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Amino Acids - Ecu

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Amino Acids

and Proteins


• Proteins are composed of amino acids.

• There are 20 amino acids commonly

found in proteins. All have:

H

NH2

C α

R

COOH


Amino acids at neutral pH are dipolar ions

(zwitterions) because their α-carboxyl and

α-amino groups are ionized.

+

NH3

H

C

R

COO


Titration curve for Glycine:

pK2

pH

8

6

4

pK1

COOH=

COO-

NH3+=

NH2

2

0. 5

[NaOH]


Structure of glycine at differing pH values:

H

H

+

NH3 C COOH

+

NH3 C COO

H

pH=1

H

H

pH=7

NH2

C

COO

H

pH=11


pK2

8

NH3+

pH

6

4

2

pK1

COOH

Isoelectric

point (no net

charge)

0. 5

[NaOH]


Aliphatic Non-Polar Amino Acids

H 2+

N

COO -

C

H

CH 2

COO -

H 3+

N- C -

H

COO -

H 3+

N- C -

CH

H

H 2 C CH 2

proline

COO -

H 3+

N - C -

CH 2

H

CH

CH 3 CH 3

leucine

CH 3

alanine

COO -

H 3+

N - C -

CH 3

H

H - C - CH 3

CH 2 isoleucine

CH 3 CH 3

valine

COO -

H 3+

N - C -

CH 2

CH 2

S

H

CH 3

methionine


Aromatic Non-Polar Amino Acids

COO -

COO -

H 3+

N - C -

H

H 3+

N - C -

H

CH 2

phenylalanine

CH 2

C

CH

N

H

tryptophan


Polar Uncharged Amino Acids

COO -

H 3+

N - C -

H

H

glycine

COO -

H 3+

N - C -

H

COO -

H 3+

N - C -

H

CH 2 OH

serine

pKa=13

COO -

COO -

H 3+

N - C -

H

CHOH

CH 3

threonine

pKa=13

CH 2

H 3+

N - C -

H

OH

tyrosine

pKa=10.1

CH 2

SH

cysteine

pKa=8.3


Serine and Threonine can be PHOSPHORYLATED:

COO -

ATP

ADP, Pi

COO -

H 3+

N - C -

H

H 3+

N

- C -

H

CH 2 OH

2-

CH 2 OPO 3 serine

serine

COO -

ATP

ADP, Pi

COO -

H 3+

N - C -

H

H 3+

N

- C -

H

CHOH

2-

CHOPO 3 CH 3

threonine

CH 3

threonine


COO -

H 3+

N - C -

CH 2

S

S

CH 2

H 3+

N- C -

H

H

COO -

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

COO -

H 3+

N - C -

CH 2

C

H

O NH 2

asparagine

COO -

H 3+

N - C -

CH 2

CH 2

C

H

O NH 2

glutamine


Acidic Amino Acids

COO -

COO -

H 3+

N - C - H

H 3+

N - C - H

O

CH 2

C

O -

aspartate

pKa=3.9

O

CH 2

CH 2

C

O -

glutamate

pKa=4.3


Basic Amino Acids

COO -

COO -

COO -

H 3+

N - C -

H

H 3+

N - C -

H

H 3+

N - C -

H

CH 2

CH 2

CH 2

CH 2

NH 3 +

Lysine

pKa=10.5

CH 2

CH 2

CH 2

NH

C

H 2+ N NH 2

arginine

pKa=12.5

CH 2

HC=

C

N NH

C

H

histidine

pKa=6.0


Chirality in Amino Acids

CHO

HO - C - H

CH 2 OH

L-Glyceraldehyde

CHO

H - C - OH

CH 2 OH

D-Glyceraldehyde

COOH

H 3+ N - C - H

CH 3

L-Alanine

COOH

+

H - C - NH 3 CH 3

D-Alanine

L amino acids occur in proteins!


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

the elements of H 2

0 are removed


H

O

H

NH - C - C - OH

2

H

N - C - COOH

H

H

H


H

O

H

NH - C - C

2

- OH

H -

N - C - COOH

H

H

H


H

O

H

NH - C - C

2

- OH

H -

N - C - COOH

H

H

H


H

O

H

NH - C - C

2

The Peptide Bond!!

H

N - C - COOH

H

H

H

O

H

NH - C - C

2

N - C - COOH

H

H

H


Functions of Proteins:

• Enzymes

• Regulatory Proteins

• Structural

• Transport

• Storage

• Contractile

Three Classes Based on Shape

and solubility:

• Fibrous (collagen)

• Globular (enzymes)

• Membrane (CP 43)


Conjugated Proteins:

• Prosthetic groups: non-amino acid

components

• Coenzyme: organic molecules (vitamins)

involved in catalysis

• Metalloproteins

• Phosphoproteins

• Glycoproteins

• Lipoproteins

• Nucleoproteins


• Protein chains have a direction.

• By convention the N-terminus is taken to

be the beginning of a polypeptide chain.

H O H O H

NH 2 - C - C - N - C - C -N - C - COOH

H

H

H

H CH 3

Glycine-Glycine-Alanine


Protein Architecture

• 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:

H

O

H

NH - C - C

2

N - C - COOH

H

H

H

H O - N +

H

NH - C - C

2

N + - C - COOH

H

H

H


Peptide bonds are

resonance

structures and

cannot freely

rotate

Rotation occurs

only about the

N-C a

(phi; φ ) and

C-C a

(psi; ψ) bonds


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.

α-Helix


C

C

N

N

N

C

Parallel;

5 sheets

or more

β-pleated

sheet

Anti-Parallel: 2 or

more sheets; silk

is an example

C

N

Glycine and

Alanine often

found in β-sheets


Composed of 4

amino acids;

the first is

hydrogen

bonded to the

fourth

β-Bend

Glycine (small and

flexible) and proline

(kinks) occur in

β-bends


• 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


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

subunits; it’s structure is designated α 2

β 2

.


Forces Driving Quaternary Association:

Hydrogen Bonding

Electrostatic Interactions

Van Der Waals Interactions

Hydrophobic Interactions


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

temperature: complete denaturation

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