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essential chemistry
 essential chemistry
Atoms, Molecules, and ­Compounds
Chemical ­Reactions
Metals
The Periodic ­Table
States of ­Matter
Acids and ­Bases
Biochemistry
Carbon ­Chemistry
Chemical ­Bonds
Earth ­Chemistry
essential chemistry
Biochemistry

Copyright © 2008 by Infobase ­Publishing

All rights reserved. No part of this book may be reproduced or utilized in any form or by
any means, electronic or mechanical, including photocopying, recording, or by any infor-
mation storage or retrieval systems, without permission in writing from the publisher. For
information ­contact:

Chelsea ­House
An imprint of Infobase ­Publishing
132 West 31st ­Street
New York NY ­10001

Library of Congress ­Cataloging-­in-­Publication ­Data

Laberge, ­Monique.
Biochemistry / Monique ­Laberge.
p. cm. — (Essential chemistry)
Includes bibliographical references and ­index.
ISBN 978–0-7910–9693–2 (hardcover)
1. ­Biochemistry—­Textbooks. I. Title. II. ­Series.

QP514.2.L33 ­2008
612'.015—­dc22     2007051316

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for businesses, associations, institutions, or sales promotions. Please call our Special Sales
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Text design by Erik Lindstrom

Cover design by Ben Peterson

Printed in the United States of ­America

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This book is printed on ­acid-­free ­paper.

All links and Web addresses were checked and verified to be correct at the time of pub-
lication. Because of the dynamic nature of the Web, some addresses and links may have
changed since publication and may no longer be ­valid.
 Contents
1 What Is ­Biochemistry? 1
2 Amino Acids 9
3 Proteins and Nucleic Acids 16
4 Enzymes 31
5 Lipids and Biological ­Membranes 40
6 Carbohydrates: Energy for
Living Organisms 48
7 Metabolic ­Pathways: The Roads
to Energy 54
8 Photosynthesis: The Basis of Life on Earth 64
9 The Human Genome ­Project 73
Periodic Table of the Elements 82
Electron Configurations 84
Table of Atomic Masses 86

Glossary 88
Bibliography 100
Further Reading 101
Photo Credits 105
Index 106
About the ­Author 112
 1

What is
biochemistry?
B iochemistry is the study of the chemistry of life. It seeks to
understand the relationship between the structure and func-
tion of the molecules that make up living organisms. This is no
easy task because of the enormous diversity and complexity of
life processes. There is a broad overlap between biochemistry
and all of the other sciences that study living organisms, from
microorganisms to plants, animals, and human beings. Areas
as diverse as cell and molecular biology, molecular genetics,
physiology, toxicology, drug design, nutrition, forensic science,
and environmental science all use biochemistry techniques and
methods.
Some biochemists try to explain how the molecules that make
up the human body function. They identify the molecules and
determine how the molecules are produced, how they interact with
each other, and the results of the chemical reactions they undergo.

1
 biochemistry

Figure ­ 1.1 The relationship between biochemistry and medicine is illustrated

above. Medical researchers attempt to find cures for the diseases shown in the
bottom half of the diagram by investigating the molecules shown in the top ­half.

These molecules are mostly found in cells, the basic structural

units of living systems, or in close proximity to ­cells.

Biomolecules
Just as there is a great diversity of living organisms, there is also
a wide variety of molecules essential to life. These biomolecules
are usually classified in four major groups: proteins, nucleic
acids, lipids, and carbohydrates. The groups differ in chemical
structure, reactivity, and function. Proteins are constructed from
compounds called amino acids. Some proteins are structural,
such as those that make up hair and cartilage; some are reactive,
such as the enzymes that carry out the numerous chemical reac-
tions of life. DNA and RNA are nucleic acids, compounds that
carry genetic information and control protein synthesis. They are
among the largest molecules known. Lipids are compounds that
include fats and oils. Carbohydrates include such important com-
pounds as sugars, starch, and cellulose. Within each of the four
main groups of biomolecules are subgroups, classified according
to structure or ­functionality.
Proteins are one of the major constituents of cells. The study
of proteins includes two important areas of biochemical specializa-
tion, namely protein synthesis and enzymology. Protein synthesis
 What Is Biochemistry? 

Figure ­1.2 The cell is the basic unit of ­life. Above is a diagram of a eukaryote cell,
the more complex of the two categories of cells. Unlike the more primitive pro-­
karyotes, eukaryotes have nuclear membranes and ­membrane-­bound organelles.

is the process of how proteins are made. Enzymology is the study

of enzymes. Enzymologists describe the sites where enzymes bind
and the molecules that can activate or stop them. They also study
how enzymes control metabolism, the chemical processes occur-
ring within a living cell or organism that are essential for life.
Other specialization areas include cell membrane transport, the
Table 1.1 Common Techniques and Methods Used
in ­Biochemistry
Technique Description Purpose
Cell culture The growing of microorganisms, Obtaining specific material
techniques cells, or tissues in a specially for study
prepared nutrient medium
Microscopy Magnification of structures too small Visualization and
to be seen by the naked eye identification of tissues,
cells, and biomolecules
Centrifugation Mechanical separation of mixtures Separation of the
placed in compartments spun about a components of a mixture
central axis to separate components
of different weights
Chromatography Separation method that uses columns Purification of biomolecules
filled with gels that separate a
mixture of molecules into individual
components by size or charge
Electrophoresis Separation of large, charged Identification of the
molecules in an electric field across components of a mixture
a porous medium
Spectroscopy Study of molecular or atomic Identification and
structure by observation of its characterization of
interaction with electromagnetic biomolecules
radiation
Kinetic Measurement of the rate at which a Understanding the nature
experiments biochemical reaction yields a product and/or function of a reaction
Radioisotope Incorporation of a radioactive label Characterization of
labeling into a compound biomolecular components;
tracing reaction pathways
­X-­ray Use of ­X-­rays to record the structure Identification of the atomic
crystallography of a molecule crystal constituents of a biomolecule
and of its 3D structure
Nuclear Monitoring of the response of Identification of the 3D
magnetic reso-­ protons to radiation when placed in a structure of biomolecules in
nance (NMR) magnetic field solution
Molecular Computer programs that allow the Used to investigate the
modeling visualization of the structure of a properties of biomolecules
biomolecule and the modeling of when experimental
their properties techniques can not be used
 What Is Biochemistry? 

study of how biomolecules pass into and out of cells, and signal
transduction, the study of how cells communicate with each other
and produce chemical signals inside cells. No matter what the area
of specialization, biochemistry basically applies the tools of biol-
ogy, chemistry, physics, and mathematics using special ­techniques,
many of which are summarized in Table 1.1.

The ­Biochemistry-­Medicine ­Connection

The genes of living organisms are the basic units of heredity. They
consist of a nucleic acid called deoxyribonucleic acid (DNA), the
large biomolecule that stores the information required for the de-
velopment and growth of a living organism. In humans, DNA codes
for hereditary characteristics such as hair color, eye color, and height,
among many other traits. Molecular genetics is the science of how
DNA is copied and passed on from generation to generation and
how the genetic information encoded into a DNA sequence is used
in organisms to produce proteins. Anything that interferes with the
copying of the DNA information or with the genes or chromosomes
may cause a genetic disease. Biochemistry is routinely applied to the
understanding of human genetic diseases. For example, biochem-
ists have discovered special enzymes, called DNA polymerases, that
can copy and, at times, even repair damaged ­DNA.
Sickle-­cell anemia is a disease of the blood that affects hemo-­
globin. Hemoglobin is the ­iron-­containing protein in red blood
cells that carries oxygen throughout the body. Normal red blood
cells are shaped like doughnuts with soft, hollow centers. In
­sickle-­cell anemia, the red blood cells clump together and become
sticky and stiff, adopting a curved, “banana” shape that impairs
the ability of hemoglobin to efficiently carry ­oxygen.
The disease is caused by a mutation of a gene that controls
hemoglobin production. A hemoglobin molecule consists of two
types of amino acid chains: alpha chains and beta chains. At the
molecular level, the ­ sickle-­cell anemia mutation involves the
replacement of one amino acid in the beta chains by another
 biochemistry

Figure ­ 1.3 The round cells are normal red blood cells. The mis-­
shapen cell on the left is a sickle cell. Sickle cells clump together and
impair blood circulation and the ability of blood to carry oxygen to
body ­tissues.

i­ ncorrect amino acid. By measuring the ability of normal and ­sickle-

­cell hemoglobin to bind oxygen, biochemists were able to describe
the effect of the mutation: less oxygen delivery to the ­tissues.
Atherosclerosis is a disease that involves the accumulation
of ­ lipid-­containing molecules in large arteries, which causes in-
flammation and a narrowing of the arteries that may eventually
lead to heart attacks. Biochemistry contributes significantly to
­understanding the details of the disease, for example by identi-
fying the molecules involved in clogging blood vessels and how
they travel in the body. Recent biochemical tests were also able to
show that high amounts of copper and iron were present in these
molecules, suggesting that these minerals, required by the body to
maintain health, may not be beneficial in older ­people.
 What Is Biochemistry? 

The Limeys of the

British ­Navy
In 1747, James Lind, a Scottish naval surgeon, discovered that
an unknown nutrient in citrus fruit prevented scurvy, a disease
that causes weakness, spontaneous bleeding, loose teeth, pain
in the joints, and finally sudden death. Before the invention of
refrigeration, scurvy was a common and deadly disease typi-­
cally afflicting sailors, who could only eat dry foods during their
­long-­distance sea journeys. According to Lind, more British
sailors were lost to scurvy than to war. However, very sick men
would recover in a week or two after reaching land, where they
could eat fresh fruit, which prompted Lind’s experiments. As a
result, the British Admiralty decided to distribute lemon juice to
the fleet in 1795. This led to British sailors being derisively nick-­
named “Limeys” because the relationship between fresh fruit
and the prevention of scurvy was not common ­knowledge.
Understanding why fresh fruit could prevent or reverse
scurvy only happened two centuries later, following the discov-­
ery of vitamin C by Albert ­Szent-­Györgyi, a Hungarian biochem-­
ist. ­Szent-­Györgyi was able to purify and isolate a compound
that he named hexuronic acid, now known as ascorbic acid, or
vitamin C. This very important substance has the chemical for-­
mula C6H8O6 . For his discovery, ­Szent-­Györgyi was awarded the
Nobel Prize for Medicine or Physiology in ­1937.

Diabetes is a disease in which the body is either unable to pro-

duce enough insulin or the cells cannot use the insulin to remove
glucose from the blood. Diabetes affects the cells of the body in
many ways. Over the past several decades, biochemical techniques
have been used to describe precisely how the body breaks down
sugars and what can interfere with the process. The monitoring
 biochemistry

of the blood’s sugar levels also involves standard biochemical tests

used by physicians to get a general idea of how diabetic patients are
reacting to their recommended diet, exercise, and medicinal plan,
and whether or not any changes need to be ­made.

Where There Is Life, There Is ­Biochemistry

Biochemistry is important in many fields of science in addition to
medicine. For instance, biochemists investigate food by studying
molecules such as vitamins, amino acids, fatty acids, various min-
erals, and water, all of which are dietary requirements for healthy
nutrition. They also explain how these nutrients are absorbed by
the body and what they do in the cells. For example, the question
of how the body derives energy from dietary fats and oils involves
a series of biochemical reactions explained by the biochemistry of
the metabolic ­pathways.
One of the major scientific discoveries of the twentieth century
involved working out the full chemical nature of all human genes.
The Human Genome Project reached this goal in 2003. Many
previously unknown genes were identified, and the identifica-
tion of their protein products now involves intense biochemical
research in new areas, such as comparing the proteins associated
with specific genes under different conditions; using computers to
explore information about genes, nucleic acids, and proteins; and
using microorganisms or proteins to perform specific industrial
or manufacturing processes. Biochemistry has always been an
­exciting area of study, but these recent advances now make it one
of the most challenging ­sciences.
 2

Amino Acids
A mino acids are the building blocks of proteins, the bio-
molecules found in all living organisms. Amino acid mole-
cules can join together to form chains called peptides. Long
peptides, containing more than 50 amino acids, are called poly-
peptides. Poly is from the Greek word that means “many,” there-
fore, a polypeptide is made up of many amino acid chains.
Amino acids all contain carbon (C), oxygen (O), nitrogen (N),
and hydrogen (H).
There are 20 standard amino acids. All share a chemical core
of the same atoms: they all have a carboxyl group (COOH),
an amine group (NH2) (also called the amino group), and a
hydrogen atom attached to the same carbon atom. This car-
bon is called the alpha carbon. Amino acids can be grouped
into families that have similar chemical properties. This is
achieved by attaching different groups, called R groups, to the
alpha carbon. The R groups of the 20 standard amino acids are

EC Biochemistry PF.indd 9 12/1/09 3:55:16 PM

10 biochemistry

The Elements of ­Life

An element is a pure substance that cannot be broken down into simpler sub-­
stances by ordinary chemical techniques. Elements combine with one another
in different amounts to form everything from air, to food, to tools, to the
human ­body.
Elements have names and chemical symbols. For example, the chemical
symbol for iron is Fe, and that of oxygen is O. When we say that a substance is
“pure,” we mean that it contains only one kind of atom. For example, a piece
of pure iron contains only atoms of the element iron, Fe. It can be heated to
high temperatures and melted. Whether melted into a liquid or a solid, the
Fe atoms are the same. Yet if left exposed to air, the iron will rust because it
will chemically react with the oxygen in the air, forming compounds called
iron oxides that contain both iron and oxygen. The chemical reaction that
causes rust is called oxidation, and the iron oxide (Fe2O3) is the resulting red-­
dish brown layer. The iron in the rusted layer is no longer pure because it has
reacted with ­oxygen.
There are some 118 known elements, but only 4 elements make up 99% of
living organisms. These elements are hydrogen (H), oxygen (O), nitrogen (N),
and carbon (C), and they are special because they are widely available every-­
where and also suitable for the chemistry of ­life.
Carbon (C) is sometimes called the single most important element to life
because the chemical properties of the carbon atom make it ideal for build-­
ing large biological molecules. Oxygen (O) is important for life, because it is
required for cellular respiration, the ­energy-­releasing reactions that sustain
life. Nitrogen (N) is a major component of proteins, without which life could
not exist. Almost 80% of the air is made up of nitrogen. In the plant kingdom,
nitrogen is one of the three main elements that make plant life possible (the
other two are potassium and phosphorus). Hydrogen (H) is the fourth most
abundant element. It is almost always bound to the carbon that living systems
are made of, and many chemical reactions that make life possible involve the
hydrogen ­ion.
 Amino Acids 11

Table 2.1 Standard Amino Acids

The table shows a list of the 20 standard amino acids and the abbreviations of their
names, which can be a 3-letter code or a single letter. For example, alanine can be
called “Ala” or simply “A.”
Amino acid 3-Letter code 1-Letter code R group
alanine Ala A -CH3
arginine Arg R -(CH2)HNBNHNH2
asparagine Asn N -CH2CONH2
aspartic acid Asp D -CH­2COOH
cysteine Cys C -CH2SH
glutamine Gln Q -CH2CH2CONH2
glutamic acid Glu E -CH2CH2COOH
glycine Gly G -H
histidine His H -CH2C3NHN
isoleucine Ile I -CHCH3CH2CH3
leucine Leu L -CH2CH(CH3)2
lysine Lys K -(CH2)4NH3+
methionine Met M -CH2CH2SCH3
phenylalanine Phe F -C6H5
proline Pro P -CH­2­CH2CH2
serine Ser S -CH2OH
threonine Thr T -COOH(CH3)
tryptophan Trp W -CH2C2NHC6H4
tyrosine Tyr Y -CH2C6H4OH
valine Val V -CH(CH3)2

listed in the fourth column of Table 2.1. For example, the chemical
formula for alanine (Ala) ­is C3H7NO2 and the structural formula is

CH3–C H–COOH
|
NH2

Like all other amino acids, the alpha carbon has a bond to a
COOH group and another to a NH2 group. But unlike the ­others,
12 biochemistry

Figure ­2.1 Amino acids are the building blocks of protein. All amino acids have
an alpha carbon linked to an amino group, a carboxylic group, a hydrogen atom,
and an ­R ­group.

its R group is CH3. Amino acids are acids because they can
release H+ (hydrogen ions) in water at both the carboxylic and
amino ­groups.

Water
Two of the four most abundant elements in living systems, hydrogen (H)
and oxygen (O), combine to form water, H2O. Without water there would be
no life as we know it. The human body is largely made up of water. Water
dissolves other ­life-­supporting substances and transports them into and
around cells. It is also a liquid in which important biochemical reactions
take ­place.
A water molecule is composed of one oxygen atom and two hydrogen
atoms. Each hydrogen atom has one electron available for bonding and each
oxygen atom has six. Hydrogen is bonded to the oxygen by sharing a pair of
electrons. This type of bond where electrons are shared is called a covalent
bond. Thus there are four pairs of electrons surrounding the oxygen atom:
two pairs involved in covalent bonds with hydrogen, and two unshared pairs
on the opposite side of the oxygen ­atom.
continues
 Amino Acids 13

continued from page 12

What makes water very special is that it is a polar molecule, meaning that
the two sides of a water molecule have different electrical charges. There is
a ­partial negative charge near the oxygen atom due to the unshared pairs
of electrons. The hydrogen atoms have slightly positive charges because the
electrons shared in the covalent bonds are pulled more toward the oxygen.
Compared to hydrogen, oxygen is an electronegative, or ­electron-­loving,
atom. When more water molecules are in contact, the partial positive charge
near the hydrogen atoms attracts the partial negative charge near the oxy-­
gen of another water molecule. This is called a hydrogen bond (or H bond).
The ability of other charged and polar molecules to dissolve in water is due
to the polarity of water. Because of its polarity, water is a very good solvent.
Charged or polar molecules, such as salts, sugars, and amino acids, dissolve
readily in water. Such compounds are said to be hydrophilic (water loving).
Uncharged or nonpolar molecules, such as lipids, do not dissolve well in water
and are said to be hydrophobic (water hating).
Many other important properties of water are due to its special ability to
form H bonds. For example, ice floats because hydrogen bonds hold water mol-­
ecules farther apart in a solid than in a liquid, where there is one less hydrogen
bond per molecule. The hydrophobic effect, or the exclusion of compounds con-­
taining carbon and hydrogen (nonpolar compounds), is another special property
of water caused by H bonds. The hydrophobic effect is very important in the for-­
mation of cell membranes, which are made up of long ­carbon-­hydrogen chains.
Water helps them to form by “squeezing” the nonpolar carbon chains ­together.
During chemical reactions, molecular parts ranging from tiny subatomic
particles, such as electrons, to entire atoms, such as hydrogen, get shuffled
around, transferred, shared, or exchanged. Because water is the most common
chemical solvent on the Earth, such reactions mostly occur in water. However,
water is not simply a passive liquid in which chemical reactions occur. In fact, it
plays an active role, constantly making and breaking chemical bonds around
reactive molecules in order to shuttle them from one compound to ­another.
continues
14 biochemistry

continued from page 13

Water is also important because when it dissociates, or splits, into ions, it
­forms:
H2O –› H+ + OH–

Two water molecules ionize as ­follows:

2H2O –› H3O+ + OH–

The charged H3O+, which is called a hydronium ion, and OH–, which is
called a hydroxide ion, form stronger H bonds with surrounding water mol-­
ecules. The amount of H3O+ will also control the pH of a solution. At pH 7.0,
a solution is ­neutral—­it is neither acid nor basic. At a lower pH (1–6), it has a
lot of H3O+ and is acidic, meaning that it can release H+ or H3O+. At higher pH
(8–14), a solution is basic, meaning that it has little H+ or H3O+ and can accept
more of these ­ions.

Figure ­2.2 Above, two water molecules are linked by a hydrogen bond.
This occurs due to the attraction of the slightly positive hydrogen atoms of
one molecule to the slightly negative oxygen atom of another molecule.
 Amino Acids 15

Figure ­2.3 In a polypeptide of five amino acids, the bold black C is the alpha car-­
bon. The amino acids are linked together by a peptide bond (red atoms) linking the
carboxylic group of one amino acid to the amino group of the next amino acid. The
­R group (blue R) can be any sidechain. The ­Cα-­C-­N-­Cα-­C-­N-­Cα-­C-­N is the “backbone.”

The Peptide ­Bond

Amino acids are linked together by a type of bond called a pep-­
tide bond. A peptide bond, −C=ONH−, is formed between the
carboxyl group of one amino acid and the amino group of another
amino ­acid.
Small peptides consist of a few amino acids. An example is ­Ala-
­Met-­Gly, a peptide consisting of alanine, methionine, and glycine.
The simplest peptide is called a dipeptide, and it contains a single
peptide bond formed between the C atom of the carboxyl group
of one amino acid and the N atom of the amino group of the sec-
ond. In a polypeptide consisting of, for instance, 58 amino acids,
there are 56 peptide bonds. The Cα–CO–N–Cα–CO–N–Cα–CO–N
atoms of a peptide chain, without the ­R ­groups, is called the “back-
bone.”
The C–N peptide bond has an interesting property: It is planar
and very rigid. This special geometry of the peptide bond makes it
very stable and ideal to maintain the structure of ­proteins.
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