BIOCHEMISTRY REVIEW
All matter is composed of fundamental types of atoms called elements.
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Of the 92 naturally occurring elements, only six make up 99% of all living tissue: carbon,
hydrogen, oxygen, nitrogen, phosphorus, and sulfur. (CHONPS)
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These six elements readily combine with each other and other atoms to form the kind
of complex yet stable materials required by living things. (see: organic molecules;
macromolecules; carbon chains)
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The diversity of life is the result of recombining these basic elements in myriad ways.
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The biochemical analysis of any given physiological or ecological system will center
on these elements, their numbers and arrangement in space and time. (see: van
Niel’s Hypothesis; carbon cycle; water cycle; nitrogen cycle; phosphorus cycle)
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Notes about Carbon: see #16
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Hydrogen ions form the basis for chemiosmotic power production in photosynthesis
and respiration.
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Oxygen is the final electron acceptor in aerobic respiration and helps create
hydrogen bonds. (see: electron transfer chain; electronegativity)
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Nitrogen is an integral part of all proteins and nucleic acids.
amino group; nitrogenous base)
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Phosphate groups containing phosphorus form the hydrophilic parts of the cell
membrane and also participate in virtually every energy transformation that occurs
within a cell. (see: phospholipids; lipid bilayer; ATP; phosphorylation)
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Sulfur atoms help form certain amino acids. (see: cysteine; methionine; disulfide
bridges)
(see: amino acid;
Trace amounts of other elements are also required by living things.
(“See Hopkins Café, mighty good salt.”)
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Potassium (K) is required for the transmission of nerve impulses in animals and for
regulating the movement of water molecules and gases into/out of leaves. (see:
resting potential; action potential; polarization; depolarization; repolarization;
stomates; guard cells)
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Iodine is required by vertebrate animals to help regulate metabolism (see: thyroxine;
thyroid)
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Calcium is required for muscle contraction in vertrebrate animals. (see: sarcomere;
T system; sarcoplasmic reticulum; actin; myosin; tropomyosin; troponin; cross-bridge
binding sites)
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Iron is found in hemeglobin, which is used to transport oxygen and carbon dioxide in
vertebrate animals; iron is also found in cytochromes, which play a role in cellular
respiration. (see: heme group; porphyrin ring; electron transfer chain)
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Magnesium is found in chlorophyll, the light-sensitive pigment used by producer
organisms during the light-dependent phase of photosynthesis. (see: photolysis;
photosystem; reaction center)
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Sodium (Na) is required for the transmission of nerve impulses in animals. (see:
resting potential; action potential; polarization; depolarization; repolarization)
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Chlorine (Cl) is required for maintaining ionic balance in cells and tissues; it is also
needed by plants during the light-dependent reactions of photosynthesis. (see:
osmosis; Loop of Henle)
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The atoms of each element have a characteristic number of positive, negative, and neutral parts.
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Different atoms of the same element may contain different numbers of neutrons. These
elemental types are called isotopes.
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Isotope assays can help estimate the age of fossils. (see: radioactive dating; carbon
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Isotopes of certain key elements (CHONPS) have been used to trace the course of
physiological processes such as photosynthesis, cellular respiration, and replication.
(see: van Niel’s Hypothesis; Meselson and Stahl)
Isotopes of certain elements can also be used in medicine to treat certain cancers
and image internal organs/passageways.
Electrons orbit atomic nuclei in prescribed ways. Electrons are said to occupy energy
levels and move within orbitals.

In the light-dependent reactions of photosynthesis, electrons within chlorophyll
molecules are boosted to higher levels by radiant energy. (see: photosystems;
reaction center)
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Outer level electrons are donated and received in oxidation-reduction reactions that
occur during photosynthesis, respiration and many other processes. (see: redox
reactions)
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In order to control the release of energy during photosynthesis and respiration,
electrons are passed along electron transfer chains. (see: cytochromes)
Electrically charged atoms are known as ions.
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Sodium, potassium, and calcium ions are required for proper nerve function. (see:
resting potential; action potential; polarization; depolarization; repolarization)
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High concentrations of hydrogen ions in solution create acidic conditions. (see:
hydronium ion; hydroxide ion; pH)
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Certain ions serve as cofactors involved in enzymatic action. For example,
magnesuim ions are required in all reactions involving the transfer of a phosphate
group from one molecule to another.
Two or more atoms can interact to form molecules and compounds.
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Two of the types of bonds that hold atoms together are ionic and covalent.
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Ionic bonds break easily in the aqueous solutions present within cells and in
interstitial tissues; the resulting ionic solutes play many physiological roles in living
systems. (see: osmosis; diffusion; electrolytes; action potential; guard cells)
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The main constituents of living cells (i.e. CHONPS) are relatively small atoms that
tend to form covalent bonds in which the shared electrons are held closely by the
nuclei. These bonds are very stable, and this leads to molecular stability within cell
parts. (see: organic molecules; macromolecules; polymers)
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Chemical energy is stored within the covalent bonds of organic molecules. (see:
dehydration synthesis; phosphorylation)
Covalent bonds that are shared unequally are known as polar covalent bonds.
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The polar covalent bonds of water molecules give it its unique physical properties.
(see: question # 13)
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Given its high electronegativity, oxygen often forms polar covalent bonds with its
partners.
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Polar covalent bonds account for the polarity of polar amino acids. (see:
asparagine; cysteine; glutamine; glycine; serine; threonine; tyrosine)
Atoms can participate in covalent bonds and fill their outer energy levels by forming
single, double, or triple bonds.
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In places where greater bond strengths are required, double (or triple) bonds form.
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“Saturated” fats possess only single bonds (C-C), while “unsaturated” fats possess
varying numbers of double bonds (C=C). This means that unsaturated fats have
more bonding possibilities than saturated fats. (see: fatty acids; polyunsaturated)
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Beta-carotene and vitamin A are molecules possessing an unusually high number of
double bonds.
Chemical reactions are exchanges of electrons among atoms.
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Three basic types of chemical reactions occur: combinations, dissociations, and
exchanges.
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Condensation synthesis reactions join substrates together and yield the product plus
one water molecule per covalent bond formed. (see: anabolism)
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Hydrolysis reactions break substrate molecules into parts by adding a water molecule
between covalent bond partners. (see: catabolism)
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Exchange reactions may occur in the environment as salts precipitate out of
saltwater.
Some chemical reactions are energy-releasing reactions and some are energy-requiring.
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The most important energy-releasing reaction in living things is the hydrolysis of ATP
to ADP + phosphate. This reaction provides the cell with its immediate energy
needs.
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The energy-requiring reaction that is coupled with the previous reaction is the
dehydration synthesis of ATP from ADP + phosphate.
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Phase changes in water are energy-requiring and endothermic, which explains why
coastal areas have moderate climates.
In all energy exchanges and conversions, if no energy leaves or enters a given system,
the potential energy of the final state will always be less than the potential energy of the
initial state.
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Each time an energy exchange or transformation occurs within a living thing, heat is
released. Organisms trap some of this heat temporarily to warm their bodies. (see:
second law of thermodynamics; entropy; free energy change)
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Organisms living in frigid environments often restrict the flow of warm blood to the
extremities so as to prevent heat loss. (see: countercurrent exchange)
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In ecosystems, the “ten percent rule of thumb” states that only about ten percent of
the energy available in a given trophic level can be passed along to the next trophic
level. The remaining energy is lost to the environment. (see: food chain; biomass;
net primary productivity)
Living things are uniquely organized.
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Every living thing shows at least the following levels of organization: subatomic, atomic,
molecular, cellular.
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In cellular respiration: electrons are passed from the centrally-located iron ion of one
cytochrome molecule to the iron ion of the next cytochrome molecule, and all of this
happens within the confines of the cell – either within the mitochondria of eukaryotic
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organisms or in the cytoplasm of prokaryotes. (see: electron transfer chain;
chemiosmosis)
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In light-dependent phase of photosynthesis: electrons boosted to a higher energy
level by sunlight travel from magnesium ions located within chlorophyll molecules to
electron carriers and back to chlorophyll molecules. All of this occurs within the
confines of the cell – either within the chloroplasts of eukaryotic organisms or in the
cytoplasm of prokaryotes. (see: photolysis; photosystem)
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Activation of rhodopsin: a pair of electrons cause a conformational change in a C-C
link (i.e. bent position changes to straight position) of a rhodopsin molecule within a
rod cell of the eye. (see: visual purple; beta-carotene; vitamin A)
As a result of their organization, living systems are capable of maintaining life. The
characteristics of life are: ability to maintain homeostasis; ability to exchange materials
with the environment; ability to move; responsiveness; ability to grow and develop; ability
to use and transform energy; adaptability; and ability to reproduce.
(“This cell is the home of the ex-Mr. Gear.”)
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Living things have a thermodynamically “open” architecture; open systems require
constant energy inputs in order to maintain their structural integrity. (see:
thermodynamics; second law of thermodynamics; entropy)
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When conditions change within or around cells, changes in organization may follow.
For example, a change in temperature or pH can cause proteins to be denatured.
(see: tertiary structure of proteins)
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Information-containing molecules are needed by living things both to serve as
construction “blueprints” and to orchestrate and coordinate cell activities. Nucleic
acids are the main information-containing molecules that perform these tasks in living
things. Without them, cells cannot be organized as they should be. (see: primary
sequence; sequencing; central dogma; replication; transcription; translation; genetic
code)
Life on Earth depends on water.
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Water’s polar molecular structure gives it the following unique set of physical properties:
high adhesion and cohesion; high specific heat, heat of vaporization and heat of fusion;
lower density as a solid than as a liquid; and the ability to be a “universal” solvent.
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The transpiration of water molecules occurs at the stomates of leaves. As each
water molecule leaves the leaf, it exerts a pull on its nearest neighbor(s). The
column of cohering water molecules within the xylem vessels is thus drawn upward
from the roots – making it available to any leaf cells in need of water. (Note: the
water column within the xylem vessels is able to move against gravity because of
adhesion between the water molecules and the xylem vessel walls.)
(see:
transpiration stream; cohesion-tension theory; stomates; guard cells; pressure-flow
mechanism).
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Because of its high heat of vaporization and high heat of fusion, water absorbs vast
amounts of heat from the environment, which it releases slowly. Thus aquatic
environments represent places with little
day-to-day or season-to-season change
in temperature.
(see: maritime climate)
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Because liquid water is more dense than ice, many water habitats remain usable
during winter. (see: density)
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Water molecules comprise 50-95% of the weight of any living system.
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An excess of hydronium ions in solution is an acid; an excess of hydroxide ions is a base.
Almost all of the chemistry of living things takes place at pHs between six and eight.
Organisms resist strong, sudden changes in the pH of tissues by means of buffers.
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Exception: The gastric juice (pH 1.5 – 2.5) produced by the stomach mucosa in
humans and other vertebrates is an extreme example of material that does not
conform to the “near neutral” state characteristic of most body fluids. This is for
good reason: gastric juice is designed to kill ingested bacteria and begin the
process of dismantling organic molecules. (see: gastric pits; gastric glands;
pepsinogen; pepsin; gastrin)
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Exception: In men the prostate gland produces an alkaline fluid that is added to
semen in order to neutralize the normally acidic conditions that exist within the female
reproductive tract.
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The major buffer system in the human bloodstream is:
CO2 + H20
carbon dioxide
water
H2C03
carbonic acid
-
HCO3 + H
+
bicarbonate ion hydrogen ion
In places that produce many CO2 molecules, such as actively metabolizing tissues,
the body will store much of the excess CO2 as bicarbonate ion plus hydrogen ion.
Conversely, in the lungs, CO2 will be liberated by the dissociation of carbonic acid.
(see: respiration; alveoli; partial pressure of CO2)
Biochemistry is to a large extent carbon chemistry.
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In general, an organic molecule derives its overall shape from the arrangement of the
carbon atoms that form the backbone or skeleton of the molecule.
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A carbon atom can form up to four covalent bonds, thus allowing for multiple
branching. (see: valence electrons)
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Molecules such as lipids possess long chains of carbon atoms. These regions are
hydrophobic. (see: fatty acid; phospholipid)
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Some organic molecules possess carbon rings. One extreme example is a steroid
molecule, which possesses a linked set of four carbon rings. (see: ring formation;
porphyrin ring)
The specific chemical properties of an organic molecule derive principally from groups of
atoms known as functional groups (e.g. hydroxyl, carboxyl, amino, phosphate).
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Certain amino acids have side groups that are either acidic or basic. (see: aspartic
acid; glutamic acid; histidine; lysine; arginine)
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The third phosphate of an ATP molecule can be added or removed relatively easily.
When a phosphate from an ATP molecule is removed, energy is made available for
use in chemical reactions within the cell. (see: coupled reactions)
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Hydroxyl groups will be involved in the formation of hydrogen bonds. (see: cohesion
of water; surface tension of water)
The four kinds of organic molecules found in large quantities in living things are: carbohydrates,
lipids, proteins, and nucleic acids.
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Certain carbohydrates (e.g. sugars, monosaccharides, double sugars, disaccharides,
starch, glycogen) are the primary energy-storage molecules in most living things; other
fulfill structural roles within cells (e.g. cellulose).
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For all organisms, glucose metabolism is fundamentally important. Glucose is the
most common energy-storing molecule used by living things. (see: cellular
respiration; glycolysis; diabetes)
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Glucose is often stored for later use in the form of starch (in plants) or glycogen (in
animals). (see: polysaccharide)
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Cellulose is the structural carbohydrate that comprises plant cell walls.
Lipids serve as energy storage molecules, as structural molecules, and as chemical
messengers within living systems.
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Fats represent a “permanent” energy molecule storage option for living things. Fats
possess six times the energy of an equal amount of glycogen. (see: triglyceride;
lipid metabolism; brown fat)
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25% of the cell membrane of a red blood cell consists of cholesterol; cholesterol also
forms part of the myelin sheath that surrounds a nerve axon. (see: liver metabolism;
LDL; HDL)
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Sex hormones, cortisol, and other corticosteroids are classified as lipids. (see:
estrogen; progesterone; testosterone; glucocorticoid; aldosterone)
Proteins are polymers of amino acids arranged in linear sequence that serve many
important functions in living systems.
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Enzymes are required catalysts for all chemical reactions that occur in living things.
(see: catalase)
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Prolactin, which stimulates milk production in mammals, is one of several
proteinaceous hormones. (see: somatotropin; TSH; ACTH; FSH; LH; ADH;
thyroxine; calcitonin; parathormone; insulin; glucagon)
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Albumin is an example of a storage protein. (see: seed protein)
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Hemoglobin and myoglobin are examples of transport proteins.
group)
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Actin and myosin are contractile proteins; these proteins allow muscle fibers to
contract. (see: myofibril; sarcomere; Z line; H zone; I band; A band)
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Antibodies are immunoglobulin proteins that protect living systems from internal
attacks. (see: B lymphocyte; plasma cell; memory cell; IgA; IgD; IgE; IgG; IgM)
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Antigens and receptor proteins are two types of membrane proteins.
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The collagen family of proteins are structural proteins. (see: tendon; ligament)
(see: heme
The information dictating protein structure is encoded in and translated by
known as nucleic acids (DNA, RNA).
molecules
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DNA is the substance that comprises genes.
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mRNA is the “working blueprint” transcribed from DNA.
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tRNA are molecules that “fetch” the amino acids needed to construct a protein.
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