1. Which regulatory mechanisms occur at the DNA-level, which occur at the protein-level?
DNA level - transcription, chromosome remodeling, acetylation/methylation, activators/repressors, siRNA
protein level - feedback inhibition; allosteric/competitive inhibition

2. How do acetylation, methylation, repressors, activators, and siRNA control gene expression? What role do inducers play?
Acetylation loosens the DNA, allowing transcription factors to bind
Methylation is the opposite of acetylation, it crams the DNA close together to that it denies access
Repressor binds to regulatory sites blocking attachment of transcription factors
Activators binds to the regulatory sites
Inducers are crucial since they have the ability to control repressors and activators

3. What is an enhancer and how does it help control how much of a particular protein is made?
An enhancer is a short region of DNA that can bind to activators - are far from the promoter site. Enhancers increase the transcription process, therefore increasing amount of protein to be made.

4. How do allosteric inhibition and competitive inhibition differ in the ways they accomplish feedback inhibition?
Allosteric inhibition binds, changing the shape of the enzyme, while competitive inhibition gets in the way by blocking the entrance to an enzyme

5. What are the three phases of the cell cycle? What occurs at each phase?
G1, S, and G2 phase. G1 and G2 is similar in that they are the phase were the cell is given time to grow to its stable size, and in the S phase, DNA synthesis occurs

6. What are the four phases of mitosis? What occurs at each phase?
Prophase - DNA condenses and mitotic spindles start to develop
Metaphase - Linear alignment of chromatids at the center of the cell
Anaphase - Mitotic spindles pull the sister chromatids apart so that they are on each side of the cell
Telophase/Cytokinesis - Nuclear envelop reforms and the cell is divided by the cell membranes separating

7. What are cell cycle checkpoints? Why are they important?
Cell cycle checkpoints are areas where the enzymes examine whether or not the cell cycle is progressing properly to prevent mutations or problems that can occur.

8.What is apoptosis? What role does it play in the cell cycle?
Apoptosis is when a cell "suicides" or kills itself, it helps in the cell cycle so that it prevents further cell division in mutated cells

9. What is the difference between chromatin and chromosomes?
Chromosomes are condensed versions of chromatin.

10. What is the role of the centromere? (What would happen without it?)
Centromere holds the sister chromatids together, without it anaphase would most likely not correctly separate to each side of the cell (the whole chromosome might go to one side).

11. What is the difference between a chromatid and a chromosome?
Two strands of chromatid forms a chromosome

12. What events must happen in order for two sister chromatids to separate from one another and move to opposite sides of the cell? (What happens at the centromere? What happens to the centromere? What is the role of the mitotic spindle?)
The kinetochore microtubules connect to the sister chromatids and line up during metaphase. During Anaphase, the sister chromatids are pulled apart, and the centromere that hold them together are actually proteins that deactivate allowing, the separation of them. The mitotic spindles are shortened and are turned into centrioles and conserved for future mitosis processes

13. What would happen if two sister chromatids moved to the same side of the cell?
Of the pair of cell through mitosis, one will have an abundance of chromosomes, while the other cell will be lacking.

14. What happens to the mitotic spindle after mitosis?
Forms into the cytoskeleton and returns back into shape of microtubules and centrioles

15. What are gametes? Where are they made in the body? How are they made?
Sex cells; eggs in females made in the ovaries, or sperm in the male made in the testes; made by meiosis

16. What are the eight phases of meiosis? What occurs during each phase? How does meiosis differ from mitosis?
Prophase I - DNA condenses and microtubles start to assembles.
Metaphase I - Homologous chromosomes alignment at center of cell; crossing over occurs
Anaphase I - Separation of homologous chromosomes
Telophase/Cytokinesis I - Cell is divided, both daughter cell gets 23 pairs of chromatids each; results in two haploids
Prophase II - Microtubules prepare for Metaphase II
Metaphase II - 23 chromatid pairs line up at the center
Anaphase II - Centromere divide and split the the 46 chromosomes; sister chromatids by mitosis
Telophase/Cytokinesis II - Divides both cells into halves, making four haploids (gametes)

17. How do crossing over and random assortment “mix up” genes so that children are genetically different from their parents?
Crossing over occurs on any part of the chromosome and since there are so much DNA in the chromosome, there are a number of possibilities where crossing over can occur. Random assortment further helps but most of the genetic variation is due to crossing over.

18. Why are insertion and deletion mutations usually more harmful than substitution mutations?
Insertion and deletion mutations is more harmful because substitution is more likely to an equivalent condon since there are 20 codons for 64 different combinations.

19. How does nondisjunction affect the genes present in an organism? Specifically, why does it cause deformities?
Nondisjunction affects cells undergoing division and result in an extra or missing one chromosome.

20. What “super powers” must a cell acquire to become cancerous? How does it acquire these powers?
Active oncogenes and inactive tumor suppressor genes; by mutation which can alter these gene's control of activation and deactivation.

21. Compare and contrast oncogenes and tumor suppressor genes. What are they? How are they similar? How are they different?
Oncogenes and tumor suppressor genes both play a role in controlling cell division. Oncogenes tells cells to keep dividing while tumor suppressor genes halt or slow the process of cell division. Oncogenes help cancer, tumor suppressors help against cancer.

22. Why is cancer primarily a disease of old age?
In old age, the wear in the body's immune system and all the regulatory functions can allow a cancerous to take advantage by "cheating the system."

23. How do mutations cause genetic variation? Is this good or bad for the organism?
Mutations can create new alleles which is expressed as a new genotype. Normally it is bad, since it can cause a defect in the organism, but if it's good, it's considered evolution

24. How do genetic diseases caused by point mutations differ from those caused by chromosomal mutations like nondisjunction?
Chromosomal mutations affect a large number of DNA vs point mutations which cause a frame change in the DNA sequence

25. What causes spontaneous mutations? What causes induced mutations?
Spontaneous mutations are caused by point mutations or nondisjunction incurred during mitosis. Induced mutations are caused by mutagens.

26. How accurate is DNA replication? (That is, how often do point mutations occur?)
Errors from point mutations occur in about every 1 in 100,000 nucleotides; when an enzyme tries to fix the problem, the error rate drops to about 1 in 10 billion nucleotides in humans.

27. What type of mutation is shown here? AGTGCCGTAAC
___________________________________TCACGGCCAGTG
Point mutations (both frameshift - a nucleotide was added - and substitution)