BIMM 120 Final questions n answers
graded A+ passed
Error-Prone DNA Repair - correct answer ✔✔ §SOS ("Save Our Ship") repair
-Induced by extensive DNA damage
-Results in expression of many DNA repair enzymes
-Among them, two "sloppy" DNA polymerases that lack proofreading activity and allow
mutations to occur
-However, the cell has no other option but to "mutate or die."
Error-Proof Repair Pathways - correct answer ✔✔ §Nucleotide excision repair
-An endonuclease removes a patch of single-stranded DNA containing certain types of damaged
bases, including dimers.
*google docs
Identifying Mutagens Using Bacterial "Guinea Pigs" - correct answer ✔✔ §The Ames test relies
on a mutant bacterial strain that has a point mutation in the hisG gene
-This histidine auxotroph cannot grow on a medium lacking histidine
-A mutagen-containing paper disk is placed on an agar plate spread with the mutant.
-The mutagen causes reversion mutations of hisG and colonies start to appear around the disk.
-Read text for full description
Mutations Arise in Diverse Ways - correct answer ✔✔ §Spontaneous mutations are rare
because of the efficiency of DNA replication proofreading and repair.
§However, they can arise for many reasons:
,1.Tautomeric (chemical) shifts in DNA bases that alter base-pairing properties
2.Oxidative deamination of bases
3.Formation of apurinic sites
4.Damage caused by reactive oxygen species
9.3 Mutations - REVIEW - correct answer ✔✔ §A mutation is a heritable change in the DNA
sequence.
§Types of mutations:
-Point mutation: change in a single base
-Transition: purine → purine; pyrimidine → pyrimidine
-Transversion: purine ↔ pyrimidine
-Insertion (addition) and deletion (subtraction) of one or more bases
-Inversion: DNA is flipped in orientation.
-Reversion: DNA mutates back to original sequence.
1. Missesnse point mutation: single nucleotide change results in diff amino acid
2. Nonsense point mutation: single nucleotide change results in stop codon
3. Insertion frameshift: changes reading frame and all downstream amino acids
4. Deletion frameshift: removing nucleotides to cause a frameshift
5. Inversion: flipping DNA sequence to change amino acids produced
Site-Specific Recombination - correct answer ✔✔ §Site-specific recombination does not utilize
RecA and is specialized for certain DNA rearrangements.
§It involves very short (10 to 20 bp), specific regions of homology between donor and target
DNA molecules.
-These are recognized specifically by dedicated enzyme systems, which catalyze a crossover.
§Example:
,-The integration of phage lambda into the host chromosome to become a prophage
Generalized Recombination and RecA - correct answer ✔✔ §There are three functions for
generalized recombination in the microbial cell:
-Internal DNA repair.
-DNA repair with DNA taken up from the same species.
-Acquisition of new genes from other organisms for genetic diversity to enhance the
competitive fitness of the cell (evolution).
CRISPR Interference - correct answer ✔✔ §CRISPR (clustered regularly interspaced short
palindromic repeats) is an adaptive system.
-An organism that manages to survive a phage attack captures a piece of the phage genome and
uses it as defense against future attack.
§CRISPRs consist of repeats and spacers that do not encode proteins
§Near them lie CRISPR-associated (CAS) gene families that encode proteins.
§CRISPR is a microbial immune-like system.
-CRISPR function can be divided into three stages: spacer acquisition, crRNA processing, and
effector stage (cleavage of foreign DNA).
1. spacer acquisition: sequences from invading DNA are incorporated into the CRISPR locus
2. crRNA processing: crRNA is transcribed and processed by Cas products
3. Effector stage: cleavage of foreign DNA
Generalized Transduction - correct answer ✔✔ During the phage lytic life cycle, bacterial
genomic DNA fragments are accidentally packed into phage virions
These transducing phage can then inject the DNA into a new host cell, and it can recombine into
the chromosome
, *google docs
Gene Transfer by Conjugation Steps - correct answer ✔✔ 1.Sex pilus attaches
2.Retraction of pilus and bridge is formed
3.oriT is nicked and ssDNA is transferred
4.Replication of DNA in donor cell
5.ssDNA circularizes and replicates
6.F- recipient is now F+
*Google docs
Viruses- Introduction - correct answer ✔✔ §"All" cells can be infected by viruses.
§Some animal viruses generate serious disease: influenza, measles, dengue, zika, HIV...
§There are also insect and plant viruses.
--§Tobacco mosaic virus (TMV) was the first virus discovered.
§Bacterial viruses are called bacteriophage or just phage
§Viruses are ubiquitous and play important roles in the environment.
§In research, viruses have provided both tools and model systems in molecular biology.
Viruses - correct answer ✔✔ §A virus is a noncellular particle that must infect a host cell to
reproduce.
-Obligate intracellular parasite
-The viral genome directs the host cell's machinery to produce progeny viral particles.
§The virus particle, or virion, consists of nucleic acid (DNA or RNA) contained within a protective
protein capsid.
§Virus genomes are usually small, some contain less than a dozen genes.
graded A+ passed
Error-Prone DNA Repair - correct answer ✔✔ §SOS ("Save Our Ship") repair
-Induced by extensive DNA damage
-Results in expression of many DNA repair enzymes
-Among them, two "sloppy" DNA polymerases that lack proofreading activity and allow
mutations to occur
-However, the cell has no other option but to "mutate or die."
Error-Proof Repair Pathways - correct answer ✔✔ §Nucleotide excision repair
-An endonuclease removes a patch of single-stranded DNA containing certain types of damaged
bases, including dimers.
*google docs
Identifying Mutagens Using Bacterial "Guinea Pigs" - correct answer ✔✔ §The Ames test relies
on a mutant bacterial strain that has a point mutation in the hisG gene
-This histidine auxotroph cannot grow on a medium lacking histidine
-A mutagen-containing paper disk is placed on an agar plate spread with the mutant.
-The mutagen causes reversion mutations of hisG and colonies start to appear around the disk.
-Read text for full description
Mutations Arise in Diverse Ways - correct answer ✔✔ §Spontaneous mutations are rare
because of the efficiency of DNA replication proofreading and repair.
§However, they can arise for many reasons:
,1.Tautomeric (chemical) shifts in DNA bases that alter base-pairing properties
2.Oxidative deamination of bases
3.Formation of apurinic sites
4.Damage caused by reactive oxygen species
9.3 Mutations - REVIEW - correct answer ✔✔ §A mutation is a heritable change in the DNA
sequence.
§Types of mutations:
-Point mutation: change in a single base
-Transition: purine → purine; pyrimidine → pyrimidine
-Transversion: purine ↔ pyrimidine
-Insertion (addition) and deletion (subtraction) of one or more bases
-Inversion: DNA is flipped in orientation.
-Reversion: DNA mutates back to original sequence.
1. Missesnse point mutation: single nucleotide change results in diff amino acid
2. Nonsense point mutation: single nucleotide change results in stop codon
3. Insertion frameshift: changes reading frame and all downstream amino acids
4. Deletion frameshift: removing nucleotides to cause a frameshift
5. Inversion: flipping DNA sequence to change amino acids produced
Site-Specific Recombination - correct answer ✔✔ §Site-specific recombination does not utilize
RecA and is specialized for certain DNA rearrangements.
§It involves very short (10 to 20 bp), specific regions of homology between donor and target
DNA molecules.
-These are recognized specifically by dedicated enzyme systems, which catalyze a crossover.
§Example:
,-The integration of phage lambda into the host chromosome to become a prophage
Generalized Recombination and RecA - correct answer ✔✔ §There are three functions for
generalized recombination in the microbial cell:
-Internal DNA repair.
-DNA repair with DNA taken up from the same species.
-Acquisition of new genes from other organisms for genetic diversity to enhance the
competitive fitness of the cell (evolution).
CRISPR Interference - correct answer ✔✔ §CRISPR (clustered regularly interspaced short
palindromic repeats) is an adaptive system.
-An organism that manages to survive a phage attack captures a piece of the phage genome and
uses it as defense against future attack.
§CRISPRs consist of repeats and spacers that do not encode proteins
§Near them lie CRISPR-associated (CAS) gene families that encode proteins.
§CRISPR is a microbial immune-like system.
-CRISPR function can be divided into three stages: spacer acquisition, crRNA processing, and
effector stage (cleavage of foreign DNA).
1. spacer acquisition: sequences from invading DNA are incorporated into the CRISPR locus
2. crRNA processing: crRNA is transcribed and processed by Cas products
3. Effector stage: cleavage of foreign DNA
Generalized Transduction - correct answer ✔✔ During the phage lytic life cycle, bacterial
genomic DNA fragments are accidentally packed into phage virions
These transducing phage can then inject the DNA into a new host cell, and it can recombine into
the chromosome
, *google docs
Gene Transfer by Conjugation Steps - correct answer ✔✔ 1.Sex pilus attaches
2.Retraction of pilus and bridge is formed
3.oriT is nicked and ssDNA is transferred
4.Replication of DNA in donor cell
5.ssDNA circularizes and replicates
6.F- recipient is now F+
*Google docs
Viruses- Introduction - correct answer ✔✔ §"All" cells can be infected by viruses.
§Some animal viruses generate serious disease: influenza, measles, dengue, zika, HIV...
§There are also insect and plant viruses.
--§Tobacco mosaic virus (TMV) was the first virus discovered.
§Bacterial viruses are called bacteriophage or just phage
§Viruses are ubiquitous and play important roles in the environment.
§In research, viruses have provided both tools and model systems in molecular biology.
Viruses - correct answer ✔✔ §A virus is a noncellular particle that must infect a host cell to
reproduce.
-Obligate intracellular parasite
-The viral genome directs the host cell's machinery to produce progeny viral particles.
§The virus particle, or virion, consists of nucleic acid (DNA or RNA) contained within a protective
protein capsid.
§Virus genomes are usually small, some contain less than a dozen genes.
