MCB 317 Final Exam Questions with Correct Answers Latest Update 2025-2026
discovering eukaryotic promoter - Answers a series of deletional analysis required
What two requirements for mutational analysis of transcription control regions (promoter) do
we need? - Answers a systemic way to make mutants
a quantitative way to assay for transcription
deletion analysis - Answers systemic way to used to define borders of transcriptional control.
sequence between last functional txn and no txn is the border.
How did we make delusion mutants? - Answers PCR with two restriction enzyme sites
Make two primers specific to genes, on one end add a sequence that corresponds to one
restriction enzyme(HIND), and the other a different restriction enzyme (BAM) to the other end
and amplify
linker scanner mutagenisis - Answers a systemic way to determine 10bp necessary for txn
Boxes indicate a place where we've lost transcription, so we need that DNA.
if we lost transcription with 3 substitutions, our promoter needs those 3 elements
construction of linker scanner mutant - Answers confusing image of take a 3' deletion and a 5'
deletion mutant and clone them together which will change the 6-8 base pairs that make up the
resctriction site. we alter sequence by substitution using restriction enzyme
in linker scanner, what codes for the 6-8 base pair substitution? - Answers the substitution is a
restriction enzyme site of Zho, so when using PCR, we use 2 different restriction enzyme like
bam and hind
site directed mutagenesis allows us to.... - Answers make single base substitution in order to
see if particular nucleotides are required for txn
steps of sire directed mutagenesis: - Answers 1. isolate a plasmid DNA from bacteria with your
gene that is methylated and denature strands
2.make primers with one base pair mismatch
3. add mutagenic oligonucleotide primers with one mismatch each and angel, now the 2
plasmids are hemimethylated
4.digest the plasmids with an "oddball" restriction enzyme that cleaves only methylated DNA
5. transform into bacteria...we now have clones with one mismatch
, why does bacteria methylate DNA? - Answers to recognize viral DNA and cleave it up if it is not
methylated.
do most restriction enzymes cut hemimethylated DNA? - Answers no because they keep to
protect DNA when they replicate
summary of finding promoters: - Answers deletion analysis: border
linker scanner: subregions
site directed mutagenisis: individual nucleotides
mutational/genetic analysis of DNA can be used to study: - Answers any DNA sequence-
dependent process
promoters, enhancers, origins of rep ORF, CEN, TEL, a
how did we quantify transcription? - Answers in vitro assays: cell extract with no other DNA,
radioactive nucleotides, and cloned DNA, run gel, quantify radioactive RNA and determined txn
efficient by radioactive RNA product...
the problem: DNA polymerase will run until it falls off, so we can't determine where promoter is
from the size of RNA
how did we determine where the promoter STARTS/ make bands of defined sites. - Answers
using linear DNA to get an RNA of defined length. so if RNA was 30 nucleotides, then we can
figure out 30 nucleotides back where promoter began.
what did the initial result of systemic (mutants) and quantification (northern blot) of RNA tell us?
- Answers promoters are sufficient for transcription. (which is false, but that's what we believed
at time)
most control regions: - Answers most control regions are not ESSENTIAL/ABSOLUTE to
transcription, only for its "basal" level of activity
response element: - Answers a DNA sequence that binds a transcription factor or protein
virtually every DNA sequence regulating any process are binding sites for proteins - Answers
DNA has no function other then that.
do all genes have TATA box? - Answers no. some lack certain elements, different promoters can
be made of different combinations of elements. no element is essential in the sense that they
are found at all promoters
discovering eukaryotic promoter - Answers a series of deletional analysis required
What two requirements for mutational analysis of transcription control regions (promoter) do
we need? - Answers a systemic way to make mutants
a quantitative way to assay for transcription
deletion analysis - Answers systemic way to used to define borders of transcriptional control.
sequence between last functional txn and no txn is the border.
How did we make delusion mutants? - Answers PCR with two restriction enzyme sites
Make two primers specific to genes, on one end add a sequence that corresponds to one
restriction enzyme(HIND), and the other a different restriction enzyme (BAM) to the other end
and amplify
linker scanner mutagenisis - Answers a systemic way to determine 10bp necessary for txn
Boxes indicate a place where we've lost transcription, so we need that DNA.
if we lost transcription with 3 substitutions, our promoter needs those 3 elements
construction of linker scanner mutant - Answers confusing image of take a 3' deletion and a 5'
deletion mutant and clone them together which will change the 6-8 base pairs that make up the
resctriction site. we alter sequence by substitution using restriction enzyme
in linker scanner, what codes for the 6-8 base pair substitution? - Answers the substitution is a
restriction enzyme site of Zho, so when using PCR, we use 2 different restriction enzyme like
bam and hind
site directed mutagenesis allows us to.... - Answers make single base substitution in order to
see if particular nucleotides are required for txn
steps of sire directed mutagenesis: - Answers 1. isolate a plasmid DNA from bacteria with your
gene that is methylated and denature strands
2.make primers with one base pair mismatch
3. add mutagenic oligonucleotide primers with one mismatch each and angel, now the 2
plasmids are hemimethylated
4.digest the plasmids with an "oddball" restriction enzyme that cleaves only methylated DNA
5. transform into bacteria...we now have clones with one mismatch
, why does bacteria methylate DNA? - Answers to recognize viral DNA and cleave it up if it is not
methylated.
do most restriction enzymes cut hemimethylated DNA? - Answers no because they keep to
protect DNA when they replicate
summary of finding promoters: - Answers deletion analysis: border
linker scanner: subregions
site directed mutagenisis: individual nucleotides
mutational/genetic analysis of DNA can be used to study: - Answers any DNA sequence-
dependent process
promoters, enhancers, origins of rep ORF, CEN, TEL, a
how did we quantify transcription? - Answers in vitro assays: cell extract with no other DNA,
radioactive nucleotides, and cloned DNA, run gel, quantify radioactive RNA and determined txn
efficient by radioactive RNA product...
the problem: DNA polymerase will run until it falls off, so we can't determine where promoter is
from the size of RNA
how did we determine where the promoter STARTS/ make bands of defined sites. - Answers
using linear DNA to get an RNA of defined length. so if RNA was 30 nucleotides, then we can
figure out 30 nucleotides back where promoter began.
what did the initial result of systemic (mutants) and quantification (northern blot) of RNA tell us?
- Answers promoters are sufficient for transcription. (which is false, but that's what we believed
at time)
most control regions: - Answers most control regions are not ESSENTIAL/ABSOLUTE to
transcription, only for its "basal" level of activity
response element: - Answers a DNA sequence that binds a transcription factor or protein
virtually every DNA sequence regulating any process are binding sites for proteins - Answers
DNA has no function other then that.
do all genes have TATA box? - Answers no. some lack certain elements, different promoters can
be made of different combinations of elements. no element is essential in the sense that they
are found at all promoters
