USC Biochemistry

Questions

2009-07-29T10:45:00.000+05:30

1. Phosphorylation of glucose by hexokinase does not contribute to:-

a) Escaping of glucose molecule out of cell.

b) Binding energy of phosphohexose isomerase.

c) Activation of glucose molecule.

d) Net negative free energy change.

2. Inhibition of Triose phosphate isomerase results in net formation of how many ATP from 1 molecule of glucose in glycol sis:

a) 4 b) 2 c) 0 d) 1

3. During glycolysis, 1 molecule of glucose yield how many molecules of H₂O:

a) 1 b) 2 c) 4 d) 0

4. During vigorous exercise, inhibition of lactate dehydrogenase in muscle does not result in:

a) High [NAD⁺] level b) lowering of pH

[NADH]

c) Inhibition of glycoysis d) shifting of equilibrium of bicarbonate buffer toward left

5. How many steps of glycolysis are endergonic in nature:-

a) 4 b) 6 c) 3 d) 2

6. The methyl group of pyruvate is formed from which carbon of glucose

a) 1 and 6 b) 2 and 5 c) 3 and 4 d) 2 and 4

7. If all the oxygen atoms of glucose were radioactively labeled, how many oxygen atom of pyruvat would be radioactive.

a) 3 b) 2 c) 1 d) None

8. Decyclization occurs in which step of glycolysis.

a) 5 b) 4 c) 3 d) 6

9. The phosphate group of glucose – 6 – phosphate is used in substrate level phosphorylation in step no. :

a) 7 b) 6 c) 10 d) 9

10. Which carbon of glucose occur in reduced state in pyruvate

a) 1 and 6 b) 2 and 5 c) 3 d) 4

11. Mannose enters glycolysis after it is converted to:

a) glycose – 6 – phosphate b) Fructose – 6 – phosphate

c) Fructose 1, 6 bisphosphate d) glucose – 1 – phosphate

12. UMP donor during conversion of galactose 1 – phosphate to UDP – glactose is

a) UTP b) UDP c) UDP – glucose d) UDP – mannose

13. No. of NADH consumed during conversion of 1 molecule of galactose to 2 molecule of pyruvate

a) 2 b) 1 c) 0 d) 3

14. Production of ethanol is inhibited by:

a) High [NADH] ratio b) presence of Mg²⁺

[NAD ⁺]

c) High CO₂ level d) presence of O₂

15. Which carbon of glucose is released as CO₂ during ethanol production?

a) 4 and 3 b) 1 and 6 c) 2 and 5 d) 3 and 5

16. Which enzymes doesn’t require Thiamine pyrophosphate

a) Pyruvate dehydcogenase b) pyruvate decarboxylase

c) Transketolase d) Succinate dehydrogenase

17. No. of ATP equivalents used in formation of 1 molecule of glucose from 2 molecule of pyruvate is

a) 4 b) 5 c) 6 d) 8

18. the most exergonic step during gluconeogenesis is

a) 1^st b) 2^nd c) 5^th d) 9^th

19. After 3 molecules of glucose – 6 – phosphate enter pentose phosphate pathway, how many molecules of CO₂ is liberated

a) 6 b) 3 c) 0 d) None

20. Defect in pentose phosphate pathway causes:-

a) Bromolecules damage by superoxide radical b) Reduced nucleotide, RNA, DNA brosynthesis

c) Both a & b d) Only a

21. Transketolase transfer how many carbon

a) 1 b) 2 c) 3 d) 4

22. Transaldolase transfer how many carbon

a) 1 b) 2 c) 3 d) 4

23. Which ractive species causes maximum damage to biomolecules

a) O₂ b) H₂O₂ c) OH^- d) OH

24. How many net ATP is used in converting glucose to pyruvate and pyruvate black to glucose.

a) 2 b) 4 c) 6 d) 8

25. Significance of lactate formation is/are

a) Prevent halting of glycolysis b) provede substrate for gluconeogenesis in liver

c) Increase [NAD⁺] ratio d) All

[NADH]

26. The final catabolic product of glucose in RBC is:

a) CO2 & H2O b) Pyruvate & lactafe c) Both a & b

27. The energy yielding pathway in RBC is

a) TCA cycle b) glycolysis c) both a & b d) pentose phosphate pathway

28. In cancerous cell much of ATP is formed by

a) TCA cycle b) glycolysis c) electron transport change d) Both a & b

29. The reactive intermediate in thiamine pyrophosphate catalysed reaction is

a) Carbocation b) Carbanion c) free radical d) All

30. In anaerobic process, there is …………………………………..of the carbons of glucose.

a) net oxidation b) net reduction c) no net oxidation or reduction

31. (α 1 → 6) glucosidase activity of debranching enzyme produce

a) glucose 1 – phosphate b) glucose – 6 – phosphate c) glucose d) glucose 1, 6 bisphosphate

32. The active residue in the phosphoglucomutase enzyme that catalyse the reaction is

a) Serine b) Threonine c) phosphorylated serine d) phosphorylated threonine

33. Glucose transporter in liver is

a) GLUT 4 b) GLUT 2 c) GLUT 1 d) All

34. Inhibition of Pi (inorganic phosphate) transporter at Endoplasmic reticulum of liver cell results in

a) Decrease level of glucose transport from liver to blood.

b) Lowers ATP concentration in liver cytosol

c) Decrease the activity of glyceraldehye 3 – phosphate dehydrogenase enzyme.

d) All

35. Glucose – 6 – phosphatase of liver is located at

a) cell membrane b) Mitochondrial inner membrane

c) cytosol d) membrane of endoplasmic reticulum

36. Which amino acid catalyse the initial attack reaction in glucogenin

a) Serine b) Threonine c) Tryptophan d) Tyrosine

37. The predominant hexokinase in liver in liver is

a) Hexokinase I b) Hexokinase II c) Hexokinase III d) Hexokinase IV

38. Which of the hexkinase have high Km value

a) Hexokinase I b) Hexokinase II c) Hexokinase III d) Hexokinase IV

39. Activity of hexokinase IV is inhibited by

a) glucose – 6 – phosphate b) glucose 1 – phosphate c) fructose – 6 phosphate d) All

40. Km of phosphofructose kinase I………………………….at high [ATP] ratio.

[ADP]

a) Increases b) Decreases d) Remain same

41. Inactivation of pyrucate kinase by phosphorylation in liver occurs when

a) Blood glucose level is high b) Glucoagon level in blood is high

c) Pyruvate level is high in cytosol d) All

42. Which of the following isn’t allosteric inhibitor of muscle pyruvate kinase?

a) Pyruvate b) Alanine c) ATP d) Acetyl coA

43. Fructose 2, 6 Bisphosphate lowers the Km value of which enzyme

a) phosphofructose kinase I b) Fructose 1, 6 bisphosphatase

c) Fructose 2, 6 bisphosphatase d) Phsphofructose kinase - 2

44. Fructose 2, 6 bisphosphate is formed when

a) Insulin level is high b) Glucose level in blood is low

c) Energy demand in liver cell is low d) TCA cycle intermediate don’t participate in biosynthesis reaction

45. Which of the following isn’t covalently attached with enzyme

a) FAD b) NAD⁺ c) lipoate d) Thiamin pyrophosphate

46. Which carbons of glucose are released as CO₂ when pyruvate is converted to Acetyl CoA.

a) 1 and 6 b)5 and 2 c) 4 and 3 d) 2 and 4

47. Avidin a protein in raw egg binds biotin and inhibits its absorption. Which enzyme activity may be inhibited when Avidin is intake?

a) pyruvate dehydroginase b) pyruvate carboxylase c) succinate dehydrogenase d) All

48. Pyruvate dehydrogenase complex is present in

a) cell membrane b) cytosol c) Mitochondria d) Endoplasmic reticulum

49. Lipoate is attached to with amino acid residue of Dihyropoyl transacetylase

a) His b) Lys c) phe d) Ser

50. No. of total electrons released when 1 molecule of glucose is converted to 2 molecule of Acetyl Coa

a) 2 b) 4 c) 8 d) 10

PHOTOSYNTHESIS REVIEW QUESTIONS FOR BIOLOGY

2009-07-24T08:16:00.001+05:30

1. What is the primary function of photosynthesis?

2. (a) Name a gas released as by-product of the light dependent reactions of photosynthesis. (B) Name the molecule that is the source of this gas. (C) Why is oxygen removed from the molecule named in 2B?

3-4. Name two molecules that are produced during the light dependent reactions of photosynthesis and serve as temporary sites for energy storage.

5. When a molecule loses an electron, the molecule has been _?_ (oxidized or reduced or destroyed)

6. When a molecule gains an electron, the molecule has _?_ (gained energy or lost energy)

7. (A) True or False All electrons contain the same amount of energy. (B) If this statement were true, could life (at least as we know it) exist? Why?

8. When chlorophyll P680 absorbs sunlight, what subatomic particle actually has a change in energy content? (electron or proton or neutron)

9. When chlorophyll P680 loses an electron, from what atom does the chlorophyll receive an electron?

10. When chlorophyll P680 loses an electron, from what molecule does the chlorophyll receive an electron?

11. Which contains more energy: one molecule of NADP or one molecule of NADP-H ?

12. What is the name of the three carbon molecule that is a product of the Calvin cycle (= “dark” reactions)?

13. Name the molecule that is taken from the air and that provides the carbon for the production of carbohydrates during the Calvin cycle.

14. Which has the most energy: one photon of green light, one photon of red light, or one photon of blue light ?

15. Chlorophyll is green because it _?_ (absorbs, reflects, or transmits) green wave lengths of light.

16. In eukaryotic cells, photosynthesis occurs in organelles named _?_

17. How many molecules of carbon dioxide must enter the Calvin cycle in order for the plant to produce a sugar containing 24 carbon atoms?

18. The term phosphorylation means:

19. True or False The Calvin cycle (= light-independent reactions) can occur in a plant that is in dark room so long as the materials carbon dioxide, ATP, and NADP-H are present.

20. Which contains more energy: three molecules of carbon dioxide or one molecule of phosphoglyceraldehyde (= PGAL) ?

21. "Packets" or "particles" of light are called ?

22. What would happen to humans and most other living organisms on Planet Earth if photosynthesis stopped?

23. What is the range of wavelengths of light that are visible to humans?

24. What is the wavelength of UV light? infrared?

25. Which has more energy, short wave lengths of electro-magnetic radiation or long wave lengths of electro-magnetic radiation?

26. Summarize, in one sentence, what happens during the light dependent reactions of photosynthesis.

27. Summarize, in one sentence, what happens during the light independent reactions of photosynthesis.

28. What happens to an electron in an atom if the electron gains energy? loses energy?

29. What happens to an electron in chlorophyll in Photosystem II when the electron absorbs light energy?

30. High energy electrons in Photosystem I are used to manufacture molecules of ?

31. High energy electrons in Photosystem II are used to manufacture molecules of ?

ANSWERS

1. The primary function of photosynthesis is to capture light energy, convert some of this light energy into chemical energy, and store this chemical energy in molecules of carbohydrates (such as phosphoglyceraldehyde, glucose, or starch).

2. (A) Oxygen is released as a by-product (= “waste material”) of photosynthesis. (B) The oxygen atoms are removed from water as the water is broken down during the light reactions. (C) Water is broken down to provide hydrogen atoms (which, in turn, provide electrons to replace electrons that are lost from chlorophyll P680). At this point, oxygen is of no value to the system and, consequently, is released from the chloroplast and from the leaf into the surrounding air.

3-4. Two high-energy molecules that are produced during the light reactions are adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADP-H). These two molecules temporarily store energy; they transfer energy into carbohydrates being produced during the light independent reactions (= Calvin cycle). The carbohydrates (PGAL, glucose, starch) can store energy for much longer periods of time.

5. When a molecule loses an electron, the molecule has been oxidized.

6. When a molecule gains an electron, the molecule has been reduced (and has gained energy that the electron brought.)

7. (A) False. Electrons vary tremendously in the amount of energy they contain. In this class, we typically do not use numbers or units to describe the energy levels of electrons. Instead, we simply refer to the electrons as being “low energy” or “high energy.” (B) If all electrons contained the same amount of energy (and could not gain or lose energy) life could not occur because living organisms must have energy available and this energy is captured and released primarily from electrons (in the reactions of photosynthesis and respiration.)

8. When chlorophyll P680 absorbs energy, an electron gains the energy. (Actually a series of electrons, one after the other, gains energy; however, if you understand what happens to one electron, then you understand what happens to each of the millions of other electrons in this series.)

9-10. When chlorophyll P680 loses an electron, the P680 molecule replaces this electron with an electron taken from an atom of hydrogen which has come out of a molecule of water. (Review: a hydrogen atom consists of one proton and one electron. If the electron is removed, only the proton remains. The proton will be used later, in Photosystem I, to join with an electron that is picked up by NADP. The result is the formation of NADP-H, one of products of the light-dependent reactions.)

11. A molecule of NADP-H contains more energy than a molecule of NADP. The NADP picks up a high-energy electron and combines the electron with a proton to form the hydrogen atom that is the “H” of the NADP-H. Compare NADP to an empty Wells Fargo armored delivery truck while NADP-H is the Wells Fargo truck loaded with money (or, in the case of NADP-H, loaded with energy).

12. The name of the 3-carbon product of the Calvin cycle is phosphoglyceraldehyde (which is also called glyceraldehyde phosphate) and is commonly symbolized as PGAL.

13. Carbon dioxide, in the form of a gas, is removed from the environment of a plant (either from the surrounding air or water, depending on whether the plant lives in air or submerged in water), taken into leaves and chloroplasts, and used as a carbon source during the manufacture of carbohydrates (such as PGAL, glucose, and starch) in the Calvin cycle.

14. The shortest wavelengths (such as violet) have more energy than do the longer wavelengths of light such as red. Of the three colors of light listed here (blue, green, red), blue has the shortest wavelength and, consequently, the most energy. If we compare the wavelengths longer than light (such as radio waves) with wavelengths shorter than light (such as X-rays), the differences in energy level are easier to appreciate. X-rays (short wavelengths with high energy levels) are dangerous to living cells because the X-rays can damage DNA in the chromosomes. Conversely, the long wavelengths of radio waves (with their low energy levels) are apparently harmless to cells.

15. Chlorophyll is green because it reflects green wavelengths of light and these are what we see.

16. Photosynthesis occurs in cell parts called chloroplasts that occur primarily in plant cells that are exposed to light. (Would the root cells of a plant be able to use chloroplasts?)

17. For each carbon atom that is released from the Calvin cycle in a high-energy carbohydrate molecule, one carbon dioxide molecule must enter the cycle. To produce one molecule of PGAL (which contains 3 carbon atoms), 3 molecules of carbon dioxide must enter the cycle; to produce one molecule of glucose (with 6 carbon atoms), 6 molecules of carbon dioxide must enter the cycle; to produce a molecule containing 24 carbon atoms, 24 molecules of carbon dioxide must enter the cycle.

18. The term phosphorylation refers to the addition of a phosphate group to an atom or molecule. The addition of the phosphate involves the addition of large amounts of energy. This energy may come from light (as in the light reactions of photosynthesis) or from the breakdown of sugars (as in cellular respiration).

19. True. The Calvin cycle requires the input of carbon dioxide (as a source of carbon for building carbohydrates) and the availability of ATP and NADP-H to provide energy to reduce the carbon dioxides and construct high-energy carbohydrates. If these materials (carbon dioxide, ATP, and NADP-H) are available, the Calvin cycle can occur, even in darkness. Normally, however, what would happen to the quantities of ATP and NADP-H shortly after the plant is placed in darkness? (The light dependent reactions would shut down and no more ATP and NADP-H would be produced. When the available supplies of ATP and NADP-H are used up, the Calvin cycle would stop.)

20. One molecule of phosphoglyceraldehyde (= PGAL) contains more energy than three molecules of carbon dioxide. During the Calvin cycle (the light independent reactions) the low energy carbon atoms in carbon dioxide are reduced (i.e., they gain energy from ATP and NADP-H).

21. Packets or “bundles” of light energy are called photons.

22. If photosynthesis stopped, most living organisms on Planet Earth, including humans, would die due either (A) to a shortage of energy because no food molecules would be available or (B) to a shortage of oxygen for cellular respiration.

23. The wavelengths of light that are visible to humans range from approximately 400 nanometers (violet) to 700 nanometers (red). Some animals can see additional wavelengths. For example, some insects can see ultraviolet light.

24. Ultraviolet light (= UV light) has a shorter wavelength than violet (which has a wavelength of about 400 nanometers; infrared has a longer wavelength than red (which has a wavelength of about 700 nanometers).

25. The shorter wavelengths have more energy; therefore, UV light has more energy per photon than does infrared. One consequence of this is that the shorter wavelengths are more likely to be dangerous to living cells.

26. Light energy is absorbed by electrons that supply energy for the formation of molecules of ATP and NADP-H which are used as temporary energy storing molecules.

27. Molecules of carbon dioxide enter the Calvin cycle where the carbons are reduced by acquiring energy from ATP and NADP-H (from the light dependent reactions) and high energy molecules of PGAL are constructed.

28. If an electron gains energy it moves to an outer shell; if the electron gains enough energy, the electron may be driven out of the atom.

If an electron loses energy it moves to an inner shell (i.e., closer to the nucleus of the atom).

29. The electron gains so much energy (by absorbing photons) that the electron leaves the chlorophyll molecule. The electron is now described as a “high-energy electron” and can provide energy for the formation of molecules of ATP.

30. High energy electrons in Photosystem I are used to manufacture molecules of NADP-H.

31. High energy electrons in Photosystem II are used to manufacture molecules of ATP.

Photosynthesis

2009-07-15T11:00:00.000+05:30

1. Excitation of P700

a) greatly reduces its reduction potential c)greatly increases its reduction potential

b) has no effect on the reduction potential d)has effects on oxidation potential only.

2. The energy required to excite PSI is

a) less than that needed to excite PSII c) more than that needed to excite PSII

b) equal to that needed to excite PSII d) it can’t be told

3. Cytochrome b₆f complex is present:

a) in the grand lamellae c) in the stromal lamellae

b) throughout the thyllakoid membrane d) exclusively in stroma

4. Which of the following is not “one electron carrier”?

a) Cytochrome b) Fe-S protein c) Quinone d) None

5. During light reaction, the direction of proton flow is from

a) Stroma to thyllakoid membrane c)Thyllakoid membrane to stroma

b) Stroma to out of chloroplast d) Lamellae to lumen

6. During cyclic electron flow which of the following is produced?

a) ATP b) NADH c) NADPH d)O_{2 e)}all

7. No. of photons required to evolve O2during oxygenic photosynthesis is

a) 4 b) 6 c) 8 d) 10

8. Which of the following is a soluble-Cu containing electron transfer protein?

a) Cytochrome b) Pheophytin c) Plastoquinone d) Plastocyanin

9. Plastocyanin is present on which side?

a) Stroma b) Lumen c) Lamellae d) All

10. During the electron flow from Cytochrome b₆f to plastocyanine which side has maximum protons?

a) Stroma b) Lumen c) Lamellae d) Grana

11. Cytochrome c₆in Cyanobacteria is homologous to

a) Mitochondrial cytochrome c b) Plastocyanin as in plants

c) Mitochondrial cytochrome bc₁ d) a & b e) a,b & c

12. How does ATP synthesized in chloroplasts get into the cytosol?
A. It is transported as sucrose.
B. It is transported directly by a membrane transporter.
C. It is transported as triose phosphate.
D. It is transported as inorganic phosphate (P_i).

13. The net outcome of light reaction in green plant is:

a)3ATP & 3NADPH b)2NADPH & 2ATP c)3ATP & 2NADPH d)2ATP & 3 NADPH

14. The large and small subunits of Rubisco are encoded respectively in the

a) Chloroplast and nuclear genome b) nuclear and chlorophyll genome

c) both in nuclear genome d) Bone in chlorophyll genome

15. Chlorophyll contains all glycolytic enzymes except

a) Phosphoglycerate mutase b) Phosphoglycerate isomerase c) Triose –P- mutase d) Triose – P – isomerase

16. Glycine decarboxylase is present at very high levels in mitochondria of:-

a) C₄plants b) CAM plants c) C₃ plants d) None

17. 11. Which of the following reactions is catalyzed by transketolase?
A. glyceraldehyde 3-phosphate + dihydroxyacetone phosphate fructose 1,6-bisphosphate
B. ribose 5-phosphate ribulose 5-phosphate
C. ribulose 5-phosphate ribulose 1,5-bisphosphate
D. fructose 6-phosphate + glyceraldehyde 3-phosphate erythrose 4-phosphate + xylulose 5-phosphate

18. CO₂ fixed by mesophyll cells gets transported to neighboring bundle-sheath cells by
A. the movement of oxaloacetate that diffuses between the neighboring cell membranes.
B. the movement of oxaloacetate that passes through channels that connect the cells.
C. the movement of malate that passes through channels that connect the cells.
D. the movement of pyruvate that passes through channels that connect the cells.

19. “Nocturnal inhibitor” 2-carboxyarabinitol1-phosphate is a structural analog of

a) Ribulose 1,5-bisphosphate b) Enediolate intermediate

c) Beta ketoacid intermediate d) Hydrated intermediate.

20. Central to the rubisco activity is the carbamoylated ____ residue

a) Lys201 b) lys 175 c) His 294 d) Leu 101.

21. Which of the following represents the sequence of electron flow in the light reactions of photosynthesis in higher plants?

(A) H2O → photosystem I → photosystem II → NADP

(B) H2O → photosystem II → photosystem I → NADP

(D) NADPH → photosystem I → photosystem II → O2

(E) Photosystem I → photosystem II → NADPH → O₂

Enzyme kinetics

2009-07-06T13:26:00.000+05:30

A catalyst alters the rate of a chemical reaction by:

A) always providing a surface on which molecules react

B) changing the products formed in the reaction

C) inducing an alternate pathway for the reaction with generallylower activation energy

D) changing the frequency of collisions between molecules

ANSWER: C

Choose the INCORRECT answer. The rate of a chemical reaction:

A) usually is increased when the concentration of one of the reactants is increased

B) is dependent on temperature

C) may be inhibited sometimes by certain catalytic agents

D) will be very rapid if the activation energy is large

ANSWER: D

If a reaction is first order with a rate constant of 5.48 x 10^-2 sec^-1, how long is required for 3/4 of the initial concentration of reactant to be used up?

A) 25.3 sec

B) 36.5 sec

C) 6.3 sec

D) 18.2 sec

E) none of these

ANSWER: A

The rate constant at 160 ^oC for the first order decomposition of ore is 0.032/min. The half-life of the reaction is:

A) 62.5 sec

B) 31.25 sec

C) 5000 sec

D) 111 sec

E) none of these

ANSWER: E

A reaction is first order. If its initial rate is 0.0200 M/sec and 25.0 days later its reaction is 6.25 x 10^-4 m/sec, then its half-life is:

A) 12.5 days

B) 5.0 days

C) 25.0 days

D) 50.0 days

E) none of these

ANSWER: B

For 2NO + O₂ --> 2NO₂ , initial rate data are:

[NO]	0.010	0.010	0.030 M
[O₂ ]	0.010	0.020	0.020 M
rate	2.5	5.0	45.0 mM/sec

The rate law is Rate = k[O₂ ]^y and

A) x = 1 y = 2

B) x = 2 y = 1

C) x = 1 y = 1

D) x = 2 y = 2

E) none of these

ANSWER: B

A and B are mixed and the reaction is timed until a color change occurs. The data are:

[A]	0.100	0.050	0.100M
[B]	0.140	0.140	0.070M
time	25 sec	50 sec	100 sec

The order of the reaction in terms of [A] is:

A) second

B) half

C) zero

D) first

E) none of these

ANSWER: D

For the reaction 2HgCl₂ + C₂O₄^2- --> products, data are:

[HgCl₂], M	0.0836	0.0836	0.0418
[C₂O₄^2- ] ,M	0.202	0.404	0.404
Init. rate, M/hr	0.26	1.04	0.53

The rate law is Rate = [HgCl ]^x [C₂O₄^2-]^y. Thus

A) x = 2 y = 1

B) x = 2 y = 2

C) x = 1 y = 2

D) x = 1 y = 1

E) none of these

ANSWER: C

The correct units of the specific rate constant for a zero order reaction are:

A) L/mol-sec

B) sec^-1

C) sec

D) L² /mol² ^.sec

E) none of these

ANSWER: E

If the half-life of a reaction depends on the concentration of the reactant, then the reaction cannot be __________ order.

A) second

B) zero

C) first

D) third

E) none of these

ANSWER: C

The reaction has the rate law Rate = k[A][B]². Which will cause the rate to increase the most?

A) doubling [A]

B) lowering temperature

C) tripling [B]

D) quadrupling [A]

E) doubling [B]

ANSWER: C

The reaction 2 H₂ + NO ---> H₂O + 1/2 N₂ is first order in H₂ and second order in NO. The rate law is:

A) k[H₂]² [NO]

B) k[H₂][NO]²

C) k[H₂]

D) k[H₂][NO]

E) none of these

ANSWER: B

For a reaction Rate = k[A][B]², what factor will NOT change k?

A) raising temperature

B) adding inhibitor

C) increasing [A]

D) adding catalyst

E) none of these

ANSWER: C

A variable that has NO EFFECT on reaction rate is:

A) energy of activation

B) temperature

C) catalyst

D) concentration

E) none of these

ANSWER: E

What is the main difference between a Pt catalyst and an enzyme catalyst?

ANSWER: enzyme has greater substrate specificity

What is the order of reaction for the following reaction. Rate = k[A]^-1/2[B]^1/2 ?

ANSWER: zero order overall

Substance A decomposes by a first-order reaction. Starting initially with [A] = 2.00 M, after 150 min [A] = 0.50 M. For this reaction what is t_1/2 ?

ANSWER: 75.0 min

For the above reaction, what is k?

ANSWER: 9.24 x 10^-3 min^-1

-------------------------------------

In the first order reaction A ---> products, [A] = 0.400 M initially and 0.250 M after 15.0 min.

What is the value of the rate constant, k?

ANSWER: 0.034 min^-1

What is the half-life of the reaction?

ANSWER: 20.4 min

At what time will [A] = 0.200 M?

ANSWER: 20.4 min

What will [A] be after 175 min.?

ANSWER: 1.04 x 10^-3 M

-------------------

The reaction A + B --> C + D is second order in A and zero order in B. The value of k is 0.012 M^-1 min^-1 . What is the rate of this reaction when [A] = 0.125 M and [B] = 0.435 M?

ANSWER: 1.88 x 10^-4 M min^-1

Which of the following statements is true about the reaction 2A --->B + C which is first order in A and first order overall:

A) The rate of the reaction will decrease at higher concentrations of B and C.

B) The time required for one half of A to react is directly proportional to the quantity of A.

C) The rate of formation of C is twice the rate of reaction of A.

D) The rate of formation of B is the same as the rate of reaction of A.

E) none of these

ANSWER: E

A catalyst

A) takes part in a reaction and speeds it up

B) appears in the rate equation of a chemical reaction

C) provides an alternate reaction pathway

D) raises the activation energy of a reaction

E) none of the above

ANSWER: C

Define heterogeneous catalysis.

ANSWER: The catalyst is present in a different phase of matter than are the reactants and products.

The rate of a specific chemical reaction is independent of the

concentrations of the reactants. Thus the reaction is

A) first order

B) second order

C) exothermic

D) catalyzed

E) none of these

ANSWER: E

Which of the following does not determine the rate of a reaction?

A) value of DELTA H⁰

B) activation energy

C) presence of a catalyst

D) temperature of reactants

E) none of these

ANSWER: A

Which of the following lowers the activation energy of a reaction?

A) adding reactants

B) lowering the temperature

C) removing products

D) adding a catalyst

E) raising the temperature

ANSWER: D

If a reaction has a rate equation of rate = k[A][B][C] then it is

A) second order

B) first order

C) third order

D) zero order

E) cannot be determined

ANSWER: C

The first-order reaction A --> Products has a half-life, t_1/2, of 55.0 min at 25 ^oC and 6.8 min at 100 ^oC. What is the activation energy for this reaction?

ANSWER: 25.8 kJ/mol

Which of the following statements is CORRECT

A) A zero order reaction depends on the concentration ofreactants.

B) A reaction rate cannot be calculated from the collision frequency alone.

C) A commonly stated rule of thumb is that reaction rates triple for a temperature increase of about 10 ^oC.

D) none of these

ANSWER: B

The first order reaction A---> products has t_1/2 = 150 sec. What percent of the sample remains unreacted after 300 sec?

ANSWER: 25%

Define rate law.

ANSWER: An experimentally determined equation that describes how the rate of reaction depends on the concentration of reactants

Define activation energy.

ANSWER: The minimum total kinetic energy that molecules must bring to their collisions for a chemical reaction to occur.

The rate constant for a first-order reaction is k = 0.00073 s^-1.

Determine the percent of reactant that has decomposed after 500 s.

ANSWER: 30.6%

---------------

For the reaction A---> products, the following data are obtained:

First Experiment		Second Experiment
[A] = 1.512 M	t = 0 min	[A] = 3.024 M	t = 0 min
[A] = 1.490 M	t = 1.0 min	[A] = 2.935 M	t = 1.0 min
[A] = 1.469 M	t = 2.0 min	[A] = 2.852 M	t = 2.0 min

Determine the order of the above reaction.

ANSWER: second order

What is the rate constant, k?

ANSWER: 9.62 x 10^-3 mol^-1 min^-1

What is the concentration of [A] in the first experiment after 4.0 min?

ANSWER: 1.429 M

What is the initial rate of the reaction in each experiment?

ANSWER: First experiment = 0.022 mol/min Second experiment = 0.089 mol/min

sources: http://itl.chem.ufl.edu/2041_f97/kinetics_quiz.html

question for oxidative phosphorylation

2009-07-06T13:01:00.000+05:30

1. Which of the following is true about the difference between oxidative phosphorylation and photophosphorylation?
A. Photophosphorylation occurs only in photosynthetic organisms and oxidative phosphorylation occurs only in non-photosynthetic organisms.
B. In oxidative phosphorylation, NADH donates electrons; in photophosphorylation NADPH donates electrons.
C. Photophosphorylation occurs only in light; oxidative phosphorylation occurs only in darkness.
D. In oxidative phosphorylation, O2 is reduced to H2O; in photophosphorylation, H2O is oxidized to O2.

2. Which of the following processes takes place in the mitochondrial matrix?
A. cellular respiration
B. glycolysis
C. fatty acid oxidation
D. photosynthesis

3. Which of the following is true about the expression of mitochondrial genes?
A. Mitochondria encode all of the proteins needed to make new mitochondria.
B. Mitochondria can translate their own genes.
C. Mitochondria import all of their proteins from the cytoplasm.
D. Mitochondrially-encoded genes are expressed in the cytoplasm.

4. Diseases caused by mutations in mitochondrial genes are invariably inherited from the mother because
A. mitochondrial genes are encoded on the X chromosome.
B. males do not have mitochondrial DNA.
C. all of the mitochondria of a developing embryo are derived from the mother's egg.
D. mitochondrial genes of males are turned off.

5. How do mitochondria eliminate the harmful superoxide free radical ·O2- that is generated with low frequency during oxidative phosphorylation?
A. Glutathione reductase reduces ·O2- to H2O.
B. Superoxide dismutase converts ·O2- to H2O2.
C. Glutathione peroxidase converts ·O2- to O2.
D. ·O2- is transported out of mitochondria.

6. Which of the following processes yields the greatest number of ATP molecules when a molecule of glucose is completely oxidized?
A. lactate fermentation
B. pyruvate oxidation
C. glycolysis
D. the citric acid cycle

7. How does thermogenin keep newborn mammals warm?
A. It makes oxidative phosphorylation more efficient.
B. It causes the transfer of electrons from ubiquinone directly to oxygen.
C. It uncouples electron transport from ATP synthesis.
D. It stimulates the accumulation of brown fat.

8. The light-dependent and carbon-assimilation reactions of photosynthesis are linked in that
A. the light-dependent reactions generate the chemical energy needed for carbon-assimilation.
B. the oxidation of carbohydrates from the carbon-assimilation reactions drives the synthesis of ATP in the light-dependent reactions.
C. carbon dioxide generated in the light-driven reactions is converted to triose phosphates in the carbon-assimilation reactions.
D. NADPH generated in the carbon-assimilation reactions drives the synthesis of ATP in the light-dependent reactions.

9. In which part of the chloroplast do the light-dependent reactions of photosynthesis take place?
A. in the thylakoid lumen
B. in the thylakoid membrane
C. in the stroma
D. in the inner membrane

10. What is the role of antenna molecules in photosynthesis?
A. to donate their electrons for use in oxidation-reduction reactions
B. to release absorbed energy as fluorescence
C. to transmit light energy to reaction centers
D. to transduce light energy into chemical energy

11. The F0 complex of mitochondrial ATP synthase
A. is inhibited by oligomycin.
B. synthesizes ATP.
C. pumps protons into the mitochondrial matrix.
D. is a peripheral membrane protein.

12. Which complex of the respiratory chain is inhibited by cyanide?
A. Complex IV
B. ATP synthase
C. Complex I
D. Complex III

13. How will oxidative phosphorylation be affected by placing intact mitochondria in a weak acid that can readily diffuse across the mitochondrial membranes?
A. Electron transfer reactions will be inhibited.
B. No H2O will be generated.
C. ATP will be able to be synthesized in the absence of an oxidizable substrate.
D. ATP synthesis will be inhibited.

14. Complexes I and II of the mitochondrial respiratory chain
A. have heme prosthetic groups.
B. transfer electrons directly to ubiquinone.
C. pump protons from the matrix to the intermembrane space.
D. transfer electrons from NADH.

15. How does NADH generated by glycolysis in the cytosol get conveyed into mitochondria for oxidation in the respiratory chain?
A. It diffuses through the inner mitochondrial membrane.
B. Its reducing equivalents are transported across the inner mitochondrial membrane.
C. It is transported across the inner mitochondrial membrane as aspartate.
D. It is transported directly across the inner mitochondrial membrane by an NADH transporter.

sources: http://bcs.whfreeman.com/lehninger/pages/bcs-main.asp?v=chapter&i=19070.01&s=19000&n=00070&o=|00510|00520|0

Lehninger Principles of Biochemistry

questions for amino acids and nucleotide biosynthesis

2009-07-01T13:15:00.001+05:30

1. Which chemical reaction depicts nitrification?
A. N₂ ® NH₄⁺
B. NO₃^- ® NH₄⁺
C. NO₂^-® NO₃^-
D. NO₃^- ® N₂

2. Glutamine is derived from which glycolysis or citric acid cycle intermediate?
A. pyruvate
B. a-ketoglutarate
C. oxaloacetate
D. 3-phosphoglycerate

3. Newborn infants sometimes develop jaundice because of an accumulation of
A. heme.
B. biliverdin.
C. urobilin.
D. bilirubin.

4. In the de novo pathway, what is the immediate precursor to dTMP?
A. dUMP
B. TMP
C. thymidine
D. dCMP

5. Which of the following is true about the de novo synthesis of nucleotides?
A. Deoxyribonucleotides are precursors of ribonucleotides.
B. Pyrimidines are precursors of purines.
C. Bases are synthesized then attached to ribose or deoxyribose.
D. Amino acids are precursors of nucleotides.

6. Plants carry out
A. reduction of nitrate.
B. denitrification.
C. nitrification.
D. nitrogen fixation.

7. Which of the following molecules is not derived from glycine?
A. glutathione (GSH)
B. heme
C. serotonin
D. phosphocreatine

8. The conversion of serine to glycine requires which of the following?
A. S-adenosylmethionine (adoMet)
B. 5-phosphoribosyl-1-pyrophosphate (PRPP)
C. NADH
D. tetrahydrofolate (H₄ folate)

9. Nucleoside diphosphate kinase catalyzes which reaction?
A. ATP + AMP 2 ADP
B. ATP + dCDP ADP + dCTP
C. ATP + dGMP ADP + dGDP
D. ATP + UMP ADP + UDP

10. Adenosine deaminase deficiency leads to
A. gout.
B. Lesch-Nyhan syndrome.
C. severe immunodeficiency disease.
D. porphyria.

11. Which of the following molecules does not result from decarboxylation of an amino acid?
A. histamine
B. spermidine
C. g-aminobutyrate (GABA)
D. dopa

12. Which of the following is true about the symbiotic relationship between leguminous plants and nitrogen-fixing bacteria?
A. Leguminous plants produce leghemoglobin to prevent oxygen from interfering with the bacterial electron-transfer system.
B. Nitrogen-fixing bacteria obtain citric acid intermediates from the leguminous plants.
C. Nitrogen-fixing bacteria are present on the leaves of the leguminous plants.
D. Leguminous plants produce the nitrogenase complex used by the bacteria to fix nitrogen.

13. Chorismate is an intermediate in the synthesis of which amino acid?
A. phenylalanine
B. proline
C. serine
D. cysteine

14. In the salvage pathway, how are nucleotides generated?
A. Free bases are attached to ribose, which is then phosphorylated to generate the corresponding NMPs.
B. Free bases exchange with the bases on NMPs.
C. Free bases react with 5-phosphoribosyl-1-pyrophosphate (PRPP) to generate the corresponding NMPs.
D. Purine and pyrimidine bases are built up while attached to ribose throughout the process.

15. Parkinson's disease is associated with
A. an underproduction of dopamine.
B. an underproduction of g-aminobutyrate (GABA).
C. an overproduction of histamine.
D. an overproduction of dopamine.

16. AMP is converted to adenosine by what enzyme?
A. nucleotidase
B. 5'-nucleotidase
C. adenosine deaminase
D. ribonucleotide reductase

17. Which of the following occurs in the degradation pathway of AMP?
A. Adenine is converted to hypoxanthine.
B. The end product is urea.
C. AMP is converted to adenosine.
D. Adenosine is converted to adenine.

sources: http://bcs.whfreeman.com/lehninger/pages/bcs-main.asp?v=chapter&s=22000&n=00070&i=22070.01&o=|00510|00520|00530|00540|00550|00PRS

questions for glycolysis

2009-07-01T13:12:00.000+05:30

1. Which process does not generate CO₂?
A. the citric acid cycle
B. the conversion of pyruvate to lactic acid
C. the conversion of pyruvate to acetyl-CoA
D. the conversion of pyruvate to ethanol

2. Which of the following is true about the fermentation of glucose?
A. It can occur under aerobic or anaerobic conditions, depending on the products generated.
B. There is no net yield of ATP.
C. The hydrogen to carbon ratio (H:C) of the reactants and products remains the same.
D. It always generates CO₂.

3. Glycogen is degraded in a
A. phosphorylation reaction.
B. hydrolysis reaction.
C. dephosphorylation reaction.
D. phosphorolysis reaction.

4. Which of the following sugars does not get converted to D-glucose before entering the glycolytic pathway?
A. D-galactose
B. glycogen
C. sucrose
D. lactose

5. Which of the following steps occurs during the payoff phase of glycolysis?
A. the conversion of phosphoenolpyruvate to pyruvate
B. the conversion of fructose 6-phosphate to fructose 1,6-biphosphate
C. the conversion of glucose 6-phosphate to fructose 6-phosphate
D. the conversion of glucose to glucose 6-phosphate

6. Under what conditions will lactic acid accumulate in skeletal muscle?
A. when citric acid enzymes are depleted
B. when ATP is depleted
C. when O₂ is depleted
D. when NADH is depleted

7. The enzyme that converts 3-phosphoglycerate to 2-phosphoglycerate is a
A. transferase.
B. kinase.
C. mutase.
D. phosphorylase.

8. Glycolysis and the pentose phosphate pathway are the same in that
A. they both generate NADPH.
B. they both generate ATP.
C. they both involve the oxidation of glucose.
D. they are reversible.

9. Which of the following reactions is catalyzed by transaldolase?
A. xylulose 5-phosphate + ribose 5-phosphate glyceraldehyde 3-phosphate + sedoheptulose 7-phosphate
B. ribose 5-phosphate xylulose 5-phosphate
C. sedoheptulose 7-phosphate + glyceraldehyde 3-phosphate erythrose 4-phosphate + fructose 6-phosphate
D. xylulose 5-phosphate + erythrose 4-phosphate glyceraldehyde 3-phosphate + fructose 6-phosphate

10. What is the role of uridine diphosphate (UDP) in the conversion of galactose to glucose 1-phosphate?
A. Its hydrolysis is needed to provide the energy to convert galactose to glucose 1-phosphate.
B. It donates a phosphoryl group to galactose to generate galactose 1-phosphate.
C. It serves as a phosphate acceptor.
D. It serves as a carrier for galactose and glucose.

11. The NADPH produced in the pentose phosphate pathway is used
A. to donate electrons to O₂ in mitrochondria.
B. to provide reducing power for biosynthetic reactions.
C. to convert superoxide free radicals (^·O₂^-) into hydrogen peroxide (H₂O₂) during detoxification.
D. to provide the energy for catabolic reactions.

12. Which of the following is true about gluconeogenesis?
A. In mammals, gluconeogenesis occurs predominately in the liver.
B. Gluconeogenesis is the pathway by which glucose is converted to glycogen.
C. The gluconeogenesis pathway is the glycolysis pathway running in the opposite direction.
D. Plants do not undergo gluconeogenesis.

13. Rapidly dividing cells have a high need for nucleotide precursors, which are provided by
A. the Cori cycle.
B. the pentose phosphate pathway.
C. glycolysis.
D. gluconeogenesis.

14. All of the bypass reactions used in gluconeogenesis
A. require high-energy equivalents.
B. involve the removal of phosphate groups.
C. are irreversible.
D. requires mitochondrial enzymes.

15. Mammals cannot convert fatty acids to glucose because
A. they have no pathway for breaking down fatty acids.
B. they cannot use pyruvate as a precursor of glucose.
C. the glycolysis pathway is not reversible.
D. they cannot convert acetyl-CoA to pyruvate.

sources: Lehninger's principle of Biochemistry

questions from Bioenergetics

2009-07-01T13:05:00.002+05:30

1. A chemical reaction is more likely to occur spontaneously if
A. the products of the reaction are more complex than the reactants.
B. the system takes up heat from its surroundings.
C. the products of the reaction are more disordered than the reactants.
D. the system gains free energy.

2. If a chemical reaction starts with 1M concentrations each of reactants A and B and products C and D, under what conditions of K'_eq and DG'^o will the reaction proceed in the forward direction (DG'^o = RT ln K'_eq)?
A. If K'_eq is greater than 1 and DG'^o is negative.
B. If K'_eq is 0 and DG'^o is negative.
C. If K'_eq is negative and DG'^o is negative.
D. If K'_eq is less than 1 and DG'^o is positive.

3. Living cells and organisms
A. exchange energy but not matter with their surroundings.
B. exchange energy and material with their surroundings.
C. are closed systems.
D. are at equilibrium with their surroundings.

4. The standard free-energy changes of two sequential chemical reactions are additive only if
A. the reactions share a common intermediate.
B. each reaction has a negative DG' ^o.
C. the overall (net) reaction has a postive DG' ^o.
D. the exergonic reaction occurs first.

5. Which of the following has a thioester bond?
A. PEP (phosphoenolpyruvate)
B. ATP
C. phosphocreatine
D. acetyl-CoA

6. What provides the energy for the synthesis in an RNA polymer?
A. The transfer of an energy-rich ribonucleoside monophosphate to the polymer.
B. The hydrolysis of two anhydride bonds in ribonucleoside triphosphates.
C. The transfer of the g phosphate of a ribonucleoside triphosphate to the polymer.
D. The transfer of an energy-rich ribonucleoside triphosphate to the polymer.

7. When a nucleophile attacks the a phosphorous atom of ATP, what kind of transfer occurs?
A. pyrophosphoryl transfer
B. phosphoryl transfer
C. adenylyl transfer
D. adenosine transfer

8. When dNTPs become depleted in the cell, which of the following enzymes will regenerate dNTPs from dNDPs?
A. nucleoside diphosphate kinase
B. polyphosphate kinase
C. creatine kinase
D. adenylate kinase

9. Which of the following enzymes can catalyze the conversion of AMP to ADP?
A. nucleoside diphosphate kinase
B. polyphosphate kinase
C. creatine kinase
D. adenylate kinase

10. Conversion of NAD⁺ to NADH is accomplished by the addition of
A. a proton.
B. an electron.
C. a hydride ion.
D. a hydrogen atom.

11. Which of the following carbon-containing molecules is most fully oxidized?
A. carbon monoxide
B. carbon dioxide
C. methane
D. ethanol

12. The oxidation-reduction reaction Fe²⁺+ Cu²⁺ Fe³⁺+ Cu⁺, can be described in terms of two half-reactions:

(1) Fe²⁺ Fe³⁺ + e^-
(2) Cu²⁺ + e^- Cu⁺

Which of the following statements is true?
A. In the overall reaction at the top, the cupric ion (Cu²⁺) is the reducing agent.
B. In half-reaction (2), cupric ion (Cu²⁺) is being oxidized.
C. In half-reaction (1), Fe³⁺ and e^- constitute a conjugate redox pair.
D. In the overall reaction at the top, the ferrous ion (Fe²⁺) is oxidized by the cupric ion (Cu²⁺).

13. Electrons can be transferred from one molecule (electron donor) to another molecule (electron acceptor) by all of the following ways except
A. as a hydride ion.
B. directly as an electron.
C. as a proton.
D. as a hydrogen atom.

14. Which of the following is true of flavin nucleotides?
A. They have no reduction potential unless bound to a protein.
B. They always accept two electrons.
C. They are utilized by oxygenases.
D. They act as prosthetic groups.

15. Below are the standard reduction potentials (E'^o) for two conjugate redox pair:

Pyruvate^-/lactate^- E'^o = –0.185

NAD+/NADH E'^o = –0.320

Which of the following is true?
A. The pyruvate/lactate conjugate redox pair has a greater tendency to lose electrons than the NAD⁺/NADH redox pair.
B. Pyruvate has a greater affinity for electrons than NAD⁺.
C. NAD⁺ is a reducing agent.
D. Under standard conditions, NAD⁺ is more likely to be converted to NADH, than pyruvate is to converted to lactate.

sources: Lehninger's principle of biochemistry

2009-07-01T12:40:00.001+05:30

1. Sex hormones are biosynthesized from cholesterol. Which one is the correct sequence
(a) Cholesterol --- Progesterone --- Pregnenolone --- Testosterone --- estradiol
(b) Cholesterol --- Progesterone --- Pregnenolone --- estradiol ---Testosterone
(c) Cholesterol --- Pregnenolone --- Progesterone --- estradiol ---Testosterone
(d) Cholesterol --- Pregnenolone --- Progesterone ---Testosterone --- estradiol

2. Does aminotransferase catalyze the last step in the biosynthesis of Phe ? (a) yes (b) No

3. His is derived from a precursor belonging to the family of (a) α– ketoglutarate
(b) Ribose – 5- phosphate (c) Pyr (d) OAA

4. Arg is derived from a precursor belonging to the family of (a) α– ketoglutarate
(b) Ribose – 5- phosphate (c) Pyr (d) OAA

5. Val is derived from a precursor belonging to the family of (a) α– ketoglutarate
(b) Ribose – 5- phosphate (c) Pyr (d) OAA

6. PRPP contributes ____ carbon atoms in His biosynthesis (a) 6 (b) 5 (c) 3 (d) 4

7. Reactants of the first step in His biosynthesis are (a) PRPP and ATP (b) PRPP and Gln
(c) PRPP and Glu (d) PRPP and Asp

105. The hormone that mediates the action of leptin is (a) epinephrine (b) norepinephrine (c) glucagon ( d) none

8. Somatostatin is released by (a) α cells of Islets of Langerhans (b) β cells of Islets of Langerhans (c) δ cells of Islets of Langerhans

9. Wrong statement about glucagons action is (a) increase is glycogen breakdown (b) decrease in glycogen synthesis (c) increase in F-2,6-BP levels (d) increase in gluconeogenesis

10. The hormone that acts during starvation is (a) glucagon (b) insulin (c) epinephrine (d) none

11. Which of the following hormones is not regulated by hypothalamus ? (a) oxytocin
(b) somatostatin (c) norepinephrine (d) progesterone

12. The site for ibuprofen action is
(a) cyclooxygenase (b) thromboxane synthase (c) lipoxygenase (d) all

13. Aldosterone is released in response to (a) (a) FSH (b) LH (c) Thyrotropin (d) ACTH

14 . Which intermediate is not involved in aminotransferase action ?
(a) aldimine (b) carbanion (c) carbonium ion (d) quinonoid

15. Which of the following statements regarding degradation of ALL amino acids in not true ?

(a) Separation of amino group from the carbon skeleton, ( b) Passage of carbon skeleton to the glucogenic pathway, (c) Excretion of excess amino groups in a form appropriate to the organism and its environment, ( d) Use of amino groups for synthesis of new amino acids or other nitrogenous products.

16. Correct statement for the biosynthesis of phosphatidyl choline in a vertebrate is
(a) First DAG reacts with CDP and then Choline reacts (b) First choline reacts with CDP and then DAG reacts (c) Both (a) and (b) (d) none

17. Correct statement for the biosynthesis of phosphatidyl choline in a bacteria is
(a) First DAG reacts with CDP and then Choline reacts (b) First choline reacts with CDP and then DAG reacts (c) Both (a) and (b) (d) none

18. The hormone that is released from tissues outside brain and interacts with hypothalamus is
(a) Leptin (b) epinephrine (c) glucagon (d) insulin

19. NAD⁺ participates in the ___ step of biosynthesis of CTP from Asp.
(a) 4^th (b) 3^rd (c) 2^nd (d) 5^th

20. CO₂ is liberated in the ___ step in biosynthesis of CTP from Asp. (a) 4^th (b) 3^rd (c) 2^nd (d) 5^th

21 Gln donates N atoms of positions number ___ of purine ring. (a) one and seven (b) one and nine (c) three and nine (d) seven and nine

22. Asp participates in ____ steps in biosynthesis of AMP from PRPP. (a) 8^th and 11^th (b) 7^th and 12^th (c) 6^th and 12^th (d) 8^th and 12^th

23. ATP is involved in steps ____ of the biosynthesis of AMP from PRPP. (a) 2, 3, 4, 5
(b) 2, 3, 4, 5, 6 (c) 2, 4, 5, 6 (d) 2, 4, 5, 6, 8

24. Common intermediate in the biosyntheses of aromatic amino acids is
(a) anthranilate (b) shikimate (c) chorismate (d) prephenate

25. Gln participates in ___ step of biosynthesis of Trp from shikimate (a) 5^th (b) 4^th (c) 6^th (7^th
77. Number pf hormones released from posterior pituitary is (a) 1 (b) 2 (c) 3 (d) 4

26. Fatty acyl – CoA desaturase is a (a) mixed – function oxidase (b) dioxygenase (c) mixed – function oxygenase (d) acyl – CoA dehydrogenase

27. Methotrexate is a chemotherapeutic agent because it is a competitive inhibitor of
(a) thymidylate synthase (b) dihydrofolate reductase (c) ribonucleotide reductase (d) serine hydroxymethyl transferase

28. Degradation of AMP to uric acid releases (a) O₂ (b) CO₂ (c) NH₃ (d) H₂O

29. Common intermediate in the degradation of AMP and GMP to uric acid is
(a) hypoxanthine (b) Xanthine (c) guanine (d) adenine

30. The cofactor of thymidylate synthase is
(a) dihydrofolate (b) methylenetetrahydrofolate (c) tetrahydrofolate (d) SAM

31. Wrong statement about ribonucleotide reductase is (a) It is a dimmer with subunits R₁ and R₂ (b) dATP is its activator (c) Its active is formed between R₁ and R₂ (d) Its action involves free radical

32. Wrong statement about ATCase is m(a) ATCase is an allosteric enzyme (b) CTP inhibits it
(c) ATP activates it (d) It catalyzes the first step in the biosynthesis of CTP

33. PRPP participates in the ____step in biosynthesis of CTP from Asp.(a) 4^th (b) 3^rd (c) 2^nd (d) 5^th

34. Which of the following actions exerted by epinephrine is not true ? (a) increase in heart rate (b) increase in insulin secretion (c) increase in blood pressure (d) dilation of respiratory passage.

35. Epinephrine is (a) neurotransmitter (b) hormone (c) both neurotransmitter and hormone

36. Which of the following hormones does not involve pituitary gland ? (a) epinephrine (b) oxytocin (c) testosterone (d) prolactin

37. Number of distinct proteins required for biosynthesis of myristic acid from acetyl – CoA is
(a) 9 (b) 8 (c) 7 (d) 10
38. Glyphosate inhibits ________ step in the biosynthesis of shikimate to chorismate
(a) 1^st (b) 2^nd (c) 3^rd (d) 4^th

39. The product of chorismate mutase is (a) shikimate (b) phenyl pyruvate (c) prephanate (d ) none

40. For the biosynthesis of Trp N atom is donated by (a) Ser (b) Gly (c) Glu (d) Ala

41. The neurotransmitter not derived from tyrosine is
(a) serotonin (b) dopamine (c) norepinephrine (d) epinephrine

42. Which is not the substrate of ribonucleotide reductase (a) ADP (b) TDP (c) CDP (d) GDP

43. The substrate of thymidylate synthase is (a) dUMP (b) UMP (c) dUDP (d) dUTP

44. Glycerol can’t be catabolized in which cell

a) Adipose b) Skeletal c) hepatic d) cardiac

45. Lovastatin competitively inbibits HMG-CoA reductase as it structurally resembles

a) HMG b) HMG-CoA c) Mevalonate d) Acetoacetyl CoA

46. High rato of protein to lipid is found in

a) Chylomicrons b) HDL c) VLDL d) LDL

47. Percentage of cholesterol is high in

a) Chylomicrons b) HDL c) VLDL d) LDL

48. Percentage of TAG is high in

a) Chylomicrons b) HDL c) VLDL d) LDL

49. The site of formation of LDL is

a) liver b) intestine c) blood plasma d) All

50. Steroid sensor in SCAP-SREBP complex is

a) SCAP b) SREBP c) Both d) None

51. The primary effect of high intracellular cholesterol

a) inhibition of migration of SCAP-SREBP complex from ER to golgi complex.

b) promotion of migration of SCAP-SREBP complex from ER to golgi complex.

c) proteolytic cleavage of SREBP d) enhanced transcription of HMG-CoA reductase.

52. Which of the following isn’t feature of amino-terminal domain of SREBP

a) it regulates gene transcription. b) it has long half life

c) it promotes uptake and synthesis of cholesterol. d) it is released in cytosol.

53. LDL receptor binds to

a) apoA-I b) apoB-48 c) apo B-100 d) apo C –II

54. By percentage, LDL is rich in

a) protein b) free cholesterol c) cholesterylester d) TAG

55. In receptor-mediated endocytosis of LDL

a) LDL receptor is destroyed by lysosomal enzyme b) LDL receptor is recycled from endosome.

c) LDL receptor is transported from endosome to ER. d) All of the above

56. Which of following protein isn’t associated with HDL

a) ACAT(acyl-CoA cholesterol acyl transferase) b) apo A – I

c) ACAT (lecithin-cholesterol acyl transferase) d) apo C- I

57. Which of following isn’t feature of SR-BI receptor?

a) it mediates endocytosis of HDL in hepatic and steroidogenic tissue

b) it is involved in reverse cholesterol transport

c) it mediates passive movement of cholesterol from cell surface into HDL. d) None

58. Which of the following apolipoprotein triggers uptake of VLDL and chylomicrons remnant in liver.

a) apo D b) apo A- I c) apo E d) apo B-48

59. How many ATPs are required to form one molecule of squalene from mevalonate?

a) 3 b) 6 c) 9 d) 18

60. How many molecules of CO₂ is released during formation of 1 molecule of squalene from mevalonate?

a) 1 b) 3 c) 6 d) 5

61. The first cyclic molecule during cholesterol biosynthesis is

a) squalene b) ergosterol c) lanosterol d) stigmasterol

62. Formation of fanesyl phosphate involves

a) head to head condensation b) tail to head condensation c) head to tail condenoation d) tail to tail condensation.

63. Formation of squalene involves.

a) head to head condensation b) tail to head condensation c) head to tail condenoation d) tail to tail condensation.

64. Choline donor during biosynthesis of sphingomyeline is

a) CDP-choline b) CTP-choline c) Phosphatidyl choline d) UDP- choline

65. During biosynthesis of sphingolipids, acyl group transfer occurs in which step

a) 2 b) 3 c) 4 d) 5

66. During biosynthesis of plasmogen, ethanolamine is attached in the form of

a) CDP-ethanolamine b) CTP-ethanolamine c) Unactivate ethanolamine d) Phosphatidyl ethanolamine

67. No. of NADPH used during formation of plasmogen

a) 2 b) 3 c) 4 d) 5

68. Cardiolipin is formed in eukaryotic cell by

a) Condensation of two phosphatidyl glycerol b) Condensation of two phosphatidyl choline

c) Condensation of two phosphatidyl glycerol and CDP-DAG

d) Condensation of two phosphatidyl choline and CDP-DAG.

69. Phosphatidyl serine in mammals is formed by

a) Condensation of CDP-DAG and serine b) Condensation of CDP serine and DAG

c) head groud exchange reaction d) both a and b

70. Inhibition of glyceroneogenis in adipose tissue doesn’t results in:-

a) increase level of free fatty acid in blood b) enhanced glyceroneogenesis in liver

c) increase glycerol level in blood d) none

71. Effect of thiazolidinediones in liver is

a) induction of transcription of PEP carboxykinasic b) Inhibition of transcription of PEP carboxykinasic

c) allosteric activator of PEP carboxykinase d) none

72. Which of following statement is false about TAG cycle?

a) TAG cycle is halted during starvation. b) TAG cycle is apparently futile cycle.

c) TAG cycle maintain free fatty acid in blood d) TAG cycle requires serum albumin and apolipoprotein.

73. Glucocorticoids

a) decreases transcuption of PEPCK in liver. b) increases level of free fatty acid in blood.

c) increases level of glycerol-3-phosphate in adipose d) hinders transport of TAG from liver to adipose tissue.

74. No. of ATPs required to form acyl bonds of 1 molecule of TAG is

a) 3 b) 6 c) 8 d) 10

75. Aspirin inhibits

a) COX-1 b) COX-2 c) both a & b d) none

76. Which of following desaturation doesn’t occurs in mammals

a) ∆⁹ b) ∆⁵ c) ∆⁶ d) ∆¹²

77. Which of the following isn’t essential fatty acid

a) linoleate b) α-linolenate c) oleate d) all

78. The fatty acid present in low amount in plant cell is

a) 18:0 b) 16:0 c) 18:3 d) 16:3

79. No. of electrons used during formation of stearate from acetyl CoA is

a) 28 b) 32 c) 36 d) 40

80. No. of carbon donated by CO₂ during plamitate biosynthesis is

a) 8 b) 4 c) 0 d) 2

81. Phenylbutyrate ingestion enhances biosynthesis of

a) glycine b) glutamine c) glutamate d) alanine

82. PLP forms aldimine linkage with which lysine residue in aminotransferase.

a) Lys²⁵⁵ b) Lys²⁵⁸ c) Lys²⁵⁹ d) Lys²⁶⁰

83. Purely ketogenic amino acid is

a) glycine b) Leucine c) Valine d) Isoleucine

84. Deficiency of Tyrosine amonitransferase cause

a) Tyrosinemia II b) Tyrosinemia I c) Alkaptonuria d) Tyrosinemia III

85. Catabolism of which amino acid involves 1 carbon metabolism

a) Phenylalanine b) Serine c) Luecine d) Lysine

86. Transcription of Urea cycle enzyme increases during

a) carbohydrate rich diet b) protein rich diet c) starvation d) both b & c

87. In reference to urea cycle inhibition of N-acetyl glutamate synthase results in

a) increased urea synthesis b) decrease ATP consumption

c) increased flow of carbon in aspartate arginosucunate pathway d) none

88. Which of the following statement is false about urea cycle?

a) A net of 0.5 ATP used per urea molecule. b) Arginine enhances urea cycle.

c) Urea cycle is dependent of TCA cycle. d) No redox reaction occur in urea cycle.

89. During metabolic acidosis, uptake of which amino acid increases in kidney

a) Glutamate b) Asparagine c) Glutamine d) Alanine

90. Amino acid that involves transamination reaction during catabolism is

a) Serine b) Tryptophan c) Cysteine d) Threonine

91. Which of following fatty acid can gives carbon for gluconeogenesis

a) odd chain FA b) phytic acid c) olecate d) a & b

92. The ratio of oxygen to carbon dioxide in complete oxidation of stearate is

a) 23:18 b) 24:18 c) 26:18 d) 28:18

93. Not true about mammalian fatty acid synthase is

a) fatty acid synthase occur in cytosol. b) fatty acid synthase is a single polypeptide

c) all seven active site act as enzyme d) AT transfers acyl group from ACP to KS.

94. Apolipoprotein isn't involved in :

a) Acting as ligand for capillary lipases b) decreasing the density of chylomicrons

c) enhancing the solubility of chylomicrons in blood. d) stabilizing chylomicrons.

95. Ammonia toxicity isn't associated with :

a) Cerebral edema b) low level of ATPs c) increased level of GABA d) inhibition of TCA cycle.

96. which of the following enzyme is found only in liver mitochondrial matrix:

a) Thiolase b) HMG-CoA synthase c) HMG- CoA lyase d) malate dehrdrogenase.

97. Carbohydrate isn't used for energy storage instead of TAG because:

a) Carbon in carbohydrate is more oxidized than carbon in fatty acids.

b) hydration of carbohydrate is problematic during storage and transportation.

c) Carbohydrate would increase osmolarity of cytosol. d) All of above.

98. Excess of benzoate intake increases the de novo biosynthesis of

a) glutamine b) Glutamate c) Valine d) Glycine

99. Fatty acids aren't primarily biosynthesized in plant and bacteria for:

a) Maintainence of membrane fluidity b) Storage of energy c) Formation of signal molecules d) None of the above

100. beta- oxidation is not favoured by:

a) low conc. of acetyl CoA b) Enhanced activity of acetyl CoA carboxylase

c) high [NAD] / [NADH] ratio d) high level of ephinephrine and glucagon

A mechanical analogy for light reactions

2009-06-19T07:08:00.001+05:30

Science Writing I Feb. 26, 2008

2008-02-26T19:37:00.000+05:30

Science Writing

It may be at first difficult to see the importance or understand the necessity of writing about science.
Science writing communicates what you know to a specific audience.
Publication of discovery, a new theory, a new phenomenon or experimental results contribute to science and advance your career.
Dissemination of scientific ideas is crucial and inseparable from science itself.

Benefits of writing :

It is a visible token of your continuing activity.
It gains prestige for you and your work.
It helps you correspond with colleagues in the field.
It helps you obtain the funding, equipment, superior colleagues, research assistants and collaborators .
It is essential for the survival of science.
It establishes the Bragging rights of scientists.

Learning to write persuasively with fervor, vigor, imagination and precision is one of the keys to success in the practice of science.

Define goals of your writing

What is your goal ?

To explain a new concept ?
To demonstrate the efficiency of a method that you have executed ?
To lay out in a clear and logical way the data you have measured in experiments ?
To describe the existing research or thinking about a problem ?

Have your purpose clearly in your mind when you begin to write

The science writing should have

A concise statement of the goal of the paper.
Clear language
Precise description of procedures.
Good graphs, charts and tables.
Definition of all technical terms
A summary of findings

It should not have

Obscure language and terms
Long, difficult – to – read sentences
Consideration of subjects which cloud the issue or take you off the main track
Poor contexts for understanding new ideas.

Scientific Report

I. Front Material

A. Write an abstract, summarizing the research in 100 – 300 words.

B. Write a title that describes the major intent of your work

II. Introduction

A. Define the problem, explaining the importance of the problem wherever possible and necessary.

B. Specify your hypothesis.

C. Describe what others have said and done in attacking a similar problem ( Literature review )

D. Brief description of the main conclusion of your research.

III. Materials and Methods

A. Describe the methods and materials you used in the lab and for data collection

IV. Results

A. Describe the data you collected

B. Analyze the data

C. Interpret the data

V Conclusions

A. Draw generalizations from analysis of the data.

B. Draw conclusions from your generalizations

VI List of Citations

My arrival

2008-02-13T05:16:00.000+05:30

Dear USC faculty, students and well wishers :

I am finishing my stay in Chicago, USA. I could not visit friends because of hostile weather ( - 10 - -20 C temp ) . But I am following American primary election very curiously. On my retrn journey I will visit IIT, Kanpur for 2 days and present a seminar. I will return Kathmandu on Feb. 21 and will join my duty on Feb. 24. On the same day I plan to meet USC students at 1 PM in seminar hall. You all are invited. Bye

Vishwanath P. Agrawal

Biochem 323 Plant Biochemistry August 8, 2007 Exam Questions

2007-08-08T16:29:00.000+05:30

1. In prokaryotic pathway for glycerolipid biosynthesis sn – 2 position is specific for (a) 18:0 (b) 16:0 (c) 18:1 d) b + c

2. fad2 gene locus is involved in desaturation of (a) 16:1 (b) 18:1 (c) 18:2 (d) 18:3

3. fad A gene is involved in desaturation of (a) 16:0-MGD (b) 16:0 - PG (c) 18:1- PG (d) none

4. The substrate for desaturase encoded by fad D gene is (a) 16:1-PG (b) 16:1-MGD (c) a + b
(d) 18:2 - PG

5. Whose gene product yields a unique FA ? (a) fad A (b) fad B (c) fad C (d) fad D

6. Which is not a substrate for fad C ? (a) 18:1-PG (b) 18:1-MGD (c) 16:1-MGD (d) 16:1-PG

7. SL derived from eukaryotic pathway has ________ in sn -1 position .
(a) 18:1 (b) 16:0 (c) a or b (d) 18:2

8. The most frequent intermediate in the TWO-PATHWAY scheme for glycerolipid biosynthesis is
(a) PG (b) DAG (c) MGD (d) PC

9. Which glycerol lipid is found in highest percentage in plants ?
(a) PC (b) MGD (c) DGD (d) DAG

10. The enzyme that determines cold tolerance or sensitivity of a plant is
(a) Acyl-ACP:G-3-P acyltransferase (b) Acyl-ACP:lyso-PA acyltransferase
(c) 18:1-PC desaturase (d) All wrong

11. The elongation of fatty acid follows (a) CoA track (b) ACP track (c) a+b (d) None

12. The conclusion that Stearoyl-ACP dasaturase is highly conserved in plant kingdom is based on
(a) high degree of identity in protein sequence (b) high degree of identity in DNA sequence
(c) high degree of identity of cDNA sequence (d) high degree of identity of mRNA sequence

13. Absence of PC in chloroplast is due to
(a) The enzyme CDP-choline: DAG cholinephosphotransferase (A) is not present in chloroplast
(b) Enzyme A is very specific for sn-2 18:1- DAG (c) a or b (d) All wrong

14. The target lipid for analyzing fatty acid composition during temperature fluctuation is
(a) MGD (b) PC (c) PG (d) SL

Answer to Biochem 323 Plant Biochemistry July 26 - 27, 2007

2007-08-01T17:48:00.000+05:30

1. Which of the following is not a lipid ?

(a) Jasmonic acid (b) lecithin (c) 18:1 : G-3-P acyltrasferase (d) All correct

2. What is the principal hurdle in understanding the regulation of glycerolipid biosynthesis ?

(a) Reactions involved are complex (b) synthesis takes place at various sites (c) solubilization of membrane-bound enzymes (d) the substrates are water insoluble.

3. In the TWO – PATHWAY model desaturation of 18:1 does not take place on ________

(a) PC (b) DAG (c) MGD (d) PG

4. _________ links prokaryotic and eukaryotic pathways according to the TWO – PATHWAY model.

(a) PG (b) PC (c) DAG (d) MGD

5. _______ is not exported to extrachloroplastidial sites . (a) 16:0 (b) 18:0 (c) 18:1 (d) a +c

6. 16:1 is synthesized by _________ pathway. (a) prokaryotic (b) eukaryotic (c) a + b (d) novel
7. In a pea plant carbon skeleton of MGD is mainly derived from _________.

(a) PA (b) PG (c) PC (d) DAG

8. In a spinach plant carbon skeleton of MGD is mainly derived from _________.

(a) PA (b) PG (c) PC (d) DAG

9. Upon shifting a plant from light to darkness the level of acetyl ACP is

(a) decreased (b) increased (c) unaffected (d) None

10. _________ pathway is also called ACP track.
(a) eukaryotic (b) prokaryotic (c) a+b (d) all wrong

Answers to 1st term Test

2007-07-12T14:42:00.000+05:30

Universal Science College Biochem 323 Plant Biochemistry July 9, 2007

Name of the student :

1. The cyclic electron flow during photosynthesis in plants does not result into (a) production of NADPH, (b) Production of ATP (c) Production of protons (d) none

2. The species having the highest reduction potential is (a) [ Mn – complex ] ⁺⁴ (b) P₆₈₀^·+ (c) NADPH (d) H₂O

3. During plant photosynthesis concentration of protons increases in (a) stroma (b) lamelle (c) chloroplast (d) lumen

4. In photosynthesis by purple bacteria which step is the slowest ? (a) charge separation (b) electron transfer from Q_A to Q_B (c) electron transfer from Cyt bc₁ to (Chl)₂^·+ (d) electron transfer from pheophytin to Q_A

5. In photosynthesis photons raise __________ of electrons (a) reduction potential (b) oxidation potential (c) flow (d) none

6. Oxidation potential of DCPIP is ______ than water (a) higher (b) lower (c) same (d) none

7. Which one is not oriented towards lumen side ? (a) OEC (b) PC (c) Cytf (d) Cyt b₆

8. Which sequence of steps can give ATP ? ( A – addition of pH 4 medium , B – removal of the medium by centrifugation , C – addition of pH 8 medium, D – addition of ADP + P_i , E – incubation for 2 hours )

(a) Chloroplast – C – E - B – D – A , (b) Chloroplast - A - E – B – C – D (c) Chloroplast – C – E - B – A – D and (d) Chloroplast - A - B – E – C – D

9. ATP synthase is located in (a) granal lamelle (b) stromal lamelle (c) lumen (d) stroma

10. Which statement is not true about OEC ? (a) It catalyzes the evolution of oxygen (b) It is oriented towards stromal side (c) It provides 4 electrons to PSII (d) It acts as a proton pump.

11. Which species accepts electrons from water in OEC ? (a) Tyr (b) [ Mn – complex ] ⁰

12. How many NADPH molecules are produced for each molecule of oxygen evolved ?

(a) 1 (b) 2 (c) 3 (d) 4

13. How many molecules of ATP are produced for each oxygen molecule evolved in photosynthesis ?

(a) 1 (b) 2 (c) 3 (d) 4

14. Under which condition electron flow during plant photosynthesis can become cyclic ?

(a) high [NADP] / [NADPH] (b) low [NADP] / [NADPH] (c) In presence of DCMU (d) In presence of DCPIP

15. Which of the following is not involved in Calvin cycle ?

(a) Ribose-5-P (b) G-3-P (c) Ribulose-1-P (d) Erythrose-4-P

16. In 4 Calvin cycles the number of Ribulose-1,5-BP formed is
(a) 0 (b) 1 (c) 2 (d) all wrong

17. During sucrose biosynthesis the direction of P_i transport by Pi – TP antiporter is
(a) stroma to cytosol (b) lumen to stroma (c) cytosol to stroma (d) all

18. Which enzymatic step ( excluding transport ) in photorespiration utilizes THF as the cofactor ?
(a) 4^th (b) 5^th (c) 6^th (d) 7^th

19. Which enzyme involved in CO₂ fixation in C₄ plants is not regulated by light ?
(a) Malate dehydrogenase (b) Malic enzyme (c) PEP carboxylase (d) Pyr phosphate dikinase

20. The pathway of CO₂ fixation in a C₄ plants has ____ enzymatic steps
(a) 4 (b) 5 (c) 6 (d) 7
( The rubisco reaction has been counted )

21. Which enzyme catalyzes the liberation of CO₂ in a C₄ plant ?
(a) Malate dehydrogenase (b) Malic enzyme (c) PEP carboxylase (d) Pyr phosphate dikinase

22. In photorespiration fixation of 2 molecules of O₂ gives _____ molecules of C₃ .
(a) 1 (b) 2 (c) 3 (d) 4;

23. The most abundant protein in mitochondria of a spinach plant is
(a) PEP carboxylase (b) glycine decarboxylase (c) Rubisco (d) None

24. In photorespiration Calvin cycle is gradually slowed down because of decreasing supply of
(a) NADPH (b) ATP (c) RuBP (d) b + c

25. Regeneration of RuBP from TP in stage 3 of Calvin cycle is accomplished in ___ distinct steps.
(a) 7 (b) 8 (c) 9 (d) 10

26. Which statement is not true about the effect of photosynthesis?
(a) Mg⁺⁺ concentration increases in stroma (b) Mg⁺⁺ concentration decreases in stroma (c) H+ concentration decreases in stroma (d) All

27. Which of the followings is not different for C3 and C4 plants ?
(a) carbon intermediates (b) ATP consumed (c) specificity for O₂ (d) Calvin cycle

28. For C₄ plants which statement is more accurate ?

(a) CO2 fixation and Calvin cycle are spatially separated (b) CO2 capture and Calvin cycle are spatially separated ( CO2 is captured in mesophyll cells and fixed in Calvin cycle in bundle sheath.)

29.Which statement is false about cyclic photophosphorylation ?
(a) ATP is produced (b) NADPH is not produced (c) Oxygen is evolved (d) all

30. When chloroplast is illuminated with a light of 700 nm, which of the following gets reduced ?

(a) Plastoquinone (b) Plastocyanin (c) Ferrodoxin (d) Pheophytin

31. Which contains only cyclic photosynthesis ? (a) Plants (b) Purple bacteria (c) green sulfur bacteria (d) All wrong

32. The reaction catalyzed by Malic enzyme is analogous to the one catalyzed by __________ enzyme.
(a) isocitrate dehydrogenase (b) α – ketogluatarate ddehydogenase (c) succinate dehydrogenase (d) none [ Notice the structural similarity of the portion undergoing decarboxylation ]

33. Starch biosynthesis is stimulated by (a) high level of Pi and low level of triose phosphate

(b) low level of Pi and high level of triose phosphate (c) high level of Pi and high level of triose phosphate (d) low level of Pi and low level of triose phosphate .

34. What will happen upon addition of DCPIP to chloroplast treated with DCMU herbicide ?
(a) Synthesis of ATP will be restored. (b) Evolution of oxygen will resume (c) NADPH production will not be restored (d) All wrong

35. Iodoacetate can inhibit an enzyme by reacting with thiol group in its active site. Which enzyme is not inhibited by iodoacetate ? (a) Malate dehdrogenase (b) Ribulose – 5 – phosphate kinase

36. In the activation of ____________ enzyme thioredoxin is involved

(a) glycine decarboxylase (b) Malic enzyme (c) F - 1,6 - bisphosphatase (d) Rubisco

37. A defect in sedoheptulose-1,7- bisphosphatase will totally inhibit the synthesis of (a) ribulose-5- phosphate (b) ribose-5-phosphate (c) xylulose-5-phosphate ( d) Erythrose-4-phosphate

38. In photophosphorylation __________ donates electrons (a) NADPH (b) NADH (c) H₂O (d) PSII.

39. Efficiency of photosynthesis would be maximum, when chloroplast is illuminated with light of _____ nm. (a) 680 nm (b) 700nm (c) a + b (d) all wrong

40. Which statement about photosynthesis is not true ? (a) Dark reaction does not occur in light (b) Dark reaction does not occur in dark (c) Dark reaction occurs in both light and dark (d) None

41. Decrease in wavelength of light in photosynthesis will favor (a) stacking of grana (b) unstacking of grana (c) a + b (d) all wrong

42. Which intermediate is not involved in the reaction catalyzed by rubisco ?
(a) endioate (b) 3-PG (c) β – hydroxyl acid (d) carbanion

43. Rubisco enzyme is activated by (a) RuBP (b) CO₂ (c) a + b (d) all wrong

44. The main reason for photorespiration is (a) high temperature (b) high O₂levels (c) rubisco possesses oxygenase activity (d) None

45. A defective Malic enzyme can inhibit CO₂ fixation in (a) C₄ plants (b) C₃ plants (c) a + b (d) None

Class Test Biochem 323 Plant Biochemistry June 27, 2007

2007-06-27T18:17:00.000+05:30

Universal Science College Class Test Biochem 323 June 27, 2007

Name of the student :…………………………………………………..

1. Which of the following is not an intermediate in Calvin cycle ?

(a) Ribose-5-P (b) G-3-P (c) Ribulose-1-P (d) Erythrose-4-P

2. In 4 Calvin cycles the number of Ribulose-1,5-BP formed is
(a) 0 (b) 1 (c) 2 (d) all wrong

3. During sucrose biosynthesis the direction of P_i transport by Pi – TP antiporter is
(a) stroma to cytosol (b) lumen to stroma (c) cytosol to stroma (d) all

4. Which enzymatic step ( excluding transport ) in photorespiration utilizes THF as the cofactor ?
(a) 4^th (b) 5^th (c) 6^th (d) 7^th

5. Which enzyme involved in CO₂ fixation in C₄ plants is not regulated by light ?
(a) Malate dehydrogenase (b) Malic enzyme (c) PEP carboxylase (d) Pyr phosphate dikinase

6. The pathway of CO₂ fixation in a C₄ plants has ____ enzymatic steps
(a) 4 (b) 5 (c) 6 (d) 7
( The rubisco reaction has been counted )

7. Which enzyme catalyzes the liberation of CO₂ in a C₄ plant ?
(a) Malate dehydrogenase (b) Malic enzyme (c) PEP carboxylase (d) Pyr phosphate dikinase

8. In photorespiration fixation of 2 molecules of O₂ gives _____ molecules of C₃ .
(a) 1 (b) 2 (3) (d) 4; the correct answer is 3, but it has been cancelled because of mistake in the question.

9. The most abundant protein in mitochondria of a spinach plant is
(a) PEP carboxylase (b) glycine decarboxylase (c) Rubisco (d) None

10. In photorespiration Calvin cycle is gradually slowed down because of decreasing supply of
(a) NADPH (b) ATP (c) RuBP (d) b + c

11. Regeneration of RuBP from TP in stage 3 of Calvin cycle is accomplished in ___ distinct steps.
(a) 7 (b) 8 (c) 9 (d) 10

12. Which statement is not true about the effect of photosynthesis?
(a) Mg⁺⁺ concentration increases in stroma (b) Mg⁺⁺ concentration decreases in stroma (c) H+ concentration decreases in stroma (d) All

13. Which of the followings is not different for C3 and C4 plants ?
(a) carbon intermediates (b) ATP consumed (c) specificity for O₂ (d) Calvin cycle

14. For C₄ plants which statement is more accurate ?

(a) CO2 fixation and Calvin cycle are spatially separated (b) CO2 capture and Calvin cycle are spatially separated ( CO2 is captured in mesophyll cells and fixed in Calvin cycle in bundle sheath.)

C4 Plants

2007-06-25T19:52:00.000+05:30

C₄ Plants

Both high light intensity and high temperature favor photorespiration. C4 plants provide a way out. They have (a) high photosynthetic rates, (b) low rates of water loss ( transpiration ), low photorespiration rates and (d) high growth rates.

In C4 plants CO2 is fixed, released and fixed again. Sites of first CO2 fixation is separate from Calvin cycle ( spatially separated ).

C3 Plants	C4 Plants
1. Product of CO2 fixation is 3 carbon intermediate 3-PG	Product of first CO2 fixation is 4 carbon intermediate OAA
2. consumes 3 ATP / CO2	Consumes 5 ATP / CO2
3. O2 is acceptable	O2 is not acceptable
4. less efficient utilization of CO2	Most efficient utilization of CO2
5. 4 enzymes are light activated	7 enzymes are light activated.
6. CO2 gas is fixed	CO2 in aqueous state ( HCO3 ^- ) is first fixed

Photorespiration

2007-06-25T11:41:00.000+05:30

Why photorespiration ?

Because Rubisco is not 100% specific for CO₂ ; Km for CO2 is 9 μM whereas for O2 is 350 μ M. In 3-4 turnovers , Rubisco catalyzes the condensation of O2 in place of CO2. As a result of this one C₃ ( 3-PG) and one C₂ ( 2- phosphoglycolate ) are formed.

Photorespiration	Normal respiration
1. Chloroplast + peroxisome + mitochondria	mitochondria
2. Gly immediate precursor	TCA intermediates
3. O2 utilized in the first step	O2 utilized in the last step
4. consumes ATP	Produces ATP
5. does not produce NADH	Produced NADH
6. Salvage pathway	Main pathway
7. No electron transfer	Electron transfer
8. Peroxide is produced	No peroxide formed

Regulation of Calvin cycle by light

2007-06-25T11:11:00.001+05:30

Regulation of Calvin cycle by light

Photosynthesis induces higher pH and higher Mg⁺⁺ in stroma. Therefore, stromal enzymes adapt to higher pH and higher Mg⁺⁺. Since Calvin cycle takes place in stroma, enzymes involved in Calvin cycle are also regulated in this manner.

Enzymes : (1) Ru-5-P kinase, (2) F-1,6- BPase, (3) SH-1,7-BPase and (4) G-3-P dehydrogenase are activated by light driven reduction of disulphide bonds of the enzymes; enzymes containing free –SH groups are active, whereas enzymes containing –S-S- are inactive.

Electrons from PSI reduce Fd , reduced Fd_red reduces Thioredoxin which reduces the disulphide linkage of enzymes to active forms. Therefore, in the day time enzymes of Calvin cycle are activated resulting in its full activity.

Starch is only synthesized during light. In night , -SH hroups are reoxidized to disulphide bonds. As a result above 4 enzymes are inactivated ; ATP is not expended, but starch synthesized and stored in day time is degraded to fuel glycolysis.

On the other hand, Glu-6-P dehydrogenase is oppositely regulated by light. In the day time when plenty of NADPH is available this enzyme is inactivated, but in the night time this enzymes becomes active and produce much needed NADPH.

Calvin cycle II

2007-06-24T08:36:00.000+05:30

Five – sixths of C3 molecules are used for Ru-1,5-P and only 1/6 th of C3 are used for sucrose and / or starch biosynthesis. What would happen to the Calvin cycle if more than 1/6 of C3 are used for carbohydrate biosynthesis ?

Functions of Pi – TP antiporter system :

Keeps Pi level in chloroplast high enough for photophosphoryalation, why ?
Maintains sucrose synthesis, how ?
Supports glycolysis by supplying ATP and NADH / NADPH to cytosol , how ?

Calvin Cycle I

2007-06-20T20:04:00.000+05:30

Carbon Assimilation Reaction ( Calvin Cycle )

Dark reaction is not that dark. It is thought as independent of light, but it turns out that it is indirectly controlled by light reaction.

In dark Calvin cycle does not occur to a significant extent.

3 stages of Calvin cycle :

First stage : CO₂ fixation ; 3C₅ + 3C₁ ---- 6C₃

Second stage : Reduction 3-GP ----- G-3-P

Third stage : Generation of receptor C₅

C3 + C3 --- C6

C6 + C3 --- C5 + C4

C4 + + C3 --- C7

C7 + C3 --- C5 + C5

C3 – Glyceraldehyde – 3- phosphate and DHAP

C4 – erythrose – 4- phosphate

C5 - Xylulose – 5 – P; Ribose – 5- P; Ribulose-5-P; Ribulose-1,5-BP

C7 – Sedoheptulose-1,7-BP, Sedoheptulose-7-P

C6 – F-1,6-BP; F-6-P

9 ATP and 6 NADPH are required for fixing 3 molecules of CO₂ ; in the same ratio they are produced in light reaction.

Photosynthesis VI

2007-06-20T19:43:00.000+05:30

Electrons from water do not pass directly to P680

Oxygen evolving complex ( OEC ) or water splitting complex ( WSC )

Tyr residue of D protein participates in OEC.

4 P₆₈₀⁺ + 4 Tyr ---- 4 P₆₈₀ + 4Tyr^·

Tyr^· radical abstracts 4 electrons in sequence from [ Mn Complex ] ⁰ and oxidizes it to [ Mn Complex ]⁺⁴

4Tyr^· + [ Mn Complex ]⁰ ---- 4 Tyr + [ Mn Complex ]⁺⁴

[ Mn Complex ]⁺⁴ accepts 4 e from water at a time .

[ Mn Complex ]⁺⁴ + 2H₂O ---- [ Mn Complex ]⁰ + 4 H⁺ + O₂

OEC acts as a proton pump driven by electron transfer.

Phtosynthesis V

2007-06-20T19:20:00.000+05:30

Comparison between chloroplast and mitochondria

Chloroplast	Mitochondria
1. Cytb₆f	Cyt bc₁
2. PQ_B	Q_B
3. PC	Cytc
4. Proton transfer ( from outside stroma ---- to inside Lumen	Proton transfer from inside ( matrix ) to outside ( inner membrane )

Sequence of reactions for proton pump

1. PQ_BH₂ participates in Q cycle.

2. Electrons released during oxidation of PQ_BH₂are equally partitioned in following electron trranfer sequences :

Rieske Fe – S protein – Cyt f –PC – PSI
Cyt b₆ funnels electron back in Q cycle for reduction of PQ_B ( stroma side )

3. The orientation of Q cycle is such that H⁺ released during oxidation of PQ_BH₂ is pumped towards lumen ( inside thylakoid)

4. Protons required during reduction of PQ_B is derived from stroma.

5. Proton concentration in lumen becomes higher than stroma and proton gradient is established resulting in ATP synthesis.

TOPOLOGY

a) PSII spans across the lamelle with P680 exposed in stroma to capture light and OEC ( oxygen evolving complex ) buried in lumen.

b) PQ on the stroma side and PQH₂ near lumen side

c) Rieske Fe – S protein and Cyt f on lumen side

d) PC on lumen side

e) Cyt b₆ on stroma side.

f) PSI spans across the lamelle with P700 exposed in stroma to capture light

g) Fd on stroma side

Spatial separation of PSII and PSI is managed to prevent larceny ( theft ) of photons

PSII is located in tightly apposed membrane stacks of grana.

Photsynthesis IV

2007-06-20T18:22:00.000+05:30

1. For every two photons ( one photon per P.S. ) one electron is transferred from H2O to NADP+.
2. For one O2 molecule transfer of 4 e are required, i.e. 8 photons ( 4 photons per P.S. )
3. Binding of PQA to protein is the site for action of many commercial herbicides like DCMU.

Cytb6f links PSII and PSI

Cytb6f is similar to Complex III of mitochondria.

Chloroplast Mitochondria

A. Cytb6f Cytbc1
B. PQB QB
C. PC Cyt c
D. Proton transfer ( outside ---inside) Proton transfer ( inside ----outside )

Ag - Biotech

2007-06-13T16:49:00.000+05:30

Recent advances in biological and agricultural research have injected new energy into efforts to improve crops and control plant pests and diseases, and thus offer better solutions to many of the agricultural problems faced by farmers in developing countries.

One technology that has generated both excitement and controversy from the start is genetic modification (GM) — the process of transferring genetic traits from one species to another, endowing the second with desirable characteristics from the first. Using this approach with crop plants, researchers are seeking to help plant breeders develop new varieties with a range of advantageous traits such as higher yields, disease or pest resistance, and tolerance of drought.

Genetically modified varieties of cotton, maize and soya have already been commercialised in developing countries, including China, India, South Africa and Brazil. Other GM crops, such as rice and aubergine or eggplant — known in India as brinjal — are also under development.

But the ability to manipulate the genetic make-up of plants is not the only outcome of research. Non-GM advances in biotechnology are also showing their value in improving crop yields and pest resistance. Take tissue culture, used to produce disease-free plants; DNA-based diagnostic tools to identify viral and bacterial plant diseases; and microbes that target pests or nourish the soil in products such as bio-pesticides and bio-fertilisers.

The purpose of this dossier is to provide an overview of the new possibilities for enhanced crop production that these novel techniques are opening up. It looks at the controversies that some of them, particularly GM crops, have sparked. And it examines how governments and other bodies have responded to agricultural biotechnology — primarily by introducing regulatory systems that seek to maximise the benefits, and minimise any potential health or environmental damage.

GM crops: behind the biggest impact

Few dispute that, whatever the relative merits and dangers of GM crops, it is through these that modern biological science is already having the most dramatic impact on crop production and agricultural practices, both in the developed and the developing world.

Proponents of GM crops point out that they could help address not only food production but also a number of related developmental challenges, including economic growth, agricultural sustainability, environmental protection and poverty alleviation.

For example, in addition to using GM to enhance growth rates and resistance to insect pests and other threats — such as drought — researchers have also boosted the nutritional value of some crops, which could be used to supplement the diets of poor consumers.

Scientists are also developing novel crops as 'biofactories' to produce pharmaceutical or industrial compounds, creating new opportunities and markets for farmers, entrepreneurs and researchers in developing countries.

At the same time, a number of concerns have been raised about the potential impact of GM crops on both the health of those who consume them and the environment. This has, in turn, generated dilemmas for politicians in developing countries who must decide whether or not to approve the planting of such crops, and if so, under what conditions.

At the heart of many such debates is the question of who will benefit most from the introduction of GM crops. Supporters of the technology argue that they benefit small farmers as well as big ones — and that all farmers should therefore have access to the new technology.

In contrast, many critics of GM technology claim that it allows multinational corporations to exploit poor farmers, and threatens to disrupt alternative forms of agricultural system. They also argue that placing too much confidence in the technology distracts attention from the socio-economic and equity issues that underlie poverty and malnutrition.

Unsurprisingly, therefore, opinions tend to be sharply divided on the appropriate ways of identifying and managing the risks and uncertainties that surround the implementation of GM crops, and often centre on issues concerning transparency, participation and accountability in decision-making.

Another element in the debate is that GM is not the only potential benefit from recent biological and agricultural research. Many scientists, economists and rural development specialists argue that more attention should be given to other advanced agricultural biotechnologies that do not involve transferring genes between organisms.

They suggest that these alternative agri-biotech tools and methods, such as cloning by tissue culture — an approach being used to produce bananas in East Africa, for instance — or selection assisted by 'molecular markers', may be more appropriate for the developing world.

Towards a pro-poor biotechnology

Whatever the social, economic and environmental impact of these new technologies, it is already clear that a number of developing countries — particularly China, India, South Africa and Brazil — have already developed the scientific and technical capacity to play a leading role in biotechnology research, and thus in shaping GM technology to their own requirements.

In fact, some developing countries have been among the most enthusiastic in adopting GM crops. So far, however, the fact that globally, most agronomic GM research has been carried out either by the private sector, or by government laboratories in developed countries, means that it has inevitably focused on crops important to commercial farmers and industrialised agriculture in these regions.

So for the most part, the focus has been on just four crops — maize, cotton, canola (rape) and soya — and two traits, insect resistance and herbicide tolerance. Relatively little attention has been paid to crops such as sorghum, millet and teff or traits such as drought resistance, which are of more interest to the developing world.

Reflecting this imbalance, many development activists and civil society groups believe that the promotion of GM crops by multinational companies undermines both the food security of the poor and the economic interests of developing countries.

Others focus on supporting the efforts of public, private and non-profit agencies — such as the members of the World Bank's Consultative Group on International Agricultural Research (CGIAR) — to develop and deliver GM technology in ways that are more 'pro-poor.

The broader debate

Both sides in the argument accept that agri-biotech, whether GM or non-GM, has enormous potential for transforming the nature of modern agriculture in the developing world. But realising this potential — for example, by developing drought-tolerant rice varieties for Africa, and ensuring that farmers and farm labourers benefit directly from them — remains a major challenge.

As the various articles, news items, policy briefs and opinion items in this dossier indicate, the issues involved are not just scientific and technical. They also touch on important and frequently controversial socio-economic, political and ethical questions.

Some have direct implications for food production and environmental sustainability. Others concern international trade, since the global nature of markets for many food and cash crops means that international rules on how they can be grown, transported and sold are a key issue for developing countries.

Differing public perceptions of both the safety of GM crops and the way they are implemented raise major dilemmas for policy-makers. Countries wishing to exploit markets for 'GM-free' and organic products, for example, need to ensure that their exports meet the exacting standards demanded by retailers and consumers in importing countries.

Concern about this issue lies at the heart of recent controversies concerning the supply of GM grain as food aid to certain African countries. Decision-makers feared that some of the grain would be planted rather than eaten, which raised the question of whether those countries' crops could still be considered 'GM-free'.

Despite the challenges, however, many developing countries are creating policy frameworks that mean they can take advantage of the opportunities arising from biotechnology, for example by implementing safety practices that comply with the international agreements discussed above.

It is not an easy task, given the complexity of the underlying science, for example, or the cost of some of the equipment involved. But various initiatives, drawing on support from a range of donors, are currently seeking to help developing countries build these capabilities.

The goals of all these efforts is to ensure that developing countries build the scientific and regulatory capacity that will enable them to articulate their concerns, needs and priorities, and to shape the direction of biotechnology research and commercialisation to follow their own interests.

SciDev.Net's Agri-biotech dossier

This dossier provides a guide to these and other issues, covering both GM and non-GM techniques, and drawing on the specialised knowledge, insights and opinions of people in both developed and developing countries.

A key element of the dossier are 'policy briefs' that explore in detail, and from various specialist perspectives, the essential scientific and policy issues in areas such as food safety and risk assessment, public–private partnerships and nutritional enhancement of crops.

Shorter opinion articles present the more personal views of stakeholders or a particular angle of the debate. News items provide information on the latest scientific, technical and political developments. And the dossier also provides short summaries of key documents, a glossary of important terms, upcoming events and annotated links to other relevant websites.

We hope you find the contents of this dossier informative and useful. We would welcome your comments, feedback and suggestions on any aspect of it.

Dominic Glover, February 2006

If you have any comments or suggestions, please contact dossiers@scidev.net.

A Good Link on Bioinformatics

2007-06-11T15:15:00.000+05:30

Here is a link to a site where you can find pdfs on different topics regarding Bioinformatics:

http://www.clcbio.com/index.php?id=30

Good book on photosynthesis

2007-06-07T16:42:00.000+05:30

Hello :

Click the link given below for a comprehensive treatise on photosynthesis .

http://books.google.com/books?id=ztpvGBelfrEC&pg=PA137&ots=XVpdlGnyz1&dq=cytb6F&sig=h5CHRX-V46Xrw6Lp2z1H3MzmH2g#PPA137,M1

Bye.

( Courtsey of Bikash Thapa, a student of 8th semester of USC, presently doing research in Yonsei University, Korea. Thanks. )

Photosynthesis Class Test

2007-06-06T17:17:00.000+05:30

1. The cyclic electron flow during photosynthesis in plants does not result into (a) production of NADPH,

(b) Production of ATP (c) Production of protons (d) none

2. The species having the highest reduction potential is (a) [ Mn – complex ] ⁺⁴ (b) P₆₈₀^·+ (c) NADPH
(d) H₂O

3. During plant photosynthesis concentration of protons increases in (a) stroma (b) lamelle (c) chloroplast (d) lumen

4. In photosynthesis by purple bacteria which step is the slowest ? (a) charge separation
(b) electron transfer from Q_A to Q_B (c) electron transfer from Cyt bc₁ to (Chl)₂^·+
(d) electron transfer from pheophytin to Q_A

5. In photosynthesis photons raise __________ of electrons (a) reduction potential (b) oxidation potential (c) flow (d) none

6. Oxidation potential of DCPIP is ______ than water (a) higher (b) lower (c) same (d) none

7. Which one is not oriented towards lumen side ? (a) OEC (b) PC (c) Cytf (d) Cyt b₆

(a) Chloroplast – C – E - B – D – A , (b) Chloroplast - A - E – B – C – D (c) Chloroplast – C – E - B – A – D and (d) Chloroplast - A - B – E – C – D

9. ATP synthase is located in (a) granal lamelle (b) stromal lamelle (c) lumen (d) stroma

10. Which statement is not true about OEC ? (a) It catalyzes the evolution of oxygen (b) It is oriented towards stromal side (c) It provides 4 electrons to PSII (d) It acts as a proton pump.

11. Which species accepts electrons from water in OEC ? (a) Tyr (b) [ Mn – complex ] ⁰

12. How many NADPH molecules are produced for each molecule of oxygen evolved ?
(a) 1 (b) 2 (c) 3 (d) 4

13. How many molecules of ATP are produced for each oxygen molecule evolved in photosynthesis ?
(a) 1 (b) 2 (c) 3 (d) 4

14. Under which condition electron flow during plant photosynthesis can become cyclic ?
(a) high [NADP] / [NADPH] (b) low [NADP] / [NADPH] (c) In presence of DCMU (d) In presence of DCPIP

Photosynthesis Part III

2007-06-05T22:02:00.000+05:30

Purple bacteria

P870 Reaction Center ( pheophytin – quinone system )

Events :

1. Capture of a photon by antenna Chl Chl + hv ----- Chl * ( exciton )

2. Exciton transfer to the Reaction Center (Chl)₂

3. Excitation ( transfer of electron from exciton ) (Chl)_{2 --------} (Chl)₂^*

4. Charge separation (Chl)₂^*+ Pheo ------- (Chl)₂^·⁺+ Pheo ^·^ˉ ( t = 3 ps )

5. Electron transfer to bound Q_A ( Manaquinone ) Pheo ^·^ˉ + Q_A----- Pheo + Q_A^·^ˉ (t = 200 ps )
6. Electron transfer to loosely bound Q_B ( ubioquinone ) Q_A^·^ˉ + Q_B ------- Q_A+ Q_B^·^ˉ ( t = 6 μs )
7. Reduction of Q_B Q_B^·^ˉ + 2 H⁺ -------- Q_BH₂

8. Diffusion of Q_BH₂ through the membrane to the Cytbc₁ complex

9. Q cycle occurs QH₂ + 2Cytc₁ (oxidized ) + 2H⁺_N = Q + 2Cytc₁( reduced ) +4H⁺_P

10. Electron transfer from Cytbc1 complex to (Chl)₂^·⁺ via Cyt c₂ (t = 270 ns )

How dose an SDS-PAGE really work?

2007-06-05T10:25:00.000+05:30

HOW DOES AN SDS PAGE GEL REALLY WORK? 06/06/2007

The system most people use for separating proteins by gel electrophoresis was formulated by Laemmli (Nature 227:680-685 [1970]). It is such a commonly used laboratory technique that nowadays we take it for granted and I dare say that many of us don’t know how a discontinuous pH gel system actually works.

First the sample. Most SDS PAGE sample buffers contain the following: SDS (sodium dodecyl sulphate, also called lauryl sulphate), b-mercaptoethanol (BME), bromophenol blue, glycerol, and Tris-glycine at pH 6.8. BME is added to prevent oxidation of cysteines and to break up disulfide bonds. Bromophenyl blue is a dye that is useful for visualizing your sample in the well and tracking its progress through the gel. Glycerol is much more dense than water and is added to make the sample fall to the bottom of the sample well rather than just flow out and mix with all the buffer in the upper reservoir. The interesting components are the buffer and the SDS.

SDS is an ionic detergent that binds to the vast majority of proteins at a constant ratio of 1.4 gm SDS/gm protein. A few proteins like tubulin do not bind at this ratio and this is one reason why some proteins migrate anomalously (there are other reasons as well so you shouldn’t put too much faith in the apparent molecular weight estimated from an SDS PAGE gel). Since SDS is an anionic detergent it imparts a negative charge to all the proteins in your sample. More importantly, these charges swamp the inherent charge of the proteins and give every protein the same charge-to-mass ratio. Because the proteins have the same charge-to-mass ratio, and because the gels have sieving properties, mobility becomes a function of molecular weight. But what about running gels, stacking gels, electrode buffer, and all these different pHs?

The velocity of a charged particle moving in an electric field is directly proportional to the field strength and the charge on the molecule and is inversely proportional to the size of the molecule and the viscosity of the medium. Adding a gel with sieving properties (that is a gel where the resistance to the motion of a particle increases with particle size) increases the differences in mobility between proteins of different molecular weights. This is the basis of separation. The problem now becomes how to line up all the proteins in an orderly fashion at the starting gate. That’s where the discontinuous pH part comes in.

Laemmli gels are composed of two different gels (stacker and running gel), each cast at a different pH. In addition, the gel buffer is at a third, different pH. The running gel is buffered with Tris by adjusting it to pH 8.8 with HCl. The stacking gel is also buffered with Tris but adjusted to pH 6.8 with HCl. The sample buffer is also buffered to pH 6.8 with Tris HCl (note all the chloride ions – they will become important in a minute). The electrode buffer is also Tris, but here the pH is adjusted to a few tenths of a unit below the running gel (in this case 8.3) using only glycine – nothing else. We run our gels at constant voltage.

So here’s what happens when you turn on the power. Glycine is a weak acid and it can exist in either of two states, an uncharged zwitterion, or a charged glycinate anion (that is to say, negatively charged). At low pH it is protonated and thus uncharged. At higher pH it is negatively charged. When the power goes on the glycine ions in the running buffer want to move away from the cathode (the negative electrode) so they head toward the sample and the stacking gel. The pH there is low and so they lose a lot of their charge and slow down. Meanwhile, in the stacker and sample the highly mobile chloride ions (which are also negatively charged) move away from the cathode too. This creates a narrow zone of very low conductance (in other words very high electrical resistance) in the top of the stacking gel. Because V=IR almost all of the voltage that you put across the gel (110 Volts is typical for stacking) is concentrated in this small zone. The very high field strength makes the negatively charged proteins move forward. The trick, however, is that they can never outrun the chloride ions. If they did they would find themselves in a region of high conductance and very low field strength and would immediately slow down. The result is that all the proteins move through the stacker in a tight band just behind the moving front of chloride ions. Behind them, the pokey glycine ions straggle along as best they can (they do move, but with lower mobility than the chloride ions).

The effect of this moving zone of high voltage is that all the proteins reach the running gel at virtually the same time so that migration of the proteins is truly a function of molecular size and not some complicated function of how carefully you loaded the gel and when you started the voltage.

When the big caravan of ions hits the running gel everything changes. The pH goes way up and the glycine becomes deprotonated (and thus more negatively charged). The mobility of the glycine goes way up and the mobility of the proteins goes way down (due to the sieving properties of the gel). The result is that the glycine races past the protein and the proteins are no longer in a narrow zone of very high resistance (and very high electric field). They find themselves in a much more relaxed, uniform electric field where they can chill out a bit. Move at their own pace.

Tips for running good gels:

1. After pouring the running gel, carefully overlay it with ethanol or another imiscible liquid. This will give you a nice flat surface. Also, since polymerization of acrylimide is inhibited by oxygen it will speed up polymerization.
2. For the mini-gels we run the minimum protein loading per well (single band) is 0.1 µg for standard Coomassie staining and 2 ng for silver staining. I haven’t tested it but my impression is that Simply Blue staining is within a factor of two as sensitive as standard Coomassie staining.
3. The maximum protein loading per well (for a mixture of proteins of different sizes) is about 40 µg. If you exceed amount this your gel will look like crap.
4. KCl causes SDS to precipitate. If you samples contain KCl you should dilute them or methanol precipitate them and resuspend them in 1X sample buffer. With low concentrations of KCl (<200 mM) you can run them on the gel but you should loaed every lane with sample buffer containing the same concentration of KCl (even if they are blanks). This will help the gel run a little less anomalously.
5. If your sample buffer turns yellow, it is at the wrong pH. Add NaOH or

Safety Notes:

- Acrylimide is extremely toxic, causing central nervous system paralysis. It can be absorbed through unbroken skin. If skin comes in contact with acrylimide solution or powder, wash immediately with soap and a lot of water. Unpolymerized acrylimide should be polymerized with excess catalyst and disposed of with solid waste. DO NOT POUR UNPOLYMERIZED ACRYLIMIDE DOWN THE SINK.
- Amonium Persulfate should be made up fresh or used from a relatively fresh stock. It goes bad after a week or two in the refrigerator. It can be disposed of by dilution with water and pouring down the sink.
- TEMED should be stored in the refrigerator in dark glass bottles. A bottle should be good for about a year, maybe longer.

A good website for photosynthesis

2007-06-04T15:17:00.000+05:30

http://www.life.uiuc.edu/govindjee/paper/gov.html

Metabolism of Glucose- Glycolysis Biochem 222

2007-06-02T18:33:00.000+05:30

Dear students
please ask me questions about the chapters we have finished viz. energetics and glycolysis by clicking on comments.

vijayendra agrawal

Photosynthesis light reaction part II

2007-06-02T16:13:00.000+05:30

Hill reaction

Hill reaction demonstrates that if an appropriate electron acceptor is provided, water can be made to loose electron in presence of light and evolove oxygen.

2H2O + A = 2AH2 +O2
A can be 2,6-dichloro phenol indophenol.
Mix A with chlorophyll, and shine, blue color becomes colorless.

Photosynthesis ( Light Reaction ) Part I

2007-06-02T15:56:00.000+05:30

Difference between oxidative phosphorylation and photophosphorylation.

1. In OP, NADH is electron donor whereas in PP water is electron donor.
2. In OP, oxygen is converted to water but in PP, water is converted to oxygen.
3. In PP, photons are required but in OP they are not required.
4. The reason for the need of photons is that water has a very low oxidation potential (-0.82 V) and therefore cannot liberate electron without additional energy. On the other hand, NADH has pretty high oxidation potential (-0.32 V) and therfore can give electrons.

Photosynthesis happens in thylakoids. The fluid surrounded by thylakoid membrane is known as lumen. Membranes of thylakoids is known as lammeli. The aqueous phase outside thylakoid but surrounded by inner membrane is known as stroma. Stroma is site of carbon assimilation reaction.

USC Biochemistry

Questions

PHOTOSYNTHESIS REVIEW QUESTIONS FOR BIOLOGY

Photosynthesis

Enzyme kinetics

more question for bioenergetics and oxidative phosphorylation

question for oxidative phosphorylation

questions for amino acids and nucleotide biosynthesis

questions for glycolysis

questions from Bioenergetics

A mechanical analogy for light reactions

Science Writing I Feb. 26, 2008

My arrival

Biochem 323 Plant Biochemistry August 8, 2007 Exam Questions

Answer to Biochem 323 Plant Biochemistry July 26 - 27, 2007

Answers to 1st term Test

Class Test Biochem 323 Plant Biochemistry June 27, 2007

C4 Plants

Photorespiration

Regulation of Calvin cycle by light

Calvin cycle II

Calvin Cycle I

Photosynthesis VI

Phtosynthesis V

Photsynthesis IV

Ag - Biotech

A Good Link on Bioinformatics

Good book on photosynthesis

Photosynthesis Class Test

Photosynthesis Part III

How dose an SDS-PAGE really work?

A good website for photosynthesis

Metabolism of Glucose- Glycolysis Biochem 222

Photosynthesis light reaction part II

Photosynthesis ( Light Reaction ) Part I