September 2002 Paper II

1) Name aromatic amino acids Describe the metabolism of tryptophan Name the important

compounds synthesized from it and metabolic disorder (feb 2006)

ANS The aromatic amino acids are phenyl alanine tyrosine tryptophan

Fig metabolism of tryptophan

The principle function of amino acids including tryptophan is as building blocks in

protein biosynthesis

In addition tryptophan functions as a biochemical precursor for the production of the

neurotransmitter serotonin (via tryptophan hydroxylase) and the vitamin niacin (with

kynurenine as an intermediate) Serotinin in turn can be converted to melatonin (a

neurohormone) via 5-hydroxyindole-O-methyltransferase

Conversion of tryptophan to niacin is insufficient to meet the demands for this vitamin

Lack of tryptophan however such as dependence on food of low tryptophan content

such as maize can contribute to the niacin-deficiency disease pellagra

In organisms which synthesize tryptophan (plants and microorganisms) high levels of

this amino acid activate a repressor protein which in turn binds to the trp operon

Binding of this repressor to its operon prevents transcription of downstream DNA that

codes for enzymes involved in the biosynthesis of tryptophan Hence high levels of

tryptophan prevent additional tryptophan synthesis through a negative feedback loop

Conversely if the cells tryptophan level drops transcription of the operons genes

resumes This is one example of how gene expression responds rapidly to changes in the

cells internal and external environment

Fig Important product derived from tryptophan

The principle function of amino acids including tryptophan is as building blocks in

protein biosynthesis

In addition tryptophan functions as a biochemical precursor for the production of the

neurotransmitter serotonin (via tryptophan hydroxylase) and the vitamin niacin (with

kynurenine as an intermediate) Serotinin in turn can be converted to melatonin (a

neurohormone) via 5-hydroxyindole-O-methyltransferase

Conversion of tryptophan to niacin is insufficient to meet the demands for this vitamin

Lack of tryptophan however such as dependence on food of low tryptophan content

such as maize can contribute to the niacin-deficiency disease pellagra

In organisms which synthesize tryptophan (plants and microorganisms) high levels of

this amino acid activate a repressor protein which in turn binds to the trp operon

Binding of this repressor to its operon prevents transcription of downstream DNA that

codes for enzymes involved in the biosynthesis of tryptophan Hence high levels of

tryptophan prevent additional tryptophan synthesis through a negative feedback loop

Conversely if the cells tryptophan level drops transcription of the operons genes

resumes This is one example of how gene expression responds rapidly to changes in the

cells internal and external environment

Fig Important product derived from tryptophan

2) Write short notes on

a) Structure and functions of tRNA (aug 2004 feb 2006 aug 2010 sep 2002)

It transfer amino acids from cytoplasm to ribosomal protein hence the name transfer

RNA

They are easily soluble also referred as sRNA

Each molecule is only 73-93 nucleotides in length shorter than mRNA

TRNA molecules are large undergoes post transcriptional modifications

Structure of tRNA It shows extensive internal base pairing and cloverleaf like

structure

It contains unusual bases They are dihydro uracil pseudo uridine hypoxanthine are

methylated

Acceptor arm is at 3acute end

It carries the aminoacids It has seven base pairs The end sequence is CCA-3acute The 3rsquo

end hydroxyl group is bonded with carboxyl end of amino acids

Anticodon Arm of tRNA

Acceptor arm recognizes the triplet nucleotide codon present in mRNA

The tRNA molecule plays a Vitol role in translation

The tRNA molecule act as mediator between the mRNA and amino acids

DHU Arm of tRNA

DHU arm serves as the recognition site for enzymes

Pseudouridine arm of tRNA

It is involved in binding tRNA to ribosomes

b) AIDS

ANS in 1981 lusters of 5 cases of pnemocystis carinii pneumonia were reported in USA

These protozoa can produce pneumonia only in immune deficient individuals Based on

the clinical manifestation the disease named as AIDS

Transmission

I) 80 of the total patients got the infection as a sexually transmitted disease

II) In about 15 of patients the disease was transmitted through blood

III) In the rest 5cases virus may be transmitted from mother to fetus through placenta

Natural course of diseases

I) Window period

When the virus enters the body it is multiplied in the body cells but it cannot be

detected easily

II) Seropositive stage

After a few months antibodies are seen circulation This is called seropositivity

During this period the person is completely normal Seropositve individuals will go for

the AIDS disease within 5 years

III) Lymphodenopathy and fever may see Non pathogenic micro organisms enter into the

body and produce lesions in skin gastro intestinal tract lungs urinary tract and brain

IV) Immunology of AIDS

The lymphocytes are decreased in number leading to immunodeficiency

Macrophages and monocytes act as the reservoir of HIV infection disseminate the

virus to various organs

T-helper count is less than 400cu mm of blood T-killer cytotoxic activity is reduced

Antibody response against a foreign antigen is poor Productions of lymphokines

such as interferon interlukin-2 etc are lowered

c) Occupational hazards

Ans Occupational health is essentially preventive medicine The joint International Labor

Organization(ILO) amp World Health Organization(WHO) Committee- occupational health

should aim at the promotion and maintenance of the highest degree of physicalmental

and social well being of the workersemployees in all occupations

An industrial workeremployee may be exposed to five types of hazards depending on

the occupations

1 Physical Hazards

2 Chemical Hazards

3 Biochemical Hazards

4 Mechanical Hazards

5 Psychosocial Hazards

b) AIDS

ANS in 1981 lusters of 5 cases of pnemocystis carinii pneumonia were reported in USA

These protozoa can produce pneumonia only in immune deficient individuals Based on

the clinical manifestation the disease named as AIDS

Transmission

I) 80 of the total patients got the infection as a sexually transmitted disease

II) In about 15 of patients the disease was transmitted through blood

III) In the rest 5cases virus may be transmitted from mother to fetus through placenta

Natural course of diseases

I) Window period

When the virus enters the body it is multiplied in the body cells but it cannot be

detected easily

II) Seropositive stage

After a few months antibodies are seen circulation This is called seropositivity

During this period the person is completely normal Seropositve individuals will go for

the AIDS disease within 5 years

III) Lymphodenopathy and fever may see Non pathogenic micro organisms enter into the

body and produce lesions in skin gastro intestinal tract lungs urinary tract and brain

IV) Immunology of AIDS

The lymphocytes are decreased in number leading to immunodeficiency

Macrophages and monocytes act as the reservoir of HIV infection disseminate the

virus to various organs

T-helper count is less than 400cu mm of blood T-killer cytotoxic activity is reduced

Antibody response against a foreign antigen is poor Productions of lymphokines

such as interferon interlukin-2 etc are lowered

c) Occupational hazards

Ans Occupational health is essentially preventive medicine The joint International Labor

Organization(ILO) amp World Health Organization(WHO) Committee- occupational health

should aim at the promotion and maintenance of the highest degree of physicalmental

and social well being of the workersemployees in all occupations

An industrial workeremployee may be exposed to five types of hazards depending on

the occupations

1 Physical Hazards

2 Chemical Hazards

3 Biochemical Hazards

4 Mechanical Hazards

5 Psychosocial Hazards

c) Occupational hazards

Ans Occupational health is essentially preventive medicine The joint International Labor

Organization(ILO) amp World Health Organization(WHO) Committee- occupational health

should aim at the promotion and maintenance of the highest degree of physicalmental

and social well being of the workersemployees in all occupations

An industrial workeremployee may be exposed to five types of hazards depending on

the occupations

1 Physical Hazards

2 Chemical Hazards

3 Biochemical Hazards

4 Mechanical Hazards

5 Psychosocial Hazards

d) PCR and its application (feb 2010

ANS it is a vitro DNA amplification procedure in which millions of a particular

sequence of DNA can be produced within few hours

Two primers of about 20-30 nucleotides with complementary sequence of the flanking

region can be synthesized

I) DNA strands are separated by heating at 95c for 15 sec to 2 min

II) The primers are annealed by cooling to 50c the primer hybridise with their

complementary single stranded DNA produced

III) New DNA strand are synthesized by taq polymerase This enzyme is derived from

bacteria that found in hot springs The polymerase reaction is allowed to take place at

72c for 30 sec in presence of dNTPs

Fig PCR

IV) Clinical applications

V) PCR detect even one bacillus present in the specimen Any other bacteria also

detect similarily This technique is widely used in the diagnosis of viral infections like

hepatitis C and HIV

VI) PCR allows the DNA in a single cell or in a hair follicle to be analysedthis is highly

useful in forensic medicine to identify the criminal

VII) PCR especially usefull for prenatal diagnosis of inherited diseases

VIII) PCR is widely used to monitor residual abnormal cells present in treated

patients

IX) Diagnosis of genetic disorder the PCR technology has been widely used to

amplify the gene segments that contain known mutations for diagnosis such as

sickle cell anemia etc

X) Real time PCR ndash quantitation of the number of virus present in the sample

can be calculated Eg viral load in HIV

3) Compare the metabolic changes in well fed state and starvation

ANS Erythrocytes lack mitochondria and hence are wholly Reliant on glycolysis and the

pentose phosphate pathway The brain can metabolize ketone bodies to meet

About 20 of its energy requirements the remainder must be supplied by glucose The

metabolic changes that occur in starvation are the consequences of the

Need to preserve glucose and the limited reserves of Glycogen in liver for use by the

brain and erythrocytes and to ensure the provision of alternative fuels for other

Tissues The fetus and synthesis of lactose in milk also

Require a significant amount of glucose

In the Fed State Metabolic Fuel

Reserves Are Laid Down

For several hours after a meal while the products of digestion are being absorbed there

is an abundant supply of metabolic fuels Under these conditions glucose is the major

fuel for oxidation in most tissues this is observed as an increase in the respiratory

quotient

Glucose uptake into muscle and adipose tissue is controlled by insulin which is secreted

by the B islet cells of the pancreas in response to an increased concentration of glucose

in the portal blood An early response to insulin in muscle and adipose tissue is the

migration of glucose transporter vesicles to the cell surface exposing active glucose

transporters (GLUT 4) These insulin- sensitive tissues will only take up glucose from the

blood stream to any significant extent in the presence of the hormone As insulin

secretion falls in the starved state so the transporters are internalized again reducing

glucose uptake The uptake of glucose into the liver is independent of insulin but liver

has an isoenzyme of hexokinase (glucokinase) with a high Km so that as the

concentration of glucose entering the liver increases so does the rate of synthesis of

glucose 6-phosphate

Metabolic Fuel Reserves Are Mobilized in the Starving State

In the postabsorptive state as the concentration of glucose in the portal blood falls so

insulin secretion decreases resulting in skeletal muscle and adipose tissue taking up less

glucose The increase in secretion of glucagon from the A cells of the pancreas inhibits

Glycogen synthase and activates glycogen phosphorylase in liver The resulting glucose 6-

phosphate in liver is hydrolyzed by glucose-6-phosphatase and glucose is released into

the blood stream for use by other tissues particularly the brain and erythrocytes

4) Write short notes on

A) Post translation modifications ( aug 2006 aug 2007 feb 2010 feb 2012)

Ans Once the protein is synthesized by the process of translation by the ribosomes it

undergoes various modifications to become a fully functional protein Those processes

are called post translational modification or post translational processing They are

Proteolytic cleavage ndashproteins like insulin are secreted as pre pro proteins

Proteinases cleave the N terminal and C-terminal portions of prepro insulin and

insulin undergoes disulphide bond creation to form insulin which is produced just

before its release

Gamma carboxylation- the gamma carbon of glutamic acid in clotting

factors(IIVIIIXXI) under influence of vitamin K is needed for them to become

active clotting factors

Hydoxylation- of lysine and proline in collagen is needed for making bonds

between them to increase the strength of collagen

Phosphorylation of serthrtyr in many regulatory enzymes like phosphorylase

are important for regulation of metabolic pathways

Glycosylation- many proteins are glycoproteins Carbohydrates are attached to

serthr residues

Clinical applications

Defective hydroxylation in collagen leads to collagen disorders like Ehlers

Danlos syndrome

Defective protein folding may lead to dangerous prion diseases like bovine

spongiform encephalopathy and Crueztfolt Jacob disease

B) Salvage pathway (Aug 2004 Aug 2005 Aug 2010 Aug 2011 Feb 2012)

- Ans Nucleotides are degraded regularly Salvage pathway recycles the

purines and make it available for nucleic acid synthesis

- Adenine is converted to AMP using PRPP by Adenine phosphoribosyl

transferase(APRTase)

- Guanine is converted to GMP using PRPP by Hypoxanthine guanine

phosphoribosyl transferase (HGPRTase)

- The salvage pathway is important for RBC and brain since denovo synthesis of

purine nucleotides are not operative

- A defect in HGPRTase will lead to Lesch Nyhan syndrome

Lesch Nyhan syndrome

it is a X-linked inborn error of purine metabolism incidence 110000

deficiency of HGPRTase which acts in salvage pathway

so the salvage pathway is stopped and PRPP accumulates which will go for catabolism

to uric acid

hyperuricemia leads to nephrolithiasis and gout

it is also characterized by self mutilation mental retardation

C) Define and explain about point mutation with eg

Ans A point mutation or single base substitution is a type of mutation that causes the

replacement of a single base nucleotide with another nucleotide of the genetic material

DNA or RNA The term point mutation also includes insertions or deletions of a single

base pair

A point mutant is an individual that is affected by a point mutation

TransitionTransversion categorization

Transitions replacement of a purine base with another purine or replacement of

a pyrimidine with another pyrimidine

Transversions replacement of a purine with a pyrimidine or vice versa

Transitions (Alpha) and transversions (Beta)

There is a systematic difference in mutation rates for transitions (Alpha) and

transversions (Beta) Transition mutations are about an order of magnitude more

common than transversions

Functional categorization

Nonsense mutations Code for a stop which can truncate the protein A nonsense

mutation converts an amino acid codon into a termination codon This causes the

protein to be shortened because of the stop codon interrupting its normal code

How much of the protein is lost determines whether or not the protein is still

functional

VI) PCR allows the DNA in a single cell or in a hair follicle to be analysedthis is highly

useful in forensic medicine to identify the criminal

VII) PCR especially usefull for prenatal diagnosis of inherited diseases

VIII) PCR is widely used to monitor residual abnormal cells present in treated

patients

IX) Diagnosis of genetic disorder the PCR technology has been widely used to

amplify the gene segments that contain known mutations for diagnosis such as

sickle cell anemia etc

X) Real time PCR ndash quantitation of the number of virus present in the sample

can be calculated Eg viral load in HIV

3) Compare the metabolic changes in well fed state and starvation

ANS Erythrocytes lack mitochondria and hence are wholly Reliant on glycolysis and the

pentose phosphate pathway The brain can metabolize ketone bodies to meet

About 20 of its energy requirements the remainder must be supplied by glucose The

metabolic changes that occur in starvation are the consequences of the

Need to preserve glucose and the limited reserves of Glycogen in liver for use by the

brain and erythrocytes and to ensure the provision of alternative fuels for other

Tissues The fetus and synthesis of lactose in milk also

Require a significant amount of glucose

In the Fed State Metabolic Fuel

Reserves Are Laid Down

For several hours after a meal while the products of digestion are being absorbed there

is an abundant supply of metabolic fuels Under these conditions glucose is the major

fuel for oxidation in most tissues this is observed as an increase in the respiratory

quotient

Glucose uptake into muscle and adipose tissue is controlled by insulin which is secreted

by the B islet cells of the pancreas in response to an increased concentration of glucose

in the portal blood An early response to insulin in muscle and adipose tissue is the

migration of glucose transporter vesicles to the cell surface exposing active glucose

transporters (GLUT 4) These insulin- sensitive tissues will only take up glucose from the

blood stream to any significant extent in the presence of the hormone As insulin

secretion falls in the starved state so the transporters are internalized again reducing

glucose uptake The uptake of glucose into the liver is independent of insulin but liver

has an isoenzyme of hexokinase (glucokinase) with a high Km so that as the

concentration of glucose entering the liver increases so does the rate of synthesis of

glucose 6-phosphate

Metabolic Fuel Reserves Are Mobilized in the Starving State

In the postabsorptive state as the concentration of glucose in the portal blood falls so

insulin secretion decreases resulting in skeletal muscle and adipose tissue taking up less

glucose The increase in secretion of glucagon from the A cells of the pancreas inhibits

Glycogen synthase and activates glycogen phosphorylase in liver The resulting glucose 6-

phosphate in liver is hydrolyzed by glucose-6-phosphatase and glucose is released into

the blood stream for use by other tissues particularly the brain and erythrocytes

4) Write short notes on

A) Post translation modifications ( aug 2006 aug 2007 feb 2010 feb 2012)

Ans Once the protein is synthesized by the process of translation by the ribosomes it

undergoes various modifications to become a fully functional protein Those processes

are called post translational modification or post translational processing They are

Proteolytic cleavage ndashproteins like insulin are secreted as pre pro proteins

Proteinases cleave the N terminal and C-terminal portions of prepro insulin and

insulin undergoes disulphide bond creation to form insulin which is produced just

before its release

Gamma carboxylation- the gamma carbon of glutamic acid in clotting

factors(IIVIIIXXI) under influence of vitamin K is needed for them to become

active clotting factors

Hydoxylation- of lysine and proline in collagen is needed for making bonds

between them to increase the strength of collagen

Phosphorylation of serthrtyr in many regulatory enzymes like phosphorylase

are important for regulation of metabolic pathways

Glycosylation- many proteins are glycoproteins Carbohydrates are attached to

serthr residues

Clinical applications

Defective hydroxylation in collagen leads to collagen disorders like Ehlers

Danlos syndrome

Defective protein folding may lead to dangerous prion diseases like bovine

spongiform encephalopathy and Crueztfolt Jacob disease

B) Salvage pathway (Aug 2004 Aug 2005 Aug 2010 Aug 2011 Feb 2012)

- Ans Nucleotides are degraded regularly Salvage pathway recycles the

purines and make it available for nucleic acid synthesis

- Adenine is converted to AMP using PRPP by Adenine phosphoribosyl

transferase(APRTase)

- Guanine is converted to GMP using PRPP by Hypoxanthine guanine

phosphoribosyl transferase (HGPRTase)

- The salvage pathway is important for RBC and brain since denovo synthesis of

purine nucleotides are not operative

- A defect in HGPRTase will lead to Lesch Nyhan syndrome

Lesch Nyhan syndrome

it is a X-linked inborn error of purine metabolism incidence 110000

deficiency of HGPRTase which acts in salvage pathway

so the salvage pathway is stopped and PRPP accumulates which will go for catabolism

to uric acid

hyperuricemia leads to nephrolithiasis and gout

it is also characterized by self mutilation mental retardation

C) Define and explain about point mutation with eg

Ans A point mutation or single base substitution is a type of mutation that causes the

replacement of a single base nucleotide with another nucleotide of the genetic material

DNA or RNA The term point mutation also includes insertions or deletions of a single

base pair

A point mutant is an individual that is affected by a point mutation

TransitionTransversion categorization

Transitions replacement of a purine base with another purine or replacement of

a pyrimidine with another pyrimidine

Transversions replacement of a purine with a pyrimidine or vice versa

Transitions (Alpha) and transversions (Beta)

There is a systematic difference in mutation rates for transitions (Alpha) and

transversions (Beta) Transition mutations are about an order of magnitude more

common than transversions

Functional categorization

Nonsense mutations Code for a stop which can truncate the protein A nonsense

mutation converts an amino acid codon into a termination codon This causes the

protein to be shortened because of the stop codon interrupting its normal code

How much of the protein is lost determines whether or not the protein is still

functional

3) Compare the metabolic changes in well fed state and starvation

ANS Erythrocytes lack mitochondria and hence are wholly Reliant on glycolysis and the

pentose phosphate pathway The brain can metabolize ketone bodies to meet

About 20 of its energy requirements the remainder must be supplied by glucose The

metabolic changes that occur in starvation are the consequences of the

Need to preserve glucose and the limited reserves of Glycogen in liver for use by the

brain and erythrocytes and to ensure the provision of alternative fuels for other

Tissues The fetus and synthesis of lactose in milk also

Require a significant amount of glucose

In the Fed State Metabolic Fuel

Reserves Are Laid Down

For several hours after a meal while the products of digestion are being absorbed there

is an abundant supply of metabolic fuels Under these conditions glucose is the major

fuel for oxidation in most tissues this is observed as an increase in the respiratory

quotient

Glucose uptake into muscle and adipose tissue is controlled by insulin which is secreted

by the B islet cells of the pancreas in response to an increased concentration of glucose

in the portal blood An early response to insulin in muscle and adipose tissue is the

migration of glucose transporter vesicles to the cell surface exposing active glucose

transporters (GLUT 4) These insulin- sensitive tissues will only take up glucose from the

blood stream to any significant extent in the presence of the hormone As insulin

secretion falls in the starved state so the transporters are internalized again reducing

glucose uptake The uptake of glucose into the liver is independent of insulin but liver

has an isoenzyme of hexokinase (glucokinase) with a high Km so that as the

concentration of glucose entering the liver increases so does the rate of synthesis of

glucose 6-phosphate

Metabolic Fuel Reserves Are Mobilized in the Starving State

In the postabsorptive state as the concentration of glucose in the portal blood falls so

insulin secretion decreases resulting in skeletal muscle and adipose tissue taking up less

glucose The increase in secretion of glucagon from the A cells of the pancreas inhibits

Glycogen synthase and activates glycogen phosphorylase in liver The resulting glucose 6-

phosphate in liver is hydrolyzed by glucose-6-phosphatase and glucose is released into

the blood stream for use by other tissues particularly the brain and erythrocytes

4) Write short notes on

A) Post translation modifications ( aug 2006 aug 2007 feb 2010 feb 2012)

Ans Once the protein is synthesized by the process of translation by the ribosomes it

undergoes various modifications to become a fully functional protein Those processes

are called post translational modification or post translational processing They are

Proteolytic cleavage ndashproteins like insulin are secreted as pre pro proteins

Proteinases cleave the N terminal and C-terminal portions of prepro insulin and

insulin undergoes disulphide bond creation to form insulin which is produced just

before its release

Gamma carboxylation- the gamma carbon of glutamic acid in clotting

factors(IIVIIIXXI) under influence of vitamin K is needed for them to become

active clotting factors

Hydoxylation- of lysine and proline in collagen is needed for making bonds

between them to increase the strength of collagen

Phosphorylation of serthrtyr in many regulatory enzymes like phosphorylase

are important for regulation of metabolic pathways

Glycosylation- many proteins are glycoproteins Carbohydrates are attached to

serthr residues

Clinical applications

Defective hydroxylation in collagen leads to collagen disorders like Ehlers

Danlos syndrome

Defective protein folding may lead to dangerous prion diseases like bovine

spongiform encephalopathy and Crueztfolt Jacob disease

B) Salvage pathway (Aug 2004 Aug 2005 Aug 2010 Aug 2011 Feb 2012)

- Ans Nucleotides are degraded regularly Salvage pathway recycles the

purines and make it available for nucleic acid synthesis

- Adenine is converted to AMP using PRPP by Adenine phosphoribosyl

transferase(APRTase)

- Guanine is converted to GMP using PRPP by Hypoxanthine guanine

phosphoribosyl transferase (HGPRTase)

- The salvage pathway is important for RBC and brain since denovo synthesis of

purine nucleotides are not operative

- A defect in HGPRTase will lead to Lesch Nyhan syndrome

Lesch Nyhan syndrome

it is a X-linked inborn error of purine metabolism incidence 110000

deficiency of HGPRTase which acts in salvage pathway

so the salvage pathway is stopped and PRPP accumulates which will go for catabolism

to uric acid

hyperuricemia leads to nephrolithiasis and gout

it is also characterized by self mutilation mental retardation

C) Define and explain about point mutation with eg

Ans A point mutation or single base substitution is a type of mutation that causes the

replacement of a single base nucleotide with another nucleotide of the genetic material

DNA or RNA The term point mutation also includes insertions or deletions of a single

base pair

A point mutant is an individual that is affected by a point mutation

TransitionTransversion categorization

Transitions replacement of a purine base with another purine or replacement of

a pyrimidine with another pyrimidine

Transversions replacement of a purine with a pyrimidine or vice versa

Transitions (Alpha) and transversions (Beta)

There is a systematic difference in mutation rates for transitions (Alpha) and

transversions (Beta) Transition mutations are about an order of magnitude more

common than transversions

Functional categorization

Nonsense mutations Code for a stop which can truncate the protein A nonsense

mutation converts an amino acid codon into a termination codon This causes the

protein to be shortened because of the stop codon interrupting its normal code

How much of the protein is lost determines whether or not the protein is still

functional

4) Write short notes on

A) Post translation modifications ( aug 2006 aug 2007 feb 2010 feb 2012)

Ans Once the protein is synthesized by the process of translation by the ribosomes it

undergoes various modifications to become a fully functional protein Those processes

are called post translational modification or post translational processing They are

Proteolytic cleavage ndashproteins like insulin are secreted as pre pro proteins

Proteinases cleave the N terminal and C-terminal portions of prepro insulin and

insulin undergoes disulphide bond creation to form insulin which is produced just

before its release

Gamma carboxylation- the gamma carbon of glutamic acid in clotting

factors(IIVIIIXXI) under influence of vitamin K is needed for them to become

active clotting factors

Hydoxylation- of lysine and proline in collagen is needed for making bonds

between them to increase the strength of collagen

Phosphorylation of serthrtyr in many regulatory enzymes like phosphorylase

are important for regulation of metabolic pathways

Glycosylation- many proteins are glycoproteins Carbohydrates are attached to

serthr residues

Clinical applications

Defective hydroxylation in collagen leads to collagen disorders like Ehlers

Danlos syndrome

Defective protein folding may lead to dangerous prion diseases like bovine

spongiform encephalopathy and Crueztfolt Jacob disease

B) Salvage pathway (Aug 2004 Aug 2005 Aug 2010 Aug 2011 Feb 2012)

- Ans Nucleotides are degraded regularly Salvage pathway recycles the

purines and make it available for nucleic acid synthesis

- Adenine is converted to AMP using PRPP by Adenine phosphoribosyl

transferase(APRTase)

- Guanine is converted to GMP using PRPP by Hypoxanthine guanine

phosphoribosyl transferase (HGPRTase)

- The salvage pathway is important for RBC and brain since denovo synthesis of

purine nucleotides are not operative

- A defect in HGPRTase will lead to Lesch Nyhan syndrome

Lesch Nyhan syndrome

it is a X-linked inborn error of purine metabolism incidence 110000

deficiency of HGPRTase which acts in salvage pathway

so the salvage pathway is stopped and PRPP accumulates which will go for catabolism

to uric acid

hyperuricemia leads to nephrolithiasis and gout

it is also characterized by self mutilation mental retardation

C) Define and explain about point mutation with eg

Ans A point mutation or single base substitution is a type of mutation that causes the

replacement of a single base nucleotide with another nucleotide of the genetic material

DNA or RNA The term point mutation also includes insertions or deletions of a single

base pair

A point mutant is an individual that is affected by a point mutation

TransitionTransversion categorization

Transitions replacement of a purine base with another purine or replacement of

a pyrimidine with another pyrimidine

Transversions replacement of a purine with a pyrimidine or vice versa

Transitions (Alpha) and transversions (Beta)

There is a systematic difference in mutation rates for transitions (Alpha) and

transversions (Beta) Transition mutations are about an order of magnitude more

common than transversions

Functional categorization

Nonsense mutations Code for a stop which can truncate the protein A nonsense

mutation converts an amino acid codon into a termination codon This causes the

protein to be shortened because of the stop codon interrupting its normal code

How much of the protein is lost determines whether or not the protein is still

functional

B) Salvage pathway (Aug 2004 Aug 2005 Aug 2010 Aug 2011 Feb 2012)

- Ans Nucleotides are degraded regularly Salvage pathway recycles the

purines and make it available for nucleic acid synthesis

- Adenine is converted to AMP using PRPP by Adenine phosphoribosyl

transferase(APRTase)

- Guanine is converted to GMP using PRPP by Hypoxanthine guanine

phosphoribosyl transferase (HGPRTase)

- The salvage pathway is important for RBC and brain since denovo synthesis of

purine nucleotides are not operative

- A defect in HGPRTase will lead to Lesch Nyhan syndrome

Lesch Nyhan syndrome

it is a X-linked inborn error of purine metabolism incidence 110000

deficiency of HGPRTase which acts in salvage pathway

so the salvage pathway is stopped and PRPP accumulates which will go for catabolism

to uric acid

hyperuricemia leads to nephrolithiasis and gout

it is also characterized by self mutilation mental retardation

C) Define and explain about point mutation with eg

Ans A point mutation or single base substitution is a type of mutation that causes the

replacement of a single base nucleotide with another nucleotide of the genetic material

DNA or RNA The term point mutation also includes insertions or deletions of a single

base pair

A point mutant is an individual that is affected by a point mutation

TransitionTransversion categorization

Transitions replacement of a purine base with another purine or replacement of

a pyrimidine with another pyrimidine

Transversions replacement of a purine with a pyrimidine or vice versa

Transitions (Alpha) and transversions (Beta)

There is a systematic difference in mutation rates for transitions (Alpha) and

transversions (Beta) Transition mutations are about an order of magnitude more

common than transversions

Functional categorization

Nonsense mutations Code for a stop which can truncate the protein A nonsense

mutation converts an amino acid codon into a termination codon This causes the

protein to be shortened because of the stop codon interrupting its normal code

How much of the protein is lost determines whether or not the protein is still

functional

C) Define and explain about point mutation with eg

Ans A point mutation or single base substitution is a type of mutation that causes the

replacement of a single base nucleotide with another nucleotide of the genetic material

DNA or RNA The term point mutation also includes insertions or deletions of a single

base pair

A point mutant is an individual that is affected by a point mutation

TransitionTransversion categorization

Transitions replacement of a purine base with another purine or replacement of

a pyrimidine with another pyrimidine

Transversions replacement of a purine with a pyrimidine or vice versa

Transitions (Alpha) and transversions (Beta)

There is a systematic difference in mutation rates for transitions (Alpha) and

transversions (Beta) Transition mutations are about an order of magnitude more

common than transversions

Functional categorization

Nonsense mutations Code for a stop which can truncate the protein A nonsense

mutation converts an amino acid codon into a termination codon This causes the

protein to be shortened because of the stop codon interrupting its normal code

How much of the protein is lost determines whether or not the protein is still

functional

Missense mutations Code for a different amino acid A missense mutation

changes a codon so that a different protein is created a non-synonymous change

Silent mutations Code for the same amino acid A silent mutation has no effect

on the functioning of the genome A single nucleotide can change but the new

codon specifies the same amino acid resulting in an unmutated codon This type

of change is called synonymous change since the old and new codon code for the

same amino acid This is possible because 64 codons specify only 20 amino acids

D) Structure of proteins (oct 2003 Aug 2006 Aug 2007 Feb 2008 Aug 2011)

Ans Proteins are an important class of biological macromolecules present in all

organisms Proteins are polymers of amino acids Classified by their physical size

proteins are nanoparticles (definition 1ndash100 nm) Each protein polymer ndash also known as

a polypeptide ndash consists of a sequence formed from 20 possible L-α-amino acids also

referred to as residues For chains under 40 residues the term peptide is frequently used

instead of protein To be able to perform their biological function proteins fold into one

or more specific spatial conformations driven by a number of non-covalent interactions

such as hydrogen bonding ionic interactions Van Der Waals forces and hydrophobic

packing To understand the functions of proteins at a molecular level it is often

necessary to determine their three-dimensional structure This is the topic of the

scientific field of structural biology which employs techniques such as X-ray

crystallography NMR spectroscopy and dual polarization interferometry to determine

the structure of proteins

Levels of protein structure

Protein structure from primary to quaternary structure

There are four distinct levels of protein structure

Primary structure

The primary structure refers to amino acid linear sequence of the polypeptide chain The

primary structure is held together by covalent or peptide bonds which are made during

the process of protein biosynthesis or translation The two ends of the polypeptide chain

are referred to as the carboxyl terminus (C-terminus) and the amino terminus (N-

terminus) based on the nature of the free group on each extremity Counting of residues

always starts at the N-terminal end (NH2-group) which is the end where the amino group

is not involved in a peptide bond The primary structure of a protein is determined by the

gene corresponding to the protein A specific sequence of nucleotides in DNA is

transcribed into mRNA which is read by the ribosome in a process called translation The

sequence of a protein is unique to that protein and defines the structure and function of

the protein The sequence of a protein can be determined by methods such as Edman

degradation or tandem mass spectrometry Often however it is read directly from the

sequence of the gene using the genetic code We know that there are over 10000

proteins in our body which are composed of different arrangements of 20 types of amino

acid residues (it is strictly recommended to use the word amino acid residues as when

peptide bond is formed a water molecule is lost so protein is made up of amino acid

Fig Primary structure

residues) Post-translational modifications such as disulfide formation phosphorylations

and glycosylations are usually also considered a part of the primary structure and cannot

be read from the gene

Secondary structure

Secondary structure refers to highly regular local sub-structures Two main types of

secondary structure the alpha helix and the beta strand or beta sheets were suggested

in 1951 by Linus Pauling and coworkers[2] These secondary structures are defined by

patterns of hydrogen bonds between the main-chain peptide groups They have a regular

geometry being constrained to specific values of the dihedral angles ψ and φ on the

Ramachandran plot Both the alpha helix and the beta-sheet represent a way of

saturating all the hydrogen bond donors and acceptors in the peptide backbone Some

parts of the protein are ordered but do not form any regular structures They should not

be confused with random coil an unfolded polypeptide chain lacking any fixed three-

dimensional structure Several sequential secondary structures may form a

supersecondary unit

Fig Secondary structure

Tertiary structure

Tertiary structure refers to three-dimensional structure of a single protein molecule The

alpha-helices and beta-sheets are folded into a compact globule The folding is driven by

the non-specific hydrophobic interactions (the burial of hydrophobic residues from

water) but the structure is stable only when the parts of a protein domain are locked

into place by specific tertiary interactions such as salt bridges hydrogen bonds and the

tight packing of side chains and disulfide bonds The disulfide bonds are extremely rare in

cytosolic proteins since the cytosol is generally a reducing environment

Quaternary structure

Quaternary structure is the three-dimensional structure of a multi-subunit protein and

how the subunits fit together In this context the quaternary structure is stabilized by

the same non-covalent interactions and disulfide bonds as the tertiary structure

Complexes of two or more polypeptides (ie multiple subunits) are called multimers

Specifically it would be called a dimer if it contains two subunits a trimer if it contains

three subunits and a tetramer if it contains four subunits