Module 4 Flashcards
(211 cards)
1
Q
What is the chi-square formula?
A
o-e^2 / e
2
Q
What is population genetics?
A
study of inherited variation within and between populations over time
3
Q
What is gene frequency?
A
- allele frequency in a population
4
Q
What is a gene pool?
A
- alleles in a population
5
Q
What do you need to know for population genetics?
A
- determine the frequency of alleles and genotypes in a population to study forces that could change a population
- genotypic array
- gametic array
6
Q
What is the hardy weinerg law?
A
- allele and geneotypic frequencies will arrive at and remain at equillibrium frequencies after 1 generation of random mating if assumptions are met
7
Q
What are the assumptions for the hardy weinberg law?
A
- infinitely large population
- random mating
- no selection
- no migration
- no mutation
8
Q
What is the genotype frequencies formula?
A
- p^2 (AA) + 2pq (Aa) + q^2 (aa)
9
Q
What is the formula for P and q ?
A
f(MM) + 1/2(MN)
10
Q
What does P+q= ?
A
1
11
Q
What is fitness?
A
- W
- ability to survive and reproduce
- different models of relative fitness
12
Q
What is directional selection?
A
- selection that favors one side over the other
- homozygous after an infinite number of generations
- additive effects
13
Q
What is disruptive selection?
A
- there is a selection advantage for both extreme
- leads to bimodal population because both alleles stay in the population
- underdominance
14
Q
What is stabilizing selction?
A
- heterozygous favored
- both alleles stay in population
- overdominance
15
Q
What is variable selection?
A
- do they survive until reproduction
16
Q
What is the variable selection formula?
A
P^2WAA + 2wpqAa + q^2 Waa
17
Q
How fast is genetic frequency change?
A
very slow and small changes
around 10^-5 rate
18
Q
What causes genetic frequency changes?
A
- mutations
19
Q
What are the effects of a small population?
A
- genetic drift
- founder populations
- inbreeding
- bottlenecks
- non-random mating
20
Q
What is genetic drift?
A
- random variation in gene frequency from generation to generation due to small population and sampling error
21
Q
What does genetic drift lead to?
A
- random fixation or a loss of alleles over time
22
Q
What is the founder population?
A
- small population that colonizes a new area
23
Q
What are the problems with founder populations?
A
- can lead to genetic drift
allele frequencies in this population could differ from the og population - selective pressure are probably different from the population causing more rapid change because they’re are often harsher
24
Q
When is inbreeing more likely to occur?
A
small populations
25
What does inbreeding cause?
- more homozygotes by descent (same allele 2x)
- affects all loci in organism
26
What is f?
- inbreeding coefficient
- if it is between 0 and 1 inbreeding is occuring
27
What is f when there is no inbreeding?
O
28
Does inbreeding alter allele frequencies?
no
29
Does inbreeding alter genetic frequences?
yes
- increases both homozygous genotype frequencies and decreases heterozygous. eventually population will al be homozygous and genotypic array will be PAA + Qaa
30
What is a bottlenecks?
- when a large amount of the population is killed/ It changes genetics to look like survivors
31
Does non-random mating change genotypes?
yes
32
Does non-random mating change allele frequency?
- no
33
What is assortative mating?
mating based on phenotype
34
What is positive assortative mating?
mating like individuals together results in more homozygotes but onli for loci under selction
35
What is negative assortative mating?
- "opposites attract"
- would keep diversity in population and results in more heterozygous for loci under selection
36
What is P?
- frequency of A allele in donor pop (mainland)
37
What is m?
- proportion of migrants after immigration occured (parent from mainland)
38
What is p?
frequency of A allele on island initially
39
What is 1-m?
- probability that a parent will come from island
40
What is p'?
- frequency of A allele after migration
= (1-m)p + mP
41
What does a change in gene frequency depend on?
- migration rate and gene frequencies of immigrants vs native
42
What are the types of genetic changes in a populatiion?
- emergence of a species
- divergence of a species
- extinction of a species
43
What are the steps to evolution?
- 1. genetic variation starts
- 2. increase or decrease frequency in gene pool
44
What is a a species?
- a group ofindividuals that could interbreed in nature
45
What is reproductive isolation?
- species become distinct when they don't exchange genes
46
What is prezygotic reproductive isolation?
- species chose not too or can't mate
- something like different environments
47
What is postzygotic isolation?
- progeny are sterile or inviable
48
What is the biological species concept?
- members of a species are capable of intermating and producing fertile progeny
49
What is allopatric specitation?
- geographic barrier intiates specitation by blocking gene flow
- example. darwins finch beaks based on available food
50
What is sympatric specitation?
- speciation within a single interbreeding population without a geographical barrier
- examples. hybridization leading to alloploidy or apple maggot fly
51
What is phylogenics?
- study of relationships between species, individuals, or genes based on charecteristics
52
What is the tree of life?
- shows specitation and extinction events for all life on earth
- related to phylogeny
53
How do you reconstruct a phylogenic tree?
- reconstruct by inferring relationships among present day organisms
54
What is anagenesis?
- evolution within a lineage over time
55
What is cladogenesis?
- splitting of 1 lineage into 2
- once cladogenesis occurs branches evolve seperately
56
What does cladogenesis lead to?
- more biological diversity since more species exist at the same time
57
What are homologs?
- related evolutionary dna sequences
58
What are paralogs?
- homologous sequences found in same species and arrive through gene duplication
59
What are orthologs?
homologous sequnces found in different species
60
What is an example of gene duplication?
- homeotic genes
61
Does the genome evolve at the same time?
- no, different parts of the genome evolve at diffferent rates
- highest mutation rates in enes that have the least effect on function
- more constraints on sequence to provide function, fewer changes tolerated bc changes might not be survivable
62
Do pseudogenes code for proteins?
- no
63
Which part of the genome has the lowest mutation rate?
- exons since introns are just removed
64
What is the molecular clock?
- assuming a constant mutation rate in DNA change, differences in sequence between the present day organisms can be used to date past evolutionary events
65
What do phylogenic trees show?
- degrees of similarities between OTUs
66
What are OTUs?
- operational taxonomic units based on differences in DNA sequences
- could be species, virsu strains, different alleles...
67
What are rooted trees?
- distance between OTUs are kown, order of divergence is inferred by comparing to an OTU out group
68
What is an outgroup?
- OTU that diverged earlier than all other OTUS outfroop roots the tree, all others share a common ancestor
69
What are unrooted trees?
- only distance between OTU is known, not order of divergenece throughout evolutionary time
70
What are terminal nodes?
- where we are now
71
What is a branch?
shows evolutionary time
72
What are internal nodes?
- most recent common anscestors between two
73
What is the distance approach?
- computing differences to infer relationships based on overall similarity of organisms typically by using multiple phenotypic characteristics or gene sequences
- doesn't require out group
- OTUs dont need to be different species
#s are calculated from dna sequnce differences and dna sequence alignment
74
What is the distance approach formula?
- number of differences/ number of bases (1000)
- higher # = more differences
75
What are cancer cells?
- serve no useful function, unlimited potential to grow
76
What is pleiotropy?
- 1 gene affects multiple traits
- can be positive or negatively correlated
77
What are limits to selection responses?
- selection response may decline over time
- two positive traits may be negatively correlated
- extremes might not be healthy
- could lose genetic variation as homozygous are bred
78
How do you map quantitative trait loci?
- QTL are identified by linkage analysis between trait and molecular markers
- if the inheritance of a genetic marker is associated with the inheritance of a quantitative trait that marker must be linked to QTL
- SNPS are often markers
- looked at through GWAS
79
What are heritability limits?
- doesn't say how much genes effect trait, it shows how much genes affect variation in trait
- an individual doesn't have hertiability
- heritabliility depends on a particulat pop. in a particular environment
- if height is .8 .8 of your height isn't genetic, it means 80% of variation is because of genetic variation
80
What do twin studies do?
- compare monozygotic and dizygotic twinse
81
What is concordance ?
in twin studies the twins are the same for the trait
82
What is disconcordance?
- in twins studies the twins are different for the trait
83
What is % concordance?
- indicates a % of twin group showing same phenotype
84
How does cancer occur?
- its errors occuring during cell cycle and increase through mitosis
- g1
- g 2
- m errors
- genetic but rarely heretible
85
What does G2 IM do?
- holds up cycle until replication and DNA repair are complete
86
What does G1 1s do?
- monitors for propper cell size and increases throuh mitosis
87
what does m do?
- proper spindle formation and attachment
88
What is a tumor?
- distinct mass of abnormal cells that don't have normal division controls
89
What does benign mean?
-doesn't invade surrounding tissues
90
What does malignant mean?
- invades surrounding tissue
91
What does metastatic mean?
- starves body, cells spread and create more tumors
92
What are the genetic causes of cancer?
- mutations in somatic cells
- single defective gene
- polygeneic (2+ defective genes)
- chromosomal aberattion
- viruses
93
What are the environmental causes of cancer?
- carcinogens
- can cause mutations
- can alter gene expression
94
What does cancer being a multi-hit diesase mean?
- most cancers are sporadic and influenced by environment
- cancers develop over time
- loss or gain og gunction mutatuons
95
What does it mean that cancers are sporadic and invludnced by environment?
- siblings rarely get same cancer
- populations that migrate typically get cancer rates of that region
96
What does it mean that cancers develop over time?
- changes in cancer rate due to envrionment tend to take deccades
97
What is the relationship between cell division and cancer risk
- more division= more risk
- mutatuoins leading to cancer are bc of replication errors
98
WHat are some of the worst places to get cancer?
= tumor supressor genes
- poroto oncogens
99
What are tumor-suppressor genes?
- prevent "bad cells" from dividing
- abnormal functino = no inibiiton = tumor if both alleles are bad (must disrupt both copies)
100
What are proto-oncogenes?
- allow good cells to divide, must be activated to be regulated propperly
101
Is a loss or gain of function mutation dominant?
- gain of function
102
What are the tumor supressor genes?
- BRCA
- RB
- p53
103
What does the BRCA gene do?
- repairs double stranded breaks, leads to breast cancer with mutations
104
What does RB do?
- regulates cell division and causes retinoblastoma and other cancers
- normally important at g1/s
- binds t e2f replication leads to RB to release E2f which leads to transcription
- RB typiclaly prevents e2f from activating replicaiton
105
What is E2f?
- transcription factor
106
What is p53?
- in 50% of tumors
- at g1
- looks for DNA damage
- if broken, damaged DNA can replicate
107
What must all tumor supressor genes have?
- 2 daamged genes
108
What are oncogenes?
-protooncogenes can cause oncogenes if mutated
- dominant, only need 1 mutation to have a problem (all oncogenes)
109
What causes burkits lymphoma?
- caused by myc mutation which is a transcription factor
- oncogene
- reciprocal translocation between 18 and 14, placing myc next to high enhanver immunoglobin causing it to be constantly expressed
110
What are viral cancers?
- retroviruses that can mutate and rearrange protooncogenes or insert a strong promotor near protooncogenes
111
What are most cancers due to?
- many mutation accumulations in several gens
112
What is clonal evolution?
- tumors can get more mutations allowing them to be more agressive in proliferation
113
What can clonal evolution effect?
- cell cycle regulation, signal trasnduction, DNA repair, telomere length, chromosome segregation, vascularization
114
How can clonal evolution effect DNA repair?
- defective nulceotide excision repair (skin cancer)
- defective mismatch repair (colerectal, endometrial, stomach cancers)
- double stranded break (brca1+brca2+
115
How does clonal evolution affect telomere length?
- telomeres shorten as they age, if cells have constant telomerase expression they can be immortal
116
How can clonal evolution affect vascularization?
- angiogenesis
- gives tumors nutrients
- angiogenesis inhibitors can be inactivated or under expressed
- metastasis is cause of death in 90% of human cancers
117
What is angiogenesis?
- growth of new blood vessels. helps tumorprogression
118
What are the levels of quantitative genetic variation?
continuous levels
119
Do quantitative genetics have a distinct F2 genes?
no
120
What is the multifactor hypothesis?
- variation due to envrionment (both strains, pure-breeding, homozygous)
- variation due to envrionment ( all plants one genotype)
- variation due to genotype and envrionment (difff. genotype) MOST GENES
121
What is the variation due to environment and genotype hypothesis?
- expresison depends on additive effects of lots of genes
- effect of each gene is small
- environment smooths curve and plays a role in the expression of trait
- a single genotype may produce a range of phenotypes
122
What kind of distribution do most traits have?
- normal distribution
- bell curve
123
What does the standard deviation affect
curve width
larger std deviation = larger curve
124
What is the mean formula?
- x= sigmax/n
125
What is the sample variance formula?
- s^2
- (e1(xi-x)^2) / n-1
126
Can distributions have the same mean and different variances?
yes
- knowing variance cna ell us width and give us more info
127
What is the phenotype formula?
- genotype + environment
128
What is the genotype formula?
- additive+ dominance effects
129
What does additive mean?
- effects of subbing A for a in genotyp
130
What does dominance mean?
- effects of allele combos
- D=0= Aa is exactly btwn values of AA and aa
131
What is the vp formula?
vp= vg+ve
132
What does vp mean?
- phenotypic variance, s^2
133
What is the vg formula?
vg= va + vd
134
What does vg mean?
genetic variance
135
What does va mean?
- additive genetic variance
136
What is vd?
- variation due to dominences
137
What does the effect of a gene depend on?
- envrionment where its found
138
What is heritability?
- proportion of phenotypic variance due to genetics
- broad sense and narrow sense
- 0-1
- 0= all vp is bc of environment
- 1 = vp due to genetic variation
139
What is broad sense heritability?
- proportion of a phenotypic variance due to genetic effect
140
What is narrow sense heritability?
- proportion of phenotypic variance due to additive genetic effects
141
What is the broad-snse heritabilty formula?
- H^2 vg/vp
142
What is narrow sense heritabilty?
- h^2 va/vp
143
What is the relationship between heritability and breeding?
- more heritability = better breeding and more progress seen
- still based on pop not individual
144
What is response to selection?
- the extent to which characteristic changes over a gene
145
What is selection diferential?
S= xs-x0
146
What is the response to selection formula?
R= x1-0`
147
What are the limits to selection responses
- selection response may decline over time
- you can lose genetic variation as homozygous is bred
- extremes might not be healthy
- 2 positive traits could be negatively corerelated
148
Who developed PCR?
Kary Mullis
149
What are the steps to PCR?
- denature DNA Aby heating to 95C and separate strands
- each strand is replication template
- primers identify target to be amplified after being cooled (3"OH)
- taq polymerase adds nucleotides to 3' end of primer and repeat
- DENATURE ANNEAL EXTEND
150
What is the correlation between distance migrated and fragment size in electrophoresis?
- distance migrated is inversely proportional to the log of the fragment size
- smallest moves fastest
- sizes can be determined based on comparing fragment migration to a known control migration
151
Where is DNA loadedd in electrophoresis?
- loaded at - and goes to +
152
What are the limitations to PCR?
- must know something about sequences surrounding gene
- easily contaminated
- taq polymerase doesn't proofread or correct errors
- fragments amplified = small
153
What are the applications of PCR?
- types of repeats can be used to reate DNA fingerprint
- allele is based on length of DNA segment
- useful for paternity and forensics; must be
- combined DNA index system
154
What types of repeats can be used to create DNA fingerprints?
- short tandem repeats
- variable number of tandem repeats
- microsatellite regions
155
Why are alleles based on length of DNA segment?
- bc diff alleles have diff # of copies of sequence
156
How can you use DNA for forensics and paternity?
- for chrime scenes DNA must be a 100% match
- if 1 bound loci its homozygous
- fbi database has a 1 in 1 billion match except for identical twins
- data put in on local level and shared at state/ national level
- DNA comes from offenders, arrestees, crime scenes, human remains, relatives of missing people, missing people, immigrants
157
What are the ethical issues of genetic testing?
- partial match can help identify suspects
- familial DNA testing
- conflict between solving crimes and protecting privacy
158
What is recombinant DNA?
- creates new molecules by combinining DNA from different sources
- creates 2 different dNA molecules
159
What makes 2 recombinant DNA pieces compatable?
if they are cut by the same restriction enzyme
160
How is recombination DNA formed?
- combines DNA from diff sources
- uses restriction enzymes to cut DNA
- produces blunt end when cut
- if cut by same restriction they are compatible
- makes 2 diff dna molecules
- dna ligase seals 2 pieces to create recombinant
161
What is a restriction enzyme?
- endonucleases that recognize sequence and cleaves there
162
What is a palindrome?
- reads 5' to 3' on both strands
163
What is a vector?
carrier DNA that is capable of independent replication into which a dna fragment can be cloned.
- purpose is to carry foreign DNA into cell
164
What are the parts of a vector?
- oriC
- selectable// insertional markers
- multiple cloning site
165
what does the oriC do?
- allows replicaiton in host cell by letting machinery work
166
What do selectable/ insertional markers do?
- allows cells containing vector and recombinant molecule to be identified
167
What were the experiments to identify recombinant DNA?
- ligation
- insertional inactivation
- transforming
- identification of different cell types
168
What is litigation?
- gains foreign DNA to vector.
- foreign DNA and vector are both cut with the same restriction enzymes
- add ligase and a recombinant is formed
169
What is insertaional inactivation?
inserted DNA inactivates a gene by inserting into that gene allows for the identification of recombinant DNA
170
What is transforming?
allows cells to take up procducts from a litigation experiment
171
What is identification of diff. celly types?
- cells with no uptake, cell that take up original vector, cell that take up recombo plasmid
172
Why are there multiple recognition sites?
- enzyme flexibility and availability
173
What tells you if foreign DNA was successfully inserted and gene is functional
- litigation marker
- lac z is an insertional marker
- if bacteria is successfully transformed and amplified it allows for selection of transformed colonies
174
What was the problem golden rice was fixing?
- lack of vitamin a
- missing enzymes that convert gpp into phytoene
175
What is reverse transcriptase?
- RNA dependant DNA polymerase
- uses mRNA as DNA template (first strand) cdNA
176
What were the problems with creating golden rice?
- needs a lot of DNA, a promotor, and a way to get into rice genome
- rice needs PSY, CRH, promotor, poly A signals. transgenic markers, LB and RB for insertion into plant genome
177
What is a transgenome?
- an organisms own altered DNA
178
What do transgenic things have?
- foreign gene in genome and transgenome
179
What is a ti plasmid?
- tumor supressor gene to have plant make own food
180
What is a modified ti plasmid?
ti tumor gene removed, dna transfer functions intact
- allows inserted genes to be functional
181
What are expression factors?
- must contain sequences required for transcfiption and translation
- RNA polymerase binds to the promotor
182
what is a southern blot?
Single strandend DNA sperated by length
183
What is a northern blot?
-rna seperated by length
184
What is a western blot?
- proteins seperated by molecular weight
185
What is blotting?
molecules that were previously sperated to a membrane that can be better tested
186
What is a probe?
- ssDNA that is a sequence we want
- binds to complementary strand
187
What is a dioxy sequencing reaction?
- 3' OH required by DNA polymerase to form phosphodiester bone
- dna replicated until deoxy nucleotide is incorporated
- no further extension occurs
- detects which position deoxynucleotide was incorporated
188
What is foward genetics?
- start with a mutant phenotype and seek out gene that causes phenotype
- use chromosome mapping to identify gene
189
What is reverse genetics?
- start with DNA sequence/ genotype and alter its function or prevent its expression and observe phenotypic effect
- starts with a gene and breaks it through Crisper, RNAI, microarray, RNAC
190
What is the RNAI breaking transgenic mice experiment?
- inject gene of interest into fertilized egg
- implant embryo
- test progeny for gene presence by marker or PCR
- always heterozygous
- have to breed heterozygous to get homozygous
- study gene function
191
How does crsipr work with reverse genetics?
- CRSPr rna and cas 9 cuases double end break, non-homologous end joinging to mutate gene
192
What does RNAI do?
- interferes with RNA, but doesn;t change DNA only changes the amount of protein produced
193
What was the knockout mice experiment?
1. normal gene is disabled by inserting Neo+ and tk is linked to target gene
2. disabled gene is transferred to embryo where it is recombined with normal gene
3. recombinant has neo + and tk-
4. cells are grown in media selective for only neo+ homologous recombo survives
5. neo_ diabled genes are injected into early mouse embryos
6. embryos are implanted
7. variated progney have miz of normal clels and disabled gene
8. variated are creossed with white then interbred ot get homozygous
194
What is a microarray?
- 2 populations of cell, compares which genes are expressed (transcribed)
-tag 1 cell type with red and one with green then compare
- yellow= it has red and green
- comapres mRNA
195
What is RNA sequencing/ RNAC
- looks at MRNA
- takes mrna turns into c dna, cuts cdna into piececes and sequences DNA
196
What is gneomics?
- feild of genetics that attempts to understand content, organization, function, evolution of genetic info contained iwthiin and between whole genomes
197
What is involved in genomics?
- need whole genome
- involves collecting sequence data, and correlating genetic cytological and physical chromosome maps. identifying DNA sequences containing genes of interest and analyzing function of gene products
198
What is map based gneome sequencing?
- seperate chromosomes, cut into peices
199
What is whole genome approach?
- cut DNA
- used today bc we have basic model already
200
What is an SNP?
- specific site in genome where DNA varies in at least 1% of the population
- different in diseases
- snps near eachtother are often inherited together and can be grouped as a halotype
201
What is a gwas?
- looks for specific association between presence of trait/phenotype and alleles
- useful for QTL
- studies populations not pedigrees
202
Qhat is a linkage disequillibrium?
- certain halplotypes/ variants are combined more frequently in pop than would be if random
203
What are tag snps?
- subset of snps used to identify haplotype
- correlates presense/ absence of snp with presence of genetic disorder
- identifies DNA sequences faster than sequencing whole genome, but correlation doesn't = causation
204
What are the types of gene therapy?
- transgenes
- genome editing
- germ-line
- somatic cell
- retrovirus
- non-viral
205
What is gene therapy?
introducing/ creating new functional copies of a gene in individuals who only have defective copies
206
what does a transgene do?
- a transgene is an introduced new coy of gene
- it will make missing gene product and restore normal phenotype
207
what is genome editing?
- crispr to correct a deffective copy
208
what is a somatic cell edit?
- non heritable, treats but doesn't cure disease
- all current gene therapies
209
What is a germ-line cell edit?
- heritable, major moral and ethical considerations
- illegal
210
What is a retroviral vector?
- integrates DNA of host cell
- transgene is transmitted to all progeny cells in lineage
- transgene may integrate so it disrupts function of anotehr gene
211
What are nonviral gene edits?
- direct injection, lipid capsuels, nanoparticles
