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BIO 184
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Fall 2006
STUDY GUIDE FOR EXAM 1
Use the study questions below to help guide you when studying for the
first exam. I encourage you to come see me during office hours to ask
questions and clarify concepts. I will also be happy to answer questions
by e-mail as long as the required answers are reasonably short and do
not require diagrams.
I.
STRUCTURE OF DNA AND RNA (LECTURE 1)
1.
What are the main criteria that characterize living organisms from inanimate
objects?
2.
Is genetic information held in digital or analog form? What is the difference
between digital and analog information? (Be able to give a few examples)
3.
What does a genetic information molecule need to do? (Be able to list 4 things).
4.
Know the Griffith experiment (1928), the Avery, MacLeod and McCarty experiment
(1940s), and the Hershey-Chase experiment (1952). Know the details of the
experimental design and what each contributed to the idea that DNA, rather than a
protein, is the genetic information molecule.
5.
Why did most biochemists in the 1920s through the 1940s believe that the genetic
information molecule was a protein?
6.
Know the structure of a nucleotide and how nucleotides are linked in singlestranded chains. Be able to identify a phosphodiester bond, the numbered carbons
of the ribose sugar, and the 5’ and 3’ end of a nucleotide or nucleotide chain. You do
not need to know the structure of the bases, but do know where the base attaches
to the sugar.
7.
How do DNA and RNA differ? (Know three fundamental ways.)
8.
What were the contributions of the following scientists to the discovery of the
molecular structure of DNA? Linus Pauling, Rosalind Franklin, Maurice Wilkins,
Erwin Chargaff, Francis Crick, and James Watson.
9.
Know the characteristics of the Watson-Crick model of DNA. (You don’t have to be
able to draw it.)
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10.
How do proteins “read” the sequence of a stretch of DNA, particularly those
proteins that don’t unwind the DNA?
11.
What is a nucleosome, a solenoid (30 nm fiber), and a radial loop? Why does DNA
need to be so heavily packaged around proteins?
12.
What is RNA secondary structure and how does it form? What stabilizes it?
13.
Why are G-C bonds stronger than A-T bonds?
14.
In what way(s) are structural RNAs (e.g. tRNAs, rRNAs) more like proteins than
DNA? In what way(s) are they more similar to DNA?
II.
GENE TRANSCRIPTION (LECTURE 2)
1.
Be able to draw out the central paradigm of molecular genetics. Why is this a very
simplistic way of depicting gene expression?
2.
What is a gene?
3.
Be able to draw out the parts of genes that are common in all organisms – from
bacteria to elephants.
4.
Be able to identify the coding and template strands of a gene (given sufficient
clues).
5.
Which strand (coding or template) is actually “read” by RNA polymerase? Which
strand has the same polarity and sequence (with U’s swapped for T’s) as the
resulting transcript?
6.
Other than coding for polypeptides, what other roles do RNAs play in the cell?
7.
Know the role of sigma factor in transcription initiation in E. coli. What is the
holoenzyme? The core enzyme? What is the closed complex versus the open
complex?
8.
9.
What is a promoter? What do E. coli promoters look like? What binds to the
promoter to initiate the transcription of a gene in E. coli?
How are promoter sequences numbered (with respect to what)?
10.
Why do promoters always contain A-T rich regions of DNA?
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11.
What is a consensus sequence?
12.
Know the two modes of transcriptional termination that operate in E. coli.
13.
How many RNA polymerases does E. coli have? How about eukaryotic organisms?
14.
What subset of genes does each eukaryotic RNA polymerase transcribe?
15.
What three features are common to almost all eukaryotic promoters?
16.
What cis element of the eukaryotic promoter is needed for a “basal level” of
transcription?
17.
What is needed for full transcription of a eukaryotic gene to occur?
18.
How can a regulatory cis element located thousands of base-pairs upstream (5’) of a
eukaryotic promoter affect the level of transcription of the gene controlled by the
promoter?
19.
What is the difference between a “cis” and a “trans” factor?
20.
What is needed for the transition between the closed and open complex during
transcription initiation in eukaryotes?
21.
Why is post-transcriptional processing possible in eukaryotes but not in
prokaryotes?
22.
What is “colinearity of gene expression?” In what types of organisms does
colinearity exist?
23.
In what three ways is a pre-mRNA molecule processed into a mature mRNA
molecule in a eukaryotic cell?
24.
What is the splicesome? What are introns and exons?
25.
Why are eukaryotic genes spliced? (What is the evolutionary logic?)
26.
What is 5’ capping? What is the chemical nature of the “cap”? What is the role of
the cap?
27.
What is the “polyadenylation signal”? What happens juts 3’ to this signal when a
pre-mRNA is processed?
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28.
How long is a typical poly A tail? What is its purpose thought to be?
III.
TRANSLATION OF mRNA (LECTURE 3)
1.
What did Archibald Garrod contribute to our understanding of the relationship
between the genetic material and proteins?
2.
What did Beedle and Tatum show in their 1940’s experiments in Neurospora?
3.
In what ways is the “one-gene-one-enzyme theory” simplistic? What is the most
correct way of rephrasing this statement?
4.
How did Khorana and his colleagues work out the details of the genetic code? Be
able to describe their experimental design and logic.
5.
What is the genetic code and how many nucleotides does each codon contain?
6.
Be able to describe the following characteristics of the genetic code: degeneracy,
stop and start signals, universality, single reading of nucleotides.
7.
What is the 5’ UTR of a mature mRNA? The 3’ UTR? The coding region?
8.
What is the first codon in the coding region of a mature mRNA? What is the final
codon? Can there be more than one possibility in each case?
9.
Be able to describe the primary, secondary, tertiary, and quarternary structure of
proteins. How is each stabilized?
10.
How many different amino acids are used by life? What are the four major
categories of amino acids and how do they differ from one another chemically?
11.
What is the “adaptor hypothesis”? When was it proposed and by whom?
12.
If the anticodon of a tRNA is 5-CCU-3’, what amino acid does it carry?
13.
Of what two types of biological macromolecules is the ribosome comprised?
14.
What 3 discrete tRNA binding sites are located on the ribosome?
15.
How does the initial recognition of the mRNA by the ribosome differ in prokaryotes
and eukaryotes?
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18.
What is the anticodon sequence on the only tRNA that ever enters the “P site”
directly?
19.
Once the first tRNA has entered the ribosome, where does the second one enter?
What defines which amino acid this second tRNA will carry?
20.
What is the reaction catalyzed by peptidyl transferase? Be able to draw out how
the polypeptide begins to form as the tRNAs cycle through the A, P, and E sites
during translation elongation.
21.
What happens when a stop codon enters the bottom of the A site?
22.
What three anticodons are never found on tRNAs?
23.
In what direction is a new polypeptide chain made? To which end of the mRNA does
its N terminus correspond? Its C terminus?
24.
How does a eukaryotic cell “know” where a particular polypeptide belongs?
25.
What happens to a polypeptide that fails to be properly localized?
IV.
MUTAGENESIS AND PROTEIN FUNCTION (LECTURE 4)
1.
Define the term “mutation.”
2.
What is a single-gene mutation? A chromosome mutation? A genome mutation? Be
able to give examples of each.
3.
What are the two main types of gene mutations?
4.
Among point mutations, what is a transition? A transversion? Which is more
common?
5.
What is a silent mutation? How does a silent mutation affect the primary structure
of the polypeptide for which the mutant gene codes?
6.
What is a missense mutation? Under what conditions is a missense mutation likely
to cause a change in the phenotype of the organism? Under what conditions is its
effect likely to be neutral?
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7.
What is a frame-shift mutation and how are such mutation related to the fact that
the genetic code contains three codons per amino acid?
8.
Under what conditions would a frame-shift mutation be likely to result in a nonfunctional protein product? Under what conditions might its effect be neutral?
9.
In what two ways can mutations in promoters affect gene expression?
10.
How is a splice-site mutation likely to affect the primary sequence of a
polypeptide?
11.
What is a trinucleotide repeat expansion (TRE) mutation? How does such a mutation
affect a protein’s level of expression if the repeat is not expanded within the
gene’s coding region? How about if the repeat is expanded within the coding region?
12.
What is the difference between a germ-line and a somatic mutation? Be able to give
an example of a somatic mutation in humans and how it affects the individual’s
phenotype.
13.
What is a reverse mutation as opposed to a forward mutation? Which is more rare
and why?
14.
Why do Siamese cats have coat pigment in the cooler areas of their bodies but not
in the core (warmer) areas?
15.
What is a lethal mutation?
16.
How might a mutation be beneficial to an organism?