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Exam 4 Flashcards

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1
Q

where can DNA mutations happen?

A

they can happen in somatic or germ-line cells and within or near genes

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2
Q

how are mutations present in germ-line cells?

A

because they are in reproductive cells, they are passed on fully to the entire individual or not at all

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3
Q

how are mutations present in somatic cells?

A

because they are not in reproductive cells, they are spread via mitosis and become a population of mutant cells “generation of a mosaic”

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4
Q

what is a codon?

A

3 nucleotides that code for a specific amino acid

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5
Q

what is a reading frame?

A

a series of codons that code for amino acids in the polypeptide chain

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6
Q

what does the reading frame always start with?

A

AUG which codes for MET (methionine)

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7
Q

what is a nonsense base substitution?

A

the introduction of a stop codon

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8
Q

what is a missense base substitution?

A

a change in the amino acid sequence

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9
Q

what is a silent base substitution?

A

no change in the amino acid sequence

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10
Q

impact of insertions:

A

shifts the reading frame

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11
Q

impact of deletions:

A

shifts the reading frame

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12
Q

impact of in-frame insertion/deletion:

A

the reading frame is maintained, so it may just code for another amino acid in the chain, changing the protein.

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13
Q

what is a transition base substitution?

A

purine for purine or pyrimidine for pyrimidine

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14
Q

what is a transversion base substitution?

A

purine for pyrimidine or vice versa

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15
Q

what is a forward mutation?

A

a mutation that alters the wild-type phenotype

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16
Q

what is a reverse mutation (reversion?)

A

changes the mutant phenotype back to the wild-type

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17
Q

what is an intragenic suppressor mutation?

A

hides or suppresses the effects of another mutation on the same gene

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18
Q

inter vs intragenic mutations:

A

intergenic mutations occur on different genes, intragenic mutations occur on the same gene

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19
Q

what is an intergenic suppressor mutation?

A

this is in a different gene than the original mutation

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20
Q

intragenic missense mutation:

A

a missense mutation will alter a single codon at one site on a gene… then a second mutation at a different site on the same gene can restore the original amino acid

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21
Q

what are the three main causes of mutations?

A

errors DURING replication, DNA damage AFTER replication, transposons/viral insertions AFTER replication

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22
Q

Errors during replication:

A

DNA Polymerase III, 3’-5’ exonuclease proofreading, mismatch repair after proofreading fails

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23
Q

DNA damage AFTER replication:

A

chemical, radiation

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24
Q

transposons/viral insertions AFTER replication:

A
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25
what if a mutation is not fixed and then is recorded?
it will remain in the DNA
26
what are expanding trinucleotide repeats?
a hairpin can form during replication causing the GTC sequence to repeat. during replication the extra GTC repeats are fixed into the genome
27
what are the three flavors of transposons?
replicative, non-replicative, retrotransposon
28
which transposon increases copy number and why?
replicative
29
what is a transposon?
a mobile genetic element
30
what is transposase?
it makes staggered cuts in the DNA that are filled in by DNA Polymerase (flanking direct repeats)
31
what are transposon insertion sequences?
they contain only the genetic information required for movement
32
what is a composite transposon?
they contain DNA sequences not related to transposition
33
what is a noncomposite transposon?
they lack insertion sequences
34
what causes variegated corn?
transposons
35
3 evolutionary theories of transposon existence:
cellular function hypothesis, genetic variation hypothesis, selfish gene hypothesis
36
cellular function hypothesis:
transposons serve a valuable function within the cell
37
genetic variation hypothesis:
transposons exist because of their mutagenic activity
38
selfish gene hypothesis:
transposons serve no purpose
39
central dogma:
DNA to RNA to Proteins
40
4 differences between DNA and RNA
ds vs ss, deoxyribose vs ribose, T vs U, storing info vs protein synthesis
41
mRNA
carries coding sequence for proteins, both euks and proks
42
rRNA
components of ribosome, both euks and proks
43
tRNA
incorporates amino acids during translation, both euks and proks
44
snRNA
snRNPs, pre-mRNA splicing, euks only
45
miRNA
regulation of translation, euks only
46
siRNA
triggers degradation of target mRNAs, euks only
47
are all genes arranged and read the same in the genome?
no
48
what are consensus sites in a prok promoter?
the most commonly encountered nucleotides at each site
49
3 critical components of the transcriptional unit
promoter, RNA-coding region, terminator
50
what is the promoter region?
core sequences recognized by RNA Polymerase holoenzyme. shows where to start transcription and directionality
51
bacterial transcription machinery:
5 subunits, sigma factor required for promoter recognition and initiation, one RNA Polymerase will synthesize all RNA
52
what would happen in bacteria without sigma factor?
RNA polymerase would initiate transcription randomly
53
stages of transcription
initiation, elongation, termination
54
transcription termination in prokaryotes
the rho-dependent or independent terminator sequence
55
rho-dependent terminator sequence
rho binds to rut site and moves toward the 3' end. rna poly enounters a terminator sequence and rho catches up. rho unwinds dna/rna and stops transcription.
56
rho-independent terminator sequence
contain inverted repeats, string of 6 adenines following 2nd repeat
57
what is polycistronic transcription?
one mRNA encodes for multiple proteins, common in prokaryotes
58
in prokaryotes, are transcription and translation coupled?
yes
59
eukaryotic transcription machinery:
multiple RNAs
60
what is a Shine-Dalgarno sequence?
a consensus sequence in the 5' untranslated region in prokaryotes for ribosomal binding
61
where does transcription/translation happen in prokaryotes?
the cytoplasm of the cell
62
where does transcription/translation happen in eukaryotes?
transcription within the nucleus, translation on ribosomes in the cytoplasm
63
what is an enhancer?
64
what is a regulatory promoter?
65
what is a core promoter?
66
what is a TATA box?
67
differences between prokaryotic and eukaryotic mRNA:
eukaryotic has the 5' cap and the 3' poly A tail.
68
what does the 5' cap do?
required for translational initiation, increases mRNA stability, involved in import from the nucleus
69
what does the 3' poly A tail do?
CPSF binds to the poly-A signal to stimulate cleavage of the mRNA downstream
70
what if TFIID and TBP (TATA-binding protein) were missing from transcriptional initiation?
the TATA box would not act as a crucial signal for initiating transcription in eukaryotic cells, binding to the TATA-binding protein (TBP) and facilitating the assembly of the pre-initiation complex, which is necessary for RNA polymerase to bind and start transcription
71
what is TFIID
a crucial multi-subunit complex that recognizes and binds to the core promoter region, specifically the TATA box, and initiates the assembly of the pre-initiation complex (PIC) for RNA polymerase II (Pol II) transcription
72
RNA Polymerase II
transcribes DNA into precursors of messenger RNA (mRNA), small nuclear RNA (snRNA), and microRNA (miRNA)
73
how are poly A tails added?
during a process called polyadenylation, where an enzyme called poly-A polymerase adds a string of adenine nucleotides
74
what are exons
regions of DNA that are transcribed to RNA and retained after introns are spliced out
75
what are introns
a segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes
76
how are snRPs related to the slicesosome?
SnRNPs (small nuclear ribonucleoproteins) are the core components of the spliceosome, a large RNA-protein complex responsible for removing introns and joining exons in pre-mRNA, a process called splicing
77
pre-mRNA splicing
occurs in the nucleus
78
3 important features of introns
5' consensus site, 3' consensus site, branch point. changing a nucleotide in these places prevents normal splicing
79
how is pre-mRNA spliced
1. cut at the 5' splice site 2. cut at 3' splice site. simultaneously, exon 1 and 2 are covalently bonded
80
what does U1 snRNP do?
attaches to 5' splice site
81
what does U2 snRNP do?
attaches to branch point
82
what do U4-6 snRNP do?
they are added to spliceosome (1 and 4 are released)
83
miRNA vs siRNA
miRNAs are naturally occurring and have multiple mRNA targets, while siRNAs are synthetic and target a specific mRNA for degradation (stability)
84
how many synthesases are there?
20
85
4 stages of translation
tRNA charging, initiation (ribosome assembly), elongation, termination
86
tRNA charging:
amino acids reacts with ATP, amino acid is transferred to tRNA. ends up with tRNA linked to amino acid.
87
translation initiation in prokaryotes
1. small and large ribosomal units, three initiation factors, initiator tRNA, GTP energy source
88
translation initiation in eukaryotes
1. small subunit recognizes the cap (elf4e factor) with initiation factors. 2. small subunit scans for the Kozak unit to start. more initiation factors, cap-binding, and poly-A
89
accomodation:
correct vs incorrect. it corrects tRNAs and fits like a lock and key.
90
what happens at A site
everything enters here except fMET-tRNA
91
what happens at P site
a peptide bond is formed between AAs at A and P site. bond is cleaved between AA and tRNA
92
what does histone acetylation lead to
activation of gene transcription HATs and HDACs
93
what does histone methylation lead to
enhanced or suppressed transcription

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