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BM 210: Introduction to Biochemistry > Block A: DNA and Gene Expression > Flashcards

Block A: DNA and Gene Expression Flashcards

1
Q

Where does translation take place?

A

The cytosol
(Lecture 1, Slide 4)

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2
Q

What is a nucleoside?

A

A base joined to a sugar
(Lecture 1, Slide 8)

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3
Q

What is a nucleotide?

A

A nucleoside joined to one or more phosphate groups
(Lecture 1, Slide 9)

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4
Q

What is a phosphate group?

A

A phosphorus atom bonded to 4 oxygen atoms
(Lecture 1, Slide 9)

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5
Q

Are the sugar phosphates and bases on the inside or outside of DNA?

A

Sugar phosphates are on the outside, bases are on the inside
(Lecture 1, Slide 12)

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6
Q

Roughly how many bases are in each DNA turn?

A

10
(Lecture 1, Slide 13)

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7
Q

What do introns and exons stand for?

A

Introns stand for intervening DNA whereas exons stand for expressed DNA
(Lecture 1, Slide 14)

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8
Q

During what stage in the cell cycle is DNA replicated?

A

During the S-phase (Synthesis phase)
(Lecture 1, Slide 15)

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9
Q

How is DNA replication semiconservative?

A

1 stand of the DNA is maintained every time it is duplicated (the original double strand is split in 2 and each half makes an entirely new double strand, leaving 1 original strand and 1 new one for each of the replicates)
(Lecture 1, Slide 16)

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10
Q

What direction does DNA polymerase synthesise the DNA strand in?

A

The 5’ to 3’ direction
(Lecture 1, Slide 16)

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11
Q

How does DNA polymerase synthesise DNA?

A

It catalyses the step-by-step addition of deoxyribonucleotide units to DNA
(Lecture 1, Slide 17)

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12
Q

What does DNA polymerase require to synthesise DNA?

A

A primer (that has a free 3’ -OH)
(Lecture 1, Slide 17)

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13
Q

What does PPi stand for?

A

Pyrophosphate
(Lecture 1, Slide 18)

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14
Q

Is the base sequence of mRNA the complement of the DNA template strand or the coding strand?

A

It is the complement of the template strand and is a copy of the coding strand (with the exception of thymine being changed out for uracil)
(Lecture 1, Slide 20)

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15
Q

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

A
  1. Initiation
  2. Elongation
  3. Termination
    (Lecture 1, Slide 22)
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16
Q

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

A

At promoters
(Lecture 1, Slide 23)

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17
Q

What is a promoter?

A

A defined DNA sequence near the transcription start site
(Lecture 1, Slide 23)

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18
Q

What are 3 examples of promoter sequences?

A

CAAT box
TATA box
GC box
(Lecture 1, Slide 23)

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19
Q

How do promoter sequences define the point of transcription?

A

By recruiting RNA Polymerase II
(Lecture 1, Slide 23)

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20
Q

Which strands can the CAAT and GC boxes be on?

A

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

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21
Q

What is the initiation stage of mRNA synthesis regulated by?

A

A group of proteins called transcription factors (TF)
(Lecture 1, Slide 24)

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22
Q

What can sequences known as “enhancers” influence?

A

Gene expression
(Lecture 1, Slide 25)

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23
Q

What do enhancer sequences binding sites bind to?

A

Transcription factors
(Lecture 1, Slide 25)

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24
Q

Are transcription factors specific?

A

Yes
(Lecture 1, Slide 27)

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25
Q

How are transcription factors specific?

A

They recognise specific DNA sequences near promoters of genes
(Lecture 1, Slide 27)

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26
Q

What are many transcription factors targets for?

A

Signalling pathways
(Lecture 1, Slide 27)

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27
Q

What can transcription factors be activated by?

A

Phosphorylation and subsequent movement into the nucleus
(Lecture 1, Slide 27)

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28
Q

What strand is unwound in the elongation stage of mRNA synthesis?

A

The coding strand
(Lecture 1, Slide 29)

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29
Q

What is created as a result of mRNA being created from the template strand in the elongation stage of mRNA synthesis?

A

A RNA-DNA hybrid helix of mRNA and the template strand
(Lecture 1, Slide 29)

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30
Q

Is mRNA stable or unstable?

A

Unstable
(Lecture 1, Slide 30)

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31
Q

What 2 ways is mRNA processed in, in order to make it more stable in the termination stage of mRNA synthesis?

A

A modified 5’ cap
A poly A tail at the 3’
(Lecture 1, Slide 30)

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32
Q

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

A

To help stability and translation
(Lecture 1, Slide 30)

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33
Q

What codon does protein synthesis always start with, and what amino acid is this codon for?

A

AUG (Methionine codon)
(Lecture 1, Slide 33)

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34
Q

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

A

Aminoacyl tRNA
(Lecture 1, Slide 34)

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35
Q

How does tRNA form it’s characteristic clover shape?

A

Hydrogen bonding between the bases
(Lecture 1, Slide 34)

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36
Q

What are amino acids attached to and where is it on a tRNA molecule?

A

They are attached to an aminoacyl moiety at the amino acid attachment site
(Lecture 1, Slide 34)

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37
Q

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

A

A flexible CAA arm
(Lecture 1, Slide 34)

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38
Q

What is the purpose of aminoacyl tRNA synthesis?

A

To link a specific amino acid with a specific tRNA
(Lecture 1, Slide 35)

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39
Q

What decides what amino acids links with the tRNA molecule?

A

The anticodon
(Lecture 1, Slide 35)

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40
Q

What is the equation of the first step of aminoacyl synthesis and what is this stage called?

A

The amino acid activation step

Amino acid + ATP ———»» Aminoacyl-AMP + PPi
(Lecture 1, Slide 35)

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41
Q

What is the equation of the second step of aminoacyl synthesis and what is this stage called?

A

Transfer of aminoacyl-AMP to a specific tRNA

Aminoacyl-AMP + tRNA ———»» Aminoacyl-tRNA + AMP
(Lecture 1, Slide 35)

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42
Q

What hydrolysis reaction drives aminoacyl tRNA synthesis and what is the equation for this?

A

The hydrolysis of pyrophosphate (PPi)

PPI + H20 ———»» 2Pi
(Lecture 1, Slide 35)

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43
Q

What is the full equation of aminoacyl tRNA synthesis?

A

Amino acid + ATP + tRNA + H2O ———»» Aminoacyl-tRNA + AMP + 2Pi
(Lecture 1, Slide 35)

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44
Q

Where does attachment of amino acids to the tRNA occur?

A

At an activator site of aminoacyl tRNA synthetase
(Lecture 1, Slide 36)

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45
Q

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

A

It is able to “reject” incorrect amino acids
(Lecture 1, Slide 36)

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46
Q

How are aminoacyl tRNA synthetases specific?

A

They can recognise the tRNA structure and anticodon
(Lecture 1, Slide 36)

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47
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 via hydrolysis
(Lecture 1, Slide 37)

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48
Q

What subunits are ribosomes made up of?

A

Ribosomes are made up of 2 rRNA subunits
(Lecture 1, Slide 38)

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49
Q

What is the function of the “P” site of a ribosome?

A

The peptide grows here through a “tunnel” in the structure
(Lecture 1, Slide 38)

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50
Q

What is the function of the “A” site of a ribosome?

A

Aminoacyl-tRNA binds here, bringing in the next amino acid
(Lecture 1, Slide 38)

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51
Q

What is the function of the “E” site of a ribosome?

A

Functions as an exit site for empty tRNAs
(Lecture 1, Slide 38)

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52
Q

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

A

Met-tRNAi
(Lecture 1,Slide 39)

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53
Q

What 3 other things does met-tRNA form a complex with in order to help initiate translation?

A

Initiation factors
GTP
30S ribosomal subunit
(Lecture 1, Slide 39)

54
Q

What does the complex formed by met-tRNA , initiation factors, GTP and the 30S ribosomal subunit do to help initiate translation?

A

It “scans” the mRNA looking for an AUG initiation codon, using energy to do this
(Lecture 1, Slide 39)

55
Q

What 2 things does the met-tRNA, initiation factors, GTP and 30s ribosomal subunit recruit once it finds an AUG initiation codon, and what complex does this then form with it?

A

It recruits the remaining 50S ribosomal subunit, along with further initiation factors in order to form the 80S initiation complex
(Lecture 1, Slide 39)

56
Q

What does formation of the 80S initiation complex during translation result in?

A

Protein synthesis beginning
(Lecture 1, Slide 39)

57
Q

What are the 3 regulatory steps of transcription / translation?

A

Selective control of gene expression
Control of mRNA synthesis rates / stability / processing
Protein synthesis / degradation rates
(Lecture 1, Slide 42)

58
Q

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

A

RNA polymerase
(Lecture 2, Slide 7)

59
Q

When does mRNA capping occur?

A

When the pre-mRNA is ~ 25 nt long
(Lecture 2, Slide 8)

60
Q

What is required to cap the pre-mRNA?

A

Specific capping proteins
(Lecture 2, Slide 8)

61
Q

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

A

Endonuclease
(Lecture 2, Slide 9)

62
Q

What is present as mRNA is made?

A

An AAUAAA cleavage signal
(Lecture 2, Slide 9)

63
Q

What does endonuclease cleaving the phosphodiester bond when mRNA is being made allow?

A

Poly(A) polymerase to function
(Lecture 2, Slide 9)

64
Q

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

A

It adds a poly(A) tail to the pre-mRNA
(Lecture 2, Slide 9)

65
Q

Why is it called a poly(A) tail?

A

It is a polymer tail of multiple adenine nucleotides (A)n where n can be >250
(Lecture 2, Slide 9)

66
Q

What is the specific adenine which is key to splicing in every intron called?

A

The branch site
(Lecture 2, Slide 11)

67
Q

What do all introns end with?

A

AG
(Lecture 2, Slide 11)

68
Q

What do all introns begin with?

A

GU
(Lecture 2, Slide 11)

69
Q

What 2 things are present in every intron which are key to splicing?

A

There is a pyrimidine-rich tract (Py)n and a specific adenine key to splicing (branch site)
(Lecture 2, Slide 11)

70
Q

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

A

They recruit other proteins into a large complex called the spliceosome
(Lecture 2, Slide 12)

71
Q

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

A

It can capture, splice and release RNA accurately and in an co-ordinated way
(Lecture 2, Slide 12)

72
Q

What is the first step to RNA splicing?

A

Splicing proteins recognise 2 specific sites, the GU at the 5’ splice site and the branch site
(Lecture 2, Slide 12)

73
Q

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

A

A careful choreography of the spliceosome components
(Lecture 2, Slide 12)

74
Q

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

A

A lariat form
(Lecture 2, Slide 13)

75
Q

What is alternate RNA splicing?

A

A process where different mRNAs are generated from the same initial primary transcript
(Lecture 2, Slide 14)

76
Q

What can alternate RNA splicing result in?

A

Proteins with different functions being generated
(Lecture 2, Slide 14)

77
Q

Why can some RNA molecules self-replicate?

A

As it can fold into distinct structures, it has the capacity to act as an enzyme and splice itself
(Lecture 2, Slide 18)

78
Q

Which 2 people discovered that RNA could act as an enzyme and that it can splice itself?

A

Tom Cech and Sidney Altman
(Lecture 2, Slide 19)

79
Q

What is RNA interference (RNAi)?

A

It is a powerful tool to disrupt gene expression
(Lecture 2, Slide 20)

80
Q

How was RNAi discovered?

A

When double stranded RNA was introduced into a cell, it was found to suppress the transcription of genes that contained sequences present in the original double stranded RNA
(Lecture 2, Slide 20)

81
Q

What does RNA interference (RNAi) rely on?

A

The key activity of small interfering RNAs (siRNA’s)
(Lecture 2, Slide 20)

82
Q

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

A

To examine the function of a particular gene product
(Lecture 2, Slide 21)

83
Q

What are 3 potential uses of CRISPR?

A

Powerful tool to create cells lines to probe specific gene function
Can produce specific mutations in the germ line
Can be used in ex vivo and in vivo genome editing for clinical therapy
(Lecture 2, Slide 23)

84
Q

State 3 reasons why cells signal.

A

Co-ordination of day-to-day physiology
Regulate behaviours in multicellular organisms
Cells respond and change to stimuli in their environment
(Lecture 3, Slide 3)

85
Q

State 5 physiological activities that cell signalling regulates.

A

Answers include:
Cell metabolism
Cell growth
Cell division
Cell motility
Cell morphology
Cell death
Differentiation and development
Co-ordination of gene expression
(Lecture 3, Slide 4)

86
Q

What is intercellular signalling?

A

Communication between cells
(Lecture 3, Slide 5)

87
Q

What does intercellular signalling permit?

A

A single cell to influence the behaviour of other cells in a specific way
(Lecture 3, Slide 5)

88
Q

What is intracellular signalling?

A

Signalling within a single cell
(Lecture 3, Slide 5)

89
Q

What does intracellular signalling happen in response to?

A

Extracellular or intracellular stimuli
(Lecture 3, Slide 5)

90
Q

What is the autocrine intercellular signalling mechanism?

A

A cell targets itself
(Lecture 3, Slide 6)

91
Q

What is the paracrine intercellular signalling mechanism?

A

A cell targets a nearby cell
(Lecture 3, Slide 6)

92
Q

What is the endocrine intercellular signalling mechanism?

A

A cell targets a distant cell through the bloodstream
(Lecture 3, Slide 6)

93
Q

What is the juxtacrine intercellular signalling mechanism?

A

A cell targets a cell connected by gap junctions
(Lecture 3, Slide 6)

94
Q

Is cell signalling a linear process?

A

No.
(Lecture 3, Slide 7)

95
Q

What are the 4 major types of cell signalling receptor?

A

Ligand-gated ion channel receptors
G-protein coupled receptors
Kinase-linked receptors
Nuclear receptors
(Lecture 3, Slide 9)

96
Q

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

A

Different signals
(Lecture 3, Slide 10)

97
Q

What 3 biases can alter the kinetics of the response of cell signalling pathways?

A

Bias with the extracellular signal,
intracellular signal or
Both
(Lecture 3, Slide 10)

98
Q

What are signalosomes composed of?

A

Unique combinations of signalling pathway components
(Lecture 3, Slide 12)

99
Q

How are signalosomes targeted to discreet intracellular localisation?

A

Via the association of anchor or adaptor proteins
(Lecture 3, Slide 12)

100
Q

How adaptable and dynamic are signalosomes?

A

They are very adaptable and dynamic
(Lecture 3, Slide 12)

101
Q

What do signalosomes allow?

A

They allow cells to construct the optimum cellular subdomain for signalling
(Lecture 3, Slide 12)

102
Q

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

A

Intracellular compartments
(Lecture 3, Slide 13)

103
Q

Where are G-protein coupled receptors internalised to?

A

Endosomes and then trafficked to a pre-Golgi compartment
(Lecture 3, Slide 13)

104
Q

What is the purpose of compartmentalisation of cAMP signalling?

A

Cells needs a way to “turn off” signalling
(Lecture 3, Slide 14)

105
Q

What catalyses the breakdown of cAMP?

A

Phosphodiesterases
(Lecture 3, Slide 14)

106
Q

What can compartmentalisation of cAMP create?

A

Discreet cAMP gradients in the cytosol
(Lecture 3, Slide 14)

107
Q

Can cells have more than 1 cAMP gradient?

A

Yes
(Lecture 3, Slide 15)

108
Q

State in order from slowest to fastest, the typical times associated with the 4 major types of signalling pathway receptors.

A

Nuclear receptors (hours/days)
Kinase-linked receptors (hours)
G-protein coupled receptors (seconds)
Ligand-gated ion channel receptors (milliseconds)
(Lecture 3, Slide 16)

109
Q

How can one signal generate many responses?

A

Some cells have the same receptor as each other
(Lecture 3, Slide 17)

110
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
(Lecture 4, Slide 3)

111
Q

What do we mean by a gene being “expressed”?

A

That it is transcribed into mRNA leading to a production of the corresponding protein
(Lecture 4, Slide 3)

112
Q

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

A

Epigenetics
(Lecture 3, Slide 4)

113
Q

What is epigenetics?

A

Modifications to the genome that affect gene expression but do not alter the DNA sequence
(Lecture 3, Slide 5)

114
Q

What are CpGs?

A

A rare dinucleotide sequence
(Lecture 4, Slide 5)

115
Q

What does the p in CpG islands represent?

A

The phosphate residue on the DNA backbone
(Lecture 4, Slide 7)

116
Q

What is methylation associated with?

A

Gene silencing
(Lecture 4, Slide 7)

117
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
(Lecture 4, Slide 7)

118
Q

What are CpG islands?

A

Regions of the genome which have a high density of CpGs
(Lecture 4, Slide 9)

119
Q

Where are CpG islands mostly found?

A

The promoter region of genes
(Lecture 4, Slide 9)

120
Q

How do CpG islands alter the binding of transcription factors?

A

By undergoing chemical modification (methylation)
(Lecture 4, Slide 10)

121
Q

Is the cytosine or the guanine methylated in CpG?

A

The cytosine
(Lecture 4, Slide 11)

122
Q

How does methylation prevent the binding of transcription factors?

A

Methyl binding proteins bind to the methylated DNA which prevents the binding of transcription factors
(Lecture 4, Slide 12)

123
Q

What is a nucleosome?

A

A DNA / histone octamer complex
(Lecture 4, Slide 16)

124
Q

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

A

Chromatin
(Lecture 4, Slide 16)

125
Q

How many histone subunits form a histone octamer?

A

4
(Lecture 4, Slide 17)

126
Q

What happens after 4 histone subunits form an octamer?

A

DNA wraps around the octamer
(Lecture 4, Slide 17)

127
Q

What are the 2 chromatin states?

A

Euchromatin and heterochromatin
(Lecture 4, Slide 18)

128
Q

What are 3 differences between euchromatin and heterochromatin?

A

Euchromatin is loosely packed whereas heterochromatin is tightly packed.
Euchromatin is enriched in genes whereas heterochromatin is usually genetically inactive.
Euchromatin is under active transcript whereas heterochromatin cannot be accessed by RNA polymerase
(Lecture 4, Slide 18)

129
Q

What 2 things regulate chromatin state?

A

Methylation and acetylation of the histones
(Lecture 4, Slide 18)

130
Q

What are 2 ways in which epigenetic changes can lead to cancer?

A

Phosphorylation of a tumour suppression gene could inhibit gene expression.
Genes could be turned on by changing histone modification pattern
(Lecture 4, Slide 20)

BM 210: Introduction to Biochemistry (12 decks)

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