Question 1. List the following items in order of size from the smallest to largest:

• A. Nucleosome smallest__C_____

• B. Mitochondrion __A_____

• C. Diameter of a DNA molecule Largest__B_____

Question 2. Give experimental evidence to support that DNA, and not protein, is a genetic material.

• See experiments by Griffiths and Avery et al. on R and S strains of Streptococcus pneumoniae [Figs. 5-3 and 5-4] or

• Experiment by Hershey and Chase on T2 virus infecting E. coli cell [Fig. 5-5].

Fig. 5-3, p. 173Griffith’s experiment regarding DNA’s characteristics.

Fig. 5-4: DNA is genetic material (Avery et al.).

Is the genetic material protein or DNA?Hershey and Chase expt. (Fig. 5-5, p. 174)

Question 3. Fill in the blanks:

• Disulfide bonds can form between two cysteine side chains in proteins.

• The 5’end of RNA is capped by the addition of 7-methylguanosine .

• Nucleotides are joined together by phosphodiester linkage between 5’and 3’ carbon atoms to form nucleic acids.

Question 4. Short answers.A. Cholesterol comprises up to 50% of membrane lipids in

many animal cells. Explain in no more than two sentences why it is not possible to form lipid bilayers with cholesterol alone.

• Membranes are stabilized by phospholipids which are strongly amphipathic, that is with very strong hydrophilic (charged, both (+) and (-) as well as with polar groups) and very strong hydrophobic hydrocarbon chains of 12-22 carbons in length. Cholesterol is not sufficiently amphipathic to form a stable bimolecular leaflet in which the only hydrophilic group is the hydroxyl, with is only weakly polar. The rest of the molecule is completely hydrophobic.

Question 4. Short answers.

b. RNA splicing is considered an important rather than a wasteful process? Explain.

RNA splicing makes genetic recombination between exons of different genes more likely, leading to formation of different mRNAs and evolution of genes for new proteins.

Question 5. Briefly describe the structure-function relationship for each of the following terms:

A. Small nuclear ribonucleoprotein particles: The snRNPs are special kind of enzymes which are composed of a complex of proteins and RNA. They catalyze removal of introns from RNA (RNA splicing). Different types of snRNPs recognize different regions of introns by complemetary base-pairing (e.g. U1 snRNP recognize 5’splice site).

b. Aminoacyl-tRNA synthetases: are the enzymes with two binding sites, one for a specific amino acid and the other for a specific tRNA. These enzymes catalyze the ATP-mediated covalent coupling of an amino acid to its appropriate set of tRNA molecules.

c. Lysosomes: Lysosomes have a number of hydrolytic enzymes e.g. proteases which function at acidic pH and cause hydrolysis of macromolecules. Low pH in lysosme is maintained by influx of proton by H+-ATPase pumps on lysosome membrane.

1. Where are Polymerases?2. Where are transcription start/stop sites?3. Where are the 3’ and 5’ ends of the transcript?4. Which direction are the RNA polymerases moving?5. Why are the RNA transcripts so much shorter than the length of the DNA that

encodes them?

See Figs. 7-9 and 7-17 for answer to this question.

Transcription of two genes seen be EM [Fig. 7-8]

Question 7: Write a short essay on the biological information flow (DNA RNA protein) in eucaryotes.

The essay should contain these points: [Fig. 7-20]• Transcription of a gene by RNA polymerase

(Fig. 7-9)• mRNA processing e.g. 5’ RNA capping, splicing,

3’ polyadenylation [Figs. 7-12, 7-17]• mRNA transport to cytosol [Fig. 7-19]• precise role of genetic code, tRNA, ribosomes,

mRNA in translation [Figs. 7-26, 7-32].

Question 8. Which of the following statements are correct? Explain your answers.

• Lipids in a lipid bilayer do not rotate rapidly around their long axis.

• Lipids in a lipid bilayer do not flip flop readily from one lipid monolayer to the other.

• Glycolipids move through different membrane-enclosed compartments during their synthesis but remain restricted to one side of the lipid bilayer.

See question 11-9 and its answer in your text book (Pages 387, A:30)

Problem Solving: Shown in the table below are the sequences of selected amino acids from different types of human hemoglobin (abbreviated Hb). Some forms of hemoglobin are defective, while others are not. From what you know about protein structure, explain why Sickle Cell and Hammersmith Hbs are defective while delta Hb is not.

Amino acid numberType of Hemoglobin (Hb) 3 4 5 6.. 9... 40

41 42 43Normal beta Hb Leu Thr Pro Glu Ser Gln Arg Phe

GluSickle Cell Hb (defective) Leu Thr Pro Val Ser Gln Arg Phe

GluHammersmith Hb (defective) Leu Thr Pro Glu Ser Gln

Arg Ser GluNormal delta Hb Leu Thr Pro Glu Thr Gln Arg Phe

Glu

Panel 2-5, p75 Acid side chains-negatively charged

Panel 2-5, p75Polar side chains-interact well with water, can form H-bonds

Panel 2-5, p75

Nonpolar groups-energetically unfavorable for them to contact water