fundamentals of genetics

Question 1

Heritability of traits - mendelian genetics

Answer 1

Pisium sativum naturally self fertilises. To do genetics you need to do crosses.
These traits were present in each parental strain in one of two mutually exclusive forms.
Each parental strain was true-breeding for the trait in question.

Question 2

Genes as units of heritability

Answer 2

In sexually reproducing organisms, both parents contribute equally to the offspring.
For each trait, each individual has two copies of a unit of inheritance, one from each parent. Each unit is a genetic LOCUS. It broadly corresponds to a GENE.
The two copies segregate away from each other during gametogenesis.
Each gamete contains exactly one copy of each gene.
Alleles Each gene comes in alternative forms.
Genotype The combination of alleles present determines the final form of the individual (PHENOTYPE).

Question 3

The principle of independent assortment

Answer 3

These ratios can only occur if the two alleles for each of the traits segregate completely independently of one another during gametogenesis.

These ratios cannot occur if the probability of inheriting a specific allele of one locus affects the probability of inheriting a specific allele of the other locus.

9:3:3:1

Question 4

Chromosome theory of inheritance

Answer 4

Chromosome behaviour in mitosis and meiosis correlates with gene behaviour
– Mitosis produces exact copies of the mother cell
– Meiosis produces daughter cells with half the number of chromosomes as the parent cell
– Fertilisation unites two gametes (produced
by meiosis) to give an individual with a new combination of genes

Question 5

Linkage and segregation

Answer 5

– Fertilisation unites two gametes (produced by meiosis) to give an individual with a new combination of genes.
– BUT, there are clearly more genes than chromosomes.
– So each chromosome carries many genes
– ie genes are linked on chromosomes

Sex linkage
Mapping linked genes to reveal their physical order
– Genetic maps
– Physical maps

Morgan found a white eyed fly
Normal flies have red eyes.
This male had white eyes.
He crossed it to normal females.

Work on this one fly led to the discovery of sex linkage and the confirmation of the chromosomal theory of inheritance.
white eyed male x red eyed females
F1 generation 1237 red eyed flies (male and female). (and 3 white eyed males.)

Final proof
All the data on white is consistent with the white gene being physically located on the X chromosome.
Final proof came from examining flies that had extra Y chromosomes.
XXY females are fertile, and can transmit a Y chromosome to their offspring.
w1 / Y males crossed to XXY females can generate w1 / Y males

Question 6

Meiosis and recombination

Answer 6

recombination:
In meiosis there can be exchange of genetic information between homologous chromosomes, or sister chromatids
– recombination (crossing over)
If the recombination is between homologous chromosomes the result is formation of a hybrid chromosome

Recombination Frequency = (Number of recombinant progeny / Total number of progeny) x 100

Question 7

Pedigree analysis

Answer 7

Pedigree analysis
Generate a family tree, including as much info as possible
Relationships
Disease status
Look for linkage of the trait with genetic markers

*Genetic mapping allows you to identify the region of the genome that carries the gene for a trait of interest
–it exploits basic Mendelian genetics
*Markers used can be visible, or can be molecular markers
–you just have to be able to tell the alleles apart.

*Mapping traits can be helped by using both the physical map and the genetic map
*Genome sequencing has been very useful to allow you to get quickly from a genetic region to a gene

Question 8

Alleles - human mendelian traits

Answer 8

Autosomal dominant
Huntingtons disease
Familial Hypercholesterolemia
Appear in both sexes with equal frequency.
Affected individuals have at least one affected parent
(unless the mutation has arisen de novo).
Trait does not (generally) skip generations

Autosomal recessive
Infantile onset epilepsy(GM3 synthase)
Cystic fibrosis
Phenylketonuria
Appear in both sexes with equal frequency
Parents can be unaffected
Parents are often related, although depends on allele frequency in the population
Trait frequently skips generations

X-linked recessive
Red-green colour blindness
Haemophilia
Appears in males more frequently than females
Parents can be unaffected
Fathers do no pt transmit the trait to their sons
Trait frequently skips generations
-affected man, unaffected daughter, affected grandson

X-linked dominant
Familial vitamin D resistant rickets

Appear in females more frequently than males
At least one parent affected(unless de novo)
Fathers do not transmit trait to their sons, do pass it on to ALL daughters
Trait does not skip generations

Question 9

dominance of alleles and multiple alleles

Answer 9

incomplete dominance
* The heterozygote of two incompletely dominant alleles has an intermediate phenotype between the two homozygotes.
* Flower colour in snap-dragons.

Co-dominance
* The heterozygote between two co-dominant alleles has the sum of the two phenotypes.
* Lentil seed pattern - spotted and dotted.
1:2:1 ratio

Over-dominance heterozygote advantage
* The fitness of the heterozygote is higher than the fitness of either homozygote (at least under some conditions)
* Sickle cell disease.
* Cystic fibrosis.
* A disease allele is present in the gene pool at higher frequencies than would be expected given the nature of the disease.

Under-dominance heterozygote disadvantage
* Human chromosome 2 formed from a fusion of two ancestral chromosomes.
* Homozygotes of either allele have a higher fitness than the heterozygote.
- Chromosomal rearrangements.
- Has significant implications for speciation because it typically causes the population to fix one of the two alleles. This can reduce immigration potential, and thus leads to populations becoming genetically isolated.

Multiple alleles - Human ABO blood group
antage
/o ancestral chromsomes.
* ABO blood types.
* Red blood cells have a glycosylated antigenic structure on their surface.
* Two antigenic variants exist - A and B.
* O individuals do not express either variant - they make antibodies to both A+B
*A individuals express only the A form - they make antibodies to the B form
* B individuals express only the B form - they make antibodies to the A form
* AB individuals express both A and B forms - they make no antibodies to these antigens

Multiple alleles of an individual locus - allelic series
* If one allele is overwhelmingly the most common in a population it is termed the “wild type” allele. Most essential genes have a single wild type allele. Genes controlling traits that are very variable in a population, eg hair colour, are don’t have a single common allele. These loci are polymorphic.

Question 10

mutation

Answer 10

Any inheritable change in the DNA sequence:
Some are detrimental
Some are neutral
Some are advantageous
Spontaneous
Random
Increased in frequency by the action of a mutagen

types of mutation:
Single base pair changes (base pair substitution)
One base pair changes to be a different base pair

transition and transversion:
Transition substitutes one purine for the other purine (or one pyrimidine to the other)
Eg. A->G or T->C

Transversion substitutes a purine for a pyrimidine or vice versa
Eg. A->T or T->G

how they arise:
DNA damage (DNA repair process)
DNA replication. (DNA repair process)
New sequences inherited in the daughter. (If damage repaired = no mutation)

Question 11

spontaneous substitution

Answer 11

Error caused by mis-pairing during DNA replication
Tautomerisation
Anomalous base pairing (Non-Watson Crick pairing)
The replication machinery inserts the wrong base during DNA replication
After replication there is a mismatch
This can be repaired to generate the original sequence or the repair machinery could repair to give the new sequence

1. A must-paired base inserted ipduring DNA replication
2. Mis paired base is detected after replication
3. EITHER mismatch not repaired= mutation occurs
4. OR DNA repair corrects mismatch= mutation not occured

Question 12

depurination

Answer 12

Loss of the purine base from a nucleotide leads to an a basic site - a gap.
During replication there is no information to direct what base should be incorporated opposite this gap. An incorrect nucleotide could be incorporated.

Question 13

deamination

Answer 13

Cytosine deamination generates Uracil.
Uracil can be recognised by the DNA repair machinery
5-Methylcytosine deamination generates Thymine.
This leads to a mismatch pair (G-T)
CG -> AT transitions are common in species where DNA methylation of cytosine is common (eg humans)

Question 14

changes induced by chemical mutagens

Answer 14

Deamination can be caused by nitrous acid.
Alkylating agents
Add an alkyl group - methyl, ethyl etc to the base
Ethyl methyl sulphonate (EMS).
Ethylates Guanine or Thymine, and leads to atransition mutations.

Base analogues.
eg 5-Bromouracil. Can be incorporated into DNA in place of thymine.
enol form is relatively stable and can base pair with guanine.

Oxidative damage
Free radicals, ozone, peroxide etc, produced during normal cellular activity can modify bases and alter pairing properties

Question 15

effects of single base pair change

Answer 15

Triplet code (3bp per codon)
64 different codons exist (43)
There are 20 amino acids used in proteins.
STOP is also encoded
The genetic code is redundant.

Question 16

effects of single base pair change within coding sequence

Answer 16

Silent mutation
Changes a codon for a specific amino acid to a different codon for the SAME amino acid. No change to sequence of encoded protein.

Missense mutation
Changes a codon for a specific amino acid to a codon for a DIFFERENT amino acid. The sequence of the encoded protein is altered.

Nonsense mutation
Changes a codon for a specific amino acid to a STOP codon. Results in truncation of the protein.

Question 17

consequences of single base pair change

Answer 17

Loss of function of a gene
Gain of a gene function
No effect on gene function
A large part of the genome can be non-coding
Proportion varies depending on species
12% of the E. coli genome is non-protein coding.
1% of the human genome is protein coding.
Point mutations outside coding regions are typically silent, but they can affect gene function

Question 18

DNA changes that affect more than a single base pair

Answer 18

Small insertions or deletions - INDELS

Replicating DNA can gain or lose single bases (or longer regions) by REPLICATION SLIPPAGE
Insertions can be caused by DNA intercalating agents - eg ethidium bromide - which fit between base pairs and are recognised as an extra base during DNA replication

Question 19

effects of small indels - within a coding sequence and outside a coding sequence

Answer 19

Within a coding sequence
Deletion or addition of bases can lead to a frame shift
Deletion or addition of 3 (or a multiple of 3) bases does not shift the frame, but does alter the protein
Triplet expansion diseases - eg Huntington’s disease

Outside coding sequence
Often the effect is silent, although small INDELs can alter gene regulatory sequences

Question 20

large insertions generated by

Answer 20

Transposon mobilisation.
Transposons DNA elements that can move to new positions in the genome. They are autonomous - ie they have this ability encoded within their own DNA

Virus insertion.
Many viruses insert their DNA into the host cell DNA during infections. This then becomes a heritable change in the host DNA - a mutation.

Retroposition.
An RNA transcript in a cell can be copied back to make DNA (reverse transcription). This DNA sequence can then be inserted into the genome

Question 21

large deletions generated by

Answer 21

Transposon mobilisation.
Some transposition events cause a region of the genome to be deleted when the transposon moves.

Incorrect repair of DNA double strand breaks.
Repair of double strand DNA breaks usually involves use of the homologous chromosome as a template to supply the correct sequence.
Sometimes this is not possible and the broken ends can be rejoined - often with a bit missing

Question 22

effects of large deletions and insertions

Answer 22

deletions:
Disruption of gene activity
Complete deletion of one or more genes

insertion:
Disruption of gene activity

Question 23

other changes that can occur(bigger)

Answer 23

Translocation
Moving a region of the genome to a different place.
Reciprocal translocations swap the positions of two genomic regions

Inversion
A region of the genome cut out from its normal location, turned around, and stuck back in again.

Duplication
Insertion of a second copy of a genomic region

Chromosome fusion / fission
Sticking two chromosomes together to make one, or taking one chromosome and splitting it to make two

Question 24

duplication

Answer 24

The result of a duplication event is the that there are now two copies of the duplicated genes.
Important for evolution if both copies are retained
One can evolve a new function
Or the original function can be split between the new copies

Question 25

mutations and their effects on gene function

Answer 25

Alleles that are dominant
Loss of function of a haplo-insufficient locus.
In this case just one copy of the normal gene sequence is not enough to provide the gene function and you get a phenotype (eg HPE4)

Gain of function.
E.g. The mutation changes the specificity of an enzyme so that it works on a new substrate. The phenotype will be caused by this activity, and the normal gene product’s presence will have no effect.
E.g. The mutation causes the gene expression pattern to be changed so that it is now expressed in cells that would normally not express it.

Dominant Negative.
In this case the mutant protein counteracts or competes with the normal protein, e.g. a mutant enzyme that bind irreversibly to the substrate, so that the substrate is no longer available for the enzyme produced by the wild type allele

Alleles that are recessive
- Loss of function of a “normal” locus.
- For most genes a single functional copy of the gene is enough, so a loss of function mutation is recessive to the wild type.
* The loss of function could be complete, eg deletion of the gene.
Partial loss of function alleles can also occur - e.g. the allele generates a protein that does the normal function but the protein is more unstable so total activity is reduced.
* Itis more common for a mutant allele to be recessive than dominant.

Question 26

DNA repair

Answer 26

DNA repair
* A change in the DNA sequence only becomes a mutation when it becomes heritable
- Changes, eg mismatch bases etc can be recognised by the cell and repaired.
- Cells that are not dividing might leave the damage unrepaired

• Several different DNA repair mechanisms are available to cells
• Direct reversal
  Mismatch repair
• Base excision repair
• Nucleotide excision repair
• Homologous recombination
• It is possible for the cell to patch up the damage without accurate repair
• Translesion DNA synthesis
• Non-homologous end joining
• The Nobel prize for Chemistry(2015)
  For “mechanistic studies of DNA repair”

Mutation rates
* DNA replication is does not have 100% fidelity.
* Not all damage is repaired.
* Mutations WILL occur
Mutation rates are hard to measure but most recent estimates are:
* Human mutation rate is about 1.2x10- single nucleotide changes per bp per generation.
* E. coli mutation rate is about 8.9x10-11 single nucleotide changes per bp per generation.
(consider the different number of cell divisions per generation in these two organisms)