Introduction to

Biochemistry
The chemistry of living organisms is called biochemistry.
Biochemical molecules tend to be very large and difficult
to synthesize.
Living organisms are highly ordered. Therefore, living
organisms have very low entropy.
Most biologically important molecules are polymers,
called biopolymers.
Biopolymers fall into three classes: proteins, polysaccharides
(carbohydrates), and nucleic acids.
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Chapter 25

Proteins

Amino Acids
Proteins are large molecules present in all cells.
They are made up of -amino acids.
There are two forms of an amino acid: one that is neutral
(with -NH2 and -OH groups) and one that is zwitterionic
(with -NH3+ and -O- groups).
A zwitterion has both positive and negative charge in one
molecule.
There are about 20 amino acids found in most proteins.
Each amino acid is assigned a three-letter abbreviation.
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Proteins
Amino acids are the basic structural units of proteins. An
amino acid is a compound that contains at least one amino
group (-NH2) and at least one carboxyl group (-COOH)
H O

H O
+H N
3

C C O- + +H3N C C OR2

R1

Peptide bond

H O
+H N
3

H O

C C N C C O- + H2O
R1

H R2
25.3

25.3

Proteins

Amino Acids
Our bodies can synthesize about 10 amino acids.
Essential amino acids are the other 10 amino acids, which
have to be ingested.
The -carbon in all amino acids except glycine is chiral
(has 4 different groups attached to it).
Chiral molecules exist as two nonsuperimposable mirror
images.
The two mirror images are called enantiomers.
Chiral molecules can rotate the plane of polarized light.
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Proteins
Amino Acids
The enantiomer that rotates the plane of polarized light to
the left is called L- (laevus = left) and the other
enantiomer is called D- (dexter = right).
Enantiomers have identical physical and chemical
properties. They only differ in their interaction with
other enantiomers.
Most amino acids in proteins exist in the L-form.

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Chapter 25

Proteins
Amino Acids

Proteins
Polypeptides and Proteins
Proteins are polyamides.
When formed by amino acids, each amide group is called
a peptide bond.
Peptides are formed by condensation of the -COOH
group of one amino acid and the NH group of another
amino acid.

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Proteins
Polypeptides and Proteins
The acid forming the peptide bond is named first.
Example: if a dipeptide is formed from alanine and
glycine so that the COOH group of glycine reacts with
the NH group of alanine, then the dipeptide is called
glycylalanine.
Glycylalanine is abbreviated gly-ala.
Polypeptides are formed with a large number of amino
acids (usually result in proteins with molecular weights
between 6000 and 50 million amu).
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Proteins

Protein Structure
Primary structure is the sequence of the amino acids in
the protein.
A change in one amino acid can alter the biochemical
behavior of the protein.
Secondary structure is the regular arrangement of
segments of protein.
One common secondary structure is the -helix.
Hydrogen bonds between N-H bonds and carbonyl
groups hold the helix in place.
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Protein Structure
Pitch is the distance between
coils.
The pitch and diameter ensure
no bond angles are strained and
the N-H and carbonyl
functional groups are
optimized for H-bonding.
Tertiary structure is the three
dimensional structure of the
protein.
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Protein Structure

Carbon

Nitrogen
Oxygen
R group

The structure is
held in position by
intramolecular
hydrogen bonds
()

Hydrogen

25.3

Protein Structure

25.3

Protein Structure
Intermolecular Forces in a Protein Molecule

ionic forces

hydrogen
bonds

dispersion
forces

ionic forces

dispersion
forces
dispersion
forces

dipole-dipole
forces
25.3

Hydrogen Bonds in Parallel and Antiparallel b-pleated Sheets

25.3

Enzymes
Enzymes are biological catalysts.
Most enzymes are protein molecules with large molecular
masses (10,000 to 106 amu).
Enzymes have very specific shapes.
Most enzymes catalyze very specific reactions.
Substrates undergo reaction at the active site of an
enzyme.
A substrate locks into an enzyme and a fast reaction
occurs.
The products then move away from the enzyme.
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Chapter 14

Catalysis
Enzymes
Only substrates that fit into the enzyme lock can be
involved in the reaction.
If a molecule binds tightly to an enzyme so that another
substrate cannot displace it, then the active site is blocked
and the catalyst is inhibited (enzyme inhibitors).
The number of events (turnover number) catalyzed is
large for enzymes (103 - 107 per second).

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Chapter 14

Catalysis
Enzymes

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Chapter 14

Enzyme Catalysis

13.6

Carbohydrates

Carbohydrates have empirical formula Cx(H2O)y.

Carbohydrate means hydrate of carbon.
Most abundant carbohydrate is glucose, C6H12O6.
Carbohydrates are polyhydroxy aldehydes and ketones.
Glucose is a 6 carbon aldehyde sugar and fructose 6
carbon ketone sugar.
The alcohol side of glucose can react with the aldehyde
side to form a six-membered ring.
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Carbohydrates
Most glucose molecules are in the ring form.
Note the six-membered rings are not planar.
Focus on carbon atoms 1 and 5: if the OH groups are on
opposite sides of the ring, then we have -glucose; if
they are on the same side of the ring, then we have glucose.
The - and - forms of glucose form very different
compounds.
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Prentice Hall 2003

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Carbohydrates

Disaccharides
Glucose and fructose are monosaccharides.
Monosaccharides: simple sugars that cannot be broken
down by hydrolysis with aqueous acids.
Disaccharides are sugars formed by the condensation of
two monosaccharides. Examples: sucrose (table sugar)
and lactose (milk sugar).
Sucrose is formed by the condensation of -glucose and
fructose.
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Carbohydrates
Disaccharides
Lactose is formed from galactose and -glucose.
Sucrose is about six times sweeter than lactose, a little
sweeter than glucose and about half as sweet as fructose.
Disaccharides can be converted into monosaccharides by
treatment with acid in aqueous solution.

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Carbohydrates
Polysaccharides
Polysaccharides are formed by condensation of several
monosaccharide units.
There are several different types. Example: starches can
be derived from corn, potatoes, wheat or rice.

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Carbohydrates
Polysaccharides
Starch is not a pure substance.
Enzymes catalyze the conversion of starch to glucose.
Starch is poly -glucose whereas cellulose is poly glucose.
Enzymes that hydrolyze starch do not hydrolyze cellulose
because of the different shapes of the polymers.
Ingested cellulose is recovered unmetabolized.

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Carbohydrates
Polysaccharides
Bacteria in the stomach of animals contain cellulases,
which are enzymes that enable animals to use cellulose
for food.

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Chapter 25

Nucleic Acids
Nucleic acids carry genetic information.
DNA (deoxyribonucleic acids) have molecular weights
around 6 - 16 106 amu and are found inside the nucleus
of the cell.
RNA (ribonucleic acids) have molecular weights around
20,000 to 40,000 amu and are found in the cytoplasm
outside the nucleus of the cell.
Nucleic acids are made up of nucleotides.
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Nucleic Acids
Nucleic acids are high molar mass polymers that play an
essential role in protein synthesis.
1. Deoxyribonucleic acid (DNA)
2. Ribonucleic acid (RNA)

DNA molecule has 2 helical strands.

Each strand is made up of nucleotides.

25.4

Nucleic Acids
There are three important parts to a nucleic acid:
phosphoric acid unit,
five carbon sugar (e.g. deoxyribose), and
nitrogen containing organic base (e.g. adenine).

DNA and RNA have different sugars (dexoyribose vs.

ribose).

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Nucleic Acids
There are only five bases found in DNA and RNA:

adenine (A),
guanine (G),
cytosine (C),
thymine (T found in DNA only), and
uracil (U found in RNA only).

Nucleic acids are formed by condensing two nucleotides

(the phosphoric acid condenses with the O-H group of
the sugar).
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The Components of the Nucleic Acids DNA and RNA

25.4

Nucleic Acids
DNA consists of two deoxyribonucleic acid
strands wound together in a double helix.
The phosphate chains are wrapped around
the outside of the DNA molecule.
Complementary base pairs are formed from
bases which optimize H-bonding: T and A
or C and G.
The complementary base pairs are held
together by hydrogen bonding.
During cell division, the DNA double helix
unwinds.

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Base-Pair Formation by Adenine and Thymine and by

Cytosine and Guanine

25.4

Nucleic Acids
A new strand is formed when bases attach to each strand
of the unwinding double helix.
Because of the optimized hydrogen bonding, there is only
one location for each base.
Therefore, the order of bases in the new strand is the
same as the order of bases in the original strand.
This is how genetic information is preserved during cell
division.
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Nucleic Acids
DNA structure provides us with the understanding of how
protein synthesis occurs, how viruses infect cells, and
other biological problems occur.

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Chapter 25

Prentice Hall 2003

Chapter 25

Lipids
Lipids: a heterogeneous class of naturally occurring
organic compounds classified together on the basis of
common solubility properties.
insoluble in water, but soluble in organic solvents including
diethyl ether, dichloromethane, and acetone

Lipids include:
fatty acids, triglycerides, sphingolipids, phosphoacylglycerols,
and glycolipids.
lipid-soluble vitamins.
prostaglandins, leukotrienes, and thromboxanes.
cholesterol, steroid hormones, and bile acids.

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Schematic diagram of simple and complex lipids.

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Protein Synthesis
The central dogma of molecular biology
Information contained in DNA molecules is expressed in
the structure of proteins.
DNA
replication

RNA
replication

DNA Transcription mRNA

Reverse transcriptase

Translation

protein

Transcription
Protein
Synthesis
Replication involves separation of the two original
strands and synthesis of two new daughter strands using
the original strands as templates.
Transcription: the process by which information encoded
in a DNA molecule is copied into an mRNA molecule.
Translation: the process whereby a base sequence of
mRNA is used to create a protein.

Metabolism
Metabolism: the sum of all chemical reactions involved
in maintaining the dynamic state of a cell or organism.
Pathway: a series of biochemical reactions.
Catabolism: the biochemical pathways that are involved in
generating energy by breaking down large nutrient
molecules into smaller molecules with the concurrent
production of energy.
Anabolism: the pathways by which biomolecules are
synthesized.

(-oxidation)

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