Name:  _________________________

 

Biological Sciences 4087

Final Exam

5/9/2007

 

Total:  150 points

1.(24pts) The following quotations are from Science 314 1308 (06). Define the term in bold.  Don’t worry about the rest of the quotation.

A.  “The peak fractions (29 to 30) from (B) were subjected to SDS-polyacrylamide gel electrophoresis”- method for separating proteins by molecular weight; can be used to determine the molecular weight of the subunits of a protein

 

B.  “S127G mutant, which was devoid of lipase activity, retained substantial liposome-disrupting activity” (Name the amino acids)- serine and glycine

 

C.  “Taq polymerase”- a heat-stable DNA polymerase used in polymerase chain reaction (PCR)

 

D.  “The expression vectors described above were transformed by heat

shock into the Rosetta-gami(DE3)pLysS strain of E. coli…”- plasmid which contains sequences for prokaryotic transcription and translation to allow synthesis of foreign proteins in E. coli.

 

E.  “…The film was hydrated with 100 mM glycine buffer…”- weak acid or base that resists changes in pH of a solution

 

F.  “one in which a stop codon was substituted…”-(give one example) terminates translation:  UAA, UAG, UGA

 

2.(5pts) In one sentence, summarize the journal article used for the take home problem set.

C. novyi-NT  in combination with liposome-encapsulated doxorubicin proved effective in reducing tumor size and extending life span in mice.

 

3.(4pts) A. Describe the structure of glycogen.

a1-4 polymer of glucose with a1-6 branches

 

B. Describe the structure of cellulose.

b1-4 polymer of glucose

 

4.(4pts)  A. For a competitive inhibitor, when the inhibitor is added to an enzyme reaction, the Vmax (CIRCLE ONE):

 

DECREASES

REMAINS THE SAME

INCREASES

 

B.  For a Lineweaver-Burk plot, the y-intercept is equal to (CIRCLE ONE):

 

-1/Km

1/Vmax

 

5.(3pts) Answer the following with respect to the Sanger method of DNA sequencing.

 

A.  The direction of synthesis is 5’ to 3’

 

B.  Is a primer required?  yes

 

C.  What terminates polymerization?  dideoxynucleotides

 

6.(6pts) A.  The T state of hemoglobin has a (CIRCLE ONE):

 

LOW AFFINITY FOR O2

HIGH AFFINITY FOR O2

 

B.  BPG stabilizes the (CIRCLE ONE): 

 

THE R STATE OF HEMOGLOBIN

THE T STATE OF HEMOGLOBIN

 

C.  Describe the subunit structure of hemoglobin.

a2b2

 

7.(4pts) For each of the following methods of regulation, name an example of an enzyme that is regulated by that method.  

 

Enzyme

 

allosteric

 

aspartate transcarbamoylase

 

reversible covalent modification

 

glycogen phosphorylase

 

isozymes

 

lactate dehydrogenase

 

proteolytic activation

 

chymotrypsin

 

8.(12pts) - The following questions refer to insulin secretion from pancreatic b cells.

A.  Name the main transporter that brings glucose into pancreatic b cells.

GLUT2

 

B.  The Kt for glucose transport by this transporter is (CIRCLE ONE):

 

MUCH LOWER THAN THE BLOOD GLUCOSE CONCENTRAION

MUCH HIGHER THAN THE BLOOD GLUCOSE CONCENTRATION

 

C.  Name the enzyme that produces most of the ATP that results from glucose oxidation.

 

ATP synthase

 

D. In b cells, ATP closes membrane K+ channels.

 

E.  This results in (CIRCLE ONE):

 

DEPOLARIZATION OF THE MEMBRANE

HYPERPOLARIZATION OF THE MEMBRANE

 

F.  As a result, voltage-dependent Ca2+ channels open and result in insulin secretion.

 

9.(7pts) A. Name 3 elements of a eukaryotic promoter.

TATA box, Inr, DPE, CAAT, GC, Enhancer

 

B. Name an example of an RNA-directed DNA polymerase.

reverse transcriptase

 

C. The enzyme that catalyzes most DNA synthesis in E. coli is

DNA polymerase III

 

10.(18pts) Identify the following structures.

 

A. fructose

 

B. heme

 

C. cerebroside

 

D. ATP

 

E. phenylalanine

 

F. S-adenosylmethionine

C.
 

C.
 

F.
 

 

11.(21pts) Fill in the blanks.

PATHWAY

FUNCTION

REGULATORY ENZYME

LOCATION IN CELL

citric acid cycle

acetyl CoA to 2 CO2; 3 NADH, FADH2, GTP

C skeletons

citrate synthase, isocitrate dehydrogenase, a-ketoglutarate dehydrogenase

mitochondrion

gluconeogenesis

make glucose from amino acids, lactate, glycerol, propionate

pyruvate carboxylase

(PEP carboxykinase, fructose 1,6 bisphosphatase, glucose 6 phosphatase)

mitochondrion, cytosol, ER

Calvin cycle (dark reactions)

fix CO2 into organic carbon

Rubisco

chloroplast stroma

fatty acid synthesis

make fatty acids from acetyl CoA using NADPH

acetyl CoA carboxylase

cytosol

pyrimidine synthesis

U, C, T nucleotides

aspartate transcarbamoylase

cytosol

fatty acid b oxidation

degrade fatty acids to acetyl CoA, make FADH2 and NADH each round

carnitine acyltransferase I

mitochondrion

glycolysis

glucose to 2 pyruvate, make 2 ATP and 2 NADH, C skeletons

hexokinase, phosphofructokinase, pyruvate kinase

cytosol

glycogen degradation

glycogen to glucose-1-phosphate

glycogen phosphorylase

cytosol

 

12.(6pts)  A.  All 27 carbon atoms in cholesterol come from the citric acid cycle intermediate:

 

acetyl CoA

 

B. Name the regulatory enzyme for cholesterol synthesis. HMG CoA reductase

 

C. Name 3 biological molecules that are synthesized using cholesterol as a precursor.

 

vitamin D

bile salts

steroid hormones

 

13.(6pts)  Name an amino acid that is

A.  synthesized from pyruvate ala, val, leu

 

B.  used to make serotonin trp

 

C.  degraded to make oxaloacetate asp, asn

 

D.  used to make the pyrimidine ring of UTP asp, gln

 

E.  used to make the purine ring of AMP asp, gln, gly

 

F.  used to make NO arg

 

14.(10pts) On the back of this sheet, write out the urea cycle. 

see Fig. 23.17

 

15.(8pts)  A. In type 1 diabetes mellitus, the absence of insulin causes unregulated

 

secretion of the hormone glucagon by the a cells of the pancreas.

 

B. What causes high blood glucose concentrations in untreated type 2 diabetes mellitus?

 

insulin resistance

 

C. Name 2 proteins that are phosphorylated by protein kinase A in adipose cells when they are stimulated by norepinephrine signaling due to the action of leptin.

 

hormone-sensitive lipase

perilipin

 

16.(12pts) Define:

A. siRNA- short interfering RNA, made by action of DICER on dsRNA, becomes part of RISC and cleaves complementary mRNAs, decreasing protein synthesis.

 

B. ferredoxin- FeS protein in photosynthetic electron transport chain

 

C. MoFe protein- part of nitrogenase, it binds N2 and reduces it to NH3

 

BONUS (5pts):  What is the brand name of liposome-encapsulated doxorubicin?

Doxil