BIOL 200 Mcgill Exam Questions with
Complete Answers
Aminoacyl-tRNA synthetase - ANSWER-Links amino acid to its corresponding tRNA.
EF hand/helix-loop-helix motif - ANSWER-Proteins with this motif will bind to Ca2+
involving ionic bonds.
coiled-coil motif - ANSWER-found in fibrous proteins
zinc-finger motif - ANSWER-RNA and DNA binding proteins
What is a Motif/Domain? - ANSWER-The activity associated with a polypeptide.
Mutation - ANSWER-Permanent, transmissible changes to the genetic material of a
cell.
Mutagens - ANSWER-Chemical compounds that increase frequency of mutations.
(Ex. UV radiation, X-rays)
Carcinogens - ANSWER-Agent that cause cancer, most carcinogens are mutagens.
What are the 6 types of DNA repair? - ANSWER-1. Proofreading by DNA
polymerase
2. Base Excision Repair (BER)
3. Mismatch Excision Repair
4. Nucleotide Excision Repair
5. Double-strand Break Repair by End-joining
6. Double-strand Break Repair by Homologous Recombination
Proofreading by DNA polymerase - ANSWER-Done by either pol d/pol e.
They have exonuclease activity for the 3' end. The DNA polymerase will stop,
remove and replace the nucleotide.
When does Base Excision Repair occur? - ANSWER-When deamination of cytosine
occurs, it forms uracil which would create an incorrect watson-crick base pair.
Methylation of cytosine, creates 5-methylcytosine if this gets deaminated, it produces
Thymine. (incorrect bp)
Base Excision Repair - ANSWER-1. DNA Glycosylase hydrolyzes the bond between
the mispaired base and the sugar-phosphate backbone. (specific DNA Glycosylase
for different bases)
2. APE1 endonuclease cuts the DNA backbone.
3. AP lyase, associated with pol beta (pol b) removes the deoxyribose phosphate.
, 4. DNA pol b fills the gap with the proper base pair and DNA ligase seals the sugar-
phosphate backbone.
Mismatch Excision Repair - ANSWER-1. MSH2 (recognizes the daughter strand)
and MSH6 (recognizes which base pair is wrong) bind to daughter strand.
2. Previous part triggers the activity of MLH1 endonuclease + PMS2. (cut one bp out)
3. DNA helicase unwinds part of the daughter strand while DNA exonuclease digests
the segment with the error.
4. Pol d and ligase repairs the gap.
When does Nucleotide Excision repair happen? - ANSWER-If there is a mutation
caused by a mutagen , which modifies bases that dirt the normal shape of DNA.
Ex. Formation of Thymine-Thymine dimer though UV radiation
Nucleotide Excision Repair (NER) - ANSWER-1. Initial damage recognition with XP-
C and 23B. 23B recruits other proteins.
2. Opening of DNA double helix with TFIIH and RPA (to keep in right conformation).
3. XP-F (3' cut) and XP-G (5' cut) endonucleases remove the damaged chunk.
4. DNA pol e and DNA ligase repair the gap.
Double Stranded Break Repair by End-joining - ANSWER-- Can introduce error
1. DNA-PK, KU80/KU70 (heterodimer) bind to the end of the break.
2. other proteins join in.
3.Ends are ligated.
Double Stranded Break Repair by homologous Recombination - ANSWER-1. Ends
digested by exonucleases leaving 3' single-stranded ends.
2. RecA or Rad51 mediated strand invasion.
3. 3' end of invading strand is extended by DNA polymerase, until displaced single-
strand base-pairs with other 3' single strand generated initially.
4. 3' end of top strand is extended by DNA polymerase
5. Ends are ligated
6. Holiday junctions are cut (4 possible ways)
what are the components of plasmids? - ANSWER-ORI: Origin of replication, to be
able to multiply as many times as we need.
ampr : Ampicillin resistance gene.
Polyinker: Region to put the DNA of interest, number of restriction endonuclease
sites that can be recognized by enzymes.
How do polyinkers work? - ANSWER-Restriction sites (palindromic sequences)
where Endonuclease will cut and create "sticky ends". The genomic DNA of interest
will anneal to the sticky ends of the plasmid. T4 DNA ligase will complete the
backbone break.
Results in a Recombinant Plasmid.
What are the steps to transformation? - ANSWER-1. Mix E.Coli, Plasmid, and
CaCl2+ Pulse of heat.
2. Place the mix on agar plate containing ampicillin. (The bacterias that got
transformed with the plasmid will survive because of ampr, the rest will die)
Complete Answers
Aminoacyl-tRNA synthetase - ANSWER-Links amino acid to its corresponding tRNA.
EF hand/helix-loop-helix motif - ANSWER-Proteins with this motif will bind to Ca2+
involving ionic bonds.
coiled-coil motif - ANSWER-found in fibrous proteins
zinc-finger motif - ANSWER-RNA and DNA binding proteins
What is a Motif/Domain? - ANSWER-The activity associated with a polypeptide.
Mutation - ANSWER-Permanent, transmissible changes to the genetic material of a
cell.
Mutagens - ANSWER-Chemical compounds that increase frequency of mutations.
(Ex. UV radiation, X-rays)
Carcinogens - ANSWER-Agent that cause cancer, most carcinogens are mutagens.
What are the 6 types of DNA repair? - ANSWER-1. Proofreading by DNA
polymerase
2. Base Excision Repair (BER)
3. Mismatch Excision Repair
4. Nucleotide Excision Repair
5. Double-strand Break Repair by End-joining
6. Double-strand Break Repair by Homologous Recombination
Proofreading by DNA polymerase - ANSWER-Done by either pol d/pol e.
They have exonuclease activity for the 3' end. The DNA polymerase will stop,
remove and replace the nucleotide.
When does Base Excision Repair occur? - ANSWER-When deamination of cytosine
occurs, it forms uracil which would create an incorrect watson-crick base pair.
Methylation of cytosine, creates 5-methylcytosine if this gets deaminated, it produces
Thymine. (incorrect bp)
Base Excision Repair - ANSWER-1. DNA Glycosylase hydrolyzes the bond between
the mispaired base and the sugar-phosphate backbone. (specific DNA Glycosylase
for different bases)
2. APE1 endonuclease cuts the DNA backbone.
3. AP lyase, associated with pol beta (pol b) removes the deoxyribose phosphate.
, 4. DNA pol b fills the gap with the proper base pair and DNA ligase seals the sugar-
phosphate backbone.
Mismatch Excision Repair - ANSWER-1. MSH2 (recognizes the daughter strand)
and MSH6 (recognizes which base pair is wrong) bind to daughter strand.
2. Previous part triggers the activity of MLH1 endonuclease + PMS2. (cut one bp out)
3. DNA helicase unwinds part of the daughter strand while DNA exonuclease digests
the segment with the error.
4. Pol d and ligase repairs the gap.
When does Nucleotide Excision repair happen? - ANSWER-If there is a mutation
caused by a mutagen , which modifies bases that dirt the normal shape of DNA.
Ex. Formation of Thymine-Thymine dimer though UV radiation
Nucleotide Excision Repair (NER) - ANSWER-1. Initial damage recognition with XP-
C and 23B. 23B recruits other proteins.
2. Opening of DNA double helix with TFIIH and RPA (to keep in right conformation).
3. XP-F (3' cut) and XP-G (5' cut) endonucleases remove the damaged chunk.
4. DNA pol e and DNA ligase repair the gap.
Double Stranded Break Repair by End-joining - ANSWER-- Can introduce error
1. DNA-PK, KU80/KU70 (heterodimer) bind to the end of the break.
2. other proteins join in.
3.Ends are ligated.
Double Stranded Break Repair by homologous Recombination - ANSWER-1. Ends
digested by exonucleases leaving 3' single-stranded ends.
2. RecA or Rad51 mediated strand invasion.
3. 3' end of invading strand is extended by DNA polymerase, until displaced single-
strand base-pairs with other 3' single strand generated initially.
4. 3' end of top strand is extended by DNA polymerase
5. Ends are ligated
6. Holiday junctions are cut (4 possible ways)
what are the components of plasmids? - ANSWER-ORI: Origin of replication, to be
able to multiply as many times as we need.
ampr : Ampicillin resistance gene.
Polyinker: Region to put the DNA of interest, number of restriction endonuclease
sites that can be recognized by enzymes.
How do polyinkers work? - ANSWER-Restriction sites (palindromic sequences)
where Endonuclease will cut and create "sticky ends". The genomic DNA of interest
will anneal to the sticky ends of the plasmid. T4 DNA ligase will complete the
backbone break.
Results in a Recombinant Plasmid.
What are the steps to transformation? - ANSWER-1. Mix E.Coli, Plasmid, and
CaCl2+ Pulse of heat.
2. Place the mix on agar plate containing ampicillin. (The bacterias that got
transformed with the plasmid will survive because of ampr, the rest will die)
