• This day is mostly about setting the stage and getting into the right frame of mind for the semester.
• Please remember that you have an assignment due next week in lab (January 23) regarding the genetic revolution.  Follow directions carefully in order to receive full credit.  10 points.
• Here is the video on the "genomic revolution" (sequencing personal genomes), which is a part of the larger genetic revolution, that I wanted you to see (11 minutes).
  

Day 2: January 15, 2014--Updated after class

1. How did Watson and Crick figure out that DNA is a double-helix and what the dimensions of the helix were? 
   
2. How did Watson and Crick figure out that A pairs with T and G pairs with C?  What did they think initially was the proper pairing?  Who helped them figure out the right pairing?  How did they figure out that the bases went on the inside of the helix (not on the outside as they originally placed them in their model)?
   

Day 3:  January 17, 2014

DNA structure:

1. What did Chargaff figure out in 1950 that helped Watson and Crick?
2. What did Rosalind Franklin's data tell Watson and Crick?
3. DNA is a polymer made up of what kind of units?
4. Name the three main components of a nucleotide. 
5. What is a phosphate group?  What kind of charge does it have?
6. What sugar is found in DNA?  How many carbons are in it?  
7. Be able to draw the general shape of deoxyribose and label each carbon by number.  Which are the three important attachment points and what do they attach to?
8. Where does the phosphate group attach to a deoxyribose?
9. On which carbon of deoxyribose does the base attach?
10. If a new nucleotide were to be added to a chain of nucleotides, on to which carbon would the new nucleotide be added?  What would be removed from the 3' Carbon to allow the new nucleotide to attach?
11. Which two parts of a nucleotide form the "backbone" of a strand of DNA?  (This may not be explicitly stated in your notes, but you should be able to figure this out!)
12. Of the four bases (adenine, guanine, cytosine, and thymine) found in DNA, which two are purines?  What is the general shape of a purine?  
13. Which two are pyrimidines?  What is the general shape of a pyrimidine?
14. Look at Figure 16.5 in your book.  Pick out a single nucleotide (sugar + phosphate + base) to examine.  How many rings do you count in the structure of a pyrimidine nucleotide?  a purine nucleotide?
15. What did What does "DNA sequence" or "nucleotide sequence" refer to?
16. What does "complementary" mean when it comes to DNA?
17. In which way are the two strands of DNA oriented in dsDNA?
18. Look at the nucleotide that you built or at a well-labeled diagram of a strand of DNA.  What is found at the 5' end of a strand of DNA?  What is found at the 3' end? What does "anti-parallel" orientation have to do with DNA?
19. What kind of bonds, and how many of them, are found between G and C?  between A and T?
20. How can DNA be easily denatured in the lab?  Which is easier to denature, GC rich DNA or AT rich DNA? 
21. Why does Ethidium bromide work as a stain for DNA?
22. When referring to DNA, what do the abbreviations for length "bp" and "nt" refer to?

1. What are the similarities between DNA and RNA?
   
2. What is different about deoxyribose and ribose?  Does the difference occur at one of the important attachment sites (i.e., 1', 3', or 5' C?)
3. On which carbon does the phosphate group attach to ribose?  Is this the same as for DNA?
4. We often think of RNA as a single-stranded molecule.  Can RNA exist as a double-stranded molecule?  Explain.
5. What is different about the bases found in DNA vs. RNA?  What base is Uracil most like?

1. Why does DNA replication happen?  When does DNA replication happen in the life of a cell (what part of the cell cycle)?
2. Will mitosis happen if DNA replication does not happen? 
   
3. What are the purposes of mitosis?
4. Know the cell cycle.  Diagram it and label it.
5. Do all cells progress through the cycle at the same rate? Explain two factors that impact the rate of progression of a normal cell through the cell cycle.
6. For a cancer cell, what is going on with the cell cycle?  Can inhibiting DNA replication help someone with cancer?
7. What does DNA replication have to do with sister chromatids?  What is a centromere? 
8. When in the cell cycle do sister chromatids become joined together: G1, S, G2, or mitosis?  What proteins hold sister chromatids together?
   
9. Remember, one chromosome = one double helix of DNA.  In a human cell (chromosome number = 46), within the nucleus of a non-dividing cell, how many DNA double-helices are there?  (1, 2, 46, 92, hundreds?)  After DNA replication, how many DNA double helices are there? (1, 2, 46, 92, hundreds)

1. You can watch the steps of DNA replication in the Chapter 16 BioFlix Animations. 
   
2. In natural DNA replication, what enzyme unwinds the DNA?
3. On a prokaryotic chromosome, will there be one or many origins of replication?
4. On a eukaryotic chromosome, will there be one or many origins of replication?
5. Knowing what you do about base pairing, what would likely be characteristic of the nucleotide sequence of origins of replication (high AT content or high GC content)?
6. What bad thing can happen to DNA during the unwinding process?
7. What enzymes deal with the stress induced by unwinding the double helix?
8. What proteins keep the newly opened DNA from "snapping back together"?
   

1. During natural DNA replication, what are primers made of? What enzyme synthesizes the primers? Why are primers necessary?
2. What enzyme builds new DNA? 
3. In which "direction" is DNA polymerase able to synthesize new DNA?  What other "rule" does DNA polymerase have to follow (i.e., what does it need to get started)?
4. How is it determined which nucleotide (dATP, dGTP, dCTP, or dTTP) is added next in a growing chain of DNA? 
5. Be able to identify on a diagram which direction new DNA is being built relative to the template strand of DNA (add in the 5' and 3' notations and use an arrow to show which way the new DNA is growing).
6. What happens to RNA primers during DNA replication?
7. What is the role of DNA ligase in DNA replication?
8. What do cohesins do in DNA replication?  Use what you know about the cell cycle to decide: When in the cell cycle do sister chromatids become joined together: G1, S, G2, or mitosis?
9. What does it mean that DNA replication is "semiconservative"?  When DNA replication is over and two sister chromatids are being held together, where does the original DNA lie (in one chromatid or some in both chromatids)?
   
10. The enzyme telomerase is important in bacterial chromosome replication (true or false?). 
    
11. What are telomeres?  What happens to our telomeres as we age?
12. What happens to the chromosomes if telomeres become shortened?  What does this have to do with mitosis?
13. What is it about DNA polymerase that makes it unable to finish the job of DNA replication at the telomeres?  Which end(s) of the newly synthesized DNA has a problem (5', 3', or 5' and 3')?  Remember, this is the fact that I asked you to look into this weekend if you don't know for sure which it would be.
    

Day 6: January 27, 2014--Snow Day!

1. Be able to diagram the DNA replication problem as it occurs at the ends of chromosomes and know what features of DNA polymerase lead to the problem.
2. What does telomerase do? Where do the instructions for making telomerase come from?  Does every body cell have the instructions (the gene) for making telomerase?  What kinds of cells have high levels of the telomerase protein?  What does this have to do with immortality in cancer cells?  What effect does stress seem to have on telomerase levels? 
   

1. Define mitosis.  What is mitosis used for?  
2. What happens to DNA in preparation for mitosis?
3. When do cohesins begin attaching sister chromatids to each other and when do cohesins begin to let go?
   

Reading assignment on Sister Chromatid Cohesion:  There is quite a bit of complexity in this article that I don't expect you to worry with.  When we talk about meiosis on Friday, that part of it will make more sense, too.  I do think that reading the article will give you a strong appreciation for the complexity of the process of mitosis (and meiosis, soon).

• Note: there are many protein names in this article, highlighting the complexity of sister chromatid cohesion.  Do not get bogged down in the names or in trying to remember or follow them all.  Concentrate on the roles of cohesins and separase.
  
• Definition you will need to know: Aneuploidy = wrong number of chromosomes, usually +1 or -1 chromosome
• Answer these questions about the article and bring them to lab next week, 2/6/14

1. What is the spindle fiber assembly checkpoint?
2. When do centromeric cohesins finally let go?  What enzyme causes them to let go?
3. What pulls sister chromatids apart?
4. What is different about cell division for plant vs. animal cells?
   
5. In mitosis, what is "disjunction" of sister chromatids? 
   
6. Be able to diagram and/or explain the steps describing what happens to chromosomes during the cell cycle to maintain constant chromosome number during mitosis.
   Start with a cell that is in G1 phase and diagram it with 4 chromosomes.  Now follow this same cell through S-phase and mitosis to show the genetic composition of the two daughter cells that are produced at the end of the cell cycle.
7. Now that you know the action of chromosomes during mitosis and leading up to it, label the phases of mitosis.
8. What is interphase?  Is "resting phase" a good name for it? 
   
9. For fun: Look at the pictures in your book and try to determine why metaphase chromosomes are what we want to observe under the microscope when assessing the chromosomes of a patient or any other organism that we want to study.
10. What does the term "nondisjunction" mean when it applies to sister chromatids?  Why are some of the reasons why it might happen?
11. I forgot to mention this, but when nondisjunction happens, the resulting cells with abnormal chromosome numbers are showing "aneuploidy" (we will cover that term on Monday; aneuploidy also is mentioned above because it is helpful to understand aneuploidy when reading the cohesins article I assigned).
    
12. Be able to diagram nondisjunction in mitosis. 
    
13. Do agressive cancer cells usually have the same chromosome content as normal body cells?  How can over-expression of separase help lead to this?

Day 9: February 3, 2014 (The importance of chromosome number; Meiosis)

1. What is a euploid number?  Does chromosome number correlate in any way with "complexity"?
2. Define "ploidy", "diploid", "haploid", "octaploid" or any other type of ploidy with a reasonable prefix (e.g., "triploidy").  What is polyploidy?
3. What is a homologous pair of chromosomes and how is it different from sister chromatids?
1. Let's check your understanding of sister chromatids vs. homologous and non-homologous chromosomes:
1. Would the two chromosomes in a homologous pair (e.g., #9 and #9 within the same cell) have a) an identical nucleotide sequence, b) a very similar, but not quite identical nucleotide sequence, or c) a radically different nucleotide sequence?
2. Would non-homologous chromosomes (e.g., #1 and #9) have a) an identical nucleotide sequence, b) a very similar, but not quite identical nucleotide sequence, or c) a radically different nucleotide sequence?
3. Would sister chromatids have a) an identical nucleotide sequence, b) a very similar, but not quite identical nucleotide sequence, or c) a radically different nucleotide sequence?
4. What does aneuploid mean?
   
5. What are autosomes?
6. Trisomy and triploidy refer to very different things.  What does each term mean?
7. Are most aneuploidies survivable for humans?  Why not?  Relate your answer to "dosage effect".
   

1. If the point of meiosis is to reduce the chromosome number of a cell by half, why does the process begin with duplicating all of the chromosomes?
2. Which of the two cell divisions in meiosis is the "reduction division" that reduces the chromosome number to half what it started at (e.g., diploid --> haploid or tetraploid --> diploid)?
3. What is synapsis?  What is the synaptonemal complex?  How is it different from "cohesins"?
4. Is there any need for the synaptonemal complex in regular cell division (mitosis)?  Why is the synaptonemal complex used in meiosis?
5. How do the synaptonemal proteins "know" to put chromosome 1 with its homolog and not with chromosome 2?  
6. What is crossing over? 
7. Be able to diagram the chromosomes of a cell in G1, after S-phase, during and after Meiosis I, and during and after Meiosis II.  When does the cell become haploid?

1. For the process of meiosis, when do cohesins begin to do their jobs?  What do cohesins hold together? When are they released?  What protein releases the cohesins?
2. For the process of meiosis, when does the synaptonemal complex begin to do its job?  What is it holding together?  When is the synaptonemal complex broken down?  Is the synaptonemal complex used for anything besides meiosis?
   
3. For the process of meiosis, when does crossing over occur?  Why is it important?  (because it generates genetic diversity among the gametes produced by an individual AND because crossing over helps with _______________[what process])  What kind of genetic problem could be caused by unequal crossing over?  Does crossing over ever occur for any other purpose other than meiosis?
   
4. How do the synaptonemal proteins "know" to put chromosome 1 with its homolog and not with chromosome 2?  How do X and Y chromosomes become synapsed even though they have very different DNA sequences from each other?
5. X and Y chromosomes synapse at their very tips.  What does this tell you about the DNA sequences at the ends of these two chromosomes?
6. Why does Turner syndrome (XO) more often result from an aneuploid sperm than from an aneuploid egg?

Nondisjunction

1. Be able to diagram non-disjunction of one chromosome pair in Meiosis I.
2. Be able to diagram non-disjunction of sister chromatids in Meiosis II.
3. Be able to explain the actions of spindle fibers, synaptonemal complex proteins, crossing over, cohesins, and separase to the point that you can identify how each of these things can fail to cause nondisjunction. 
   
4. Extra practice: What kind of nondisjunction event could cause a normal dad and a normal mom to have a child with an XYY karyotype?