The following are one-two word answer questions.
1. The bond between a phosphate group and the ribose sugar group in RNA is called which of the following?
2. Alternative Splicing is the process that does what to the exons and introns?
3. What codon starts a protein open reading frame?
4. Which of the codons cannot be recognized by a tRNA molecule?
5. What is the rate of DNA translation?
6. During DNA replication, the 3' -OH of the growing DNA chain attacks which phosphate of an incoming nucleotide?
7. The 5' capping process creates what type of linkage?
8. Codons that code for the same amino acid are called what?:
9. What is the rate of mammalian DNA replication?
10. What signals the end of transcription?
11. What is the function of the poly A tail?
12. What is the rate of mutation per round of DNA replication?
13. Give an example of a missense DNA mutation?
14. What provides the energy that drives the addition of nucleotides to a growing DNA chain during replication?
15. Name the four RNA bases.
16. What is the name of a mutation that changes the reading frame of an RNA molecule?
17. How many base pairs make up a codon?
18. How many amino acids are there?
19. How many hydrogen bonds are formed between one A:T base pair?
20. Are hairpin loops involved in the RNA splicing reaction?
21. How many nucleotides specify an amino acid?
22. What links codons and anti-codons together during DNA translation?
23. At which position on the cytosine ring is it methylated by the methyltransferase?
24. Which is the biological molecule that contains the genetic information that is transmitted hereditarily and controls the cellular functioning?
25. The first procedure used for DNA sequencing and still used at times is named after its creator. Name it.
26. If you inject a foreign protein into a human it will elicit what type of reaction?
27. With the TALEN technology you want to recognize a 20 nucleotide sequence of DNA. How many TALEN repeats will be in the construct?
28. In molecular biology what does GFP stand for?
29. If you want to find information on the web about a specific miRNA what database would you search?
30. The size of gene families usually increases from lower organisms to higher organisms. What is the name of one of the gene processes that has been proposed due to gene homology measurements?
31. Which raps around histones? RNA or DNA?
32. When electron micrographs were taken of eukaryotic chromosomal DNA were hybridized with mRNA hairpins of non-base pair bonded DNA were found. What structure of DNA was this the first evidence of?
33. I molecular bioinformatics what does EST stand for?
34. RTRACS stands for what?
35. What is in the center of the Dynabeads we used in the CHiPs assay that makes it easy to pellet them.
36. What is the name of the synthetic biology technique that can join multiple DNA pieces simultaneously in one reaction?
37. What does IPSC stand for?
The following are couple sentence answer questions.
1. What is the genetic code?
2. What is the role of messenger RNA and ribosomes for the protein synthesis?
3. Of what RNA subunits are ribosomes are made in prokaryotes and eukaryotes?
4. How different are the location of ribosomes in eukaryotic and in prokaryotic cells?
5. Where in eukaryotic cells does mRNA synthesis occur? To where do these molecules migrate?
6. You want to determine the full complement of H3K4Me3 histone methylation sits in a cell what procedure would you use instead of qPCR?
7. Which two nucleotides of the TALEN sequence give the variable recognition for nucleotides?
8. Define microbiome in humans.
9. miRNA are stable in serum while messenger RNA would degrade quickly. What two properties of miRNA give it its stability?
10. You have a eukaryotic gene that has five exons and four introns. How many theoretical alternative splice variants do you have?
11. What are the key nucleotide sequences in the human genome introns that drive alternative splicing?
12. Name or draw a light sensitive entity used to chemically link small molecules to their potential protein receptor target.
The following are more than a couple of sentence answer questions.
1. Nanopore sequencing is the up and coming new technology for DNA sequencing. Explain how it works.
2. Compare and contrast the benefits and pitfalls of the TALEN and Zinc finger procedures.
3. For zinc finger technology the Fok I nuclease is used. What class of enzymes does Fok I belong? What is special about Fok I that makes it useful for zinc finger cleavage?
4. Explain the process for miRNA processing.
5. Explain the hypothesis of the speed bump model for histone modification of alternative splicing.
6. Different histone methylation modifications effect whether an exon is included or excluded from a final mRNA. Explain the process.
7. Alternative splice variants are theorized as the reason that organisms can become more complex without necessarily adding more genes. Explain how this works.
8. Explain the CLIP assay for discovery of splice accessory proteins. Remember very close to CHiP assay.
9. For determination of sites where DNA is methylated we discussed a couple different techniques. Name and explain ONE of these procedures.
10. You several libraries of EST sequences derived from a dozen different specific cell types. Explain how this helps you define the intron exon boundaries for genes in the organism.
11. You wish to determine which alternative splice variants are expressed in a specific cell culture. Name and explain a technique to do this.
12. A gene for a membrane protein has a series of different exon that all will code for different cytoplasmic regions of the protein. How does this help increase the diversity of the function for this one gene depending on which exon selected in a certain cell type?
13. Synthetic biology was used to produce the malaria drug artemisinic acid in yeast. Explain thesynthetic biology steps changed in order to produce the artemisinic acid.
14. For communication between RTRACS modules engineers wanted a natural molecule that is easy to make, and nicely unstable so signal controllable. What is this molecule and what properties make it useful for a signal transfer molecule?
15. When defining the stability of a biological or a small molecule after injection what four letter acronym is used and what does each letter stand for?
16. Explain target based drug screening.
17. If you wanted to use Zebrafish as a model organism for a human disease what analytic comparisons of the two genomes should be done first?
18. What are the standard gene factors that need to be expressed in skin fibroblasts in order to potentially produce IPSCs
19. We discussed epigenetic states that have been found to differ between ESC and IPSC cells. Name and explain one of these.