Chapter 9

Proteins

Chapter Objectives:
• Learn about amino acid structure and classification.
• Learn about the formation of zwitterions and isoelectric points.
• Learn about reactions of amino acids, including the formation of disulfides, peptides and
proteins.
• Learn about the characteristics, classification structure, and functions of proteins.
• Learn about the structures and characteristics that give rise to the primary, secondary,
tertiary, and quaternary structure of proteins.
• Learn about protein hydrolysis and denaturation.

Mr. Kevin A. Boudreaux

Angelo State University
C H E M 2353 Fundamentals of Organic Chemistry
Organic and Biochemistry for Today (Seager & Slabaugh)
www.angelo.edu/faculty/kboudrea
 Proteins
• Proteins (Greek proteios, “primary” or “of first
importance”) are biochemical molecules consisting
of polypeptides joined by peptide bonds between
the amino and carboxyl groups of amino acid
residues.
• Proteins perform a number of vital functions:
– Enzymes are proteins that act as biochemical
catalysts.
– Many proteins have structural or mechanical
functions (e.g., actin and myosin in
muscles).
– Proteins are important in cell signaling,
immune
responses, cell adhesion, and the cell cycle.
2
–
Amino Acids

3
 Amino Acids
• All proteins are polymers containing chains of
amino acids chemically bound by amide
(peptide) bonds.
• Most organisms use 20 naturally-occurring amino
acids to build proteins. The linear sequence of the
amino acids in a protein is dictated by the
sequence of the nucleotides in an organisms’
genetic code.
• These amino acids are called alpha ()-amino
acids because the amino group is attached to the
first carbon in the chain connected to the carboxyl
carbon.
H O H O
amino group carboxylate group
H2N C C OH H3 O-
N  carbon
R R 4
 Amino Acids
• The amino acids are classified by the polarity of
the R group side chains, and whether they are
acidic or basic:
– neutral, nonpolar
– neutral, polar
– basic, polar (contains an additional amino
group)
– acidic, polar (contains an additional
carboxylate group)
• All of the amino acids are also known by a
three- letter and one-letter abbreviations.

5
 Table 9.1: The Common Amino Acids
Neutral, nonpolar side chains
H O H O H O H O

H3N C C O- H3N C C O- H3N C C O- H3N C O-

C
H CH3 CH CH3 CH2 CH CH3
Glycine (Gly) G Alanine (Ala) A
CH3 CH3
Valine (Val) V Leucine (Leu) L
H O H O H O

H3N C C O- H3N C O- H2N C C O-

C
CH CH2 CH3 CH2 H2C CH2
CH2
Phenylalanine (Phe) F Proline (Pro) P
CH3
Isoleucine (Ile) I
H O

H3N C O-
C
CH2 CH2 S CH3
Methionine (Met) M 6
 Table 9.1: The Common Amino Acids
Neutral, polar side chains
H O H O H O

H3N C C O- H3N C C O- H3N C O-

C
CH2 OH CH OH CH2 OH
Serine (Ser) S
CH3 Tyrosine (Tyr)Y
Threonine (Thr) T

H O
H O
H3N C C O-
H3N C O-
C H O
CH2 SH
CH2 Cysteine (Cys) C H3N C C O-
O
H
CH2 CH2 C
N H3N O C O- NH2
Glutamine (Gln) Q
H C
Tryptophan (Trp) W CH2 C
O NH2
Asparagine (Asn) N 7
 Table 9.1: The Common Amino Acids
H O
Basic, polar side chains
H O
H3N C O- -
H3N C C
C
O NH2
H O
CH2 CH2 CH2 CH2 NH C NH2
HN H3N C O- Arginine (Arg) R
C
NH CH2 CH2 CH2 CH2
Histidine (His) H NH3
Lysine (Lys) K

Acidic, polar side chains

H O H O

H3N C O- C O-
H3N O
C
CH2 C O- C O CH2 CH2 O-
Aspartate (Asp) D C
Glutamate (Glu) E
8
 Stereochemistry of the Amino Acids
• Since the amino acids (except for glycine) contain
four different groups connected to the -carbon,
they are chiral, and exist in two enantiomeric
forms:
CO2 - CO2-

H3N C H H C NH3

R R
an L-amino acid an D-amino acid

• The amino acids in living systems exist primarily

in the L form.

9
 Zwitterions
• Because amino acids contain both an acidic and a
basic functional group, an internal acid-base
reaction occurs, forming an ion with both a positive
and a negative charge called a zwitterion:
basic N acidic H
O O

H2N CH C OH H3N CH C O-

R R
nonionized form zwitterion
(does not exist) (present in solid form
and in
solutions)
• In solution, the structure of an amino acid
can change with the pH of the solution:

10
 Zwitterions
• Lowering the pH of the solution causes
the zwitterion to pick up a proton:
O O

H3N CH C + H O+ H3N CH C
O- 3
OH
R R
zwitterion (positive net charge)
(0 net charge)
• Increasing the pH of the solution causes
the zwitterion to lose a proton:
O O

H3N CH C + OH- H2N CH C

O- O-

R R
zwitterion (negative net charge)
11
(0 net charge)
 Zwitterions
• Since the pH of the solution affects the charge on
the amino acid, at some pH, the amino acid will
form a zwitterion. This is called the isoelectric
point.
• Each amino acid (and protein) has a characteristic
isoelectric point: those with neutral R groups are
near a pH of 6, those with basic R groups have
higher values, and those with acidic R groups
have lower values.
• Because amino acids can react with both H3O+ and
OH-, solutions of amino acids and proteins can act
as buffers. (E.g., blood proteins help to regulate the
pH of blood.)

12
 Examples: Amino Acid Structures
• Identify the following amino acid R groups as
being polar or nonpolar, and acidic or basic:
H O H O H O

H3N C O- H3N C C O- H3N C O-

C C
CH2 CH2 CH2 CH2
CH2 CH2 OH NH3

• Draw the structure of the amino acid leucine (a)

in acidic solution at a pH below the isoelectric
point, and (b) in basic solution at a pH above the
isoelectric point.
H O

H3N C O-
C
CH2 CH CH3

CH3
Leucine (Leu) L 13
 Examples: Amino Acid Structures
• Draw Fischer projections representing the D and
L form of aspartate and cysteine.

14
Reactions of
Amino Acids

15
 Oxidation of Cysteine
• Amino acids can undergo any of the
reactions characteristic of the functional
groups in the structure.
• Cysteine is the only amino acid that contains a
sulfhydryl (thiol, R—SH) group. Thiols are
easily oxidized to form disulfide bonds (R—S—S
—R). This allows cysteine to dimerize to form
cystine:
O
H3N CH O- H3N CH C O-
C
O
CH2
CH2 [O]
SH oxidizing agent S

SH S

CH2 reducing agent CH2

H3N O- H3N CH C O-

O
C 16
Cystine
 Peptide Formation
• Amides can be thought of as forming from
the reaction of an amine and a carboxylic
acid:
O H O H
R HOH
C OH + R' N H R C N

R' +

carboxylic acid amine amide linkage

• In the same way, two amino acids can combine to
form a dipeptide, held together by a peptide
bond:
peptide linkage
H O H O H O
H3N C
H C O O- + H3N C C O- H3N C C NH C C O- +
HOH
H CH3
glycylalanine
glycine alanine (a dipeptide)
H CH3 17
 Peptide Formation
• The two amino acids can connect the other way
as well, forming a structural isomer of the
dipeptide, with a unique set of physical
properties:
H O H O H O H O
H3N C C O- + H3N C C O- H3N C C NH C O- + HOH
C
CH3 H
alanine glycine CH3 alanylglycine
(a dipeptide)

• A third amino acid can join the chain

H
to form
a tripeptide:
H O H O
H O
H3N C C NH C C NH C C O-

CH3 CH CH3

CH 3
H
alanylglycylvaline
(a tripeptide) 18
 Peptides
• A fourth amino acid would form a tetrapeptide,
a fifth would form a pentapeptide, and so on.
• Short chains are referred to as peptides, chains of
up to about 50 amino acids are polypeptides, and
chains of more than 50 amino acids are proteins.
(The terms protein and polypeptide are often used
interchangeably.)
• Amino acids in peptide chains are called amino
acid residues.
– The residue with a free amino group is called the
N-terminal residue, and is written on the left
end of the chain.
– The residue with a free carboxylate group is
called the C-terminal residue, and is written
on the right end of the chain. 19
 Peptides
• Peptides are named by starting at the N-terminal
end and listing the amino acid residues from left to
right.
• Large amino acid chains are unwieldy to draw in
their complete forms, so they are usually
represented by their three-letter abbreviations,
separated by dashes:
– Gly-Ala (Gly = N-terminal, Ala = C-terminal)
– Ala-Gly (Ala = N-terminal, Gly = C-terminal)
• The tripeptide alanylglycylvaline can be written as
Ala-Gly-Val. (There are five other arrangements of
these amino acids that are possible.)
• Insulin has 51 amino acids, with 1.551066 different
possible arrangements, but the body produces only 20
one.
 Examples: Reactions of Amino Acids
• Write two reactions to represent the formation of
the two dipeptides that form when valine and serine
react.

• Write a complete structural formula and an

abbreviated formula for the tripeptide formed
from aspartate, cysteine, and valine in which the
C- terminal residue is cysteine and the N-terminal
residue is valine.

21
 Examples: Reactions of Amino Acids
• How many tripeptide isomers that contain one
residue each of valine, phenylalanine, and lysine
are possible? Write the abbreviated formulas for
these peptides.

22
Important Peptides

23
 Vasopressin and Oxytocin
• More than 200 peptides have been identified as being essential
to the body’s proper functioning.
• Vasopressin and oxytocin are nonapeptide hormones secreted by
the pituitary gland. Six of the amino acid residues are held in a
loop by disulfide bridges formed by the oxidation of two
cysteine residues. Even though the molecules are very similar,
their biological functions are quite different:
– Vassopressin is known as antidiuretic hormone (ADH) because
it reduces the amount of urine formed, which causes the body
to conserve water. It also raises blood pressure.
– Oxytocin causes the smooth muscles of the uterus to contract,
and is administered to induce labor. It also stimulates the
smooth muscles of mammary glands to stimulate milk
ejection.

24
 Adrenocorticotropic hormone
• Adrenocorticotropic hormone (ACTH) is a 39-residue peptide
produced in the pituitary gland. It regulates the production of
steroid hormones in the cortex of the adrenal gland.

25
 Examples of Peptide and Protein Hormones
Name Origin Action
Adrenocorticotropic
Pituitary Stimulates production of adrenal hormones
hormone (ACTH)
Angiotensin II Blood plasma Causes blood vessels to constrict
Follicle-stimulating Stimulates sperm production and follicle
Pituitary
hormone (FSH) maturation
Gastrin Stomach Stimulates stomach to secrete acid
Glucagon Pancreas Stimulates glycogen metabolism in liver
Human growth
Pituitary General effects; bone growth
hormone (HGH)
Insulin Pancreas Controls metabolism of carbohydrates
Stimulates contraction of the uterus and other
Oxytocin Pituitary
smooth muscles
Prolactin Pituitary Stimulates lactation
Somatostatin Hypothalamus Inhibits production of HGH
Vasopressin Pituitary Decreases volume of urine excreted

26
Characteristics of
Proteins

27
 Size of Proteins
• Proteins are very large polymers of amino acids
with molecular weights that vary from 6000 amu to
several million amu.
– Glucose (C6H12O6) = 180 amu
– Hemoglobin (C2952H4664O832N812S8Fe4) = 65,000 amu
Molecular Number of Amino
Protein Weight (amu) Acid Residues
Insulin 6,000 51
Cytochrome c 16,000 104
Growth hormone 49,000 191
Rhodopsin 38,900 348
Hemoglobin 65,000 574
Hexokinase 96,000 730
Gamma globulin 176,000 1320
Myosin 800,000 6100
28
 Size of Proteins
• Proteins are too large to pass through cell
membranes, and are contained within the cells
where they were formed unless the cell is damaged
by disease or trauma.
– Persistent large amounts of protein in the
urine are indicative of damaged kidney cells.
– Heart attacks can also be confirmed by the
presence of certain proteins in the blood that
are normally confined to cells in heart tissue.

29
 Acid-Base Properties
• Proteins take the form of zwitterions. They have
characteristic isoelectric points, and can behave
as buffers in solutions.
• The tendency for large molecules to remain in
solution or form stable colloidal dispersions
depends on the repulsive forces acting between
molecules with like charges on their surfaces.
– When proteins are at a pH in which there is a net
positive or negative charge, the like charges
cause the molecules to repel one another, and
they remain dispersed.
– When the pH is near the isoelectric point, the net
charge on the molecule is zero, and the repulsion
between proteins is small. This causes the
protein molecules to clump and precipitate from
solution. 30
 Protein Function
• Proteins perform crucial roles in all
biological processes.
1. Catalytic function: Nearly all reactions in living
organisms are catalyzed by proteins functioning
as enzymes. Without these catalysts, biological
reactions would proceed much more slowly.
2. Structural function: In animals structural materials
other than inorganic components of the skeleton are
proteins, such as collagen (mechanical strength of
skin and bone) and keratin (hair, skin, fingernails).
3. Storage function: Some proteins provide a way to
store small molecules or ions, e.g., ovalbumin
(used by embryos developing in bird eggs), casein
(a milk protein) and gliadin (wheat seeds), and
ferritin (a liver protein which complexes with iron
ions). 31
 Protein Function
4. Protective function: Antibodies are proteins that
protect the body from disease by combining with
and destroying viruses, bacteria, and other foreign
substances. Another protective function is blood
clotting, carried out by thrombin and fibrinogen.
5. Regulatory function: Body processes regulated
by proteins include growth (growth hormone) and
thyroid functions (thyrotropin).
6. Nerve impulse transmission: Some proteins act
as receptors for small molecules that transmit
impulses across the synapses that separate nerve
cells (e.g., rhodopsin in vision).
7. Movement function: The proteins actin and
myosin are important in muscle activity,
regulating the contraction of muscle fibers.
32
 Protein Function
8. Transport function: Some proteins bind small
molecules or ions and transport them through
the body.
– Serum albumin is a blood protein that carries
fatty acids between fat (adipose) tissue and other
organs.
– Hemoglobin carries oxygen from the lungs to
other body tissues.
– Transferrin is a carrier of iron in blood plasma.
• A typical human cell contains 9000 different
proteins; the human body contains about
100,000 different proteins.

33
Table 19.4 Biological Functions of Proteins
Function Examples Occurrence or role
Catalysis lactate dehydrogenase Oxidizes lactic acid
cyctochrome c Transfers electrons
DNA polymerase Replicates and repairs DNA
Structure viral-coat proteins Sheath around nucleic acid of virus
glycoproteins Cell coats and walls
-keratin Skin, hair, feathers, nails, and hooves
�-keratin Silk of cocoons and spiderwebs
collagen Fibrous connective tissue
elastin Elastic connective tissue
Storage ovalbumin Egg-white protein
casein A milk protein
ferritin Stores iron in the spleen
gliadin Stores amino acids in wheat
zein Stores amino acids in corn

34
Table 19.4 Biological Functions of Proteins
Function Examples Occurrence or role
Protection antibodies Form complexes with foreign proteins
fibrinogen Involved in blood clotting
thrombin Involved in blood clotting
Regulation insulin Regulates glucose metabolism
growth hormone Stimulates growth of bone

Nerve impulse rhodopsin Involved in vision

transmission acetylcholine receptor protein Impulse transmission in nerve cells
Movement myosin Thick filaments in muscle fiber
actin Thin filaments in muscle fiber
dynein Movement of cilia and flagella
Transport hemoglobin Transports O2 in blood
myoglobin Transports O2 in muscle cells
serum albumin Transports fatty acids in blood
transferrin Transports iron in blood
ceruloplasmin Transports copper in blood
35
 Classification by Structural Shape
Proteins can be classified on the basis of
their structural shapes:
• Fibrous proteins are made up of long rod-shaped or
stringlike molecules that can intertwine with one
another and form strong fibers.
– insoluble in water
– major components of connective tissue, elastic tissue,
hair, and skin
– e.g., collagen, elastin, and keratin.
• Globular proteins are more spherical in shape
– dissolve in water or form stable suspensions.
– not found in structural tissue but are transport proteins, or
proteins that may be moved easily through the body by
the circularoty system
– e.g., hemoglobin and transferrin.
36
 Classification by Composition
Proteins can also be classified by composition:
• Simple proteins contain only amino acid residues.
• Conjugated proteins also contain other organic
or inorganic components, called prosthetic
groups.
– nucleoproteins — nucleic acids (viruses).
– lipoproteins — lipids (fibrin in blood, serum
lipoproteins)
– glycoproteins — carbohydrates (gamma globulin in
blood, mucin in saliva)
– phosphoproteins — phosphate groups (casein in
milk)
– hemoproteins — heme (hemoglobin, myoglobin,
cytochromes) 37
Protein Structure

39
 Protein Structure
• The structure of proteins is much more complex
than that of simple organic molecules.
– Many protein molecules consist of a chain of
amino acids twisted and folded into a
complex three-dimensional structure
– The complex 3D structures of proteins
impart unique features to proteins that allow
them to function in diverse ways.
• There are four levels of organization in
proteins structure: primary, secondary, tertiary,
and quaternary.

40
 Primary Structure of Proteins
• The primary structure of a protein is the linear
sequence of the side chains that are connected to
the protein backbone:
O O O O O

NH CH C NH CH C NH CH C NH CH C NH CH C

R R' R'' R'''

R''''
protein backbone
• Each protein has a unique sequence of amino acid
residues that cause it to fold into a distinctive
shape that allows the protein to function properly.
• Primary structure of human insulin:

41
 Secondary Structure — The  Helix
• Hydrogen bonding causes protein chains to fold
and align to produce orderly patterns called
secondary structures.
• The -helix is a
single protein
chain twisted to
resemble a coiled
helical spring.

42
 Secondary Structure — The  Helix
• The -helix is held in this shape O
by hydrogen bonding interactions C N
between amide groups, with the
side chains extending outward H
from the coil.
O
• The amount of -helix coiling in
C N
proteins is highly variable.
H
• In -keratin (hair, pictured below), myosin
(muscles), epidermin (skin), and fibrin (blood clots),
two or more helices coil together (supracoiling) to
form cables. These cables make up bundles of
fibers that strengthen tissues in which they are
found:

43
Secondary Structure — The �-Pleated
• Another secondary structure is the �-pleated
Sheet
sheet, in which several protein chains lie side by
side, held by hydrogen bonds between adjacent
chains:

44
Secondary Structure — The �-Pleated
• The �-pleated sheet structure is less common
Sheet
than the -helix; it is found extensively only in
the protein of silk.
• The figure below shows both types of
secondary structures in a single protein.

45
 Tertiary Structure of Proteins
• The tertiary structure of a protein refers to the
bending and folding of the protein into a
specific three-dimensional shape.
• These structures result from four types of
interactions between the R side chains of the
amino acids residues:
1. Disulfide bridges can form between two
cysteine residues that are close to each other in
the same chain, or between cysteine residues in
different chains. These bridges hold the protein
chain in a loop or some other 3D shape.
2. Salt bridges are attractions between ions that
result from the interactions of the ionized side
chains of acidic amino acids (—COO-) and the side
chainsamino
basic of acids (—NH3 +).
46
 Tertiary Structure of Proteins
3. Hydrogen bonds can form between a variety of
side chains, especially those that contain:
O

OH NH2 C
NH2
Hydrogen bonding also influences the secondary structure, but here the
hydrogen bonding is between R groups, while in secondary structures it
is between the C=O and NH portions of the backbone.

4. Hydrophobic interactions result from the attraction

of nonpolar groups, or when they are forced
together by their mutual repulsion of the aqueous
solvent. These interactions are particularly
important between the benzene rings in
phenylalanine or tryptophan. This type of
interaction is relatively weak, but since it acts over
large surface areas, the net effect is a strong
interaction. 47
 Tertiary Structure of Proteins
4. cont. The compact structure of globular proteins
in aqueous solution, in which the nonpolar groups
are pointed inward, away from the water
molecules.

48
Tertiary Structure of Proteins — Summary

49
 Examples: R-Group Interactions
• What kind of R-group interaction might be
expected if the following side chains were in close
proximity?
CH CH2 CH3 CH2 CH CH3

CH3 CH3

CH2 C NH2 CH2 OH

CH2 C O- CH2 CH2 CH2 CH2 NH3

50
Visualizing Protein Structure

51
 Quaternary Structure of Proteins
• When two or more polypeptide chains are held
together by disulfide bridges, salt bridges,
hydrogen bond, or hydrophobic interactions,
forming a larger protein complex.
• Each of the polypeptide subunits has its
own primary, secondary, and tertiary
structure.
• The arrangement of the subunits to form a larger
protein is the quaternary structure of the protein.

52
 Hemoglobin
• Hemoglobin is made of four subunits: two
identical alpha chains containing 141 AA’s and two
identical beta chains containing 146 AA’s. Each
subunit contains a heme group located in crevices
near the exterior of the molecule.

53
 Hemoglobin
• A hemoglobin molecule in a person suffering from
sickle-cell anemia has a one-amino acid difference
in the sixth position of the two �-chains of
normal HbA (a glutamate is replaced with a
valine).
• This changes the shape of red blood cells that
carry this mutation to a characteristic sickle shape,
which causes the cells to clump together and
wedge in capillaries, particularly in the spleen, and
cause excruciating pain.
• Cells blocking capillaries
are rapidly destroyed,
and the loss of these red
blood cells causes
anemia.
54
Protein Hydrolysis
and Denaturation

55
 Protein Hydrolysis
• Amides can be hydrolyzed under acidic or
basic conditions.
• The peptide bonds in proteins can be broken
down under acidic or basic conditions into
smaller peptides, or all the way to amino acids,
depending on the hydrolysis time, temperature,
and pH
H+ or OH- H+ or OH-
protein + H 2O smaller peptides amino
acids
– The digestion of proteins involves
hydrolysis reactions catalyzed by digestive
enzymes.
– Cellular proteins are constantly being broken
down as the body resynthesizes molecules
and tissues that it needs.
56
 Denaturation
• Proteins are maintained in their native state
(their natural 3D conformation) by stable
secondary and tertiary structures, and by
aggregation of subunits into quaternary
structures.
• Denaturation is caused when the folded native
structures break down because of extreme temps.
or pH values, which disrupt the stabilizing
structures. The structure becomes random and
disorganized.

57
 Denaturation
• Most proteins are biologically active only over
a temperature range of 0ºC to 40ºC.
• Heat is often used to kill microorganisms and
deactivate their toxins. The protein toxin from
Clostridium botulinum is inactivated by being
heated to 100ºC for a few minutes; heating also
deactivates the toxins that cause diphtheria and
tetanus.
• Heat denaturation is used to prepare vaccines
against some diseases. The denatured toxin can no
longer cause the disease, but it can stimulate the
body to produce substances that induce immunity.

58
 Denaturation
• Proteins can also be denatured by heavy-metal ions
such as Hg2+, Ag+, and Pb2+ that interact with —SH
and carboxylate groups.
– Organic materials containing Hg (mercurochrome
and merthiolate) were common topical
antiseptics.
– Heavy-metal poisoning is often treated with large
doses of raw egg white and milk; the proteins in
the egg and milk bind to the metal ions, forming
a precipitate, which is either vomited out or
pumped out.

59
 Substances That Denature Proteins
Substance or condition Effect on Proteins

Disrupt hydrogen bonds and ionic attractions by

Heat and ultraviolet light making molecules vibrate too violently; produce
coagulation, as in cooking an egg

Organic solvents (ethanol

Disrupt hydrogen bonds in proteins and probably
and others miscible with
form new ones with the proteins
water)

Disrupt hydrogen bonds and ionic attractions;

Strong acids or bases
prolonged exposure results in hydrolysis of protein

Disrupt hydrogen bonds, hydrophobic interactions,

Detergents
and ionic attractions.

Heavy-metal ions (Hg2+, Form bonds to thiol groups and precipitate proteins
Ag+, and Pb2+) as insoluble heavy-metal salts
60