Exam 2 Review/Summary
Day 12, 11
Take a look at this Scientific American article on DNA
organization (Inner Life
of the Genome) if you are interested in the figures or
information I told you about in class today.
- What is a nucleosome?
- What are "histones"? How
much of the composition of a mitotic chromosome do histones make
- What kind of non-histone proteins
are involved in a mitotic chromosome?
- When you look at a mitotic
chromosome, what proportion of it is actually DNA? What
other types of molecules are you looking at?
- In an interphase cell, what kinds
of molecules are associated with DNA and in what proportions?
- Are chromosome territories
constant within a particular cell type (i.e., are they the same
for all liver cells)?
- Are chromosome territories the
same in different cell types?
- Where do active genes of a
chromosome tend to reside?
- What are transcription factories?
- Where do inactive genes of a
chromosome tend to reside? What holds them there?
chromosomal translocations "random", or are certain
translocations between certain chromosomes common in cancer
cells? Explain how this phenomenon could be related to
Day 13, 13 February 2013:
**Assignment (6 points): Read this article on cystic fibrosis.
Fill out this study sheet (due
in lab, Thursday, 21 February 2013).
What are genes?
Introduction to protein-coding genes
- What is a gene? Be able to give a good definition that
would include what a gene is made up of and what its function
is. Do not call it a "unit of heredity".
- What are the two different kinds of genes that we have?
- List three examples of functional RNA's.
- What is an allele?
- Would it be more accurate to say a
person from a healthy family has "good genes" or that they have
"good alleles"? Does someone have a "disease gene" or a
- What are the symptoms of cystic
- In cystic fibrosis, does everyone
with the "c" allele have pretty much the same DNA sequence, or
is it different in different families? What does the
protein from the C allele do? In a Cc heterozygote, does
the dominant allele in any way "repress" the recessive disease
allele at the molecular level, or does it just function well
enough by itself to produce a normal phenotype?
- What is transcription? Where
does it take place in eukaryotes? Why is the term
"transcription" a good description of the process?
- What is translation and where does
it take place in eukaryotes? Why is "translation" a good
term for the process?
- What feature of a protein
determines if/how it will function?
- Be able to take a DNA sequence and
transcribe it to mRNA (you will need to know base pairing rules
and 5'-->3' orientation rules).
- Be able to take a mRNA sequence
and translate it (you will need to know which end of the
sequence the ribosome starts on and how to read the genetic code
Day 14, 15 February 2013:
Introduction to RNA processing
- When transcription is going on, is every gene within a cell
- Know the "anatomy" of a gene including: core promoter,
enhancer, exons, introns, and termination sequence.
- What is a core promoter and what are the things that bind
to it called? What process begins at the proximal
- What are generalized transcription factors? Do they work
for all genes, or just for some genes?
- What are enhancers of a gene? Can a single gene have
more than one enhancer?
- What are specialized transcription factors?
- What is one type of molecule that you have heard of before
that acts as an "activator" for the enhancer of many
- In real life, who is "the scribe"? (name of the enzyme)
In real life, where is "the scribe" locked up?
- In the initiation stage of transcription, what events happen?
- An RNA transcript gets ______ (longer or shorter) as RNA
polymerase travels from the promoter of a gene toward the
- In which "direction" does RNA polymerase work?
- At the end of every gene is a termination sequence. What is the function
of this sequence?
- Once initiation has happened, is a gene only transcribed once,
or are multiple RNA polymerases used?
- Be able to give the RNA sequence that would result from a
given DNA sequence, including 5' and 3' ends. See figure
17.7 and remember the rules you learned earlier about base
Day 15, 18
- Roughly how many tRNA genes are in the
human genome? When tRNA genes are transcribed, what is
the transcript called? What kind of processing must
happen to a tRNA to make it active?
Conclusion to RNA processing
- How many rRNA genes are there in the human
genome? When rRNA genes are transcribed, what is the
transcript called? What kind of processing must happen
to a rRNA to make it active?
- Roughly how many miRNA genes are there in
the human genome? When miRNA genes are transcribed and
processed, what is the product called?
- What is the name of the transcript from a
- For the bacteria and the archaea, is mRNA
processing complicated? How separated in time and space
are the processes of transcription and translation?
- In eukaryotes, what 3 things happen to the
transcript of a protein-coding gene before it is allowed to
leave the nucleus?
- For most protein-coding genes in
eukaryotes, is more of the length of the immature mRNA made up
of coding (exon) sequence or non-coding (intron) sequence?
question: Why can't you just sequence a piece of DNA
and know exactly what amino acid sequence would be produced
from that DNA in a particular cell?--What else do you need
to know about the sequence?
thinking question: Why might a geneticist want to look
at the sequence of a mature mRNA instead of just looking at
the gene sequence that the mRNA came from?
- What is alternative splicing and why is it
- How can
alternative splicing increase the number of different
proteins made by our genes? Could this help explain
the complexity of humans, since we turn out to have
surprisingly few genes?
- What is mature mRNA? Be able to draw
one and label its parts.
- What is the start codon? Which end of
the mRNA is it nearest? How far away from the tip of the
mRNA is it?
- What is the stop codon? Which end of
the mRNA is it nearest? How far away from the poly-A
tail of the mRNA is it?
- Define 5' UTR. Define 3'
UTR. Where do the instructions for making the sequence
of the 5' and 3' UTR's come from?
- Place the following mRNA components in
order by length (as they would be for a typical gene) from
longest to shortest: 3' UTR, 5'UTR, coding region of mRNA,
Day 16, 20 February 2013:
- Transcription and translation process video
- When a ribosome "reads" an mRNA, the first ribonucleotide used
is at the ________ (5' or 3') end.
- Be familiar with the steps of translation.
- What "ingredients" come together at the initiation of
- How is it determined which amino acid will be added to a
growing protein chain?
- What happens at a stop codon?
- How long (period of time) is a particular mRNA translated?
What determines the timespan?
- The DNA sequence of a protein-coding gene determines the
shape(s) of the protein(s) that will be made from the gene's
mRNA product. The part of the DNA sequence of a gene that
codes for the 3' UTR also determines the _____________ of
- Why does the lifespan of a mRNA matter? What would
happen in a cell if an mRNA were built but never destroyed?
- Can translation of a mRNA be prevented by the folding (secondary structure)
of the mRNA? How does Listeria
prevent translation of its PrfA mRNA's at low temperatures, but
"allow" translation of these same mRNA's at high temperatures?
How exactly does high temperature change gene activity
(protein production) in this case?
- Why does the order of amino acids matter in a protein?
Day 17, 25 February 2013:
Gene Regulation: Examples
you have learned already (5' UTR folding and alternative
- Define "gene expression". Define "gene
- Approximately what percent of our genes are expressed in any
- What are house-keeping genes? Give an example.
- What does "tissue-specific" gene expression refer to?
Give an example.
- When in the process of making a protein can a gene be
- Is the Listeria prfA gene regulated pre-transcription or
- Is alternative splicing pre-transcriptional or
post-transcriptional regulation? Is it good for regulating
housekeeping genes or for regulating tissue-secific gene
expression? What does "exon skipping" mean? Is exon
skipping the only mechanism of alternative splicing? Is
this pre-transcriptional regulation or post-transcriptional
- "Switches" = Regulatory
elements that can enhance or repress transcription depending
on which molecules are present in the cell to activate them
(different cells have different "environments" within them)
Day 18, 27 February 2013:
Gene Regulation: Switches and Epigenetics (We watched 3 video clips today! Links are
below if you want to see them again.)
1: Katie Pollard's work on switches in humans starts at 1hour,
44 minutes; Video 2: Sean
Carroll's work on switches in flies
- Enhancer" is a name for a distal control element (section of
DNA) that increases transcription rates for a gene when it is
bound by the right molecules (transcription factors). Where are enhancers located
relative to a gene? Can they be located in more than
one place? Can there be more than one enhancer for a
- "Silencer" is a name for a distal control element (section
of DNA) that prevents transcription for a gene when it is
bound by the right molecules (repressors).
- I forgot to refer you to figure
18.10, but here it is to help clarify our discussion of
- Be able to explain how enhancers and silencers can help
guide tissue-specific gene expression.
- Are the same switch DNA sequences present in all cells
within an individual's body (e.g., liver cells and skin
- Are the same types of activator molecules present in all
cell types? Explain.
- Think back to what we've said in the past about Vitamin D
(picture above on Day 14 material)... How does vitamin D fit
into this type of gene regulation?
Epigenetics from Nova
- What is heterochromatin? What is euchromatin?
- What is epigenetic
change? How can activity of a gene change
without the DNA sequence of the gene (or the DNA sequence of
DNA surrounding the gene) changing?
- How does the degree of DNA methylation relate to DNA
- If the DNA of a gene's promoter is methylated, will it be
transcribed? Will the gene make proteins?
- Can two individuals with the same DNA sequences
(e.g., identical twins or inbred strains of mice) have
different phenotypes due to DNA methylation?
- Based on research in mice (small, brown vs. fat, yellow),
does it seem likely that environmental factors, such as
maternal diet, can influence DNA methylation patterns?
Day 19, 1 March 2013
- Can two individuals with the same DNA sequences
(e.g., identical twins or inbred strains of mice) have
different phenotypes due to DNA methylation?
- Based on research in mice (small, brown vs. fat, yellow), does
it seem likely that environmental factors, such as maternal
diet, can influence DNA methylation patterns?
- What happens to X-chromosomes during the fetal development of
female mammals? How does this process show up in the
phenotype of calico/tortoise-shell cats?
- Is the methylation pattern of a parent cell's genes usually
passed on to the daughter cells it creates via mitosis?
How? Are methylation patterns typically heritable (with
some notable exceptions) from cell to cell and from generation
- Is DNA methylation pattern the same from one cell type to
another? Does DNA methylation pattern affect embryonic
development and cell differentiation?
- What is genomic imprinting? How does genomic imprinting
explain the fact that it takes both egg and sperm to make a
mammal baby (i.e., mammals cannot be parthenogenetic)?
- Based on research in rats, it seems likely that environmental
stimulation, such as parental care, also can influence DNA
methylation patterns. For fun, check out what kind of rat mother are you?
Click on "lick a rat pup" to find out.
- What do the yellow mouse studies
show about the influences of chemicals and diet on epigenetic
control of gene expression? Was the epigenetics of a
developing fetus dependent on its mother's diet? Does
the epigenetic gene-expression status of a mouse influence the
status of its offspring and grand-offspring?
- What do twin studies show about
the stability of epigenetic patterns through a human lifetime?
- Do chemicals in our environment
(think about BPA, arsenic, cadmium, and methyl-mercury) affect
expression of particular genes?
March 4, 2013: microRNA's
Day 21, March
6, 2013: Classical genetics meets molecular genetics: Dominance
- Are microRNA genes transcribed? Are microRNA's
translated or do they do a job in some other way?
- What makes miRNA's fold into a double-stranded conformation?
- Do miRNA's typically inhibit or enhance
protein production for the gene(s) that they correspond
- Explain how miRNA silencing works. What does Dicer do? What does
the silencing complex do?
- What process is
prevented by the action of a fully processed miRNA/silencing
- How could a researcher studying micro-RNA genes know which
protein-coding gene(s) the microRNA helps regulate?
- How many miRNA genes do you have in your genome? What do
they do? Are these miRNA genes transcribed all the time?
(use what you know from the miRNA10b gene example to answer this
- Do miRNA's have to come from an endogenous source to work in a
- Are there miRNA's in the foods we eat? Can they affect
our own gene function? (give the example of a food and its
effect that we discussed)
- What does RNAi do as a therapeutic treatment, and how is it
similar to miRNA gene activity? How is RNAi used as a
- Remember our lab using RNAi
- Be very comfortable with the following terms:
gene, allele, genotype, phenotype, heterozygous,
homozygous, dominant, recessive, carrier
- Are dominant alleles more common than recessive alleles
in a population? Explain why or why not and provide a
- Are dominant alleles "healthier" than recessive
alleles? Explain why or why not and provide a real-world
- Do dominant alleles "shut down" the recessive allele at the
molecular level? Explain why or why not and provide a
- Define "haplo-sufficient".
- Define loss-of-function
- If a gene is not
transcribed because of a problem with its promoter, is this
likely a LOF mutation or not?
- In cystic fibrosis, does everyone with the "c" allele have
pretty much the same DNA sequence, or is it different in
different families? What does the protein from the C
allele do? What is usually wrong with the "c" DNA
sequence? Is the "c" LOF allele transcribed? Is a
protein built from its mRNA? Why is this considered a LOF?
In a Cc heterozygote, does the dominant allele in any way
"repress" the recessive disease allele at the molecular level,
or does it just function well enough by itself to produce a
- Why is the O allele for blood type considered a LOF mutation?
Is it harmful? Is the allele likely to be
transcribed? Why is this allele considered recessive?
In blood types, is this
recessive allele common or rare in the population?
- For recessive, LOF mutations (like the cystic fibrosis disease
allele or the O allele in blood type), the dominant allele makes
a heterozygote phenotypically like a normal homozogote because
the good allele is ________-_____________.
- Huntington's Disease is caused by
a dominant/recessive (circle one) autosomal/sex-linked (circle
one) allele. Is the recessive allele a LOF mutation?
Is the dominant allele a LOF mutation? Does the dominant
allele do anything with/to the recessive allele at the molecular
remember that 2 labs are included on this
- Explore a Gene: The Gene,
immature mRNA and mature mRNA diagrams are helpful
- Cat Lab: Know how to do
autosomal and sex-linked inheritance problems (don't
worry about Chi-square tests)
If you are given a stretch
of DNA, and if you are told which strand of the DNA is the
template strand for a gene, be able to determine the
corresponding mRNA sequence and the corresponding amino acid
sequence that would be generated from it. You will need
to remember four things: 1) base pairing rules for
transcription; 2) RNA strands will be built with an
antiparallel orientation to the DNA strands they are built
from; 3) the ribosome will start at the 5' end of the mRNA and
read toward the 3' end; 4) the genetic code table gives the
amino acid that goes with the mRNA sequence.
Transcription/Translation problem with answer.
Additional interactive practice for
transcription and translation here (remember to pay attention to
5' and 3' ends: http://learn.genetics.utah.edu/content/begin/dna/transcribe/
~End of Exam 2
~Good luck with your studying!~