Module III: Proteins

Definition, classification of amino acids – Essential and non essential, structure of proteins,
digestion, absorption, transport, distribution, storage and excretion. Protein Metabolism –
Transamination, Deamination and Urea Cycle, Amino acid pool, Protein biosynthesis.

DEFINITION - AMINO ACIDS:

“They are basic structural unit of proteins consisting of an amino group (-NH2), a carboxyl
group (-COOH), a hydrogen atom (H) and a distinctive variable (R) group. These groups are
attached to a central carbon atom”

General Formula

CLASSIFICATION OF AMINO ACIDS

Structural Classification

Aliphatic : Glyciene,, Alanine, Valine, Leucine, Isoleucine

Aromatic: Phenylalanine, Tyrosine, Tryptophan

Sulphur containing: Cysteine, Methionine

Biological or physiological classification

Essential - Methionine, Arginine, Tryptophan, Threonine, Valine, Isoleucine,

Leucine,Phenylalanine, Lysine, Histidine

Non -Essential - Alanine, Aspargine, Aspartic acid, Cystiene, Glutamic acid, Glutamine,
Glycine, Proline, Serine, Tyrosine.

Semi- essential- Arginine, Histidine

Electrochemical Classification

Acidic- Aspartic acid, Glutamic acid

Basic – Lysine, Arginine

Neutral- Serine, Threonine, Aspargine, Glutamine

 Fate of amino acid

Glucogenic - Alanine, Cysteine, Glycine, Arginine, Glutamine, Isoleucine, Tyrosine

Ketogenic : Phenylalanine, Tyrosine, Tryptophan, Isoleucine , Leucine , Lysine

PEPTIDE BOND FORMATION

PEPTIDE

It is a condensation product of two or even more amino acids.

α – amino group of one amino acid condenses with α – carboxyl group of another amino
acid.

Two amino acids - Dipeptide

Three amino acids - Tripeptide

Four amino acids - Tetrapeptide

PROTEINS

Diverse group of macromolecules.

Essential nutritionally because of their constituent amino acids.

Using amino acids body synthesize different proteins and nitrogen containing molecules.
 Each body protein is unique in characteristic and pattern of sequencing amino acids.

There are 20 amino acid monomers.

CLASSIFICATION OF PROTEINS

Functional classification

Based on chemical nature

Based on nutritive value

FUNCTIONAL CLASSIFICATION

1. Enzymes, Hormones, Structural component, Immunoproteins, Buffers, Messengers,

Fluid Balancers, Transporters

Enzymes

 They are protein molecules.

 Acts as biological catalyst.

 Classified as:

» Hydrolases

» Isomerases

» Ligases

» Oxidoreductases

» Transferases

Hormones

 Act as messenger proteins.

 Helps to co-ordinate certain bodily activities

Eg: Insulin – Maintain blood glucose level & Prolactin – Action on mammary gland

On Chemical Nature

I. Simple proteins

Albumins : Egg albumin & serum albumin

 Globulins : Serum globulin, Tuberin (potato), arachin & conarchin (peanuts).

Glutelins : Glutelin of wheat.

II. Conjugated Protein

Glycoprotein : Mucin (saliva)

Lipoprtoteins : LDL/ HDL in blood

Neucloproteins : Nucleoproteamines

Phosphoproteins : Caseinogen

III. Derived Protein

- Primary : Metaproteins, Coagulated proteins

- Secondary : Proteoses, Peptones, peptides.

Based on Nutritive value

Complete protein :– Provide all EAA’s & promote growth. Eg: Egg protein

Partially incomplete Protein: - Partially lack one or more amino acid & promote only
moderate growth. Eg: Wheat proteins

Incomplete protein :- Completely lack one or more Proteins. They do not promote
growth. Eg: Zein.

STRUCTURE OF PROTEINS
PRIMARY STRUCTURE

 Refer to the number nature and sequence of amino acids.

 The sequence determines the further levels of organisation of the protein molecule.

 Left end – free amino Group

 Right end – free COOH group

SECONDARY STRUCTURE

 Two forms of secondary structure.

 α – helix and β – pleated sheet.

• α – helix

 Three to six amino acid residues per complete run.

 Structure is stabilized by intra-molecular hydrogen bonding.

 NH group of 1st amino acid comes in close proximity of C = O group of 4th amino acid
residue.

• β – pleated sheet

 Results from hydrogen bonding.

 The chains may be parallel or antiparallel.

 Parallel chain – N – atoms points in same direction.

 Anti parallel – Alternate chains are oriented in the same direction.

TERITARY SRUCTURE

 Secondary chain undergo coiling and folding to form tertiary structure.

 Final shape is ellipsoid.

 Shape is determined by the hydrogen bond, ionic bond, hydrophobic bond.

 Binds active amino acids together.

QUATERNARY STRUCTURE
  2 or more polypeptide chain may associate to give the quaternary structure.

 Association is brought by hydrophobic interactions, hydrogen bonds, electrostatic bonds.

 If proteins have identical unit – Homogenous.

 If proteins have dissimilar units – Heterogeneous

• HEMOGLOBIN

PROTEIN METABOLISM

• Amino acid pool

The amount of free amino acid distributed throughout the body.

Plasma levels of amino acid range between – 4 to 8mg/dl.

Sources of amino acid pool

Dietary protein

Breakdown of tissue protein

Biosynthesis of NEAA

Fate of amino acid pool

Biosynthesis of structural protein. Eg: Tissue protein

Biosynthesis of functional protein. Eg: Hb, Mb, enzymes

Biosynthesis of small peptides. Eg: Glutathione

Biosynthesis of non – protein compounds. Eg: Urea, uric acid, Creatinine.

CATABOLIC PATHWAY
TRANSAMINATION

Transfer of amino group form α-amino acid to α – keto acid with formation of a new
amino acid & keto acid.

Liver is the main site.

All amino acids except lysine, threonine, proline, hydroxy proline.

 They are reversible reactions

Catalysed by aminotransferases (Transaminases)

Co-enzyme is pyridoxal phosphate (PLP)

I. ALANINE TRANSAMINASE

 Also known as Serum glutamate pyruvate transaminase (SGPT)

 Catalytic transfer of amino group from glutamic acid to pyruvic acid to form alanine and
α – keto glutarate.

 SGPT is present in cytoplasm of liver cells.

II. ASPARTATE TRANSAMINASE

 Also known as Serum glutamate Oxaloacetate transaminase (SGOT)

 Catalytic transfer of amino group from glutamic acid to oxaloacetate to form aspartate
and α – ketoglutarate.

 SGPT is present in cytoplasm of liver, heart and skeletal muscles.

CLINICAL SIGNIFICANCE

 They are intracellular enzymes.

 Plasma levels are low under normal conditions.

 SGPT is present mainly in cytoplasm of liver cells.

  SGOT is seen both in cytoplasm and mitochondria.

 Any organ failure may increase their levels.

 Liver disease – SGOT & SGPT Level rises

 Acute liver disease (Acute viral hepatitis) – SGPT rises.

 Chronic liver disease (Liver cirrhosis) – SGOT rises

 In heart disease – SGOT rises

 In skeletal disease – (Myasthenia gravia) – SGOT rises.

DEAMINATION

Removal of amino group from α – amino acid in the form of ammonia with formation
of an α – keto acid.

Liver and kidney are the main site.

It can be either oxidative or non – oxidative.

I. OXIDATIVE DEAMINATION

 Catalyzed by following enzymes

a. L – Amino acid oxidases

b. D – amino acid oxidases

c. Glutamate dehydrogenase

a) L – Amino acid oxidases

 Present in liver and kidney. Its activity is low. It is an anaerobic dehydrogenase. It

needs FMN as co- enzyme. Deaminates most of the naturally occuring L – amino acids.

b) D – Amino acid oxidases

 Present in plants and bacterial cell wall. It is an aerobic dehydrogenase. It needs FAD as
co – enzyme.

c) Glutamate dehydrogenase
 It is present in almost all tissues. Present both in cytoplasm & mitochondria. Activity is very
high. It is an anaerobic dehydrogenase. Co-enzyme needed as NAD & NADP. It
deaminates glutamic acid.
II. Non – Oxidative Deamination

 Catalyzed by

Dehydratases & Desulfhydrases

UREA CYCLE
 Also known as Krebs – Henseilet cycle or ornithine cycle.

 First metabolic cycle elucidated.

 There occur five major reactions.

 Each of the reaction utilises specific enzymes.

 The first two reactions are mitochondrial and the rest are cytoplasmic.

5 – enzymes of urea cycle

Carbonyl phosphate synthase 1

Ornithine carbamoyl transferase or citrulline synthase

Arginosuccinate synthatase

Arginosuccinate lyase

Arginase

STEP I - SYNTHESIS OF CARBAMOYL PHOSPHATE

1 molecule of NH3 or NH4+ condenses with CO2 in the presence of two molecules of ATP
to form carbamoyl phosphate.

Catalysed by carbamoyl phosphate synthase 1 (CPS I)

CPS – I requires N – acetylglutamate (NAG) for its activity.

This reaction is the rate limiting step in urea formation.

It is an irreversible reaction.

It consumes 2 ATP.
STEP II - FORMATION OF CITRULINE

The second reaction is also mitochondrial.

The carbamoyl group is transferred to the NH2 group of ornithine to form

CITRULLINE.

The reaction is catalysed by ornithine trans carbamoylase.

Ornithine is regenerated and used in urea cycle.

Citrulline leaves mitochondria.

Further reaction takes place in cytoplasm.

STEP 3 - FORMATION OF ARGINOSUCCINATE

One molecule of aspartic acid adds to citrulline forming arginosuccinate.

Catalysed by arginosuccinate synthase.

Second amino group is introduced to urea in this reaction.

This needs hydrolysis of ATP to AMP level, so two high energy phosphate bonds are
utilized.

STEP IV - FORMATION OF ARGININE

Arginosuccinate is cleaved to form arginine and fumerate.

It is catalysed by arginosuccinate lyase or arginosuccinase.

The fumerate formed may be funneled into TCA cycle.

It is then converted to malate and then to oxaloacetate.

Thus area is linked to TCA cycle through fumerate as thus the cycle is also called urea
bicycle.

STEP V-FORMATION OF UREA

The final reaction of the cycle is the hydrolysis of arginine to urea and ornithine.

It is catalysed by arginase. It is found in liver.

Arginase is activated by Co2+ and Mn2+.

Ornithine returns to mitochondria to react with another molecule of carbamoyl phosphate.

 ENERGETICS
The endergonic (energy requiring) urea cycle utilises energy.

It is equivalent to 4 high energy phosphate bonds.

OTHER CONSIDERATIONS

Fumerate formed in the 4th step may be converted to malate.

Malate when oxidised to oxaloacetate produces 1 NADH equivalent to 3 ATP.

Net energy expenditure is only one high energy phosphate.

NET UTILISATION

PROTEIN BIOSYSNTHESIS

 Protein synthesis is the process in which cells make proteins. It occurs in two stages:
transcription and translation.
 Transcription is the transfer of genetic instructions in DNA to mRNA in the nucleus. It
is processed, it carries the instructions to a ribosome in the cytoplasm.

 Translation occurs at the ribosome, which consists of rRNA and proteins. In translation,
the instructions in mRNA are read, and tRNA brings the correct sequence of amino acids
to the ribosome.
 Then, rRNA helps bonds form between the amino acids, producing a polypeptide chain.
 After a polypeptide chain is synthesized, it may undergo additional processing to form
the finished protein.
 Translation is the second part of the central dogma of molecular biology: RNA → Protein.
 It is the process in which the genetic code in mRNA is read to make a protein.
 After mRNA leaves the nucleus, it moves to a ribosome, which consists of rRNA and
proteins.
 The ribosome reads the sequence of codons in mRNA, and molecules of tRNA bring amino
acids to the ribosome in the correct sequence.
 To understand the role of tRNA, you need to know more about its structure. Each tRNA
molecule has an anticodon for the amino acid it carries.
 An anticodon is complementary to the codon for an amino acid.
 For example, the amino acid lysine has the codon AAG, so the anticodon is UUC.
Therefore, lysine would be carried by a tRNA molecule with the anticodon UUC.
 Wherever the codon AAG appears in mRNA, a UUC anticodon of tRNA temporarily binds.
 While bound to mRNA, tRNA gives up its amino acid. With the help of rRNA, bonds form
between the amino acids as they are brought one by one to the ribosome, creating a
polypeptide chain. The chain of amino acids keeps growing until a stop codon is reached.

Ribosome Structure

 Ribosomes are composed of two subunits, one small and one large. Four binding sites are
located on the ribosome, one for mRNA and three for tRNA.
 The three tRNA sites are labeled P, A, and E. The P site, called the peptidyl site, binds to the
tRNA holding the growing polypeptide chain of amino acids.
 The A site (acceptor site), binds to the aminoacyl tRNA, which holds the new amino acid to
be added to the polypeptide chain.
 The E site (exit site), serves as a threshold, the final transitory step before a tRNA now bereft
of its amino acid is let go by the ribosome.