Principles of

BIOCHEMISTRY
Third Edition

HORTON MORAN OCHS RAWN SCRIMGEOUR

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 Chapter 1
Introduction to Biochemistry

• Adenovirus: Viruses consist of a nucleic

acid molecule surrounded by a protein coat

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 1.1 Biochemistry Is a Modern Science

• Urea was synthesized by heating the inorganic

compound ammonium cyanate (1828)
• This showed that compounds found exclusively
in living organisms could be synthesized from
common inorganic substances

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 Two notable breakthroughs in the
history of biochemistry

(1) Discovery of the role of enzymes as

catalysts
(2) Identification of nucleic acids as
information molecules

Flow of information: from nucleic acids to proteins

DNA RNA Protein

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 1.2 The Chemical Elements of Life

• Only six nonmetallic elements: oxygen, carbon,

hydrogen, nitrogen, phosphorous, and sulfur
account for >97% of the weight of most organisms
• These elements can form stable covalent bonds
• Water is a major component of cells
• Carbon is more abundant in living organisms than
it is in the rest of the universe

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 Fig 1.1 Periodic Table of the elements

• Important elements found in living cells are

shown in color
• The six abundant elements are in red
(CHNOPS)
• Five essential ions are in purple
• Trace elements are in dark blue (more
common) and light blue (less common)

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Prentice Hall c2002 Chapter 1 7
 Functional groups in biochemistry

• Functional groups - specific parts of molecules

involved in biochemical reactions
• Figure 1.2 shows the general formulas of:
(a) Organic compounds
(b) Functional groups
(c) Linkages common in biochemistry
(R represents an alkyl group (CH3CH2)n-)
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 Fig 1.2 (a) General formulas

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 Fig 1.2(b) General Formulas

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 Fig 1.2 (c) General Formulas

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 1.3 Many Important Biomolecules
are Polymers

• Biopolymers - macromolecules created by

joining many smaller organic molecules
(monomers)
• Condensation reactions join monomers
(H2O is removed in the process)
• Residue - each monomer in a chain

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 Molecular mass

• Molecular weight is more correctly termed the

relative molecular mass (Mr) - the molecular
mass relative to 1/12 mass of a carbon atom (12C)
• Mr is a relative quantity and is dimensionless
• A typical protein may have an Mr = 38,000
• The absolute molecular mass of this protein =
38,000 daltons (1 dalton = 1 atomic mass unit)

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 A. Proteins

• Proteins are composed of 20 common amino acids

• Each amino acid contains:
(1) Carboxylate group (-COO-)
(2) Amino group (-NH2)
(3) Side chain (R) unique to each amino acid

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 Fig 1.3 Structure of an amino acid
and a dipeptide

(a) Amino group (blue), carboxylate group (red)

(b) Dipeptides are connected by peptide bonds

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 Polypeptides

• Polypeptides - amino acids joined end to end

• Conformation - the three dimensional shape of
a protein which is determined by its sequence
• Active site - a cleft or groove in an enzyme that
binds the substrates of a reaction

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 Fig 1.4 Egg white lysozyme

(a) Free enzyme

(b) Enzyme, bound substrate in active site cleft

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 B. Polysaccharides

• Carbohydrates, or saccharides, are

composed primarily of C,H and O
• Polysaccharides are composed of saccharide
monomers
• Most sugar structures can be represented as
either linear (Fischer projection) or cyclic

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 Fig 1.5 Representations of the
structure of ribose

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 Fig 1.6 (a) Glucose, (b) Cellulose

Glycosidic bonds
connecting glucose
residues are in red

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 C. Nucleic Acids

• Polynucleotides - nucleic acid biopolymers

are composed of nucleotide monomers
• Nucleotide monomers are composed of:
(1) A five-carbon sugar
(2) A heterocyclic nitrogenous base
(3) Phosphate group(s)

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 Fig 1.7 Deoxyribose

• Deoxyribose lacks a hydroxyl group at C-2.

It is the sugar found in DNA.

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 Nitrogenous bases

• Major Purines:
Adenine (A)
Guanine (G)
• Major Pyrimidines
Cytosine (C)
Thymine (T)
Uracil (U)
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 Fig 1.8 Adenosine Triphosphate (ATP)

• Nitrogenous base (adenine), sugar (ribose)

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 Fig 1.9 Structure of a dinucleotide

• Residues are
joined by a
phosphodiester
linkage

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Fig 1.10 Short segment
of a DNA molecule

• Two polynucleotides
associate to form a
double helix
• Genetic information is
carried by the sequence
of base pairs

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 D. Lipids and Membranes

• Lipids are rich in carbon and hydrogen, but

contain little oxygen
• Lipids are not soluble in water
• Fatty acids are the simplest lipids: long chain
hydrocarbons, a carboxylate group at one end
• Fatty acids are often components of
glycerophospholipids

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 Fig 1.11 Structures of (a) glycerol 3-
phosphate, (b) a glycerophospholipid

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 Fig 1.12 Model of a membrane lipid

• Hydrophilic (water-loving)
head interacts with H2O
• Hydrophobic (water-
fearing) tail

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Fig 1.13 Structure of a biological membrane

• A lipid bilayer with associated proteins

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 1.4 The Energetics of Life

• Photosynthetic organisms capture sunlight

energy and use it to synthesize organic
compounds
• Organic compounds provide energy for all
organisms

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 Energy Flow

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 Metabolism and energy

• Metabolism - collection of reactions by

which organic compounds are synthesized
and degraded
• Bioenergetics - study of the changes in
energy during metabolic reactions

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 Free energy (DG)

• Free energy change (DG) can predict the equilibrium

concentrations and direction of a reaction where:
DH = enthalpy change, DS = entropy change, T = temp
• When DG<0, the reaction will proceed spontaneously
in the direction written
• When DG>0, the reaction requires energy to proceed

DG = DH - TDS
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 1.5 Biochemistry and Evolution

• Prokaryotes - do not have a membrane-

bounded nucleus
• Eukaryotes - possess nucleus and other
complex internal structures
• Prokaryotes and eukaryotes appear to have
evolved from a common ancestor over three
billion years ago

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 1.6 The Cell is the Basic Unit of Life

• Plasma membrane - surrounds aqueous

environment of the cell
• Cytoplasm - all materials enclosed by the
plasma membrane (except the nucleus)
• Cytosol - aqueous portion of the
cytoplasm minus subcellular structures
• Bacteriophage or phage - viruses that
infect prokaryotic cells
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1.7 Prokaryotic Cells: Structural Features

• Prokaryotes, or bacteria are usually single-

celled organisms
• Prokaryotes lack a nucleus (their DNA is
packed in a nucleoid region of the cytoplasm)
• Escherichia coli (E. coli) - one of the best
studied of all living organisms
• E. coli cells are ~0.5mm diameter, 1.5mm long

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 Fig. 1.14 E. coli cell

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 1.8 Eukaryotic Cells: Structural Features

• Eukaryotes: plants, animals, fungi, protists

• Have a membrane-enclosed nucleus containing
the chromosomes
• Are commonly 1000-fold greater in volume than
prokaryotic cells
• Have an intracellular membrane network that
subdivides the interior of the cell

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 Fig 1.15 (a) Eukaryotic cell (animal)

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 Fig 1.15(b) Eukaryotic cell (plant)

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 A. The Nucleus

Nuclear envelope and endoplasmic

reticulum of a eukaryotic cell

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 B. Endoplasmic Reticulum and
Golgi Apparatus

• Endoplasmic reticulum - network of

membrane sheets and tubules extending from
the nucleus
• Golgi apparatus - responsible for modification
and sorting of some biomolecules.

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 Golgi apparatus

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 C. Mitochondria and Chloroplasts

• Mitochondria are the main sites of energy

transduction in aerobic cells.

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Chloroplasts - sites of photosynthesis in
plants, green algae

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 D. Specialized Vesicles

• Lysosomes - contain specialized digestive

enzymes
• Peroxisomes - carry out oxidative reactions in
animal and plant cells
• Vacuoles - fluid-filled vesicles, used as storage
sites for water, ions and nutrients such as glucose

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 E. The Cytoskeleton

• A protein scaffold is required for support, internal

organization and movement of a cell
• Actin filaments form ropelike threads
• Microtubules are rigid fibers packed into bundles
- Serve as an internal skeleton
- Form the mitotic spindle during mitosis
- Form movement structures (e.g. cilia, flagella)
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Fig 1.16

Fluorescently labeled:
(a) Actin filaments

(b) Microtubules

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1.9 A Picture
of Living Cell

Fig 1.17 Cytosol

of an E. coli cell.
Magnification:
Top 106X
Bottom 107X
(shows water,
other small
molecules)
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 1.10 Biochemistry is Multidisciplinary

• Various disciplines contribute to

understanding biochemistry:
Physics Genetics
Chemistry Physiology
Cell biology Evolution

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 Textbook organization

• Horton is organized into four sections:

1. PART ONE: Introduction
2. PART TWO: Structure and Function of
Biomolecules
3. PART THREE: Metabolism and
Bioenergetics
4. PART FOUR: Biological Information Flow
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