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Nucleic Acids Flashcards

(80 cards)

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1
Q

what is the central dogma of molecular biology

A

replication - transcription - translation

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2
Q

how was the structure of DNA found

A

using aspects from biology, chemistry, and physics
Watson and Crick found the double helical structure of DNA using x-ray crystallography from Rosalind Franklin, Chargaff’s rule, and the knowledge of purine and pyrimidine bases

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3
Q

what is chargaffs rule

A

A=T C=G

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4
Q

what would happen if:
purine + purine
pyrimidine + pyrimidine

A
  • too thick

- too thin

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5
Q

what did erwin chargaff find

A

phosphate and functional groups of nucleic acids

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6
Q

what is the semi-conservative, conservative, and dispersive models?

A
  • recombining to create 2 strands, each with 1 parental and 1 new daughter strand
  • creates 3 new strands and 1 new strand
  • strands mix together to make 4 identical double helices
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7
Q

how was the semi-conservative model found to be true (experiment)

A
  • using heavy and light N isotopes, the samples were centrifuged
  • conservative model: was too dense
  • dispersive model: was too light
  • semi-conservative model: in the middle, just right
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8
Q

where does DNA replication start

A

origin of replication

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9
Q

how is the leading strand synthesized

A

continuously, moving towards the replication fork

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10
Q

how is the lagging strand synthesized

A

as a series of Okazaki fragments because replication can only happen in a 3’-5’ direction
- strands are antiparallel so this happens in the 5’-3’ direction

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11
Q

what is the function of dna polymerase

A

catalyze replication

- adds new nucleotides onto the free 3’ end

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12
Q

what does dna polymerase require in order to function

A
  • an RNA primer
  • template DNA
  • Mg2+
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13
Q

what does Mg2+ do for dna polymerase

A

helps nucleotides attach onto the 3’ OH end

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14
Q

what does dna helicase do

A

unwinds the parental double helix

- breaks the hydrogen bonds

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15
Q

what does the single-stranded binding proteins do

A

keeps structure in a linear orientation

- keeps unwound, reduces super-coiling

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16
Q

what does dna topoisomerase I do

A

produces single stranded breaks in dna

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17
Q

what does dna topoisomerase II do

A

produces double-stranded breaks in dna

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18
Q

what does dna gyrase do with dna topoisomerase II

A

folds the molecule across itself and cleaves it to create 2 negative supercoils

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19
Q

what is the general function of both topoisomerases

A

to correct over-winding ahead of the forks by breaking and rejoining the DNA strands

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20
Q

how is the leading strand synthesized?

A

starts at the origin of replication and the primer RNA is added, the daughter strand has one parental and one new strand

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21
Q

how is the lagging strand synthesized?

A

the Okazaki fragments are synthesized and dna polymerase I replaces the RNA primer with dna
- dna ligase joins the sugar phosphate backbones into a continuous strand

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22
Q

how is dna proofread?

A

dna polymerase proofreads and replaces incorrect nucleotides

- dna ligase rebuilds the sugar phosphate backbone of dna where dna polyermase replaced the incorrect nucleotides

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23
Q

why is crispr a problem

A

once there is a change in the germ cell line, there is no going back

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24
Q

what is the evolutionary significance of altering dna nucleotides

A
  • organisms with more dna were able to better adapt to mistakes because there was a lot of dna left over to use for repairs
  • if there was a mistake made, it was passed onto future generations
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25
what is the source of genetic variation
mutations and mistakes in genes
26
what is progressive shortening and why does it happen
- after repeated rounds of replication, the dna become shorter and shorter - happens because the 5' end can never be completed
27
what are telomeres
special nucleotide sequence at the end of eukaryotic chromosomes (TTAGGG) - postpone the erosion of genes near the end
28
what cells lack telomeres and what does this affect
somatic cells, short telomeres are associated with cell death
29
what is progeria and how is it caused
premature aging of telomeres, rapid aging of a person
30
what is telomerase
catalyzes the lengthening of telomeres in germ cells
31
where is the best place to stop coding for a protein
preventing the polymerase from binding, can be done by adding a molecule that is similar but not exactly like the rna molecule (locks the binding site)
32
what is transcription
one of the 2 dna strands (template strand) provides a template for ordering the sequence of complementary nucleotides in an rna transcript - synthesizes rna
33
what type of cells undergo a lot of replication
organs that renew a lot, immune cells, cells that maintain homeostasis
34
which strand is the template strand
the top strand | the bottom strand is identical to the mRNA transcription
35
what is a promotor
dna sequence where rna polymerase attaches
36
what is the terminator, what organism has them
the sequence that signals the end of the transcript, only in bacteria
37
what are the three stages of transcription
1. initiation 2. elongation 3. termination
38
how is transcription initiated
the TATA box helps to form the initiation complex in eukaryotes - the promotor signals transcription start - transcription factors mediate the binding of rna polymerase and the initiation of transcription
39
what is the transcriptional initiation complex
the transcription factors and rna polymerase II bound to a promotor
40
what are MYC and FOS
transcription factors in transcription | - initiation of transcript
41
what is elongation of the transcript
rna polymerase unwinds the dna and untwists the dna | - nucleotides are added to 3' end
42
what drives elongation in transcription
feedback inhibition
43
what is termination of transcription
rna polymerase II transcribes the polyadenylation signal sequence before being released
44
what is polyadenylation and 5' methylation and why do they occur
- protect from nucleotide degradation from nucleases
45
in bacteria, how is transcription terminated
polymerase stops at the end of the terminator (no modifications occur)
46
after the pre-mRNA is transcribed, what does it undergo?
5' end: 5' cap | 3' end: poly-A tail
47
why must there be post-transcriptional modifications to the mRNA
- facilitates the export of mRNA to the cytoplasm - protects the mRNA from hydrolytic enzymes - helps ribosomes attach to the 5' end
48
what can introns contain (why are they not transcribed)
- may contain sequences that regulate genes expression - not actually gene code - these may code for a polypeptide that is already being transcribed by the exons
49
what is rna splicing
removing introns and joining exons together
50
what is a codon
three-nucleotide word that codes for an amino acid, using the genetic code table - 64 in total
51
how is the genetic code redundant
more than one codon specifies an amino acid
52
how is the code not ambiguous
no codon specifies more than one amino acid | - 1 codon = 1 amino acid
53
what is translation and where does it occur
protein synthesis on the ribosomes
54
what is the translational process
a fully mature mRNA molecule is fed into the translation apparatus and the sequence of amino acids comes out
55
what are 2 things that needs to happen for translation
a correct match between tRNA and an amino acid | a correct match between the tRNA anticodon and a mRNA codon
56
what is a tRNA
- functional - links mRNA to the amino acid - has anticodon
57
what is an anticodon
base pairs with a complementary codon on mRNA
58
what is a wobble on tRNA
flexible pairing at the third base of the codon that allows some tRNAs to bind to more than one codon
59
what is aminoacyl-tRNA synthase
an enzyme that ensures a correct match by joining a specific amino acid to a specific tRNA
60
what is the difference between an uncharged and a charged tRNA
uncharged: no amino acid attached charged: amino acid is attached
61
what are the three binding sites that ribosomes have
E, P, A
62
what is each ribosomal site used for
A site: initial attachment, holds the tRNA that carries the next amino acid to be added to the chain P: central site, holds the tRNA that carries the growing polypeptide chain E: exit site, where the tRNA leaves the ribosome
63
what are the three stages of translation
1. initiation 2. elongation 3. termination
64
how is translation initiated
- the small ribosomal subunit binds with mRNA and the initiator (tRNA) - the small subunit moves along the mRNA unit it reaches a start codon - initial factors brings the large ribosomal subunit to complete the translational initiation complex
65
what are initial factors in translation
proteins
66
what is elongation in translation and what is requires
when amino acids are added to the C-terminus end of the polypeptide - energy and elongation factors
67
what is termination of translation
when the stop codon reaches the A site, the A site then accepts a release factor which releases the polypeptide chain
68
what does the acceptance of a release factor do in translation
water is added instead of another amino acid, this breaks the bond and translation assembly comes apart - tRNA becomes uncharged
69
what happens to the polypeptide chain after it is translated, what helps it do this
- needs to fold and coil into its 3D shape | - chaperon protein helps it fold properly
70
what are some post-translational modifications that the polypeptide undergoes
- adding sugar/lipid/phosphate - removing amino acids - cleaving - combining with others to form subunits of a protein
71
what is prion disease
when there is an error in folding
72
what are the 6 types of rna
- messenger: carries genetic information - transfer: adaptor between amino acids and codons in mRNA - ribosomal: structural component of ribosomes - small nuclear: structural component of spliceosomes - micro: blocks expression of mRNAs
73
eukaryotes: where does transcription and translation take place
transcription/replication: nucleus | translation: cytoplasm
74
prokaryotes: where does transcription and translation take place
in the cytoplasm
75
what can prokaryotes do to aid humans
can be genetically modified to complete tasks (make insulin, etc.)
76
what are mutations and when do they occur and what do they affect
changes in genetic material, happen spontaneously | - protein structure/function, amino acid sequence
77
what are point mutations? what are the two types
- small scale chemical changes in just one base pair in gene | - nucleotide-pair substitutions and nucleotide-pair insertion or deletion
78
what are nucleotide-pair substitutions
silent: still codes for correct amino acid missense: may not be the right amino acid that is coded nonsense: changes amino acid into a stop codon, which creates a non-functional protein
79
what are nucleotide-pair insertions/deletions, what can they lead to
- adding or deleting a nucleotide from the sequence | - can lead to a frameshift mutation which alters the reading frame of the sequence
80
how does antibiotic resistance happen?
when proteins that recognize penicillin mutate and prevent the drug from binding which renders the penicillin from binding and is ineffective

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