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Biochemistry > DNA and Proteins > Flashcards

DNA and Proteins Flashcards

1
Q

What is the Central Dogma?

A

The process by which DNA is converted to mRNA and then to a protein

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2
Q

d: genome

A

the entire genetic material that makes up an organism

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3
Q

d: allele

A

each of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome

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4
Q

d: nucleotides

A

are organic molecules that serve as the monomer units for forming DNA and RNA

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5
Q

name the two nucleotides that transcription occurs between

A

DNA

RNA

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6
Q

what is a nucleoside compared to a nucleotide?

A

nucleotides without a phosphate group

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7
Q

composition of nucleoside

A

base

sugar

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8
Q

composition of a nucleotide

A

base
sugar
phosphate group

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9
Q

eg of a nucleoside

A

adenosine

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10
Q

d: nucleic acid

A

a complex organic substance present in living cells, especially DNA or RNA, whose molecules consist of many nucleotides linked in a long chain

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11
Q

name the two classes of nucleic acids

A

purines

pyrimidines

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12
Q

name the two purines

A

Adenine

Guanine

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13
Q

name the three pyrimidines

A

uracil
thymine
cytosine

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14
Q

are purine or pyrimidines larger molecules

A

purines are larger

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15
Q

Name the bases present in DNA

A

Guanine
Cytosine
Adenine
Thymine

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16
Q

Name the bases present in RNA

A

Uracil
Adenine
Cytosine
Guanine

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17
Q

What are the components of AMP? (C present etc)

A 
5 C
1 phosphate group
adenine
1 oxygen in centre
2 hydroxyl groups
6 hydrogens in centre
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18
Q

what does AMP stand for?

A

Adenosine 5’-monophosphate

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19
Q

d: chromosome

A

a threadlike structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes.

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20
Q

how is the polymer DNA formed?

A

through a condensation reaction of many nucleotides

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21
Q

f: DNA

A

code for polypeptides

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22
Q

Where is DNA found?

A

nucleus

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23
Q

what is the bond called that forms during the condensation reaction of DNA nucleotides which holds them together?

A

phosphodiester bond

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24
Q

f: phosphodiester bond

A

holds the sugar phosphate backbone of DNA together

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25
Q

d: purines

A

bases with a double ring structure

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26
Q

d: pyrimidines

A

bases with a single ring structure

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27
Q

What type of bonds form between adenine and thymine and how many?

A

Hydrogen bonds

2

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28
Q

What type of bonds form between cytosine and guanine and how many?

A

hydrogen bonds

3

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29
Q

How are the two DNA strands described motion wise? Why?

A

Antiparallel

run in opposite directions to one another

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30
Q

What is the end of the DNA strand with the phosphate group attached called?

A

5’ end

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31
Q

What is the end of the DNA strand without the phosphate group attached called?

A

3’ end

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32
Q

Why does DNA have to be replicated (duplicated) before cell division?

A

so that the daughter cells have a complete complement of the genome

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33
Q

d: semiconservative

A

denoting replication of a nucleic acid in which one complete strand of each double helix is directly derived from the parent molecule

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34
Q

how is DNA replication described?

A

as semi-conservative

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35
Q

why must DNA polymerase enzyme only go in one direction?

A

its active site can only bind to nucleotides at one end

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36
Q

what does DNA polymerase require and where is it placed before it starts building up the backbone?

A

Primase ( RNA primer)

3’ end

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37
Q

how many sights of origin do eukaryotic cells have for DNA replication?

A

multiple

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38
Q

why does replication start simultaneously at several points in the genome and bidirectionally?

A

ensures that replication can be finished in a reasonable time

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39
Q

what is the only end nucleotides can be added to?

A

3’

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40
Q

how do you know if its the leading strand?

A

always has a free 3’ end

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41
Q

d:lagging strand

A

the strand of forming DNA whose direction of synthesis is opposite to the direction of the growing replication fork

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42
Q

which DNA strand is replicated in short fragments? what are they called?

A

lagging strand

Okazaki fragments

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43
Q

why is lagging strand replicated in fragments?

A

Copying lagging strand template is more complex

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44
Q

what separates the h-bonds in DNA replication?

A

DNA helicase enzyme

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45
Q

how are the free nucleotides joined together?

A

by forming phosphodiester bonds via DNA polymerase enzyme

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46
Q

incorporating the wrong type of nucleotide during DNA replication can cause which type of mutation?

A

deleterious

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47
Q

DNA polymerase has 3’ to 5’ exonuclease activity, how does this improve replication?

A

removes incorrect nucleotide

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48
Q

name the 3 main classes of RNA

A

ribosomal
messenger
transfer

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49
Q

f: rRNA

A

combines with proteins to form ribosomes where protein synthesis takes place

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50
Q

f: tRNA

A

carries the amino acids to be incorporated into the protein

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51
Q

f: mRNA

A

carries the genetic information for protein synthesis

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52
Q

name the stable RNAs

A

ribosomal

transfer

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53
Q

describe the structure of RNA

strands, loops, bases

A

single stranded
stem loops
contains Uracil (U)

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54
Q

what is a stem loop in RNA?

A

local stretches of intramolecular base-pairing

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55
Q

which RNA type has the highest % of total cellular RNA?

A

rRNA

56
Q

which RNA type has the LOWEST % of total cellular RNA?

A

mRNA

57
Q

d: anticodon

A

sequence of three nucleotides forming a unit of genetic code in a tRNA molecule, corresponding to a complementary codon in mRNA.

58
Q

what type of structure do tRNA molecules have?

A

3D

59
Q

describe the structure when tRNA is flattened into 2D

A

cloverleaf structure

60
Q

what end is the specific AA attached to in tRNA? what does this depend on?

A

3’

anticodon sequence

61
Q

What makes RNA?

A

RNA polymerases

62
Q

How many types of RNA polymerase do prokaryotic cells have?

A

1

63
Q

How many types of RNA polymerase do Eukaryotic cells have? and names

A

3
POL I
POL II
POL III

64
Q

How can the 3 POL’s be distinguished?

A

by their sensitivity to toxins eg alpha-amanitin

65
Q

What POL synthesises all mRNA?

A

POL II

66
Q

describe the steps of transcription (5)

A

RNA polymerase binding
detection of initiation sites (promoters) on DNA

DNA chain separation
local unwinding of DNA
to gain access to the nucleotide sequence

Transcription initiation
selection of the first nucleotide of the growing RNA

Elongation
addition of further nucleotides to the RNA chain

Termination

67
Q

What is the promoter of RNA?

A

Pol II

68
Q

Where does transcription start?

A

at nucleotide +1

69
Q

Where is the TATA box present?

A

about 25 nucleotides before the transcriptional start

70
Q

How does RNA polymerase know where to start transcription?

A

promoter shows it

71
Q

What does TBP stand for?

A

TATA box binding protein

72
Q

f: TATA box

A

regulates gene expression by providing a binding site for enzymes involved in transcription

73
Q

What does TFIID stand for?

A

transcription Factor II D

74
Q

f: TBP

A

Introduces kink into DNA
determines transcriptional start and direction
Provides a binding site for further transcription factors and for RNA polymerase

75
Q

What does transcription require to be initiated?

A

additional general transcription factors

76
Q

What allows transcription to occur at low basal rates?

A

TFIID remains at promoter, a new initiation complex can assemble

77
Q

d:elongation (transcription)

A

elongation is the stage when the RNA strand gets longer, due to the addition of new nucleotides.

78
Q

describe the termination step in transcription

A

Newly synthesised RNA makes a stem-loop structure
followed by a stretch of Us

A specific enzyme cleaves the (now finished) RNA
and the RNA is released

79
Q

What happens to the RNA polymerase II after transcription?

A

it dissociates

80
Q

What is required for regulation of transcription?

A

Requires ‘specific’ transcription factors that
Bind to specific DNA sequences in the vicinity of a promoter
Regulating transcription positively or negatively

81
Q

name the two functional domains which can be physically separated in specific transcription factors in the regulation of transcription

A

DNA-binding domain

transcriptional activation domain

82
Q

How do specific transcription factors bind to DNA sequences in regulation of transcription?

A

via enhancers

83
Q

d: transcription factor

A

a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence

84
Q

give two egs of transcription factors which control gene expression

A

Steroid receptors

glucocorticoid receptor

85
Q

where are steroid receptors found?

A

cell cytoplasm

86
Q

How do steroids enter target cells?

A

by diffusion

87
Q

what is the name for a coding region in eukaryotic cell?

A

exon

88
Q

what is the name for a non-coding region in eukaryotic cell?

A

intron

89
Q

what has to happen to introns before mRNA is translated to a protein? why?

A

spliced out

introns and exons are transcribed together

90
Q

How are the ends of mRNAs processed?

A

Addition of poly(A) tail

Addition of 5’ cap

91
Q

What is mRNA called before and after regulation?

A

pre-mRNA

mature mRNA

92
Q

d: codon

A

a sequence of 3 bases that code for 1 AA

93
Q

how many different combinations of bases?

A

64

94
Q

d: reading frame

A

one of three possible ways of reading a nucleotide sequence, depending where translation starts

95
Q

how is the AA attached to tRNA molecule?

A

via Aminoacyl-tRNA synthetase enzyme

96
Q

what are the sources of energy for translation?

A

ATP and GTP

97
Q

what is the energy source for formation of bond that binds tRNA and AA?

A

ATP

98
Q

what bond forms between tRNA and AA?

A

covalent

99
Q

how many rRNA molecules does a ribosome contain? What else do ribosomes contain?

A

4

protein components

100
Q

Name the 3 tRNA binding sites in Ribosomes

A

exit
peptidyl
aminoacyl

101
Q

what provides energy for translation initiation?

A

hydrolysed GTP

102
Q

What is required for initiation of translation?

A

Initiation factors

103
Q

describe initiation of translation

A

Small ribosomal subunit binds to 5’ end of mRNA
Moves along the mRNA until AUG (start codon) is found (ATP-dependent)
Special ‘initiator’ tRNA with UAC anticodon base-pairs with the start codon
carries methionine
Large subunit joins assembly and initiator tRNA is located in P site

104
Q

what codon is for methionine?

A

AUG

105
Q

What is the start codon in translation?

A

methionine

106
Q

f: elongation factor in translation

A

brings the next aminoacyl-tRNA to the A site

107
Q

describe elongation process translation

A

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

GTP is hydrolysed, EF is released from tRNA

A second elongation factor (EFbg) regenerates EF1a to pick up the next aminoacyl-tRNA

108
Q

What is the name of the enzyme which catalyses peptide bond formation between AA and what sites are these AA between?

A

peptidyl transferase

P and A

109
Q

Which site is the peptide located after it is formed?

A

A

110
Q

Describe peptide bond formation and translocation process

A

Peptidyl transferase catalyses peptide bond formation
Elongation factor EF-2 moves ribosome along the mRNA by one triplet
‘Empty’ tRNA moves to E site and can exit and become reloaded with an amino acid
tRNA with the growing peptide moves from the A to the P site
A site is free for the next aminoacyl-tRNA

111
Q

When does termination of translation occur?

A

when the A site of the ribosome encounters a stop codon

112
Q

give 3 stop codons

A

UAA, UAG or UGA

113
Q

describe termination of translation process

A

No aminoacyl-tRNA base-pairs with stop codons
Release factor RF binds stop codon
GTP hydrolysis
Finished protein is cleaved off tRNA
The components – rRNA, mRNA and tRNA – dissociate from one another
Whole process starts all over again with small subunit being bound by IF ready for translation of a new protein

114
Q

d:polysome

A

a cluster of ribosomes held together by a strand of messenger RNA that each ribosome is translating.

115
Q

name the 5 types of mutations of protein synthesis

A 
point
missense
nonsense
silent
frameshift
116
Q

d:point mutation

A

change in a single base in DNA

117
Q

d: missense mutation

A

results in a change of amino acid sequence

can change protein function,

118
Q

d: nonsense mutation

A

creates a new termination codon

changes length of protein due to premature stop of translation

119
Q

d: silent mutation

A

no change of amino acid sequence

due to degeneracy of the genetic code

no effect on protein function

120
Q

d: frameshift mutation

A

addition or deletion of a single base (or two!)

changes reading frame of translation into protein

121
Q

give 4 chromosome mutations

A

deletions
duplications
inversions
translocations

122
Q

give three things that happen to the finished protein

A

targeting
modification
degradation

123
Q

describe targeting of protein

A

moving a protein to its final cellular destination
many possible locations within a cell
depends on the presence of specific amino acid sequences within the translated protein

124
Q

d: modification of a protein

A

addition of further functional chemical groups

125
Q

d: degradation

A

unwanted or damaged proteins have to be removed

126
Q

where free ribosomes found?

A

cytosol

127
Q

what do free ribosomes make proteins destined for?

A

cytosol
nucleus
mitochondria
translocated post-translationally

128
Q

what do bound ribosomes make proteins destined for?

A 
plasma membrane
ER
Golgi apparatus
secretion
translocated co-translationally
129
Q

where are bound ribosomes found?

A

rough endoplasmic reticulum

130
Q

d: co-translationally

A

happens during synthesis

131
Q

d:post-translationally

A

happens after translation

132
Q

list some post-translational modifications (3)

A

Glycosylation
Formation of disulfide bonds in the ER
Folding and assembly of multisubunit proteins in the ER
Specific proteolytic cleavage in the ER, Golgi, and secretory vesicles

133
Q

d: glycosylation

A

addition and processing of carbohydrates in the ER and the Golgi

134
Q

what does the hereditary form of emphysema result from?

A

misfolding of the protein a1-antitrypsin in the ER

135
Q

name a disease that originates from inherited recessive disorder of protein targeting

A

I-cell disease (mucolipidosis II)

Biochemistry (5 decks)

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