Chapter 13 - Bacterial Genome

Question 1

Briefly summarize the experiments of Griffith; Avery, MacLeod, and McCarty; and Hershey and Chase.

Answer 1

• Griffith used mice
  
  • Avery, macleod, mccarty used enzymes to degrade protein, rna, and dna
    Hershey and chase used bacteriophages

Question 2

Explain how protein was ruled out as the molecule of genetic information storage in each of the experiments performed by these important microbiologists

Answer 2

• Griffith noticed that clean r strain became virulent only when put together with s strain. This suggested something is responsible for transformation
• Avery and group noticed that transformation did not occur when dna was destroyed. Suggested dna carries genetic info
  Hershey and chase noticed that bacteriophage injected dna into cell not protein

Question 3

What are nucleic acids? How do DNA and RNA differ in structure

Answer 3

• Nucleic acids are macromolecules that store and transmit genetic info
• Nucleic acids are composed of nucleotides
• Nucleotides have a sugar, phosphate and nitrogenous base
  DNA and RNA

Question 4

Outline the transcription cycle observed in bacteria. Which steps require the following: RNA polymerase core enzyme, sigma factor, and RNA polymerase holoenzyme?

Answer 4

• Transcription is when RNA polymerase holoenzyme binds to promotor region of DNA. DNA unwinds and RNA polymerase synthesizes RNA nucleotides
• Elongation is when RNA polymerase moves along template strand synthesizing in 5’ to 3’ direction. DNA unwinds infront of enzyme and newly synthesized RNA detaches behind enzyme
  Termination is when a termination sequence or Rho protein binds to RNA and RNA transcript is released and machinery disassembles

Question 5

What is a consensus sequence? What happens at the –35 and –10 sequences during transcription initiation?

Answer 5

• A consensus sequence is a sequence of DNA that represents the most common nucleotide patten found at a specific position in a set of related DNA sequences. Ex promotor regions
• The -35 and -10 sequences are promotor sequences that are recognized by the sigma factor of RNA polymerase holoenzyme
• The sequences act as initial binding sites for RNA polymerase holoenzyme
• -35 sequence = recognition and binding of RNA polymerase
  -10 sequence = facilitates unwinding of DNA to start transcription

Question 6

What is the difference between a codon and an anticodon?

Answer 6

• A codon is a sequence of nucleotides on mRNA that encode info for the polypeptide chain. Written in 5’ to 3’ direction
  Anticodon is a sequence of nucleotides on tRNA that encode for the corresponding amino acid to the codon. Written in 3’ to 5’ direction

Question 7

What is meant by code degeneracy (redundancy)? How does wobble help alleviate the energy cost exacted on a cell due to code degeneracy?

Answer 7

• 1st and 2nd codon are most important
• 3rd codon can be different and code for the same amino acid as long as first two are the same
• 64 codons only 20 amino acids
  Wobble reduces energy cost because it allows one tRNA to recognize multiple codons

Question 8

In which direction are polypeptides synthesized?

Answer 8

• From the N terminus to the C terminus
• N terminus is amino group
  C terminus is carboxyl group

Question 9

Briefly describe the structure of transfer RNA and relate this to its function. How are amino acids activated for protein synthesis, and why is the specificity of the aminoacyl-tRNA synthetase reaction so important?

Answer 9

Key regions
1. Anticodon loop = 3 complementary bases to mRNA codon
2. Acceptor stem = 3’ (CCA) end where amino acid is attached
3. D and T loops = allow tRNA to interact w ribosomes and enzymes
4. Variable loop = add flexibility and diversity
Amino acid activation
- Aminoacyl tRNA synthetases catalyze a two step reaction that attach amino acid to tRNA molecule
- This reaction is important because each aminoacyl tRNA synthetase is specific to one amino acid and corresponding tRNA
Attaching the wrong amino acid result in incorrect protein synthesis

Question 10

What roles do ribosomal RNAs have?

Answer 10

• Provide structure for tRNA and mRNA interaction
• Catalyze formation of peptide bonds using 23S rRNA
• APE sites where tRNA binds
• 16S rRNA aligns mRNA by recognizing shine dalgarno sequence
  Ensures translation is accurate between codons and anticodons