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Chemistry 20
Chapter 14
Proteins
Function of proteins
Fibrinogen helps blood clotting
Proteins
100,000 different proteins in human body.
Fibrous proteins:
Insoluble in water – used for structural purposes.
Globular proteins:
More or less soluble in water – used for nonstructural purposes.
Amino acids
•
•
•
•
•
Are the building blocks of proteins.
Contain carboxylic acid and amino groups.
Are ionized in solution (soluble in water).
They are ionic compounds (solids-high melting points).
Contain a different side group (R) for each.
R
│
side chain
H2N— C —COOH
│
H
R
│
+
Zwitterion
H3N— C —COO−
│
H
ionized form
Amino acids
Only difference: containing a different side group (R) for each.
H
│
+
H3N—C —COO−
│
H
glycine
CH3
│
+
H3N—C —COO−
│
H
alanine
Amino acids
Amino acids are classified as:
• Nonpolar amino acids
(hydrophobic) with hydrocarbon
(alkyl or aromatic) sides chains.
• Polar amino acids (hydrophilic)
with polar or ionic side chains.
• Acidic amino acids (hydrophilic)
with acidic side chains (-COOH).
• Basic amino acids (hydrophilic)
with –NH2 side chains.
Amino acids
There are many amino acids.
There are only 20 different amino acids in the proteins in humans.
Are called α amino acids.
Nonpolar amino acids
COONH3
+
COONH3
+
Glycine
(Gly, G)
-
+
COO
NH3 +
S
COONH3 +
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
Polar amino acids
COO-
H2 N
O
NH3 +
-
As paragine
(As n, 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- Threon in e
(Thr, T)
NH3 +
Acidic and basic amino acids
-
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
Histidine
(His , H)
+
-
COO
NH3
+
Lysine
(Lys, K)
Fischer projections
All of the α-amino acids are chiral (except glycine)
Four different groups are attached to central carbon (α-carbon).
-
COO
H
N H3
COO
+
+
H 3N
CH3
D-Alanine
COO-
-
H
CH3
L-Alanine
(Fischer projections)
H
N H3 +
CH23SH
COO+
H 3N
H
CH23SH
CH
D-Alanine
L-Alanine
D-cysteine
L-cysteine
(Fischer projections)
L isomers is found in the body proteins.
Ionization and pH
pH: 5 to 6
Isoelectric point (pI)
O
O
+
charges
-Positive charges = Negative
H3 N-CH-C-O + OH
H2 N-CH-C-O + H2 O
No net charge - Zwitterion
R
R
pH: about 2 or 3
-COO- acts as a base and accepts an H+
O
+
+
H3 N-CH-C-O + H3 O
R
pH: 7.6 to 10.8
O
+
H3 N-CH-C-O + OH
R
O
+
H3 N-CH-C-OH + H2 O
R
-NH3+ acts as an acid and loses an H+
O
H2 N-CH-C-O- + H2 O
R
Ionization and pH
The net charge on an amino acid depends on the
pH of the solution in which it is dissolved.
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
OHH3 O+
O
H2 N-CH-C-OR
pH 10.0
N et ch arge -1
Ionization and pH
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
Each amino acid has a fixed and constant pI.
Peptide
A dipeptide forms:
• When an amide links two amino acids.
• Between the COO− of one amino acid and
the NH3 + of the next amino acid.
peptide
bond
CH3
+
H 3N
O-
O
Alanine (Ala)
+
+
H 3N
O
OCH2 OH
Serine (Ser)
CH3 H
O
+
N
H 3N
O - + H2 O
O
CH2 OH
Alanyls erine
(Ala-Ser)
Peptide
•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.
Naming of peptides
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
Naming of peptides
- Begin from the N terminal.
- Drop “-ine” and it is replaced by “-yl”.
- Give the full name of amino acid at the C terminal.
O
O
O
+
-
H3N-CH-C-NH-CH2-C-NH-CH-C-O
CH3
CH2OH
From alanine
alanyl
From glycine
glycyl
From serine
serine
Alanylglycylserine
(Ala-Gly-Ser)
Structure of proteins
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
Primary Structure of proteins
- The order of amino acids held together by peptide bonds.
- Each protein in our body has a unique sequence of amino acids.
- The backbone of a protein.
CH3
CH3
+
CH3 O
+
S
CH CH3
SH
CH2
CH O
CH2 O
CH2 O
H3N CH C N CH C N CH C N CH C OH
H
Ala─Leu─Cys─Met
H
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
bon d
S
S
CH2
+
H3 N-CH-COO
Cystine
NH3+
Primary Structure of proteins
NH3+
The primary structure of insulin:
- Is a hormone that regulates the glucose level
in the blood.
- Was the first amino acid order determined.
- Contains of two polypeptide chains linked by
disulfide bonds (formed by side chains (R)).
O
C
O-
- Chain A has 21 amino acids and
chain B has 30 amino acids.
- Genetic engineers can produce it for
treatment of diabetes.
O
C
O-
Chain A
Chain B
Secondary Structure of proteins
Describes the way the amino acids next to or near to each other
along the polypeptide are arranged in space.
1. Alpha helix (α helix)
2. Beta-pleated sheet (-pleated sheet)
3. Triple helix (found in Collagen)
Secondary Structure - α-helix
• A section of polypeptide chain coils into
a rigid spiral.
• Held by H bonds between the H of N-H
group and the O of C=O of the fourth
amino acid down the chain (next turn).
• looks like a coiled “telephone cord.”
• All R- groups point outward from the
helix.
H-bond
Secondary Structure - -pleated sheet
• Consists of polypeptide chains arranged side by side.
• Has hydrogen bonds between the peptide chains.
• Has R groups above and below the sheet (vertical).
• Is typical of fibrous proteins such as silk.
O
H
Secondary Structure – Triple helix (Collagen)
- Collagen is the most abundant protein.
- Three polypeptide chains (three α-helix) woven
together.
- Typical of collagen, connective tissue, skin,
blood vessels, tendons, and cartilage.
-
Consists of glycine (33%), proline (22%), alanine (12%), and
smaller amount of hydroxyproline and hydroxylysine.
-
We need vitamin C (special enzyme).
Tertiary Structure
The tertiary structure is determined by attractions and repulsions
between the side chains (R) of the amino acids in a polypeptide chain.
Interactions between side
chains of the amino acids
fold a protein into a specific
three-dimensional shape.
-S-S-
Tertiary Structure
(1) Disulfide (-S-S-)
(2) salt bridge (acid-base)
(3) Hydrophilic (polar)
(4) hydrophobic (nonpolar)
(5) Hydrogen bond
Globular proteins
- Have compact, spherical shape.
- Almost soluble in water.
- Carry out the work of the cells:
Synthesis, transport, and metabolism
Myoglobin
Stores oxygen in muscles.
153 amino acids in a single polypeptide chain (mostly α-helix).
Fibrous proteins
- Have long, thin shape and insoluble in water.
- Involve in the structure of cells and tissues.
α-keratin: hair, wool, skin, and nails
Three α-helix bond together by disulfide bond (-S-S-)
-keratin: feathers of birds
Large amount of -pleated sheet
Quaternary Structure
• Occurs when two or more protein
units (polypeptide subunits) combine.
α chain
 chain
• Is stabilized by the same
interactions found in tertiary
structures (between side chains).
• Hemoglobin consists of four
polypeptide chains as subunits.
 chain
• Is a globular protein and transports
oxygen in blood (four molecules of O2).
α chain
Hemoglobin
Summary of protein Structure
Summary of protein Structure
Denaturation
Active protein
- Is a process of destroying a protein
by chemical and physical means.
- We can destroy secondary, tertiary,
or quaternary structure but the primary
structure is not affected.
- Denaturing agents: heat, acids and bases,
organic compounds, heavy metal ions, and
mechanical agitation.
- Some denaturations are reversible,
while others permanently damage the protein.
Denatured protein
Denaturation
•Heat: H bonds, Hydrophobic interactions
•Detergents: H bonds
•Acids and bases: Salt bridges, H bonds.
•Reducing agents: Disulfide bonds
•Heavy metal ions (transition metal ions Pb2+, Hg2+): Disulfide bonds
•Alcohols: H bonds, Hydrophilic interactions
•Agitation: H bonds, Hydrophobic interactions