Study Guide for Test 5

DNA replication

1. When did we find out that DNA was the substance that stored our genetic information?

2. What do the following terms mean?Transformation, Transcription, Translation?

3. Who described the structure of DNA?Who took the photograph that made this possible?What technique was used to take this photograph?

4. Who figured out that the backbone of a strand is made of sugar and phosphate?Who figured out that the nucleic acids were pointed towards the middle?

5. what do these binding chemicals do in DNA replication?helicase, binding protein, primer, topoisomerase, primase, DNA polymerase, DNA ligase, nuclease, aminoacyl-tRNA synthetase

6. what is a primer made of

7. what is dATP?What sugar does it contain?

8. what is a leading strand?What is a lagging strand?What is an okizaki fragment

9. Which end of a strand do we add nucleotides to?What direction does a strand grow in?

10. which enzymes excise (remove) mismatches between strands?

11. what are telomeres?What is their purpose?what does telomerase do to them?

12. what is chromatin?What two things is it made of?

13. what is a spliceosome

14.

genes, Transcription and Translation

1. What are genes and chromosomes made of?

2. What is a gene?What is a genome?

3. What type of organisms express recessive traits?What type of organisms express dominant traits?

4. Name three ways that DNA and RNA differ.What are the backbones of DNA and RNA made of?What part of the DNA and RNA molecules contains the genetic information?

5. What are these types of RNA used for:rRNA, tRNA, mRNA, siRNA

6. Where does transcription happen?What molecule(s) do it?What are they reading?What are they making?

7. Where does translation happen?What molecule(s) do it?What are they reading?What are they making?

8. What is a codon?What is an anticodon?What type of RNA has a codon in it?What type of RNA has an anti-codon in it

9. Where are start and stop codons found?What process do they control?

10.Where are promotors and terminators found?What process do they control?

11.Be able to explain how gene regulation affects what cells make and what cell type they belong to.Be able to list three ways of shutting off transcription of a gene

12.What are templates?What are complimentary strands

13.Be able to explain the relationship between Codons and Amino Acids

14.When we copy a DNA molecule, where do the template strands from the original molecule end up?

15.What are some possible side effects of replication errors?How do we “proofread” for replication errors?

16.What is a mutagen? 

17.What type of DNA errors can be caused by UV radiation

18.What are introns, exons, transposons, 

19.Can genes be turned on or off by environmental conditions? Can signals from cell to cell regulate gene expression

20.Most cells in your body have the same DNA.What causes them to form different cell types

21.How does the wrapping/packing of DNA around histone affect gene expression

22.How does methylation affect gene expression?

23. Be able to explain the following terms: Operon, repressor, co-repressor

24. what is the difference in a repressible operon and a inducible operon. Which is common in catabolic pathways? Which is common in anabolic pathways?

25. explain how methylation and acetylation can affect transcription and epigenetics. Can these changes be passed on to the next generation?

26. What is alternative RNA splicing?

27. how are siRNA and miRNA similar? How are they different?

28. In cell division and animal development, what does the term “induction” mean? How does it affect the formation of thing like wings, limbs, or even head formation?

29. What are stem cells? What does it mean to be totipotent? What does it mean to be pleuripotent? How long can they divide? What can they differentiate into?

30. What are proto-oncogenes? What are oncogenes? What are some ways that proto-oncogenes can change to cause disease?

Viruses

1. Are viruses alive? Explain why or why not?

2. What two things do all viruses have?

3. What is a viral “envelope” made of

4. Which types of nucleic acids can they contain?

5. What are the lytic and lysogenic cycles? Which method do virulent viruses use? Which method do temperate phages use?

6. What is prophage DNA? How is it different from a provirus?

7. What is a retrovirus? What enzyme does it contain?

8. What is a capsid? What is a capsomere?

9. What organisms to phages infect?

10. What are restriction enzymes? What are plasmids? What do bacteria use them for?

11. What are prions?

Mutations

1. How are enzymes related to phenotypes (think of mouse coat colors)How are enzymes related to metabolic disorders

2. Which sugar and base are used in RNA?Which sugar and base are used in DNA?

3. How does a ribosome know which tRNA has the appropriate amino acid?

4. How are RNA polymerase and ribosomes similar?How are they different?(think of codons and promoters)

5. How is RNA polymerase different than DNA polymerase

6. What happens during RNA splicing

7. How many nucleotides are in a codon

8. What are the three characteristics of the genetic code

9. What is a type of mutation is called a “substitution”

10.Be able to use the charts in your book to discuss the effects of mutations.Be able to use the charts to compare the following mutations: AAAèAAG, AAGèAGG, AGGèAUG.Which of these will cause no change?Which will change an amino acid without denaturing the protein?Which will cause an amino acid change that might denature the protein? 

11.What will happen if a mutation in the middle of a gene causes the resulting mRNA codon to change from UGG to UGA

12.What are ribosomes made of?

13.What is a point mutation?

14.What is an insertion?What is a deletion?Why are insertions and deletions some of the mutations most likely to alter the shape/structure of a protein

15. Why are insertions and deletions classified as “frame shift” mutations

16.What is a “silent mutation”

17.Is it possible for a mutation to make an enzyme work better?Is this common?

Biotechnology and genetic engineering

1. Why do we say the genetic code is “universal”

2. Is it possible to manipulate the genes of a population WITHOUT using genetic engineering

3. Which of these are used in genetic engineering:turning a gene on, turning a gene off, adding a new gene

4. Be able to define the term Gene therapy

5. What do we use restriction enzymes for in biotech?What do bacteria use them for?

6. What do we use DNA ligase for in biotech?What do eukaryotes use it for?

7. What are “sticky ends”, and why are they useful in biotech? 

8. What is recombinant DNA?Why do we need to use the same restriction enzyme on both DNA sources when we are making recombinant DNA?

9. What is a plasmid?What do bacteria use plasmids for?

10. What are two ways to amplify DNA?Which one is used to make insulin, clotting factors and enzymes to dissolve clots?Which method is used for crime scene investigation and paternity tests?

11. Eukaryotic cells normally use enzymes to unzip and unwind the DNA before duplicating it.In PCR, we do this another way.Explain how.

12.Why does PCR require precise temperature control?What bonds are we trying to break?What bonds are we trying to NOT break?

13.What is special about the DNA polymerase used in PCR?Where was it found?

14. What is a vector?Be able to list three types of vectors

15.What technique is used in the lab as part of DNA fingerprinting

16. Which fragments move fastest and furthest through an electrophoresis gels?

17. How long have we been able to clone plants?Describe the technique for cloning a plant.

18.Describe the three steps in cloning an animal.Are cloned animals identical to the DNA donor?

19. What is the goal of gene therapy?Therapy to which type of cells is more likely to be controversial?

20. What is RNAi?What type of RNA do the protection mechanisms of the cell destroy?

21. What is a GMO?Why do we make them?(How can they be beneficial) What is a “transgenic organism”

22. Scientists have added the gene for Green Fluorescent Protein (GFP) to rabbits, dogs, monkeys and fish.What organism did this gene originally come from?

23. One environmental factor that worries some people about GMOs is the potential for pollution.How could GMO plants increase soil/water pollution? How could GMO salmon increase water pollution?

24.What are some of the other ethical concerns of GMOs?How could people prevent gene transfer?

25. How does PCR work? What chemicals are needed to make it happen?

26. Why would genomic libraries be stored in viruses?

27. What is cDNA?

28. Why is radioactive DNA used as a probe

29. How does size of a molecule affect movement in electrophoresis gel? How does charge affect it?

30. What is southern blotting used for? Explain how it is related to electrophoresis? Explain how it is related to DNA hybridization?

31. How is nuclear transplantation used in cloning?

32. What are vectors?

33. What does it mean to be “transgenic?” What is a “Pharm animal?”

34.