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GTS 351 > The Process Of Transcription And Translation > Flashcards

The Process Of Transcription And Translation Flashcards

1
Q

What is a major level of regulation

A

Transcription

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2
Q

Three sequential stages of transcription.

A
  1. Transcription initiation
  2. Transcript elongation
  3. Termination of transcription
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3
Q

Transcription initiation

A
  1. Requires open chromatin structure at the promoter region.
  2. Transcription factors locate and bind to short DNA control regions in promoter of genes.
  3. Transcription factors recruits RNA polymerase
  4. Additional activator and repressor Prots determine the level of transcription.
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4
Q

Genes transcribed by RNA polymerase 1

A

5.8S, 18S and 28S rRNA genes

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5
Q

Genes transcribed by RNA polymerase 2

A

All protein coding genes, plus snoRNA genes, miRNA genes, siRNA genes, IncRNA genes and most snRNA genes.

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6
Q

What genes do RNA polymerase 3 transcribe.

A

TRNA genes, 5S-rRNA genes, some snRNA genes and genes for other small RNAs.

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7
Q

Function of mRNA

A

Messenger RNA, code for proteins

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8
Q

Function rRNA

A

Ribosomal RNAs, form the basic structure of the ribosome and catalyse protein synthesis.

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9
Q

Function of tRNA

A

Transfer RNAs, central to protein synthesis as adaptors between mRNA and amino acids.

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10
Q

SnoRNAs

A

Small nucleolar RNAs, help to process and chemically modify rRNA’s.

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11
Q

SnRNA FUNCTION

A

Small nuclear RNA, function in a variety of nuclear processes, including the splicing of pre-mRNA.

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12
Q

MiRNA

A

MicroRNAs, regulate gene expression by blocking translation of specific mRNAs cause their degradation.

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13
Q

SiRNA

A

Small interfering RNAs, turn off gene expression by directing the degradation of selective mRNAs and the establishment of compact chromatin structure.

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14
Q

PiRNA

A

Piwi-interacting RNA, bind to piwi proteins and protect the germ line from transposable elements.

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15
Q

IncRNAs

A

Long non-coding RNAs, many of which serve as scaffolds, they regulate diverse cell processes, including X-chromosome inactivation.

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16
Q

Where does transcription initiation occur?

A

It Occurs at the TATA box, 30 bp upstream of +1 start site in promoter.

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17
Q

Function of TFIID

A
  1. It recognises and binds to the TATA box more specifically by the TBP *(TATA box binding protein) subunit of TFIID.
  2. This causes a dramatic distortion in DNA of the TATA box
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18
Q

Steps in binding of transcription factor to form the basal complex

A
  1. TFIID binds to TATA box
  2. TFIIA binds to TFIID
  3. Then TFIIB binds
  4. TFIIB binds to RNA polymerase 2
  5. TFIIF binds next
  6. Next TFIIE and TFIIH
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19
Q

Function of TFIIA

A

Helps to stabilise the TBP-DNA interaction

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20
Q

Function of TFIIB

A
  1. Recruits RNA pol2 in association with TFIIF.

2. Accurately positions RNA pol2 at the start site.

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21
Q

Function of TFIIH

A
  1. Unwinds DNA at the transcription start point
  2. TFIIH has kinase activity: it phosphorylase’s the C-terminal repeat domain (CTD) of RNA pol2 releasing RNA pol2 from the promoter.
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22
Q

Function of TFIIE

A

Attracts and regulates TFIIH

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23
Q

Function of TFIIF

A
  1. Stabilises RNA polymerase interaction with TBP and TFIIB.

2. Helps attracts TFIIE and TFIIH

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24
Q

What does PIC stand for

A

Pre-initiation complex

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25
Q

What is a holoenzyme

A

An enzyme in need of a coenzyme to function.

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26
Q

What Transcription factors make up TFIID.

A
  1. TBP: TATA-binding protein

2. TBP-associated factors (TAFs)

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27
Q

Function of TBP-associated factors (TAFs)

A

Allows TFIID to respond to activators.

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28
Q

What structure of the TFIID forms the groove that fits the DNA.

A

Molecular clamp structure

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29
Q

Function of Molecular clamp structure of the TFIID.

A

Domains form a groove that fits the DNA.

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30
Q

What is the structure of the TBP and how this affects the DNA.

A

TBP has a saddle -like structure and bends the DNA.

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31
Q

What terminus of the TBP do the transcription factors TFIIA and TFIIB bind to.

A
  1. TFIIA binds to N-terminus

2. TFIIB binds to C-terminus

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32
Q

How does the basal transcription factor open the chromatin structure.

A

One of the TAFs in the TFIID contains histone acetyltransferase- activity. It can acetylate histones to open chromatin structure.

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33
Q

How is initiation of transcription started.

A

RNA pol2 is phosphorylated by TFIIH at ser5.

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34
Q

Why does RNA pol2 pause after producing a short 20-30 nt

A

To cap the 5’ prime end of the mRNA.

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35
Q

After RNA pol 2 has paused what has to happen for elongation to continue.

A

RNA pol 2 needs further elongation. This is done by the 5’ cap which recruits pTEF-b kinase a enzyme that phosphorylase’s pol2 at Ser2.

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36
Q

What happens at termination of transcription.

A

The RNA is cleaved downstream of the AAUAAA and a poly-A-tail is added to the 3’ prime site.

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37
Q

Core/basal promoters and its relationship to transcription

A
  1. At minimum the core promoter is required for transcriptional initiation.
  2. Alone, they produce only low rate of transcription.
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38
Q

What does the core/basal promoter include.

A

TATA box and/or Inr element allows initial binding of TFIID and other general TFs.

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39
Q

Relationship of Upstream promoter element in the promoter element and transcription

A

Increase rate of transcription when activators bind

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40
Q

TATA box in the core promoter position?

A

-30

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41
Q

Inr or start site position

A

+1

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42
Q

Example of general control elements

A
  1. TATA
  2. CCAAT
  3. Sp1
  4. Inr
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43
Q

General control element

A
  1. Common to many promoters
  2. Are active in all cell types, but cause low rate of transcription .
  3. Some promoters have more than one of a particular elements.
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44
Q

Specific/ unique control elements

A
  1. Regulate the response to a specific regulatory signal.

2. Generally shared by a smaller set of genes (related function)

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45
Q

Examples of specific/unique control elements

A

Heat shock elements

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46
Q

Function of heat shock protein 70 (Hsp70)

A
  1. Heat shock protein assist in (A) correctly folding nascent protein, and (B) re-folding or degrading proteins that denature under heat stress.
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47
Q

What element is unique to heat -inducible genes

A

Heat shock element (HSE)

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48
Q

Heat shock elements (HSE)

A
  1. HSE is recognised by a heat shock factor protein (HSF)

2. HSE allows these genes to respond to elevated temps, via increased transcription of these genes.

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49
Q

HSF stands for

A

Heat shock factor protein

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50
Q

Steps of inducing transcription by heat induction .

A
  1. In-un-induced cells: TFIID is bound to TATA, GAGA protein is bound to its element. This causes nucleosome displacement and opens the chromatin structure. Gene is ready to be activated.
  2. When heat is induced: HSF binds to HSE activating transcription.
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51
Q

HSF state before heat shock and after heat shock.

A

HSF is pre-formed protein, but its inactive form (monomers) in the cytoplasm of the cell. Heat induction changes its shape becomes a trimmer and allows binding to HSE.

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52
Q

Common characteristics of DNA cis elements

A
  1. Can be short (4bp) or long (>100bp), but. Typically 6-18bp
  2. Their orientation relative to a gene generally does not matter
  3. Many occur as (semi) palindromes
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53
Q

Some ways to identify and characterise regulatory elements.

A
  1. Identify the different regulatory elements of a specific promoter?
  2. Measure the specificity/ activity of any promoter elements?
  3. Finding which proteins bind to promoters elements?
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54
Q

Experiments to identify and characterise regulatory elements.

A
  1. Reporter
  2. Deletion mutation analysis
  3. Mobility shift assay
  4. ChIP analysis
  5. DNase 1 foot printing
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55
Q

How do regulatory elements activate transcription .

A
  1. DNA-binding protein causes altered chromatin structure.
    Or
  2. DNA-binding protein directly activates transcription.
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56
Q

DNA-binding protein causes altered chromatin structure.

A

TF binding causes nucleosome displacement, this unmasks other DNA binding sites.

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57
Q

DNA -binding protein directly activates transcription.

A

Protein binds and interacts with other proteins at promoter, this causes formation of stable PIC which increases transcription.

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58
Q

Importance of receptors.

A

A particular receptor is specific for a particular hormone, Cells have multiple receptors for different hormones. Some hormones have more than one type of receptor. Presence of a receptor is necessary for response in cell.

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59
Q

General characteristics of enhancers

A
  1. Increases transcription dramatically
  2. From a far distance (>50 kb away)
  3. Enhances activity in either orientation relative to a promoter.
  4. Can occur upstream, downstream or within transcription unit.
  5. Many enhancers are cell or tissue type specific
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60
Q

Mechanism of action of enhancers.

A

Enhancers share sequences similar and different to element of promoters. Regulatory proteins bind to enhancer sequences working together to enhance gene activation.

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61
Q

What are clusters of enhancer elements, together with the different proteins that assemble on enhancers called?

A

Enhanceosome

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62
Q

The role of enhanceosomes

A

Enhancers upregulate transcription by increasing the concentration of transcription factors in the vicinity of promoters.

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63
Q

What mechanism do enhancer elements and promoter elements have in common.

A
  1. Can change the chromatin structure, leading to nucleosome displacement and formation of hypersensitive sites.
  2. Can directly interact with proteins of the basal transcription complex.
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64
Q

Models for enhancer action.

A
  1. Activator proteins bind to enhancer, triggering DNA bending.
  2. Activators interact with coactivators to stimulate chromatin remodelling and histone acetylation.
  3. Activators bind to mediator, triggering assembly of RNA polymerase and general transcription factors at the promoter site.
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65
Q

How binding of activator protein to enhancer can recruit basal transcription complex and start transcription.

A
  1. Activator protein will bind and recruit the basal transcription complex.
  2. When the cell receives a signal, basal complex is then transferred to the promoter to initiate transcription by the looping /bending of the DNA
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66
Q

What type of histone modification is common in enhancer sequences.

A

H3K4me1 rather than H3K4me3 is more common in enhancers than promoters.

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67
Q

General characteristics of silencers

A
  1. Elements(on the DNA) that recruit proteins that act in an entirely negative manner.
  2. Act on promoter over great distance. In either orientation
  3. Mode of action is similar to that of enhancers
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68
Q

Action of silencers

A
  1. Silencers can recruit proteins that direct a closed chromatin conformation in the region of the gene
    Or
  2. Silencers can recruit proteins that directly inhibit transcription, by interacting with RNA pol and associate Transcription factor.
69
Q

Example of a protein that binds to a silencer

A

Polycomb transcription factor.

70
Q

How do polycomb Transcription factor work?

A
  1. Binding of polycomb to silencer element recruits a histone methyltransferase enzyme .
  2. The enzyme methylates histones, hence resulting in tightly packed chromatin .
71
Q

Function of PRC2

A

Has histone methyltransferase activity, establishes H3K27me3 reversibly.

72
Q

Function of PCR1

A

PRC1 recognises and binds to H3K27me3 and results in stable chromatin compaction.

73
Q

What do activator proteins bind to and how do they work?

A

The activator protein binds to the enhancer.
When they bind they cause the DNA to bend, bringing them near a gene promoter, even though they may be thousands of base pairs away.

74
Q

What protein has to bind to promoter region to stop the enhancer region from binding.

A

CTCF this protein reacts with the insulator region.

75
Q

How does methylation stop the effects of an insulator.

A

The addition of A methylated group to the cytidine prevents CTCF from attaching to the insulator, turning it off, allowing the enhancers to bind to the promoter.

76
Q

What are the characteristics of transcription factors.

A
  1. DNA-binding domain

2. Regulatory domain ( activation- or repressor domain)

77
Q

Define the DNA binding domain of the transcription factor.

A

They recognise and bind to specific DNA control elements, usually only one per Transcription factor.

78
Q

Define the regulatory domain of the transcription factor.

A

They interact directly with other proteins to stimulate/ repress transcription of a promoter. There may be more than one per transcription factor.

79
Q

Define a motif.

A

Alpha -helix and beta-sheets associate, with loops that connect them.

80
Q

Define a domain.

A

Different motifs bind to each other form a tertiary structure, has a specific molecular function.

81
Q

What is DNA affinity chromatography used for?

A

screening for clone containing appropriate TF gene

82
Q

The principle of DNA affinity chromatography.

A

Purify transcription factors by making use of the fact that it binds very specifically to its DNA-binding site.

83
Q

Requirements for DNA affinity chromatography.

A
  1. Nucleotide sequence of specific DNA-binding site of transcription factors.
  2. Need to obtain a small amount of purified Transcription factors
84
Q

Basic steps of DNA affinity chromatography.

A
  1. Protein extract is loaded onto a column containing resin.
  2. A DNA oligo ligand is attached to the resin.
  3. The ligand will bind target transcription factor, all other non-specific proteins pass through.
  4. Elution: Wash out the transcription factor with a solvent.
  5. Sequence the Transcription factor and compare to know TF on databases.
85
Q

Types of DNA-binding domains

A
  1. Helix-turn helix motif
  2. Homeodomain
    .3. Zinc fingers
  3. Leucine zipper domain
  4. Helix-loop-helix domain
86
Q

What in the binding domain enables it to very specifically recognise and bind to nucleotides of a specific DNA element.

A

Amino acids

87
Q

Which is one of the most common structural domains.

A

Helix turn-helix

88
Q

Structure of the helix-turn helix motif.

A
  1. Consists of two alpha-helixes that are connected by a short chain of amino acids that form a beta-sheet turn.
  2. The two alpha-helixes are held at a fixed angle.
89
Q

Which part of the helix-turn-helix motif is responsible for nucleotide-specific recognition.

A

One alpha-helix

90
Q

Where does the the helix-turn helix motif attach to the DNA.

A

They lie across a major groove.

91
Q

Characteristics of the helix-turn-helix motif.

A
  1. Helix helps to position the recognition helix correctly and stabilises it.
  2. Transcription factors with this domain bind to DNA as homodimers.
  3. Additional motifs or regulates
92
Q

What do homeotic genes encode?

A

They encode homeotic transcription factors.

93
Q

What is the homebox that is found in the homeotic gene.

A

It is a coding nt sequence within the homeotic genes. It is a 180bp region with sequence homology amongst all homeotic genes

94
Q

What is the Homeobox domain.

A

It is a domain that consists of 60 amino acid that folds as a helix-turn-helix structure., responsible for DNA binding.

95
Q

Homeotic genes play an important role in what part of development.

A

Early embryonic development

96
Q

What are Hox genes

A

A subset of homebox genes, are a group of related genes that specify regions of the body plan of an embryo along the head tail axis of animals.

97
Q

What happens when there is inactivation/mutations in homeotic genes.

A

Homeotic genes encode transcription factors that are used in the synthesis of proteins used in the body plan of an embryo along the head-tail axis of animals. If there is a mutation in these genes there will be incorrect development in the animal.

98
Q

Example of inactivation/ mutation in these genes.

A

Ectopic expression of Antennapedia (required for normal leg development) in the head resulting in legs in the place of antennae.

99
Q

Zinc finger motifs: Cys2-His2

A
  1. Zink finger motif is approximately 30aa in length.
  2. Classic zinc finger has 2 cysteine and 2 histidine (Cys2-His2)a arranged so that they can bind a single zinc atom.
  3. Has a looped amino acid chain held together at the stem by a zinc atom.
100
Q

How does the four cysteine zinc fingers differ from the conventional zinc fingers

A

The cysteine zinc fingers look like two conventional zinc fingers but the His are replaced with Cys.

101
Q

What is the 1st finger of the four cysteine zinc finger domain used for .

A

It binds to DNA

102
Q

What is the 2nd finger of the four cysteine zinc finger domain used for .

A

It modulates binding of the domain

103
Q

What is an example of DNA that have Cys4 zinc fingers as DNA binding domain.

A

Steroid-thyroid hormone receptor family of transcription factors.

104
Q

Why would DNA that encodes for a transcription factor also contain hormone binding domains.

A

The hormone binding domain ensures that the transcription factor is only transcribed when the hormone is present.

105
Q

What happens when hormone binding domains are swapped between receptors.

A

The transcription factors that are up regulated by the presents of one hormone will now be controlled by another hormone. Example Glucose binding domain attached to a DNA-binding domain of oestrogen receptor . Therefore glucose now controls the transcription of transcription factors that are associated with genes that are associated with oestrogen.

106
Q

What change in the zinc finger can alter the specificity of a transcription factor and its ability to activate gene

A

Changes in the amino acids

107
Q

Changes in the amino acids of a zinc finger can result in?

A

The alteration of specificity of a transcription factor and its ability to activate genes.

108
Q

How does the leucine zipper binding domain motif work.

A

The two DNA-binding domains of the dimeric protein are also alpha helixes “grip” the DNA like a pair of scissors, very tight binding.

109
Q

Where does the leucine zipper occur relative to the DNA binding domain.

A

The leucine zipper occurs at the C-terminal side.

110
Q

Interaction between transcription factors increase gene control by?

A
  1. The binding of homodimers and heterodimers that allow different binding strengths to the same element.
  2. An example of this is the Jun-Fos leucine zipper, the Jun-Fos heterodimer binds to the same recognition site as the homodimer, but with 30-fold greater affinity.
111
Q

Heterodimerisation allows for transcription factors to do what?

A

It allows for them to increase the number of DNA sequences/ promoters, transcription factors can recognise.

112
Q

Structure of helix-loop-helix motif

A

Consists of a short alpha helix connected by a loop to a second longer alpha helix.

113
Q

Why do leucine zippers come in dimer formation.

A

Dimerisation modifies the transcription structure, so that DNA binding domain can directly interact with DNA.

114
Q

What formation do helix-loop-helix motifs come in and what is the function of this formation.

A
  1. This motif can only bind in the form of dimers.

2. Dimerisation facilitates binding to DNA via adjacent DNA-binding motif

115
Q

In what ways can the activation domains of transcription factor initiate

A
  1. Directly interact with basal transcription complex at TATA box.
  2. Facilitate binding of other transcription factor and thereby activate transcription indirectly.
116
Q

Why are Transcriptional factors modular?

A

Make it possible to exchange domains between different transcription factors using recombinant techniques.

117
Q

How to identify/map an activation domain?

A
  1. Generate hybrid transcription factors in which DNA-binding domain of known Transcription factor 1 is linked to unknown regions of transcription factors 2.
  2. Evaluate which of these hybrids can activate transcription of gene X that has DNA-binding domain for transcription factor 1.
  3. Hybrids will all bind to DNA-binding domain of gene recognised by transcription factor 1 but only hybrid with appropriate activation domain of transcription factor 2 will activate expression.
118
Q

Different classes of activation domains.

A
  1. Acidic region
  2. Glutamine-rich region
  3. Proline-rich region
119
Q

Activator binds to an activator binding site in promoter of gene can?

A
  1. Stimulate assembly of basal transcription complex or

2. Increase activity of the already assembled complex.

120
Q

Overall effect of activator?

A

Enhances activity of the basal transcription complex

121
Q

What is the first target for activation is …

A

TFIID

122
Q

How does activator affect the rate of assembly.

A
  1. It enhances binding of TFIID to TATA box which improves assembly rate.
  2. This allows binding of other required transcription factors.
123
Q

How does the activator alter conformation of TFIID.

A
  1. Interaction with activator changes shape of TFIID.

2. Increases its ability to recruit other Prots or enhances stability of basal complex.

124
Q

Activator can interact either.

A
  1. Directly with TATA-box binding protein (TBP)

2. Or indirectly with TATA-box binding protein via TAFs.

125
Q

Which type of TAFs do acidic activator target.

A

They target TAFII31

126
Q

Which type of TAFs do glutamine-rich activator target.

A

It activates TAFII110

127
Q

Which type of TAFs do proline -rich activator target.

A

TAFII55

128
Q

Why would activators target TFIIB.

A

So that components of basal transcription complex can bind more efficiently which will increase efficiency of the transcription complex.

129
Q

How do activators interact with the RNA pol if they do not directly interact with the RNA pol.

A
  1. The activators bind to mediator complex that binds to the C-terminal domain of the RNA pol.
  2. Binding to the mediator allows mediator to receive signals from activators and transmits it to RNA polymerase which enhancers transcription.
130
Q

How does the binding of the activator to the mediator cause activation of transcription.

A
  1. Activators may stimulate the ability of the mediator to interact with TFIIH.
  2. TFIIH is a kinase that phosphorylates the C-terminal domain (CTD) of the polymerase.
  3. This phosphorylation is essential to start transcription.
131
Q

Function of mediator?

A

The mediator acts as a ‘gatekeeper’ to consolidate all these signals and then the overall signal to basal transcription complex, to either activate or repress transcription initiation.

132
Q

Why do activators and repressors act on mediator and not directly with the RNA pol.

A

Provides a better/tighter control to the regulation of genes.

133
Q

Define Co-activator

A

Protein that does not itself bind DNA, but assembles on other DNA-bound regulatory Prots to activate transcription of a gene.

134
Q

What is a common well known co-activator.

A

CREB-binding protein (CBP)

135
Q

What protein does CREB-binding protein bind to and what is its function.

A
  1. CBP binds to the CREB transcription factor but only if CREB has been phosphorylated.
  2. Function : plays an important role to activation transcription by binding to a wide variety of transcription factor activators.
136
Q

By mechanisms do co-activators act?

A
  1. Linking activator to basal transcription complex.

2. Promoting chromatin from closed to an open structure.

137
Q

How does the co-activator link the activator to basal transcription complex.

A

CBP interacts with TATA-binding protein, TFIIB and RNA pol II

138
Q

How does the co-activator promote chromatin from closed to an open structure.

A

CBP has histones-acetyl-transferase activity.

139
Q

Explain the Synergistic effect of binding of more than one activator.

A

Activation is much stronger than the binding of either factor alone.

140
Q

Activators can act synergistically by interacting with:

A
  1. Mediators complex
  2. Different TAFs within TFIID
  3. HAT enzymes
  4. Chromatin-modifying complexes such as SW1/SNF
141
Q

What functional domain do transcriptional factor that repress transcription have.

A

DNA binding domain and repression domain.

142
Q

Repressors can act by different mechanisms to either:

A
  1. Indirectly inhibit the positive effect of An activator or

2. Direct inhibit the function of the basal transcription complex

143
Q

Ways in which repressors can inhibit transcription.

A
  1. Repressor causes a closed chromatin structure, meaning activator cannot bind.
  2. Activator cannot bind due to occupancy of its binding site.
  3. Activator bound to repressor in solution therefore unable to bind to DNA
  4. Activity of activator neutralised by repressor
  5. Activator degraded but repressor
  6. Direct repression
144
Q

What is MDM2 ?

A

A transcription factor with ubiquitin ligase activity.

145
Q

Examples of degration of activators by repressors.

A
  1. MDM2 repressor binds to p53 activator, causes its ubiquitination and target p53 for degradation by a protease (P).
  2. Repressor AEBP1 binds to activator and degrades activator directly.
146
Q

What is AEBP1

A

A transcription factor with protease activity.

147
Q

What is erbAalpha ?

A

It is thyroid hormone receptor that regulates transcription of thyroid responsive genes.

148
Q

What happens to transcription of the thyroid responsive genes in the absence of thyroid hormone.

A

Inhibitory domain of erbAalpha recruits a co-repressor (CoR) that inhibits assembly of PIC (promoter initiation complex) on promoter which inhibits transcription.

149
Q

What happens to transcription of the thyroid responsive genes in the presence of thyroid hormone.

A

ErbAalpha undergoes conformational change. This releases CoR and leads to binding of a co-activator (CoA) that allows assembly of PIC (promoter initiation complex) on promoter therefore transcription is initiated.

150
Q

For most genes, expression levels are regulated at what stage of transcription

A

Initiation stage

151
Q

The regulation at level of transcription initiation is related to?

A

It’s related to the number of RNA polymerase molecules transcribing a gene. Therefore the more RNA pol complexes = more transcripts

152
Q

Example of cases where transcription is regulated at elongation stage.

A

RNA pol 2 is selectively inhibited during elongation of the c-myc oncogene in differentiated cells.

153
Q

Why is c-myc expression in undifferentiated cells 10x higher than in differentiated cells.

A

Because in differentiated cells functional full length transcripts are not produced and this is caused by polymerase pausing that prevents elongation from taking place in differentiated cells.

154
Q

What is the function of a super elongation complex (sec).

A

The sec has pTEF-b kinase activity, which phosphorylase’s CTD of RNA pol to stimulate elongation.

155
Q

How does the c-Myc oncogene over come the pausing of elongation?

A
  1. A super Elongation complex (SEC) can be recruited to c-myc promoter by a mediator .
  2. SEC has pTEF -b kinase activity, which phosphorylates CTD of the RNA pol2 to stimulate elongation.
156
Q

Transcriptional elongation also a factor in HIV infection

A
  1. After reverse transcription, HIV genome integrates into host cell genome.
  2. Viral genes begin transcription, but pause shortly after transcription is initiated.
  3. Tat viral protein recruits SEC-pTEF -b complex to phosphorylate stalled RNA pol 2 complex.
157
Q

Abortive Transcription

A

RNA polymerase is synthesising very short transcripts in the beginning of transcription, usually less than ten nucleotides. This is because the RNA poly needs enough energy to overcome the forces of the promoter.

158
Q

What amino acids are found in activation domains.

A

Asp- D
Glutamate - E
Glutamine - Q
Proline- P

159
Q

What amino acids are commonly found in DNA binding domains

A

Basic amino acids
Arginine- R
Histidine - H
Lysine -K

160
Q

Where does translation of mRNA take place?

A

On a cytoplasmic ribosome

161
Q

Breakdown the physical structure of a eukaryotic ribosome.

A
  1. Eukaryotic ribosome weighs 80s
  2. 80s ribosome has 2 subunits = 60s large subunit and 40s small subunit
  3. 60s consists of ribosomal RNA and 49 ribosomal proteins
  4. 40s consists of ribosomal RNA and 33 ribosomal proteins
162
Q

Mechanism of translational initiation.

A
  1. ELF4E binds to the cap structure of the mRNA this is followed by the binding of Elf4A and ElF4G to ELF4E forming the ELF4F complex.
  2. The elf4f complex is then recognised by a complex consisting of the 40s ribosomal subunit, the initiator tRNA and elf2.
  3. The 40s subunit then migrates along the RNA until it reaches the initiator AUG codon/ start codon.
  4. The elf2 is released and then the 60s large ribosomal subunit binds to the 40s small ribosomal subunit.
  5. Initiator tRNA bearing a methionine amino acid to the AUG codon in the P-site of the ribosome.
163
Q

Mechanism of translation elongation.

A
  1. A second tRNA is recruited in association with the eEF1, binds to the next codon in the A site of the ribosome via its corresponding anticodon.
  2. A peptide bond is formed between the methionine and the next amino acid, the elongation factor eEf2 then initiates translocation of the ribosome 3 bases along the mRNA and the first tRNA moves to the E site of the ribosome and is released and the tRNA carrying the peptide chain to the P site.
  3. The cycle then repeats itself with a new tRNA being recruited to the next three bases, with consequent peptide bond formation producing a 3-amino acid peptide.
164
Q

Explain the wobble hypothesis

A

The partial degeneracy of the genetic code due to the fact that some t-RNA molecules can recognise more than one codon.

165
Q

What are the three stop codons and what recognises these stop codons.

A
  1. The 3 Stop codons= UAA, UAG, UGA
  2. They are not recognised by a specific tRNA but rather a release factor (eRF1) )which catalyses the release of the completed polypeptide from the ribosome.
166
Q

Mechanism of translation termination

A
  1. The stop codon recruits the binding of release factor eRF1 that binds to the A site in the ribosome.
  2. As there is no amino acid in the A site, a water molecule is added to the end of the peptide chain which is bound at the P site.
  3. This causes the release of the peptide chain and tRNA from the ribosome and the termination of translation.
167
Q

In what situations do release factors bind to codons that are not stop codons.

A

This happens when the wrong tRNA is bound in error by the mRNA resulting in a codon-anticodon mismatch in the A-site. This results in the insertion of an incorrect amino acid into the protein.

168
Q

The function of PABP.

A
  1. The PABP protein binds to the poly(A) tail of the mRNA and interacts with the eLF4G factor bound at the 5’ end.
  2. This circularises the mRNA and facilitates re-initiation of protein synthesis by ribosomes which have dissociated at the 3’ end of the mRNA.
  3. There are multiple ribosomes on one circular mRNA at a time.

GTS 351 (9 decks)

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