Amina Larbah (alarbah@uci.edu) Bio 97 Edinger/Cinquin/Bardwell (Sec.

D) Office Hours: MW 11-12 (SH 149) Week 2

1. Which of the following statements is TRUE?

a. One difference between DNA and RNA nucleotides is the presence of a 3 hydroxyl on the pentose sugar. b. In DNA replication, gyrase (topoisomerase II) relieves torsional stress by making a single strand break in the DNA backbone, swiveling the DNA, and then rejoining the strand. c. Helicase provides the energy necessary to unzip double stranded DNA and break hydrogen bonds between the strands.
d. DNA polymerase has a proofreading activity known as the 3 to 5 exonuclease

activity that allows it to excise the most recently added nucleotide during replication. 2. Ciprofloxacin (Cipro) is a drug used to treat anthrax and other more common bacterial infections. Cipro works by inhibiting bacterial topoisomerase II (gyrase). What impact does this drug have on bacterial cells?
3. Which of the following statements is FALSE regarding DNA sequencing?

a. A part of the sequence of the DNA needs to be known before DNA sequencing can occur. b. The sequence of the DNA could be determined even if the chain terminating nucleotides were not labeled. c. Chain-terminating bases, also called diterminators, are present in low concentrations and once added to a chain of nucleotides polymerization is terminated

Amina Larbah (alarbah@uci.edu) Bio 97 Edinger/Cinquin/Bardwell (Sec. D) Office Hours: MW 11-12 (SH 149) d. Chains of nucleotides of varying lengths (due to termination by a dideoxynucleotides) are separated by length via gel electrophoresis with the shortest strands travelling the fastest through the gel. 4. Fill in the spaces in the chart below to identify similarities and differences between PCR, DNA sequencing, and DNA replication. DNA Replication Primer (DNA or RNA) DNA Polymerase Type Heat or Helicase Ligase (Yes/No) Semiconservative or conservative Type of nucleotides
5. Determine the sequence of the primer used for DNA replication, DNA sequencing, and PCR.

DNA Sequencing

PCR

For PCR, determine the Tm for that specific primer Template: 5 ACTGCCGACTTACA. 3 Primer for replication Primer for sequencing Primer for PCR Tm for PCR primer =
6. Fill in the blanks to the statement below (one word/blank).

5 5 5

3 3 3

Both exon shuffling and alternative splicing can give rise to new______. In both processes, the order of the ______ does not change. However, the exon shuffle model can involve ____ transcript(s) while alternative splicing involves _____ transcript(s).

Amina Larbah (alarbah@uci.edu) Bio 97 Edinger/Cinquin/Bardwell (Sec. D) Office Hours: MW 11-12 (SH 149) 7. Fill in the chart to compare transcription and translation in eukaryotes and prokaryotes. Energy for transloc ation Prokaryotes Eukaryotes UTR (Y/N) Coupling Initiation factors (Y/N) Scanning (Y/N) Starting Ribosomal amino acid Subunits mRNA processing (Y/N) #Protein /mRNA

8. Which of the following statements is TRUE?

a. Aminoacyl tRNA synthetase is the enzyme responsible for translating the genetic code by binding an amino acid to it proper tRNA (correct anticodon). b. Initiation factors in prokaryotes bind to the 5 cap of the mRNA. c. The first tRNA carrying methionine enters the ribosome at the A (acceptor) site. d. RNA polymerase binds to promoter sequences in double stranded DNA to initiate translation. e. DNA ligase seals a nick in the DNA backbone by forming a phosphodiester bond between a free 3 OH and an incoming deoxynucleotide triphosphate.
9. Assume that a DNA sequence (sense strand shown) reads 5 .ACTTGCAACGCA3.

Look at the sequences below and identify what possible mutation might have occurred in the original sequence.
a. 5... ACTGCAACGCA3

__________________________ ___________________________

b. 5..ACTTGCAAACGCA..3

Amina Larbah (alarbah@uci.edu) Bio 97 Edinger/Cinquin/Bardwell (Sec. D) c. 5.. ACCTGCAACGCA..3 d. 5.. ACTTGCAAGGCA..3 Tips and helpful notes: Make sure to do the problems assigned on the syllabus and those assigned in lecture. Form a study group. The best way to learn sometimes is to teach others. Be careful of how a question is worded. Read carefully! Check it out: http://learn.genetics.utah.edu/content/begin/dna/ DNA sequencing: http://www.youtube.com/watch?v=SRWvn1mUNMA Acronym: ReMember This rRNA, mRNA, tRNA 1, 2, 3: rRNA= RNA Polymerase I, mRNA= RNA Polymerase II, tRNA= RNA Polymerase III Office Hours: MW 11-12 (SH 149) ___________________________ ___________________________