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bm210 biochemistry > A1 eukaryotic gene expression and function > Flashcards

A1 eukaryotic gene expression and function Flashcards

1
Q

where is DNA copied into

A

RNA in the nucleus

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2
Q

where is processed RNA exported to

A

cytosol

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3
Q

where does translation take place

A

cytosol

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4
Q

what is the 5’ end of DNA usually attached to

A

phosphoryl group

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5
Q

what is usually at the 3’ end of DNA

A

free hydroxyl group (OH)

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6
Q

what bases are purines

A

adenine and guanine

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7
Q

what bases are pyrimidines

A

cytosine and thymine

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8
Q

the 4 DNA bases

A

adenine, guanine, cytosine, and thymine

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9
Q

the 4 RNA bases

A

adenine, guanine, cytosine, and uracil

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10
Q

what is a nucleoside

A

a base (A, T, G, C) conjugated to a sugar

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11
Q

nucleoside bases (DNA)

A

deoxyadenosine
deoxyguanosine
deoxycytosine
thymidine

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12
Q

nucleoside bases (RNA)

A

adenosine
guanosine
cytidine
uridine

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13
Q

what is a nucleotide

A

a nucleoside conjugated to one or more phosphoryl group

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14
Q

nucleotide bases in DNA

A

deoxyadenylate (dATP)
deoxyguanylate (dGTP)
deoxycytidylate (dCTP)
thymidylate (dTTP)

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15
Q

what sugar is DNA and RNA based on

A

RNA- ribose
DNA- deoxyribose

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16
Q

what bond holds bases together

A

hydrogen bonds

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17
Q

structure of DNA

A

2 polynucleotide chains coiled round common axis with a right handed screw
chains are anti-parallel
double helix

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18
Q

location of sugar phosphates and bases on DNA helix

A

sugar phosphates on outside
bases on inside

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19
Q

what degree are bases at to helix axis

A

90 degrees

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20
Q

how do the stacked bases at the core of the double helix attract each other

A

van der waals forces

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21
Q

is the double stranded DNA stable or unstable

A

very stable

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22
Q

why does DNA replication need to be error free

A

to avoid mutation

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23
Q

what are the stages of the cell cycle

A

G1 growth
S dna synthesis
G2 growth and prep for mitosis
M- mitosis (cell div)

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24
Q

at what phase in the cell cycle does DNA replication take place

A

S phase

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25
Q

why is DNA replication said to be semi conservative

A

because one complete strand of each double helix is directly derived from the parent molecule and one complete new strand

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26
Q

what is the key enzyme involved in DNA replication

A

DNA polymerase

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27
Q

what does DNA pol require to begin synthesis

A

primer (with a free 3’-OH)

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28
Q

what does DNA pol do in DNA replication

A

catalyses step by step addition of deoxyribonucleotide units too DNA

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29
Q

what is the new DNA assembled onto

A

template DNA

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30
Q

in what direction does new DNA grow at

A

3’ end

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31
Q

what direction is DNA synthesis

A

5’-3’

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32
Q

what are the 2 strands in DNA replication called

A

leading and lagging strand

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33
Q

explain the lagging strand

A

short sequences of DNA are synthesised (okazaki fragments)

34
Q

what enzyme joins okazaki fragments

A

DNA ligase

35
Q

what are introns

A

intervening DNA
non coding regions

36
Q

what are exons

A

expressed DNA
coding regions

37
Q

what are the 3 main types of RNA

A

messsenger RNA (mRNA)
transfer RNA (tRNA)
ribosomal RNA (rRNA)

38
Q

what is mRNA

A

template for synthesis of proteins

39
Q

what is mRNA transcribed by

A

RNA polymerase II

40
Q

what is tRNA

A

carries activated amino acids to ribosomes

41
Q

what is tRNA synthesised by

A

RNA polymerase III

42
Q

what is rRNA

A

major component of ribosomes

43
Q

what is rRNA synthesised by

A

RNA polymerase I

44
Q

what do the 3 main types of RNA require to copy template DNA

A

ATP
UTP
CTP
GTP
together with Mg2+ ions

45
Q

what are the three steps of mRNA synthesis

A
  1. Initiation
  2. Elongation
  3. Termination
46
Q

summary of initiation in mRNA synthesis

A

RNA Pol II and transcription factors assemble at promoter sites ; RNA synthesis then initiates

47
Q

summary of elongation in mRNA synthesis

A

-RNA pol moves along DNA template to synthesis mRNA which grows in a 5’-3’ direction
-Sequence of growing mRNA driven by base pairing to DNA strand- faithful copy of DNA template produced

48
Q

summary of termination in mRNA synthesis

A

RNA pol II ceases transcription at defined site
mRNA transcript is then stabilised by specific modifications

49
Q

what are the two promotor boxes

A

CAAT box (sometimes present)
TATAAA box (Hogness box)

50
Q

what strands can the CAAT and TATA box be on

A

CAAT can be on either
TATA can only be on one

51
Q

transcription goes from

A

DNA to RNA

52
Q

translation goes from

A

RNA to protein

53
Q

are mRNA and DNA complementary

A

yes

54
Q

what are the names of the coding and template strand

A

coding - sense
template -antisense

55
Q

approximately how many base pairs of DNA are unwinded

A

17

56
Q

what direction is DNA strand read in during elongation

A

3’-5’

57
Q

what protective features are added to the transcript

A

cap at 5’
long poly (A) tail at 3’

58
Q

can transcription factors turn gene expression on or off

A

yes

59
Q

are transcription factors specific

A

yes

60
Q

what are transcription factors activated by

A

by phosphorylation and subsequent movement into the nucleus

61
Q

what is used as a template for protein synthesis

A

mRNA

62
Q

what is the role of tRNAs in protein synthesis

A

translate the genetic code and allow specific amino acids to be added to a growing protein chain

63
Q

where does translation occur

A

on ribosomes

64
Q

what is essential for protein synthesis and how are they delivered to the ribosome

A

amino acids
delivered to ribosome on tRNAs (aminoacyl-tRNA)

65
Q

what is the start codon for protein synthesis

A

AUG (methionine)

66
Q

what structure is adopted by tRNAs and how

A

clover leaf structure
H bonding between bases

67
Q

where is the anticodon located on the clover leaf structure of tRNA

A

at the base
will then base pair with corresponding condon in mRNA being translated ensuring specificity

68
Q

amino acids are attached as what and where on tRNA

A

attached as an aminoacyl moiety and the amino acid attachment site

69
Q

what do aminoacyl tRNA synthetases do

A

link a specific amino acid with a specific tRNA (defined by its anticodon)

70
Q

what are the 3 steps for linking aa to specific tRNa with chem eqn

A

amino acid activation step
transfer of aminoacyl-AMP to specific tRNA
driven by hydrolysis of pyrophosphate (PPi)

aa+ATP — aminoacyl-AMP + PPi
aminoacyl-AMP + tRNA — aminoacyl-tRNA +AMP
PPi + water — 2Pi

71
Q

overall equation of the 3 step process to link aa to tRNA

A

amino acid + ATP + tRNA + H2O — Aminoacyl-tRNA + AMP + 2Pi

72
Q

how many aminoacyl-tRNA synthetases are there per amino acid

A

one

73
Q

how do synthetases reject the incorrect amino acid

A

they have a proof reading ability
can recognise the tRNA structure and its anticodon allowing specificity

74
Q

what are ribosomes made up of

A

50S and 30S rRNA subunits

75
Q

what are the 3 sites on ribosomes (P, A, E)

A

P- peptide grows here through a tunnel in the structure
A- amino acyl-tRNA binds here, bringing in next amino acid
E- exit site for empty tRNA

76
Q

what is Met-tRNAi

A

special intiation tRNA bearing methionine key for translation initiation

77
Q

what two things (with initiation factors) form a complex in translation initiation

A

GTP and 30S ribosomal subunit

78
Q

what does the complex scan mRNA for and what is the energy source in translation initiation

A

looking for AUG (initiation codon)
uses ATP

79
Q

what occurs when complex finds AUG in translation initiation

A

once AUG is found, the remaining ribosomal subunit (50S) is recruited with further initiation factors to form the 80S initiation complex, allowing protein synthesis to begin

80
Q

what are some of the many regulatory steps of protein synthesis

A

selective control of gene expression
control of mRNA synthesis rates
protein synthesis/degradtion rates

bm210 biochemistry (19 decks)

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