Exam 2 Answer Key | Biochemistry 2006 | CHEM 431 | Exams Biochemistry

CHEM 431/531 - Biochemistry I/Exam II/October 9. 2006 Answer Key

Each Question is Worth 7 Points. Maximum Points Possible = 112 Points (12 Bonus Points).

1. Describe the Watson - Crick Model of double-stranded DNA.

Watson-Crick Model:

(i) Two helical polynucleotide chains are coiled around a common axis. The chains run in

opposite directions.

(ii) The sugar-phosphate backbones are on the outside and the purine and pyrimidine bases lie

on the inside of the helix..

(iii) The bases are nearly perpendicular to the helix axis and adjacent bases are

separated by 3.4 A. The helical structure repeats every 34 A, so there are 10 bases (=34A

per repeat/3.4 A per base) per turn of helix. There is a rotation of 36 degrees per base (360

degrees per full turn/10 bases per turn).

(iv) The diameter of the helix is 20 A.

2. Briefly describe the Meselson and Stahl experiment that indicated that DNA replication is

semi-conservative.

Meselson and Stahl grew bacteria in the presence of 15

N, or “heavy” nitrogen. They rapidly replaced

the 15

N media with 14

N, or light nitrogen. DNA was extracted at various time intervals during the

growth of the bacteria, representing different stages of replication (generations). They examined the

DNA using density-gradient equilibrium sedimentation and observed that no “heavy” DNA was

present in the first generation, but that the DNA was intermediate between light and heavy. After the

second generation, there were equal amounts of intermediate and light. This confirmed that one

strand of the parent DNA is present in each daughter strand of replicated DNA.

3. What is DNA hybridization?

DNA hybridization is the process whereby strands of complimentary DNA strands or

one strand of complementary DNA and one strand of RNA base pair to form a helix.

4. Compare and contrast DNA polymerase and RNA polymerase.

DNA polymerase catalyzes the addition of deoxyribonucleotide units to a DNA chain and RNA

polymerase catalyzes the addition of ribonucleonucleotide units to a RNA chain. The direction of

synthesis for both enzymes is in the 5’



3’ direction. The enzymes have a similar mechanism of

elongation and the synthesis is driven in the forward direction by the hydrolysis of pyrophosphate.

However, RNA polymerase does not require a template and lacks the nuclease capability used by

DNA polymerase to excise mismatched nucleotides.

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CHEM 431/531 - Biochemistry I/Exam II/October 9. 2006 Answer Key

Each Question is Worth 7 Points. Maximum Points Possible = 112 Points (12 Bonus Points).

Describe the Watson - Crick Model of double-stranded DNA. Watson-Crick Model: (i) Two helical polynucleotide chains are coiled around a common axis. The chains run in opposite directions. (ii) The sugar-phosphate backbones are on the outside and the purine and pyrimidine bases lie on the inside of the helix.. (iii) The bases are nearly perpendicular to the helix axis and adjacent bases are separated by 3.4 A. The helical structure repeats every 34 A, so there are 10 bases (=34A per repeat/3.4 A per base) per turn of helix. There is a rotation of 36 degrees per base ( degrees per full turn/10 bases per turn). (iv) The diameter of the helix is 20 A.
1. Briefly describe the Meselson and Stahl experiment that indicated that DNA replication is semi-conservative. Meselson and Stahl grew bacteria in the presence of 15 N, or “heavy” nitrogen. They rapidly replaced the 15 N media with 14 N, or light nitrogen. DNA was extracted at various time intervals during the growth of the bacteria, representing different stages of replication (generations). They examined the DNA using density-gradient equilibrium sedimentation and observed that no “heavy” DNA was present in the first generation, but that the DNA was intermediate between light and heavy. After the second generation, there were equal amounts of intermediate and light. This confirmed that one strand of the parent DNA is present in each daughter strand of replicated DNA.
2. What is DNA hybridization? DNA hybridization is the process whereby strands of complimentary DNA strands or one strand of complementary DNA and one strand of RNA base pair to form a helix.
Compare and contrast DNA polymerase and RNA polymerase. DNA polymerase catalyzes the addition of deoxyribonucleotide units to a DNA chain and RNA polymerase catalyzes the addition of ribonucleonucleotide units to a RNA chain. The direction of synthesis for both enzymes is in the 5’  3’ direction. The enzymes have a similar mechanism of elongation and the synthesis is driven in the forward direction by the hydrolysis of pyrophosphate. However, RNA polymerase does not require a template and lacks the nuclease capability used by DNA polymerase to excise mismatched nucleotides.

What are two features of eukaryotic mRNA that are unique as compared to prokaryotic mRNA. Eukaryotic mRNA has a special nucleotide “cap” at the 5' end and a poly A tail at the 3' end. NOTE: Prokaryotic DNA contains only exons; eurkaryotic DNA contains exons and introns. Mature prokaryotic mRNA has no introns. Mature eurkaryotic mRNA has no introns (introns are removed and exons spliced together by splicosomes).
Design a potential DNA-restriction enzyme site. Show both strands. Any palindromic site of four or more base pairs would be appropriate 5’GGATCC3’ 3’CCTAGG5’
What is the basis of the Sanger method? This technique uses sequence -specific termination of a DNA synthesis reaction using modified nucleotide substrates (ddNTPs) resulting in various sizes of DNA fragments. By including limited amounts of radioactive bases, strands differing by one base in length can be observed. By reading the bands, the sequence can be determined. (Fluorescent or dye tags can also be used in an automated process.)
Explain the basis of the polymerase chain reaction (3 steps; explain what happens at each step). Using primers that flank the sequence of interest and carrying out repetitive replication reactions can make copies of a particular DNA fragment. Template DNA, DNA polymerase, dNTPs, and other necessary reagents are added to the reaction mixture. The DNA is heated to separate the strands, cooled to allow the primers to anneal, and then replicated. The process is repeated many times, each time doubling the number of DNA copies present. The enzyme used is thermostable, and can withstand the repetitive heating and cooling steps.
Distinguish between a primer and a template DNA strand and describe the function of each. Template Strand – A strand of nucleic acid such as DNA that serves as a pattern for the synthesis of a macromolecule, as of RNA. Template strand dictates the sequence on the newly synthesized strand of DNA because the new strand’s bases are complementary to the bases on the template strand. Primer Strand – A short segment of nucleic acid that serves as a starting point for DNA replication. A primer is required because most DNA polymerases cannot begin synthesizing a new DNA strand from scratch, but can only add to an existing strand of nucleotides.

You are given two solutions containing different purified DNAs. One is from the bacterium (prokaryotic) and has an adenine composition of 25%, whereas the other is from a fungus cell (eukaryotic) and has an adenine composition of 37%. a. What relative proportions of adenine, guanine, thymine, and cytosine would you expect to find in the two DNA samples? A C G T Bacterium: 25% ____25%__ ____25%___ 25% Fungus: 37% 13% 13% 37% b. You measure the absorbance of ultraviolet light of each solution as a function of increasing temperature. Which solution will yield the higher Tm value and why? The bacterium will have a higher Tm value because it has a higher G:C content. The G:C base pair has three hydrogen bonds and is more stable to heat denaturation than the A:T base pair which has only two hydrogen bonds. c. After melting the two solutions, mixing them together, and allowing them to cool, what would you expect to happen? The single stranded DNA (ssDNA) of the bacterium will hybridize to each other to produce double stranded DNA (dsDNA). Likewise, the ssDNA of the fungal DNA will reanneal with each other to produce dsDNA. d. One of these species was isolated from a hot spring (95oC). Suggest which sample is the thermophilic organism. What is the basis for your answer? The bacterium is most likely the thermophilic organism since it contains a higher GC content which would be more stable to heat.
Human myoglobin a protein found in human muscle that facilitates the diffusion of oxygen in muscle fibers. The human myoglobin gene contains three exons separated by two introns. Which DNA type should be used to transform and express human myoglobin in E. coli? Human myoglobin complementary DNA or human myoglobin genomic DNA? ( 1 Point) Explain why (Remaining 6 Points). Since E. coli lack the machinery to excise introns and splice exons, they would make a meaningless mRNA if presented with human myoglobin genomic DNA. Therefore, if you wish to express the human myoglobin gene in E. coli, you must use its complementary DNA (cDNA), which contains the information in the three exons, but no introns.

Exam 2 Answer Key | Biochemistry 2006 | CHEM 431, Exams of Biochemistry

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Download Exam 2 Answer Key | Biochemistry 2006 | CHEM 431 and more Exams Biochemistry in PDF only on Docsity!

Each Question is Worth 7 Points. Maximum Points Possible = 112 Points (12 Bonus Points).