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Biology II:
Exam II Content Review
Supplemental Instruction
Iowa State University
Leader:
Course:
Instructor:
Date:
Safwan Elkhatib
BIO 212 (2,3)
Coffman & Manz
February 21st, 2016
Nucleic Acid Structure
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If given two nucleotides, you will be able to diagram the formation of a dimer via a
polymerization/condensation reaction.
You will be able to state which base pairs are complementary in DNA and RNA, what types of bonds they form
with each other, and why that dictates the antiparallel structure in DNA and RNA.
You will be able to state two compositional differences between DNA and RNA.
Diagram the formation of a nucleotide trimer via condensation, noting differences between DNA and
RNA. Don’t worry about the structure of the bases. How do we modify these structures to sequence our
genome?
DNA Replication
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If given the base sequence and directionality/polarity of a single strand of DNA, you will be able to write the
base pairs that would be added to it during replication and in which direction they would be added.
You will be able to describe the steps of DNA synthesis and state which enzymes are associated with each step
(for both leading and lagging strands).
You will be able to compare and contrast the synthesis of leading and lagging strands.
You will be able to explain why telomerase is not active in bacteria or on the leading strand of linear
chromosomes.
You will be able to predict how telomeres change as a person ages and support your prediction using your
knowledge of how lagging strands are synthesized and the activity of telomerase in somatic cells.
You will be able to describe how DNA polymerase and mismatch repair work to reduce errors during
DNA synthesis.
Draw out of all of DNA replication. Make sure to note the following:
[Double helix strand, single-strand binding proteins, DNA topoisomerase, Replication fork,
DNA helicase, DNA ligase, DNA Polymerase, Okazaki fragments, Leading strand, Lagging Strand, DNA Primase,
RNA Primers, Clamp proteins]
Address the learning outcomes relating to telomeres and telomerase.
Transcription
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You will be able to describe the process of RNA synthesis, particularly with regard to how RNA polymerase
interacts with the DNA molecule during elongation (Fig. 17.1, Fig. 17.3)
You will be able to explain how transcription is initiated (Fig. 17.2) and terminated (Fig. 17.4) in bacteria
You will be able to compare and contrast transcription in bacteria and eukaryotes. (Table 17.1)
Discuss transcription stepwise from initiation, to elongation, and termination. Draw out how RNA
Polymerase works to complete transcription.
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You will be able to explain why the product of transcription in eukaryotes is called the primary transcript, why
it requires processing, and how this is different from RNA transcribed in bacteria
You will be able to list the processes that are performed on pre-mRNA to produce a mature mRNA (processes
involved in RNA processing)
You will be able to describe the process of RNA splicing (what is being cut out of the RNA strand, which
molecules/complexes are involved, and how it is done). (Fig. 17.6)
You will be able to explain the function of the 5’ cap and poly(A) tail in mRNA.
1060 Hixson-Lied Student Success Center  515-294-6624  sistaff@iastate.edu  http://www.si.iastate.edu
Address the learning outcomes discussing RNA splicing.
Translation
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You will be able to compare and contrast translation in bacteria and eukaryotes, particularly in relation to where
and when those processes occur. (Figs. 17.8 and 17.9)
You will be able to describe/diagram the basic structure of tRNA (Fig. 17.12) and explain its role in translating
mRNA to amino acid chains.
You will be able to describe how the correct amino acids are attached to particular tRNAs so that aminoacyltRNAs are formed and explain what would happen if this process were less precise
You will be able to describe/diagram the basic structure of a ribosome (Fig. 17.14a) during translation and
explain its role in how an amino acid chain is elongated (Fig. 17.16)
You will be able to explain how translation is initiated (Fig. 17.15) and terminated (Fig. 17.17)
Draw out the connection between tRNA and mRNA, and how this allows us to create polypeptides. Diagram
the ribosome and its different “sites.” Show the general steps of translation using this.
Prokaryotic Gene Regulation
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You will be able to describe the general processes that can occur during any of the three major types of gene
expression control and state when they occur within the central dogma. (Fig. 18.1)
You will be able to compare and contrast the three major types of gene expression control in terms of efficiency
and speed
You will be able to name at least two ways that a protein can be activated or deactivated during posttranslational control
Write out the central dogma, and explain how control can occur at the different steps.
Lac Operon
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You will be able to explain how genes are regulated in a normally operating lactose metabolism model system,
relating the specific molecules and genes involved to their general terms. (Fig. 18.4, 18.5, 18.7)
You will be able to predict what will happen if particular elements within the lactose metabolism model system
are inhibited or mutated so that they do not behave in a normal way. (Table 18.1, Fig. 18.7)
You will be able to compare negative and positive control of transcription, state which one of these is exhibited
in the lactose metabolism model system, and explain why. (Fig. 18.6, 18.7)
You will be able to explain the “Operon model” in general and relate it specifically to the lactose metabolism
model system. (Fig. 18.8)
You will be able to explain the importance of the specific findings in the lactose metabolism/lac operon model
to the general understanding of bacterial control of gene expression
Draw out the Lac Operon. What are the key components? What are their functions?
Eukaryotic Gene Regulation
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You will be able to list and briefly describe the six levels at which eukaryotes can control gene expression.
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Learning outcome: You will be able to describe the basic structure of chromatin and implications that this
structure has on gene regulation in eukaryotes.
Chromatin is a way to tightly pack DNA. It consists of DNA wrapped around histone proteins. The DNA is
negatively charged and the histones are positively charged, causing the tightly packed structure of chromatin.
In order for RNA polymerase to bind to the promoter of a particular gene, the chromatin must be decondensed
so the primer can be exposed. This means that the default state of eukaryotic genes is “off” and chromatin exerts
a form of negative control on eukaryotic genes.
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19.3: Learning outcome: You will be able to compare and contrast methods of transcriptional gene regulation
in eukaryotes to what we saw in bacteria. You should be familiar with the processes occurring in Figure 19.8.
The promoter is the binding site on DNA where RNA polymerase must bind before transcription can begin. In
eukaryotes, promoters are more complex than in bacteria, but many eukaryotic promoters have a TATA box.
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Instead of the sigma regulatory protein we saw in bacteria, eukaryotes have many proteins that signal the start
of transcription and help RNA polymerase bind to the promoter.
In bacteria, related genes are regulated together via operons. In eukaryotes, related genes are not located next to
each other in DNA, but they can be regulated together because they share regulatory sequences of DNA that
bind the same regulatory proteins near the promoters. These regulatory sequences are called promoter-proximal
elements.
Some eukaryotic regulatory sequences are far from the promoter. Of these, sequences that activate genes and
exert positive control on transcription are called enhancers. (Fig. 19.6) Sequences that shut down gene
expression and exert negative control on transcription are called silencers.
Regulatory proteins that bind to promoter-proximal elements, enhancers, or silencers are collectively called
transcription factors. Production of different transcription factors depending on signals the cell receives is an
important way that eukaryotes perform gene regulation.
You will be able to explain how alternative splicing can lead to the production of different proteins from the
same gene and the implications this has for eukaryotic genomes. (Fig. 19.9)
You will be able to explain how mRNA stability and mRNA interference (Fig. 19.10) act as forms of gene
regulation in eukaryotes.
You will be able to describe at least two examples of post-translational control in eukaryotes. d. You will be
able to compare and contrast how bacteria and eukaryotes regulate gene expression at the six different levels of
regulation. (Table 19.1)
List the 6 steps of Eukaryotic gene regulation. Briefly describe each using the information provided in the
study guide, found above.
Review how alternative splicing affects the proteome of eukaryotes.
Biotechnology
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You will be able to describe the steps of PCR, explain the purpose of each step, and explain why a
scientist would want to do PCR. (Fig. 20.8)
You will be able to describe the steps of dideoxy sequencing, explain the purpose of each step, and explain
why a scientist would want to do dideoxy sequencing. (Fig. 20.9)
You will be able to describe the steps of shotgun sequencing, explain the purpose of each step, and
explain why a scientist would want to do shotgun sequencing. (Fig. 20.9)
You will be able to explain how PCR, dideoxy sequencing, and shotgun sequencing are related and what each
technique accomplishes and if and how they could be used together.
You will be able to describe how genes are identfied within bacterial genomes and why it is much more
complicated to identify genes in eukaryotes. (Fig. 21.3)
You will be able to describe the basic relationship of bacterial genome size to estimated number of genes and
metabolic capabilities of the organism. You will be able to contrast this with the relationship between these
things in eukaryotes. (Fig. 21.4)
You will be able to explain what lateral gene transfer is and how it is identified in a given species
You will be able to explain what transposable elements and short repeated sequences are and how they
propagate in the genome. (Fig 21.6, 21.7)
You will be able to explain how STRs are used to uniquely identify individuals or test paternity (DNA
fingerprinting). (Fig. 21.8)
You will be able to explain how gene duplication can give rise to gene families. f. You will be able to explain
why there is no simple relationship between the size of the eukaryotic genome and the complexity of the
organism
You will be able to estimate the ratio of protein-coding portions of the human genome to the rest of the human
genome. (Fig. 21.10)