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GSBS Biochem > DNA 4 > Flashcards

DNA 4 Flashcards

1
Q

Examples of RNA

A

messenger
transfer
ribosomal
micro
long non-coding
riboswitches

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2
Q

each type of RNA has a different function and a

A

different secondary and tertiary structure

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3
Q

more complicated dogma of biochemistry

A

DNA to mRNA to tRNA to protein via rRNA

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4
Q

in terms of RNA, how are prokaryotes and eukaryotes different?

A

Eukaryotes have to transfer the RNA out of the nucleus

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5
Q

many RNAs are inherently

A

single stranded

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6
Q

secondary and tertiary structures in RNA

A

stems
loops
bulges

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7
Q

how are secondary and tertiary structures formed in RNA

A

the strand finds complementary sections and pair with itself

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8
Q

messenger RNA is formed by

A

reading the DNA

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9
Q

how is DNA transcribed to mRNA

A

by RNA polymerase

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10
Q

the complementary nature of the mRNA produces a temporary mix of RNA-DNA called

A

RNA-DNA double helix D-loop

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11
Q

what do helicases do

A

twist and untwist DNA

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12
Q

twisting equation

A

Lk=Wr+Tw
linking number = writhe + twist

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13
Q

when DNA is being untwisted, what breaks first

A

TATA box

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14
Q

when the TATA box is broken, what happens to the persistance length

A

it goes from 500A to 6-10A
the DNA becomes weak

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15
Q

DNA relieves torsional stress with

A

localized sequence dependent structural failures

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16
Q

what are minicircles

A

like mini plasmids but programmable.
one strand is knicked and then is twisted or untwisted before religating

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17
Q

the number of twists affects the

A

shape

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18
Q

names for mini circles shapes

A

open circle
curved circle
8 shape
racquet
handcuff
needle
rod

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19
Q

Cryo-EM shows that mini circles break at

A

the TATA box

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20
Q

it takes how many bases to code for an amino acid

A

3

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21
Q

messenger RNA carries the code from the DNA to the

A

synthesis machinery

22
Q

before mRNA can be read by the ribosome it must

A

be processed into a mature form

23
Q

in the final mature form, we find that the genetic code has some

A

redundancies in the third slot of the codon

24
Q

what makes mRNA

A

RNA polymerase

25
Q

on an immature mRNA what are the two parts

A

introns or intervening material
exons

26
Q

what part of an immature mRNA is transcribed

A

exon

27
Q

introns are cleaved at specific splice sites by

A

the RNA itself

28
Q

catalytic RNA is known as a

A

ribozyme

29
Q

all the RNA is synthesized and then the … are chopped out and the … are rejoined to make a fully processed or mature and functional mRNA

A

introns
exons

30
Q

RNA splicing only happens at specific sites and creates

A

a lariat structure from the introns

31
Q

RNA splicing reaction occurs in a complex region called the

A

spliceosome which contains proteins and RNA

32
Q

in the spliceosome the individual reactions with proteins are specific and require what to drive the precursors of the processing reactions

A

ATP

33
Q

how does RNA splice itself

A

the strands find self-complimentary regions and form stem-loop structures
creates mRNA, tRNA, rRNA, siRNA, snRNA, lncRNA and more

34
Q

what kind of RNA must also be processed after transcription by splicing into a mature form

A

tRNA

35
Q

tRNA is formed during transcription in an

A

immature form

36
Q

tRNA is processed to form the

A

clover leaf form

37
Q

tRNA folds up into specific shape with common domains which are stabilized by

A

specific and unusual base pairs and triplets

38
Q

tRNA folding is important to its

A

function

39
Q

nucleosides unique to RNA

A

ribothymidine
pseudouridine

40
Q

uncommon pairings and triplets form at the

A

domain junctions in tRNA

41
Q

inosine is a very versitile

A

hydrogen bonder

42
Q

what ion is required for tRNA to fold

A

Mg2+

43
Q

once folded, tRNA forms the familiar shape with some

A

pseudo two-fold symmetry

44
Q

in the tRNA folded state what kinds of binding is present

A

some watson and crick double helices
a number of more interesting regions of structure

45
Q

tRNA must attatch to mRNA at

A

triplet codons and hold an activated amino acid in place

46
Q

silencing RNA is also called

A

RNA interference
RNAi
gene silencing

47
Q

what kind of RNA is used to regulate transcription

A

miRNA
micro RNA

48
Q

how to turn off a gene

A

chromatin conformation must be remodeled
RNAi initiates chromatin silencing
chemical markers on histone proteins shift the equilibrium and allow recognition

49
Q

types of epigenetic markers that can be used to silence a gene

A

acetylation
methylation
phosphorylation
ubiquitination

50
Q

two fragments of rRNA

A

30S and 50S

GSBS Biochem (10 decks)

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