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Cell > Nucleic Acids > Flashcards

Nucleic Acids Flashcards

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
Q

what is the source of genetic variation

A

mutations and mistakes in genes

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26
Q

what is progressive shortening and why does it happen

A
  • after repeated rounds of replication, the dna become shorter and shorter
  • happens because the 5’ end can never be completed
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27
Q

what are telomeres

A

special nucleotide sequence at the end of eukaryotic chromosomes (TTAGGG)
- postpone the erosion of genes near the end

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28
Q

what cells lack telomeres and what does this affect

A

somatic cells, short telomeres are associated with cell death

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29
Q

what is progeria and how is it caused

A

premature aging of telomeres, rapid aging of a person

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30
Q

what is telomerase

A

catalyzes the lengthening of telomeres in germ cells

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31
Q

where is the best place to stop coding for a protein

A

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)

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32
Q

what is transcription

A

one of the 2 dna strands (template strand) provides a template for ordering the sequence of complementary nucleotides in an rna transcript
- synthesizes rna

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33
Q

what type of cells undergo a lot of replication

A

organs that renew a lot, immune cells, cells that maintain homeostasis

34
Q

which strand is the template strand

A

the top strand

the bottom strand is identical to the mRNA transcription

35
Q

what is a promotor

A

dna sequence where rna polymerase attaches

36
Q

what is the terminator, what organism has them

A

the sequence that signals the end of the transcript, only in bacteria

37
Q

what are the three stages of transcription

A
  1. initiation
  2. elongation
  3. termination
38
Q

how is transcription initiated

A

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
Q

what is the transcriptional initiation complex

A

the transcription factors and rna polymerase II bound to a promotor

40
Q

what are MYC and FOS

A

transcription factors in transcription

- initiation of transcript

41
Q

what is elongation of the transcript

A

rna polymerase unwinds the dna and untwists the dna

- nucleotides are added to 3’ end

42
Q

what drives elongation in transcription

A

feedback inhibition

43
Q

what is termination of transcription

A

rna polymerase II transcribes the polyadenylation signal sequence before being released

44
Q

what is polyadenylation and 5’ methylation and why do they occur

A
  • protect from nucleotide degradation from nucleases
45
Q

in bacteria, how is transcription terminated

A

polymerase stops at the end of the terminator (no modifications occur)

46
Q

after the pre-mRNA is transcribed, what does it undergo?

A

5’ end: 5’ cap

3’ end: poly-A tail

47
Q

why must there be post-transcriptional modifications to the mRNA

A
  • facilitates the export of mRNA to the cytoplasm
  • protects the mRNA from hydrolytic enzymes
  • helps ribosomes attach to the 5’ end
48
Q

what can introns contain (why are they not transcribed)

A
  • 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
Q

what is rna splicing

A

removing introns and joining exons together

50
Q

what is a codon

A

three-nucleotide word that codes for an amino acid, using the genetic code table
- 64 in total

51
Q

how is the genetic code redundant

A

more than one codon specifies an amino acid

52
Q

how is the code not ambiguous

A

no codon specifies more than one amino acid

- 1 codon = 1 amino acid

53
Q

what is translation and where does it occur

A

protein synthesis on the ribosomes

54
Q

what is the translational process

A

a fully mature mRNA molecule is fed into the translation apparatus and the sequence of amino acids comes out

55
Q

what are 2 things that needs to happen for translation

A

a correct match between tRNA and an amino acid

a correct match between the tRNA anticodon and a mRNA codon

56
Q

what is a tRNA

A
  • functional
  • links mRNA to the amino acid
  • has anticodon
57
Q

what is an anticodon

A

base pairs with a complementary codon on mRNA

58
Q

what is a wobble on tRNA

A

flexible pairing at the third base of the codon that allows some tRNAs to bind to more than one codon

59
Q

what is aminoacyl-tRNA synthase

A

an enzyme that ensures a correct match by joining a specific amino acid to a specific tRNA

60
Q

what is the difference between an uncharged and a charged tRNA

A

uncharged: no amino acid attached
charged: amino acid is attached

61
Q

what are the three binding sites that ribosomes have

A

E, P, A

62
Q

what is each ribosomal site used for

A

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
Q

what are the three stages of translation

A
  1. initiation
  2. elongation
  3. termination
64
Q

how is translation initiated

A
  • 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
Q

what are initial factors in translation

A

proteins

66
Q

what is elongation in translation and what is requires

A

when amino acids are added to the C-terminus end of the polypeptide
- energy and elongation factors

67
Q

what is termination of translation

A

when the stop codon reaches the A site, the A site then accepts a release factor which releases the polypeptide chain

68
Q

what does the acceptance of a release factor do in translation

A

water is added instead of another amino acid, this breaks the bond and translation assembly comes apart
- tRNA becomes uncharged

69
Q

what happens to the polypeptide chain after it is translated, what helps it do this

A
  • needs to fold and coil into its 3D shape

- chaperon protein helps it fold properly

70
Q

what are some post-translational modifications that the polypeptide undergoes

A
  • adding sugar/lipid/phosphate
  • removing amino acids
  • cleaving
  • combining with others to form subunits of a protein
71
Q

what is prion disease

A

when there is an error in folding

72
Q

what are the 6 types of rna

A
  • 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
Q

eukaryotes: where does transcription and translation take place

A

transcription/replication: nucleus

translation: cytoplasm

74
Q

prokaryotes: where does transcription and translation take place

A

in the cytoplasm

75
Q

what can prokaryotes do to aid humans

A

can be genetically modified to complete tasks (make insulin, etc.)

76
Q

what are mutations and when do they occur and what do they affect

A

changes in genetic material, happen spontaneously

- protein structure/function, amino acid sequence

77
Q

what are point mutations? what are the two types

A
  • small scale chemical changes in just one base pair in gene

- nucleotide-pair substitutions and nucleotide-pair insertion or deletion

78
Q

what are nucleotide-pair substitutions

A

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
Q

what are nucleotide-pair insertions/deletions, what can they lead to

A
  • adding or deleting a nucleotide from the sequence

- can lead to a frameshift mutation which alters the reading frame of the sequence

80
Q

how does antibiotic resistance happen?

A

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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