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Fundamentals Block 2 > Hebert 1-6 > Flashcards

Hebert 1-6 Flashcards

1
Q

what percentage of our genome is repetitive?

A

50%

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2
Q

what percent of our genes actually codes for protein?

A

1.5%

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3
Q

what are the 5 classes of DNA?

A

repetitive
heterochromatin
regulatory
intronic
coding

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4
Q

what are the 3 classes of RNA?

A

protein coding
catalytic
regulatory

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5
Q

what is the significance of AT-rich regions on DNA?

A

it is where the origin of replication can happen because it is easier to break 2 hydrogen bonds rather than the 3 found in GC regions

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6
Q

SS DNA binding proteins

A

keep DNA single stranded and protect from nucleases

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7
Q

how do eukaryotes differ from bacteria in DNA replication?

A

it occurs at multiple sites in eukaryotes and only a single site in bacteria

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8
Q

helicase

A

enzyme that unwinds DNA at both replication forks
-requires ATP

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9
Q

topoisomerase

A

cut a nick in supercoil strand so it can unwind then uses ligase to restitch it back together

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10
Q

type I vs type II topoisomerase

A

-type I doesn’t require ATP, cuts only one strand
-type II cuts both strands and allows a double strand to pass through the break

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11
Q

what is the significance of the OH on the 3’ end?

A

DNA polymerase III binds in order to continue making DNA

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12
Q

DNA polymerase III

A

-reads parental strand from 3-5
-synthesizes new DNA from 5-3

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13
Q

okazaki fragments

A

multiple RNA primers in the lagging strand

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14
Q

DNA polymerase I

A

-removes primers in 5-3 exonuclease activity

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15
Q

what enzyme fuses the DNA ends together after the okazaki fragments have been cut out

A

ligase

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16
Q

telomeres

A

-ensure that genes are fully replicated
-protect ends of chromosomes
-shorten with age

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17
Q

why don’t telomeres shorten in cancer cells?

A

these cells express telomerase

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18
Q

telomerase

A

-an enzyme comprised of protein and a short piece of RNA
-reverse transcriptase activity (can make DNA from RNA template)
-maintains telomere length
-expressed in primary cell lines which makes them immortal

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19
Q

what is the approximate length of DNA?

A

6.5 feet

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20
Q

how do histones work

A

histones are positively charged and DNA is negative so they attract each other
-H1 binds the DNA between the nucleosome beads

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21
Q

what histone modifications can impact gene expression?

A

acetylation, methylation, and phosphorylation

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22
Q

mismatch repair reduces the error of replication to how many errors per replication?

A

3.2

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23
Q

repairs bulky lesions as those caused by pyrimidine dimers

A

nucleotide excision repair

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24
Q

-removes only the problem base
-takes care of bases lost to deamination

A

base excision repair

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25
how are double strand breaks repaired?
nonhomologous end-joining (error prone) homologous recombination (less error prone)
26
protein coding rna
mRNA
27
catalytic RNA
rRNA tRNA snRNA snoRNA scaRNA
28
regulatory RNA
miRNA riboswitch
29
RNA modifications enable ~_________________genes in the human genome to produce ~_____________different proteins.
30,000 100,000
30
what percentage of RNA in a cell is mRNA?
5%
31
monocistronic vs polycistronic mRNA
-eukaryotes (mono): RNA carries info from 1 gene -prokaryotes (poly): RNA carries info from more than 1 gene (operon)
32
rRNA accounts for what percent in a cell?
80%
33
-has unusual bases and intrachain pairing -3 sizes in prokaryotes -4 sizes in eukaryotes
rRNA
34
what percent of RNA in a cell does tRNA account for?
15%
35
-at least one for each amino acid -has unusual bases and intrachain pairing -needs to be processes to form clover structure
tRNA
36
-some are spliceosomal (remove introns) -has unusual bases and intrachain pairing -base pairs with heterogenous nuclear RNA (hnRNA) to facilitate splicing
snRNA (small nuclear)
37
small nuclear ribonucleoproteins (snRNPs)
part of the spliceosome which removes introns from pre-mRNA
38
what is the leading genetic cause of infant mortality?
spinal muscular atrophy caused by mutations in the survivor of motor neurons protein which helps in snRNP biogenesis
39
guide RNAs that determine where modification takes place by base pairing with the rRNA
snoRNA (small nucleolar)
40
-guide RNAs found in a nuclear subdomain -guide modifications found in snRNAs
scaRNA (small cajal body-specific)
41
-base pair with specific mRNAs in the 3'UTR region and promote mRNA degradation or reduced translation -around 400 different ones expressed in humans
miRNA (micro)
42
-short sequences of RNA that can change conformation upon binding of small molecules -folding can disrupt transcription -common in bacteria
riboswitch
43
Name two diseases that have poly Q expansion
-Huntington disease -Spinocerebellar ataxia type I
44
repeats induce gene silencing via DNA methylation
Fragile X syndrome
45
repeats reduce mRNA stability and induce heterochromatin
Myotonic dystrophy
46
repeats induce heterochromatin and decrease transcription
Friedreich ataxia
47
non-template strand
coding, sense strand
48
template strand
noncoding, antisense strand
49
compare and contrast prokaryotic and eukaryotic transcription
-RNA polymerase: prokaryotes have 1 and eukaryotes have 3 -prokaryotes have a sigma factor and eukaryotes have general transcription factors -eukaryotes have nucleosomes and higher order chromatin -eukaryotes undergo extensive mRNA modification while prokaryotes have no modifications
50
51
RNA is complementary to which strand?
template, antisense
52
RNA is identical to which strand?
coding, sense
53
what portion of the holoenzyme reads the DNA and makes RNA? (prokaryote)
core enzyme
54
what protein binds to the promotor region so that RNA polymerase can start transcription? (eukaryote)
transcription factor
55
a protein that helps bacteria start transcription by allowing RNA polymerase to bind to gene promoters (prokaryote)
sigma factor
56
what type of RNA does RNA polymerase I make? (eukaryote)
rRNA
57
what type of RNA does RNA polymerase III make? (eukaryote)
tRNA snRNA
57
what type of RNA does RNA polymerase II make? (eukaryote)
mRNA snRNA
58
Rifampin
inhibits prokaryotic transcription inititation
59
Actinomycin D
blocks transcription elongation; the first antibiotic used to treat cancer
60
a-amanitin
inhibits RNA polymerase II (eukaryotic)
61
rho-dependent termination (prokaryote)
rho protein cause RNA polymerase to break away from the DNA
62
rho-independent termination (prokaryote)
CG repeats are attracted to each other and forms hairpin structure which removes the RNA polymerase
63
describe termination of eukaryote transcription
polyadenylation signal (AAUAA) activates enzymes that cleave RNA from RNA polymerase
64
hnRNA (heterogenous nuclear RNA)
rna that has just been transcribed but has to undergo modifications before becoming mRNA
65
what splices introns in hnRNA to make mRNA
SNRPs
66
what is the major mechanism by which chromatin is remodeled?
modification of histone lysine acetylation
67
binds to transcription factors and and increases transcription of genes
enhancer
68
what are the three hnRNA modifications
5' capping splicing poly A tail
69
what is the purpose of the 5' cap?
protects RNA from nucleases and allows for efficient translation initiation
70
nonsense mutation
a codon for aa changed to stop codon
71
missense mutation
a codon for one aa changed to codon for another aa
72
silent mutation
mutation does not change desired aa
73
transition
purine for purine or pyrimidine for pyrimidine
74
transversion
purine for pyrimidine or pyrimidine for purine
75
why cant transcription and translation take place concurrently in eukaryotes?
eukaryotes have introns so you have to splice them first
76
where does eukaryotic translation take place?
cytoplasm
77
A site
binds incoming charged tRNA
78
P site
carries peptidyl tRNA with nascent peptide chain
79
E site
occupied by empty tRNA about to leave
80
large subunit
catalyzes formation of peptide bonds that link amino acids in proteins
81
small subunit
binds mRNA; ensures proper pairing between codon and anticodon
82
what sequence in prokaryotes initiates translation?
shine-delgarno sequence
83

Fundamentals Block 2 (10 decks)

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