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BM210 (chored from Ryan) > Block A > Flashcards

Block A Flashcards

1
Q

Where does translation take place?

A

Cytosol

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2
Q

What is a nucleoside?

A

A base joined to a sugar

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3
Q

What is a nucleotide?

A

A nucleoside joined to one or more phosphate group

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4
Q

What is a phosphate group?

A

A phosphorus atom bonded to 4 oxygen atoms (PO₄³⁻)

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5
Q

Where are the sugar phosphates and bases on a DNA strand?

A

The sugar phosphates on outside, bases inside

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6
Q

Roughly how many bases are in each DNA turn?

A

10

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7
Q

What is intron short for?

A

intervening DNA

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8
Q

What is exon short for?

A

expressed DNA

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9
Q

What stage of the cell cycle is DNA replicated?

A

S-phase (synthesis phase)

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10
Q

What makes DNA replication semiconservative?

A

one strand of the DNA is maintained every time its duplicated (original strand is split in 2 making each half making new strand half original half new)

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11
Q

What direction is a DNA strand synthesised by DNA polymerase?

A

5’ to 3’

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12
Q

How does DNA polymerase synthesise DNA?

A

catalyses the step-by-step addition of deoxyribonucleotide units to DNA

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13
Q

What is needed by DNA polymerase to synthesise new DNA ?

A

A primer (that has a free 3’ -OH)

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14
Q

What is PPi?

A

Pyrophosphate

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15
Q

The base sequence of mRNA is the complement of which DNA strand?

A

Template strand (is a copy of coding strand but with U for T)

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16
Q

What are the 3 stages of mRNA synthesise, in order?

A
  1. initiation
  2. elongation
  3. termination
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17
Q

Where does the initiation stage of mRNA synthesis occur in the DNA?

A

At promoters

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18
Q

What is a promoter?

A

A defined DNA sequence near the transcription start site

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19
Q

Give 3 examples of promoter sequences

A
  1. TATA box
  2. CAAT box
  3. GC box
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20
Q

How do promoter sequences define the point of transcription?

A

BY recruiting RNA Polymerase II

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21
Q

Which strand can the CAAT and GC boxes be on?

A

PLEASE HELPPPPP
The template (antisense) strand and more commonly the coding (sense) strand
(Lecture 1, Slide 23)??????????

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22
Q

What is the initiation stage of mRNA synthesis regulated by?

A

transcription factors (TF)

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23
Q

What can sequences known as “enhancers” influence?

A

Gene expression

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24
Q

What are enhancer sequences binding sites for?

A

transcription factors

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25
Q

Are transcription factors specific?

A

Yes

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26
Q

How are transcription factors specific?

A

They recognise DNA sequences near promoters of genes

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27
Q

The template (antisense) strand and more commonly the coding (sense) strand
(Lecture 1, Slide 23)

A

signaling pathways

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28
Q

What can transcription factors be activated by?

A

phosphorylation and subsequent movement into the nucleus

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29
Q

In the elongation phase of mRNA synthesis which strand is unwound?

A

The coding strand

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30
Q

What is created during the elongation stage of mRNA synthesis

A

A RNA-DNA hybrid helix of mRNA and the template strand

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31
Q

Is mRNA stable?

A

No

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32
Q

Give 2 ways mRNA is processed to make it more stable in the termination stage of mRNA synthesis

A
  1. modified 5’ cap
  2. poly A tail at the 3’
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33
Q

Give 2 reasons the modified 5’ cap and poly A tail at the 3’ end are added in the termination stage of mRNA synthesis

A

Help stability and translation

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34
Q

What codon does protein synthesis always start with?

A

AUG

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35
Q

What amino acid does the codon AUG code for

A

Methionine

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36
Q

What is the tRNA that carries amino acids to the site of translation?

A

aminoacyl tRNA

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37
Q

How does tRNA form its clover shape?

A

Hydrogen bonding between bases

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38
Q

What amino acids attached to, and where, on a tRNA molecule?

A

They are attached to an aminoacyl moiety at the amino acid attachment sie

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39
Q

What is present at the amino acid attachment site on a tRNA molecule?

A

A flexible CAA arm

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40
Q

What is the purpose of aminoacyl tRNA synthesis

A

To link a specific amino acid with a specific tRNA

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41
Q

What decided what amino acid links with the tRNA molecule?

A

The anticodon

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42
Q

What is first stage of aminoacyl synthesis called?

A

The amino acid activation step

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43
Q

Give the equation for the first stage of aminoacyl synthesis

A

Amino acid + ATP —-> Aminoacyl-AMP +PPi

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44
Q

What is second stage of aminoacyl synthesis?

A

Transfer of aminoacyl-AMP to a specific tRNA

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45
Q

Give the equation for the second stage of aminoacyl synthesis

A

Aminoacyl-AMP + tRNA —-> aminoacyl-tRNA + AMP

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46
Q

What is the hydrolysis reaction that drives aminoacyl tRNA synthesis

A

The hydrolysis of pyrophosphate (PPi)

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47
Q

Give the equation for the hydrolysis of PPi

A

PPi + H2O —-> 2Pi

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48
Q

Give the full equation for aminoacyl tRNA synthesis

A

Amino acid + ATP + tRNA + H20 —-> Aminoacyl-tRNA + AMP + 2Pi

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49
Q

Where does the attachment of amino acids to tRNA occur?

A

At an activator site of aminoacyl tRNA synthetase

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50
Q

What is the proof reading ability of aminoacyl tRNA synthetase able to do?

A

“Reject” incorrect amino acids

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51
Q

What makes aminoacyl tRNA synthetases specific?

A

They recognise the tRNA structure and anticodon

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52
Q

How do aminoacyl tRNA synthetases proof read?

A

The CCA arm can move amino acids between the activation and editing sites
If the amino acid fits well into the editing site, it is removed by hydrolysis

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53
Q

What are the subunits of ribosomes made up of?

A

Ribosomes are made up of 2 rRNA subunits

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54
Q

Give the function of the “P” site of a ribosome

A

Where the peptide grows (through a “tunnel” in structure)

55
Q

Give the function of the “A” site of a ribosome

A

Aminoacyl-tRNA binds here, bringing the next amino acid

56
Q

Give the function of the “E” site of a ribosome

A

Exit site for empty tRNAs

57
Q

Which special tRNA bears methionine in order to help initiate translation?

A

Met-tRNAi (i is a subscript)

58
Q

Give 3 things Met-tRNAi forms a complex with in order to help initiate translation

A
  1. initiation factors
  2. GTP
  3. 30s ribosomal subunit
59
Q

Give 2 things Met-tRNAi, initiation factors, GTP and 30s ribosomal subunit recruit once they find an AUG codon
What complex does this form?

A
  1. recruits remaining 50s subunit
  2. recruits further initiation factors

Forms the 80s initiation complex

60
Q

What does the formation of the 80s initiation complex result in?

A

protein synthesis occuring

61
Q

Give the 3 regulatory steps of transcription/translation

A
  1. selective control of gene expression
  2. control of mRNA synthesis rate/stability/processing
  3. protein synthesis/degradation rates
62
Q

Which enzyme synthesises the primary transcript of mRNA before it is spliced?

A

RNA polymerase

63
Q

When does mRNa capping occur?

A

When the pre-mRNA is ~ 25nt long

64
Q

What is required to cap the pre-mRNA?

A

Specific capping proteins

65
Q

What enzyme cleaves the phosphodiester bond to e when mRNA is being made?

A

Endonuclease (DOUBLE CHECK THIS CARD 2 slide 9)

66
Q

Give the name of the specific adenine which is key to splicing every intron

A

The branch site

67
Q

What is present as the mRNA is made?

A

An AAUAAA cleavage signal

68
Q

What do all intron end with?

A

AG

69
Q

Endonuclease cleaving the phosphodiester bond when mRNA is being made allows what?

A

Poly(A) polymerase to function

70
Q

What does poly(A) polymerase do after it has been activated by endonuclease cleaving the phosphodiester bond when mRNA is being made?

A

Adds a poly(A) tail to the pre-mRNA

71
Q

What gives a poly(A) tail its name?

A

It is a polymer tail of multiple adenine nucleotides (A)n where n can be >250

72
Q

What do splicing proteins recruit and what complex does this create?

A

Other proteins to form complex called spliceosome

73
Q

What do all introns begin with?

A

GU

74
Q

Give 2 thins present in every intron which are key to splicing

A
  1. pyrimidine rich tract (Py)
  2. specific adenine
75
Q

Give 3 things the spliceosome can do to RNA and in what way

A

Capture, splice and release RNA accurately and in a coordinated way

76
Q

Give the first step to RNA splicing

A

Splicing proteins recognise 2 specific sites, the GU at the 5’ splice site and the branch site

77
Q

What does the spliceosome capturing, splicing and releasing RNA require?

A

Careful choreography of spliceosome components

78
Q

What form are the introns released in, in RNA splicing?

A

lariat form

79
Q

What is alternative RNA splicing?

A

A process where different mRNAs are generated from the same initial primary transcript

80
Q

What can alternative RNA splicing result in?

A

Proteins with different functions being formed

81
Q

Why can some RNA molecules self replicate?

A

They can fold into distinct structures ( having the capaity to act as an enzyme and splice themselves)

82
Q

Who discovered RNA can act as an enzyme and splice itself?

A
  1. Tom Cech
  2. Sidney Altman
83
Q

What is RNA interference (RNAi)

A

A powerful tool to distrupt gene expression

84
Q

How was RNAi discovered?

A

Double stranded RNA was introduced to a cell and it suppressed the transcription of genes that contained sequences present in the original double stranded RNA

85
Q

What does RNA interference (RNAi) rely on?

A

The key activity of small interfering RNAs (siRNAs)

86
Q

How can exploitation of RNA interference be used in cell biology?

A

To examine the function of a particular hene product

87
Q

Give 3 potential uses of CRISPR

A
  1. Create cell lines to probe specific gene function
  2. Produce specific mutations in the germ line
  3. used in ex vivo and in vivo genome editing for clinical therapy
88
Q

Give 3 reasons why cells signal

A
  1. Co-ordination of day-to-day physiology
  2. Regulate behaviours in multicellular organisms
  3. Cells respond and change to stimuli in their environment
89
Q

Give 5 physiological activities that cell signaling regulates

A

(answers include):
1. cell metabolism
2. cell growth
3. cell division
4. cell motility
5. cell morphology
6. cell death
7. Co-ordination and development of gene expression

90
Q

What is intercellular signalling?

A

Communication between cells

91
Q

What does intercellular signalling permit?

A

A single cell to influence the behaviour of other cells in a specific way

92
Q

What is intracellular signalling?

A

Signalling within a single cell

93
Q

What does intracellular signalling happen in response to?

A

extracellular or intracellular stimuli

94
Q

What is autocrine intercellular signalling?

A

A cell targets itself
(double check this one)

95
Q

What is paracrine intercellular signalling?

A

A cell targets a nearby cell

96
Q

What is endocrine intercellular signalling?

A

A cell targets a distant cell through the blood stream

97
Q

What is the juxtacrine signalling?

A

A cell targets a cell connected by gap junctions

98
Q

Is cell signalling a linear process?

A

NO

99
Q

Give the 4 major types of cell signalling receptors

A
  1. ligand-gated ion channel receptors
  2. G-protein coupled receptors
  3. kinase-linked receptors
  4. nuclear receptors
100
Q

What can alter the “what”, “where” and “when” parameters of G-protein coupled receptor function?

A

Different signals

101
Q

Give 3 biases that can alter the kinetics of the response of cell signalling pathways

A

Bias with extracellular signal, intracellular signal, or both

102
Q

What are signalosomes composed of?

A

A unique combination of signalling pathway components

103
Q

How are signalosomes targeted to discreet intracellular localisation?

A

via the association of anchor or adaptor proteins

104
Q

How adaptable and dynamic are signalosomes?

A

Very

105
Q

What do signalosomes allow?

A

Cells to construct the optimum cell subdomain for signalling

106
Q

Where can G-protein coupled receptors generate unique signals from?

A

intracellular compartments

107
Q

Where are G-protein coupled receptors internalised to?

A

Endosomes and then trafficked to a pre-Golgi compartment

108
Q

What is the purpose of compartmentalisation of cAMP signalling?

A

Cells need a way to “turn off” signalling

109
Q

What catalyses the breakdown of cAMP?

A

Phosphodiesterases

110
Q

What can the compartmentalisation of cAMP create?

A

cAMP gradients in the cytosol

111
Q

Can cells have more than one cAMP gradient?

A

Yes

112
Q

State the 4 major types of signalling pathway receptors and the typical times associated with these

A
  1. ligand-gated ion channel receptors (milliseconds)
  2. G-protein coupled receptors (seconds)
  3. Kinase-linked receptors (hours)
  4. nuclear receptors (hours/days)
113
Q

How can one signal generate many responses?

A

Different cells can have the same receptor

114
Q

What makes different types of cells different?

A

All cells contain the same DNA sequences (genes) but are made different by which genes are expressed, this is different in different cell types

115
Q

What is meant by a gene being “expressed”?

A

it is transcribed into mRNA leading to a production of the corresponding protein

116
Q

What has a major role in determining what genes are expressed?

A

Epigenetics

117
Q

What is epigenetics?

A

Modifications to the genome that affect gene expression but do not alter the DNA sequence

118
Q

What are CpGs?

A

A rare dinucleotide sequence

119
Q

What does the p in CpG islands represent?

A

The phosphate residue on the DNA backbone

120
Q

What is methylation associated with?

A

Gene silencing

121
Q

How does methylation cause gene silencing?

A

The methyl group protrudes into the major groove of DNA which interferes with the binding of transcription factors

122
Q

What are CpG islands?

A

Regions of the genome which have a high density of CpGs

123
Q

Where are CpG islands mostly found?

A

The promoter region of genes

124
Q

How do CpG islands alter the binding of transcription factors?

A

By undergoing chemical modification (methylation)

125
Q

What bases is methylated by CpG

A

cytosine

126
Q

How does methylation prevent the binding of transcription factors?

A

Methyl binding proteins bind to the methylated DNA preventing the binding of transcription factors

127
Q

What is a nucleosome?

A

A DNA / histone octamer complex

128
Q

What is the overall DNA-histone complex referred to as?

A

Chromatin

129
Q

How many histone subunits form a histone octamer?

A

4

130
Q

What happens after 4 histone subunits form an octamer?

A

DNA wraps around the octamer

131
Q

What are the 2 chromatin states?

A

Euchromatin and heterochromatin

132
Q

Give 3 differences between euchromatin and heterochromatin

A
  1. Euchromatin is loosely packed whereas heterochromatin is tightly packed
  2. Euchromatin is enriched in genes whereas heterochromatin is usually genetically inactive
  3. Euchromatin is under active transcript whereas heterochromatin cannot be accessed by RNA polymerase
133
Q

Give 2 things regulate chromatin state

A

Methylation and acetylation of the histones

134
Q

Give 2 ways in which epigenetic changes can lead to cancer

A
  1. Phosphorylation of a tumour suppression gene could inhibit gene expression.
  2. Genes could be turned on by changing histone modification pattern

BM210 (chored from Ryan) (2 decks)

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