: The periodic table (BJ p 39 not in AP) of the chemical elements or just
the periodic table is a table of all the element based upon the atomic number of the
element
–
–
–
–
–
–
–
Atomic– number – number of protons of an atom or ion – also number of electrons of a
neutral atom - always a who number usually in the upper left corner of element on table . It is
the atomic number or number of protons that determines the number of valence electrons
that in turn determines the chemical properties of an atom. So the type of atom is defined by
the number of protons.
Atomic Mass- the mass of an atom expressed in atomic mass units. The atomic mass of an
atom may be considered to be the total mass of protons, neutrons and electrons in a single
atom
Average Atomic Mass (weight): - the average mass of an atom and it isotopes expressed in
atomic mass units. This is the number on the periodic table.
Series – the line of element in increasing atomic number
Groups – the column of elements that group element with same valence or outer electrons.
Valence electrons: outer shell electrons
Rule of the octave (eights): The shells of an atom want 8 electrons (except inner) most shell
– s- which only needs 2.
Bohr or planetary atomic
model
• Show picture of Bohr model (BJ p
40, AP p 130.
Division of Matter
• Matter
• Mixtures Pure Substances
• Heterogeneous Homogeneous
Elements
• Compounds
• Elements and Their Symbols –
see periodic table
Chemical Bonds:
•
•
•
•
•
•
•
•
•
•
•
Sharing or “borrowing” outer shell – valence – electrons.
Follow rule of the octave
S - , P 8, D 8 and so on
Ionic bonds – borrowing electrons – not really consider a bond, but
an ionic attraction’note – electron with proton is intra-molecular
interactions
Intermolecular interaction Example Na+ ClCovalent Bonds - sharing of electrons – true bond – very strong
bonds
Intermolecular bond
Single Bond
Double Bond
Triple Bond
Vader Walls Bonds
• Vader Walls – Hydrogen Bonds –
weak interactions – not a true bonds
cases by
• permanent dipole–permanent dipole
forces
• permanent dipole–induced dipole
forces
• induced dipole-induced dipole
Molecules and Chemical
Compounds (AP p 134 – 136)
•
•
•
•
•
Single atoms Monatomic: In physics and chemistry, monatomic is a combination of
the words "mono" and "atomic," and means "single atom." It is usually applied to
gases: a monatomic gas is one in which atoms are not bound to each other.
At standard temperature and pressure (STP), all of the noble gases are monatomic.
These are helium, neon, argon, krypton, xenon and radon. The heavier noble gases
can form compounds, but the lighter ones are unreactive. All elements will be
monatomic in the gas phase at sufficiently high temperatures.
Molecules: Molecules are formed when atoms linked together (AP 134 – 135)
Diatomic molecules are molecules composed only of two atoms, of either the same
or different chemical elements. The prefix di- means two in Greek. Common diatomic
molecules are hydrogen, nitrogen, oxygen, and carbon monoxide. Most elements
aside from the noble gases form diatomic molecules when heated, but high
temperatures - sometimes thousands of degrees - are often required.
Chemical compound: a substance consisting of two or more elements chemicallybonded together in a fixed proportion by mass. The basic unit (smallest unit that has
these properties) of a compound is the molecule.
Chemical Symbols and
Formulas of Compounds
• -- Use of subscript - goes with
prior symbol
• -- Use of coefficient - in front of
atom or compound
Chemical and Physical Properties
and changes (AP p 136 – 137)
• -- Physical properties can be observed or measured without
changing the composition of matter. Physical properties are used to
observe and describe matter. Physical properties include:
appearance, texture, color, odor, melting point, boiling point, density,
solubility, polarity, and many others.
• -- Chemical properties of matter describes its "potential" to
undergo some chemical change or reaction by virtue of its
composition. What elements, electrons, and bonding are present to
give the potential for chemical change. It is quite difficult to define a
chemical property without using the word "change". Eventually you
should be able to look at the formula of a compound and state some
chemical property.
Chemical and Physical
Changes
• -- Physical changes occur when objects undergo a change that
does not change their chemical nature. A physical change involves a
change in physical properties. Physical properties can be observed
without changing the type of matter. Physical changes are
reversible. Examples of physical properties include: texture, shape,
size, color, odor, volume, mass, weight, and density.
• -- Chemical changes are the changes in a substance through
chemical reactions. The chemical reactants form a new product with
equal mass.
• The following can indicate that a chemical change took place,
although this evidence is not conclusive:
– * Change of color (e.g., rusting of iron causes a change in color from silver to
reddish-brown).
– * Change in temperature or energy, such as the production (exothermic) or loss
(endothermic) of heat.
– * Change of form (burning paper) (this change is difficult to reverse).
– * An unexpected change in color
– * Light, heat, or sound is given off.
– * gasses formed, often appearing as bubbles.
– * Formation of precipitate (insoluble particles).
– * The decomposition of organic matter (rotting food)
•
For example, placing a pot of water on a hot stove element causes a change in
temperature and gas to be released (water vapor) but a chemical change did not take
place. It was simply a physical change / change of state. An example could be a log
that is burning.
•
A chemical reaction produces new substances by changing the way in which atoms
look. In a chemical reaction old bonds are broken and new bonds are formed
between different atoms. This breaking and forming of bonds takes place when
particles of the original materials collide with one another. An example of a chemical
change is fireworks.
2A2 Energy (BJ 43)
• Energy: the ability to perform work (move something
over a distance) ability to do work - to cause motion
(create a force and act over a distance)
• Forms or Energy Different forms of energy include
kinetic, potential, thermal, gravitational, sound, light,
elastic, and electromagnetic energy. The forms of energy
are often named after a related force.
• Transformation of Energy Any form of energy can be
transformed into another form, but the total energy
always remains the same. This principle, the
conservation of energy.
Thermodynamics:
•
Zeroth law of thermodynamics: If two thermodynamic systems are each in thermal equilibrium
with a third, then they are in thermal equilibrium with each other.
•
First law of thermodynamics: Law of energy conservation - first law of thermodynamics. Energy
can neither be created or destroyed, but can transformed from one form of energy to the other.
•
Law of conservation of mass-energy (E=mc2) - Matter is very concentrated energy - consistent
with scripture?
•
Second Law of Thermodynamics: The second law of thermodynamics is an expression of the
universal law of increasing entropy, stating that the entropy of an isolated system which is not in
equilibrium will tend to increase over time, approaching a maximum value at equilibrium.
•
There are many versions of the second law, but they all have the same effect, which is to explain
the phenomenon of irreversibility in nature.
•
Third law of thermodynamics: Heat flows (conducts) from Hot to Cold As temperature
approaches absolute zero, the entropy of a system approaches a constant.
• Combined law of thermodynamics: a mathematical
summation of the first law of thermodynamics and the
second law of thermodynamics subsumed into a single
concise mathematical statement as shown below:
• dU - TdS + pdV <= 0
• Here, U is internal energy, T is temperature, S is entropy,
p is pressure, and V is volume. In theoretical structure in
addition to the obvious inclusion of the first two laws, the
combined law incorporates the implications of the zeroth
law, via temperature T, and the third law, through its use
of free energy as related to the calculation of chemical
affinities near absolute zero.
Energy, Heat, Temperature
• Energy - Ability to do work (displace) cause movement (Force)
• Heat: Thermal energy in transit Kinetic Energy - Energy of motion,
consists of both potential and kinetic energy or the total energy of
the molecules.
• Temperature - Average KE of motions
• Kinetic Energy – energy by virtue of motion (1/2mv2)
• Kinetic Molecular Energy –KE of moving molecules (BJ: p 44)
• Thermal Energy - All motion (KE) straight, vibration, rotation
• Potential Energy - Energy by virtue OF position.
• Potential Energy of a Molecule - Energy by virtue of position Page
45.
The Measurement of
Energy
• Energy - SI Joule F x ds = n - meter = ma meter
= m m2/s2
• Erg - cgs = dyne - cm
• - British - BTU
• - Calorie - amount of energy to raise one gram
of water 1 degree C
– -- Food calorie is actually a Kilocalorie
Temperature Scales
• Celsius – based upon freezing and
boiling point of water (0 and 100 C)
• Kelvin - Based upon absolute scale 0
K = no energy K = 273 + C)
• Fahrenheit – Based on normal
temperature range humans
experience (in UK) 0 coldest – 100
warmest C = 5/9 (F-32) F = (9/5C)+32
States of Matter (AP p 138)
•
Solids, Liquid, Gas, Plasma and Ne very low Bose-Einstein
condensate)
•
- Progressively Higher energy states
•
- Plasma
•
-New Bose-Einstein condensate - at close to absolute 0 matter acts as
one large atom
•
Change of States
– Melting - Freezing (water T = 0 C for both)
– Evaporation – Condensation
– Sublimation - Deposition
Types of reactions
•
-- Exothermic - gives off energy A + B -> C + D + energy
•
-- Endothermic -- Absorbs energy A + B + energy -> C + D
•
Catalyst (AP 145): Catalysis is the process in which the rate of a chemical reaction is either
increased or decreased by means of a chemical substance known as a catalyst. Unlike other
reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself.
The catalyst may participate in multiple chemical transformations. Catalysts that speed the
reaction are called positive catalysts. Catalysts that slow down the reaction are called negative
catalysts or inhibitors. Substances that increase the activity of catalysts are called promoters and
substances that deactivate catalysts are called catalytic poisons.
•
Enzymes: Enzymes are biomolecules (organic molecules) that catalyze (i.e., increase the rates
of) chemical reactions. Nearly all known enzymes are proteins. However, certain RNA molecules
can be effective biocatalysts too. These RNA molecules have come to be known as ribozymes. In
enzymatic reactions, the molecules at the beginning of the process are called substrates, and the
enzyme converts them into different molecules, called the products. (see BJ pp56-57)
BJ 2 (p 47) A-3 Solutions (AP p138)
•
Solution: a homogeneous mixture of one or more substances with another substance
•
Solute: A substance that dissolved in another substance, usually the component of a solution
present in the lesser amount.
•
Solvent: A solvent is a liquid or gas that dissolves a solid, liquid, or gaseous solute, resulting in a
solution
•
Concentration: In chemistry, concentration is the measure of how much of a given substance
there is mixed with another substance. This can apply to any sort of chemical mixture, but most
frequently the concept is limited to homogeneous solutions, where it refers to the amount of solute
in the solvent.
•
Concentration Gradient (BJ p50): A gradient is a measurement of how much something
changes as you move from one region to another. So a concentration gradient is a measurement
of how the concentration of something changes from one place to another.
http://www.mit.edu/~kardar/teaching/projects/chemotaxis(AndreaSchmidt)/gradients.htm
•
Diffusion – BJ p51 AP 140
• Diffusion – BJ p51 AP 140: the process by which molecules
spread from areas of high concentration, to areas of low
concentration.
• Diffusion Pressure: The concentration gradient will create a force
that can be expressed as energy per unit volume (E/V) or pressure
(F/A).
• Osmosis – BJ p52 AP 141: Osmosis is a selective diffusion process
driven by the internal energy of the solvent molecules.
• Semi-Permermeable Membrane: A semi-permeable membrane,
also termed a selectively-permeable membrane, a partiallypermeable membrane or a differentially-permeable membrane, is a
membrane that will allow certain molecules or ions to pass through it
by diffusion and occasionally specialized "facilitated diffusion."
Acids, Bases Buffers (BJ: pp 53-54)
• There is actually no completely unique definition of an
acid ion bases. But the following is the most basic and
useful for biology
• Acid: Any substances that give up a proton (H+) when
dissolved
• Base; Any substance that give up a hydroxyl ion OHwhen dissolved
• Ph: a measure of the acidity or basicity of a solution. It is
defined as a relative measure (from 0 – 14) of the activity
of dissolved hydrogen ions (H+). The lower the number
the more acidic. The higher the number the more basic.
0 – 6.9 is acid, 7 is neutral and 7.1 – 14 is basic.
• Buffer: any substance that will combine with an H+ or
OH- (whichever is in excess) to maintain proper Ph
• Acid Base reaction: This is when an
acid and base reactive to neutralize
each other. The general formula is
• Acid + Base ỵ→ Salt + water example
HCL + NaOH =>→ NaCl + H2O
BJ 2B Organic Chemistry
AP p 146 - 161
•
Inorganic versus Organic Chemistry
•
Inorganic Chemistry: Inorganic chemistry is the branch of chemistry concerned with
the properties and behavior of inorganic compounds. This field covers all chemical
compounds except the myriad organic compounds (compounds containing C-H
bonds), which are the subjects of organic chemistry. The distinction between the two
disciplines is far from absolute, and there is much overlap, most importantly in the
sub-discipline of organometallic chemistry.
•
Organic Chemistry: Organic chemistry is a discipline within chemistry which
involves the scientific study of the structure, properties, composition, reactions, and
preparation (by synthesis or by other means) of chemical compounds that contain
carbon. These compounds may contain any number of other elements, including
hydrogen, nitrogen, oxygen, the halogens as well as phosphorus, silicon and sulfur.
•
Vitalism: chemistry alone and that life is in some part self-determining.
2B-1 Organic Compounds
•
An organic compound is any member of a large class of chemical compounds
whose molecules contain carbon. For historical reasons discussed below, a few types
of compounds such as carbonates, simple oxides of carbon and cyanides, as well as
the allotropes of carbon, are considered inorganic. The division between "organic"
and "inorganic" carbon compounds while "useful in organizing the vast subject of
chemistry...is somewhat arbitrary"
•
Carbon Bonds: Carbon has four valence bonds, giving it the greatest possible
covalent bonding potential. Because of the unique bonding properties of carbon,
there are millions of different organic chemicals. Each one has unique properties.
There are organic chemicals that make up your hair, your skin, even your fingernails.
All life as we know it is made up of organic compounds. Carbon (C) appears in the
2nd row of the periodic table and has atomic number of 6. Given our discussion of
electron shells it is easy to see that carbon has 4 electrons in its valence shell. Since
carbon needs 8 electrons to fill its valence shell, it forms 4 bonds with other atoms
(each bond consisting of one of carbon's electrons and one of the bonding atom's).
Every valence electron participates in bonding, thus a carbon atom's bonds will be
distributed evenly over the atom's surface. These bonds form a tetrahedron, as
illustrated below:
An organic molecule (hydrocarbon) is formed when
carbon bonds to hydrogen. The simplest hydrocarbon
consists of 4 hydrogen atoms bonded to a carbon atom
(called methane):
• Carbon Backbone: Chain or ring of carbon that forms
the basis for the rest of the atoms.
• Functional Groups: In organic chemistry, functional
groups are specific groups of atoms within molecules
that are responsible for the characteristic chemical
reactions of those molecules. The same functional group
will undergo the same or similar chemical reaction(s)
regardless of the size of the molecule it is a part of.
However, its relative reactivity can be modified by nearby
functional groups. (see p56 for table of functional
groups)
2B -2 Carbohydrates and Lipids
• Biomolecules: A biomolecule is any organic molecule that is
produced by a living organism, including large polymeric molecules
such as proteins, polysaccharides (carbohydrates), and nucleic
acids as well as small molecules such as primary metabolites,
secondary metabolites, and natural products.
• As organic molecules, biomolecules consist primarily of carbon and
hydrogen, nitrogen, and oxygen, and, to a smaller extent,
phosphorus and sulfur. Other elements sometimes are incorporated
but are much less common.
• A diverse range of biomolecules exist, including:
* Small molecules:
• o Lipid, phospholipid, glycolipid, sterol,
glycerolipid
• o Vitamin
• o Hormone, neurotransmitter
• o Carbohydrate, sugar
•
* Monomers:
• o Amino acids
• o Nucleotides
• o Monosaccharides
* Polymers:
• o Peptides, oligopeptides, polypeptides,
proteins
• o Nucleic acids, i.e. DNA, RNA
• o Oligosaccharides, polysaccharides
(including cellulose)
• o Lignin
Carbohydrates
•
Carbohydrates [α] or saccharides[β] are the most abundant of the four major classes of
biomolecules of . , lipids, carbohydrates (saccharides), proteins, and nucleic acids.
•
the four major chemical groupings of carbohydrates are: monosaccharide, disaccharide,
oligosaccharide, and polysaccharide.
•
They fill numerous roles in living things, such as the storage and transport of energy (eg: starch,
glycogen) and structural components (eg: cellulose in plants and chitin). Additionally,
carbohydrates and their derivatives play major roles in the working process of the immune system,
fertilization, pathogenesis, blood clotting, and development.
•
Carbohydrates make up most of the organic matter on Earth because of their extensive roles in all
forms of life. First, carbohydrates serve as energy stores, fuels, and metabolic intermediates.
Second, ribose and deoxyribose sugars form part of the structural framework of RNA and DNA.
Third, polysaccharides are structural elements in the cell walls of bacteria and plants. In fact,
cellulose, the main constituent of plant cell walls, is one of the most abundant organic compounds
in the biosphere. Fourth, carbohydrates are linked to many proteins and lipids, where they play
key roles in mediating interactions between cells and interactions between cells and other
elements in the cellular environment.
• Chemically, carbohydrates are simple organic
compounds that are aldehydes or ketones with many
hydroxyl groups added, usually one on each carbon
atom that is not part of the aldehyde or ketone functional
group. The basic carbohydrate units are called
monosaccharides; examples are glucose, galactose, and
fructose. The general stoichiometric formula of an
unmodified monosaccharide is (C·H2O)n, where n is any
number of three or greater; however, not all
carbohydrates conform to this precise stoichiometric
definition (eg: uronic acids, deoxy-sugars such as
fucose), nor are all chemicals that do conform to this
definition automatically classified as carbohydrates.[2]
Monosaccharides
• Monosaccharides The basic carbohydrate units– examples:
glucose, galactose, and fructose - can be linked together into what
are called polysaccharides (or oligosaccharides) in a large variety of
ways. Many carbohydrates contain one or more modified
monosaccharide units that have had one or more groups replaced or
removed. For example, deoxyribose, a component of DNA, is a
modified version of ribose; chitin is composed of repeating units of
N-acetylglucosamine, a nitrogen-containing form of glucose.
• While the scientific nomenclature of carbohydrates is complex, the
names of carbohydrates very often end in the suffix -ose.
Glycoinformatics is the specialized field of study that deals with the
specific and unique bioinformatics of carbohydrates.
• Glucose – example of monosaccharide
Disaccharides
• A disaccharide is the carbohydrate formed when two
monosaccharides undergo a condensation reaction
(dehydration synthesis) which involves the elimination of
a small molecule, such as water, from the functional
groups only. Like monosaccharides, disaccharides also
dissolve in water, taste sweet and are called sugars.[1]
• 'Disaccharide' is one of the four chemical groupings of
carbohydrates (monosaccharide, disaccharide,
oligosaccharide, and polysaccharide).
Example of a disaccharides
Lactose
Sucrose
Oligosaccharide
• Oligosaccharide is a saccharide polymer containing a
small number (typically three to ten of component
sugars, also known as simple sugars. The name is
derived from the Greek word oligos, meaning "a few",
and from the Latin/Greek word sacchar which means
"sugar". Oligosaccharides can have many functions for
example, they are commonly found on the plasma
membrane of animal cells where they can play a role in
cell-cell recognition.
• They are generally found either O- or N-linked to
compatible amino acid side chains in proteins or to lipid
moieties
Polysaccharides
•
Polysaccharides are polymeric carbohydrate structures, formed of repeating units
(either mono- or di-saccharides) joined together by glycosidic bonds. These
structures are often linear, but may contain various degrees of branching.
Polysaccharides are often quite heterogeneous, containing slight modifications of the
repeating unit. Depending on the structure, these macromolecules can have distinct
properties from their monosaccharide building blocks. They may be amorphous or
even insoluble in water.
•
When all the monosaccharides in a polysaccharide are the same type the
polysaccharide is called a homopolysaccharide, but when more than one type of
monosaccharide is present they are called heteropolysaccharides.
•
Examples include storage polysaccharides such as starch and glycogen, and
structural polysaccharides such as cellulose and chitin.
•
Polysaccharides have a general formula of Cx(H2O)y where x is usually a large
number between 200 and 2500. Considering that the repeating units in the polymer
backbone are often six-carbon monosaccharides, the general formula can also be
represented as (C6H10O5)n where 40≤n≤3000
Starch
• Starch: Starch or amylum is a polysaccharide carbohydrate
consisting of a large number of glucose units joined together by
glycosidic bonds. Starch is produced by all green plants as an
energy store and is a major food source for humans.
• Pure starch is a white, tasteless and odorless powder that is
insoluble in cold water or alcohol. It consists of two types of
molecules: the linear and helical amylose and the branched
amylopectin. Depending on the plant, starch generally contains 20 to
25% amylose and 75 to 80% amylopectin. Glycogen, the glucose
store of animals, is a more branched version of amylopectin.
• Starch can be used as a thickening, stiffening or gluing agent when
dissolved in warm water, giving wheatpaste.
Glycogen
•
Glycogen is the molecule which functions as the secondary short term
energy storage in animal cells. It is made primarily by the liver and the
muscles, but can also be made by glycogenesis within the brain and
stomach. Glycogen is the analogue of starch, a less branched glucose
polymer in plants, and is commonly referred to as animal starch, having a
similar structure to amylopectin. Glycogen is found in the form of granules in
the cytosol in many cell types, and plays an important role in the glucose
cycle. Glycogen forms an energy reserve that can be quickly mobilized to
meet a sudden need for glucose, but one that is less compact than the
energy reserves of triglycerides (fat). In the liver hepatocytes, glycogen can
compose up to 8% of the fresh weight (100–120 g in an adult) soon after a
meal. Only the glycogen stored in the liver can be made accessible to other
organs. In the muscles, glycogen is found in a much lower concentration
(1% to 2% of the muscle mass), but the total amount exceeds that in the
liver. However the amount of glycogen stored in the body , especially within
the red blood cells liver & muscles, mostly depends on physical training,
basal metabolic rate and eating habits . Small amounts of glycogen are
found in the kidneys, and even smaller amounts in certain glial cells in the
brain and white blood cells. The uterus also stores glycogen during
pregnancy to nourish the embryo.
Cellulose
•
Cellulose is an organic compound with the formula
(C6H10O5)Template:Chem/dispAAA, a polysaccharide consisting of a linear chain of
several hundred to over ten thousand β(1→4) linked D-glucose units.
•
Cellulose is the structural component of the primary cell wall of green plants, many
forms of algae and the oomycetes. Some species of bacteria secrete it to form
biofilms. Cellulose is the most common organic compound on Earth. About 33
percent of all plant matter is cellulose (the cellulose content of cotton is 90 percent
and that of wood is 50 percent).
•
For industrial use, cellulose is mainly obtained from wood pulp and cotton. It is mainly
used to produce cardboard and paper; to a smaller extent it is converted into a wide
variety of derivative products such as cellophane and rayon. Converting cellulose
from energy crops into biofuels such as cellulosic ethanol is under investigation as an
alternative fuel source.
•
Some animals, particularly ruminants and termites, can digest cellulose with the help
of symbiotic micro-organisms that live in their guts. Cellulose is not digestible by
humans and is often referred to as 'dietary fiber' or 'roughage', acting as a hydrophilic
bulking agent for feces.
Chitin
• Chitin (C8H13O5N)n (pronounced /ˈkaɪtɨn/) is a longchain polymer of a N-acetylglucosamine, a derivative of
glucose, and is found in many places throughout the
natural world. It is the main component of the cell walls
of fungi, the exoskeletons of arthropods, such as
crustaceans (e.g. crabs, lobsters and shrimps) and
insects, including ants, beetles and butterflies, the radula
of mollusks and the beaks of cephalopods, including
squid and octopuses. Chitin has also proven useful for
several medical and industrial purposes. Chitin is a
biological substance which may be compared to the
polysaccharide cellulose and to the protein keratin.
Although keratin is a protein, and not a carbohydrate like
chitin, both keratin and chitin have similar structural
functions.
Lipids
•
Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fatsoluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids,
and others. The main biological functions of lipids include energy storage, as structural
components of cell membranes, and as important signaling molecules.
•
Lipids may be broadly defined as hydrophobic or amphiphilic small molecules; the amphiphilic
nature of some lipids allows them to form structures such as vesicles, liposomes, or membranes
in an aqueous environment. Biological lipids originate entirely or in part from two distinct types of
biochemical subunits or "building blocks": ketoacyl and isoprene groups. Using this approach,
lipids may be divided into eight categories: fatty acyls, glycerolipids, glycerophospholipids,
sphingolipids, saccharolipids and polyketides (derived from condensation of ketoacyl subunits);
and sterol lipids and prenol lipids (derived from condensation of isoprene subunits).
•
Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids
called triglycerides. Lipids also encompass molecules such as fatty acids and their derivatives
(including tri-, di-, and monoglycerides and phospholipids), as well as other sterol-containing
metabolites such as cholesterol. Although humans and other mammals use various biosynthetic
pathways to both break down and synthesize lipids, some essential lipids cannot be made this
way and must be obtained from the diet.
Fatty acid
•
Fatty acid is a carboxylic acid often with a long unbranched aliphatic tail (chain),
which is either saturated or unsaturated. Carboxylic acids as short as butyric acid (4
carbon atoms) are considered to be fatty acids, whereas fatty acids derived from
natural fats and oils may be assumed to have at least eight carbon atoms, caprylic
acid (octanoic acid), for example. Most of the natural fatty acids have an even
number of carbon atoms, because their biosynthesis involves acetyl-CoA, a
coenzyme carrying a two-carbon-atom group (see fatty acid synthesis).
•
Fatty acids are produced by the hydrolysis of the ester linkages in a fat or biological
oil (both of which are triglycerides), with the removal of glycerol. See oleochemicals.
•
Fatty acids are aliphatic monocarboxylic acids derived from, or contained in esterified
form in an animal or vegetable fat, oil, or wax. Natural fatty acids commonly have a
chain of four to 28 carbons (usually unbranched and even numbered), which may be
saturated or unsaturated. By extension, the term is sometimes used to embrace all
acyclic aliphatic carboxylic acids. This would include acetic acid, which is not usually
considered a fatty acid because it is so short that the triglyceride triacetin made from
it is substantially miscible with water and is thus not a lipid.
Hydrophilic:
•
Hydrophile, from the Greek (hydros) "water" and φιλια (philia) "friendship," refers to a
physical property of a molecule that can transiently bond with water (H2O) through
hydrogen bonding. This is thermodynamically favorable, and makes these molecules
soluble not only in water, but also in other polar solvents. There are hydrophilic and
hydrophobic parts of the cell membrane.
•
A hydrophilic molecule or portion of a molecule is one that is typically chargepolarized and capable of hydrogen bonding, enabling it to dissolve more readily in
water than in oil or other hydrophobic solvents. A hydrophilic is made up of alcohol
and fatty acyl chains. Hydrophilic and hydrophobic molecules are also known as polar
molecules and nonpolar molecules, respectively. Some hydrophilic substances do not
dissolve. This type of mixture is called a colloid. Soap has a hydrophilic head and a
hydrophobic tail, which allows it to dissolve in both waters and oils, therefore allowing
the soap to clean a surface.
•
An approximate rule of thumb for hydrophilicity of organic compounds is that solubility
of a molecule in water is more than 1 mass % if there is at least one neutral
hydrophile group per 5 carbons, or at least one electrically charged hydrophile group
per 7 carbons.
Hydrophobic:
•
hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear
phobos) refers to the physical property of a molecule (known as a hydrophobe) that is
repelled from a mass of water.
•
•
Hydrophobic molecules tend to be non-polar and thus prefer other neutral molecules
and nonpolar solvents. Hydrophobic molecules in water often cluster together forming
micelles. Water on hydrophobic surfaces will exhibit a high contact angle.
•
Examples of hydrophobic molecules include the alkanes, oils, fats, and greasy
substances in general. Hydrophobic materials are used for oil removal from water, the
management of oil spills, and chemical separation processes to remove non-polar
from polar compounds.
•
Hydrophobic is often used interchangeably with lipophilic, "fat loving." However, the
two terms are not synonymous. While hydrophobic substances are usually lipophilic,
there are exceptions—such as the silicones and fluorocarbons.
Triglyceride
•
Triglyceride (help·info) (more properly known as Triacylglycerol.ogg triacylglycerol
(help·info), TAG or triacylglyceride) is a glyceride in which the glycerol is esterified
with three fatty acids. It is the main constituent of vegetable oil and animal fats.
•
Triglycerides are the chemical form in which most fat exists in food as well as in the
body. They're also present in blood plasma and, in association with cholesterol, form
the plasma lipids.
•
Triglycerides in plasma are derived from fats eaten in foods or made in the body from
other energy sources like carbohydrates. Calories ingested in a meal and not used
immediately by tissues are converted to triglycerides and transported to fat cells to be
stored. Hormones regulate the release of triglycerides from fat tissue so they meet
the body's needs for energy between meals.
•
Excess triglycerides in plasma is called hypertriglyceridemia. It's linked to the
occurrence of coronary artery disease in some people. Elevated triglycerides may be
a consequence of other disease, such as untreated diabetes mellitus. Like
cholesterol, increases in triglyceride levels can be detected by plasma
measurements. These measurements should be made after an overnight food and
alcohol fast.
Saturates versus Unsaturated:
• An unsaturated fat is a fat or fatty acid in which there are one or
more double bonds in the fatty acid chain. A fat molecule is
monounsaturated if it contains one double bond, and
polyunsaturated if it contains more than one double bond. Where
double bonds are formed, hydrogen atoms are eliminated. Thus, a
saturated fat is "saturated" with hydrogen atoms. In cellular
metabolism hydrogen-carbon bonds are broken down – or oxidized
– to produce energy, thus an unsaturated fat molecule contains
somewhat less energy (i.e fewer calories) than a comparable sized
saturated fat. The greater the degree of unsaturation in a fatty acid
(ie, the more double bonds in the fatty acid), the more vulnerable it
is to lipid peroxidation (rancidity). Antioxidants can protect
unsaturated fat from lipid peroxidation. Unsaturated fats also have a
more enlarged shape than saturated fats.[citation needed]
Phospholipids
• Phospholipids are a class of lipids and
are a major component of all cell
membranes. Most phospholipids contain a
diglyceride, a phosphate group, and a
simple organic molecule such as choline;
one exception to this rule is
sphingomyelin, which is derived from
sphingosine instead of glycerol. They are
a type of molecule. They form a lipid
bilayer within a cell membrane.
Sterols
• Sterols are an important class of organic
molecules. They occur naturally in plants,
animals and fungi, with the most familiar type of
animal sterol being cholesterol, which has been
shown to contribute to high blood pressure and
heart disease. Within the past decade, interest in
plant sterols as a dietary supplement has
increased, due to studies showing that they can
contribute to lower cholesterol levels.
2B-3 Proteins and Nuclear Acids
(p62)
•
Proteins (also known as polypeptides) are organic compounds made of amino acids arranged in a linear chain. The amino acids in a
polymer chain are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The
sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic
code specifies 20 standard amino acids, however in certain organisms the genetic code can include selenocysteine — and in certain
archaea — pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational
modification, which alter the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins.
Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.
•
Amino Acids: amino acid is a molecule containing both amine and carboxyl functional groups. These molecules are particularly
important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic
substituent. In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon.
The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a
hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan.
•
Amino acids are critical to life, and have a variety of roles in metabolism. One particularly important function is as the building blocks of
proteins, which are linear chains of amino acids. Amino acids are also important in many other biological molecules, such as forming
parts of coenzymes, as in S-adenosylmethionine, or as precursors for the biosynthesis of molecules such as heme. Due to this central
role in biochemistry, amino acids are very important in nutrition.
•
The amino acids are commonly used in food technology and industry. For example, monosodium glutamate is a common flavor enhancer
that gives foods the taste called umami. Beyond the amino acids that are found in all forms of life, amino acids are also used in industry,
with the production of biodegradable plastics, drugs and chiral catalysts being particularly important applications.
Peptides:
•
Peptides are short polymers formed from the linking, in a defined order, of α-amino acids. The link
between one amino acid residue and the next is known as an amide bond or a peptide bond.
•
Proteins are polypeptide molecules (or consist of multiple polypeptide subunits). The distinction is
that peptides are short and polypeptides/proteins are long. There are several different conventions
to determine these, all of which have caveats and nuances.
•
Four levels of a Protein structure and Peptide to functioning protein – (BJ p 63-64)
•
Nucleic Acids: A nucleic acid is a macromolecule composed of chains of monomeric nucleotides.
In biochemistry these molecules carry genetic information or form structures within cells. The most
common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids
are universal in living things, as they are found in all cells and viruses. Nucleic acids were first
discovered by Friedrich Miescher in 1871.
•
Artificial nucleic acids include peptide nucleic acid (PNA), Morpholino and locked nucleic acid
(LNA), as well as glycol nucleic acid (GNA) and threose nucleic acid (TNA). Each of these is
distinguished from naturally-occurring DNA or RNA by changes to the backbone of the molecule.
DNA:
•
DNA: Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in
the development and functioning of all known living organisms and some viruses. The main role of
DNA molecules is the long-term storage of information. DNA is often compared to a set of
blueprints or a recipe, or a code, since it contains the instructions needed to construct other
components of cells, such as proteins and RNA molecules. The DNA segments that carry this
genetic information are called genes, but other DNA sequences have structural purposes, or are
involved in regulating the use of this genetic information.
•
DNA – Structure: Chemically, DNA consists of two long polymers of simple units called
nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These
two strands run in opposite directions to each other and are therefore anti-parallel. Attached to
each sugar is one of four types of molecules called bases. It is the sequence of these four bases
along the backbone that encodes information. This information is read using the genetic code,
which specifies the sequence of the amino acids within proteins. The code is read by copying
stretches of DNA into the related nucleic acid RNA, in a process called transcription.
•
Within cells, DNA is organized into X-shaped structures called chromosomes. These
chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic
organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and
some of their DNA in the mitochondria (animals and plants) and chloroplasts (plants only).
Prokaryotes (bacteria and archaea) however, store their DNA in the cell's cytoplasm. Within the
chromosomes, chromatin proteins such as histones compact and organize DNA. These compact
structures guide the interactions between DNA and other proteins, helping control which parts of
the DNA are transcribed.
Nucleotides
• Nucleotides are molecules that, when joined together,
make up the structural units of RNA and DNA.
Additionally, nucleotides play central roles in metabolism.
In that capacity, they serve as sources of chemical
energy (adenosine triphosphate and guanosine
triphosphate), participate in cellular signaling (cyclic
guanosine monophosphate and cyclic adenosine
monophosphate), and are incorporated into important
cofactors of enzymatic reactions (coenzyme A, flavin
adenine dinucleotide, flavin mononucleotide, and
nicotinamide adenine dinucleotide phosphate).
DNA – Replication:
•
DNA – Replication: Cell division is essential for an organism to grow, but when a cell divides it must replicate the
DNA in its genome so that the two daughter cells have the same genetic information as their parent. The doublestranded structure of DNA provides a simple mechanism for DNA replication. Here, the two strands are separated
and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This
enzyme makes the complementary strand by finding the correct base through complementary base pairing, and
bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction,
different mechanisms are used to copy the antiparallel strands of the double helix. In this way, the base on the old
strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.
•
DNA replication, the basis for biological inheritance, is a fundamental process occurring in all living organisms to
copy their DNA. This process is "semiconservative" in that each strand of the original double-stranded DNA
molecule serves as template for the reproduction of the complementary strand. Hence, following DNA replication,
two identical DNA molecules have been produced from a single double-stranded DNA molecule. Cellular
proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.
•
In a cell, DNA replication begins at specific locations in the genome, called "origins". Unwinding of DNA at the
origin, and synthesis of new strands, forms a replication fork. In addition to DNA polymerase, the enzyme that
synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are
associated with the fork and assist in the initiation and continuation of DNA synthesis.
•
DNA replication can also be performed in vitro (outside a cell). DNA polymerases, isolated from cells, and artificial
DNA primers are used to initiate DNA synthesis at known sequences in a template molecule. The polymerase
chain reaction (PCR), a common laboratory technique, employs such artificial synthesis in a cyclic manner to
amplify a specific target DNA fragment from a pool of DNA.
RNA
•
RNA: Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide
units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to
DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is
usually double-stranded; RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that
lacks one oxygen atom); and RNA has the base uracil rather than thymine that is present in DNA.
•
RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other
enzymes. RNA is central to the synthesis of proteins. Here, a type of RNA called messenger RNA carries
information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal
RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the
information they carry into proteins. There are many RNAs with other roles – in particular regulating which genes
are expressed, but also as the genomes of most viruses.
•
Transcription is the synthesis of RNA under the direction of DNA. RNA synthesis, or transcription, is the process
of transcribing DNA nucleotide sequence information into RNA sequence information. Both nucleic acid sequences
use complementary language, and the information is simply transcribed, or copied, from one molecule to the other.
DNA sequence is enzymatically copied by RNA polymerase to produce a complementary nucleotide RNA strand,
called messenger RNA (mRNA), because it carries a genetic message from the DNA to the protein-synthesizing
machinery of the cell. One significant difference between RNA and DNA sequence is the presence of U, or uracil in
RNA instead of the T, or thymine of DNA. In the case of protein-encoding DNA, transcription is the first step that
usually leads to the expression of the genes, by the production of the mRNA intermediate, which is a faithful
transcript of the gene's protein-building instruction. The stretch of DNA that is transcribed into an RNA molecule is
called a transcription unit. A DNA transcription unit that is translated into protein contains sequences that direct
and regulate protein synthesis in addition to coding the sequence that is translated into protein. The regulatory
sequence that is before (upstream (-), towards the 5' DNA end) the coding sequence is called 5' untranslated
region (5'UTR), and sequence found following (downstream (+), towards the 3' DNA end) the coding sequence is
called 3' untranslated region (3'UTR). Transcription has some proofreading mechanisms, but they are fewer and
less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than DNA
replication.
RNA replication
•
As in DNA replication, RNA is synthesized in the 5' → 3' direction (from the
point of view of the growing RNA transcript). Only one of the two DNA
strands is transcribed. This strand is called the template strand, because it
provides the template for ordering the sequence of nucleotides in an RNA
transcript. The other strand is called the coding strand, because its
sequence is the same as the newly created RNA transcript (except for uracil
being substituted for thymine). The DNA template strand is read 3' → 5' by
RNA polymerase and the new RNA strand is synthesized in the 5'→ 3'
direction.
•
•
A polymerase binds to the 3' end of a gene (promoter) on the DNA template
strand and travels toward the 5' end.
•
•
Transcription is divided into 5 stages: pre-initiation, initiation, promoter
clearance, elongation and termination.
Photosynthesis – see AP p 144
•
Photosynthesis[α] is a process that converts carbon dioxide into organic
compounds, especially sugars, using the energy from sunlight.Photosynthesis
occurs in plants, algae, and many species of Bacteria, but not in Archaea.
Photosynthetic organisms are called photoautotrophs, since it allows them to
create their own food. In plants, algae and cyanobacteria photosynthesis uses
carbon dioxide and water, releasing oxygen as a waste product.
Photosynthesis is vital for life on Earth. As well as maintaining the normal level
of oxygen in the atmosphere, nearly all life either depends on it directly as a
source of energy, or indirectly as the ultimate source of the energy in their
food.The amount of energy trapped by photosynthesis is immense,
approximately 100 terawatts: which is about six times larger than the power
consumption of human civilization.As well as energy, photosynthesis is also the
source of the carbon in all the organic compounds within organisms' bodies. In
all, photosynthetic organisms convert around 100,000,000,000 tonnes of
carbon into biomass per year.
• Although photosynthesis can occur in different ways in different
species, some features are always the same. For example, the
process always begins when energy from light is absorbed by
proteins called photosynthetic reaction centers that contain
chlorophylls. In plants, these proteins are held inside organelles
called chloroplasts, while in bacteria they are embedded in the
plasma membrane. Some of the light energy gathered by
chlorophylls is stored in the form of adenosine triphosphate (ATP).
The rest of the energy is used to remove electrons from a substance
such as water. These electrons are then used in the reactions that
turn carbon dioxide into organic compounds. In plants, algae and
cyanobacteria this is done by a sequence of reactions called the
Calvin cycle, but different sets of reactions are found in some
bacteria, such as the reverse Krebs cycle in Chlorobium. Many
photosynthetic organisms have adaptations that concentrate or store
carbon dioxide. This helps reduce a wasteful process called
photorespiration that can consume part of the sugar produced
during photosynthesis.