1. What is a nucleosome?
2. What are "histones"?  How much of the composition of a mitotic chromosome do histones make up?
   
3. What kind of non-histone proteins are involved in a mitotic chromosome?
4. When you look at a mitotic chromosome, what proportion of it is actually DNA?  What other types of molecules are you looking at?
5. In an interphase cell, what kinds of molecules are associated with DNA and in what proportions?
6. Are chromosome territories constant within a particular cell type (i.e., are they the same for all liver cells)?  
7. Are chromosome territories the same in different cell types?
8. Where do active genes of a chromosome tend to reside?
9. What are transcription factories?
   
10. Where do inactive genes of a chromosome tend to reside?   What holds them there?
11. Are chromosomal translocations "random", or are certain translocations between certain chromosomes common in cancer cells?  Explain how this phenomenon could be related to nuclear architecture.

Day 13, 13 February 2013:
What are genes?
Introduction to protein-coding genes

1. 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".
   
2. What are the two different kinds of genes that we have? 
   
3. List three examples of functional RNA's.
4. What is an allele?
5. 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 "disease allele"?
   
6. What are the symptoms of cystic fibrosis?
7. 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?
8. Define loss-of-function mutation. 
   
9. Define "haplosufficient".
   
10. What is transcription?  Where does it take place in eukaryotes?  Why is the term "transcription" a good description of the process?
    
11. What is translation and where does it take place in eukaryotes?  Why is "translation" a good term for the process?
12. What feature of a protein determines if/how it will function?
13. 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).
14. 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 table).

Day 14, 15 February 2013:
Transcription

1. When transcription is going on, is every gene within a cell transcribed?  Explain.
2. Know the "anatomy" of a gene including: core promoter, enhancer, exons, introns, and termination sequence.
   
3. What is a core promoter and what are the things that bind to it called?  What process begins at the proximal promoter?
4. What are generalized transcription factors?  Do they work for all genes, or just for some genes?
5. What are enhancers of a gene?  Can a single gene have more than one enhancer? 
   
6. What are specialized transcription factors?
7. What is one type of molecule that you have heard of before that acts as an "activator" for the enhancer of many genes? 
8. In real life, who is "the scribe"?  (name of the enzyme)  In real life, where is "the scribe" locked up?
9. In the initiation stage of transcription, what events happen?
   
10. An RNA transcript gets ______ (longer or shorter) as RNA polymerase travels from the promoter of a gene toward the termination sequence.
11. In which "direction" does RNA polymerase work?
12. At the end of every gene is a termination sequence.  What is the function of this sequence?
13. Once initiation has happened, is a gene only transcribed once, or are multiple RNA polymerases used?
14. 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 pairing.

1. 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?

1. 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?
2. Roughly how many miRNA genes are there in the human genome?  When miRNA genes are transcribed and processed, what is the product called?
   
3. What is the name of the transcript from a protein-coding gene? 
   
4. For the bacteria and the archaea, is mRNA processing complicated?  How separated in time and space are the processes of transcription and translation?
5. In eukaryotes, what 3 things happen to the transcript of a protein-coding gene before it is allowed to leave the nucleus?
6. 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?
   
7. Thinking 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?
8. Related 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?
9. What is alternative splicing and why is it important?
10. 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?
    
11. What is mature mRNA?  Be able to draw one and label its parts.
12. What is the start codon?  Which end of the mRNA is it nearest?  How far away from the tip of the mRNA is it?
13. 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?
14. Define 5' UTR.    Define 3' UTR.  Where do the instructions for making the sequence of the 5' and 3' UTR's come from?
15. 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, introns.

Day 16, 20 February 2013:
Translation

1. Transcription and translation process video from PBS
2. When a ribosome "reads" an mRNA, the first ribonucleotide used is at the ________ (5' or 3') end.
3. Be familiar with the steps of translation. 
4. What "ingredients" come together at the initiation of translation?
5. How is it determined which amino acid will be added to a growing protein chain?
6. What happens at a stop codon? 
7. How long (period of time) is a particular mRNA translated?  What determines the timespan?
8. 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 protein made.
9. Why does the lifespan of a mRNA matter?  What would happen in a cell if an mRNA were built but never destroyed?
10. 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?
11. 
12. 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 splicing)

1. Define "gene expression".  Define "gene regulation". 
2. Approximately what percent of our genes are expressed in any given cell?
3. What are house-keeping genes?  Give an example.
4. What does "tissue-specific" gene expression refer to?  Give an example.
5. When in the process of making a protein can a gene be regulated?
6. Is the Listeria prfA gene regulated pre-transcription or post-transcription?
7. 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 regulation?
   
8. "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.)

Switches

Switches: Video 1: Katie Pollard's work on switches in humans starts at 1hour, 44 minutes; Video 2: Sean Carroll's work on switches in flies

1. 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 single gene?
   
2. "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).
3. I forgot to refer you to figure 18.10, but here it is to help clarify our discussion of switches:

1. Be able to explain how enhancers and silencers can help guide tissue-specific gene expression. 
   
1. Are the same switch DNA sequences present in all cells within an individual's body (e.g., liver cells and skin cells)?
2. Are the same types of activator molecules present in all cell types?  Explain.
2. 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

Video 3: Epigenetics from Nova

1. What is heterochromatin?  What is euchromatin?  
2. 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?
3. How does the degree of DNA methylation relate to DNA packing?  
4. If the DNA of a gene's promoter is methylated, will it be transcribed?  Will the gene make proteins?
5. Can two individuals with the same DNA sequences (e.g., identical twins or inbred strains of mice) have different phenotypes due to DNA methylation?
6. 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
Epigenetics (continued):

1. Can two individuals with the same DNA sequences (e.g., identical twins or inbred strains of mice) have different phenotypes due to DNA methylation?
2. 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?
3. 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?
4. 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 to generation?
5. Is DNA methylation pattern the same from one cell type to another?  Does DNA methylation pattern affect embryonic development and cell differentiation?
6. 
7. 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)?
   
8. 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? at:  http://learn.genetics.utah.edu/content/epigenetics/rats/  Click on "lick a rat pup" to find out.
9. 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?
10. What do twin studies show about the stability of epigenetic patterns through a human lifetime?
11. Do chemicals in our environment (think about BPA, arsenic, cadmium, and methyl-mercury) affect expression of particular genes? 
    

Day 20, March 4, 2013: microRNA's

1. Are microRNA genes transcribed?  Are microRNA's translated or do they do a job in some other way?
   
2. What makes miRNA's fold into a double-stranded conformation?
3. Do miRNA's typically inhibit or enhance protein production for the gene(s) that they correspond with?  
4. Explain how miRNA silencing works.  What does Dicer do?  What does the silencing complex do?
5. What process is prevented by the action of a fully processed miRNA/silencing complex?
6. How could a researcher studying micro-RNA genes know which protein-coding gene(s) the microRNA helps regulate?
7. 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 question)
   
8. Do miRNA's have to come from an endogenous source to work in a cell?
   
9. 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)
   
10. What does RNAi do as a therapeutic treatment, and how is it similar to miRNA gene activity?  How is RNAi used as a research tool?
11. Remember our lab using RNAi on Planaria

1. Be very comfortable with the following terms:  gene, allele, genotype, phenotype, heterozygous, homozygous, dominant, recessive, carrier
2. Are dominant alleles more common than recessive alleles in a population?  Explain why or why not and provide a real-world example.
3. Are dominant alleles "healthier" than recessive alleles?  Explain why or why not and provide a real-world example.
4. Do dominant alleles "shut down" the recessive allele at the molecular level?  Explain why or why not and provide a real-world example.
   
5. Define "haplo-sufficient".
6. Define loss-of-function mutation.  
7. If a gene is not transcribed because of a problem with its promoter, is this likely a LOF mutation or not?
8. 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 normal phenotype?
9. 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?
10. 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 ________-_____________.  
11. 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 level?

~Please remember that 2 labs are included on this exam~

• 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. 

Additional Practice Transcription/Translation problem with answer.