BCM BT513-II Biochemistry Model Question.

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Model Questions for Biochemistry (M.Sc. Biotechnology, I-Semester, set II)

Long Answer Question: (7.5 × 1 = 7.5) (any one)

1. Write the structure and function of polysaccharides in the living organisms.
2. Classify the lipids and describe the structure of saturated and unsaturated fatty acids.
3. Explain the major enzyme-catalyzed reactions with examples.
4. What is PUFA? Describe the structure and functions of steroids.
5. Write the structure and function of mono-saccharides.
6. Define Michaelis-Menten expression for single substrate single enzyme catalyzed reaction. What is the significance of Michaelis constant?

Short Answer Question: (2.5 × 3 = 7.5) (any three)

1. Write a short note on competitive inhibitor.
2. What are the biological roles of nucleic acids?
3. Describe the structure and biological role of glycoprotein.
4. Explain the two major hypotheses for mode of enzyme action.
5. Define enzyme. Describe Six-major types of enzyme-catalysed reaction.
6. Suppose we have a mixture of an enzyme that contains total number of enzyme 0.1M. At this concentration (when all active site are filled), the maximal rate of reaction is 60,000M/S. Calculate the turnover number of that enzyme and time it takes to convert one substrate into a product molecule.
7. Draw the structure of lactose.
8. Draw the structure of sucrose.
9. Write a short note on starch.

Very Short Answer Question: (1 × 5 = 5) (any five)

1. Write the Michaelis-Menten equation.
2. Write the Henderson and Hasselbach equation.
3. What do you mean by Turnover Number of an enzyme?
4. Define cofactor and coenzyme.
5. What is an isoenzyme?
6. What do you mean by steady state assumption?
7. Draw the structure of alpha-D-glucose.
8. Draw the structure of alpha-D-fructose.
9. Draw the structure of dGTP.
10. What is glycogenin?
11. Write a short note on sphingolipid.

 

Molecular and Cell Biology; and Genetics

Long Answer Question: (8)

1. Describe the initiation of the replication process.
2. Describe the structure and type of gene.
3. What is a nucleosome? Describe the formation of a solenoid (condensed fiber) of DNA.
4. What are the functions of RNA? Describe mRNA.
5. Describe transcription briefly (in Prokaryotes).
6. What are the Post-transcriptional Modifications? Describe in brief.
7. Describe the initiation of the translation process in Prokaryotes.
8. What are the Post-translational Modifications? Describe in brief.
9. Describe the type of mutation and results due to base substitution. 
10. Describe in  brief about the chemical mutagens.
11. Describe the lac operon system.
12. How is gene regulation promotor work in prokaryotes? illustrate with diagram.
13. What is DNA cloning? Describe restriction enzymes (type II endonuclease).
14. Illustrate with diagram of pUC19 and pBR322 as cloning vector.
15. What are the applications of genetic engineering in biomedical sciences?
16. Describe phenol-chloroform extraction method of DNA isolation.
17. Describe the southern blot hybridization.
18. Describe the steps in PCR.
19. Highlight some gene editing techniques.
    
    

Short Answer Question: (5)

1. Enlist the enzymes involved in the replication of DNA.
2. Describe the proof-reading process of DNA polymerase.
3. Describe tRNA.
4. Draw the structure of adenine and cytosine. 
5. Write a very short note on the human genome. 
6. List the RNA polymerases and their product in Eukaryotes.
7. Differentiate between RNA polymerase and DNA polymerase.
8. Describe briefly inhibitors of transcription and their mode of action in Prokaryotes.
9. What are the genetic codes and their characters?
10. Describe translocation process during protein synthesis.
11. Shine-Dalgarno sequence. 
12. What is base excision repair.
13. TATA binding protein.
14. Inhibitors of DNases.
    
    

BCM 513-I List of Practicals

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List of Practicals (M.Sc. Biotechnology, I-Semester)

1. Preparation of normal, molar, Parts per million (PPM), and percent solutions.
2. Preparation of different buffer solutions and measure their pH.
3. Estimation of given protein concentration by Bradford, Lowry (Folin) protein assay and by Biuret test.
4. Determination of the isoelectric point of casein (of milk).
5. Titration of amino acids and find the physical constants.
6. Qualitative detection of glucose in urine (the Trommer reaction).
7. Quantitative determination of glucose in blood by a glucose-oxidase method.
8. Determination of total cholesterol concentration in serum.
9. Determination of urea concentration in serum and urine.
10. Determination of saponification value of the fat.
11. Qualitative tests for carbohydrates(Iodine test, Benedict’s test, Barfoed’s  test, Seliwanoff’s test, Bial’s test)
12. Separation of amino acids by chromatographic techniques and detection by nin-hydrin test.
13. Separation of lipids by TLC, and detection.

BCM 513-I Biochemistry Model Question

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Model Questions for Biochemistry (M.Sc. Biotechnology, I-Semester)

Long Answer Question: (7.5 × 1 = 7.5) (any one)
1) Explain the biological functions of proteins with examples.
2) Explain the essential amino acids.
3) Explain the Ramachadran plot.

Short Answer Question: (2.5 × 3 = 7.5) (any three)
1) Describe how peptide bond is formed.
2) Draw the structures of non-polar and non-charged aliphatic amino acids.
3) Mention the the enzymes and co-factors involved in hydroxylation of proline and lysine in collagen synthesis.
4) Differentiate between fibrous and globular proteins.
4) Describe the structure of collagen.

Very Short Answer Question: (1 × 5 = 5) (any five)
1) Define denaturation of proteins.
2) Which bonds are flexible for rotation in a dipeptide?
3) Mention the replaced amino acids that leads to sickle cell anaemia.
4) Define the quaternary structure of proteins.
5) What are the major amino acids in collagen?
6) Describe the supersecondary structure of protein.
7) Describe in brief about the structure of haemoglobin.
8) What are chaperones.

Model Questions for Biochemistry-IV

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for M.Sc. Biotechnology
Long Answer Questions        (@7)

1. Describe the regulation of cholesterol synthesis.
2. Describe the terpenoids biosynthesis.
3. Describe the reaction that involves pyridoxal-5-phosphate and explain the mechanism of any one of them.
4. Describe the beta-oxidation of odd-chain fatty acids.
5. Describe the gluconeogenesis pathway and its regulation.
6. Describe the degradation of purine.
7. Describe the biosynthesis of flavonoids.
8. Describe the urea cycle.

Short Answer Questions      (@2)

1. Write a brief note on fate of shikimate in metabolism.
2. Why alkaloids are imporatant?
3. Describe the metabolic role of niacin.
4. Describe the link between TCA and urea cycle.
5. Explain the mechanism of digestion of carbohydrate in brief.
6. What are steroid? Mention their role in metabolism.
7. What are the pharmacological role of coumarin?
8. Write a short note on monoterpenes.
9. Describe allelopathy.
10. Biosynthesis of ribose sugar.

Very Short Answer Questions                             (@1)

1. Write a short note on carbamoyl phosphate synthetase?
2. Enlist some organic reaction mechanisms.
3. Function of biotin.
4. What are saponin?
5. Write a short note on flavanone.
6. Glucocorticosteroid
7. Role of carnitine.
8. PUFA
9. Ascorbic acid
10. Cholecalciferol

Structure, properties and classification of amino acids

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Some key-words are:
Proteins
What is the structure ?
What is the role of Proteins?

1. The function of a protein is intrinsically dependent on its structure.
2. Since its structure is maintained by combinations of chemical interactions which are individually weak and flexible, the environment in which a protein finds itself can affect its structure.
3. Heat and pH affect protein structure.
4. The cell uses factors such as phosphorylation or ligand-binding to affect the structure, and therefore the function, of many proteins

Amino Acid

1. The first discovered Amino Acid was asparagine, in 1806.
2. The last, threonine, 1938.
3. All the amino acids have trivial or common names, in some cases derived from the source from which they were first isolated.
4. Asparagine was first found in asparagus,
5. Glutamate in wheat gluten;
6. Tyrosine was first isolated from cheese (its name is derived from the Greek tyros, “cheese”); and glycine (Greek glykos, “sweet”) was so named because of its sweet taste.

Essential Amino acids: They are not synthesized by the body and must be supplied from the diet. These are; Isoleucine, Leucine, Lysine, Methionine, Phenylanine, Threonine, Tryptophan, Valine, Arginine*, and Histidine*
PVTtim H*A*LL (private team  hall)
*Semi essential amino acid
Rest of the materials are found in pdf file. Please, wait in case of slow internet.

Model Questions for Biochemistry-III

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 Model Questions for Biochemistry (Microbiology) 
1. Explain in brief about lipolysis.
2. Explain the urea cycle.
3. What is the salvage pathway, enlist the steps?
4. Why TCA is said to be amphibolic?
5. What are the ketone bodies? Explain their metabolism.

6. What are enzymes, explain with the classification?
7. Give some examples of the special molecules of the body whose precursor are amino acids.
8. Enlist the enzymes involved in TCA cycle and estimate the number of ATP generation.
9. Describe the stoichiometry for palmitic acid oxidation.
10. What are the differences between fatty acid biosynthesis and breakdown.

11. Derive Michaelis-Menten equation.
12. What are coenzymes and isozymes? Explain in brief with examples.
13. Explain pyruvate dehydrogenase complex.
14. What is the glyoxylate cycle? Show its relationship to the citric acid cycle.
15. Explain the De novo synthesis of Pyrimidine (steps only).

Salivary amylase and starch

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Salivary amylase is a digestive enzyme secreted by the salivary glands, and about 1.7 liters of saliva is produced everyday by a healthy human. It is responsible for breakdown of the polysaccharide “starch” into dextrins (oligosaccharides), maltose (disaccharide) and glucose (monosaccharide) in the mouth.

Starch consists of two types of molecules, “amylose” (20-30%) and “amylopectin” (70-80%) and both are polymers of glucose. Amylose is a linear chain of glucose units that are linked by α-1,4 bonds, whereas amylopectin is a branched molecule in which glucose units are linked by α-1,4 bonds in the straight chain region in addition to α-1,6 bonds at the branching points. The relative proportions of amylose to amylopectin depend on the source of the starch.

Branch of amylopectin

Salivary amylase hydrolyses only the α-1,4 bonds that link glucose units. Therefore, starch and glycogen, which consist of α-1,4 bonds, are hydrolyzed by amylase while. The cellulose consisting of β-1,4 bonds, cannot be hydrolyzed by salivary amylase. The α -amylase constitute a family of endo-amylases that catalyze the initial hydrolysis of starch into shorter oligosaccharides through the cleavage of α-D-(1-4) glycosidic bonds. Neither terminal glucose residues nor α-1,6-linkages can be cleaved by α-amylase.

The conformation of (α-1→4) linkages in amylose, amylopectin causes these polymers to assume coiled helical structures. The iodine ion will be trapped in the coiled helical structures of starch and gives blue color. After digestion of starch by salivary amylase, no more helical structures available, and no color will be produced in addition of iodine. Therefore iodine can be taken as indicator to measure the activity of amylase, and sometimes, to find the inhibitor of amylase.

Nelson DDL, Cox MM (2005) Lehninger Principles of Biochemistry, 5th edition, W.H. Freeman and Co. Publisher, New York, USA, 248-252.

Model Questions for Biochemistry-II

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Model Questions for Biochemistry (Microbiology)

Long Answer Question: (5 × 5 = 25)
1) Explain the biological functions of proteins with examples.
2) Explain the essential amino acids.
3) What is the transamination process? Mention its significance.
4) What are the nucleotides? Explain the biological roles of nucleotides.
5) What are the denaturation and renaturation processes of DNA?

Multiple Choice Question: (1 × 5 = 5) (any five)
1. Marfan's syndrome is thought to be a mutation affecting
A. hemoglobin synthesis                       B. insufficient thyroid production
C. metabolism of homogentisic acid     D. collagen and/or elastin synthesis

2. Protein folding is
A. automatic, mediated by the protein itself
B. mediated by other proteins called chaperones
C. mediated by the ribosomes
D. by the protease enzyme

3. The isoelectric point of an amino acid is defined as the pH
A. where the molecule carries no electric charge
B. where the carboxyl group is uncharged
C. where the amino group is uncharged
D. of maximum electrolytic mobility

4. What is the heaviest of the twenty amino acids?
A. phenylalanine             B. tryptophan
C. tyrosine                       D. histidine

5. D-Alanine and L-Alanine are technically known as
A. polymer                       B. enantiomers
C. epimers                        D. anomers

6. Which of the following pairs of amino acids would carry a negative charge on their side chain at pH 8.0?
A. leucine & glycine              B. asparagine & glutamine
C. histidine & lysine              D. aspartate & glutamate

7. Which of the following amino acid do not fall under the category of essential amino acid?
A. leucine             B. histidine            C. glycine           D. methionine

8. What is the end product of leucine metabolism?
A. acetyl-CoA                            B. pyruvic acid
C. oxaloacetic acid                    D. acetyl carnitine

9. The nitrogen atoms of urea produced in the urea cycle are derived from
A. ammonia                                   B. ammonia and aspartic acid
C. nitrite                                         D. nitrate

10. The products of urea cycle are
A. 1 molecule of urea, 1 molecule of ammonia, 3 molecules of GTP and 1 molecule of fumaric acid
B. 1 molecule of fumaric acid, 1 molecule of urea, 1 molecule of AMP, 2 molecules of ADP
C. 1 molecule of aspartic acid, 1 molecule of ammonia, 1 molecule of fumaric acid, 1 molecule of ATP
D. 1 molecule of urea, 1 molecule of ammonia, 1 molecule of ATP and 1 molecule of fumaric acid

11. Which of the following is used as carbon atom source while producing urea in the urea cycle?
A. arginine                                         B. aspartic acid
C. carbon dioxide                               D. glucose

12. Urea cycle converts
A. ammonia into a less toxic form
B. urea into nitrogen
C. amino acids into ketoacids
D. ketoacids into amino acids

13. The inputs to one cycle of the urea cycle are
A. 1 molecule of aspartic acid, 1 molecule of ammonia, 1 molecule of carbon dioxide, 3 molecules of ATP
B. 1 molecule of urea, 1 molecule of ammonia, 3 molecules of ATP and 1 molecule of fumaric acid
C. 1 molecule of fumaric acid, 1 molecule of urea, 3 molecules of AMP
D. 1 molecule of acetic acid, 1 molecule of urea, 3 molecules of GTP

Model Questions for Biochemistry

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Model Questions for Biochemistry (Biotechnology)

Long Answer Question: (6 × 1 = 6) (any one)
1) Explain the biological functions of proteins with examples.
2) Explain the essential amino acids.

Short Answer Question: (2.5 × 2 = 5) (any two)
1) Describe how peptide bond is formed.
2) Draw the structures of non-polar and non-charged aliphatic amino acids.
3) Mention the the enzymes and co-factors involved in hydroxylation of proline and lysine in collagen synthesis.

Very Short Answer Question: (1 × 4 = 4) (any four)
1) Define denaturation of proteins.
2) Which bonds are flexible for rotation in a dipeptide?
3) Mention the replaced amino acids that leads to sickle cell anemia.
4) Define the quaternary structure of proteins?
5) What are the major amino acids in collagen?
6) What is the Ramachandran Plot?

Multiple Choice Question: (1 × 5 = 5) (any five)

1. Marfan's syndrome is thought to be a mutation affecting
A. hemoglobin synthesis                       B. insufficient thyroid production
C. metabolism of homogentisic acid     D. collagen and/or elastin synthesis

2. Protein folding is
A. automatic, mediated by the protein itself
B. mediated by other proteins called chaperones
C. mediated by the ribosomes
D. by the protease enzyme

3. The isoelectric point of an amino acid is defined as the pH
A. where the molecule carries no electric charge
B. where the carboxyl group is uncharged
C. where the amino group is uncharged
D. of maximum electrolytic mobility

4. What is the heaviest of the twenty amino acids?
A. phenylalanine             B. tryptophan
C. tyrosine                       D. histidine

5. D-Alanine and L-Alanine are technically known as
A. polymer                       B. enantiomers
C. epimers                        D. anomers

6. Which of the following pairs of amino acids would carry a negative charge on their side chain at pH 8.0?
A. leucine & glycine              B. asparagine & glutamine
C. histidine & lysine              D. aspartate & glutamate

7. Which of the following amino acid do not fall under the category of essential amino acid?
A. leucine             B. histidine            C. glycine           D. methionine

Qualitative Detection of Glucose in Urine

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Glucose is not present in urine, in general because in the kidneys, glucose is reabsorbed from the filtrate of glomerulus, across the tubular epithelium of proximal tubule into the bloodstream. Therefore, normal glucose range in urine is 0 mg/dL, or rarely up to 15 mg/dL. If higher than normal levels of glucose (0-15 mg/dL) is found in urine, then it can be suspected as diabetes, pregnancy, or renal glycosuria. Presence of glucose in urine was commonly tested to monitor diabetes in the past. Now, blood tests for glucose is easier than urine test. The glucose urine test may be done when there is suspect of renal glycosuria.

One of the test is based on the basis of character of glucose as it is a reducing carbohydrate because of a free aldehyde group. During the reduction process of Cu(OH)₂ to CuOH by the glucose aldehyde group, and itself is converted into a carboxyl group. CuOH and its degradation product, Cu₂O, are colored compounds. In excess of CuSO₄, the high Cu(OH)₂ content may lead to the formation of black CuO particles. This is called Trommer’s reaction and explained in the following equations;

Trommer's Explannation

Karl Trommer (1806-1879), German chemist first developed this copper reduction test in 1841, and more stable copper sulphate reagent was explained by Hermann von Fehling (1812-1885) in 1850. Even more sensitive copper reagent was described in 1908 by Stanley Benedict (1884-1936). Later, Ames (1945), the research team led by Albert & Helen Free, developed Clinitest tablet, which contained cupric sulfate, sodium hydroxide, and citric acid mixed with a bit of carbonate to make it fizz. Helen M. Free (1923-) and Alfred Free (1913–2000), revolutionized diagnostic urine testing with their invention of a chemically coated paper dipstick that measures a patient’s blood/urine sugar by changing color when dipped in a blood/urine sample.

Determination of protein concentration

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Introduction
Finding the exact quantity of proteins in a solution is very often necessary in the biochemical practice and to analyse clinical samples as well as in research. There are many ways to measure protein concentration. In chromogenic methods, the absorbance of a coloured product formed by the protein and an organic molecule is measured. Protein concentration can also be determined from the protein's own (intrinsic) UV absorbance. However, these methods may give different results for different proteins of the same concentration. Also, different methods can yield somewhat different results for the same protein. Also, dilution factor may be a important parameter.

Text source

There is no absolute photometric protein concentration assay. All methods have advantages and disadvantages and we must choose among them by taking the following aspects into consideration: specificity, sensitivity, the measurable range of concentration, the accuracy, the nature of the protein to be examined, the presence of materials interfering with the measurement, and the time required for the measurement.

Principle
Biuret test
Molecules with two or more peptide bonds react with Cu²⁺ ions in alkaline solution and form a purple complex. Nitrogen atoms of the peptide bonds form a coordination bond with the metal ion. The quantity of the complexes formed is proportional to the number of peptide bonds.

In practice, the determination of protein concentration is done using a calibration curve created using samples of known concentration. The protein treated with biuret reagent is measured at 540 nm after the purple product is formed.

The advantages of the method include that only few materials (e.g. Tris and amino acid buffers) interfere with it, it can be done in a short time and does not depend on the amino acid composition of the protein. Its disadvantages are its low sensitivity and that it requires at least 1 mg of protein.

Lowry (Folin) protein assay
This is sensitive technique where a coloured product is formed similarly to the biuret reaction, but a reagent strengthen the colour, which is kown as Folin–Ciocalteu reagent (a mixture of phosphotungstic acid and phosphomolybdic acid in the Folin–Ciocalteu reaction). The reaction mechanism is not well understood, but involves reduction of the Folin–Ciocalteu reagent and oxidation of aromatic residues (mainly tryptophan, also tyrosine). The strong blue colour is created by two reactions: (1) formation of the coordination bond between peptide bond nitrogens and a copper ion and (2) reduction of the Folin-Ciocalteu reagent by tyrosine (phosphomolybdic and phosphotungstic acid of the reagent react with phenol). The measurement is carried out at 750 nm.

As in the biuret reaction, a calibration curve is created (for example using BSA, bovine serum albumin), and the concentration of the unknown protein is determined from the curve.

The advantages of the method include that it is quite sensitive and is able to detect even 1 µg of protein. Its disadvantages are that it takes rather long to carry out, is disturbed by various materials (including ammonium sulphate, glycine and mercaptans) and that the incubation time is critical. As different proteins contain different amounts of tyrosine, the amount of the coloured product will also be different. As a consequence, this method is more suited to compare the concentration of solutions of the same protein than to absolute measurement.
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List of Experiments for Biochemistry Laboratory work

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                        List of Experiments for Laboratory work
Course Title: Laboratory work I: Biochemistry (Microbiology)
Credit: 1                                                                                                                                  

1. Preparation of normal, molar and percent solutions.
2. Preparation of different buffer solutions and measure their pH.
3. Determination of the isoelectric point of casein (of milk).
4. Titration of amino acids and find the physical constants.
5. Study the effects of temperature and pH on the enzymatic activity of salivary amylase.
6. Estimation of given protein concentration by Bradford, Lowry (Folin) protein assay and by Biuret test.
7. Qualitative detection of glucose in urine (the Trommer reaction).
8. Quantitative determination of glucose in blood by a glucose-oxidase method.
9. The determination of activity of the Krebs cycle dehydrogenases in the liver.
10. Determination of total cholesterol concentration in serum.
11. Determination of urea concentration in serum and urine.
12. Quantitative determination of phospholipids concentration in serum.
13. Determination of saponification value of the fat.
14. Separation of amino acids by chromatographic techniques and detection by nin-hydrin test.