19 - Genetics of living systems Flashcards
1
Q
What is a mutation?
A
Change in the base sequence of DNA
2
Q
What are the 3 types of mutation?
A
- Substitution 2. Deletion 3. Insertion
3
Q
What is a substitution mutation?
A
Replacement of one or more DNA bases with others
4
Q
What is a deletion mutation?
A
When one or more nucleotides are removed (i.e., deleted) from the DNA sequence
5
Q
What is an insertion mutation?
A
Where one or more bases are added to the DNA sequence
6
Q
What is it called when a mutation only affects one nucleotide?
A
Point mutation
7
Q
When might a mutation affect a protein’s primary structure?
A
When it creates a new codon which codes for a different amino acid
8
Q
What are the 3 different types of mutation effects?
A
- No effect 2. Damaging 3. Beneficial
9
Q
When would a frameshift mutation occur?
A
When a deletion or addition mutation occurred in a number of bases that is not a multiple of 3
10
Q
What would a frameshift mutation cause?
A
Every successive codon from the point of the mutation onwards would be different, so the protein produced would be completely different
11
Q
Would a protein still be affected by a deletion or insertion mutation which wasn’t a frameshift mutation?
A
Yes, as there would still be a new amino acid added, but the effects would likely be less
12
Q
What are 3 possible reasons why a mutation may have a neutral effect on a protein’s structure?
A
- Mutation changes a base, but the amino acid which the triplet codes for is the same 2. Mutation causes a different amino acid to be produced which is chemically similar to the original 3. The triplet affected may code for an amino acid which isn’t essential to the protein’s function, such as one located away from the active site
13
Q
Would a mutation with a neutral effect affect the whole organism?
A
No it wouldn’t affect the whole organism
14
Q
How can a mutation make a protein more or less active?
A
By changing the shape of its active site
15
Q
Does a mutation which changes a protein’s active site mean the organism is less likely to survive?
A
Not necessarily- the mutation may even be beneficial
16
Q
Give an example of a mutation with a beneficial effect for an organism?
A
A mutation which enabled a bacterial enzyme to break down an antibiotic more effectively
17
Q
Give an example of a mutation with a negative effect for an organism?
A
Deletion mutation causing changes in the CFTR protein which lead to cystic fibrosis
18
Q
How can a mutation prevent a protein from being produced?
A
If the mutation is at the start of the gene and RNA Polymerase can’t bind to it, so the protein won’t be produced
19
Q
What are 2 reasons a mutation may be harmful to an organism?
A
- Protein may not be produced at all 2. Protein may be produced, but in a non-functional form
20
Q
What increases the rate of mutation?
A
Mutagens
21
Q
What is a mutagen?
A
A chemical, biological or physical agent which causes mutations
22
Q
What is depurination?
A
The loss of a purine base from DNA
23
Q
What is depyrimidination?
A
Loss of a pyrimidine base from DNA
24
Q
How does depurination or depyrimidination usually happen?
A
Spontaneously
25
What type of mutation could depurination or depyrimidination lead to?
Insertion if a new base filled the gap left
26
What are 2 chemical mutagens?
1. Free radicals 2. Deaminating agents
27
What could a deaminating agent do to cytosine?
Change it to uracil
28
Why are antioxidants also known as carcinogens?
Due to their ability to negate the effects of mutagenic free radicals
29
What is an example of a physical mutagen?
Ionising radiation such as x-rays
30
How would x-rays act mutagenically?
Break one or both DNA strands, with the repair of the strand often causing mutations
31
What are 3 examples of biological mutagens?
1. Alkylating agents 2. Base analogues 3. Viruses
32
How does a virus act as a mutagen?
By inserting viral DNA into the genome
33
How do alkylating agents act as mutagens?
Attach methyl or ethyl groups to bases, causing incorrect pairing during replication
34
How do base analogues act as mutagens?
They are incorporated into DNA in lieu of a normal base
35
What is a chromosome mutation?
One which affects the whole chromosome or a number of chromosomes within the cell
36
When do most chromosome mutations occur?
During meiosis
37
What is a deletion chromosome mutation?
A section of a chromosome breaks off and is lost within a cell
38
What is a duplication chromosome mutation?
Sections of a chromosome duplicated
39
What is a translocation chromosome mutation?
A section of one chromosome breaks off and attaches to a non-homologous chromosome
40
What is an inversion chromosome mutation?
A section of chromosome breaks off, is reversed, and then rejoins onto the chromosome
41
What is a housekeeping gene?
One which codes for enzymes necessary for metabolic processes such as respiration
42
What are tissue-specific genes?
Ones which code for protein-specific hormones
43
What is a transcription factor?
Proteins which bind to DNA and switch genes on or off by increasing or decreasing the rate of transcription
44
What are the two types of transcription factor?
1. Activators 2. Repressors
45
What do activators do?
Factors which increase the rate of transcription
46
What do repressors do?
Factors which decrease the rate of transcription
47
How do transcription factors work?
Bind to specific DNA sites near the start of their target genes (in eukaryotes) and promote/repress the action of RNA Polymerase
48
What do transcription factors bind to in prokaryotes?
Operons
49
What 3 things can be contained in an operon?
1. Clusters of structural genes 2. Control elements 3. A regulatory gene (sometimes)
50
What do structural genes do?
Code for useful proteins i.e. enzymes
51
What 2 things do control elements contain?
1. Promoter 2. Operator
52
What is a promoter?
DNA located before the structural genes, which RNA polymerase binds to
53
What is an operator?
A DNA sequence which transcription factors bind to
54
What 2 things can regulatory genes code for?
Activators or repressor
55
What allows bacteria to respond to environmental changes?
Gene regulation
56
What 4 things is gene regulation necessary for in eukaryotes?
1. Responding to changes in external environment 2. Responding to changes in internal environment 3. Cell specialisation 4. Cell coordination
57
What are the 4 stages at which genes can be regulated?
1. Transcriptional 2. Post-transcriptional 3. Translational 4. Post-translational
58
How can genes be regulated at a transcriptional level?
Genes can be turned on or off
59
How can genes be regulated at a post-transcriptional level?
mRNA can be modified, which regulates translation and the types of proteins produced
60
How can genes be regulated at a translational level?
Can stop or start translation
61
How can genes be regulated at a post-translational level?
Proteins can be regulated after translation, which changes their function
62
What are 4 methods of transcriptional gene regulation?
1. Cyclic AMP 2. Histone modification 3. Chromatin remodelling 4. Lac operon
63
What is a chromatin?
DNA molecules that are tightly coiled around proteins call histones.
64
What is heterochromatin?
Tightly packed chromatin
65
When does heterochromatin allow chromosomes to be seen?
During cell division
66
When does euchromatin allow chromosomes to be seen?
During interphase
67
What is euchromatin?
Loosely packed chromatin
68
In which of heterochromatin and euchromatin can genes be transcribed and why?
Euchromatin, as heterochromatin is too tightly packed
69
Does protein synthesis occur during cell division, and why/why not?
No as you can't transcribe genes from heterochromatin
70
Why is it important that genes cannot be transcribed from heterochromatin?
Prevents complex and energy-consuming process of protein synthesis occurring when cells are dividing
71
What type of gene regulation is the fact that genes can't be transcribed from heterochromatin?
Transcriptional
72
Why does DNA condense around histones?
Because they are positively charged and DNA is negatively charged
73
What are 2 methods of making histone groups less positive?
Acetylation and phosphorylation
74
How is the acetylation or phosphorylation of a histone an example of transcriptional gene regulation?
Makes DNA bind to histones more loosely, allowing certain genes to be transcribed
75
How does methylation of histones affect them?
Makes them more hydrophobic
76
How is methylation of histones an example of transcriptional gene regulation?
Because it makes them more hydrophobic they bind together more tightly, so the DNA coils around them more tightly and less gene transcription can take place
77
What is epigenetics?
The control of gene expression by the modification of DNA
78
What is an operon?
A unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis. Its genes are expressed at the same time
79
Are operons present in eukaryotes?
Yes
80
Why are operons more common in prokaryotes?
Prokaryotic genomes are smaller and simpler
81
What is an advantage of using operons?
They are a very efficient way of saving resources as if certain gene products aren't needed you can switch off all the genes involved in their production
82
What 3 genes make up the lac operon?
lacZ, lacY, lacA
83
What is the lac operon involved in?
The metabolism of lactose
84
What types of genes are lacA, lacY and lacZ and why?
Structural genes as they code for enzymes and are transcribed onto one long piece of mRNA
85
What is the preferred respiratory substrate of E.coli?
Glucose
86
When would E.Coli use lactose as a respiratory substrate?
When glucose is in short supply
87
What is located near the lac operon and what does it code for?
The regulatory gene lac L, which codes for a repressor protein that prevents the transcription of the structural genes in the absence of lactose
88
What is down regulation?
Binding of repressor protein to an operator, whcih prevents binding of RNA polymerase
89
What happens to the lac operon when lactose is present?
Lactose binds to the repressor protein and causes it to change shape so that it can no longer bind to the operator, so gene transcription can occur
90
When is CRP binding possible?
When CRP is bound to cyclic AMP
91
How can the rate of transcription of RNA polymerase be increased?
By binding CRP
92
How does glucose regulate the lac operon?
1. When glucose levels are high, cAMP levels are low. 2. cAMP receptor protein (CRP), aka CAP, binds cAMP 3. cAMP-CRP acts as an activator of the operon
93
What is a cap?
Modified nucleotide
94
What is a tail?
Long chain of adenine nucleotides
95
Which ends do the cap and tail bind to?
Cap to 5' end, tail to 3' end
96
What 2 things do the cap and tail both do?
1. Stabilise mRNA 2. Delay degradation in the cytoplasm
97
What does the cap do which the tail doesn't?
Aids binding of mRNA to ribosomes
98
Where does splicing and the addition of cap and tail occur?
In the nucleus
99
Why would point mutations be done deliberately by the cell?
So that a greater range of proteins can be produced from the same mRNA molecule or gene
100
What are 2 methods of post-transcriptional gene regulation?
1. RNA processing 2. RNA editing
101
What are 4 methods of translational gene regulation?
1. Degradation of mRNA, with quicker degradation in cytoplasm meaning less protein synthesis 2. Protein kinases 3. Activation of initiation factors which aid binding of mRNA to ribosomes 4. Binding of inhibitory proteins to mRNA which prevent it from binding to ribosomes
102
What are protein kinases?
Enzymes that activate or inactivate other proteins by phosphorylating them
103
What often activates protein kinases?
cAMP
104
How does phosphorylating a protein activate it?
Changes its tertiary structure
105
What are 5 methods of post-translational gene regulation?
1. Addition of non-protein groups 2. Modifying amino acids 3. Formation of bonds such as disulfide bridges 4. Folding and shortening of proteins 5. Modification by cAMP
106
What is morphogenesis?
The regulation of the pattern of anatomical development
107
What is a body plan?
The general structure of an organism
108
What are body plans controlled by?
Proteins produced by Hox genes
109
What are homeobox genes?
Sequences of genes that control the development of specific structures
110
What is a homeobox?
A 180-nucleotide sequence within homeotic genes and some other developmental genes that is widely conserved in animals, plants and fungi
111
What does the homeodomain do?
Binds to DNA and switches other genes on or off
112
What do homeobox sequences code for?
Part of a protein called the homeodomain
113
What 2 processes are involved in the development of body plans?
Mitosis and apoptosis
114
What are Hox genes found in in animals?
Clusters
115
What are Hox genes?
A group of homeobox genes only present in animals
116
What does the order in which Hox genes appear along the chromosome determine?
The order in which their effects are expressed in the organism
117
What is the difference between diploblastic and triploblastic animals?
Diploblastic have 2 primary tissue layers, triploblastic have 3
118
What is a common feature of animals?
They are segmented
119
What are somites?
Segmented blocks of tissue in the embryo that later differentiate into vertebrae, ribs, and skeletal muscles due to the effects of Hox genes
120
What 2 types of symmetry are found in the body shape of animals?
1. Radial 2. Bilateral
121
Do all types of animal show symmetry?
No, for example sponges show asymmetry. But most do.
122
What are 2 ways apoptosis can regulate the development of the body?
1. Remove unwanted cells and tissues 2. Release chemical signals which stimulate mitosis and cell proliferation
123
What can influence the expression of regulatory genes?
The internal and external environmental
124
What is an example of a drug which interferes with Hox genes?
Thalidomide
125
what are the different types of chromosome mutations?
deletion
inversion
translocation
duplication
126
what is a chromosome mutation?
where large sections of the chromosome are altered rather than just a single base
127
what is a nonsense mutation?
where there is a mutation that changes the codon into a stop codon so cuts the sequence short
128
what is a missense mutation?
where the codon is changed completely so it codes for a different amino acid
129
what are the three effects of a mutation?
1) silent
2) beneficial
3) damaging
130
what causes a silent mutation?
when there is a change in the base sequence but because the genetic code is degenerate, this means that even after a mutation it could still code for the same amino acid.
131
what increases the chance of a mutation occuring?
mutagen/mutagenic agent
132
what does a deletion/insertion mutation lead to?
frameshift mutation which changes all subsequent codons
133
what are the three levels of controlling gene expression?
1) transcriptional
2) post transcriptional
3) translational
4) post translational
134
what controls whether transcription can occur or not?
transcription factors
135
what are transcription factors?
molecules that bind to DNA and can either inhibit or allow transcription to occur
136
if there is no transcription factor bound to the DNA, what is the state of the gene?
the gene is inactive so therefore transcription will not occur and the protein will not be made
137
what happens when the transcription factor is bound?
once the transcription factor binds to DNA, transcription can begin and mRNA can be made and will undergo translation to create the protein
138
what type of molecule is a transcription factor?
protein
139
how do transcription factors prevent transcription?
they bind to the DNA which prevents RNA polymerase from binding
140
describe the control of transcription in eukaryotes?
- transcription factors move from the cytoplasm to the nucleus and attach to DNA
- they either initiate or inhibit transcription by turning genes on/off
- therefore either allow/prevent certain proteins from being made
141
DNA is wrapped around proteins called...
histones
142
what is chromatin?
the tightly bound DNA wrapped around histones
143
what is heterochromatin and when is it present?
the tightly wound DNA in cell division (tightly wound to prevent damage)
144
how does the shape of heterochromatin affect RNA polymerase?
because the heterochromatin is so tightly bound this means the gene is compact inside so does not allow RNA polymerase to bind
145
what is euchromatin and when is it present?
the loosely wound DNA in interphase (to allow transcription to occur)
146
how does the shape of euchromatin affect RNA polymerase?
because it is loosely bound this means the gene is exposed so that allows the RNA polymerase to bind to the gene therefore allowing transcription to occur
147
how do you convert heterochromatin to euchromatin?
add an acetyl or phosphate group - which increases the negative charge so causes DNA to less tightly wind around the histones
148
what is the charge of histones?
positive
149
what is the charge of DNA?
negative
150
how do you convert euchromatin to heterochromatin?
add a methyl group to euchromatin and this increases the hydrophobic nature of the histones so makes DNA tightly wind around again
151
what is the example of gene expression in prokaryotes?
lac operon (lactose breakdown)
152
what is an operon?
a group of genes controlled by the same regulatory mechanism and are all expressed at the same time
153
what are structural genes?
codes for proteins that are not involved in DNA regulation
154
what are the three structural genes in lac operon and what enzymes do they produce?
lac Z: B-galactosidase
lac Y: lactose permease
lac A: lactose transacetylase
^all these enzymes metabolise lactose
155
the structural genes in lac operon produce enzymes that do what?
metabolise lactose
156
what are regulatory genes?
code for proteins that are involved in DNA regulation
157
what is the regulatory gene in lac operon and what does it code for?
lac I: repressor protein
158
what does the repressor protein do?
it inhibits the processes of the structural genes so it does not produce the enzymes that will metabolise lactose
159
what is the operator region?
(DNA sequence) where the repressor protein binds
160
what is the promoter region?
(DNA sequence) where the RNA polymerase binds
161
what is the order of components in the lac operon?
LacI
operator
promoter
LacZ
LacY
LacA
162
describe how to lac operon works when glucose is present?
- when glucose is present the prokaryotes wants to use this for respiration
- the LacI gene produces the repressor protein
- which binds to the operator region
- due to the shape of the repressor protein, it blocks the promoter region, SO the RNA polymerase cannot bind
- this means the transcription of the structural genes cannot occur
163
describe how the lac operon works when glucose is no longer present but lactose is?
- when glucose is no longer present that means lactose needs to be metabolised
- the lactose binds to the repressor protein which causes it to change shape
- so the repressor protein can no longer bind to the operator
- this leaves the promoter region exposed allowing the RNA polymerase to now bind to the promoter
- allows transcription of the structural genes
- therefore lactose can be metabolised
164
in the lac operon with lactose how can transcription be made more efficient (what molecule)?
CRP can bind to cAMP and this forms a complex (CRP-cAMP) which then binds to the RNA polymerase speeding up the transcription of the structural genes
then it can move along the structural genes and produce the proteins/enzymes which can then be used to metabolise lactose for respiration and energy
165
when the lac operon is working in the presence of lactose, what happens when glucose once again becomes available?
the lactose unbinds from the repressor protein which allows it to bind again to the operator , and once again blocks to promoter region
166
in the lac operon, what is the relationship between glucose and cAMP?
glucose leads to a decreases in cAMP conc. and therefore the cAMP unbinds to the CRP so transcription becomes less efficient.
167
CRP only works is ? is bound to it.
cAMP
168
in control of gene expression, what is made in the transcriptional level?
mRNA
169
in control of gene expression, what needs to be done in the post-transcriptional level?
the mRNA needs to be modified
170
what is an intron?
sections of DNA that do not code for proteins
171
what is an extron?
sections of DNA that do code for proteins
172
the mRNA strand produced in translation contains a mix of ? and ?
introns and extrons
173
why does the mRNA produced in transcription need to be modified?
the mRNA contains a mix of introns and extrons sop before it is taken to the ribosomes for translation, it needs to be modified
this strand is called pre-mRNA
174
what is pre-mRNA?
the mRNA strand that contains a mix of introns and extrons that needs to be spliced and modified before it can move to translation.
175
what are the three stages of converting pre-mRNA into mRNA that can be taken to the ribosomes (aka mature mRNA)?
1) RNA splicing where the introns are removed
2) add a cap (modified nucleotide)
3) add a tail of adenine (stabilises mRNA)
steps 2+3 are to protect the mRNA strand from damage and degradation when travelling to the ribosomes
176
how can the mature mRNA strand be edited further?
can be edited to get different versions of the mRNA that code for different proteins
177
in the translational level of gene expression, how can the translation be decreased? (2)
1) degrade the mRNA so the protein cannot be produced
2) use inhibitory proteins that bind to the mRNA - stops it from being able to bind to ribosomes
178
in the translational level of gene expression, how can the translation be increased?
1) activate initiation factors
^ these allow the mRNA to bind to the ribosomes
^ occurs by phosphorylation and protein kinases catalyse the addition of phosphate groups to the protein
179
in the translational level of gene expression, to increase the translation, what helps activate protein kinases?
cAMP (secondary messenger)
179
what is the post translational level of gene expression?
this is when the polypeptide chains made can be further modified for specific functions
180
explain the 4 ways that a polypeptide chain is modified in the post translational level of gene expression?
- adding a non protein group like a lipid, carbohydrate or phosphate group
- amino acids can be modified to form different bonds like disulphide bridges
- folding or shortening of proteins
- modification by cAMP
181
what are homeobox genes?
sequences of genes that code for proteins and are important in the early stages of development of the body
182
homeobox gene sequences are very similar in __, __ and __
animals, plants and fungi
183
what are hox genes?
a type of homeobox gene found in animals
184
what are hox genes responsible for?
correct body development and positioning of body parts
the order of the genes in the DNA is the order in which they are expressed in the organism
185
what does mitosis do?
increases the number of cells which leads to growth
186
what does apoptosis do?
removed unwanted cells through programmed cell death
187
what is the cell cycle controlled by and why?
controlled by genes to ensure that new cells being produced are actually needed for growth and prevents tumour formation
188
mitosis and apoptosis are regulated by what genes?
hox genes
189
what factors affect the expression of regulatory genes?
- drugs
- internal stimuli: psychological stress, hormones
- external stimuli: temp, intensity of light
