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Amino Acids and Proteins

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(1)

Amino Acids

and Proteins

Amino Acids

and Proteins

(2)

Proteins are composed of amino acids.

There are 20 amino acids commonly

found in proteins. All have:

C

α

COOH

NH

2

H

(3)

Amino acids at neutral pH are dipolar ions

(

zwitterions

) because their

α

-carboxyl and

α

-amino groups are ionized.

C

COO

NH

3

H

R

+

(4)

[NaOH]

[NaOH]

0. 5

0. 5

2

2

4

4

6

6

8

8

pK

1

pK

1

pK

2

pK

2

Titration curve for Glycine:

Titration curve for Glycine:

pH

pH

COOH=

COO-COOH=

COO-NH

3+

=

NH

2

NH

3+

=

NH

2

(5)

Structure of glycine at differing pH values:

C

COOH

NH

3

H

H

+

pH=1

C

COO

NH

3

H

H

+

pH=7

H

C

COO

NH

2

H

pH=11

(6)

[NaOH]

[NaOH]

0. 5

0. 5

2

2

4

4

6

6

8

8

pK

1

pK

1

pK

2

pK

2

pH

pH

COOH COOH

NH

3+

NH

3+

[NaOH]

[NaOH]

0. 5

0. 5

2

2

4

4

6

6

8

8

pK

1

pK

1

pK

2

pK

2

pH

pH

COOH COOH

NH

3+

NH

3+

Isoelectric

point (no net

charge)

Isoelectric

point (no net

charge)

(7)

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

(8)

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

(9)

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 threonine

pKa=13

tyrosine COO C -H3+N H CH2 CH2 OH OH

pKa=10.1

COO C -H3+N H CH2 CH2 SH SH cysteine

pKa=8.3

(10)

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

(11)

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.

(12)

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

(13)

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

(14)

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 arginine

pKa=12.5

COO C -H3+N H N N CH2 CH2 C C NH NH C C H H HC HC= histidine

pKa=6.0

(15)

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!

(16)

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

(17)

C - OH

NH

2

- C -

C

-

OH

H

H O

O

N

N

- C - COOH

H

H

H

H

H

H

(18)

N

N

- C - COOH

H

H

H

H

C

NH

2

- C -

C

H

H O

O

H

H

-OH

-

OH

(19)

N

N

- C - COOH

H

H

H

H

C

NH

2

- C -

C

H

H O

O

H

H

-OH

-

OH

(20)

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!!

(21)

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)

(22)

Conjugated Proteins:

Conjugated Proteins:

• Prosthetic groups: non-amino acid

components

• Coenzyme: organic molecules (vitamins)

involved in catalysis

• Metalloproteins

• Glycoproteins

• Lipoproteins

• Nucleoproteins

• Phosphoproteins

(23)

• 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

33

Glycine-Glycine-Alanine

Glycine-Glycine-Alanine

(24)

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.

(25)

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

(26)

Peptide bonds are resonance structures and cannot freely rotate Rotation occurs only about the N-Ca (phi; φ ) and C-Ca (psi; ψ) bonds

(27)

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.

(28)

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 example

Glycine and Alanine often

(29)

β

-Bend

Composed of 4 amino acids; the first is hydrogen bonded to the fourth

Glycine (small and flexible) and proline (kinks) occur in

(30)

• Secondary structures are arranged into

domains or modules.

3) Tertiary Structure: the way in which the

secondary structural elements are

folded; the spatial distribution of side

chains.

• Hydrophobic effect is a major factor in

determining the folding pattern

• Secondary structural elements fold first to

maximize H-bonds; then interactions

between these elements occur

(31)

4) Quaternary Structure: subunit

organization; kinds of subunits, number

of subunits and the ways in which they

interact with one another.

• Multisubunit proteins are also referred to as

oligomers.

• Proteins composed of a single type of

monomer are homomultimeric; those

composed of two or more different subunits

are heteromultimeric.

• Hemoglobin has two each of two different

(32)

Forces Driving Quaternary Association:

Hydrogen Bonding

Electrostatic Interactions

Van Der Waals Interactions

(33)

Structure determines function: one way to study

this relationship is to alter the structure and

determine its effect on function.

Protein Denaturation: Loss of tertiary and

quaternary structure (sometimes 2

o

structure).

β

-mercaptoethanol:

disulfide reducing agent

SDS:

detergent; disrupts hydrophobic core

urea:

disrupts hydrogen bonds

water:

disrupts electrostatic interactions

organic solvents:

disrupts interactions of

hydrophobic residues

References

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