WEEK 4

define genetic variation

the differences in DNA sequences or gene arrangements among individuals within a species

is genetic variation always visible

no, some variations will not affect the phenotype, only the genotype

when does a mutation become a polymorphism

when it persists in a population

define polymorphism

when there is 2 or more different forms of a species

what is each allele of a polymorphism called

variant

describe the variation gradient

variation is at its greatest when species are very distantly related

as species become mroe related, the less variation exists between them

why are diploid organisms forgiving with variation

because there are 2 copies of genes present, so we have a “back up”

what are the 2 types of genetic variation

continuous

discontinuous

describe continuous genetic variation

controlled by multiple genes

describe discontinuous genetic variation

controlled by one or very few genes

what are 4 applications of genetic variation

forensics - crime scenes, ID

evolutionary relationships - comparative genomics, phylogenetic trees

production - selective breeding etc

biotechnology - vectors, vaccines

what are the 2 sources of genetic variation

experimental

natural

describe the experimental source of genetic variation

induced mutagens

cloning

describe the natural source of genetic variation

errors in replication

natural mutagens

natural selection

sexual reproduction

what are the 4 mechanisms of population variation

mutation

migration

genetic drift

natural selection

explain mutation

it is a new variation, resembling neither parent, which occurs by chance

it is a permanent change in the gene or chromosome

explain migration

it is when individuals of a population move and join a different population, introducing new genes potentially

explain genetic drift

random change in frequency of genes in a population as a result of a chance event

this includes the founder effect and the bottleneck effect

explain natural selection

when organisms with a survival advantage reproduce and pass on their genes, and those without the advantage do not

what is the hardy weinberg principle

that genotype frequencies (and therefore allele frequencies) remain constant over succeeding generations

what conditions must be met for the hardy weinberg principle to be true

1. members of the population mate randomly

2. selection is unbiased and does not favour or disfavour a particular allele or genotype

3. mutation does not change allele frequency

4. migration does not occur and change allele frequencies

5. a large population is studied

how do we find allele frequency

it is the number of given copies of a given allele divided by the total number of copies of all alleles in that locus

what do natural selection and genetic drift require to operate

genetic variation

what are the 3 types of genetic variation at the DNA level

chromosomal

small segment

single nucleotide (point mutation)

what are the 2 types of chromosomal variance

chromosomes can vary in structure and in number

explain chromosomal structure variance

structure can change because of:

• deletions

• duplications

• inversions

• recombination

(this is on large scale)

explain chromosomal number variance (give examples)

sometimes organisms inherit too many or too little chromosomes

examples are of too many are klinefelters, down syndrome, patau syndrome and edwards syndrome

example of too little is turner syndrome

describe klinefelters syndrome

XXY in sex chromosomes

they are usually taller, some breast devleopment, have reproductive issues

they otherwise live a normal life

describe patau syndrome

trisomy 13

it generally results in prenatal death, due to the body naturally aborting before the 12th week

if born they may have extra digits, smaller heads, large foreheads, small ears and mental retardation

describe turner’s syndrome

only have one X chromosome in the sex chromosomes

most foetus’ will be aborted before pregnancy goes to term

if born they will be shorter, webbed fingers, short necks, bad spatial awareness, and no secondary sex characteristics

explain small segment variation

the variation is small relative to the size of a chromosome

these include insertions, deletions, inversions, duplications and repetitive elements

what is the effect of point mutations on proteins

most proteins have core regions, so if a deletion occurs then the species likely will not persist

mutations can affect the coding, non coding, regulatory and intergenic regions of a protein

these mutations might result in: incorrect protein, no protein, incorrect splicing, incorrect sorting and/or stability of RNA

describe thalassemia

a condition due to the mutation of alpha or beta globin genes

the mutation is either a transition, transversion, deletion or insertion point mutation

It affects the production of haemoglobin, which is crucial for carrying oxygen in red blood cells

what is a transition point mutation

when one purine base transitions into another purine base (or a pyrimidine into another pyrimidine)

what is a transversion point mutation

when a pyrimidine base transforms into a purine base and vice versa

what can point mutations cause

frameshift, nonsense and missense

these lead to problems with RNA splicing, RNA cleavage and transcription

what is a molecular marker

a measurable attribute in the DNA that is exhibiting mendelian inheritance

what is a morpholigcial marker

qualities like colour, size, shape

things we can see

what is a biochemical marker

presence of enzymes, proteins etc

what are the 10 characteristics of an ideal marker

1. discriminating - allows differentiation between related individuals

2. Multi-allelic - has several alleles at a single locus

3. Co-dominant - a heterozygote displays characteristics intermediate between its homozygous parents

4. Non-epistatic - the genotype can be determined regardless of the genotype at other loci

5. Polymorphic - there is variation between individuals

6. Independent of the environment - fixed regardless of the environment during development

7. Neutral - no selective advantage of any allele or combination of alleles

8. Uniformly distributed - spread throughout the entire genome

9. Reproducible - across the time and place of analysis

10. Economical - cost effective and able to be handled at high temperatures

    

what does epistatic mean

epistatic means that the gene of interest is under the control of other genes

why are morpholigcal markers a poor choice

• poor polymorphism level

• affected by environment

• dominant

• not always neutral

• may be epistatic

why are biochemical markers a poor choice

• few loci

• not neutral

• not evenly distributed

• can be expensive

why are molecular markers a good choice

• thousands available

• evenly distributed

• independent of environment

• cheap and can be automated

• co-dominant

• highly polymorphic

what are 6 applications of molecular markers

1. parentage

2. extended kinship

3. geographic location

4. forensics

5. genetic divergence

6. gene detection

what can molecular markers distinguish between

homology and analogy

define homology

descent from a common ancestor

define analogy

the convergence of different ancestors into one or two species

how do we use molecular markers to identify genes

They are used to identify genes by acting as signposts along the DNA, indicating the location of specific traits or genetic differences

We create genetic maps, which show the relative locations of genes and other DNA sequences on chromosomes

what can a molecular marker be

tandem repeats; micro and minisatellites

short or long interspersed nuclear elements

single nucleotide polymorphisms

describe minisatellites

a repeating section of DNA that is 7-50bp long

the overall marker length is less than or equal to 5kb

too long for PCR, so southern blotting is used

who discovered minsatellites

Alex Jeffreys

1985

what are minisatellites also know as

variable nucleotide tandem repeats

describe microsatellites

DNA repeats of 2-6bp

overall marker length is up to 300bp long

characterised by motif length

highly polymorphic and can be used in PCR, then detected with gel electrophoresis

what are the different microsatellite motif lengths

dinucletoide e.g (AG)n

trinucleotide e.g (AGA)n

tetranucleotide e.g. (AGTC)n

pentanucleotide e.g. (AGGCT)n

why is a trinucleotide motif length uncommon

because 3 bases generally codes for an amino acid

describe a single nucleotide polymorphism

a change to a single base

usually bi-allelic

most common polymorphism type

arise by spontaneous mutation and can occur in non-coding regions

what is another name for a single nucleotide polymorphism

single nucleotide variant

explain sickle cell anaemia

due to a single nucleotide polymorphism

an A becomes a T on the beta globin gene, so valine is coded for isntead or glutamic acid

under low oxygen, valine aggregates to form fibrous precipitates

explain the ABO blood group

A, B and O are the alleles

A and B are co-dominant, whilst O is recessive

O is due to a single deletion, and no functional receptor is produced

there are 6 genotypes but only 4 phenotypes