18 Regulation of Gene Expression Flashcards
KEY CONCEPTS 18.1 Bacteria often respond to environmental change by regulating transcription 18.2 Eukaryotic gene expression is regulated at many stages 18.3 Noncoding RNAs play multiple roles in controlling gene expression 18.4 A program of differential gene expression leads to the different cell types in a multicellular organism 18.5 Cancer results from genetic changes that affect cell cycle control (185 cards)
1
Q
What are some basic reasons that regulation of gene expression is important?
A
- Differentiation and Development of tissues
- Prevents enzyme being produced in the absence of substrate
- Organism won’t produce an amino acid if it already present readily
2
Q
What are some basic reasons that regulation of gene expression is important?
A
- Differentiation and Development of tissues
- Prevents enzyme being produced in the absence of substrate
- Organism won’t produce an amino acid if it already present readily
3
Q
What does ’biosynthesis’ refer to?
A
The producing of organic molecules by biological organisms
4
Q
What is an example of a concept of gene expression regulation?
A
The operon
5
Q
In what organisms are operons found?
A
Only bacteria
6
Q
How do operons work?
A
They have an ‘operator’ in the promoter region which can selectively prevent the RNA polymerase from passing and thus prevents transcription.
The ‘operator’ prevents transcription only when it is bound to a ‘repressor’
Past the ‘operator’ are a group of genes which code for related functions.
This entire length of DNA consisting of the promotor (includes the ‘operator’) and the related genes is collectively called the ‘operon’
7
Q
What is it called when multiple genes are simultaneously regulated?
A
Those genes are ‘coordinately controlled’
8
Q
What does ’coordinately controlled’ refer to?
A
Gense whose expression is simultaneously regulated.
For example all the genes of the operon are co-ordinately controlled.
9
Q
What does ’trp operon’ refer to?
A
A operon found in many bacteria which regulates the production of the amino acid ’tryptophan’
10
Q
What does ’regulatory gene’ refer to?
A
A gene which codes for a protein which regulates gene expression
11
Q
What is a gene which regulates the expression of others called.
A
A ‘regulatory gene’
12
Q
What are the basic types of operons?
A
’Repressible operons’ and ‘inducible operons’
13
Q
What are ‘repressible operons’ and how are they regulated?
A
In repressible operons the ‘repressor’ is transcribed form the ‘regulatory gene’ in its inactive form. Therefore the ‘operator’ region remains unbound and thus transcription occurs unimpeded.
If a ‘corepressor’ is present it binds to the ‘repressor’ aden thus activates it. This allows the repressor to binds to the operator region and thus transcription is halted.
Eventually the active repressor degrades. Therefore if the corepressor is removed the newly formed repressors will not be activated and thus transcription will resume
14
Q
What class of proteins are the repressors of operons?
A
‘Allosteric proteins‘
15
Q
What are ‘inducible operons’ and how are they regulated.
A
The ‘repressor’ is transcribed from the ‘regulatory gene’ in its active form.
Therefore only when an ‘inducer’ binds to the repressor and inactivates is the operator cleared and thus transcription of the operon allowed to continue
16
Q
What does ’inducer’ refer to?
A
A substance which binds to the repressor to inactivate it.
Therefore their presence allows the transcription of the genes of a inducible operon.
17
Q
What does ’co-repressor’ refer to?
A
A substance which binds to a repressor and thus activates it.
This allows the repressor to bind to the operator and thus transcription is prevented in ‘repressible operons’
18
Q
What are the factors which allosterically prevent transcription of operons called?
A
‘Corepressors’
19
Q
What are the factors which allosterically stimulate transcription of operons called?
A
‘Inducers’
20
Q
What are ‘repressible operons’ typically involved in?
A
Anabolic pathways i.e. biosynthesis.
This is because they can prevent wasting resources on building substances which are already abundant if those end products act as ‘corepressor’
21
Q
What are ‘inducible operons’ typically involved in?
A
Catabolic pathways i.e. the breakdown of substrates.
This is because only when the substate is present will it stimulate the transcription of genes to break it down.
22
Q
What is a further method of regulating operons?
A
The use of ‘activators’
23
Q
How do activators stimulate transcription?
A
When activated they bind to the DNA in the promoter region. This increases the affinity of the DNA to the RNA polymerase. This encourages it to bind more regularly and thus transcription rate increases
24
Q
What is the use of activators in the regulation of gene expression called?
A
‘Positive gene control’
25
What does ’positive gene control’ refer to?
The use of ‘activators’ to affect gene expression
26
What does ’activators’ refer to?
Substances which affect gene expression through ‘positive gene expression'
27
What is a specify example of an operon?
The ‘lac operon'
28
What is the lac operon control?
An inducible operon which causes the release of enzymes involved in the metabolism of lactose.
The inducer it uses is ‘allolactose’ which is an alternative form of lactose.
If the glucose levels in the cell are low, cAMP is produced. This activates a catabolite activator protein (CAP) which binds to the promoter region and thus increases the rate of transcription.
This form of ‘positive gene control’ is important as it ensures that the enzymes to break down lactose are not produced if both glucose and lactose are present.
29
If no ‘activator’ binds to the promoter region during ‘positive gene control’, can transcription still occur?
Yes albeit at a slower rate.
30
What is an analogy for the repressor/inducer’s affects on an operon versus an activator during positive gene control?
The repressors are like on-off switches which turn the operon on or off i.e transcription either occurs or doesn’t
Transcription can occur even if the activator is not present. Therefore ‘positive gene control’ is more like a volume switch of transcription.
31
What does ’biosynthesis’ refer to?
The producing of organic molecules by biological organisms
32
What is an example of a concept of gene expression regulation?
The operon
33
In what organisms are operons found?
Only bacteria
34
How do operons work?
They have an 'operator' in the promoter region which can selectively prevent the RNA polymerase from passing and thus prevents transcription.
The ‘operator’ prevents transcription only when it is bound to a ‘repressor'
Past the ‘operator’ are a group of genes which code for related functions.
This entire length of DNA consisting of the promotor (includes the 'operator’) and the related genes is collectively called the ‘operon'
35
What is it called when multiple genes are simultaneously regulated?
Those genes are ‘coordinately controlled'
36
What does ’coordinately controlled’ refer to?
Gense whose expression is simultaneously regulated.
For example all the genes of the operon are co-ordinately controlled.
37
What does ’trp operon’ refer to?
A operon found in many bacteria which regulates the production of the amino acid ’tryptophan'
38
What does ’regulatory gene’ refer to?
A gene which codes for a protein which regulates gene expression
39
What is a gene which regulates the expression of others called.
A 'regulatory gene'
40
What are the basic types of operons?
’Repressible operons’ and ‘inducible operons'
41
What are ‘repressible operons’ and how are they regulated?
In repressible operons the ‘repressor’ is transcribed form the ‘regulatory gene’ in its inactive form. Therefore the ‘operator’ region remains unbound and thus transcription occurs unimpeded.
If a ‘corepressor’ is present it binds to the ‘repressor’ aden thus activates it. This allows the repressor to binds to the operator region and thus transcription is halted.
Eventually the active repressor degrades. Therefore if the corepressor is removed the newly formed repressors will not be activated and thus transcription will resume
42
What class of proteins are the repressors of operons?
‘Allosteric proteins‘
43
What are ‘inducible operons’ and how are they regulated.
The ‘repressor’ is transcribed from the ‘regulatory gene’ in its active form.
Therefore only when an ‘inducer’ binds to the repressor and inactivates is the operator cleared and thus transcription of the operon allowed to continue
44
What does ’inducer’ refer to?
A substance which binds to the repressor to inactivate it.
Therefore their presence allows the transcription of the genes of a inducible operon.
45
What does ’co-repressor’ refer to?
A substance which binds to a repressor and thus activates it.
This allows the repressor to bind to the operator and thus transcription is prevented in ‘repressible operons'
46
What are the factors which allosterically prevent transcription of operons called?
‘Corepressors'
47
What are the factors which allosterically stimulate transcription of operons called?
‘Inducers'
48
What are ‘repressible operons’ typically involved in?
Anabolic pathways i.e. biosynthesis.
This is because they can prevent wasting resources on building substances which are already abundant if those end products act as ‘corepressor'
49
What are ‘inducible operons’ typically involved in?
Catabolic pathways i.e. the breakdown of substrates.
This is because only when the substate is present will it stimulate the transcription of genes to break it down.
50
What is a further method of regulating operons?
The use of ‘activators'
51
How do activators stimulate transcription?
When activated they bind to the DNA in the promoter region. This increases the affinity of the DNA to the RNA polymerase. This encourages it to bind more regularly and thus transcription rate increases
52
What is the use of activators in the regulation of gene expression called?
‘Positive gene control'
53
What does ’positive gene control’ refer to?
The use of ‘activators’ to affect gene expression
54
What does ’activators’ refer to?
Substances which affect gene expression through ‘positive gene expression'
55
What is a specify example of an operon?
The ‘lac operon'
56
What is the lac operon control?
An inducible operon which causes the release of enzymes involved in the metabolism of lactose.
The inducer it uses is ‘allolactose’ which is an alternative form of lactose.
If the glucose levels in the cell are low, cAMP is produced. This activates a catabolite activator protein (CAP) which binds to the promoter region and thus increases the rate of transcription.
This form of ‘positive gene control’ is important as it ensures that the enzymes to break down lactose are not produced if both glucose and lactose are present.
57
If no ‘activator’ binds to the promoter region during ‘positive gene control’, can transcription still occur?
Yes albeit at a slower rate.
58
What is an analogy for the repressor/inducer’s affects on an operon versus an activator during positive gene control?
The repressors are like on-off switches which turn the operon on or off i.e transcription either occurs or doesn’t
Transcription can occur even if the activator is not present. Therefore ‘positive gene control’ is more like a volume switch of transcription.
59
What are the fundamental ways proteins are modified?
Cleaved, chemical modification i.e the addition of carbohydrates.
60
What are the basic ways in which gene expression in Eukaryotes is regulated?
Regulation of the chromatin structure, regulation of Transcription Initiation and methods of Post-Transcriptional regulation.
61
What are the basic ways the regulation of chromatin structure affects DNA expression?
Histone modification, DNA Methylation and Epigenetic inheritance.
62
Besides affecting histone tails, how does acetylation affect gene expression?
Some enzymes that acetylate or deacetylate histones are closely associated with or even components of the transcription factors that bind to promoters.
This suggest that histone acetylation enzymes also promote transcription by binding to and thus “recruiting” components of the transcription machinery.
63
What are the basic stages of gene expression in eukaryote?
Chromatin Modification forms transcriptable DNA, then:
Transcription → RNA processing → Transport to Cytoplasm → Translation → Protein Processing → Transport to cellular destination.
64
Where does Transcription occur in Eukaryotes?
Nucleus
65
Where does RNA Processing occur in Eukaryotes?
Nucleus
66
Where does Translation occur in Eukaryotes?
Cytoplasm (free ribosomes) or on E.R. (bound ribosomes)
67
What are the fundamental ways proteins are modified?
Cleaved, chemical modification i.e the addition of carbohydrates.
68
Why is the regulation gene expression particularly important in multicellular organisms?
It allows “differential gene expression” where the gene dosage can be adjusted to lead to specialised cells or for temporal fluctuations i.e. puberty.
69
What is it called when the rates of gene expression varies between cells?
“Differential gene expression"
70
What does ’differential gene expression’ refer to?
The expression of different genes by cells with the same genome.
71
What are the basic ways in which gene expression in Eukaryotes is regulated?
Regulation of the chromatin structure, regulation of Transcription Initiation and methods of Post-Transcriptional regulation.
72
What are the purposes of DNA packing?
It ensures the DNA fits in the nucleus and helps alter gene expression
73
What are the basic ways the regulation of chromatin structure affects DNA expression?
Histone modification, DNA Methylation and Epigenetic inheritance.
74
What are the basic ways in which histone modification can lead to the regulation of gene expression?
'Histone acetylation', ‘histone methylation’ and the phosphorylation.
75
What is the structure of a acetyl group?
-COCH3
76
What is the structure of a methyl group?
-CH3
77
What is histone acetylation and how does it regulate gene expression?
The addition of acetyl (COCH3) groups to lysines in histone tails. Deacetylation is the removal of these groups.
When the lysines are acetylated, their positive charges are neutralised so the histone tails no longer bind to neighbouring nucleosomes. This promotes the folding of chromatin into a more compact structure.
This folded structure makes the DNA less accessible for transcription so acetylation inhibits gene expression.
78
Besides affecting histone tails, how does acetylation affect gene expression?
Some enzymes that acetylate or deacetylate histones are closely associated with or even components of the transcription factors that bind to promoters.
This suggest that histone acetylation enzymes also promote transcription by binding to and thus “recruiting” components of the transcription machinery.
79
What is histone methylation and how does it regulate gene expression?
The addition of Methyl groups (CH3) to histone tails which promotes condensation of chromatin and thus inhibits transcription
80
What is histone phosphorylation and how does it regulate gene expression?
The addition of phosphate groups to an amino acid next to a methylated amino acid.
This prevents chromatin packing and thus promotes gene expression.
81
What theory explains how the various histone modifications regulate gene expression?
The 'histone code hypothesis'
82
What is the ‘histone code hypothesis’?
The idea that the specific combinations of modifications, as well as the order in which they have occurred, help determine the chromatin configuration and thus transcription.
83
What is the basic idea behind DNA methylation?
Enzymes add methyl groups to actual DNA (not histone tails), most commonly on Cytosine, which causes these areas to be transcribed less.
84
What chemical/molecule does DNA methylation most frequently involve the transfer of methyl groups to?
Cytosine.
85
In what organism does DNA methylation occur?
Most plants, animals and fungi.
86
What are some general general places DNA methylation is used in the regulation of gene expression?
In some cases long stretches of DNA, i.e. the inactivated mammalian X chromosomes (Barr body etc.) are highly methylated and thus inhibited.
In other cases individual genes are methylated to inhibit gene expression.
Specifically it is often used to inhibit gene only needed for embryonic development.
87
What is broader purpose of DNA methylation?
Methylation patterns are inherited by the daughter cells of mitosis.
Therefore such patterns of gene expression can be made permanent in what is called ‘genomic imprinting'
88
What does ’genomic imprinting’ refer to?
When methylation permanently regulates gene expression of either the parental or maternal allele of a particular gene at the start of development.
Therefore it allows the body to “choose” which allele to use depending on environmental etc. factors.
89
What does ’epigenetic inheritance’ refer to?
A form of inheritance in which traits are conveyed not through the nucleotide sequence but by modifications, such as methylation, applied to the DNA
90
What is the inheritance of traits that is not dependant on the nucleotide sequence called?
Epigenetic inheritance.
91
What does ’genomic imprinting’ refer to?
When methylation permanently regulates gene expression of either the parental or maternal allele of a particular gene at the start of development.
Therefore it allows the body to “choose” which allele to use depending on environmental etc. factors.
92
What is broader purpose of DNA methylation?
Methylation patterns are inherited by the daughter cells of mitosis.
Therefore such patterns of gene expression can be made permanent in what is called ‘genomic imprinting'
93
What are some general general places DNA methylation is used in the regulation of gene expression?
In some cases long stretches of DNA, i.e. the inactivated mammalian X chromosomes (Barr body etc.) are highly methylated and thus inhibited.
In other cases individual genes are methylated to inhibit gene expression.
Specifically it is often used to inhibit gene only needed for embryonic development.
94
In what organism does DNA methylation occur?
Most plants, animals and fungi.
95
What chemical/molecule does DNA methylation most frequently involve the transfer of methyl groups to?
Cytosine.
96
What is the basic idea behind DNA methylation?
Enzymes add methyl groups to actual DNA (not histone tails), most commonly on Cytosine, which causes these areas to be transcribed less.
97
What is the ‘histone code hypothesis’?
The idea that the specific combinations of modifications, as well as the order in which they have occurred, help determine the chromatin configuration and thus transcription.
98
What theory explains how the various histone modifications regulate gene expression?
The 'histone code hypothesis'
99
What is histone phosphorylation and how does it regulate gene expression?
The addition of phosphate groups to an amino acid next to a methylated amino acid.
This prevents chromatin packing and thus promotes gene expression.
100
What is histone methylation and how does it regulate gene expression?
The addition of Methyl groups (CH3) to histone tails which promotes condensation of chromatin and thus inhibits transcription
101
What is the structure of a methyl group?
-CH3
102
What is the structure of a acetyl group?
-COCH3
103
What are the basic ways in which histone modification can lead to the regulation of gene expression?
'Histone acetylation', ‘histone methylation’ and the phosphorylation.
104
What is it called when the rates of gene expression varies between cells?
“Differential gene expression"
105
Where does Translation occur in Eukaryotes?
Cytoplasm (free ribosomes) or on E.R. (bound ribosomes)
106
Where does RNA Processing occur in Eukaryotes?
Nucleus
107
What are the basic stages of gene expression in eukaryote?
Chromatin Modification forms transcriptable DNA, then:
Transcription → RNA processing → Transport to Cytoplasm → Translation → Protein Processing → Transport to cellular destination.
107
Where does Translation occur in Eukaryotes?
Cytoplasm (free ribosomes) or on E.R. (bound ribosomes)
107
What are the fundamental ways proteins are modified?
Cleaved, chemical modification i.e the addition of carbohydrates.
107
Why is the regulation gene expression particularly important in multicellular organisms?
It allows “differential gene expression” where the gene dosage can be adjusted to lead to specialised cells or for temporal fluctuations i.e. puberty.
107
What does ’differential gene expression’ refer to?
The expression of different genes by cells with the same genome.
107
What are the basic ways in which gene expression in Eukaryotes is regulated?
Regulation of the chromatin structure, regulation of Transcription Initiation and methods of Post-Transcriptional regulation.
107
What are the purposes of DNA packing?
It ensures the DNA fits in the nucleus and helps alter gene expression
107
What are the basic ways the regulation of chromatin structure affects DNA expression?
Histone modification, DNA Methylation and Epigenetic inheritance.
107
What is histone acetylation and how does it regulate gene expression?
The addition of acetyl (COCH3) groups to lysines in histone tails. Deacetylation is the removal of these groups.
When the lysines are acetylated, their positive charges are neutralised so the histone tails no longer bind to neighbouring nucleosomes. This promotes the folding of chromatin into a more compact structure.
This folded structure makes the DNA less accessible for transcription so acetylation inhibits gene expression.
107
Besides affecting histone tails, how does acetylation affect gene expression?
Some enzymes that acetylate or deacetylate histones are closely associated with or even components of the transcription factors that bind to promoters.
This suggest that histone acetylation enzymes also promote transcription by binding to and thus “recruiting” components of the transcription machinery.
107
What is the inheritance of traits that is not dependant on the nucleotide sequence called?
Epigenetic inheritance.
107
What does ’epigenetic inheritance’ refer to?
A form of inheritance in which traits are conveyed not through the nucleotide sequence but by modifications, such as methylation, applied to the DNA
107
What is the fundamental concept in which regulation of Transcription Initiation is used to regulate gene expression?
Proteins bind to regions of DNA which facilities or inhibits the binding of RNA polymerase and thus regulates transcription.
107
What enzyme performs the synthesis of RNA in eukaryotes?
RNA polymerase II
107
What is the region of DNA that regulates transcription of that gene called?
‘Control elements'
107
What are ‘control elements’ are how are they involved in the regulation of gene expression?
Segments of noncoding DNA that serve as binding sites for proteins called 'transcription factors', which in turn regulate transcription.
107
What can ‘control elements’ be divided into?
'Proximal control elements’ which are sections of DNA close to the promoter (sometimes classed as part of the promoter)
‘Distal control elements’ are located a lot farther upstream. Groups of them are known as ‘enhancers'
107
What are ‘enhancers’ in terms of gene expression?
They refer to a group of ‘distal control elements’ which are regions of DNA that are far upstream from the promoter
107
What is the basic way control elements regulate gene expression?
They are bound proteins called ‘transcription factors’ which increase or decrease the affinity of the region to RNA polymerase and thus affects transcription.
107
What are ’transcription factors’?
Proteins which bind to ‘control elements’ caning an increase or decrease the affinity of the region to RNA polymerase and thus they affect transcription.
107
What are ’transcription factors’ divided into?
‘General transcription factors’ and ’specific transcription factors'
107
What are ‘general transcription factors’?
Transcription factors which are needed for the transcription of all genes and thus their presence determines the rate at which transcription occurs of all genes.
A few general transcription factors independently bind a DNA sequence, such as the TATA box within the promoter; the others primarily bind proteins, including each other and RNA polymerase II.
107
What are ’specific transcription factors’?
Proteins which bind to specific genes and thus lead to the correct rate of transcription of specific genes/proteins.
107
What is the basic structure of a transcription factor?
It has two domains: A ‘DNA-bindign domain’ and an ‘Activation domain’ which binds to an RNA polymerase etc. to regulate gene expression.
107
What are ‘co-ordinately controlled genes’?
A group of genes whose expression is regulated by a single promoter.
108
How specifically do enhancers regulate gene expression?
‘DNA-bending proteins’ bend the DNA so that the enhancer region is over the promoter
Each of the enhancer's ‘distal control elements are bound by an ‘activator' (a type of transcription factor)
These bound ‘activators’ then bind to ‘general transcription factors’ and groups of ‘mediator proteins’ which intern bind with the promotor to regulate transcription by recruiting RNA polymerases.
109
In the context of genetics, what are ‘activators’?
A specific form of transcription factors which bind to the distal control elements of an enhancer.
110
What is the difference between distal control elements and ‘enhancers’?
A distal control element is a specific region of DNA in which transcription factors can bind.
An ‘enhancer’ is a collection of multiple distal control elements.
A gene might have multiple enhancers with each being active only if all of its distal control elements have bound to the correct transcription factors.
111
How can the activity of ‘enhancers’ be regulated?
Proteins called ‘repressors’ bind to the enhancer and thus block activators from binding.
112
What are the proteins which bind to and block enhancers called?
‘Repressors'
113
How are activators and repressors involved in the regulation of gene expression besides by interacting with the promotor?
Some activators recruit proteins that acetylate histones near the promoters of specific genes to promote transcription.
Some repressors recruit proteins that deacetylate histones, leading to reduced transcription, a phenomenon referred to as 'silencing'.
114
In the context of genetics, what is ’silencing’?
When repressors recruit proteins that deacetylate histones which reduces transcription.
115
What is the most common method of repressing the expression of genes in eukaryotes?
Recruitment of chromatin-modifying proteins
116
Are operons found in eukaryotes?
No (a few minor exceptions)
117
How do ‘co-ordinately controlled genes’ work in eukaryotes?
Each gene has multiple ‘distal control elements’ in each ‘enhancer.’ Between genes the combination of these distal control elements varies.
Genes which are co-ordinately controlled have distal control elements which bind to the same activators. Therefore if levels of those activators increases so will transcription of all the genes with enhancers which bind to these activators. Therefore they are coordinately controlled.
118
Why is the co-ordinate control of genes important in eukaryotes?
It allows cell differentiation as different types of cells have unique combinations of ‘activators’ and thus differential expression occurs.
119
What is are some advantages of the eukaryotic method of coordinately controlled genes?
- The genes can be located across different chromosomes
| - It allows logic i.e if Activator A and Activator C then express this gene
120
What is ‘albumin’?
A major blood protein
121
Where is ‘albumin’ produced?
In the liver
122
What is the main protein component in the lens of the eye?
‘Crystallin'
123
What is ‘crystallin?'
The main protein component in the lens of the eye
124
Where is ‘crystallin' produced?
In ‘lens cells’ i.e. in the lens of the eye.
125
What are methods that regulate gene expression by controlling transcription initiation divided into?
Transcription factors, Coordinate control and Nuclear Architecture
126
What is ’Nuclear Architecture’?
During interphase the nucleus consists of multiple regions called ’territories’, each of which consists of a single condensed chromosome.
127
How does ’nuclear architecture’ regulate gene expression?
Loops of chromatin extend from individual chromosomal territories into specific sites in the nucleus called ’transcription factories’.
Different loops from the same chromosome and loops from other chromosomes may congregate in such sites, some of which are rich in RNA polymerases and other transcription-associated proteins.
It is thought that each transcription factory has a specific role and thus also leads to the coordinate control of genes.
128
What are ’transcription factories’?
Regions in the chromosome which contain a collection of chromatin loops.
They have many RNA polymerases and thus increase transcription of the genes on these ‘chromatin loops'
129
What are the fundamental forms of Post-Translational that regulate gene expression?
RNA processing, mRNA degradation and Protein Processing & Degradation
130
How can the activity of ‘enhancers’ be regulated?
Proteins called ‘repressors’ bind to the enhancer and thus block activators from binding.
131
What are the proteins which bind to and block enhancers called?
‘Repressors'
132
How are activators and repressors involved in the regulation of gene expression besides by interacting with the promotor?
Some activators recruit proteins that acetylate histones near the promoters of specific genes to promote transcription.
Some repressors recruit proteins that deacetylate histones, leading to reduced transcription, a phenomenon referred to as 'silencing'.
133
In the context of genetics, what is ’silencing’?
When repressors recruit proteins that deacetylate histones which reduces transcription.
134
What is the most common method of repressing the expression of genes in eukaryotes?
Recruitment of chromatin-modifying proteins
135
Are operons found in eukaryotes?
No (a few minor exceptions)
136
What are some ways that regulation of gene expression by Initiation of Translation is important?
Eggs store mRNA in an form that have short poly-A tails and are thus not translated until extra Adenine is added when appropriate
Some plants and algae store mRNAs during periods of darkness; light then triggers the reactivation of the translational apparatus.
137
Why is the co-ordinate control of genes important in eukaryotes?
It allows cell differentiation as different types of cells have unique combinations of ‘activators’ and thus differential expression occurs.
138
What is are some advantages of the eukaryotic method of coordinately controlled genes?
- The genes can be located across different chromosomes
| - It allows logic i.e if Activator A and Activator C then express this gene
139
What is the fundamental way in which gene expression is regulated through Protein Processing and Degradation?
Any at any steps involved in modifying, transporting or degrading proteins regulates the prevalence of that protein.
140
Where is ‘albumin’ produced?
In the liver
141
What is the main protein component in the lens of the eye?
‘Crystallin'
142
What is ‘crystallin?'
The main protein component in the lens of the eye
143
Where is ‘crystallin' produced?
In ‘lens cells’ i.e. in the lens of the eye.
144
What are methods that regulate gene expression by controlling transcription initiation divided into?
Transcription factors, Coordinate control and Nuclear Architecture
145
What is ’Nuclear Architecture’?
During interphase the nucleus consists of multiple regions called ’territories’, each of which consists of a single condensed chromosome.
146
How does ’nuclear architecture’ regulate gene expression?
Loops of chromatin extend from individual chromosomal territories into specific sites in the nucleus called ’transcription factories’.
Different loops from the same chromosome and loops from other chromosomes may congregate in such sites, some of which are rich in RNA polymerases and other transcription-associated proteins.
It is thought that each transcription factory has a specific role and thus also leads to the coordinate control of genes.
147
What are ’transcription factories’?
Regions in the chromosome which contain a collection of chromatin loops.
They have many RNA polymerases and thus increase transcription of the genes on these ‘chromatin loops'
148
What are the fundamental forms of Post-Translational that regulate gene expression?
RNA processing, mRNA degradation and Protein Processing & Degradation
149
What is ‘RNA processing’?
The process which occurs in eukaryotes wherein the ‘primary transcript’ (RNA) is modified so that mature ‘mRNA’ is yielded.
150
How specifically does RNA processing regulate gene expression?
With alternative RNA splicing, in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns.
Regulatory proteins specific to a cell type control intron-exon choices by binding to regulatory sequences within the primary transcript.
151
How does mRNA degradation regulate gene expression?
Certain processes i.e. enzymatic destruction regulate how long RNA molecules are present and thus how many times they are transcribed.
152
How is the rate of mRNA degradation controlled?
Nucleotide sequences in the untranslated region (UTR) at the 3' end of the RNA
153
What are some specific places where regulation of the degradation of mRNA is seen?
- In bacteria it is generally high so that they can quickly affect their pattern of protein production as environmental conditions change.
- In developing red blood cells the mRNA of hemoglobin polypeptides (α-globin and β-globin) are unusually stable.
154
How does ‘Initiation of Translation’ regulate gene expression?
For some mRNAs, initiation of translation is blocked by regulatory proteins that bind to sequences/structures in the untranslated region at the 5' or 3' end (5' or 3' UTR), to prevent the attachment of ribosomes.
In many eggs mRNAs produced by the parents are stored until needed. Initially, these stored mRNAs lack poly-A tails of sufficient length to allow translation initiation. At the appropriate time during embryonic development cytoplasmic enzymes add more adenine (A) nucleotides to initiate translation.
The rate of translation for all mRNA can be controlled though the activation or inactivation of one or more of the protein factors required to initiate translation.
155
What are some ways that regulation of gene expression by Initiation of Translation is important?
Eggs store mRNA in an form that have short poly-A tails and are thus not translated until extra Adenine is added when appropriate
Some plants and algae store mRNAs during periods of darkness; light then triggers the reactivation of the translational apparatus.
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What is ‘pro-insulin’?
The “raw” polypeptide which is cleaved to form functional insulin.
157
What are some specific ways protein processing occurs?
Many proteins undergo chem- ical modifications that make them functional. Regulatory pro- teins are commonly activated or inactivated by the reversible addition of phosphate groups, and proteins destined for the sur- face of animal cells acquire sugars. Cell-surface proteins and many others must also be transported to target destinations in the cell in order to function.
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What is the fundamental way in which gene expression is regulated through Protein Processing and Degradation?
Any at any steps involved in modifying, transporting or degrading proteins regulates the prevalence of that protein.
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Why is the regulation of protein degradation important?
Some proteins need to be short lived so that they lead to only short term effects.
For example ‘cyclin’ (cell cycle) is quickly degraded so that the checkpoints operate correctly.
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How are protein degraded?
Multiple ubiquitin molecules are attached to a protein by enzymes in the cytosol.
The ubiquitin-tagged protein
is recognized by a proteasome. The protein enters the hollow interior of the proteasome where it is unfolded.
Enzymatic components of the proteasome cut the protein into small peptides, which can be further degraded by other enzymes in the cytosol.
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What is the structure of a proteasome?
It is a spiral with a hollow central cavity.
