Bio 111B

Study Questions 13: DNA, Replication & DNA Technology I

 

1. What information do genes carry?

 Genes carry the information (base sequences) to build proteins

2. How are DNA, enzymes, and metabolic pathways related?

 DNA codes for the proteins that are enzymes that catalyze the steps in a metabolic pathway.

3. How do alleles differ at the DNA level? at the protein level? at the phenotype level?

 At the DNA level, alleles are different base sequences that occupy the same positions (genes) on homologous chromosomes. At the protein level, alleles are proteins that differ in their function for a specific task. At the phenotype level, alleles are different versions of the same trait (brown vs. blue eye color).

4. Why do we say that a DNA double helix runs antiparallel?

 The two strands have opposite polarity; if one strand is oriented 5'--> 3', then the other strand is oriented 3' --> 5'.

5. What is the importance of complementarity to replication?

 Complementarity allows an existing DNA strand to serve as a template for the synthesis of a new strand.

6. What are the functions of DNA polymerase, RNA polymerase, and ligase?

 DNA polymerase is the enzyme that adds nucleotides to an existing 3' end. RNA polymerase makes the primers that provide the existing 3' ends for DNA polymerase to work with. Ligase seals up breaks in the backbone after primers have been removed and DNA polymerase has filled in the primer space with DNA.

7. What is a replication fork?

 A replication fork is the point at which the two template strands are separating to allow replication to continue.

8. Why is there a leading strand and a lagging strand? What are each of their polarities?

 The leading strand is the strand along which continuous synthesis takes place. It is called "leading" because continuous synthesis is a bit faster than discontinuous synthesis, so the leading strand is usually a bit ahead of the lagging strand (along which discontinuous synthesis is occurring). There have to be leading and lagging strands because the two templates differ in polarity. The leading template strand is being read 3'-->5' (so that continuous synthesis can occur 5'-->3'); the lagging strand is being read 5'-->3' (and discontinuous synthesis occurs).

9. What are Okazaki fragments? Why are they formed?

 Okazaki fragments are the products of discontinuous synthesis. They form because the overall direction of synthesis forces a template strand to be read in the 5'-->3' direction, and new DNA can be synthesized only 5'-->3'. The Okazaki fragment consists of an RNA primer and a segment of newly synthesized DNA polymerized from the primer's 3' end.

10. Why do we call DNA synthesis semi-conservative?

 DNA synthesis is called semi-conservative because whole DNA strands are kept intact, but newly synthesized double helices consist of one old strand and one new strand.

11. What is a restriction endonuclease? Where are they naturally found? What is their natural function?

 Restriction endonucleases are enzymes that cut the S-P backbone bonds of DNA in the interior of the molecule. They are naturally found in bacteria as the bacterial "immune system." They cut up foreign (viral) DNA to inactivate it before it can destroy the bacterial cell.

12. Which way does DNA move in an electrical field and why does it move? How does gel electrophoresis separate DNA molecules? How do we make the DNA visible in an electrophoresis gel?

 DNA is negatively charged so it moves toward the positive pole. Gel electrophoresis separates DNA molecules on the basis of size...short DNA molecules find their way through the pores in the gel much more quickly than do large DNA molecules. DNA becomes visible on a gel by adding ethidium bromide, a chemical that binds to DNA and fluoresces under UV light.

13. What is PCR? Why is it useful to so many applications, from molecular genetics to forensic pathology? What enzyme is used in PCR and why?

 PCR, or polymerase chain reaction, is a way to amplify a specific segment of DNA if you know the sequence of flanking regions to construct the primers. It can be used to amplify sequences for analysis in applications as diverse as forensics, molecular genetics, and phylogenetics. Taq polymerase is the DNA polymerase used in PCR because it is thermally stable...it doesn't denature when heated to 95^oC in the process of denaturing the DNA templates.

14. In the following diagram, an origin of replication is shown. On the diagram,

a. in the boxes, label the remaining polarities of the DNA

b. indicate in which segments DNA synthesis will be continuous and in which it will be discontinuous

c. indicate the direction in which DNA polymerase will elongate the newly-made DNA

  

15. If one single strand of DNA has a ratio of purines to pyrimidines of 0.5, what is the ratio of purines to pyrimidines in the complementary strand?

 If one strand has a ratio of purines/pyrimidines of 0.5, then the other strand has a ratio of 2 purines/pyrimidines.

16. If a single strand of DNA has a C+T proportion of 0.2 (there are 20% C's and T''s in that strand), the C+T proportion in the complementary strand is…

a. 0.2

b. 5.0

c. 0.8

d. 1.25

e. impossible to determine from the information given

 

17. Consider the following gel of a drop of blood from the perpetrator (P) left at the scene of a crime and blood samples of the 3 prime suspects (S1, S2 & S3).

a. Which suspect is the perpetrator? Explain how you know. Suspect 2 matches the DNA banding pattern of the perpetrator. b. What procedures were likely applied to the crime scene blood sample to be able to produce this gel? PCR was used to amplify the sequences and restriction endonucleases were used to cut the DNA before the fragments were separated on the gel.

18.Once again, two men were involved in a paternity suit brought by a woman against her estranged husband. The woman was seeking child support for her infant from her husband, but the husband accused the woman's lover of being the biological father. Unfortunately, blood typing was inconclusive: both men had the same blood type. So the judge ordered DNA analysis. A sample of blood was taken from the mother, the baby, and both men. The results are shown below.

a. With this information, who is the father of the baby? The lover, is the father, not the husband. b. Which bands (1-11) are most useful for determining the father of the baby? Why? Bands 4 and 8 are the useful bands; they occur in the baby but not in the mother, so the baby must have gotten them from the father.