Week 2 Flashcards
1
Q
How can DNA change?
A
Change during replication or due to unrepaired DNA damage
2
Q
What are types of DNA changes?
A
Point mutations
Recombination
Dulication (genes or chromosomes)
Chromosome rearrangements
3
Q
What can cause point mutations?
A
Normally a mistake during DNA replication
Also be caused by exposire to xrays, UV and chemicals
4
Q
What are the types of point mutations?
A
Substitution mutations
Insertions
Deletions
5
Q
What are the 2 types of substitution mutations?
A
Transitions - purine to purine or pyrimidine to pyrimidine
Transversion - purine to pyrimidine or pyrimidine to purine
6
Q
What is a key trait about the genetic code?
A
Degenerate
64 codons only encode 20 amino acids
Each amino acid is coded for by more than one codon
7
Q
What is a key trait about the 3rd most amino acid in a codon?
A
It is the most degenerate
8
Q
What causes sickle cell anaemia?
A
Point mutation changing CTC to CAC causing change from glutamic acid and valine
9
Q
WHat are diseases caused by frameshift mutations?
A
Cancer, Crohn’s, cystic fibrosis
10
Q
What are frameshift mutations?
A
Insertions or deletions that cause a knock on effect impacting a the remaing amino acids on the gene
11
Q
What are substitutions?
A
Mutations that have been passed in across generations
12
Q
What are used to measure the divergence from a recent common ancestor?
A
Look at coding DNA (exons) of two species diverging from
a recent common ancestor
13
Q
What are the two key features of substitions?
A
Synonymous substitutions accumulate at a faster rate than non-synonymous substitutions
Transitions accumulate faster than transversions
14
Q
What can impact the rate of substitution?
A
Low rate of substitution at non-degenerate sites (where mutations cause amino acid sequence changes)
High rate of substitution at degenerate sites (which do not change the amino acid sequence)
15
Q
What is recombination?
A
Based on alignment of DNA in homologous chromosomes during meiosis (cell division to produce gametes)
Shuffles gene combinations as a normal function of meiosis
16
Q
What are the two forms of recombination?
A
Inter-genic (between genes)
Intra-genic (within genes)
17
Q
What is the advantage of recombination?
A
Allows molecular change through new combinations
18
Q
What is linkage disequilibrium?
A
Linkage disequilibrium is the non-random association of alleles at different genes
19
Q
Whats the difference between complete linkage disequilibrium and linkage equilibrium?
A
If alleles always inherited together, genes are in complete linkage disequilibrium
If inheritance of alleles is random, genes are in linkage equilibrium
20
Q
How does recombination reduce linkage disequilibrium?
A
Bad - breaks up linked genes/alleles - destroys beneficial genetic combinations
Good - allows adaptation by shuffling gene combinations and bringing together mutations from different sources
21
Q
What organisms does recombination occur?
A
Recombination only occurs in sexually reproducing species
22
Q
What are the benefits of recombination?
A
The benefits of recombination in facilitating evolutionary
adaptation are thought to be a key reason behind the evolution of sex
23
Q
What is DNA duplication?
A
Duplication of sections of DNA, entire genes or chromosomes
24
Q
What are examples of DNA duplications?
A
Unequal crossing over
Transposition (back to later)
Non-segregation of chromosomes during cell division
25
What is gene family?
Set of similar genes formed by duplication from a single gene
26
How can gene families vary?
Duplicated genes in families can
take on new functions
27
What is an example of duplication in a gene family?
Duplication has been an important source of new genes with different properties (e.g. foetal haemoglobin) also seen in the difference in the evolution in the ancestral beta-globin gene across birds and different groups of mammals
28
What is polyploidy?
Increase in chromosome number (>2n)
“Even” polyploids (4x, 6x) are often fertile, but “odd” polyploids (3x, 5x) are usually sterile
29
What causes polyploidy?
Failed seperation of chromosomes in meiosis
30
Can polyploid organisms reproduce with original diploid individuals?
Polyploids cannot usually reproduce with original diploid individuals – leads to rapid divergence and speciation
31
What is a key trait of polyploids?
Have many duplicated genes (genetic innovation)
32
What is ployploidy like in animals?
Relatively rare in animals (found in some
invertebrates, fish & amphibians)
33
How common is polyploidy in plants?
Common in plants (50-80% of naturally occurring plant species)
34
What is polyploidy like in crops?
Many crops are polyploid (e.g. wheat,
sugar cane)
Even odd number (i.e. sterile) polyploids are useful as crops
Produce fruits that lack seeds (bananas and grapes)
But limits further development of the crop, as reproduction must be vegetative.
35
What are the key features of translocation?
Movement of DNA between non-homologous chromosomes
Usually rare
Implicated in number of diseases (usually caused by disruption of gene function)
36
What are the key features of fission/fusion?
Chromosomes can split (fission) – thought to be important in avian evolution
They can also combine (fusion)
Human chromosome 2 formed by fusion of two ancestral chromosomes (hence 23 pairs of chromosomes in humans vs 24 in chimps and gorillas)
37
What is the overview of inversions?
End-to-end re-arrangement of a chromosome segment
Recombination reduced between inverted and non-inverted chromosomal regions (because they no longer align)
Seen as a key mutational force in evolution
38
What are examples of inverison?
Breeding polymorphisms in ruff the result of 2 inversions on the same chromosome
39
What other method can cause DNA changes?
Changes resulting from DNA repair
40
How does gene conversion occur?
DNA change is countered by repair - ‘proof reading' enzymes carry this out
‘Repair’ of one chromosome is made by copying the oher
41
What are the two types of gene conversion?
Part of one allele is copied across to the other = allelic or intra- locus gene conversion
Similar process can occur across duplicated genes = non-allelic or inter-locus gene conversion
42
What is the link between gene conversion and genetic diversity?
Gene conversion can both increase and decrease genetic diversity
43
How does gene conversion impact genetic diversity?
Like recombination, gene conversion can generate new alleles by ‘shuffling’ sections of DNA between alleles and duplicated genes
Continued gene conversion will eventually homogenise genes – thought to be why duplicated genes are often very similar to each other, even if duplication events are ancient (concerted evolution)
44
How can new DNA be added to a genome?
Transposition
Horizontal gene transfer
Hybridisation
45
What are transposable elements (jumping genes)?
Genetic elements capable of moving from one
location in a genome to another
Usually encode their own ‘transposase’ enzyme
Parasitic or ‘selfish’ DNA
46
What are class I: Reterotransposons (copy and paste)?
Common in plants (90% of wheat genome)
Include long interspersed elements (LINEs); around 100,000 of these in your genome (~17%)
47
Where are class 2: DNA transposons found?
Rare in humans (<2% genome); common in bacteria
P elements in Drosophila (used in making GM flies
48
What are the effects of transposable elements?
If a transposon lands in the middle of a gene, it may disrupt function (and cause disease)
Causes unequal crossing over
Can cause inversions, translocations and deletions
Effects on gene expression currently debated
49
What is vertical transmission?
Inheritance of DNA from parents to offspring
50
What is horizontal gene transfer?
Horizontal gene transfer is movement of genetic material between organisms other than via vertical transmission
51
What is transformation?
Natural taking up of external DNA which integrates into the host genome
52
What is transduction?
Movement of DNA between organisms via a virus
53
What is conjugation?
Transfer of DNA via a plasmid during cell-to-cell contact
54
How does horizontal gene transfer impact antibiotic resistance?
Antibiotics place strong selection pressure on bacteria to evolve resistance
Antibiotic resistance genes can rapidly spread among bacterial species via HGT
Don’t have to wait around for the mutation to come along independently
55
How does horizontal gene transfer impact cellular organelles?
Mitochondria originated via endosymbiosis of a proteobacterium
Mitochondrial genes now found in the nuclear genomes of eukaryote cells
There has been horizontal gene transfer from the organelles to the nucleus
Prevents build-up of deleterious mutations in the mitochondrial genome?
56
What is hybridisation?
Acquisition of new DNA through hybridising with another species
57
What are the different types of hybridisation?
Chromosomes from each parent species in offspring
Recombination shuffles genes from both species together
58
What is an example of hybridisation?
In Heliconius butterflies, mimetic colour patters evolved by hybridisation and exchange of colour genes among species
59
What is molecular evolution?
Molecular evolution is a change in DNA sequence composition across generations
60
How does molecular evolution occur?
Many mutations do not lead to evolution, but mutations are essential for evolution to occur
Other evolutionary forces (genetic drift, natural selection) act on mutations, which leads to evolution
61
What does natural selection impact?
Natural selection the major driver of phenotypic evolution
Is natural selection important in molecular evolution?
62
What is the selection-neutralism debate?
Debate of the evolutionary processes in molecular evolution
63
What is neutralism?
Originated with Motoo Kimura
Most variation at molecular level is selectively neutral, fixed by genetic drift
Most non-neutral mutations eliminated by selection
64
What were Darwins four postulates of evolution in the Origin of Species?
1 - Individuals within species are variable
2 - Some variations are passed on to offspring
3 - In every generation more offspring are
produced than can survive
4 - Individuals who survive and go on to reproduce
are are naturally selected
65
What is natural selection based on?
Heritable variation within populations
66
What was Darwin's prevailing belief in heritable variation?
Blending inheritance, in which heritable factors blend to produce an intermediate phenotype
67
What is wrong with the idea of blending inheritance?
But this doesn’t work, because if offspring phenotypes must always be intermediates of parents, all individuals would look the same after just a few generations
68
Who developed the theory of particulate inheritance?
Gregor Mendel 1866, the theee "laws"
69
What is the the law of segregation?
Individuals possess two alleles at each gene – one from each parent
70
What is the law of independant assortment?
Genes for separate traits are passed on independently from parents to offspring (NB this is not always true - remember linkage disequilibrium)
71
What is the law of dominance?
Recessive alleles will always be masked by dominance alleles
72
What happened in the 1930s with respect to evolutionairy biology?
Unification of Darwin and Mendel's theories
73
What were the 5 main unification points between Darwin and Mendel's theories?
*Heritable genetic variation is the principal material for natural selection.
*Fixation of beneficial changes by natural selection is the main driving force of evolution
*Natural selection operates on ‘infinitesimally small’ variations, so evolution is gradual
*Species are a central unit of evolution, and speciation a key evolutionary process
*The entire evolution of life can be depicted as a single ‘big tree
74
What was Darwin’s four postulates after the modern synthesis?
1 - As a result of mutation, gene flow and recombination, individuals within populations are variable for most traits.
2 - Individuals pass their alleles to their offspring intact.
3 - More offspring are produced than can survive.
4 - The individuals that survive and reproduce are those with alleles that best adapt to their environment.
75
What three things determine genetic variation within a population?
1 - What fraction of loci are polymorphic?
2 - How many alleles are present at each locus?
3 - What are the frequencies of the different alleles at loci?
76
What were the two schools of though for genetic variation within population until the sixties?
Classical school and Balanced school
77
What is the classical school for genetic variation?
Genetic polymorphisms are rare and mainly deleterious. Each locus, the best allele being fixed by natural selection
78
What is th balanced school for genetic variation?
Large amounts of genetic variation are maintained in populations. At each locus, polymorphisms are maintained by “balancing” natural selection
79
What was right classical school or balanced school?
Neither, they were both wrong though they didnt have any data
80
What did scientists use until the 196os to measure genotype variation?
Until the 1960s, scientists had to use variation in phenotype as a proxy for variation in genotype
81
What can using phenotype variation be useful for?
This works well for discrete variation, where a trait follows a simple Mendelian inheritance pattern
In snow geese (Chen caerulescens) two distinct colour morphs occur, caused by two alleles at a single loci
82
What can't phenotype variation be useful for genetic variation?
Measuring genetic variation is much more difficult for continuous traits
These are mostly polygenic (controlled by many genes)
Human height a classic example
83
When was gel electrophoresis first used?
In 1966, gel electrophoresis was used to visualise genetic (protein) variation for the first time
DNA or protein fragments migrate along a gel according to their size or configuration (shape)
84
What can gel electrophoresis determine?
Can distinguish homozygotes and heterozygotes at individual genes
85
What did gel electrophoresis discover?
Lewontin and Hubby (2 papers on Drosophila), and Harris (humans)
Found that ~40% loci were variable – more than expected
86
What is microsatelillite genotyping?
Rapidly mutating repeat units of DNA (TTC(lower)16 or TTC(lower)18) prone to insertions and deletions
Amplified using PCR
Can distinguish genotypes based on size differences
Useful for DNA profiling and paternity analysis
87
What was the original sequencing?
Sanger sequencing
88
How do you undergo sanger sequencing?
Add your PCR to different tubes with low concentration of either ddATP, ddTTP, ddGTP or ddCTP. Then run them on a gel electrophoresis, then at each position you will be able to identify what each nucleotide is and its sequence
89
What are the next generation sequencing?
Illumina and Pacbio
90
What is the process for library prep for Illumina?
Target DNA is randomly sheared c.500 bps with no overhangs (transposases are used by Illumina)
Ligase an A tail onto the 3' end
A T adapter is added on to the sequence joining the A tail
This is repeated on the 5' end
You add two different indices on the adapters, this allows you to multiplex as the different indices can be pulled apart
91
What happens to DNA created in the library prep?
Polymerases then duplicate this piece of DNA so its now bound to the flow cell. It then forms a bridge structure. The forward strand curls over latching onto the reverse strand primers. Polymerase works its way down, meaning you have a forward and reverse copy of the target DNA. This process happens lots of time. creating a custering effect with the large amounts of DNA formed.
92
What happens to the forward and reverse strand on the flow cell?
The reverse strand is washed away. A blocker around preventing the forming of bridges between these molecules
93
How does the forward sequence on the flow cell get sequenced?
A sequence primer ligates onto the loose end of the target DNA.
Rather than PCR there are lots of free floating nucleotides that have fluoresce attatched to them.
When they bind to the target DNA they fluoresce which is read by a tiny computer in real time
Each different nucleotide has a different colour.
All the clonal strands are read by the computer at the same time requiring 24 to 48 hours
The index is read back allowing you to create an idea where those strands come from
94
What happens when the forward strand is sequenced?
The reverse strand is sequenced
95
How is the reverse strand sequenced?
The bridge like structure is formed again and the Index 2 is read
Polymerases create the reverse strand and the forward strand is washed away
The same process occurs again allowing for the reading the reverse strands sequence
96
What happens when both strands are fully sequenced?
You will get a series of DNA fragment sequences which using analytical methods the fragments can group similar fragments together and aligned correctly for a fairly decent size of genome
97
How can you measure cross-species analysis of nucleotide diversity?
Cross-species analysis of nucleotide diversity (π)
π = proportion (or %) nucleotide sites at which sequences randomly taken from a population differ e.g. 30 base sequence with 3 varying sites, π = 0.1 (10%)
98
What does cross-species analysis of nucleotide diversity show?
Lots of diversity in all species, but also lots of variation
Termite Reticulitermes grassei, 1 in 1000 bp that are variable
Slipper shell Bostrycapulus aculeatus, 1 in 12 bp that are variable
99
What is a case study with scarlet tiger moth (Callimorpha dominula)?
Three colour morphs in Oxfordshire population, differ in white spotting on forewing, and black on red hindwings.
Fisher and Ford wanted to know why these morphs existed at certain proportions, and how these changed over time
100
What did they find about the genes of scarlet tiger moth?
Three colour morphs, differ in white spotting on forewing, and black on red hindwings.
Crosses among individuals showed that colour patterning was due to 2 alleles at a single locus (A and a)
101
What was the proportion of a population of Tiger moths collected by EB Ford of a certain genotype?
AA this is 400 / 1000 = 0.4 (Dominant)
Aa this is 400 / 1000 = 0.4 (Heterozygous)
aa this is 200 / 1000 = 0.2 (Recessive)
102
What is the observed genotype frequency?
Observed genotype frequency = the proportion of a population that has a certain genotype
103
What is allele frequency?
The proportion of a given allele in the population
104
How many alleles are there at the colour locus?
Each moth has two alleles at the colour locus
So there are 1000 x 2 = 2000 alleles in the total sample
105
How many alleles are there at the colour locus?
Each moth has two alleles at the colour locus
So there are 1000 x 2 = 2000 alleles in the total sample
106
What is the frequency of tiger moth allele A?
Dominants have two copies of allele A, heterozygotes have one, so:
The number of copies of A in the sample is: (400 x 2) + (400 x 1) = 1200
The frequency of allele A in the sample is: 1200 / 2000 = 0.6
107
How would you calculate genotype frequencies?
D = nD /N (number of dominant homozygotes divided by sample size)
H = nH /N (number of heterozygotes divided by sample size)
R = nR /N (number of recessive homozygotes divided by sample size)
All individuals have a genotype, therefore: D + H + R = 1
108
How would you calculate the number of alleles?
Num. copies of allele A: nA = 2nD + nH
(dominant homozygotes have 2 A copies)
N of copies of allele a: na = nH + 2nR
(recessive homozygotes have 2 a copies)
109
How would you calculate allele frequencies?
p and q are traditionally used symbols for dominant and recessive allele
frequencies. In a two allele system p + q = 1
110
How would you calculate the frequency of allele A?
The frequency of allele a can be denoted as:
q = na / 2N, or q = (H / 2) + R
111
How would you calculate the frequency of allele a?
The frequency of allele a can be denoted as:
q = na / 2N, or q = (H / 2) + R
112
What is the function of the hardy-weinburg model?
Gives us a way to calculate expected genotype frequencies, given the allele frequencies we observe. for two autosomal alleles
After one generation of random mating, the genotype
frequencies will be
113
What is the hardy-weinburg formula?
p^2 + 2pq + q^2 = 1
p and q are the frequencies of 2 alleles at a single locus
114
What happens if observed and expected genotype frequencies are the same?
A population is in Hardy-Weinberg equilibrium. Allele frequencies will not change over generations
115
What are the 5 assumptions for the hardy-windburg principle and forming of the hardy-weinburg equilibrium?
1 - infinitely large population size
2 - no mutation
3 - no selection
4 - no gene flow
5 - random mating
