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22
General, Organic, and
Biochemistry, 8e
Bettelheim, Brown
CAmpbell, and Farrell
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22-1
22Chapter 22
Proteins
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22-2
22Proteins
• Proteins serve many functions, including the
following. Given are examples of each.
• 1.Structure: collagen and keratin are the chief
constituents of skin, bone, hair, and nails.
• 2. Catalysts: virtually all reactions in living systems are
catalyzed by proteins called enzymes.
• 3. Movement: muscles are made up of proteins called
myosin and actin.
• 4. Transport: hemoglobin transports oxygen from the
lungs to cells; other proteins transport molecules
across cell membranes.
• 5. Hormones: many hormones are proteins, among
them insulin, oxytocin, and human growth hormone.
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22-3
22Proteins
• 6. Protection: blood clotting involves the protein
fibrinogen; the body used proteins called antibodies to
fight disease.
• 7. Storage: casein in milk and ovalbumin in eggs store
nutrients for newborn infants and birds; ferritin, a
protein in the liver, stores iron.
• 8. Regulation: certain proteins not only control the
expression of genes, but also control when gene
expression takes place.
• Proteins are divided into two types:
• fibrous proteins
• globular proteins
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22-4
22Amino Acids
• Amino acid: a compound that contains both an
amino group and a carboxyl group.
• -Amino acid: an amino acid in which the amino group
is on the carbon adjacent to the carboxyl group.
• Although -amino acids are commonly written in the
un-ionized form, they are more properly written in the
zwitterion (internal salt) form.
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O
R-CH-COH
O
R-CH-CO-
NH2
Un-ionized
form
NH3 +
Zwitterion
22-5
22Chirality of Amino Acids
• With the exception of glycine, all protein-derived
amino acids have at least one stereocenter (the carbon) and are chiral.
• The vast majority of protein-derived -amino acids
have the L-configuration at the -carbon.
COOH
N H3 +
COO+
H 3N
CH3
D-Alanine
H
CH3
L-Alanine
(Fischer projections)
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22-6
22Chirality of Amino Acids
• A comparison of the stereochemistry of L-alanine
and D-glyceraldehyde (as Fischer projections):
-
-
COO
H
NH3 +
COO
+
H3 N
CH3
D-A lanine
H
OH
CH2 OH
D -Glycerald ehyde
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H
CH3
L-Alan ine
CHO
the n aturally
occu rring form
the n aturally
occu rring form
CHO
HO
H
CH2 OH
L-Glycerald ehyde
22-7
2220 Protein-Derived AA
• Nonpolar side chains (at pH 7.0)
COO-
NH3
+
COONH3
+
Glycine
(Gly, G)
-
+
COO
NH3 +
S
COO-
+
NH
3
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Leucin e
(Leu, L)
Meth ion in e
(Met, M)
H
-
COO
Isoleucin e
(Ile, I)
-
-
COO
N
H
COO
NH3
COO- Phen ylalan ine
(Phe, F)
+
NH3
A lanine
(A la, A)
N
H
NH3
+
Prolin e
(Pro, P)
Tryptoph an
(Trp , W)
COO- Valine
(Val, V)
+
NH3
22-8
2220 Protein-Derived AA
• Polar side chains (at pH 7.0)
COO-
H2 N
O
NH3 +
-
As paragine
(As n, N )
COO
HS
NH3
O
-
H2 N
COO
NH3
Glutamine
(Gln, Q)
+
HO
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NH3
+
COO-
HO
NH3
+
Serine
(Ser, S)
OH
-
COO
+
Cysteine
(Cys, C)
Tyrosine
(Tyr, Y)
COO- Threon in e
(Thr, T)
NH3 +
22-9
2220 Protein-Derived AA
• Acidic and basic side chains (at pH 7.0)
-
COO-
O
O
NH3
As partic acid
(As p, D )
+
NH2 +
H2 N
O
-
COO
N
H
NH3
+
Arginin e
(Arg, R)
-
-
O
COO Glutamic acid
+
(Glu, E)
NH
N
3
N
H
+
H3 N
COONH3
-
COO
NH3
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Histidine
(His , H)
+
+
Lysine
(Lys, K)
22-10
2220 Protein-Derived AA
1. All 20 are -amino acids.
2. For 19 of the 20, the -amino group is primary; for
proline, it is secondary.
3. With the exception of glycine, the -carbon of each is a
stereocenter.
4. Isoleucine and threonine each contain a second
stereocenter.
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22-11
22Ionization vs pH
• The net charge on an amino acid depends on the
pH of the solution in which it is dissolved.
• If we dissolve an amino acid in water, it is present in
the aqueous solution as its zwitterion.
• If we now add a strong acid such as HCl to bring the pH
of the solution to 2.0 or lower, the strong acid donates
a proton to the -COO- of the amino acid turning the
zwitterion into a positive ion.
O
+
+
H3 N-CH-C-O + H3 O
R
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O
+
H3 N-CH-C-OH + H2 O
R
22-12
22Ionization vs pH
• If we add a strong base such as NaOH to the solution
and bring its pH to 10.0 or higher, a proton is
transferred from the NH3+ group to the base turning the
zwitterion into a negative ion.
O
+
H3 N-CH-C-O + OH
R
O
H2 N-CH-C-O + H2 O
R
• to summarize:
O
+
H3 N-CH-C-OH
R
pH 2.0
Net charge +1
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OH
+
H3 O
O
+
H3 N-CH-C-O
R
pH 5.0 - 6.0
Net charge 0
OHH3 O+
O
H2 N-CH-C-OR
pH 10.0
N et ch arge -1
22-13
22Isoelectric Point
• Isoelectric
point, pI:
The pH at
which the
majority of
molecules of
a compound
in solution
have no net
charge.
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Nonpolar &
polar side chains
alanine
asparagine
cys teine
glutamine
glycine
isoleucine
leucine
methionine
phenylalanine
proline
serine
threonine
tyros ine
tryptophan
valine
pI
6.01
5.41
5.07
5.65
5.97
6.02
6.02
5.74
5.48
6.48
5.68
5.87
5.66
5.89
5.97
Acidic
Side Chains
aspartic acid
glutamic acid
Bas ic
Side Chains
arginine
histidine
lysine
pI
2.77
3.22
pI
10.76
7.59
9.74
22-14
22Cysteine
• The -SH (sulfhydryl) group of cysteine is easily
oxidized to an -S-S- (disulfide).
+
2 H3 N-CH-COOCH2
SH
Cysteine
oxidation
reduction
+
H3 N-CH-COO
CH2
a disulfide
bon d
S
S
CH2
+
H3 N-CH-COO
Cystine
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22-15
22Other Amino Acids
• Hydroxylation (oxidation) of proline, lysine, and
tyrosine, and iodination for tyrosine, give these
nonstandard amino acids.
O
HO
C-O N
H 3N C H
COO-
H H
Hydroxyproline
I
I
O
+
H 3N
OH
COO-
N H3 +
Hydroxylysine
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I
I
OH
Thyroxine
22-16
22Peptides
• In 1902, Emil Fischer proposed that proteins are
long chains of amino acids joined by amide
bonds.
• peptide bond: The special name given to the amide
bond between the -carboxyl group of one amino acid
and the -amino group of another.
peptide
bond
CH3
+
H 3N
O-
O
Alanine (Ala)
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+
+
H 3N
O
OCH2 OH
Serine (Ser)
CH3 H
O
+
N
H 3N
O - + H2 O
O
CH2 OH
Alanyls erine
(Ala-Ser)
22-17
22Peptides
• Peptide: A short polymer of amino acids joined by
peptide bonds; they are classified by the number of
amino acids in the chain.
• Dipeptide: A molecule containing two amino acids
joined by a peptide bond.
• Tripeptide: A molecule containing three amino acids
joined by peptide bonds.
• Polypeptide: A macromolecule containing many amino
acids joined by peptide bonds.
• Protein: A biological macromolecule containing at least
30 to 50 amino acids joined by peptide bonds.
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22-18
22Writing Peptides
• By convention, peptides are written from the left,
beginning with the free -NH3+ group and ending with
the free -COO- group on the right.
• C-terminal amino acid: the amino acid at the end of the
chain having the free -COO- group.
• N-terminal amino acid: the amino acid at the end of the
chain having the free -NH3+ group.
+
H 3N
N-terminal
amino acid
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O
C6 H5
O
H
N
C-terminal
amino acid
N
OH
O
OH
COOSer-Phe-Asp
22-19
22Peptides and Proteins
• Proteins behave as zwitterions.
• Proteins also have an isoelectric point, pI.
• At its isoelectric point, the protein has no net charge.
• At any pH above (more basic than) its pI, it has a net
negative charge.
• At any pH below (more acidic than) its pI, it has a net
positive charge.
• Hemoglobin, for example, has an almost equal number
of acidic and basic side chains; its pI is 6.8.
• Serum albumin has more acidic side chains; its pI is
4.9.
• Proteins are least soluble in water at their isoelectric
points and can be precipitated from solution at this pH.
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22-20
22Levels of Structure
• Primary structure: the sequence of amino acids in
a polypeptide chain; read from the N-terminal
amino acid to the C-terminal amino acid.
• Secondary structure: conformations of amino
acids in localized regions of a polypeptide chain;
examples are -helix, b-pleated sheet, and
random coil.
• Tertiary structure: the complete threedimensional arrangement of atoms of a
polypeptide chain.
• Quaternary structure: the spatial relationship and
interactions between subunits in a protein that
has more than one polypeptide chain.
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22-21
22Primary Structure
• Primary structure: the sequence of amino acids in
a polypeptide chain.
• The number peptides possible from the 20
protein-derived amino acids is enormous.
• there are 20 x 20 = 400 dipeptides possible.
• there are 20 x 20 x 20 = 8000 tripeptides possible.
• the number of peptides possible for a chain of n amino
acids is 20n.
• for a small protein of 60 amino acids, the number of
proteins possible is 2060 = 1078, which is possibly
greater than the number of atoms in the universe!
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22-22
22Primary Structure
• Figure 22.6 The
hormone insulin
consists of two
polypeptide chains
held together by two
interchain disulfide
bonds.
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22-23
22Primary Structure
• Just how important is the exact amino acid
sequence?
• Human insulin consists of two polypeptide chains
having a total of 51 amino acids; the two chains are
connected by two interchain disulfide bonds.
• In the table are differences between four types of
insulin.
Human
Cow
Hog
Sh eep
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A Chain
p ositions 8-9-10
B Chain
p os ition 30
-Thr-Ser-Ile-A la-Ser-Val-Thr-Ser-Ile-Ala-Gly-Val-
-Thr
-Ala
-Ala
-Ala
22-24
22Primary Structure
• Vasopressin and oxytocin are both nonapeptides but
have quite different biological functions.
• Vasopressin is an antidiuretic hormone.
• Oxytocin affects contractions of the uterus in childbirth
and the muscles of the breast that aid in the secretion
of milk.
Cys S S Cys Pro Gly NH2
Tyr
A sn
Ph e Gln
Vas op res sin
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Cys S S Cys Pro Leu NH2
Tyr
A sn
Ile
Gln
Oxytocin
22-25
22Secondary Structure
• Secondary structure: conformations of amino
acids in localized regions of a polypeptide chain.
• The most common types of secondary structure are helix and b-pleated sheet.
• -Helix: a type of secondary structure in which a
section of polypeptide chain coils into a spiral, most
commonly a right-handed spiral.
• b-Pleated sheet: a type of secondary structure in which
two polypeptide chains or sections of the same
polypeptide chain align parallel to each other; the
chains may be parallel or antiparallel.
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22-26
22-Helix
• Figure 22.8(a) The -helix structure.
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22-27
22-Helix
• In a section of -helix;
• There are 3.6 amino acids per turn of the helix.
• The six atoms of each peptide bond lie in the same
plane.
• N-H groups of peptide bonds point in the same
direction, roughly parallel to the axis of the helix.
• C=O groups of peptide bonds point in the opposite
direction, also roughly parallel to the axis of the helix.
• The C=O group of each peptide bond is hydrogen
bonded to the N-H group of the peptide bond four
amino acid units away from it.
• All R- groups point outward from the helix.
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22-28
22b-Pleated Sheet
• Figure 22.8(b). The b-pleated sheet structure.
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22-29
22b-Pleated Sheet
• In a section of b-pleated sheet;
• The six atoms of each peptide bond lie in the same
plane.
• The C=O and N-H groups of peptide bonds from
adjacent chains point toward each other and are in the
same plane so that hydrogen bonding is possible
between them.
• All R- groups on any one chain alternate, first above,
then below the plane of the sheet, etc.
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22-30
22Collagen Triple Helix
• Figure 22.11 The collagen triple helix.
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22-31
22Collagen Triple Helix
• Consists of three polypeptide chains wrapped around
each other in a ropelike twist to form a triple helix
called tropocollagen.
• 30% of amino acids in each chain are Pro and Lhydroxyproline (Hyp); L-hydroxylysine (Hyl) also
occurs.
• Every third position is Gly and repeating sequences are
X-Pro-Gly and X-Hyp-Gly.
• Each polypeptide chain is a helix but not an -helix.
• The three strands are held together by hydrogen
bonding involving hydroxyproline and hydroxylysine.
• With age, collagen helices become cross linked by
covalent bonds formed between side chains of Lys
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22-32
22Tertiary Structure
• Tertiary structure: the overall conformation of an
entire polypeptide chain.
• Tertiary structure is stabilized in four ways:
• Covalent bonds, as for example, the formation of
disulfide bonds between cysteine side chains.
• Hydrogen bonding between polar groups of side
chains, as for example between the -OH groups of
serine and threonine.
• Salt bridges, as for example, the attraction of the -NH3+
group of lysine and the -COO- group of aspartic acid.
• Hydrophobic interactions, as for example, between the
nonpolar side chains of phenylalanine and isoleucine.
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22-33
22Tertiary Structure
• Figure 22.13 Forces that stabilize 3° structure of
proteins
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22-34
22Quaternary Structure
• Quaternary structure: the arrangement of
polypeptide chains into a noncovalently bonded
aggregation.
• The individual chains are held in together by hydrogen
bonds, salt bridges, and hydrophobic interactions.
• Hemoglobin
• Adult hemoglobin: two alpha chains of 141 amino acids
each, and two beta chains of 146 amino acids each.
• Each chain surrounds an iron-containing heme unit.
• Fetal hemoglobin: two alpha chains and two gamma
chains; fetal hemoglobin has a greater affinity for
oxygen than does adult hemoglobin.
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22-35
22Hemoglobin
• Figure 22.15 The 4° structure of hemoglobin.
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22-36
22Hemoglobin
• Figure 22.16 The structure of heme.
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22-37
22Quaternary Structure
• Figure 22.17 Integral membrane protein of
rhodopsin made of -helices.
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22-38
22Quaternary Structure
• Figure 22.18 The b-barrel of an integral membrane
protein of the outer membrane of a
mitochondrion is made of eight b-pleated sheets.
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22-39
22Denaturation
• Denaturation: the process of destroying the
native conformation of a protein by chemical or
physical means.
• Some denaturations are reversible, while others
permanently damage the protein.
• Denaturing agents include:
• Heat: heat can disrupt hydrogen bonding; in globular
proteins, it can cause unfolding of polypeptide chains
with the result that coagulation and precipitation may
take place.
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22-40
22Denaturation
• 6 M aqueous urea: disrupts hydrogen bonding.
• Surface-active agents: detergents such as sodium
dodecylbenzenesulfate (SDS) disrupt hydrogen
bonding.
• Reducing agents: 2-mercaptoethanol (HOCH2CH2SH)
cleaves disulfide bonds by reducing -S-S- groups to SH groups.
• Heavy metal ions: transition metal ions such as Pb2+,
Hg2+, and Cd2+ form water-insoluble salts with -SH
groups; Hg2+ for example forms -S-Hg-S-.
• Alcohols: 70% ethanol, for example, which denatures
proteins, is used to sterilize skin before injections.
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22-41
22Proteins
End
Chapter 22
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22-42