Proteins Biochemistry Essay Question And Answers

Proteins

Question 1. Name the sulfur-containing amino acids. Describe the metabolism of any one of them.
Answer:

Sulfur-containing amino acids:

• Cysteine
• Cystine
• Methionine

Metabolism of methionine:

• The metabolism of methionine is divided into three parts.

Read And Learn More: BDS Previous Examination Question And Answers

1. Utilization of methionine for transmethylation reaction.
2. Conversion of methionine to cysteine and cystine.
3. Degradation of cysteine and its conversion to specialized products.

1. Transmethylation reactions.

• The transfer of methyl group from active methionine to an acceptor is known as transmethylation.
• For this methionine need to be first activated to S-adenosylmethionine.
• It occurs by the transfer of an adenosyl group from ATP to the sulfur atom of methionine by the methionine S- adenosyl – transferase enzyme.
• As a result, sulfur becomes a sulfonium atom.
• 3 ATP molecules are consumed in it.
• Functions of S-adenosylmethionine.
  • Transfer methyl group to an acceptor from methionine.
  • Gets converted to S-adenosyl homocysteine.
• This is hydrolyse to

1. Homocysteine.

• • Remethylated to methionine by N-methyl tetrahydrofolate.
  • This methionine can be reused.
• Adenosine.
• -S-adenosyl methionine is also involved in the synthesis of polyamines like spermine.

2. Conversion of methionine to cysteine.

• Homocysteine, a precursor of cysteine is initially synthesized from methionine.
• Homocysteine then condenses with serine to form cystathionine by PLP-dependent cystathionine synthase.
• Cleavage and deamination of cystathionine to cysteine and a-ketobutyrate occur by cystathionine synthase and cystathionine.

3. Degradation of cysteine

1. Cysteine and cystine are interconvertible by an NAD+ – dependent cystine reductase.
2. Meraceptothanolamine.
   • Cysteine on decarboxylation produces it.
   • Mercaptoethanolamine is involved in the biosynthesis of coenzyme A.
3. Cysteine sulfite.
   • Cysteine oxidizes to cysteine sulfinate by cysteine dioxygenase enzyme.
   • It cleaves alanine to sulfite. S
   • Sulfite is converted to sulfate and excreted in the urine.
4. Cysteic acid.
   • Cysteine sulfinate oxidizes to cysteic acid.
   • This produces
     1. Taurine by decarboxylation and
     2. Pyruvate by degradation.
5. Cysteine can be degraded by desulfhydrase to liberate sulfur, ammonia, and pyruvate.

Question 2. Name the aromatic amino acids. Describe the metabolism of any one of them.
Answer:

Aromatic amino acids:

1. Phenylalanine
2. Tyrosine
3. Tryptophan.

Metabolism of phenylalanine:

1. Conversion of phenylalanine to tyrosine.
2. Phenylalanine is hydroxylated at the para position by phenylalanine hydroxylase to produce tyrosine.
3. It involves the incorporation of one atom of molecular oxygen into the para position of phenylalanine while the other atom of O2 is reduced to form water.
4. It is an irreversible reaction.
5. It requires specific coenzyme biopterin.
6. The active form of biopterin is tetrahydrobiopterin.
7. Tetrahydrobiopterin is oxidized to dihydrobiopterin.
8. Then tetrahydrobiopterin is regenerated by NADPH – dependent dihydropterin reductase.

 

 

1. Fumarate- uses:
   • Intermediate of the citric acid cycle.
   • Precursor for gluconeogenesis.
2. Acetoacetate – uses:
   • Source for fat synthesis.

Question 3. Describe the urea cycle and its disorders/inborn errors.
Answer:

Urea cycle:

• It is the first metabolic cycle described by Hans Krebs and Kurt Her select.
• Thus, it is known as Krebs – Henseliet cycle.
• Urea is a synthesized liver.
• It has two amino groups.
  • Derived from ammonia.
  • Second, derived from aspartate.
• It requires five enzymes.

Urea cycle Steps:

Urea cycle Disorders/Inborn Errors:

Question 4. What is a normal blood urea level? Describe the synthesis and fate of urea in our body.
Answer:

Normal Blood Urea Level:

• In healthy individuals, the normal blood urea level is 10 – 40 mg/ dl.

Normal Blood Urea Level Synthesis:

Normal Blood Urea Level Fate:

1. Urea produced gets easily diffused and is transported by the blood to the kidneys excreted in the urine.
2. A small amount of it enters the intestine.
   • Here it gets degraded to CO2 and NHg by urease.
   • Ammonia thus formed is excreted in feces or absorbed by tire blood.

Question 5. What is Urea? Enumerate the steps in its synthesis. Mention its significance.
Answer:

Urea:

• It is the end product of protein metabolism.
• B 80 – 90% of the nitrogen-containing substances excreted in urine contain urea.
• It has two amino groups – one from ammonia and the other from aspartate.

Steps in Urea Synthesis:

1. Synthesis of carbamoyl phosphate.
2. Formation of citrulline
3. Synthesis of arginosuccinate
4. Cleavage of arginosuccinate
5. Formation of urea.

Urea Significance:

• Blood urea is used as a screening test for the evaluation of kidney function.
• Elevation in blood urea is categorized into.
  1. Pre-renal
  2. Renal
  3. Post-renal.

Question 6. Describe the synthesis of urea and add a note on its regulation.
Answer:

Synthesis of Urea Regulation:

1. Carbamoyl phosphate synthase -1.
   • It is involved in the first reaction of the urea cycle.
   • Activated by N-acetylglutamate which is synthesized from glutamate and acetyl CoA by synthase.
   • It’s regulation.
     • Increased level of arginine increases N-acetyl glutamate (NAG)
     • The protein-rich diet increases NAG.
2. Other enzymes of the urea cycle.
   • Controlled by the concentration of their respective substrates.

Question 7. Describe the different processes of catabolism of amino acids. Mention the different fates of the carbon skeleton of amino acids after catabolism.
Answer:

Catabolism of amino acids:

• Amino acids undergo transamination and deamination to liberate ammonia.

Transamination Definition:

• The transfer of an amino group from an amino to a keto acid is known as transamination.

Enzymes involved:

• Group of transaminases.

Enzymes Features:

• Enzymes require pyridoxal phosphate for their activity.
• Enzymes are specific for specific amino acids.
• Only amino groups are transferred in the reaction without any liberation of ammonia.
• It is a reversible reaction.
• It involves the catabolism of amino acids as well as the synthesis of non-essential amino acids.
• It uses, excess of amino acids for energy production.
• It results in concentrating nitrogen in glutamate.
• All amino acids with some exception undergoes transamination.
• It is not restricted to a-amino groups.
• Enzymes involved in this reaction are used for diagnostic am! prognostic purposes.

Enzymes  Mechanism:

1. The amino group is transferred to the coenzyme pyridoxal phosphate.
   • Results in the formation of pyridoxamine phosphate.
2. The amino group is transferred from pyridoxamine phosphate to a keto acid.
   • Produces a new amino acid.

2. Deamination Definition:

• The removal of amino groups from the amino acids as NH3 is deamination.

Deamination Types:

1. Oxidative deamination:
   • It is the liberation of free ammonia from the amino group of amino acids along with oxidation.
   • Glutamate dehydrogenase.
     • It catalyzes glutamate by oxidative deamination to liberate ammonia.
   • Amino acid oxidases.
     • They act on corresponding amino acids to produce cx-koto acids and NH3.
2. Non-oxidative determination:
3. It is the deamination of amino acids without undergoing oxidation
   • Amino acid dehydrases.
     • Hydroxy amino acids undergo non-oxidative deamination by PEP-dependent dehydrases.
   • Amino acid desulfhydrases.
     • Sulfur amino acids undergo non-oxidative deamination by desulfhydrases.
4. Mislidases.
   • It acts on histidine to undergo non-oxidative deamination.

Fates of the carbon skeleton of amino acids:

• Generation of energy.
• Glucose synthesis
• Formation of fat or ketone bodies.
• Production of non-essential amino acids.

Question 8. How are proteins digested? Indicate the specific site at which Proteolytic enzymes act. Add a note on the amino acid pool.
Answer:

Digestion of Proteins:

• Proteins are digested in the stomach, pancreas, and small intestine.
• It doesn’t occur in the mouth due to the absence of proteases in saliva.

1. Digestion by gastric secretion in the stomach.

• Gastric juice contains hydrochloric acid and pepsinogen.
• Renin also helps in digestion, which is found in infants.

1. Hydrochloric acid.
   • It is secreted by the parietal cells of the gastric gland.
   • It has two important functions.
     • Denaturation of proteins.
     • Killing of micro-organisms.
2. Pepsin.
   • Produced by serous cells of the stomach as pepsinogen.
   • It cleaves peptide bonds formed by amino groups of phenylalanine or tyrosine.
   • It results in the formation of peptides and a few amino acids which act as stimulants for the release of the hormone cholecystokinin.
3. Renin.
   1. Involved in curdling of milk in infants.
   2. Converts milk protein casein to calcium paracaseinate which can be digested by pepsin.

2. Digestion by proteases present in the pancreas.

• Proteases are secreted by zymogens.
• They are initiated by cholecystokinin and secret in hormones.
• Zymogens produce active proteases namely chymotrypsin, elastase, and carboxypeptidase.
• Trypsin cleaves the peptide bond.
• Carboxypeptidase acts on peptidase bonds of COOH – terminal amino acid.
• The combined effect of all pancreatic proteases causes the formation of free amino acids and small peptides.

3. Digestion in the small intestine.

• It occurs by aminopeptidases and dipeptidases are present.

1. Aminopeptidase.
   • It cleaves N-terminal amino acids one by one to produce free amino acids and smaller peptides.
2. Dipeptidases.

• Acts on different dipeptides to liberate amino acids.

Amino acid pool:

1. An adult has about 100 g of free amino acids which represent tire amino acid pool of the body.
2. Glutamate and glutamine constitute about 50% and essential amino acids about 10% of the body pool.
3. This amino acid pool is maintained by the balance between the sources and utilization of amino acids.

Question 9. Functions of proteins.
Answer:

• Proteins have a variety of specialized and essential functions.
• Its functions are grouped into static and dynamic functions.

Question 10. Classification of Amino acids.
Answer:

Question 11. Limiting amino acids
Answer:

• It refers to essential amino acids in the protein which fall short of meeting the amino acids required by humans.
• They are determined by comparing the number of amino acids in a gram of protein to the number of amino acids per gram of protein required.
• These are limiting amino acids because if a person’s diet is deficient in any one of the amino acids, it will limit the usefulness of the others even if they are present in large quantities.
• It includes.

1. Sulfur-containing amino acids.
2. Methionine.
3. Lysine.

Question 12. Structure of proteins.
Answer:

• Proteins are the polymers of L -α – amino acids.
• Its structure is divided into four levels.

1. Primary structure:

• It is the linear sequence of amino acids forming polypeptides.
• Amino acids are held together by peptide bond which is formed between the amino group of one amino acid and the carboxyl group of another amino acid,

2. Secondary structure:

• The spatial arrangement of protein formed by twisting of the polypeptide chain is referred as secondary structure.

Types:

1. α-Helix.
   • Proposed by Pauling and Corey.
   • It is a tightly packed coiled structure with amino acid side chains extending outwards from the central axis.
   • It is stabilized by extensive hydrogen bonding formed between the H atom attached to peptide N and
     O atom attached to peptide C.
   • It is the common spatial arrangement.
   • It has a rigid arrangement of the polypeptide chain
   • A right-handed helix is more stable than a left-handed one.
2. β – pleated sheet.
   • Proposed by Pauling and Corey.
   • It is composed of two or more segments of fully extended peptide chains.
   • Hydrogen bonds are formed in between the neighboring segments of polypeptide chains.

3. Tertiary structure:

• The three-dimensional arrangement of protein is referred to as a tertiary structure.
• It consists of hydrophobic side chains inside the molecules while hydrophilic on the surface of the molecule.

4. Quaternary structure:

• Some of the proteins contain two or more polypeptide chains called subunits.
• The spatial arrangement of it is referred to as a quaternary structure.
• Subunits are held together by non-covalent bonds like hydrogen bonds, hydrophobic bonds, and ion bonds.

Question 13. Denaturation of Proteins.
Answer:

• It is the phenomenon of the disorganization of native protein structures.

Denaturation of Proteins Agents:

1. Physical agents.
   • Heat
   • Violent shaking
   • X-rays
   • UV radiation.
2. Chemical agents.
   • Acids
   • Alkalis
   • Organic solvents.
   • Urea.
   • Salicylate.

Denaturation of Proteins Features:

• Irreversible process
• Results in loss of secondary, tertiary, and quaternary structure with primary structure intact.
• The native structure is lost.
• Biological activity is lost.
• Protein becomes insoluble.
• society increases
• Surface tension decreases.
• Sulfhydryl groups and the ionicity of proteins increase.
• Digestion becomes easy.
• It cannot be crystalline.

Question 14. What are conjugated proteins? Give examples.
Answer:

Conjugated Proteins:

• Along with amino acids, if a protein contains a non-protein component/prosthetic group, it is known as a conjugated protein.

Examples:

Question 15. Biologically important peptides.
Answer:

Question 16. How is creating – P synthesized?
Answer:

Question 17. Phenylketonuria.
Answer:

• It is a common metabolic disorder.

Phenylketonuria Causes:

• Deficiency of the hepatic enzyme phenylalanine hydroxylase.

Phenylketonuria Mechanism:

1. Deficiency of enzyme phenylalanine hydroxylase
↓

Impairs synthesis of tetrahydrobiopterin
↓
Causes accumulation of phenylalanine in tissues and blood.
↓
Excess of it is excreted in the urine.

2. Phenylalanine is diverted to alternate pathways.

• This results in the excessive production of

1. Phenylpyruvate
2. Phenylacetate
3. Phenyllactate
4. Phenylglutamine.

Phenylketonuria Clinical Features:

1. Effects of CNS:

• Mental retardation.
• Failure to walk or talk.
• Retarded growth
• Seizures and tremor
• Low IQ

2. Effect on pigmentation:

• Hypopigmentation due to impaired melanin formation.

3. Urine:

• Contains phenylalanine and its metabolic products.
• Mousey odor – due to the presence of phenylacetate.

Phenylketonuria Diagnosis:

• Detected by screening newborn babies.

1. Guthrie test.

• It is a bacterial bioassay for phenylalanine.

2. Ferric chloride test.

• Detects phenylpyruvate in urine.
• The positive test gives green color.

Phenylketonuria Treatment:

• Intake of the diet with low phenylalanine content
• Synthetic amino acid preparations can be used.
• As tyrosine cannot be synthesized, it should be provided in the diet.
• In serious conditions – 5 – hydroxytryptophan and dopa are administered.
• This restores the synthesis of serotonin and catecholamines.

Question 18. Immunoglobulin
Answer:

• They are specialized groups of proteins

Immunoglobulin Structure:

• Consists of 2 heavy chains and 2 light chains
• These chains are held together by disulfide bonds
• Thus it forms Y shaped structure
• Heavy chains are linked to carbohydrates

Immunoglobulin Classes:

• They are named according to the heavy chain they contain

Question 19. What is S adenosyl methionine? How is it formed and what is its importance?
Answer:

S adenosyl methionine:

• It is sulfur-containing amino acids

S adenosyl methionine Formation:

• It is formed by a transmethylation reaction
• It occurs by the transfer of an adenosyl group from ATP to a sulfur atom of methionine by the methionine S adenosyl transferase enzyme
• As a result, sulfur becomes a sulfonium atom
• 3 ATP molecules are consumed in it

S adenosyl methionine Significance:

• Transfer methyl group to an acceptor from methionine
• Hydrolyses to homocysteine – remethylated to methionine by N- methyl tetrahydrofolate
• S adenosyl methionine is also involved in the synthesis of polyamines like spermine

Question 20. Name different types of immunoglobulin and their functions, (or) Structure and functions of immunoglobulin.
Answer:

Immunoglobulin:

• All immunoglobulin consists of two identical heavy chains and two light chains held together by disulfide bonds.
• The variable region is present at the amino-terminus while the constant region is at the carboxy-terminal.
• Based on the heavy chain, immunoglobulin is classified into 5 classes.

Question 21. Active Methionine.
Answer:

Active Methionine Formation:

• Methionine is activated by ATP in the presence of the enzyme methionine-adenosyl transferase.
• Methionine + ATP → active methionine.

Active Methionine Structure:

• The s-methyl bond is a high-energy bond.
• The Methyl group is liable and gets readily transferred to an acceptor during transmethylation reactions.

Question 22. Essential amino acids and their functions.
Answer:

The amino acids which cannot be synthesized in the body and need to be supplied through diet are known as essential amino acids.

Question 23. Primary Structure of Proteins.
Answer:

• The linear sequence of amino acids forming the backbone of proteins is referred to as the primary structure.
• Amino acids are held together by peptide bonds.
• This bond is formed between the amino groups of one
  amino acid and the carboxyl group of another amino acid.
• The sequence of amino acids is determined by genes in DNA.

Primary Structure of Proteins Determination:

• It involves 3 stages.

1. Determination of amino acid composition.
2. Degradation of proteins.
3. Determination of the amino acid sequence.

Question 24. Classification of proteins.
Answer:

Question 25. Semi-essential amino acids.
Answer:

• Those amino acids which can be synthesized by adults and not by growing children is known as semi-essential acids.
• Example: Arginine and histidine.

Question 26. Name the aromatic amino acids and inborn errors in them.
Answer:

Aromatic amino acids:

• Phenylalanine
• Tyrosine
• Tryptophan.

Question 27. Name sulfur-containing amino acids.
Answer:

• Cysteine
• Cystine
• Methionine.

Question 28. What are Zwitterions?
Answer:

• Zwitter ion, the word is derived from the Greek word meaning hybrid.

Zwitterions Synonym:

• Dipolar ion.

Zwitterions Definition:

• It is a hybrid molecule containing positive and negative ionic groups.
• In a strong acidic medium, the amino acid exists as positively charged while in a strong alkaline medium, it is negatively charged.
• Each amino acid at isoelectric pH carries both positive and negative charges and exists as ad Zwitter ion.

Zwitterions Example:

• Leucine at isoelectric pH = 6 is found as a Zwitter ion, below it exists as a cation and above 6 it exists as an anion.

Question 29. Transamination.
Answer:

Transamination Definition:

• The transfer of an amino group from an amino acid to a keto acid is known as transamination.

Transamination Enzyme involved:

• Transaminases catalyses transamination.

Transamination Mechanism:

1. Transfer of amino group to the coenzyme pyridoxal phosphate to form pyridoxamine phosphate.
2. Next transfer of the amino group of pyridoxamine phosphate to a keto acid.

Question 30. Where is urea synthesized?
Answer:

1. Urea is synthesized in the liver by the process called the urea cycle.
2. It required five distinct enzymes.

Question 31. Describe the urea cycle.
Answer:

• The urea cycle is tire first metabolic cycle described by Hans Krebs and Kurt Henseliet.

Urea Cycle Steps:

1. Synthesis of carbamoyl phosphate.
2. Formation of citrulline.
3. Synthesis of arginosuccinate.
4. Cleavage of arginosuccinate.
5. Formation of urea.
6. Enzyme involved:

Urea Cycle Overall reaction:

NH4+ + CO2 + Aspartate + 3ATP → urea + fumerate + 2ADP + 2Pi + AMP + PPi

Question 32. Name two non-protein nitrogen substances and mention their serum levels.
Answer:

• All nitrogen-containing substances other than proteins are referred to as non-protein nitrogen substances (NPN).

Question 33. Name the inborn errors of metabolism in the phenylalanine pathway and mention the enzymes that are missing in each case.
Answer:

Question 34. A substance formed from tyrosine.
Answer:

Question 35. Dietary sources of essential amino acids.
Answer:

• Egg, soya protein, sesame, beef, peanuts, and mustard seeds are the main food sources of essential amino acids.

Question 19. Name conjugated proteins and their functions.
Answer:

Question 36. Give one example each for transamination and deamination of amino acids.
Answer:

Example of transamination reaction:

• Transfer of amino group to coenzyme pyridoxal phosphate to form pyridoxamine phosphate

Example of deamination of amino acids:

1. Oxidative deamination

• Catalyzation of glutamate by glutamate dehydrogenase to liberate ammonia

2. Non-oxidative deamination

• Deamination of hydroxy amino acids by PLP-dependent hydrates

Question 37. Oxidative deamination
Answer:

It is the liberation of free ammonia from the amino group of amino acids along with oxidation

Example:

• Amino acids oxidases act on respective amino acids to produce a ketoacid and ammonia.

Question 38. Classify amino acids based on their nutritional importance and give two examples of each.
Answer:

1. Essential amino acids

• They cannot be synthesized by the body
• Example: valine, leucine, lysine

2. Semi-essential amino acids

• Can be synthesized by adults but not by children
• Examples: arginine, histidine

3. Nonessential amino acids

• They are synthesized in the body
• Examples: glycine, serine, aspartate, alanine

Question 39. Define isoelectric pH and denaturation.
Answer:

Isoelectric pH:

• It is defined as the pH at which a molecule exists as a Twitter ion and carries no net charge.
• The molecule is neutral with
  • Minimum solubility
  • Maximum precipitability
  • Least buffering capacity
• Value
  • Casein – 4.6
  • Albumin – 4.7
  • Haemoglobin – 6.7

Denaturation of proteins:

• It is the phenomenon of the disorganization of native protein structures.

Question 40. Write the enzyme defect and the metabolite excreted in the urine of the following disorder

1. Phenylketonuria
2. Alkaptonuria
3. Albinism

Answer:

Question 41. Name the various products formed from glycine
Answer:

1. Products formed from glycine:
2. NH4
3. Carbon dioxide
4. One carbon fragment as N5,
5. N10 methylene THF.