BIL 255 UPDATED CORRECT ACTUAL QUESTIONS
AND ANSWERS SURE A+
✔✔DNA polymerase can introduce mutations in the genome - ✔✔*Error rates*
• Polymerization site: 1 error every 1x10⁵ bases.
• Editing site: Decreases error rate 100 times to 1 error every 1x10⁷ bases.
*Error calculations*
• Human genome = 3.4 x 109 bp
• DNA Pol error rate 1x107 base
• 340 errors per cell cycle
✔✔Silent mutation - ✔✔A nucleotide-pair substitution that has no observable effect on
the phenotype; for example, within a gene, a mutation that results in a codon that codes
for the same amino acid.
✔✔Errors made during DNA replication must be corrected to avoid mutation - ✔✔•They
excise the mismatching nucleotide pairs on daug hter strand and then replace it with
new nucleotides
• Errors repaired during replication do not become fixed in the genome
• Errors fixed after replication may result in mutations 50% of the time.
✔✔Defective DNA Repair - ✔✔• Genetic mutations in mismatch repair machinery will
cause *accumulation of somatic mutations* -> *cancer* (e.g. colon cancer)
✔✔Deaminated C - ✔✔•The loss of an amino group in cysteine makes it into a uracil,
which then pairs with A
✔✔Depurinated A - ✔✔•The A is not there and the mutated strand is missing a
nucleotide, which causes the entire rest of the strand to shift
•Mutation es no bueno
,✔✔What can UV radiation do to thymine? - ✔✔It can cause it two successive thymines
to become a dimer and cause melanoma
✔✔Double Strand Break Repair - ✔✔1. *Non-homologous end joining*:
•Can either be processed by nuclease where some DNA is cleaved off to level it off and
joined together by DNA ligase (causes loss of nucleotides at repair site)
2.
*Homologous recombination:*
•Will work right after replication
•Special nucleases process the broken ends and use the homologous chromosome as
template to add nucleotides and there are *no loss of nucleotides*
✔✔What causes double stranded breaks in DNA? - ✔✔Environmental exposure to
irradiation, other chemical agents, or ultraviolet light (UV).
✔✔*Homologous recombination* - ✔✔process by which a cell replaces a stretch of DNA
with a segment that has a similar nucleotide sequence
✔✔Transcription Part 1 - ✔✔Transcription Part 1
✔✔How cells use genetic information? - ✔✔• DNA stores information as linear order of
nucleotides (*sequence*)
• Information is copied into RNA (*transcription*)
• RNA information is used to make proteins (*translated*)
•Aka the *central dogma of molecular biology*
✔✔What is a gene? - ✔✔•A unit of heredity that is transferred from a parent to offspring
and is held to determine some characteristic of the offspring.
•The segment of a DNA molecules that are transcribed into RNA, *doesn't* necessarily
*have to be protein coding*
✔✔Transcription Start Site (Gene Region) - ✔✔•The site at which the first RNA
nucleotide is added; also known as the +1 site.
✔✔Coding sequence (Gene Region) - ✔✔•Part of the gene that codes for the protein,
can be further down stream from the transcription start site
✔✔Promoter (Gene Region) - ✔✔•A specific nucleotide sequence in DNA that binds
RNA polymerase and indicates where to start transcribing RNA.
•*Promoter is upstream compared to transcription start site*
•When the polymerase binds to the sequence, it opens the DNA double helix
immediately in front of the promotor
•Every promoter *has a certain polarity*: : it contains two different nucleotide
sequences, laid out in a specific 5ʹ-to-3ʹ order, upstream of the transcriptional start site.
,These asymmetric sequences position the RNA polymerase such that it binds to the
promoter in the correct orientation
✔✔Template Strand - ✔✔•The DNA strand that provides the template for ordering the
sequence of nucleotides in an mRNA transcript.
✔✔Non-template strand - ✔✔•The strand of DNA that is not transcribed into RNA during
transcription
•Matches the mRNA with the T replaced with the U
✔✔Genes can be expressed with different efficiency. - ✔✔•Differences in expression
underlie most of the differences between sister taxa
•One promoter is more active than another
•A lot of regulation in transcription and translation
✔✔Gene Expression - ✔✔•The process by which information encoded in DNA directs
the synthesis of proteins or, in some cases, RNAs that are not translated into proteins
and instead function as RNAs.
✔✔Expression also makes cells different.... - ✔✔....by driving developmental change. A
neuron and a blood cell have the same genome, but differences in gene expression
lead to their differences since they synthesize different proteins which leads to different
cell structure and function.
✔✔Single-cell transcriptomics - ✔✔•Measurement of gene expression levels (*quantify
mRNA*) in each individual cell of an organism or tissue.
•See what types of mRNA is made in different cell types
✔✔RNA Chemistry and Synthesis - ✔✔•Similar to the structure of DNA, but RNA has
*ribose* instead of deoxyribose (*ribonucleotides*)
•RNA has *uracil* instead of thymine
•RNA synthesis *grows from 5' to 3'*, just like DNA
•RNA is single stranded mostly, however RNA can form hairpin loops (with both
complementary and non complementary base pairing) that are double stranded and
functional
✔✔RNA has.........roles. - ✔✔....structural, regulatory, or catalytic....
✔✔The structure of the polymerase/DNA/RNA complex - ✔✔•The RNA polymerase
opens up a short stretch of DNA (~9 nucleotides) and synthesizes the new mRNA that
goes out the exit groove and is growing at the 3' end.
•There is area where a DNA:RNA hybrid strand come together for a short period of time.
•The RNA polymerase moves in the direction of the 5' end of the DNA template strand
•After the RNA is formed, the DNA double helix reforms
, •There is a ribonucleoside triphosphate uptake channel that takes up the incoming
ribonucleotides which become covalently bonded (phosphodiester) to the growing RNA
strand
•The RNA strand being transcribed are very short, less than a few thousand nucleotides
long
✔✔Structure of RNA Pol II at Atomic Resolution - ✔✔•There are different types of RNA
polymerase, RNA polymerase II is responsible in eukaryotes for synthesizing mRNA in
transcription
•Composed of 10 protein subunits
•Has a pore for the incoming ribonucleotides
✔✔RNA Polymerase II vs. DNA Polymerase - ✔✔•RNA polymerase uses
ribonucleoside triphosphates as substrates, so it catalyzes the linkage of
ribonucleotides, not deoxyribonucleotides
•RNA polymerases can start an RNA chain without a primer and do not accurately
proofread their work.
✔✔Stop site - ✔✔•Terminator sequence that signals RNA pol to release and stop
transcription
•The terminator sequence itself is also transcribed, and it is the interaction of this 3ʹ
segment of RNA with the polymerase that causes the enzyme to let go of the template
DNA.
✔✔RNA polymerase: Initiation - ✔✔• Polymerase binds to *promoter* sequence in
duplex DNA. "Closed complex"
• Polymerase melts duplex DNA near transcription start site, forming a transcription
bubble. "Open complex"
• Polymerase catalyzes phosphodiester linkage of two initial rNTPs (doesn't require a
primer)
✔✔Both DNA and RNA synthesis require primers. (True/False) - ✔✔False, only DNA
requires primers. RNA synthesis only uses promoters.
✔✔RNA polymerase: Elongation, Termination - ✔✔*Elongation*
•Polymerase advances 3' --> 5' down template strand, melting duplex DNA and adding
rNTPs to growing RNA in the 5' --> 3' direction
*Termination*
•At the transcription stop site, polymerase releases completed RNA and dissociates
from DNA when protein phosphatases strip off the phosphates on its tail
✔✔Does RNA polymerase have an error correction mechanism? - ✔✔•RNA
polymerase synthesizes many proteins, so if one is wrong, it doesn't make a difference
•If there is a incorrect protein, they will be degraded quickly anyways
•The mRNA synthesized isn't inherited
AND ANSWERS SURE A+
✔✔DNA polymerase can introduce mutations in the genome - ✔✔*Error rates*
• Polymerization site: 1 error every 1x10⁵ bases.
• Editing site: Decreases error rate 100 times to 1 error every 1x10⁷ bases.
*Error calculations*
• Human genome = 3.4 x 109 bp
• DNA Pol error rate 1x107 base
• 340 errors per cell cycle
✔✔Silent mutation - ✔✔A nucleotide-pair substitution that has no observable effect on
the phenotype; for example, within a gene, a mutation that results in a codon that codes
for the same amino acid.
✔✔Errors made during DNA replication must be corrected to avoid mutation - ✔✔•They
excise the mismatching nucleotide pairs on daug hter strand and then replace it with
new nucleotides
• Errors repaired during replication do not become fixed in the genome
• Errors fixed after replication may result in mutations 50% of the time.
✔✔Defective DNA Repair - ✔✔• Genetic mutations in mismatch repair machinery will
cause *accumulation of somatic mutations* -> *cancer* (e.g. colon cancer)
✔✔Deaminated C - ✔✔•The loss of an amino group in cysteine makes it into a uracil,
which then pairs with A
✔✔Depurinated A - ✔✔•The A is not there and the mutated strand is missing a
nucleotide, which causes the entire rest of the strand to shift
•Mutation es no bueno
,✔✔What can UV radiation do to thymine? - ✔✔It can cause it two successive thymines
to become a dimer and cause melanoma
✔✔Double Strand Break Repair - ✔✔1. *Non-homologous end joining*:
•Can either be processed by nuclease where some DNA is cleaved off to level it off and
joined together by DNA ligase (causes loss of nucleotides at repair site)
2.
*Homologous recombination:*
•Will work right after replication
•Special nucleases process the broken ends and use the homologous chromosome as
template to add nucleotides and there are *no loss of nucleotides*
✔✔What causes double stranded breaks in DNA? - ✔✔Environmental exposure to
irradiation, other chemical agents, or ultraviolet light (UV).
✔✔*Homologous recombination* - ✔✔process by which a cell replaces a stretch of DNA
with a segment that has a similar nucleotide sequence
✔✔Transcription Part 1 - ✔✔Transcription Part 1
✔✔How cells use genetic information? - ✔✔• DNA stores information as linear order of
nucleotides (*sequence*)
• Information is copied into RNA (*transcription*)
• RNA information is used to make proteins (*translated*)
•Aka the *central dogma of molecular biology*
✔✔What is a gene? - ✔✔•A unit of heredity that is transferred from a parent to offspring
and is held to determine some characteristic of the offspring.
•The segment of a DNA molecules that are transcribed into RNA, *doesn't* necessarily
*have to be protein coding*
✔✔Transcription Start Site (Gene Region) - ✔✔•The site at which the first RNA
nucleotide is added; also known as the +1 site.
✔✔Coding sequence (Gene Region) - ✔✔•Part of the gene that codes for the protein,
can be further down stream from the transcription start site
✔✔Promoter (Gene Region) - ✔✔•A specific nucleotide sequence in DNA that binds
RNA polymerase and indicates where to start transcribing RNA.
•*Promoter is upstream compared to transcription start site*
•When the polymerase binds to the sequence, it opens the DNA double helix
immediately in front of the promotor
•Every promoter *has a certain polarity*: : it contains two different nucleotide
sequences, laid out in a specific 5ʹ-to-3ʹ order, upstream of the transcriptional start site.
,These asymmetric sequences position the RNA polymerase such that it binds to the
promoter in the correct orientation
✔✔Template Strand - ✔✔•The DNA strand that provides the template for ordering the
sequence of nucleotides in an mRNA transcript.
✔✔Non-template strand - ✔✔•The strand of DNA that is not transcribed into RNA during
transcription
•Matches the mRNA with the T replaced with the U
✔✔Genes can be expressed with different efficiency. - ✔✔•Differences in expression
underlie most of the differences between sister taxa
•One promoter is more active than another
•A lot of regulation in transcription and translation
✔✔Gene Expression - ✔✔•The process by which information encoded in DNA directs
the synthesis of proteins or, in some cases, RNAs that are not translated into proteins
and instead function as RNAs.
✔✔Expression also makes cells different.... - ✔✔....by driving developmental change. A
neuron and a blood cell have the same genome, but differences in gene expression
lead to their differences since they synthesize different proteins which leads to different
cell structure and function.
✔✔Single-cell transcriptomics - ✔✔•Measurement of gene expression levels (*quantify
mRNA*) in each individual cell of an organism or tissue.
•See what types of mRNA is made in different cell types
✔✔RNA Chemistry and Synthesis - ✔✔•Similar to the structure of DNA, but RNA has
*ribose* instead of deoxyribose (*ribonucleotides*)
•RNA has *uracil* instead of thymine
•RNA synthesis *grows from 5' to 3'*, just like DNA
•RNA is single stranded mostly, however RNA can form hairpin loops (with both
complementary and non complementary base pairing) that are double stranded and
functional
✔✔RNA has.........roles. - ✔✔....structural, regulatory, or catalytic....
✔✔The structure of the polymerase/DNA/RNA complex - ✔✔•The RNA polymerase
opens up a short stretch of DNA (~9 nucleotides) and synthesizes the new mRNA that
goes out the exit groove and is growing at the 3' end.
•There is area where a DNA:RNA hybrid strand come together for a short period of time.
•The RNA polymerase moves in the direction of the 5' end of the DNA template strand
•After the RNA is formed, the DNA double helix reforms
, •There is a ribonucleoside triphosphate uptake channel that takes up the incoming
ribonucleotides which become covalently bonded (phosphodiester) to the growing RNA
strand
•The RNA strand being transcribed are very short, less than a few thousand nucleotides
long
✔✔Structure of RNA Pol II at Atomic Resolution - ✔✔•There are different types of RNA
polymerase, RNA polymerase II is responsible in eukaryotes for synthesizing mRNA in
transcription
•Composed of 10 protein subunits
•Has a pore for the incoming ribonucleotides
✔✔RNA Polymerase II vs. DNA Polymerase - ✔✔•RNA polymerase uses
ribonucleoside triphosphates as substrates, so it catalyzes the linkage of
ribonucleotides, not deoxyribonucleotides
•RNA polymerases can start an RNA chain without a primer and do not accurately
proofread their work.
✔✔Stop site - ✔✔•Terminator sequence that signals RNA pol to release and stop
transcription
•The terminator sequence itself is also transcribed, and it is the interaction of this 3ʹ
segment of RNA with the polymerase that causes the enzyme to let go of the template
DNA.
✔✔RNA polymerase: Initiation - ✔✔• Polymerase binds to *promoter* sequence in
duplex DNA. "Closed complex"
• Polymerase melts duplex DNA near transcription start site, forming a transcription
bubble. "Open complex"
• Polymerase catalyzes phosphodiester linkage of two initial rNTPs (doesn't require a
primer)
✔✔Both DNA and RNA synthesis require primers. (True/False) - ✔✔False, only DNA
requires primers. RNA synthesis only uses promoters.
✔✔RNA polymerase: Elongation, Termination - ✔✔*Elongation*
•Polymerase advances 3' --> 5' down template strand, melting duplex DNA and adding
rNTPs to growing RNA in the 5' --> 3' direction
*Termination*
•At the transcription stop site, polymerase releases completed RNA and dissociates
from DNA when protein phosphatases strip off the phosphates on its tail
✔✔Does RNA polymerase have an error correction mechanism? - ✔✔•RNA
polymerase synthesizes many proteins, so if one is wrong, it doesn't make a difference
•If there is a incorrect protein, they will be degraded quickly anyways
•The mRNA synthesized isn't inherited
