Module 3 Flashcards
(220 cards)
1
Q
are all mutations bad?
A
no
- humans have 10,000 gene mutations per day
2
Q
What is a mutation?
A
- change in genetic material
3
Q
What was the first found mutation?
A
alkaptonuria
4
Q
What did garrod do?
A
- tried changing diets to change genetic mutations
- diets typically go record, restrict, replace
5
Q
What is a biochemical pathway?
A
- stepwise series of reactions
- each reaction is enzyme catalyzed
6
Q
What did beadle and tatum say?
A
-1 gene = 1 enzyme
- its actually 1 gene = 1 polypeptide chain
- if there is a mutation in a gene coding for an an enzyme a block occurs
7
Q
What is a wiltdtype pathway?
A
normal state of a protein, will grow on minimal media
8
Q
What is a mutant pathway?
A
protein doesn’t function normally, needs a different environment
9
Q
What is a germline mutation?
A
- eggs, sperm,
- meiosis allows the mutation to be passed on?
10
Q
What is a somatic mutation?
A
- non reproductive cell
- through mitosis so it can’t be passed on
11
Q
What is a loss of function mutation?
A
- a mutation that causes a complete or partial loss of protein function
- recessive mutation
12
Q
What is a gain of function mutation?
A
- cell can produce a protein that’s not typically there
- dominant
- new gene product, product at a new location, product at new time in development, excess product
- tumor growth
13
Q
What is a point mutation?
A
- a single codon change
- substitute one base for another
14
Q
Whats an example of a point mutation?
A
sickle cell
15
Q
What is a transition point mutation?
A
- purine to purine or pyrimidine to pyrimidine
16
Q
What is a transversion?
A
- purine to pyrimidine or pyrimidine to purine
17
Q
What are the effects of a point mutation?
A
- missense
-nonsense - silent
- readthrough
18
Q
What is a missense mutation?
A
- changes AA
- if nuetral doesn’t affect protein function
19
Q
What is a nonsense mutation?
A
- codon gets changed to stop codon
- negative because its cut short
20
Q
What is a silent mutation?
A
codes for same AA
21
Q
What is a readthrough mutation?
A
- stop codon changes to extra AA
- causes a longer chain
22
Q
What are spontaneous point mutations?
A
- depurination
- deamination of cytosine
- wobble
23
Q
What is depurination?
A
- removes a bond at a g or a, bases creating missing purine/ apurine site
- problem: base opposite of AP site isnt specified and improper base could be put in causing transitions and transversions
- if replicated twice total it becomes permanent
24
Q
What is deamination of cytosine?
A
- causes GC to AT transition resulting in uracil
25
What is a wobble mutation?
- mispairing due to helix flexibility resulting in transitions after replication
- A+C and T+G can bair with 2-h bonds
- 2 rounds of replication are needed ot alter both strands of DNA
26
What are examples of chemically induced point mutations?
- base analogs
- alkylating elements
-deamination
- hydrozxyl amine
- oxidative reagents
- intercalating agents
27
What are base analogs?
- mispair more frequently than normal bases
- 1 round of replication incorporates base analog
- 2 more rounds of replication (3 total) cause permanent transition
28
What are frameshift mutations?
- addition or deletion of a base causing reading frame to change
- can alter stop and start site
-alters multiple codons
29
What is an example of a frameshift replication?
- CF
30
What do repeat regions cause?
- expansions
- could occur during hairpin
- same region could be replicated 2+ times and leads to even more replication in daughter cells
31
What causes frameshift mutations?
- intercalating agents
- strand slipage during replication
- unequal crossing over (misalignment of homologous chromosomes where 1 has insertion and 1 has deletion
32
What do x-rays do?
- chromosome breakage
- leads to abberations by breaking phosphodiester bonds
- could cause point mutations
- most damage in dividing cells
- used in cancer treatments
33
What can uv -light do?
- cause pyrimidine dimers
- distorts DNA helix and inhibits replication
34
Who discovered trasnposable elements?
- McClintok
35
What are transposable elements?
elementa that can move from sites on genes
- can go from one site to antoher
- to a different chromosome
- can alter phenotypes by disrupting a gene or regulatory area
36
What is an AC activator?
- complete trasnposable element with functional transposase and repeats
- has enzymes to move itself
37
What is DS dissociation?
- lacks functional transposase (deletion) so it requires AC transposase to move
- can only move with transposase
38
Does the human genome have trasnposons?
-45% of the human genome has transposon elements but there are no active transposons
39
How do transposons affect gene expression?
- could move regulatory sequences to new places affecting gene expression
40
What is an example of transposon remminants in humans?
antibodies may have evolved from transposons
41
What are the methods for DNA repair?
- direct repair
- proof reading
- mismatch repair
- nucleotide excision repair
- base excision repair
- double strand break repair
42
What is direct DNA repair?
- corrects structure of abnormal nucleotide without replacing nucleotide
43
What are the methods of direct repair?
- bacteria use photoreactivation repair of pyrimidine dimers using photolyase
- methyltransferase restores correct form to incorrect form to incorrectly methylated guanine base
44
What cells undergo proofreading
eukaryotes and prokaryotes
45
How does dna polymerase know if there is a mistake during replication?
looks if 3' OH is in the wrong spot
46
What happens during DNA proofreading?
- DNA polymerase finds mistake
- DNA polymerase stalls replication
- exonuclease from pooymerase removes incorrect nulceotide and then DNA polymerase inserts correct nucleotide
- errors are 1 in 10 million
47
What cells undergo mismatch repair?
eukaryotes and prokaryotes
48
How does mismatch repair work?
- ecoli methylation distinguishes old DNA from new DNA
- mismatched repair proteins recognize abnormal helical structure and identify incorrect base
- exonuclease removes an area of new strand from methylated sequence to mismatch
- dna polymerase fills in the gap and ligase seals the nick
- doesn't remove lesions (damaged DNA)
-
49
What are the steps to nulceotide excision repair?
- enzyme complex recognized distortion in helix (like thymine dimers)
- strands of DNA are separated and held apart by SSB
- enzymes cleave sugar-phosphate bonds on both sides of lesion renaming several nucleotides including defective area
- dna polymerase fills in gaps
- dna ligase seals nick
- can remove lesions unlike MMR
50
What is nucleotide excision repair?
- removes bulky lesions
- happens in all organisms
51
What is base excision repair?
- removes modified bases
52
What are the steps to base excision repair?
- glycosylases recognize and remoce defective bases resulting in apurinic site
- 1 glycosylase for each specific modified base
- AP endonuclease cleaves phosphodiester bond next ot missing base causing a nick and removes rest of nucleotide
- dna polymerase fills in gaps
- dna ligase seals nick
53
What are the methods of double strand break repair?
- homologous recombination repair
- non-homologous end joining
54
What is homologous recombination repair?
- uses sister chromatid to repair break
- uses many of same enzymes as homologous recombination in meiosis
55
What is non-homologous end joining?
- often used in G1
- joins broken bonds
- often leads to translocations, deletions, insertions
56
What is translesion DNA polymerase?
- specialized polymerases that can bypass lesion on DNA during replication
- these polymerases often make errors
- allows replication to proceed at the cost of introducing mutations
- if you constantly use these the mutations will build up
57
What are chromosomal abberations?
- deletions
- inversions
- duplications
58
What are deletions?
missing chunk of chromosome
59
What is a terminal deletion?
- acentric/ end fragment lost during division
60
What is an interstitial deletion?
requires two dates
61
Describe the form of deletions?
- in prophase one chromosomes try to come together put then cant find match so it loops out
62
What are the effects of deletions?
- segments that don't contain a centromere (accentric fragments) are lost
- deletions could cause an imbalance in amount of gene product produced
- haploinsufficiency
- mutant phenotype
- pseudodominance
- some are viable some are not
63
How does a deletion cause a mutant phenotype?
deletion of normal allele on 1 chromosome may allow the recessive allele on homolog to be visible causing mutant phenotype
64
What is haploinsufficiency?
having one copy of gene isn;t enough to allow wildtype phenotype to occur
65
What is psuedodominance?
- expression of normally recessive phenotype because there is no homologous allele
66
What is a duplication?
- extra copy of part of chromosome
- could be on same or different section of chromosome
67
What are deletions caused by?
duplicdaitons and deletions are from unequal crossing over
68
Are duplicaitons survivable
yes, not as severe as deletions
69
Why are duplicaitons good?
essential for evolution
70
What is the ohno theory?
- uique genes are essential to survavie and when some genes can't mutate the duplicated copy has mutations and develops different function over time
71
What is an inversion?
section of chromosome is cut out, flipped 180 put back in
72
What is a paracentric inversion?
doesn't include centromere
73
What is a pericentric inversion?
- includes centromere
74
When do inversions happen?
when there is a double strand break
75
What is the problem with inversions?
- often doesn't change phenotype
- problem comes during meiosis, forms loop, not all genes copied, only 1/2 gametes viable
76
What are translocations?
when a piece of a chromosome moves locations
77
What are reciprocal translocations?
- 2 non-homologus chromosomes exchange arms or piece of arms
- no gain or loss of DNA
78
What are non-reciprocal translocations?
- segment from 1 chromosome is moved to a non-homologous chromosome
- no gain or loss of DNA
79
What is a robertsonian translocation?
- 2 telocentric/ nearly telocentric chromosomes combine to make a larger more metacentric chromosome
- some small amount of DNA is lost, but not noticeable
80
What are isochromosomes?
- 2 chromosomes joined are homologs
81
What are the resulting gametes of translocations?
- only 1/2 viable
- ones that go diagnol = viable
- robertsonian would join 14+21
- isochromosomes if the 2 21s join
- familial is rare
82
What is poisition effect?
chromosome location alters phenotype
83
What are the regulatory elements of genes?
- strucutral genes
- regulatory genes
- regulatory elements
84
What are structural genes?
- encode proteins that are used in metabolism or play a structural role in cell
85
What are regulatory genes?
- encode products that interact with other sequences and affect the transcription of these sequences
86
What are regulatory elements?
- DNA sequences that aren't transcribed but play a role in regulating other nuclotide sequences
87
When does prokaryotic gene regulation take place?
- often happens during transcription and transcription factors
- look at AA sequence to see if binding occurs
88
How is transcription regulatred?
- rapid turn on-off
- sequential gene expression
- constitutive expression
positive vs negative
- inducible control
89
What is the rapid turn on/ off?
provides ability to rapid respond to sudden changes
90
What is sequential gene expression?
- cascades of gene expression that turn on in order these are frequently cyclical
91
What is constitutive expression?
- continuosly expressed under normal conditions
92
What does constitutively mean?
- always on
- like rRNA and tRNA genes
93
What is positive control?
- regulator proteins binds to DNA to stimulate transcription
94
What is negative control?
- regulator protein binds to DNA to prevent transcription
95
What is inducible control?
- transcription is normally off and is turned on when a molecule binds to regulatory protein
96
What is repressible control?
- transcription is normally on and turned off when a molecule binds to regulatory protein
97
What is an operon?
- multople genes controlled by 1 promotor
98
What type of regulator does the lac operon have?
- + or -
- if negative it blocks polymerase binding
99
What is an operator?
- DNA sequence that regulating protein binds to
100
What type of control does the lac operon have?
- negative inducible control
101
Who discovered the lac operon?
- Jacob and manad
102
How does the lac operon work?
- lactose is broken down into galactase and glucose with beta galctidase
- if no lactase its not needed so it needs to be turned off
- so normally off, only on (induced transcription) when lactose is present
103
What is an allosteric change?
- in repressor, operator binding site is altered physically when repressor binds to allolactase
104
What are cis-acting mutations?
- action of an element affects only the genes adjacent to it
- operator and promoter
105
What is a trans-acting mutation?
- diffusible product produced mutant gene doesn't need to be adjacent to other genes to affect them
- repressor
106
What are the regulatory genes?
I+
I-
Is
107
What is I+?
normal repressor
108
What is I-?
- repressor can't bind to operator, always on
109
What is Is?
repressor cant bind allolactose, always off, super operator
110
What is Oc?
- operator, constituative opperator, operator can't bind, always on
111
What is p-?
- promotor can't bind RNA polymerase, always off
112
What are structural genes?
z-
y-
a-
results in defective enzymes
113
GO Review Lac operon
114
What is negative repressible control?
- repressor binds when the molecule is there
- have enough of a substance so it turns off the operon
115
Describe tryptophan control?
- negative repressible control
- tryp turns off repressible
- allosteric action
- constitutive mutants
- feedback inhibiiton
116
What is allosteric action?
- change in conformation when repressor binds TRP
117
What are the constitutive mutants?
-R-
- Oc
118
What does R- mean?
- inactive repressor, always on
119
What does Oc mean?
- operator can't bind, always on
120
Wheat is feedback inhibition?
- excess TRP in cell decreases production of enzymes used to make TRP
121
What is operon attenuation?
- separate from - repressible
- premature termination of transcription
- deletion of a leader sequence leads to an increase in transcription even when TRP is there
122
What is an attenuator?
- in leader sequence decreases transcription when TRP is present
123
When does operator attenuation happen with TRP?
- if TRP is low regions 2-3 pair, and no termination signal
- if trp is high regions 3-4 pair and theres a termination signal
124
What does anti-sense RNA do?
inhibits translation
125
What is ASRNA?
- small RNA complementary to parts of mRNA and inhibit translation
- same idea as RNAI
126
What is prokaryotic main way of regulation?
transcription
127
What are riboswitches?
- RNA sequences in mRNA that affect translation of mRNA
- translation regulation
128
What are the levels of eukaryotic gene regulation?
- chromatin regulation
- initiation of transcription
- RNA processing and stability
- protein modification
129
How are eukaryotic genes regualted?
- chromatin structure, RNA processing, cell differentiation, organism development
130
How is chromatin regulated in eukaryotes ?
- histone modification
- chromatin remodeling
- dna methylation
131
How is the initiation of transcription regulated in eukaryotes?
- transcription factors like activators and repressors
- transcription factor binding sites
- insulators
132
How is RNA processing and stability regulated in eukaryotes?
- RNA splicing
- RNA degradation
- RNA interference
133
What state must chromatin be in before transcription?
- must be decondensed
134
Describe transcriptionally active DNA?
- loosely coiled
- puffs and balbiani rings are active in active areas
135
What are DNased hypersensitive sites?
- small regions typically upstream from start of transcription
- nucleosome is missing
- binding site for regulatory proteins
136
What are the histone modification methods?
- histone structure
- methylation of tails of histones
- acytlation tails
- chromatin remodeling with repositioning nucleosomes
137
How is histone structure modified?
- globular domain interacts with other histones and DNA
- positively charged tail areas interact with phosphate groups on DNA
138
What are the forms of acytlation of tails negating charge?
- histone desacetlyation
- histone acetylation
- both negate charge and let transcription factors bind to DNA
139
What is histone deacetylation?
- done by histone deacetylase ( HDAC)
- tightens assoicaiton between histones and DNA
140
What is histone acetylation?
- done by histone acetyl transferase (HAT)
- loosens DNA- hisotne associaiton by nuetralizing the + charge on histone
141
What does a + histone charge mean?
- + = tightly associated
- no charge = loose
142
What does histone coding do?
- helps regulate chromatin structure and transcription
143
What is a histone code?
combination of modifications resent that help regulate chromatin structure and transcription
144
When does chromatin remodeling with repositioning nucleosomes?
- with genes we use constantly
145
What is chromatin remodeling with repositioning nucleosomes?
- conformational changes in the DNA or Nucleosomes to allow DNA bound to nucleosome to be more exposed and bind more transcriptional activators
- repositioning nucleosomes along DNA so DNA can change from being part of nucleosome to being part of area between nucleosome
146
What is histone methylation?
- can activate or repress expression of a gene (usually repress)
147
What is DNA methylation and the recognition sequence?
- tends to cause genes to be turned off (silencing)
- 5' CG 3' is recognition sequence
- NOT 5' GC 3'
- heavily methylated = silenced
- methylated CPG sequences attracts deaclytases furhtre repressing transcription since deacytlases remove acetyl groups from histon tails
148
What are examples of things that are helvily methylated?
- barr bodies
- repetitive sequences
- imprinting of genes conveyed from partents to offsoring
149
What is the relationship between methylation and dna transcription?
- increase in methylation leads to a decrease in DNA transcription
- association between increased DNA methylation and deacetylation of hisotnes in areas with little transcription
150
What are phenotypes caused by?
- epigenetic changes not genotypic change
151
What is cell differentiation?
- changes in DNA methylation and chromatin structure occur as a cell differentiates
- treating adult cells causes some cells to become pluripotent and undergo extensive reprogramming, changing methylation patterns, and histone modification
- only one copy of a gene is expressed or biased expression is seen
- imprinting si highly variable and only seen in certain tissues or times of development
152
What is the core/ basal promoter?
- basal transcription apparatus binds
- includes RNA polymerase and general transcription factors
- is required for transcription of nearly all RNA polymerase two
153
Do regulatory factors activate or repress?
- either
154
What do distal transcription factor binding sites do?
- binds to DNA at transcription factor binding sites
- interacts with transcription apparatus
- can bind to DNA, other transcription factors, and/ or RNA polymerase to regulate transcription
155
Describe DNA binding domains?
- sequence specific
- crystal structure of transcription factor bound to DNA as a dimer
- 1 gene may have many transcription factor binding sites (each protein binds to a different specific DNA sequence)
- different transcription factors are found in different cell types
- 1 gene can be seen in many places, just expressed differently
156
What do insulator DNA sequences do?
- block transcription factors
- since transcription factors can act at a distance and transcription factor binding site are orientation independent there needs to be an element that blocks/ insulates genes from the effects of other genes
157
What are insulators?
- cis DNA elements that block transcription factors from interacting with wrong gene
158
What is an example of environmental factors altering transcription?
- transcription of the RBC is stimulated by light in plants
- saw increase in the RBC trancsripts in leaves after exposure to light, the roots didn't see exposure
159
How can hormones alter trasncription?
- some hormones bind to cytoplasmic receptors and then complex binds to regulate gene expression (steroids)
- some hormones act at cell surface and appear to signal transcription factors (insulin)
160
What can transcription factors do?
- interact with other proteins
- be modified
- be localized
- be degraded
161
What transcribes premrna?
- RNA poly 2
162
Where is mature MRNA found by?
- 5' GTP cap,
- splicing
- intron removal
163
What are teh steps to RNA processing and stability?
1. cleaage and splicing
2. process and splicing
164
What do alternitive splice sites do?
- result in different proteins in different tissues or at different times in development
- regulation of splicing is very important for controlling eukaryotic gene expression
165
What does splicing affect in drosophila?
- phenotype/ sex
166
What does the amount of a protein synthesized depend on?
- availability of mRNA for translation
167
What does the amount of MRNA available depend on?
- rate of synthesis and rate of degradation
168
how do ribonucleases effect RNA stability
- poly a tail is shortened by RNAses
- once tail is at critical length 5' cap is removed
- RNA is then degraded by 5'
169
What does RNAI do?
- shuts off gene expression by using double stranded RNA
170
What does DSRNA do?
- cleaved by dicer to form mirna and sirna
171
What does miRNA do?
- from mRNA, transposons, or viral RNA and tarets genes it comes from
172
What does mirna do?
- transcribed from a distinct gene and targets other genes for regulation
173
What do miRNA and SiRNA do?
bind with proteins to form RNA induced silencing complex that base pairs with MRNA to inhibit trasnlation (mirna) or degrades mRNA (sirna)
174
What is Lac z?
b-galactosidase
175
What is lac y?
permease
176
What is lac A?
transacetylase
177
What is lac P?
- promotor, where polymerase binds to allow transcription
178
What is lac O?
- operator, interacts with repressor
179
What is lac I?
- regulator, codes for repressor.
180
How many antigens does a b-cell code for?
- specific for 1 antigen
181
How are B-cells replicated?
- b-cell binding to antigen clones the b cells bound
182
What happens to B-cells once they are created?
- some become plasma cells that produce antibodies and some become memory cells
183
What is the antibody structure?
- 2 chains a heavy and a light
- each chain has a variable and constant region
- antigen binds to the variable region
- heavy chain codes for immunoglobulins
184
When does somatic recombination happen?
in b-cells during b-cell differentiation
185
What is somatic recombination?
- dna processing to choose constant region and variable region for heavy and light chains
186
How is development regulated?
- is a programmed sequence of events
- regulated growth from an interaction of genome, cytoplasm, and environment
- usually not reversible
187
What is differentiation?
- an aspect of development
- forming different types of cells, organs, etc through specific regulation of gene expression
188
What is the importance of cloning?
- fist the frog cloned then the mammals
- shows that adult differentiated cells retain a complete set of genetic info
189
What are specific drosophila traits?
- maternal genes and egg polarity
- establishes anterior posterior polarity and dorsal ventral polarity
- transcribed during egg development
- translated after fertilization
- maternal effect, what mom has kids have
190
What is biccoid?
- MRNA anchored at the anterior end
- MRNA is translated to bicoid protein that diffuses from anterior end
- creates protein gradient
191
What is nanos?
- MRNA anchored at posterior end
- translated to protein that diffuses from posterior end
- creates protein gradient
192
What do biccoid and nanos do?
- regulate translation of maternal hunchback and caudal
- hunchback and caudel mrna are uniformly distributed through egg
- biccoid represes caudal mrna translation by binding caudal 3' UTR (prevents caudal from being made in anterior)
- biccoid activates hunchabck transcription by binding a transcription factor
- nanos initiates hunchback by binding to its poly-A-tail and destroying it
193
What are the four protein drosophila protein gradients?
- anterior to posterior hunchback
- anterior to posterior biccoid
- posterior to anterior nanos
- posterior to anterior caudel
194
look at hunchback graph
195
What are segmentation genes?
- affect number and organization of segments
- transcribed after fertilization so no maternal effect.
- regulated by bicoid and nanos
196
What are the segmentation genes?
- gap genes
- pair rule genes
- segment polarity genes
-
197
What are gap genes?
- divide embryos into broad segments
198
What are pair-rule genes?
- affect some part of a pattern in every other segment
199
What are segment polarity genes?
- affect anterior/ posterior polarity of each segment
200
What are homeotic genes?
- gives specificity to segments
- all on same chromosome
- genes in order from anterior to posterior
- each gene is on specefic segments based on concentration of earlier gene products
- found in most animals
201
what are homeobases?
most common dna sequences
202
What is homeodomain?
- region of protein formed from homeobox
- binds to specific dna squences and regulates transcription
203
What are dna binding sequences?
- proteins containing homeodomain
204
What are ABC homeogametic genes?
- make transcription factors which bind to DNA to allow transcription of specific genes at specific times in development
- go look at chart
205
What is ploidy?
- number of set of chromosomes
206
What is aneuploidy?
- change in number of chromosomes (missing or extra)
207
What is monoploidy?
- missing 1 chromosome
208
What is nullploidy?
- missing 2 copies of one chromosomes
209
What is doublemonoploidy?
- missing 2 different species
210
What is tripolody?
- estrachromosome
211
What causes aneuploidy?
non-disjunction
212
When is aneuploidy typcically seen?
- sex chromosomes especially x
213
What is polypoloidy?
- more than 2 copies of haploid genome
214
What is autopolyploid?
extra sets of their own chromosomes
215
What is alloploidy?
- new species from parents
- behabes like diploids and can double chromosmes creating amphidiploid
216
What is an amphidiploid?
- contains two diploid genomes of two different genomes
- only seen in plants
- type of allopolyploid
217
What causes alloploidy?
non-disjunction of all chromosomes
- happens in anaphase
218
Is alloploidy in animals?
no not often
219
Can polyploids reproduce?
- no they are sterile
220
