清华大学XX年生物化学1本科期末考试试题

考试科目：生物化学

考试时间：

考试类型：期末试题

1: how many carbons does Arachidic acid have? (20 carbons)

2: how many double bonds does Arachidonic acid have? (4 double bonds)

3: list two advantages that fats have over sugars as stored fuels (more energy gram for gram; no hydration needed)

4: where inside the cells are most of the phospholipids degraded (lysosomes) 5: oligosaccharide head groups determine the blood type of an individual. How are they attached to the plasma membrane? (glycosphingolipids or lipids and surface proteins)

6: list at least one genetic disease that could result from abnormal accumulation of membrane lipids (Tay-Sachs, Sandhoffa€?s, Fabrya€?s, Gauchera€?s, or Niemann-Pick diseases)

7: list the three main eicosanoids that produced from arachidonic acid (prostaglandins; thromboxanes; and leukotrienes).

8: list one NASID you know (aspirin, ibuprofen, or acetaminophen or meclofenamate) 9: list two fat-soluble vitamins (A, D, E, K)

10: which vitamin can be derived from beta-carotene (A).

11: which year was the fluid mosaic model proposed? (1972)

12: why the thickness of most biological membranes is thicker than 3nm, the standard thickness of lipid bilayer? ( due to association of proteins to the membrane and carbohydrates on the membrane)

13: Please define the transition temperature of the lipid bilayer (the temperature above which the paracrystalline solid changes to fluid)

14: If a membrane protein has its N-terminus exposed to the outside of the cell while its C-terminus resides in the cytosolic compartment, is it a type I transmembrane protein ? (yes).

15: How can you predict if a protein has a transmembrane domain? (hydropathy or hydropathy index, or hydropathy plot).

16: Name the two cell surface receptors that HIV use to enter cells (CCR5 and CD4).

17: For the Na+ K+ ATPase, how many Na+ and K+ can it move across the membrane for the hydrolysis of one ATP (2 K+ in, 3 Na+ out).

18: what drives F-type ATPases to synthesize ATP? (proton or proton gradients) 19: The acetylcholine receptor is a _____-gated channel (Ligand)

20: The neuronal Na+ channel is a _____-gated channel (voltage)

II.

D and H

(3 points) The antiparallel orientation of complementary strands in duplex DNA was elegantly determined in 1960 by Arthur Kornberg by nearest-neighbor analysis. In this technique, DNA is synthesized by DNA polymerase I from one

(alpha-32P)-labelled and three unlabelled deoxynucleoside triphosphates. The resulting product is then hydrolyzed by a Dnase that cleaves phosphodiester bonds on the 3a€? sides of all deoxynucleotides. For example, in the labeled dATP reaction,

ppp*A + pppC + pppG +pppT --?€?? a€|pCpTp*ApCpCp*ApGp*Ap*ApTpa€| -?€??

a€|+Cp+Tp*+Ap+Cp+Cp*+Ap+Gp*+Ap*+Ap+TpTa€|

If in the dATP labeled reaction the relative radioactivity of Tp*, Gp*, Cp* and Ap* is 0.2, 0.3, 0.4 and 0.1.

In the labeled dGTP reaction, Tp* radioactivity will be

A) 0.1

B) 0.2

C) 0.3

D) 0.4

E) 0

In the labeled dCTP reaction, Tp* radioactivity will be

F) 0.1

G) 0.2

H) 0.3

I) 0.4

J) 0

(B)

(1 point) A molecule of amylopectin consists of 1000 glucose residues and is branched every 25 residues. How many reducing ends does it have?

A) 0

B) 1

C) 25

D) 40

E) 41

F) 1000

(1 point) (D)

A mirror image of

B form DNA is

A) Z-DNA

B) A-DNA

C) B-DNA

D) does not exist in nature

(1 point) (A)

Which of the following statements is not true?

A) all natural occurring DNA is in B form

B) A-DNA probably does not exist in vivo

C) Both major groove and minor grove of B-DNA are deep

D) B-DNA is right handed, while Z-DNA is left handed.

(1 point) (A)

Lung fish has 100,000,000 kb (kb=1000 base pairs) for its haploid genome. The total length of this DNA is

A) 34 m

B) 3.4 m

C) 1 m

D) 17 m

E) 1.7 m

F) 34 mm

(3 points?) (1.5 point) A, D, E

Both tubes X and Y contain the same DNA in 0.1 M NaCl solution. In tube X more NaCl is added and in tube Y some ethanol is added. Which of the following is (are) correct?

A) tube X will have higher Tm than Y

B) tube Y will higher Tm than X

C) tube X and Y will have the same Tm

D) tube X will have higher Tm than original

E) tube Y will have lower Tm than original

(1 point) (D)

Which of the following is NOT correct?

A) Glycosaminoglycan chains are linear

B) Glycosaminoglycan chains are acidic

C) Glycosaminoglycans are composed of repeating disaccharide units

D) Different glycosaminoglycans have the same disaccharide units

(1 point) (C)

The so-called table sugar or cane sugar is a disaccharide of

A) galactose and glucose

B) 2 glucose units

C) glucose and fructose

D) galactose and fructose

(1 point) (A)

Lactose is a disaccharide of

A) galactose and glucose

B) 2 glucose units

C) glucose and fructose

D) galactose and fructose

(1 point) (B)

Choose the INCORRECT statement. In dideoxy sequencing or Sangera€?s method,

A) the newly synthesized DNA is labeled while the template is not

B) the template has to be labeled

C) a primer has to be used

D) ddNTPs are used to terminate elongation

(1 point) (B)

Choose the INCORRECT statement. In Maxam-Gilbert sequencing or chemical method,

A) the template is labeled

B) a primer is needed

C) enzyme is not needed

D) nucleotide analogues are not used

(1 point) (D)

uv radiation in the solar light directly cause which kind of the following DNA damage?

A) deamination

B) methylation

C) DNA breakage

D) pyrimidine dimer formation

E) depurination

(1 point) (C)

RNA is sensitive to alkaline hydrolysis because

A) RNA has uridine instead of thymidine in its sequence

B) RNA has hydroxyl group at 4th and 5th positions of its ribose

C) RNA has hydroxyl group at 2nd and 3rd positions of its ribose

D) RNA is mostly single stranded

E) RNA forms three dimensional structure

(1 point) (D)

Which of the following is NOT a carbohydrate

A) glucose

B) maltose

C) glycogen

D) proteglycan

E) glycosaminoglycan

(3 points?)(1.5 point) C, E, F

Which of the following is (are) NOT branched

A) glycogen

B) starch

C) cellulose

D) amylopectin

E) amylose

F) chitin

(1 point) (A)

Shown on the right is

A) A

B) G

C) T

D) C

E) U

(1 point) (C)

Shown on the right is

A) A

B) G

C) T

D) C

E) U

III.

1) The follows are the important features of signal transduction systems EXCEPT :

A. Amplification

B. Desensitization/turn-off

C. Specificity

D. Simplicity

E. Integration

2) Relative to the outside of a cell, calcium concentration inside the cell is:

A. Higher

B. Lower

C. Approximately equal

3) Hydrolysis of GTP to GDP is essential for the normal function of all the GTP-binding proteins

A. True

B. False

4) cAMP-dept kinase (PKA) regulates only sugar metabolism

A. True

B. False

5) The follows are among the intracellular second messengers EXCEPT:

A. cAMP

B. cGMP

C. Ca2+

D. IP3

E. ATP

6) How does IP3 work as a second messenger?

A??? By activating phaspholipase C

B??? By activating protein kinase C

C. By activating Ca2+ channels

D. By activating G?±S

7) The insulin receptor has tyrosine kinase activity which phsophorylates several different proteins including itself

A. True

B. False

8) The insulin signal is amplified via the MAP kinase cascade

A. True

B. False

9) All signaling pathways are very unique and very specific, and they dona€?t talk to each other

A. True

B. False

10) Which of the followings is UNIQUE to TGF?2receptors?

A. transmembrane proteins

B. Ser/The receptor kinases

C. Ligand binding activity present in the extracellular domain

D. Become activated upon ligand binding

11) The activity of CDK proteins is tightly regulated by the following events EXCEPT :

A. Phosphorylation

B. Dephosphorylation

C. Cyclin binding

D. Ubiquitination

E. CDK inhibitors

12) Caspases play essential roles in apoptosis. The following are among their effects EXCEPT:

A. Activation of DNase

B. Activation of other caspases

C. Inducing cell shrinkage

D. Stimulating gene expression

13) Cancer can be a result of the following events EXCEPT

A. Activation of mitogenic signals

B. Cell cycle arrest

C. Inactivation of negative regulators for cell growth

D. Blockage of cell apoptosis

14) In 2002, the Nobel Price for Physiology or Medicine was awarded for the research on

A. Phosphorylation

B. Cell cycle

C. Apoptosis

D. G protein

E. Oncogenes

Answers for Biosignaling:

1) D

2) A

3) A

4) B

5) E

6) C

7) A

8) A

9) B

10) B

11) D

12) D

13) B

14) C

IV.

1. Which of the following statement about 2,3-bisphosphoglycerate (BPG) is wrong:

(d)

(a) BPG binds at a site distant from the oxygen-binding site of hemoglobin.

(b) BPG regulates the oxygen-binding affinity of hemoglobin in relation to the pO2 in the lungs.

(d) BPG greatly increases the affinity of hemoglobin for oxygen.

2. Antibodies of the IgG class : (d)

(a) consist of four subunits.

(b) have noncovalent bonds and disulfide crosslinks.

(d) All three choices are correct.

3. ELISA allows for rapid screening and quantification of the presense of an antigen in a sample. Which of the following steps of ELISA is wrong: (a)

(a) Proteins in a sample are adsorbed to an inert surface, and the surface is washed with a solution of specific protein similar to the protein of interest, to block proteins in subsequence steps from also adsorbing to these surfaces.

(b) The sample was treated with a solution containing antibodies against the protein of interest. Unbound antibody is washed away, and the sample is treated with with a solution containing antibodies against the primary antibody.

(d) After unbound secondary antibody is washed away, the substrate of the antibody-linked enzyme is added and the product formation is proportional to the concentration of the protein of interest in the sample.

4. The major proteins of muscle are: (c)

(a) Myosin and hemoglobin

(b) Actin and troponin

(d) Myoglobin and actin

5. Positive cooperative binding can be identified by (c)

(a) a hyperbolic binding curve.

(b) a Hill plot with a slope less than one.

(d) Choices a) and b) are both correct.

6. Which pair of amino acids absorbs the most UV light at 280 nm? (b)

(a) Thr & His.

(b) Trp & Tyr.

(d) Phe & Pro.

7. The strong conclusion from Anfinsen's work on RNaseA was that: (b)

(a) 100% enzyme activity corresponds to the native conformation.

(b) the sequence of a protein determines its structure.

(d) disulfide bonds (S-S) in proteins can be reduced in vitro.

(e) irreversible denaturation of proteins violates the "Thermodynamic Hypothesis".

8. Which of the following statement about protein folding is wrong: (c)

(a) Some proteins undergo assisted folding by chaperons.

(b) Polypeptides fold rapidly by a stepwise process.

(d) A loss of 3-d protein structure sufficient to cause loss of function is called denaturation.

9. Hydrogen bonds in a-helices are (d)

(a) more numerous than Van der Waals interactions.

(b) not present at Phe residues.

(d) roughly parallel to the helix axis.

(e) about 5 ?… in length.

10. What is the appoximate molecular weight of a protein with 200 amino acid residues in a single polypeptide chain: (b)

(a) 11000

(b) 22000

(d) 66000

1. What are the two most striking characteristics of enzymes? (1 pt, 0.5 pt x

Answer:

The two most striking characteristics of enzymes are their 1) catalytic power, 2) specificity.

2??? How does an enzyme gain its catalytic power? (2 pt, 1 pt x 2)

Answer:

1) Enzymes bring substrates together in an optimal orientation;

2) They catalyze reactions by stabilizing transition states;

3. Is the structure of the binding site of an enzyme complementary to its substrate or to transition state? Why? (1 pt, 0.5 pt x 2)

Answer: An enzyme is in complementary in structure to the transition state of the substrate because the activation barrier is lowered during such a binding. 4???How many general ways of regulations on enzyme Activity? (2 pts, 0.5 pt x 4)

Answer:

1) Feed-back Inhibition

2) Regulatory Proteins

3) Covalent Modification

4) Proteolytic Activation

5. List the common features of enzymes (2.5 pts, 0.5 pt x 5)

Answer:

1) The active site take up small volume compare with the entire protein volume;

2) The active sites are composed of amino acid residues located in different positions on a linear sequence;

3) An enzyme binds to its substrate via multiple weak interactions;

4) Active sites are clefts or crevices;

5) The specificity of binding depends on precisely defined arrangement of atoms in an active site.

6. How many types of weak interactions involved in the binding of a substrate by an enzyme? (2 pts, 0.5 x 4)

Answer:

1) Electrostatic interactions; 2) Hydrogen bonds; 3) van der Waals forces; 4) Hydrophobic interactions.

7. Write down the Michaelis-Menten equation (0.5 pt), what is the meaning of Km?

(0.5 pt) Under which condition the Km is a measure of the affinity of the enzyme for the substrate? (1 pt), what is the meaning of Vmax? (0.5 pt) What is the physical limit of the value of k3/km? (1 pt)

Answer:

Michaelis-Menten equation: V = Vmax S/(S + Km)

Km is equal to the substrate concentration at which the reaction rate is half its maximal rate value.

Km is a measure of the enzymea€?s affinity only when K2 >> K3 (i.e., the dissociation rate constant of ES is much greater than the catalytic rate constant) Vmax is reached when all the catalytic sites on an enzyme are saturated with substrate.

The physical limit of the value of k3/km is that the enzyme-catalyzed reaction rate is rate of diffusion of both the substrate and the enzyme.

VI.

The following statements are true (T) or false (F)?

1. The biological system is an open system; living organisms are at equilibrium with their surroundings. 1.5

False: The biological system is indeed an open system, able to absorb and exchange materials with the environment. However the living organisms use energy to, for example, keep their own concentrations of ions inside the cells, which are not necessarily of the same concentrations in the environment.

2. Activation energy for a chemical reaction is the energy required for a chemical reaction to convert the reactant to transition state, but does not measure the free energy change between the reactants and products. 1.5

True

3. The mitochondrion is an organelle that functions as an energy regeneration powerhouse, but does not participate in the regulation of cell survival. 1.5

False: Mitochondria indeed play the most important role in energy production; however, they are also a key organelle in the regulation of cell death. In fact, most critical apoptotic or antiapoptotic factors regulate cell death through functional interaction with mitochondria.

4. The Buchnersa€? discovery of fermentation supported the view, as asserted by Pasteur, that fermentation can take place only in living cells. 1.55

False: The Buchnersa€? finding that fermentation can t ake place in yeast cell extracts demonstrated that cell-free extracts possess all the elements for fermentation from sucrose to alcohol. Pasteura€?s view that fermentation is inextricably tied to living cells was wrong. This finding has been regarded as one of the earliest biochemical experiments.

5. Endoplasmic reticulum is a place for posttranscriptional RNA processing, translation, and protein modification. 1.5

False: The ER is a place for protein synthesis (translation), protein modification such as glycosylation and signal peptide cleavage, but not for RNA processing.

6. Carbohydrates function as structural components in nucleic acids, amino acids, and protein modification. 1.5

E. False: Everything but amino acids

7. The present day biochemistry is the interweaving product of historical traditions of biochemistry, cell biology, molecular biology and genetics. 1.5 True