PBIO 3300/5300-Spring 2017 NAME___ANSWER KEY___________

Practice Exam II
You have the entire class period to complete all three parts of this exam (i.e., I. General
genetics knowledge, II. Multiple choice, and III. Short answer/Genetics problems). Good luck!
I. General genetics knowledge-20 points (2 points/question)
1. What contribution did Matthew Meselson and Frank Stahl make to genetics?

They showed DNA replication is semiconservative.

2. What contribution did James Watson and Francis Crick make to genetics?

They discovered the double helix structure of DNA.

3. What is the name of the molecular machine that removes introns from eukaryotic RNAs?

The spliceosome.

II. Multiple Choice (select the best answer and answer all 20 questions)-40 points
e____ 1. Which of the following is synthesized 3’ to 5’?
a. the leading strand b. the lagging strand c. mRNA d. a and c e. none of these
e____ 8. Which of the following is a polar, negatively charged amino acid?
a. Lysine b. Arginine c. Histidine d. Serine e. Aspartate
d____ 9. Which of the following is not involved with RNAi?
a. DICER b. dsRNA c. RISC d. DNA polymerase III e. all of these
c____ 14. What molecules are represented in a cDNA library?
a. genomic DNA b. tRNAs c. mRNAs d. rRNAs e. b, c, and d
e____ 19. What do toolkit genes encode?
a. enhancers b. RNA polymerase II c. insulators d. DNA gyrase e. transcriptional activators
a____ 20. Which of the following is not a part of the replisome?
a. RNA polymerase II b. DNA polymerase III c. Helicase d. Primase e. Ligase

III. Short answer/Genetics Problems-40 points (5 points per question)

1. What are enhancers and how do they work?

2. What is the purpose of PCR and how is it performed?

3. Explain how Dideoxy (Sanger) sequencing is performed?

4. Describe the two experiments which first indicated that DNA is the genetic material.

5. What is epigenetics? Name three different epigenetic marks found in eukaryotic genomes and
how each affects gene expression. And finally, explain why should epigenetics be of interest to
you if you have a poor diet or if you smoke?

6. Compare enhancer-blocking insulators to barrier insulators. How do they differ?

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III. Short answer/Genetics Problems-40 points (5 points per question)

1. What are enhancers and how do they work?

Enhancers are short DNA sequences that serve to up-regulation transcription of a nearby
gene. They work by binding to transcriptional activator proteins which in turn bind to co-
activators, which also bind to transcription factors that bind to promoter regions. This
forms a transcription complex that attracts and binds RNA polymerase with high affinity,
resulting in increased or enhanced transcription of the gene.

2. What is the purpose of PCR and how is it performed?

The purpose of PCR is to amplify a DNA sequence (often a particular gene sequence). PCR
requires template DNA, 2 primer sequences which flank the template DNA, the 4 dNTPs, a
heat stable DNA polymerase (Taq Polymerase), a buffer solution with Mg++, and a
thermocylcer (a machine which rapidly changes and holds various temperatures). A PCR
experiment involves approximately 25 cycles with 3 steps per cycles. In step 1, the template
DNA is denatured at 95C, in step 2 the primers are annealed to the template at ~50C, and
in step 3 the Taq Polymerase extends the primer sequences amplifying the template DNA.

3. Explain how Dideoxy (Sanger) sequencing is performed?

Sanger sequencing involves, a DNA template (i.e., the DNA you wish to sequence), a
complementary DNA primer sequence, a DNA polymerase, 4 dNTPs, 4 ddNTPs each of
which is labeled with a different colored fluorescent dye. After annealing the primer to the
template, the DNA polymerase will extend the primer and allow for the incorporation of
the dNTPs and ddNTPs (which will terminate the reaction) at each of the nucleotide
positions. The sequencing reaction is than run through a capillary gel column to separate
the various primer extension products. A laser is used to excite each primer extension
product terminated by one of the 4 ddNTPs and a detector and computer is used to record
the particular ddNTP to reveal the sequence.

4. Describe the two experiments which first indicated that DNA is the genetic material.

Fred Griffith used mice infected by two bacterial strains (a deadly S strain and a mild R
strain) and Avery and coworkers showed that DNA was transferred from the deadly S
strain to the R strain converting or transforming it into the deadly S strain. Subsequently,
Hershey and Chase used radioactive P and S to label bacteriophages (viruses), which infect
E. coli, to show that radioactive P (and hence DNA) was transferred to the E. coli upon
virus infection to genetically reprogram the E. coli to produce new viruses.

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5. What is epigenetics? Name three different epigenetic marks found in eukaryotic genomes and
how each affects gene expression. And finally, explain why should epigenetics be of interest to
you if you have a poor diet or if you smoke?

Epigenetics involves the regulation of gene expression over and above that possible with
conventional genetics, which relates to the sequence of As, Ts, Gs, and Cs in the DNA.
Three important epigenetic marks found in eukaryotic genomes include DNA methylation
(usually of C residues), histone acetylation, and histone methylation. Poor diet and smoking
can alter your epigenetic marks (modifications), which may result in your early demise.
More importantly, you pass on your epigenetic marks to your children, so they may pay the
price for your poor choices in life.

6. Compare enhancer-blocking insulators to barrier insulators. How do they differ?

Enhancer-blocking insulators restrict the activity of an enhancer to a particular gene (in a

particular DNA loop), while barrier insulators are used to bind proteins (including histone
acetyltransferase or HAT) which restrict the spread of heterochromatin (and gene
silencing).