Amino Acids
and Proteins
Amino Acids
and Proteins
•
Proteins are composed of amino acids.
•
There are 20 amino acids commonly
found in proteins. All have:
C
α
COOH
NH
2H
Amino acids at neutral pH are dipolar ions
(
zwitterions
) because their
α
-carboxyl and
α
-amino groups are ionized.
C
COO
NH
3H
R
+
[NaOH]
[NaOH]
0. 5
0. 5
2
2
4
4
6
6
8
8
pK
1pK
1pK
2pK
2Titration curve for Glycine:
Titration curve for Glycine:
pH
pH
COOH=
COO-COOH=
COO-NH
3+=
NH
2NH
3+=
NH
2Structure of glycine at differing pH values:
C
COOH
NH
3H
H
+
pH=1
C
COO
NH
3H
H
+
pH=7
H
C
COO
NH
2H
pH=11
[NaOH]
[NaOH]
0. 5
0. 5
2
2
4
4
6
6
8
8
pK
1pK
1pK
2pK
2pH
pH
COOH COOHNH
3+NH
3+[NaOH]
[NaOH]
0. 5
0. 5
2
2
4
4
6
6
8
8
pK
1pK
1pK
2pK
2pH
pH
COOH COOHNH
3+NH
3+Isoelectric
point (no net
charge)
Isoelectric
point (no net
charge)
Aliphatic Non-Polar Amino Acids
Aliphatic Non-Polar Amino Acids
C H2+N COO -H2C H2C CHCH22 CH2 CH2 H proline COO C -H3+N H CH3 CH3 alanine COO C -H3+N H CH CH CH3 CH3 CHCH33 valine COO C -H3+N H CH2 CH2 CH CH CH3 CH3 CHCH33 leucine COO C -H3+N H H C H - C -CH3 CH3 CH2 CH2 CH3 CH3 isoleucine COO C -H3+N H CH2 CH2 S S CH3 CH3 CH2 CH2 methionine
Aromatic Non-Polar Amino Acids
Aromatic Non-Polar Amino Acids
COO C -H3+N H CH2 CH2 phenylalanine COO C -H3+N H CH2 CH2 CH CH C C N N tryptophan H H
Polar Uncharged Amino Acids
Polar Uncharged Amino Acids
COO C -H3+N H H H glycine COO C -H3+N H CH2OH CH2OH serine
pKa=13
CH3 CH3 COO C -H3+N H CHOH CHOH threoninepKa=13
tyrosine COO C -H3+N H CH2 CH2 OH OHpKa=10.1
COO C -H3+N H CH2 CH2 SH SH cysteinepKa=8.3
Serine and Threonine can be PHOSPHORYLATED:
Serine and Threonine can be PHOSPHORYLATED:
COO C -H3+N H CH2OH CH2OH serine CH3 CH3 COO C -H3+N H CHOH CHOH threonine ATP ADP, Pi ATP ADP, Pi COO C -H3+N H CH2OPO3 2-CH2OPO3 2-serine CH3 CH3 COO C -H3+N H CHOPO3 2-CHOPO3 2-threonine
COO C -H3+N H CH2 CH2 S S COO C -H3+N H CH2 CH2 S S
Disulfide Bond:Two cysteine residues condense. Disulfide bonds may occur between cyteine residues within the same protein (intrachain) or between two cystein residues occuring in different proteins (interchain). Disulfide
formation is a major factor in the determination of protein structure.
Permanent waving is the result of the reduction of disulfides in the α-keratin protein (that hair is made of) and spontaneous
re-oxidation of those disulfide bonds in air.
Polar Uncharged Amino Acids
Polar Uncharged Amino Acids
COO C -H3+N H CH2 CH2 C C O O NHNH22 asparagine COO C -H3+N H CH2 CH2 C C O O NH 2 NH2 CH2 CH2 glutamine
Acidic Amino Acids
Acidic Amino Acids
COO C -H3+N H CH2 CH2 C C O O aspartate O -O
-pKa=3.9
COO C -H3+N H CH2 CH2 C C O O CH2 CH2 glutamate O -O-pKa=4.3
Basic Amino Acids
Basic Amino Acids
CH2 CH2 COO C -H3+N H NH3+ NH3+ CH2 CH2 CH2 CH2 CH2 CH2 Lysine
pKa=10.5
COO C -H3+N H H2+N H2+N NH 2 NH2 CH2 CH2 CH2 CH2 CH2 CH2 NH NH C C argininepKa=12.5
COO C -H3+N H N N CH2 CH2 C C NH NH C C H H HC HC= histidinepKa=6.0
Chirality in Amino Acids
Chirality in Amino Acids
HO - C - H HO - C - H CHO CHO CH2OH CH2OH L-Glyceraldehyde L-Glyceraldehyde CH2OH CH2OH CHO CHO H - C - OH H - C - OH D-Glyceraldehyde D-Glyceraldehyde H3+N - C - H H3+N - C - H COOH COOH CH3 CH3 L-Alanine L-Alanine COOH COOH H - C - NH3+ H - C - NH3+ CH3 CH3 D-Alanine D-Alanine
L amino acids occur in proteins!
The Peptide Bond
The Peptide Bond
• Bond occurs between the
α
-amino
group of one amino acid and the
α
-carboxyl group of another amino
acid
• A condensation reaction where
C - OH
NH
2- C -
C
-
OH
H
H O
O
N
N
- C - COOH
H
H
H
H
H
H
N
N
- C - COOH
H
H
H
H
C
NH
2- C -
C
H
H O
O
H
H
-OH
-
OH
N
N
- C - COOH
H
H
H
H
C
NH
2- C -
C
H
H O
O
H
H
-OH
-
OH
N
N
- C - COOH
H
H
H
H
C
NH
2- C -
C
H
H O
O
C
NH
2- C -
C
H
H O
O
N
N
- C - COOH
H
H
H
H
The Peptide Bond!!
The Peptide Bond!!
Functions of Proteins:
Functions of Proteins:
• Enzymes
• Regulatory Proteins
• Structural
• Transport
• Storage
• Contractile
Three Classes Based on Shape
and solubility:
Three Classes Based on Shape
and solubility:
• Fibrous (collagen)
• Globular (enzymes)
• Membrane (CP 43)
Conjugated Proteins:
Conjugated Proteins:
• Prosthetic groups: non-amino acid
components
• Coenzyme: organic molecules (vitamins)
involved in catalysis
• Metalloproteins
• Glycoproteins
• Lipoproteins
• Nucleoproteins
• Phosphoproteins
• Protein chains have a direction.
• Protein chains have a direction.
• By convention the N-terminus is taken to
be the beginning of a polypeptide chain.
• By convention the N-terminus is taken to
be the beginning of a polypeptide chain.
NH
2- C - C - N - C - C -N - C - COOH
NH
2- C - C
- N - C - C
-N - C - COOH
O
O
O
O
H
H
H
H
H
H
H
H
H
H
H
H
H
H
CH
CH
33Glycine-Glycine-Alanine
Glycine-Glycine-Alanine
Protein Architecture
• Conformation
• Conformation: The spatial arrangement
of atoms in a protein.
• There are 4 levels of organization:
1) Primary Structure: linear sequence
of amino acids in a polypeptide.
2) Secondary Structure: local conformation
of the peptide backbone.
The Peptide Bond is a Resonance Structure:
C
NH
2- C -
C
H
H O
O
N
N
- C - COOH
H
H
H
H
C
NH
2- C -
C
H
H O
O
-N
+N
+- C - COOH
H
H
H
H
Peptide bonds are resonance structures and cannot freely rotate Rotation occurs only about the N-Ca (phi; φ ) and C-Ca (psi; ψ) bonds
α
-Helix
Each carboxyl oxygen is hydrogen bonded to the amino group of the amino acid four residues above Single turn =
0.56 nm = 3.6 amino acids
Stretches of + and - charged
amino acids destabilize; proline destabilizes; amino acids with bulky R groups destabilize;
polyleucine and polyalanine are good helix formers.
C N N N C C C N
β
-pleated
sheet
Parallel; 5 sheets or more Anti-Parallel: 2 or more sheets; silk is an exampleGlycine and Alanine often
β
-Bend
Composed of 4 amino acids; the first is hydrogen bonded to the fourthGlycine (small and flexible) and proline (kinks) occur in