MCB4403 Exam 2 Study Guide With
Complete Solution
What is horizontal gene transfer? - ANSWER transferring of genes from other species
Can be done by virus pirating genes from hosts
What is a mutation? - ANSWER A heritable change in DNA
Explain the kinds of point mutations? - ANSWER Point mutation: change in single base
Transition: purine -> purine or pyrimidine-> pyrimidine
Transversion: purine->pyrimidine
Explain insertion/deletion, inversion, reversion? - ANSWER Insertion/deletion:
Addition/Subtraction of bases
Inversion: DNA flipped in orientation
Reversion: DNA mutates back to original sequence
Explain Silent, missense, Nonsense, frameshift mutation? - ANSWER Silent: does not
change amino acid
Missense: changes the amino acid to another
Nonsense: changes amino acid to stop codon
Frameshift: insert or deletion of single base changes ORF of gene or all codons after it
Mutations that change an amino acid into a similar do what to the protein? - ANSWER
The protein retains normal function
Where can mutations occur? - ANSWER at different positions of genes (promoters,
coding regions, 5'-3', between genes)
Why can mutations arise spontaneously ? - ANSWER 1. Tautomeric shifts in bases that
alter base-pairing like G-T/A-C
2. Oxidative deamination of bases changing it to uracil
3. Formation of apurinic sites
4. Damage caused by reactive oxygen species that interfere with polymerase
What mutagens can cause mutations? - ANSWER Chemical agents: base analogs, base
modifiers, intercalators
,Electromagnetic radiation: X-rays and gamma that break DNA, UV rays that form
pyrimidine dimers
What can base analogs do? - ANSWER substitute look-alike molecule for normal base
during replication: point mutation
What is a way to identify mutagens using ames test? - ANSWER Ames test:
mutagen-containing disk is placed on agar with a mutant, mutagen causes reversion
mutations and colonies appear around disk
It relies on mutant bacterial strains lacking hisG
What is a way to identify mutagens using bacterial guinea pigs? - ANSWER Mixing
mutagens with rat liver mimics effect of human liver on mutagens
Growth: reversion mutation created by the hisG mutant bacteria, so mutagenic
What are the two kinds of DNA repair? - ANSWER 1. Error-proof repair (prevent
mutation) : Methyl mismatch repair, photoreactivation, nucleotide excision repair, base
excision repair, recombinational repair
2. Error-prone repair pathways (risk introducing mutations): operate only when damage
to cell is too severe
Explain methyl mismatch repair? - ANSWER Uses methylation pattern of DNA bases of
the parental strand to discriminate from newly replicated DNA
Because parental will contain proper DNA sequence
explain photoreactivation? - ANSWER enzyme photolyase binds to the pyrimidine dimer
and cleaves the cyclobutane ring
Explain nucleotide excision repair? - ANSWER Endonuclease removes a patch of
single-stranded DNA containing damaged bases like dimers
Explain base excision repair? - ANSWER Enzymes recognize damaged bases and
remove them without breaking phosphodiester bond leaves abasic site recognized and
cleaved by endonuclease
The abasic site or apurinic/apyrimidic allows DNA pol 1 to synthesize replacement
strand with proper base
Explain recombinational repair? - ANSWER Single-strand of undamaged daughter
strand used to replace gap in damaged daughter strand
carried out by RecA at replication fork
Explain Save our Ship repair? - ANSWER - Extensive DNA damage causes RecA
coprotease activity to stimulate autodigestion of LexA repressor
, - Expression of DNA repair enzymes with 2 DNA pol that lack proofreading activity
causing cell to mutate or die
Why can the taking up of foreign DNA be beneficial/natural transformation ? - ANSWER
Imported DNA used as alternative food source
Repair damaged chromosomes
Genome evolution
What is transformation?
Who discovered DNA as the transforming principle? - ANSWER Uptake/import of free
DNA into bacterial cells
Avery, Macleod, Mccarty
What cells are capable of normal transformation, what artificial manipulations help? -
ANSWER Capable: Gram +
Incapable: Gram-, need CaCl2 to pertrube membrane or electroporation
What substance from the heat-inactivated encapsulated bacteria transformed
nonencapsulated? - ANSWER Smooth strain
Explain bacterial sex conjugation gene transfer? - ANSWER Type 4 secretion system
DNA in pilus proteins encoded on F factor gets transferred to recipient at oriT site
Female cells become male
Explain F' factor, Hfr factor? Conjugation process. - ANSWER F' factor: F plasmid
contains extra genes that gets transferred extra genes to recipient
Hfr: F factor integrated on bacterial chromosome, requires 100 minutes transferring
genes in order, used to determine order of genes on chromosome
What is an examples of a bacteria that can transfer genes across biological domains? -
ANSWER Agrobacterium tumefaciens (crown gall disease)
Contains tumor-inducing plasmid transferred by conjugation to plant cells, used to make
transgenic plants
What is transduction? - ANSWER Bacteriophage carries host DNA to cell
What are the two types of transduction? - ANSWER Generalized: transfers any gene
from donor to recipient
Specialized: transfer only few closely linked genes between cells
Explain horizontal gene transfer in the intestine? - ANSWER GI tract ideal bc
Complete Solution
What is horizontal gene transfer? - ANSWER transferring of genes from other species
Can be done by virus pirating genes from hosts
What is a mutation? - ANSWER A heritable change in DNA
Explain the kinds of point mutations? - ANSWER Point mutation: change in single base
Transition: purine -> purine or pyrimidine-> pyrimidine
Transversion: purine->pyrimidine
Explain insertion/deletion, inversion, reversion? - ANSWER Insertion/deletion:
Addition/Subtraction of bases
Inversion: DNA flipped in orientation
Reversion: DNA mutates back to original sequence
Explain Silent, missense, Nonsense, frameshift mutation? - ANSWER Silent: does not
change amino acid
Missense: changes the amino acid to another
Nonsense: changes amino acid to stop codon
Frameshift: insert or deletion of single base changes ORF of gene or all codons after it
Mutations that change an amino acid into a similar do what to the protein? - ANSWER
The protein retains normal function
Where can mutations occur? - ANSWER at different positions of genes (promoters,
coding regions, 5'-3', between genes)
Why can mutations arise spontaneously ? - ANSWER 1. Tautomeric shifts in bases that
alter base-pairing like G-T/A-C
2. Oxidative deamination of bases changing it to uracil
3. Formation of apurinic sites
4. Damage caused by reactive oxygen species that interfere with polymerase
What mutagens can cause mutations? - ANSWER Chemical agents: base analogs, base
modifiers, intercalators
,Electromagnetic radiation: X-rays and gamma that break DNA, UV rays that form
pyrimidine dimers
What can base analogs do? - ANSWER substitute look-alike molecule for normal base
during replication: point mutation
What is a way to identify mutagens using ames test? - ANSWER Ames test:
mutagen-containing disk is placed on agar with a mutant, mutagen causes reversion
mutations and colonies appear around disk
It relies on mutant bacterial strains lacking hisG
What is a way to identify mutagens using bacterial guinea pigs? - ANSWER Mixing
mutagens with rat liver mimics effect of human liver on mutagens
Growth: reversion mutation created by the hisG mutant bacteria, so mutagenic
What are the two kinds of DNA repair? - ANSWER 1. Error-proof repair (prevent
mutation) : Methyl mismatch repair, photoreactivation, nucleotide excision repair, base
excision repair, recombinational repair
2. Error-prone repair pathways (risk introducing mutations): operate only when damage
to cell is too severe
Explain methyl mismatch repair? - ANSWER Uses methylation pattern of DNA bases of
the parental strand to discriminate from newly replicated DNA
Because parental will contain proper DNA sequence
explain photoreactivation? - ANSWER enzyme photolyase binds to the pyrimidine dimer
and cleaves the cyclobutane ring
Explain nucleotide excision repair? - ANSWER Endonuclease removes a patch of
single-stranded DNA containing damaged bases like dimers
Explain base excision repair? - ANSWER Enzymes recognize damaged bases and
remove them without breaking phosphodiester bond leaves abasic site recognized and
cleaved by endonuclease
The abasic site or apurinic/apyrimidic allows DNA pol 1 to synthesize replacement
strand with proper base
Explain recombinational repair? - ANSWER Single-strand of undamaged daughter
strand used to replace gap in damaged daughter strand
carried out by RecA at replication fork
Explain Save our Ship repair? - ANSWER - Extensive DNA damage causes RecA
coprotease activity to stimulate autodigestion of LexA repressor
, - Expression of DNA repair enzymes with 2 DNA pol that lack proofreading activity
causing cell to mutate or die
Why can the taking up of foreign DNA be beneficial/natural transformation ? - ANSWER
Imported DNA used as alternative food source
Repair damaged chromosomes
Genome evolution
What is transformation?
Who discovered DNA as the transforming principle? - ANSWER Uptake/import of free
DNA into bacterial cells
Avery, Macleod, Mccarty
What cells are capable of normal transformation, what artificial manipulations help? -
ANSWER Capable: Gram +
Incapable: Gram-, need CaCl2 to pertrube membrane or electroporation
What substance from the heat-inactivated encapsulated bacteria transformed
nonencapsulated? - ANSWER Smooth strain
Explain bacterial sex conjugation gene transfer? - ANSWER Type 4 secretion system
DNA in pilus proteins encoded on F factor gets transferred to recipient at oriT site
Female cells become male
Explain F' factor, Hfr factor? Conjugation process. - ANSWER F' factor: F plasmid
contains extra genes that gets transferred extra genes to recipient
Hfr: F factor integrated on bacterial chromosome, requires 100 minutes transferring
genes in order, used to determine order of genes on chromosome
What is an examples of a bacteria that can transfer genes across biological domains? -
ANSWER Agrobacterium tumefaciens (crown gall disease)
Contains tumor-inducing plasmid transferred by conjugation to plant cells, used to make
transgenic plants
What is transduction? - ANSWER Bacteriophage carries host DNA to cell
What are the two types of transduction? - ANSWER Generalized: transfers any gene
from donor to recipient
Specialized: transfer only few closely linked genes between cells
Explain horizontal gene transfer in the intestine? - ANSWER GI tract ideal bc
