Download Primary structure: the sequence of amino acids in a polypeptide chain

Proteins serve many functions, including the following. Given are
examples of each.
Structure: collagen and keratin are the chief constituents of skin,
bone, hair, and nails
Catalysts: virtually all reactions in living systems are catalyzed by
proteins called enzymes
Movement: muscles are made up of proteins called myosin and
actin
Transport: hemoglobin transports oxygen from the lungs to cells;
other proteins transport molecules across cell membranes
Hormones: many hormones are proteins, among them insulin,
oxytocin, and human growth hormone
See p 525 - 526
Storage: casein in milk and ovalbumin in eggs store nutrients
for newborn infants and birds; ferritin, a protein in the liver,
stores iron
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
Protection: blood clotting involves the protein fibrinogen; the
body used proteins called antibodies to fight disease
globular proteins
Amino 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
O
R-CH-COH
O
R-CH-CO-
NH2
Un-ionized
form
NH3 +
Zwitterion
Chirality of Amino Acids
• With the exception of glycine, all proteinderived amino acids have at least one
stereocenter (the -carbon) and are chiral
– the vast majority of -amino acids have the Lconfiguration at the -carbon
COOH
N H3 +
CH3
D-Alanine
COO+
H 3N
H
CH3
L-Alanine
(Fischer projections)
Chirality of Amino Acids
• A comparison of the stereochemistry of Lalanine and D-glyceraldehyde
-
-
COO
H
NH3 +
COO
+
H3 N
CH3
D-Alanine
the naturally
H
occurring form
CH2 OH
D-Glyceraldehyde
H
CH3
L-Alanine
CHO
OH
the naturally
occurring form
CHO
HO
H
CH2 OH
L-Glyceraldehyde
20 Protein-Derived AA
• Nonpolar side chains (at pH 7.0)
COONH3
+
COONH3
+
-
+
-
COO
NH3 +
S
COO- Phenylalanine
(Phe, F)
+
NH3
Glycine
(Gly, G)
COONH3 +
Table 21-2 p 527
Isoleucine
(Ile, I)
Leucine
(Leu, L)
Methionine
(Met, M)
-
Proline
(Pro, P)
-
Tryptophan
(Trp, W)
COO
N
H
COO
NH3
Alanine
(Ala, A)
H
COO
N
H
NH3
+
COO- Valine
(Val, V)
+
NH3
20 Protein-Derived AA
• Polar side chains (at pH 7.0)
COO-
H2 N
O
NH3 +
-
Asparagine
(Asn, N)
COO
HS
NH3
O
-
H2 N
COO
NH3
+
Glutamine
(Gln, Q)
HO
NH3
+
COO-
HO
NH3
+
Serine
(Ser, S)
OH
-
COO
+
Cysteine
(Cys, C)
Tyrosine
(Tyr, Y)
COO- Threonine
(Thr, T)
NH3 +
20 Protein-Derived AA
• Acidic and basic side chains (at pH 7.0)
acidic
-
basic
COO-
O
O
NH3 +
Aspartic acid
(Asp, D)
NH2 +
H2 N
O
-
COO
N
H
NH3
+
Arginine
(Arg, R)
-
-
O
COO Glutamic acid
+
(Glu, E)
NH
N
3
N
H
+
H3 N
COONH3
+
Histidine
(His, H)
-
COO
NH3
+
Lysine
(Lys, K)
20 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 contain a second
stereocenter
isoleucine
threonine
Electrophoresis
• Electrophoresis: the process of separating
compounds on the basis of their electric charge
– electrophoresis of amino acids can be carried out
using paper, starch, agar, certain plastics, and
cellulose acetate as solid supports
• In paper electrophoresis
– a paper strip saturated with an aqueous buffer of
predetermined pH serves as a bridge between two
electrode vessels
Electrophoresis
– a sample of amino acids is applied as a spot on
the paper strip
– an electric potential is applied to the electrode
vessels and amino acids migrate toward the
electrode with charge opposite their own
– molecules with a high charge density move
faster than those with low charge density
– molecules at their isoelectric point remain at the
origin
– after separation is complete, the strip is dried
and developed to make the separated amino
acids visible
Isoelectric Point
• Isoelectric
point, pI:
the pH at
which the
majority of
molecules
of a
compound
in solution
have no net
charge
Nonpolar &
polar side chains
alanine
asparagine
cysteine
glutamine
glycine
isoleucine
leucine
methionine
phenylalanine
proline
serine
threonine
tyrosine
tryptophan
valine
pI
6.02
5.41
5.02
5.65
5.97
6.02
6.02
5.74
5.48
6.30
5.68
6.53
5.63
5.89
5.97
Acidic
Side Chains
pI
aspartic acid 2.98
glutamic acid 3.08
Basic
Side Chains
arginine
histidine
lysine
pI
10.76
7.64
9.74
Values given in table
21-1 p527
Ionization 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
O
O
ion
+
-
H3 N-CH-C-O + OH
R
– to summarize
O
+
H3 N-CH-C-OH
R
pH 2.0
Net charge +1
OH
+
H3 O
O
+
H3 N-CH-C-O
R
pH 5.0 - 6.0
Net charge 0
-
H2 N-CH-C-O
R
OHH3 O+
+ H2 O
O
H2 N-CH-C-OR
pH 10.0
Net charge -1
Ionization 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
O
+
H3 N-CH-C-OH + H2 O
R
D:\GOB.exe
Go to 21 – 3 simulation
Cysteine
• 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
bond
S
S
CH2
+
H3 N-CH-COO
Cystine
Peptides
• 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
+
H3 N
O-
O
Alanine (Ala)
+
+
H3 N
O
-
O
CH2 OH
Serine (Ser)
CH3 H
O
+
N
H3 N
O- + H2 O
O
CH2 OH
Alanylserine (Ala-Ser)
Peptide Bond Geometry
• The four atoms of a peptide bond and the
two alpha carbons joined to it lie in a plane
with bond angles of 120° about C and N
C
C
C
C
Fig 21.1, p.532
Peptide Bond Geometry
– to account for this geometry, Linus Pauling
proposed that a peptide bond is most
accurately represented as a hybrid of two
contributing structures
– the hybrid has considerable C-N double bond
character and rotation about the peptide bond
is restricted
••
••
O
C
••
C
H
(1)
O
-
C
N
C
••
••
••
+
C
N
C
H
(2)
Peptides
– 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
Writing 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
O
C6 H5
O
H
N
N
OH
O
OH
COOSer-Phe-Asp
C-terminal
amino acid
Fig. 22.UN, p.530
Peptides and Proteins
• proteins behave as zwitterions
• proteins also have an isoelectric point, pI
– hemoglobin 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
their solutions
Fig21.2 – p 533
In acid solution
solubility of polypeptide
depends on pH – least
soluble at isoelectric point
In neutral solution
In basic solution
Levels 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 overall
conformation of a polypeptide chain
Quaternary structure: the
arrangement of two or more
polypeptide chains into a
noncovalently bonded aggregation
Levels of structure
Primary
secondary
tertiary
Primary Structure
• Primary structure: the sequence of amino
acids in a polypeptide chain
• The number peptides derived 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!
Primary 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 disulfide bonds
– in the table are differences between four types
of insulin
Human
Cow
Hog
Sheep
A Chain
positions 8-9-10
B Chain
position 30
-Thr-Ser-Ile-Ala-Ser-Val-Thr-Ser-Ile-Ala-Gly-Val-
-Thr
-Ala
-Ala
-Ala
Primary 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
Asn
Phe Gln
Vasopressin
Cys S S Cys Pro Leu NH2
Tyr
Asn
Ile
Gln
Oxytocin
Secondary 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
-Helix
The h-bonding in the alpha helix is between
amino and acid groups in the backbone
C
hydrogen
bonding
C
C
C
-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 itall R- groups
point outward from the helix
b-Pleated Sheet
b-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.
Collagen Triple Helix
Collagen Triple Helix
– every third position is Gly and repeating sequences
are X-Pro-Gly and X-Hyp-Gly
– 30% of amino acids in each chain are Pro and Lhydroxyproline (Hyp); L-hydroxylysine (Hyl) also
occurs
– each polypeptide chain is a helix but not an -helix
– the three strands are held together by hydrogen
bonding involving hydroxyproline and hydroxylysine
– consists of three polypeptide chains wrapped around
each other in a ropelike twist to form a triple helix
called tropocollagen
– with age, collagen helices become cross linked by
covalent bonds formed between Lys residues
Fig 21.UN, p.540
Collagen – triple helix
( 3 intertwined
helices )
Each helix stabilized by
steric repulsions between
proline rings
Structure further
stabilized by H-bonding
between NH of glycine &
CO of amino acids on
other chains and by
covalent cross links
formed between lysine
side chains.
Tertiary Structure
• Tertiary structure: the overall conformation of a
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
Quaternary 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
Hemoglobin
D:\GOB.exe
Go to 21-5
Denaturation
• 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