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Principles: biochemistry > DNA to protein > Flashcards

DNA to protein Flashcards

1
Q

nucleoside =

A

base and sugar

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2
Q

nucleotide =

A

nucleoside and phosphate group

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3
Q

what is the difference between ribose and deoxyribose?

A

on C2 of ribose there is an OH instead of an H

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4
Q

what are the two purines?

A

adenine and guanine

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5
Q

what are the three pyramidines?

A

uracil, thymine and cytosine

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6
Q

in polymerisation a phosphodiester bond is formed between a free 3’ __ group and a 5’ ________

A

A phosphodiester bond is formed between a free 3’ OH group and a 5’ triphosphate

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7
Q

polymerisation releases 2 __ enegy bonds

A

high

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8
Q

new nucleotides are only added to a free _’ end

A

3

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9
Q

analogues of thymidine (ZDV=AZT=retrovir) can be used as drugs. The analogue is incorporated into the growing viral DNA
Lacks _’ __ group, therefore, chain elongation is terminated

A

Is incorporated into the growing viral DNA

Lacks 3’ OH group, therefore, chain elongation is terminated

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10
Q

the nucleotide analogue mechanism only works because viral _____ ______ has higher affinity for ZDV than human DNA polymerases

A

reverse transcriptase

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11
Q

Replication is semi-______

A

conservative

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12
Q

replication is catalysed by ________

A

DNA polymerase

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13
Q

DNA polymerase requires a ____ primer to start replication

A

RNA

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14
Q

in eukaryotes Replication starts simultaneously at several points in the genome
and is bidirectional, what is the advantage of this?

A

ensures that replication can be finished in a reasonable time

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15
Q

the leading strand template runs from __’ to __’

A

5 to 3

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16
Q

the lagging strand template runs from __’ to __’

A

3-5

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17
Q

which enzyme synthesises the primer for replication?

A

primase

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18
Q

DNA ______ unwinds the double helix

A

helicase

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19
Q

after the okazaki fragments have been generated the ____ are degraded and filled in by DNA -_______

A

primers, polymerase

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20
Q

DNA polymerase has 3’ → 5’ _______ activity

A

exonuclease which removes incorrect nucleotide

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21
Q

RNA is usually ___ stranded with local stretches of _______ base-pairing

A

single, intramolecular

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22
Q

what are the three main classes of RNA

A
  1. ribosomal RNA
  2. transfer RNA
  3. messenger RNA
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23
Q

what are the stable RNAs?

A

ribosomal and transfer

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24
Q

what is the function of ribosomal RNA?

A

combines with proteins to form ribosomes where protein synthesis takes place

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25
Q

what is the function of transfer RNA?

A

carries the amino acids to be incorporated into the protein

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26
Q

what is the function of messenger RNA?

A

carries the genetic information for protein synthesis

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27
Q

RNA contains __ instead of thymine

A

uracil

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28
Q

rRNA has __ units to it

A

4

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29
Q

in tRNA specific amino acid is attached to the _’ end

depends on _______ sequence

A

Specific amino acid is attached to the 3’ end

depends on anticodon sequence

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30
Q

RNA is made by ___ _______

A

RNA polymerases

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31
Q

eukaryotic cells have __ types of RNA polymerase, what are they

A

3

- pol I,II,III

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32
Q

how can the different RNA polymerases be distinguished

A

by their sensitivity to toxins like alpha-amantin

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33
Q

pol__ synthesised all mRNA

A

II

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34
Q

the ____ region is foun just upstream of the initiation site for transcription

A

PROMOTOR

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35
Q

____ ___ is present about 25 nucleotides before the transcriptional start (-25)

A

TATA box

36
Q

_____ is a general transcription factor required for all pol ___ transcribed genes

A

TFIID, II

37
Q

___ is part of TFIID and is responsible for recognising the TATA box

A

TBP

38
Q

TFIID Provides a landing platform for further ____ _____ and for ___ _______

A

Provides a landing platform for further transcription factors and for RNA polymerase

39
Q

what part of transcription process allows transcription to happen at low basal rates?

A

TFIID remains at the promotor region

40
Q

RNA chain is synthesised in a __ to __ ’ direction

A

5 to 3

41
Q

New RNA sequence is ______ to the template strand and it is _____- to the coding strand

A

complementary, identical

42
Q

in transcription termination newly synthesised RNA makes a ____ -____ structure
followed by a stretch of __

A

Newly synthesised RNA makes a stem-loop structure

followed by a stretch of Us

43
Q

when proteins are to be made in response to a signal

they require ‘specific’ ____ ____.

A

transcription factors

44
Q

regulatory transcription fatcprs can bind to either the&raquo_space; 2 things

A

DNA-binding domain

transcriptional activation domain

45
Q

the ______ receptors are a family of transcription factors, subset of (much larger) family of nuclear hormone receptors

A

steroid

46
Q

they have 3 binding domains, whatare they

A
  • Transactivation domain
  • DNA-binding domain
  • Ligand-binding domain
47
Q

steroid receptors are located in the _____ (inactive). On binding ligand (steroid) move to _____ and bind to DNA at ___ ____ _____ (SREs)

A

cytoplasm, nucleus, steroid response elements

48
Q

what is an example of a steroid receptor ?

A

glucocorticoid receptor

49
Q

Coding regions _____ are interrupted by non-coding regions ______

A

exons, introns

50
Q

introns are removed by ___

A

splicing

51
Q

what changes are made to pre-mRNA to make it into mature mRNA?

A
  1. a cap of modified GTP is added to the 5’ end
  2. specific sequence is recognised and cut by an enzyme
  3. a poly A tail is added to the cut 3’ end
52
Q

where is mRNA processing done?

A

in the nucleus

53
Q

During translation, _____ of tRNA molecules form base pairs with _____ on mRNA

A

anticodons, codons

54
Q

how many different triplet combinations are possible?

A

64

55
Q

the genetic code is ____ meaning that many amino acids have more than one codon

A

degenerate

56
Q

the genetic code is ____ meaning that each codon codes for only one amino acid (or a Stop)

A

unambiguous

57
Q

what is a start triplet?

A

AUG

58
Q

give some examples of stop codons

A

UAA, UAG, UGA

59
Q

translation is an ____ reaction

A

anabolic

60
Q

___ _____ ______ bind amino acids to their corresponding tRNA molecule(s)

A

Aminoacyl-tRNA synthetases - this is highly specific

61
Q

ATP provides energy for the formation of the ___ bond between AAs and the tRNA molecule

A

covalent

62
Q

what are the three tRNA binding sites called?

A
  1. exit
  2. peptidyl (start)
  3. aminoacyl
63
Q

initiation of translation: ____ is hydrolysed to provide energy for initiation. Small ribosomal subunit binds to __ end of mRNA.
Moves along the mRNA until ___ (start codon) is found (ATP-dependent). Special ‘initiator’ tRNA with___ anticodon base-pairs with the start codon- carries ____

A

GTP, 5’, AUG, UAC, methionine

64
Q

elongation of translation: An ______ ______ brings the next aminoacyl-tRNA to the A site. GTP is hydrolysed, __ is released from tRNA. A second elongation factor (EFβγ) regenerates ____ to pick up the next aminoacyl-tRNA

A

An elongation factor (EF-1α), brings the next aminoacyl-tRNA to the A site,

EF

EF1alpha

65
Q

For EF-1a to be active, it must have a -__ molecules attached to it.

A

GTP

66
Q

____ _____ catalyses peptide bond formation between amino acids in the P and A sites

A

peptidyl transferase

67
Q

______ moves ribosome along the mRNA

A

Elongation factor EF-2 moves ribosome along the mRNA

68
Q

No aminoacyl-tRNA base-pairs with ___ codons. the ___ factor binds to stop codons

A

stop, release

69
Q

the _____ is where ribosomes will bind to mRNA wherever they find space

A

polysome

70
Q

what is a point mutation?

A

change in a single base in DNA

71
Q

what are the two point mutations>

A
  • missense and nonsense
72
Q

what happens in a missense mutation

A

there is a change in the amino acid sequence

73
Q

what happens in a nonsense mutation?

A

this creates a new termination code

74
Q

what is a silent mutation?

A

no change of amino acid sequence
due to degeneracy of the genetic code
no effect on protein function

75
Q

what is a frameshift mutation?

A

addition or deletion of a single base (or two!) not three , doesnt change the frame
changes reading frame of translation into protein

76
Q

chromosomal mutations affect ___ portions of the genome

A

larger

77
Q

what are the 4 chromosomal mutations?

A

deletions
duplications
inversions
translocations

78
Q

the location of the final protein depends on the presence of specific amino acid sequences within the _-_____ _____

A

translated protein

79
Q

what three things can happen to a finished protein?

A
  1. targeting
  2. modification
  3. degradation
80
Q 
\_\_\_ ribosomes in the cytosol make proteins destined for:
cytosol
nucleus
mitochondria
translocated post-translationally
A

free

81
Q 
\_\_\_\_\_ ribosomes on the rough endoplasmic reticulum make proteins destined for:
plasma membrane
ER
Golgi apparatus
secretion
translocated co-translationally
A

bound

82
Q

what is glycosylation/

A

addition and processing of carbohydrates in the ER and the Golgi

83
Q

post translational modificaron:

  • specific proteolytic cleavage in the ER, Golgi, and secretory vesicles e.g insulin
  • formation of disulfide bonds in the ___
A

ER

84
Q

Hereditary form of emphysema results from misfolding of the protein __________ in the ER

A

Hereditary form of emphysema results from misfolding of the protein α1-antitrypsin in the ER

85
Q

what happens in I-cell disease?

A
  • proteins normally destined for lysosomes are not properly sorted in the Golgi
  • end up secreted from cell
  • lysosomes can not properly digest material, become clogged

Principles: biochemistry (7 decks)

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