Exam 5 Flashcards
1
Q
Proteomics
A
- Study of the proteome (complete set of proteins found in a given cell)
- Protein microarrays can be used to analyze protein-protein interactions
2
Q
Limitations of PCR
A
- The sequence of gene of interest needs to be known to synthesize primer (needs to be complementary enough)
- Potential DNA contamination:
- wrong DNA will be amplified - Accuracy of DNA polymerase:
- the entire transcription complex isn’t available, just polymerase is present, no proof-reading - Amplification size
- limited on how large can be synthesized
3
Q
Testing for HWE
A
- After one generation of random mating, the genotype frequencies for two alleles can be calculated as:
p^2 + 2pq + q^2 = 1 - Proportion of AA in population= p^2
- Proportion of aa in population= q^2
- Proportion of Aa in population= 2pq
- They result mostly from random mating
if in Hardy-Weinberg equilibrium -> allelic freq. determine genotypic freq.
4
Q
Migration and its affects on allelic frequencies
A
- influx of genes from other populations (gene flow)
- Prevents genetic divergence between populations and increase variation within population
- As Migration increases -> change in allelic freq increases
- If allelic frequencies similar, migration has less effect on allelic frequency change
- Also depends on how much migration takes place
- Populations WANT variation, adds genetic variation to pops
- Through time, migration will cause frequencies of two populations to become similar
5
Q
Calculations to deterimine # of genes/phenotypes
A
- Self-cross F1 and get F2
2. ¼ homozygous additive, half are heterozygous, ¼ are homozygous non-additive
6
Q
Narrow-Sense Heritability
A
- determines degree of resemblance of parents and offspring
- use for quantitative traits
- used to determine the proportion of phenotypic variance due to additive genetic variance (additive effects of genes on phenotype!)
- h2 = VA/VP
- High value = offspring resemble parents
7
Q
Heritability
A
- The proportion of total phenotypic variation in a specific population that is due to genetic factors
- NOT FIXED FOR A TRAIT (varies)
- applies to a specific POPULATION at any given time
- can NOT be applied to other populations
8
Q
Genotypic frequency is determined by allelic frequency
They are directly related in..
A
- Hardy-weinberg
9
Q
Biotechnology
A
- any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use
10
Q
Types of genomics (4):
A
- Proteomics
- Structural genomics
- Comparative genomics
- Functional genomics
11
Q
short term effect of mutation, migration, genetic drift, and natural selection
A
- change in allelic frequency
12
Q
Mass spectrometry
A
- Method for precisely determining molecular mass of a molecule
- Mass-to-charge ratio (m/z)
- Identify proteins and post-translational modifications, or characterize multi-protein complexes
13
Q
Hardy-Weinberg Law
A
- Mathematical model that evaluates the effect of reproduction on genotypic and allelic frequencies in a population
- The sum of the allele frequencies must equal 1
- THE PURPOSE OF HWL is to consider the impact of reproduction on the gene pool - once we know this, we can look at migration and natural selection
14
Q
Phenotypic Correlation
A
- could be caused by genetic or environmental correlations
15
Q
What increases genetic variation between populations?
A
- Mutation
2. Genetic drift
16
Q
Genetic drift
A
- deviation from expected allelic frequency due to chance
- a form of sampling error
- Has a bigger impact in smaller populations (tends to even out in large ones)
- Changing the ratio of sexes lowers effective pop. (Remember, 1/2 of genes come from each sex)
- When one sex is under-represented, genetic drift increases
- Alleles can be permanently lost if frequency fluctuates to zero
- Alternative allele is said to be fixed
1. Population suffers severe size reduction - aka BOTTLENECK
2. Founder Effect - when a small number of individuals start a population, gene pool is limited
3. A population may be reduced in size for a period of time b/c of limited resource (space, for example)
17
Q
fitness (W)
A
- relative reproductive success of a genotype (relative to the reproductive success of another genotype!)
- values from 0 to 1
- Part of natural selection
18
Q
Library screening steps
A
- used to isolate only the clones that contain your gene of interest
1. Colonies of library lysed, and DNA denatured
2. Non-/radioactive probe combined w/ colony solution on membrane; probe hybridizes w/ denatured DNA
3. Membrane rinsed for excess probe
4. X-ray film detects hybridized probe (gene of interest)
5. Cell transferred to medium for growth/analysis
19
Q
Quantitative real-time PCR (qPCR)
A
- measures gene expression levels
- checks how much DNA amplification we get in real time
- The approach to determine amount of PCR product made during experiment
20
Q
Quantitative Trait Locus (QTL)
A
- represent traits controlled by more than one gene that can be quantified
- Identifying QTLs using markers
- Compare the inheritance of some marker gene with a QTL (or a polygenic trait)
- These genes control polygenic traits
- QTL typically linked to or contains the genes that control that phenotype
- Can find where all the largest tomatoes have the same alleles for these markers
- Able to identify some QTLs in tomatoes and find which had additive alleles for these genes and which ones didn’t
- Tiny change between two bottom tomatoes (B) caused by just one particular gene
21
Q
Positive assortative mating (PAM)
A
- like individuals mate
- Similar genotypes are more likely to mate than dissimilar ones
ex: tall humans mate with tall humans
22
Q
Standard deviation (s)
A
- Also measures spread (like variance) but defines it within standard variables
- The square root of variance
Note: the mean plus or minus one standard deviation - includes ~ 66% of measurements in normal distribution - plus or minus 2 = 95.5%
- plus or minus 3 = 99.74%
23
Q
Multifactorial/complex traits have phenotypic ranges of diff genotypes that…?
A
- Can overlap
24
Q
Gene silencing
A
- using RNA interference: allows the gene to be turned off temporarily
Requirements
1.Must be recognized by Dicer
2. Complementary ONLY to target sequence - Delivery - Digestion (C. elegans), injection directly into cells
- Gene Trial for macular degeneration
25
What was the first human gene product manufactured by recombinant DNA technology?
- Insulin
26
Additive genetic variance (Va)
- additive effect of genes on phenotype
27
Knock-in
- the sequence is inserted at a specific location
- Gene addition in which a gene of interest is added to a genome to observe the over expression of a gene/ observe allele's effects
ex. Can replace a mouse allele with a human allele
28
Reproductive isolating mechanisms
- Biological factors that prevent gene exchange
1. Prezygotic
- prevents species from mating in the first place
- Prevents zygote formation
Ex: animals from diff populations
2. Postzygotic
- Reproduction isolation even when members of two populations are willing/able to mate
- Zygote is formed but no gene flow occurs
Ex: genetic divergence prevents viability/fertility of hybrids
29
Cows without the PrP gene
- cow that does not make prion gene so they cannot pass to humans bsc disease
30
Key characteristics of DNA vectors:
1. Contains several/unique restriction sites
- unique restriction enzyme sites on cloning vectors to know this is where we cut the vector
2. Must be introduced into host cells to allow independent replication of vector DNA
3. Marker genes carried by vector to distinguish whether host cells have taken up vector
4. Origin of replication
31
Agricultural biotech
- this technology modifies gene in just a few generations to get to desired trait
- both plants and animals
- Genetic manipulations done to produce transgenic crop plants of agricultural value
Ex: alter genes to confer insect resistance, herbicide resistance, nutritional characteristics
32
Molecular clock
- Time of divergence from a common ancestor estimated based on changes in amino acids/nucleotide sequence
33
Allopatric speciation
- Occurs when 2 populations that can interbreed are geographically/physically isolated from another and lose ability to interbreed
34
Artificial selection
- The process of choosing specific individuals w/ preferred phenotypes for future breeding purposes.
- Response to selection (R) = extent to which a characteristic subjected to selection changes in 1 generation...
Determined by two factors:
1. Narrow-sense heritability
2. Amount of selection(Selection Differential, S)
35
Whole-genome shotgun sequencing
- Approach used to decode a genome by shotgunning into smaller DNA fragments (by restriction enzymes)
- Fragment sequences then ordered based on overlaps in genetic code, and finally reassembled into a complete sequence.
- uses restriction enzymes to digest DNA into contigs which are aligned using computers to assemble the entire chromosome
- Relies on computers, maps are not needed
36
Most populations contain a high degree of...?
- Heterozygosity
37
Restriction fragment length polymorphism (RFLP)
- fragments of DNA with variations in nucleotide sequences
- changes in DNA sequence that introduce/remove restriction sites, restriction enzymes can't cut
- base changes between individuals will introduce/remove RE sites
- these cuts/DNA markers show differences in availability and placement of restriction sites in a species' genome.
- results in unique patterns in individuals
- can trace within families
- To test if someone has this alteration:
- use PCR and do a restriction digest (expect to have two restriction enzyme sites)
- observe numerous affected and unaffected individuals and observing which known RFLPs are inherited in tandem with the disease
38
Nonsynonymous substitution
- Nucleotide changes that DO alter amino acid sequence
39
Northern Blot
- process of transferring RNA fragments from gel to membrane
- Same process used as Southern blotting, but for RNA fragments
- Used to detect specific sequences of RNA by hybridization with complementary DNA.
40
Gene-expression microarray
- Analyzes gene-expression patterns in genetic diseases b/c progression of healthy tissue to diseased is accompanied by changes in expression of hundreds to thousands of genes
- Hundreds of thousands of experiments can be done at the same time
- Allows for direct comparison of 2 samples
- Expression arrays can also detect host response to certain pathogens
- Allows faster diagnosis/identification of pathogen
- Could provide target for treatment
Ex: cancerous cells vs. not
41
HW equilibrium
- at this point, expected genotypic frequencies are the square of the allelic frequencies and allelic frequencies determine the frequencies of genotypes
- For a single AUTOSOMAL locus
42
cDNA library
- RNA undergoes reverse transcription to form DNA, many fragments of cDNA
- Contains DNA sequences only from genes that are transcribed, so noncoding sequences not included
- a look at what is being expressed at the moment mRNA was collected
43
Quantitative measure of phenotype
- Phenotypic variance (VP) = differences between members of a group
44
What quantitative characteristic yield similar phenotypes even if genotypes are different?
- Polygenic Characteristics
45
Goals for modifying plants
- resistance to insects, environmental changes, herbicides
| ex: golden rice had vitamin A added
46
If Hardy-Weinberg is met...
- Evolution does NOT occur
B/c there is no change in allelic frequency
- reproduction alone does not alter allelic or genotypic frequencies AND ALLELIC FREQUENCIES determine FREQUENCIES OF GENOTYPES
47
long term effect of natural selection
- directional selection; fixation of one allele
| - overdominant selection; equilibrium reached
48
Structural genomics
- Studies the organization/sequence of genetic info contained within in a genome
49
Polygenic trait
- A trait controlled by two or more genes that contributes to phenotype
- The alleles in the genes are additive and quantitative
50
Two-dimensional gel electrophoresis (2DGE)
- Separates proteins based on isoelectric point (the pH their net charge= 0, horizontal separation) then size (vertical separation)
- Thus, 2 dimensions: proteins move along Y-axis and X-axis
51
Genetic-environmental variance (Vge)
- The environmental effect on a gene
| Ex: AA grows better in dry environment, aa grows better in wet environment
52
Transcriptome
- All the RNA molecules transcribed from a genome
| - The full range of mRNA molecules expressed by an organism
53
Intensity of wheat kernels' red pigmentation experiment
A good model for this consists of:
1. Genes affecting color segregate at 2 loci (in this case)
2. Gene effect is additive
3. environment plays no role
4. Unlinked loci
54
Gene pool
- The genetic information carried by members of a population
55
PCR is a diagnostic tool for:
1. Genetic testing
2. Identification
3. Parentage
56
Bioinformatics
- Emerging field consisting of molecular biology and computer science that centers on developing databases, computer-search algorithms, gene-prediction software, and other analytical tools
- an interdisciplinary field that develops and improves upon methods for storing, retrieving, organizing and analyzing biological data.
57
Biopharming
- The production of valuable(therapeutic) proteins in GMOs (animals and plants)
58
Low heritability estimate
- this indicates environmental factors may have a greater impact on phenotypic variation
59
Genetic bottleneck
- Following population reduction, drift can causes loss of alleles
- genetic diversity of population is reduced
60
Population
- A group of individuals belonging to the same species that live in a defined geographic area and actually/potentially interbreed
61
How do we determine if a population is in Hardy-Weinberg Equilibrium?
- Find out if the genotypic frequencies expected (under HWE) are the same as those that are actually observed
1. p = f(A) = (2nAA +nAa)/2N
2. q = f(a) = (2naa +nAa)/2N
3. nAA = of AA individuals
4. nAa = of Aa individuals
5. naa = of aa individuals
6. N = total # of individuals (2N b/c diploid, so two alleles at a locus)
62
How to read gel electrophoresis/DNA sequence for Sanger sequencing:
1. Template DNA strand:
- read bottom to top 5'->3' direction (smaller frag at bottom larger at top)
2. Complementary strand:
- find template and antiparallel of that 3'->5' direction
63
Mutation and its affect on allelic frequencies
- All genetic variants arise through mutation
| - BUT mutation alone has little impact on changing allelic frequencies (takes a LONG time, many generations)
64
Contiguous fragments (contigs)
- A group of overlapping clones of DNA fragments representing regions of the genome
- Result of whole genome shotgun sequencing
65
Mean (x bar)
- The average, the center of a normal distribution
| - Calculated by adding characters of all members and dividing by total # of members
66
Founder effect
- New, isolated populations may have an atypical gene pool because they are founded by just a few individuals
- The smaller the group, worse the diversity
67
Selective breeding
- The selection and breeding of naturally occurring or mutagen-induced variants
- Used to enhance food production from plants and animals
- Done through artificial selection and genetic crosses
68
Transformation
- DNA in the environment is taken up by the cell
| Ex: plasmid
69
Phylogenetic Tree
- graphical representation of evolutionary relationships
| - Nodes, Branches, Rooted
70
Biopharmaceuticals
- Creating a product that is of medical importance through biotechnology
- cloning, cloning vectors
- Insulin was first human gene product manufactured by recombinant DNA technology
71
Epistasis
- A type of gene interaction in which one gene alters the phenotypic effects of another gene that is independently inherited.
72
RNA interference
- The process in which the introduction of dsRNA into a cell causes degradation of mRNAs containing the same sequence
73
Western Blot
- process of transferring protein fragments from gel to membrane
- Same process used as Southern blotting, but for proteins
- Used to identify specific amino-acid sequences in proteins w/ a probe
74
Subunit vaccine
- Vaccines that use only part of the disease-causing virus
| - Utilizes a single or few proteins from a bacterium/virus to stimulate immune response
75
Flourescent In Situ Hybridization (FISH)
- Detects/locates a specific DNA sequence on a chromosome by exposing chromosomes to fluorescent probe
- Probe is hybridized to specific chromosome, reveals location of gene on that chromosome
- Tissues probed for a specific mRNA
- In situ= in cells/tissues
76
Multiple alleles
- are different forms of the same gene
77
Species
- Group of individuals that are able to reproduce
78
Transgenic organism
- Its genome has been permanently changed by the addition of DNA
- The genome is heritable, passed to generations
- "knock in"
Ex: in plants, a resistance to insects; nutritional value
79
Transgene
- in these animals there is foreign DNA in a transgenic organism
80
Reverse Transcription (RT-PCR)
- Detects RNA expression
1. RNA undergoes reverse transcription
2. Resultant cDNA then amplified using PCR
81
Twin studies for heritability
1. Fraternal twins(dizygotic): 50% relatedness, theoretically same env't.
2. Identical twins(monozygotic): 100% relatedness (same genes in common), theoretically same env't
- These twin studies can be used to calculate heritability
82
Non-additive alleles (0)
- alleles that do not contribute to phenotype
83
Chimeras
- genes where some cells have transgene products and others do not
84
Genomic library
- Consists of many overlapping fragments of the genome, w/ at least one copy of every DNA sequence in an organism's genome
- contains every single base pair in someone's genome in one cloning vector in hopes that you have multiple copies and that they overlap (should be identical from one cell type to another but mutations happen)
85
Total genetic variance(Vg)
VG = VA + VD + VI
86
Meristic characters
- Not continuous (discontinuous, also complex), but are determined by genes & environment
Ex: dog litter size (3, 7, 4, not 4.5)
87
What is needed for PCR
1. Template DNA (any nucleotide source)
2. Primers (identifies target and provides starting point)
3. nucleotides (for new strand synthesis)
4. polymerase (to synthesize DNA)
88
Ti Plasid
- this plasmid is tumor inducing
- foreign DNA is inserted into plant host genome
- used to create transgenic plants
89
Haplotype
- A group of alleles inherited together
90
Glofish
- first approved genetically modified pet
- byproduct of attempt to make a bioassay (fish that have ability to glow in response to the trigger of heavy metal contamination) but this did not work out because the glow gene was always expressed, not just in the presence of metal
91
Annealing
- Occurs when recombinant DNA that are single-stranded complementary sequences pair by hydrogen bonds to form double-strand
92
Plasmids
- Type of vector
- Replicate independently of bacterial chromosome
- can be constructed to have all the traits we need
93
Genome-wide association studies (GWAS)
- A method to compare the whole genomes of unassociated people either w/ or without the particular disease
- Utilizes molecular markers (SNP, RFLP, etc.)
- Look for alleles of markers (microsatellites or SNPs) that are more often associated with the “disease” phenotype than the control phenotype
- Does not require use of genomic library
- Goal: Find regions (markers) of genome that are associated w/ the disease
94
Mutation
- all genetic variants arise through mutation
- Alleles mutate via forward and reverse mutation
- Mutations all by themselves have very little impact on allelic frequencies
- Necessary to get new allele, but then the actual change takes thousands of generations
- Mutation on its own isn't enough to lead to evolution, but any other factors come in and influence it, you can see rapid changes in allelic frequencies
95
Gene Cloning
- amplification of a specific piece of DNA
| - most often in bacterial cells
96
Restriction enzymes/endonuclease
- Produced chiefly by bacteria
- Restriction endonuclease: Recognizes, binds, then cuts DNA at restriction site, specific sequence of bases
- recognize and degrade viral DNA, thus preventing viral infection; defense mechanism against infection by viruses
- Double-strand cut by cleaving phosphodiester bonds
- Type 2 is the only cut within the recognition site
97
Recombinant DNA Technology is instrumental in developing:
1. More sensitive crime scene forensics
2. Transgenic plants and animals
3. Pharmaceuticals
4. Whole-genome sequencing
98
Both calculations for quantitative traits require what?
1. The use of homozygous strains
2. Assumption that genes have equal influence in determining character
3. Loci are unlinked
4. F2 phenotypes are not affected by environment
99
Negative Number for Correlation
genes that cause an increase in one trait cause a decrease in the other trait
100
Predictions of hardy-weinberg law
ASSUMES:
- there is an equal rate of survival and reproduction (no selection)
- no new alleles arise or are created by mutation
- there is no migration into or out of the population
- the population is infinitely large
- random mating occurs
Predictions
1. Allelic frequencies of a population do not change
2. Genotypic frequencies will not change after one generation
101
Quantitative characteristics (2 types)
- continuously varying traits
1. Polygenic:
- result from the action of many genes
- traits that result from genes at more than one loci (lots of variation)
2. Multifactorial/complex traits:
- phenotypes result from genes and environment
- Environment can impact
Ex: height, number of seeds
102
What decreases genetic variation within populations?
- Genetic drift
103
When taking samples of a population:
1. Must be taken at random
| 2. Must be large enough that chance does NOT influence
104
Different genetic tests using molecular markers (3):
1. Restriction fragment length polymorphism (RFLP):
- changes in DNA sequence that introduce/remove restriction sites, restriction enzymes can't cut
2. Variable number of tandem repeats (VNTR):
- differences in copy number of a sequence in DNA
- mini-/microsatellite
3. Single nucleotide polymorphism (SNP):
- a single base change
105
Prokaryote Genomes
1. Smaller DNA range
2. Number of genes Average: 1 gene per 1000 bp
- KNOW THIS
3. About 50% of genome have assigned function
106
Transgenic Atlantic salmon
- these altered animals overexpress a growth hormone gene; brings value to producers
- Weigh an average of 10 times more than nontransgenic strains
107
Realized heritability
- The heritability determined by selective breeding and measuring the response in the offspring
- h2 = R/S
(Selection Response divided by Selection Differential)
108
Subcomponents of genetic variance (Vg)
1. Additive genetic variance (Va):
- additive effect of genes on phenotype
2. Dominance genetic variance (Vd):
- not additive, some genes have dominant influence
3. Genic interaction variance (Vi):
- genes at diff loci may interact like alleles at same locus (so impact is not additive)
109
Blunt ends
- DNA fragments that are both cut as same nucleotide pair (no overhanging ends) by restriction enzymes
110
Calculating number of polygenes for a low number of polygenes
- 2n + 1 = # of distinct phenotypic classes observed
- If 2 polygenes involved, n=2
- Then 2n + 1= 5 and each phenotype is the result of 4, 3, 2, 1, or 0 additive alleles
111
Threshold characteristic
- A characteristic that is either present or absent
112
Probe
- DNA or RNA that is complementary and antiparallel to a sequence from gene of interest
- Short segment of radioactive DNA/RNA that will hybridize with gene of interest and allow its presence to be detected (fluorescent)
- Is complementary to the gene of interest
113
Natural Selection
- differential reproduction, individuals with certain genotypes produce more offspring
Keys:
1. More individuals are produced each generation than survive to reproduce
2. Lots of phenotypic variation
3. Some phenotypic variation is heritable (due to genetic variance)
- THEREFORE, ADAPTIVE TRAITS INCREASE IN A POPULATION THROUGH TIME!
114
Gene-expression microarrays also used to detect host response to pathogens.
The purpose of this is to:
1. Allow faster diagnosis/identification of pathogen
| 2. Provide a target for treatment
115
Biological Evolution
- Genetic change takes place in a group of 2 organisms
| - Changes that occur in the gene pool(genetic changes in groups)
116
Which characteristic can vary continuously in a population?
- A Quantitative character
| ex: Human height
117
Discontinuous/qualitative characters
- Possess only a few distinct phenotypes
- Can be measured in an individual
Ex: green vs. yellow peas (characters that Mendel studied)
118
PCR (Polymerase Chain Reaction)
- taking process of replication out of cell and using it in tube to amplify piece of DNA and target the amplification piece
119
Gene Deserts
- large area on genome with no known genes
| - versus gene-rich clusters
120
DNA library
- Collection of clones containing all DNA fragments from one source (tissue type, cell type, or single individual)
121
Dominance genetic variance (Vd)
- Not additive
| - some genes can have dominant influence
122
Total Phenotypic variance (Vp)
- The total differences between members of a group/population
- Consists of genetic, environmental, and genetic-environmental variances
- VP = VG + VE + VGE
123
Multiple-gene hypothesis
- Many genes contribute to phenotype in a cumulative, quantitative way
- Each gene behaves in a Mendelian fashion
- As the # of loci affecting a character increases, the # of phenotypic classes increases
124
As the number of loci affecting a character increases...
- The number of phenotypic classes also increases
125
Genomics
- Field of genetics that attempts to understand the organization, function, evolution of genetic info contained in whole genomes
126
Calculating the number of genes contributing to a quantitative trait (# of polygenes)
1. Usually: 1/4^n
- where n= number of loci that affect character
- Set this equal to the extremes in the offspring
- 4 pigment genes make it all purple, so 1/16 of the offspring are all purple and this is the extreme
- 1/16 = 1/4^n
- n = 2
Ex: If 1/16 of F2, then n=2
127
Synonymous substitutions
- Nucleotide changes that do NOT alter amino acid sequence
128
Transgenic Cows
- Expresses lysostaphin transgene in milk
| - can kill Staphyloccus aureus before it can cause inflammation and damage to mammary tissue
129
Functional Genomics
- Determining what DNA sequences do
| - what their function is
130
Environmental variance (Ve)
- Different phenotypes in a population are due to environmental differences
131
Humulin
- was first produced by cloning the human gene for insulin and expressing it in bacterial cells.
132
long term effect of genetic drift
- fixation of one allele
133
Severe Combined Immunodeficiency (SCID)
- in this disease there are no functional T and B lymphocyte
- First human disorder treated with gene therapy successfully
- bone marrow transplant in "bubble boy"
134
Expression Vector
- this vector allows protein production and has additional sequences that allow transcription and translation to occur
- prokaryotic and eukaryotic host cells
ex: Ti plasmid
135
Microarray
- Monitors gene expression in different tissues (diff tissues have same genome as other cells but diff gene expression)
- Hundreds of thousands of experiments can be done at the same time
- Nucleic acid hybridization occurs from a probe
- Each dot/color on microarray corresponds to hybridization of probe and level of expression
Ex: bright fluorescence means highly expressed gene in tissue sample
136
Broad-Sense Heritability
- H2 = VG/VP
- this calculation yields the proportion of phenotypic variance due to genetic variance
- 0 = none of phenotypic variance is due to differences in genotype, prob due to environment
- 1 = all variance due to differences in genotype, not due to environment
137
Gene Therapy
- Therapeutic technique that aims to transfer normal genes into a patient's cells
- limited to SOMATIC gene therapy: will ONLY affect person undergoing therapy, not inheritable
- Exception: mitochondrial therapy for females only
Goal: to cure the disease, not just treat
138
What increases as eukaryote complexity increases?
- Number and length of introns
139
Genic interaction variance (Vi)
- genes at diff loci may interact like alleles at same locus (so impact is not additive!)
140
Effective population size
- The number of individuals in a population who contribute offspring to the next generation
141
What decreases genetic variation between populations?
- migration
142
Inbreeding coefficient
- (F)
- Quantifies the probability that 2 alleles of a gene in an individual are identical because they descended from the same single copy of the allele in an ancestor
- F=0 , no individ has 2 alleles derived from common ancestral copy (mating is random)
- F=1, all individs in pop are homozygous, identical by descent (complete inbreeding)
143
calculating fitness
- average the number of offspring/genotype divided by the mean number of offspring produced by the most prolific genotype
144
Recombinant DNA technology: "gene splicing"
- set of molecular techniques for locating, isolating, altering, and studying DNA segments
- allows the creation and manipulation of different DNA sequences that come from different sources
- "gene splicing"
145
What type of characteristic occurs in which each genotype produces one(or a few, depending on dominance/epistasis) phenotype?
- Discontinuous characteristics
146
long term effect of mutation
- equilibrium reached between forward and reverse mutations
147
Inbreeding
- a type of nonrandom mating
- preferential mating between related individuals
- is a form of PAM for relatedness, leads to increase in homozygotes in a population
- Whole genome is affected
148
Systems Biology
- Combines transcriptome, proteome, and genome information, makes connections between them
149
How much of DNA in human genome is derived from transposable elements?
- ~45% of DNA in human genome is derived from transposable elements
150
Additive alleles (+)
- contribute (equally) to quantitative phenotype
- The basis of continuous variation
- Each allele contributes equally to a trait, and contribute to most observable traits (phenotypes)
- alleles of different genes that affect the same trait
Ex: height, weight, eye color
151
Biotechnology
- use of living organisms to create a product or a process that helps improve the quality of life for humans and other organisms
152
Test For Heritability
- Cross the extremes of parental generation
- In the same environment, if genetics play a role in phenotype, means will be different
- Take extremes of a population and will see a shift in population mean if it's heritable
- Use other extreme, shift the other direction
- Not heritable: still get same amount of variation since you haven't changed the environment
- For P1 cross: both parents from genetic extremes, very divergent.
- This artificial selection creates homozygosity, so that any phenotypic differences are the result of the environment. (i.e. heritability decreases as natural selection takes place)
- > Artificial and natural selection begin to compete
153
Hybridization
- Attachment of probe to its complementary base sequences in the target DNA, complimentary to gene of interest
154
Impact of genetic drift
1. Changes allelic frequency in a population
- increase or decrease = drift!
2. Reduces genetic variation in a population
- An allele can reach a final frequency = 0 the allele is lost!
- Or = 1, which means the allele is FIXED (process = fixation)
3. Different populations diverge differently Fixation occurs for different alleles!
- Can cause genetic divergence between populations to increase
155
PCR Stages
1. Denaturation
- heating DNA to break hydrogen bonds and split into single strands; 92-95 DEGREES
- uses Taq polymerase bc resistant to heat
2. Annealing
- cooling DNA so some hydrogen bonds can form and targeted primer can stick to the strands, region between primers is what we want to amplify; 45-65 degrees
3. Extension
- polymerase attached to the 3' OH and starts synthesizing that fragment of DNA; 65-75 degrees
- repeat this process around 30X
- DNA can be amplified exponentially
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Differential Selection (S)
- Difference between the mean phenotype of select parent and mean phenotype of original population
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Sanger Sequencing
- very similar to PCR but uses ddNTP, which causes the elongation to stop because there is no 3' OH group (polymerase gets 3' OH group from primer)
- if polymerase grabs a regular base it keeps going, if it adds a dd base, it stops
- ddCTP, ddATP, ddGTP, ddTTP used to locate exact DNA sequence b/c each strand synthesized differs in length by one nucleotide
- Fragments separated by gel electrophoresis
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Normal distribution
- A function that represents the distribution of variables as a symmetrical bell-shaped graph when the sample is large
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Physical maps
- Based on direct DNA sequence and distance between genes
| Ex: whole-genome & map-based shotgun sequencing
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Process of gene cloning
1. Identify restriction enzyme sites that are the same between the fragment of interest and the cloning vector
2. Cut cloning site with restriction enzyme
3. Fragment is incorporated into the cloning vector and ligase seals them together (recombinant cloning)
4. Transformation takes place
5. Check whether transformation AND ligation were successful with selectable markers
Ex:
- if cells survive with ampicillin, they contain the cloning vector and were successfully transformed
- cells that are BLUE are nonrecombinant and cells that are WHITE are recombinant
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Edible vaccine
- these vaccines hope to use recombinant technology to modify naturally growing plant to be able to cause immune response when eaten
Ex: eating a banana will trigger an immune response to a pathogen
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EnviroPig
- this animal breaks down dietary phosphorous
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Multiple Cloning Sites
- Multiple restriction sites for commonly used restriction enzymes, found on plasmid vectors
- this site is where a whole group of restriction enzyme sites are needed to allow the vector to be functional for making different pieces of DNA
- want to have sticky ends to match up to what we will be cutting this vector with
- cohesive ends are preferable
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When investigating Hardy-Weinberg, how many loci are considered?
- One single locus
| - Because one locus may be in HW equilibrium, while another is not.
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Genetic Maps
- Based on recombination frequencies
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Negative assortative mating(NAM)
- unlike individuals mate
- Dissimilar genotypes are more likely to mate
Ex: plant species have pollen/stigma recognition system that prevent fertilization between plants w/ same alleles at key loci
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Microinjection
- A technique for introducing a solution of DNA into a cell using a fine microcapillary pipette
- Injects many copies of a transgene into pronucleus of a gamete
- 10-30% eggs survive; even less contain integrated transgene
- If in germ-line, then passed on to generations (can be in somatic cells, not inherited)
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Variance (s^2)
- Indicates variability of a group
(amount of spread in a distribution)
- The greater the variance, the more spread out the distribution is about the mean
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Proteome
- All the proteins encoded by the genome
| - The set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions
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Non-random mating
- Some subgroups within population either preferentially mate with each other or refrain from mating with each other.
- Does NOT change allelic freq
- Changes hetero/homozygotes in pop
- just how they end up together in the next generation
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Cloning Vectors
- Stable, replicating DNA molecule that can be attached to a piece of foreign DNA and introduced into a cell
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Selection coefficient (s)
- relative selection AGAINST a genotype
- s = 1-W
- Selection for a genotype means selection AGAINST a genotype!
- It is the fitness of the inferior genotype
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Stats
- Normal Distribution has most individuals in middle with extremes on either end
- Can take samples that must be large and random to find averages
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Estimating allelic frequencies
- can do this with info on homozygous recessive traits
- Assume population is in HWE, expected genotypic frequencies are the square of the allelic frequencies
- Frequency of homozygous recessive (aa) = q2
- So, q = square root of frequency of a
Ex: Cystic fibrosis - 1 in 2000 people
= 0.0005
q =Square root of 0.0005 = 0.02 (so about 2% of alleles are recessive)
p= 1 - q= 0.98
Use these values to find frequency of AA and A:
f(AA)= p2 = (.98)2 = 0.96
f(Aa) = 2pq = 2(0.02)(0.98) = 0.0392
So, ~ 4% of population is heterozygous for allele that cause CF!
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What increases genetic variation within populations?
1. Mutation
| 2. Migration
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Biological Species Concept
- Members of the same species have the potential to exchange genes; different species cannot
- A species is a group of organisms that can interbreed and produce fertile offspring.
- They do not have to be interbreeding, they just CAN
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Genome evolution examples
1. Gene duplication
- leads to multigene families
2. Whole-genome duplication
3. Horizontal gene transfer
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Knock-out
- Occurs when researchers have inactivated (knocked out) an existing gene by replacing it or disrupting it with an artificial piece of DNA
- this causes a gene to be completely disabled
- synthesize a transgene that is homologous to target gene and has selectable markers
- produces a giant marker in the middle of chromosome instead of a functional gene product
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High heritability estimate
- this indicates genetic factors cause much of the variation and environment has less of an impact
- does not indicate that environment has NO impact on trait
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Selection Response (R)
- The extent to which a characteristic subjected to selection changes in 1 generation.
Determine by:
1. Narrow-sense heritability
2. Amount of selection (Selection Differential, S)
- R= h2 x S
(this is the expected change in the offspring's characteristic in original population)
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Southern blotting
- Edwin Southern
| - Process of transferring DNA fragments from gel electrophoresis to membrane w/ a probe
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Limitations of Heritability
- Selection can be very effective, but it can be limited
| - usually puts competing genes in natural selection
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Genetic variance (Vg)
- Different phenotypes in a population are due to different genotypes
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Map-based sequencing
- Used to first create genetic/physical maps of genome
| - Provides known locations of genetic markers at regularly spaced intervals along each chromosome
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Comparative genomics
- Compares similarities/diff in gene content, function, organization among genomes of different organisms
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What causes genetic changes in a population?
1. Mutation
2. Migration
3. Assortive mating
4. Recombination
5. Genetic drift
6. Natural selection
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Plasmids contain...
1. Origin of replication
2. Multiple cloning site
3. Selectable marker: Genes that confer resistance to particular antibiotics or lets the cell use a specific nutrient
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Genetic Correlation
- often result of pleiotropy (one gene that affects multiple characteristics)
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Palindrome
- Most restriction sites are nucleotide sequences that read the same on both DNA strands when read 5' to 3'
- restriction sites are 4-8 bp long
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How to make dna libraries
- cut up genomic DNA, want overlapping fragments that can be hooked together
1. Colonies of the library are overlaid with a DNA-binding membrane such as nylon
2. Colonies are transferred to membrane, lysed, and DNA is denatured
3. Membrane is placed in a heat-sealed bag with a solution containing the labeled probe; the probe hybridizes with denatured DNA from colonies
4. Membrane is rinsed to remove excess probe, then dried; X-ray film is placed over the filter for autoradiography
5. Using the original plate, cells are picked from the colony that hybridized to the probe
6. Cells are transferred to a medium for growth and further analysis
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Alignment
- Similar sequences of bases such as contigs are lined up for comparison and to create a complete DNA sequence
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Positive number for correlation
- Genes that cause increase in one trait causes an increase in another trait
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Sympatric speciation
- No external/physical barrier
- Speciation that occurs in populations that live in the same area
- RIMs evolve within a single population
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Eukaryote Genomes
1. Genomes larger than proks
2. No relation between genome size and complexity/number of genes
3. Gene deserts
4. Transposable elements
- ~45% of DNA in human genome is derived from transposable elements
5. Protein diversity
- Modifications greatly increase number of proteins
6. Number and length of introns increases in more complex eukaryotes
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DNA Ligase
- The enzyme that seals phosphodiester bonds through covalent bonding
- Forms recombinant DNA
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Sticky ends
| cohesive ends
- End of a DNA double strand at which a few unpaired nucleotides of one strand extend beyond the other
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Frequency distribution
- large number of factors contribute to a measurement
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long term effect of migration
- equilibrium reached when allelic frequencies of source and recipient population are equal
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Genetic engineering
- Altering an organism's genome
| - Creating genetically modified organisms (GMOs)
