UNIT‐ 2Amino acids and Proteins

Significance of Proteins

1. Keep the cells and tissues growing, renewing and mending

2. Takepart in some kinds of important physiological

activities

3. Oxidation and supply energy

Structural

Movement

Transport

Storage

Hormone

Protection

Enzymes

Collagen; bones, tendons, cartilageKeratin; hair, skin, wool, nails, feathers

Myosin & Actin; muscle contractions

Hemoglobin; transports O2Lipoproteins; transports lipids

Casein; in milk. Albumin; in eggs

Insulin; regulates blood glucoseGrowth hormone; regulates growthImmunoglobulins; stimulate immunitySnake venom; plant toxins; Sucrase; catalyzes sucrose hydrolysisPepsin; catalyzes protein hydrolysis

Amino acids • Are the building blocks of proteins.• Contain a carboxylic acid group and an amino 

group on the alpha (α) carbon.• Are ionized in solution.• Each contain a different side group (R).

RR

│+  │H2N—C —COOH    H3N—C —

COO−│ │

HH

ionized form

H+ │

H3N—C—COO−│

H glycine

CH3+  │

H3N—C—COO−│

H alanine

Amino acids are classified as• Nonpolar (hydrophobic) 

with hydrocarbon side chains.

• Polar (hydrophilic) with polar or ionic side chains.

• Acidic (hydrophilic) with acidic side chains.

• Basic (hydrophilic) with –NH2 side chains.

Nonpolar Polar

Acidic Basic

Essential amino acids

• Must be obtained from the diet.

• Are the ten amino acids  not synthesized by the body.

• Are in meat and diary products.

• Are missing (one or more) in grains and vegetables.

TABLE 19.3

Basic Amino Acids

Amino acids • Are chiral except for glycine.• Have Fischer projections that are stereoisomers.• That are L are used in proteins.

L‐alanine D‐alanine L‐cysteine D‐cysteine

CH2SHH2N H

COOH

CH2SH H NH2

COOH

CH3

H NH2

COOH

CH3

H2N H

COOH

A zwitterion• Has charged —NH3

+ and COO‐ groups.• Forms when both the —NH2 and the —COOH 

groups in an amino acid ionize in water.• Has equal + and − charges at the isoelectric point 

(pI).  

O                                               O║ + ║

NH2—CH2—C—OH H3N—CH2—C—O–

Glycine Zwitterion of glycine

In solutions more basic than the pI,• The —NH3

+ in the amino acid donates a proton.

+ OH–

H3N—CH2—COO– H2N—CH2—COO–

Zwitterion Negative ionat pI   pH > pICharge: 0 Charge: 1−

In solutions more acidic than the pI,• The COO− in the amino acid accepts a proton.

+ H++

H3N—CH2—COO– H3N—CH2—COOH 

Zwitterion Positive ionat pI  pH< pICharge: 0 Charge: 1+

H+ OH−

+ +

H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO–

positive ion zwitterion negative ion

(at low pH) (at pH) (at high pH)

A peptide bond• Is an amide bond. • Forms between the carboxyl group of one amino 

acid and the amino group of the next amino acid.

O CH3 O+          ||                     + |       ||

H3N—CH2—C—O– +    H3N—CH—C—O–

O    H CH3 O+  ||     | |        || 

H3N—CH2—C—N—CH—C—O– + H2Opeptide bond

The primary structure of a protein is

• The particular sequence of amino acids.

• The backbone of a peptide chain or protein.

CH3

SHCH2

CH3

S

CH2

CH2CH O

O-CCH

H

N

O

CCH

H

N

O

CCH

H

N

O

CCHH3N

CH3

CH3CH

Ala─Leu─Cys─Met

The secondary structures of proteins indicate thethree‐dimensional spatial arrangements of thepolypeptide chains.

An alpha helix has• A coiled shape held in place by hydrogen bonds between the amide groups and the carbonyl groups of the amino acids along the chain.

• Hydrogen bonds between the H of a –N‐H group and the O of C=O of the fourth amino acid down the chain.

A beta‐pleated sheet is a secondary structure that

• Consists of polypeptide chains arranged side by side.

• Has hydrogen bonds between chains.

• Has R groups above and below the sheet.

• Is typical of fibrous proteins such as silk.

A triple helix• Consists of three alpha 

helix chains woven together. 

• Contains large amounts glycine, proline, hydroxyproline, and hydroxylysine that contain  –OH groups for hydrogen bonding.

• Is found in collagen, connective tissue, skin, tendons, and cartilage.

The tertiary structure of a protein• Gives a specific three dimensional shape to the polypeptide chain. 

• Involves interactions and cross links between different parts of the peptide chain.

• Is stabilized byHydrophobic and hydrophilic interactions. Salt bridges.Hydrogen bonds.Disulfide bonds.

Globular proteins• Have compact, spherical shapes.

• Carry out synthesis, transport, and metabolism in the cells.

• Such as myoglobin store and transport oxygen in muscle.

Myoglobin

Fibrous proteins• Consist of long, fiber‐like shapes.• Such as alpha keratins make up hair, wool, skin, and nails.

• Such as feathers contain beta keratins with large amounts of beta‐pleated sheet structures.

The quaternary structure• Is the combination of two or more tertiary units.

• Is stabilized by the same interactions found in tertiary structures.

• Of hemoglobin consists of two alpha chains and two beta chains. The hemegroup in each subunit picks up oxygen for transport in the blood to the tissues.

hemoglobin

Protein hydrolysis

• Splits the peptide bonds to give smaller peptides and amino acids. 

• Occurs in the digestion of proteins.

• Occurs in cells when amino acids are needed to synthesize new proteins and repair tissues.

• In the lab, the hydrolysis of a peptide requires acid or base, water and heat.

• In the body, enzymes catalyze the hydrolysis of proteins.

+

H3N CH COHOCH3

+

H2O, H+

++

heat,

CH2

OH

H3N CH C

O

N

H

CH C

O

OH

CH3

CH2

OH

CH C

O

OHH3N

Denaturation involves • The disruption of bonds in the secondary, tertiary and quaternary protein structures.

• Heat and organic compounds that break apart H bonds and disrupt hydrophobic interactions.

• Acids and bases that break H bonds between polar R groups and disrupt ionic bonds.

• Heavy metal ions that react with S‐S bonds to form solids.

• Agitation such as whipping that stretches peptide chains until bonds break.

Denaturation of protein occurs

when • An egg is cooked. • The skin is wiped with alcohol.

• Heat is used to cauterize blood vessels.

• Instruments are sterilized in autoclaves. 

Transamination of Amino acids 

Transamination is the process by which an amino group, usually from glutamate, is transferred to an  α‐keto acid, with formation of the corresponding amino acid plus  α‐

ketoglutarate. 

C

R1

H

NH3

COO + C

R2

O

COO C

R2

H

NH3

COO+C

R1

O

COO

Aminotransferases

amino acid-1 amino acid-2keto acid-2keto acid-1

Deamination of Amino acids

COOHCHNH2

(CH2)2

COOHL-Glu

L-Glu Dehydrogenase

NAD+NADH+H+ COOH

C NH(CH2)2

COOH

COOHC

(CH2)2

COOH

H2O NH3 O

¦Á-ketoglutarate

Sources and Outlet of NH31. Sources:

⑴ Endogenous sources:

① Deamination of AAs‐‐main source

② Catabolism of other nitrogen containing compounds

③ Kidney secretion (Gln)

Alanine Glucose Cycle

protein

amino acid

NH3

pyruvate

¦Á-keto acid

G

muscle

pyruvate

G

NAD+ + H2O

NADH + H+

blood liver

urea

Glu

Ala Ala Ala

Glu

G

¦Á-keto acid

+ NH3

Transportation of NH3 by Gln

CONH2

(CH2)2

CHNH2

COOH

Gln synthetaseCOOH

(CH2)2

CHNH2

COOH

+ NH3

ATP ADP + Pi

Glu GlnGlutaminase

H2O

Formation of Urea1. Site: liver (mitochondria and cytosol)

2. Process --------- ornithine cycle

ornithine NH3 + CO2

H2O

NH3H2O

H2O

urea

arginase

Arg citrulline

Metabolism of amino acids

• Decarboxylation of amino acids

• Metabolism of one carbon unit

• Metabolism of sulfur‐containing AAs

• Metabolism of aromatic AAs

• Metabolism of branched‐chain AAs

Metabolism of Sulphur Containing amino acids

NH2CHCH2

S CH3

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COOH

2

adenosyl transferase

ATPPPi+Pi

NH2CHCH2

S CH3

£¨ £©

COOH

2

RH

RCH3

methyl transferase

NH2CHCH2

SH£¨ £©

COOH

2

S-adenosyl homocysteine

H2O

NH2CHCH2

SH£¨ £©

COOH

2

homocysteine

N5 -CH3FH4

FH4Met synthase

VB12£¨ £©

A

SAM

A

Met

A

Metabolism of Cysteine and Cystine

NH2CHCH2

SH

COOHcysteine

NH2CHCH2

SH

COOHcysteine

+NH2CH

CH2

S

COOHNH2CH

CH2

S

COOH

2H

2Hcystine

Metabolism of Aromatic amino acids

CH2CHNH2COOH

+ O2

CH2CHNH2COOH

+

OH

H2O

tetrahydro- biopterin

dihydro- biopterin

Phe hydroxylase

NADPH+H+NADP+

PheTyr

Metabolism of Tryptophan

N

CH2CHNH2COOH

H

O2

NHCHO

CCHNH2COOH

O

N-formyl kynurenine

H2O

NH2

CCHNH2COOH

OHCOOH

kynurenine

N10 -CHOFH4 synthetase

FH2+ATPADP+Pi

N10 -CHOFH4

Trp

Metabolism of TyrosineCH2CHNH2COOH

OH

CH2CHNH2COOH

OHHO

CO2CH2CH2NH2

OHHO

CH2CH2NH2

OHHO

OH

CH2CH2NHCH3

OHHO

OH

CH2CHNH2COOH

OO

OO

NH

CH2CCOOH

OH

O

OH

OH

CH2COOH

dopa dopamine

dopa quinone norepine-

phrine

indole-5,6- quinone

fumarate +acetoacetate

Tyr

epinephrine

SAM

Tyr transaminase

melanin

hydroxy-phenyl-pyruvate

homogentisate

Summary of Metabolism