Name: _________________________

 

Biological Sciences 4087

Exam I

2/14/08 <3

Total:  100 points

Be sure to include units where appropriate.

1.(24pts) The following quotations are from Science 318  1780 (07). Define the terms in bold.  Do not worry about the rest of the sentence.

A.  “The samples…were…subject to SDS PAGE…” (give the definition; don’t just say what the letters stand for)

Sodium dodecyl sulfate polyacrylamide gel electrophoresis is a technique used to separate proteins based on their molecular weight.  It can be used to obtain an estimate of the molecular weight of the subunits of a protein.

 

B. “Monoclonal antibodies (mAbs) were produced against the CTD…”

Monoclonal antibodies are produced from clones of a single antibody-producing cell and bind to a single epitope on the antigen.  They are made by fusing spleen cells with myeloma cells to obtain hybridomas.  The hybridomas which produce the desired antibody are selected and grown in culture.

 

C. ”RNA polymerase II is distinguished by its large…repeat domain  …”

RNA polymerase II is a eukaryotic RNA polymerase that produces mRNAs.

 

D. “Western blots of protein extracted from cell lines expressing WT.”

Western blot is a technique used to detect a single protein in an SDS gel.  The sample protein mixture is run on SDS PAGE, blotted to a nitrocellulose sheet, and then probed with an antibody to detect the protein of interest.

 

E. “The epitope is lacking from the Ser5-P band that appears just above the IIa form.”

Epitope is the site on an antigen to which an antibody binds.

 

F. “Ser7 was phosphorylated on transcribing Pol II, appearing strongly at the promoter…”  (in your definition, give an example of part of a eukaryotic promoter)

Promoter is the DNA sequence to which RNA polymerase binds to begin transcription.  Eukaryotic promoters can contain a TATA box, a GC box, a CAAT box, an Inr sequence, or a downstream promoter element (DPE).

 

2.(12pts) RNA polymerase II is phosphorylated at the peptide sequence YSPTSPS.

A. Write out the complete name of the amino acids.

 

Y = tyrosine

P = proline

T = threonine

 

B.  Draw the complete structure of the amino acid Y at pH 7.0.

 

See Fig. 2.10

 

C.  At pH 7, the side chain of the amino acid Y can take part in (CIRCLE ALL THAT APPLY):

 

HYDROGEN BONDS

ELECTROSTATIC INTERACTIONS

VAN DER WAALS INTERACTIONS

 

D. For the peptide YSPTSPS, the amino terminal amino acid is Y

 

3.(6pts)  Phosphate buffers with a pKa of 7.2.  What is the ratio of the concentrations of the base to acid forms of phosphate that is needed to achieve a pH = 7.9?

 

pH = pKa + log [A-]/[HA]

7.9 = 7.2 + log [A-]/[HA]

0.7 = log [A-]/[HA]

5.0 = [A-]/[HA]

 

4.(6pts) Draw the structure of guanosine-5’-triphosphate.  You can do it on the back of this sheet.

See Fig. 4.6

 

5.(11pts)A.  Name this monosaccharide:

glucose

 

B.  This figure shows the (CIRCLE ONE):

 

a ANOMER

b ANOMER

 

C. Describe the structure of cellulose.

Cellulose is a b1-4 polymer of glucose.

 

D. An N-linked carbohydrate is attached to the amino acid (write out the complete name of the amino acid):

asparagine

 

6.(9pts) Name and give the function of the proteins that are required for the elongation phase (that is, not initiation or termination) of DNA replication in E. coli.  Include in your answer the proteins required for complete synthesis of the lagging strand.

 

At the replication fork, helicase serves to unwind the double-stranded DNA.  SSB (ssDNA-binding protein) stabilizes the single-stranded DNA.  Primase synthesizes RNA primers for DNA synthesis.  DNA polymerase III synthesizes DNA in the 5’ to 3’ direction; it has a 3’5’ exonuclease proofreading function, a b clamp to enhance processivity, and a clamp loading complex.  DNA polymerase I removes primers and fills in new DNA on the lagging strand.  DNA ligase seals the nick left by primer removal.

 

7.(3pts) If [H+] = 3.3 x 10-4 M, pH = 3.5

 

8.(7pts) A. Name three types of posttranscriptional processing of eukaryotic mRNAs.

 

5’ 7-methylguanosine cap

 

splicing

 

3’ polyadenylation

 

B. Name 2 types of RNA processing that produce more than one protein from a single gene. 

 

alternative splicing                 RNA editing

 

9.(14pts) Give the specific function of each of the following in prokaryotic translation.

 

A. UAG-stop codon

 

B. GTP-provides energy for initiation, EF-Tu (brings aa-tRNA to ribosome), and EF-G (translocation)

 

C. 16S rRNA-aligns small subunit of ribosome with Shine-Dalgarno sequence

 

D. 23S rRNA-peptidyl transferase; forms peptide bond

 

E. EF-G-translocates ribosome with respect to mRNA; breaks up ribosome after termination of translation

 

F. AUG-initiation codon for methionine

 

G. EF-Tu-brings aminoacyl-tRNA to ribosome

 

 

10.(8pts) Define:

A. hyaluronate-glycosaminoglycan, negatively charged heteropolymer

 

B. buffer-weak acid or base that resists the change in pH of a solution