Last updated 9/6/23

Week 5 Pre-Class Study Guide

DNA replication and mutation

General Format:
These study guides (SGs) will have several parts; only parts 1 and 2 will be turned in
for class credit. All the SGs that are turned in are individual work (you are to express
everything here in your own words). Any instances of copying from other students or
resources will be considered academic misconduct.

Part 1: Reflection/Metacognition: Part of studying is reflecting on what you have learned

and reflecting on the process of your learning, how it may have changed your thinking,
what concerns you have or how you reacted to the material. This is called
metacognition.
Part 2: Learning objectives: We want you to learn how to use a textbook in a way that is
helpful to your learning and is efficient for this class. Texts often have a lot of
information that can be overwhelming when you first read. Not everything in the text will
be covered in detail in the class.
Part 3: Terms (not graded, but feel free to define)
Part 4: Exploration questions, study question, study tips (not graded)

Part 1: Reflection/Metacognition
Length guidelines for weekly metacognitions: We are looking for 1-2 decent paragraphs
or about 200 words. These will be graded on the basis of whether or not your writing
shows evidence of thoughtful reflection on your learning.
Answer 1-2 of the following questions, or add your own.
1. Describe the difference between a forward genetics and reverse genetics screen.
2. Describe two differences between transcription initiation and initiation of DNA
replication.
3. What is the function of telomerase and why is it needed for DNA replication in
eukaryotes?
4. Would a silent, missense, or frameshift mutation be expected to have the
greatest impact on the function of the encoded protein? Why?
5. Compare the rate (i.e., how many base pairs are added per second) of DNA
polymerase and RNA polymerase.
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Part 2: Learning Objectives

Instructions: Prior to class on Monday you should fill out the learning objectives as you
read the assigned reading. This work should indicate a good effort to understand the
upcoming week’s material. You may not be able to completely fill out each learning
objective, and that is ok. We are expecting 80-90% of these objectives filled out. This
document will serve as a good study guide. As you learn more about the topics during
class, fill out this document more fully.

Week 5 DNA Replication and Mutation Learning Objectives

Students will be able to:
● Explain how regulation of gene expression is essential for development of
multicellular organisms.
● Illustrate with a drawing how the DNA replication process works in bacteria and
humans, showing how it is semi-conservative, bi-directional with synthesis
occurring exclusively 5’->3’, and in a primer-dependent and template-dependent
manner.
● Based on your understanding of DNA structure and how DNA polymerase works,
explain why replication of the two strands of a DNA helix needs to involve activity
of enzymes other than DNA polymerase itself.
● Explain how the ends of linear chromosomes are replicated and how this special
process relates to aging, cancer, and stem cells.
● Describe potential sources of mutation and use correct terms for evaluating the
impact of various types of mutations at both the molecular and organismal level.
● Given an example of a particular mutation in the coding or regulatory region of a
gene, predict what effect it could have on the gene’s expression and protein’s
abundance or activity.
● Given an experimental procedure similar to Meselson-Stahl, make predictions
about the results if replication were conservative, semiconservative or dispersive.

Part 3: Terms (be able to understand & use correctly):

We will expect that you will understand and be able to correctly use these terms. We
will not necessarily be defining them during class. You may find it helpful to look these
terms up to check your understanding, however you do not need to fill the terms out for
the LRR you turn in (though you may choose to for your own studying).

Terms from Week 5

 Last updated 9/6/23

nucleotides origin of replication RNA primer

strand replication bubble histones
double helix replication fork semiconservative
purines DNA helicase conservative
pyrimidines topoisomerase discontinuous
5’, 3’ DNA polymerase missense mutation
phosphodiester linkage DNA primase silent mutation
complementary base leading strand nonsense mutation
pairing lagging strand frameshift mutatioH
antiparallel Okazaki fragment
major/minor groove DNA ligase

Exploration Questions, Study Questions & Tips (Not-graded)

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Common Difficulties and Misconceptions
• You may have difficulty understanding the significance of the 5’ to 3’ directionality
of nucleic acids and its relationship to replication along the leading and lagging strand of
the DNA helix. The leading/lagging strand concept is related to this. Remember, the
leading and lagging strands are both nucleic acid strands being synthesized, not the
template strands.

• Primers are required for DNA polymerases. Often, in vivo, those primers are
RNA primers laid down by the DNA-dependent RNA polymerase primase. These
primers are later replaced by synthesizing new DNA where they are made by a DNA
polymerase, with the final phosphodiester bond between DNA segments made by DNA
ligase.

We use the word primers differently when discussing molecular techniques such as
PCR or DNA sequencing. There we use DNA primers – and they are not replaced.

• A common misconception about mutations is that all mutations are harmful. The
majority of mutations are neutral – changing nothing of significance. While most of the
non-neutral ones may be harmful, beneficial adaptations can arise from mutations, too.

• Mutations bring the different forms of genes (called alleles) that we observe in
populations into existence. Thus an allele named “a” at the A locus (where the wild
allele is “A”) results from mutation. The various forces of evolution change the frequency
of alleles once they arise.

Study Questions:
1. When does DNA replication generally occur in eukaryotic cells?
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2. DNA replication is semi-conservative: What other models of DNA replication

were proposed and based on what evidence were they rejected?
3. What is the difference between the leading strand and the lagging strand in DNA
replication? What is the fundamental reason for this difference?
4. What is the role of the following in DNA replication: helicase, primase, DNA
polymerase, ligase, topoisomerase, single-stranded binding proteins, and telomerase.
5. How does one type of error that arises during DNA replication get detected and
repaired?
6. What, fundamentally, does mutation do? Explain how mutation creates new
alleles.
7. Explain in what sense mutation is considered a random process.
8. Are all mutations deleterious? If a mutation is deleterious, what should happen to
the frequency of this mutation? If a mutation is neutral, would you predict the same
outcome?
9. What is a point mutation? How is it possible that some point mutations have no
phenotypic effect while other point mutations do have a phenotypic effect?
10. What is a substitution mutation? Describe three possible outcomes a point
mutation that was also a substitution mutation could have on the polypeptide coded or
by a gene. Which is likely to have the largest effect on the phenotype of the organism?
11. What are insertion and deletion mutations?
12. What are frameshift mutations and explain why they are so named (e.g., what is
the "frame" and how does it get "shifted"?). Are substitution mutations or
deletion/insertion mutations generally more likely to produce frameshifts? Explain.
13. What is a somatic mutation? Of what evolutionary significance are somatic
mutations? Of what evolutionary significance are germ-line mutations?
14. Why is heritable variation necessary for evolution and natural selection to
operate? Summarize the importance of the mutational process for the evolution of
adaptations.
15. Compare & contrast DNA replication with DNA transcription. What is the template
for each? What are the enzymes for each? Products of each? Cellular location in
prokaryotes vs. eukaryotes of each? The name of the place/sequence where each
process is directed to start? What are the general features of the regulation of each
process?
16. Use a sketch to illustrate why the replication fork arriving at the end of one of your
chromosomes can’t finish the job. Illustrate how the problem is resolved by telomerase.