12 - Prokaryotic Gene Function

Question 1

Identify the sequence of standard “start” and “stop” codons

Answer 1

• AUG is the start codon or initiator codon
• UAA, UAG, UGA are the stop codons also known as nonsence or termination codons

Question 2

Identify the function of “start” and “stop” codons

Answer 2

• a codon is a three- letter code made up of three bases
• A start codon is the first translated codon in any mRNA. it specifies the amino acid methionine
• Stop codons do not specify amino acids. They indicate the end of a polypeptide-encoding sentence.
  
  • when a ribosome reaches one of the stop codons, polypeptide synthesis stops and the new polypeptide chain is released from the ribosome.

Question 3

Compare the overall gene expression of prokaryotic vs. eukaryotic cells.

Answer 3

• Prokaryotic genes are usually under the control of operons.
• In eukaryotes, there are no operons but there are many other methods of gene control such as chromatin remodeling, RNA breakdown, miRNA inhibition, protein tagging by ubiquotin.

Question 4

relative location of such DNA sequence “signals” as promoter, 5’ and 3’ UTR, “SD box”, start codon, stop codon, transcription terminator etc.

Answer 4

• The promoter is located upstream of the gene to be transcribed but is not transcribed itself,
• the 3’ and 5’ UTR are transcribed, but occur before and after the start and stop codon and therefore are not translated.
• The SD box is in prokaryotes and is transcribed but not translated. It serves as a docking station for ribosomes through complementary base pairing of mRNA and rRNA.
• The start codon is transcribed and translated (codes for methionine) and is always the very first codon to be read and translated.
• The stop codon does not code for an amino acid, but instead attracts a protein release factor in translation. The stop codon is not translated.
• The transcription terminator sequence only functions after being transcribed. It is not translated.

Question 5

mechanism by which each signal is interpreted, or understood, by the cell

Answer 5

• The promoter is understood as DNA by the RNA polymerase and by proteins that bind to DNA,
• the SD box is understood as mRNA by rRNA.
• The start and stop codons are recognized as RNA signals by tRNA with the corresponding anti-codons.
• The transcription terminator sequence is understood as a DNA sequence (it is transcribed by RNA polymerase) but it only functions as a RNA sequence which forms a hairpin loop.
• In Eukaryotes, the clipping sequence is understood as RNA by an RNA’ase enzyme

Question 6

relationship between DNA sequence of signals and their function (ie. how would low efficiency promoters be different than high efficiency promoters?

Answer 6

• some promoters are very attractive
• The sequence of some promoters is such that polymerase makes a stable bind and initiates transcription very frecuently
• there can be promoters the are less atractive and are less efficient at transcription

Question 7

characteristics of promoters that require a particular position and direction

Answer 7

• Promoters are both location and direction dependent.
• They are location dependent since they must be located directly upstream of the gene to be transcribed.
• They are direction dependent since they must send RNA polymerase in a specific direction (towards the gene)

Question 8

change in amino acid code, given a change in the DNA sequence (and Genetic Code table)

Answer 8

A change in the DNA sequence corresponds to a change in the RNA sequence, which consequentially results in a different codon and therefore a different amino acid

Question 9

base sequence of start and stop codons as mRNA and DNA

Answer 9

• START codon: AUG (DNA sequence = TAC)
• STOP codons: RNA sequences: UAG, UAA, UGA… DNA sequences are ATC, ATT, ACT respectively.