Genetics: mutations

Monday

Observations on the fact that the rate of mutation varies from organism to organism.

Deleterious mutations.

5-10% of the DNA in an organism actually codes for protein. Majority of mutations are in non-coding regions.
Deleterious mutation: Any mutation that causes a change in phenotype.
On average you will see 1.6 deleterious mutations/person/generation

(6:00) Specific changes a mutation can create on a DNA sequence

Missense mutation: a single nucleotide change in the sequence of a gene. EFFECT: Typically is that there is a single amino change (sickle-cell anemia). Also known as Point Mutation and Base substitution.

deletion or insertion: change the reading frame (way a gene is read to be converted to protein) for the gene. Change both the sequence and the length of the protein.

create a mutation which creates a stop codon where a stop codon was not present previously. Results in prematrue termination of translation.

(15:15) Chemical agents that can damage DNA

Tautomeric Shift - alternative versions of a compound. Nitrogenous bases have tautomeres.
If a nitrogenous base undergoes a tautomeric shift. The tautomere of the nitrogenous base typically experiences non-watson&crick base pairing.
Compounds that function as base analogs: Mutagenic chemicals with the ability to substitute for one of the bases.

(19:45) EX. 5-Bromouracil: a derivative of uracil. Functions as an analog for thymine. Normal version of 5-Bromouracil base pairs with adenine. 5- Bromouracil can undergo tautomeric shift. When this happens base pairs with guanine. The presnce of 5-Bromouracil makes DNA more susceptible to mutagenesis with UV light.
(23:45) EX. 2-aminopurine: analog for adenine. Base pairs with cytosine.

Alkylating agents --> EMS (Ethylmethyl sulfonate). Add an alkyl group to a base. Creates bases that act like base analogs. EMS alkylates guanine and creates 6-ethyl guanine which functions as an analog for adenine and thus binds to thymine.
(29:45) Arsidine Dyes - cause frameshift mutations. They tend to remove 1 to 2 bases from a sequence of DNA in their role as an intercalating agent. Intercalating agent - a compound that is similar in size to a nitrogenous base pair. Because of this it is able to slip in between spaces in a DNA sequence. This creates torsion on the DNA and the DNA loses 1 to 2 BP in order to relieve the torsion.

(33:40)Environmental/ Spontaneous changes to DNA

Depurination: spontaneous loss of a purine base from its sugar-phosphate backbone.
Apurinic site - gap in the sequenc of bases. This is a problem in DNA replication
EFFECTS:

DNA replication STOPS.
DNA polymerase gets to the opening and inserts any base (most likely to be wrong)

Deamination: nitrogenous base has an amino group converted to a keto group. Cytosine is converted to uracil. The uracil then base pairs with adenine. Adenine can also undergo a deamination. Adenine will become hypoxanthine and then base pairs with cytosine.
Thymine Dimers: occur when you have two bases of thymine next to each other on a single strand of DNA. UV (260nm wavelength) hits the DNA and the two bases of thymine break their bonds with the base that they are paired to. Instead they form a double bond with each other. This can cause large scale mutations during DNA replication to the point that you can see the death of an organism. This is why UV light can be used to sterilize things.

Friday

DNA repair and mutation
Looking specifically at alterations to the chemical composition of DNA

(1:45) Mutation is the basis of genetic study. Mutate a gene and the determine the phenotype
Certain organisms are easier to mutate, for example: bacteria, fungi, yeast, viruses and fruit flies. THey have shorter lifespans.

(4:35) How mutations arise.

EX. Antibiotic resistance: the cell will mutate in response to the presence of the antibiotic.
1943 - Luria and Delbruck set out to test the two models. They set up a number of cultures of e. coli. Sensitive to infection with the T1 phage. Prior to starting the counted the total number of cells. They then exposed the cells to phage. Following exposure they counted number of survivors.

if it happens ealy 1 cell picks up a mutation and divides. All cells from this cell have the mutation. High percentage of cells with a mutation
if it happens late you get orginal cell with the mutation and a few rounds of cell division and a small percentage of resistant cells.

in the experiment they looked at 10 cultures. SPontaneous model would propose that there would be variety in the number of resistant cells in the cultures. In the adaptive model mutation is the result of environmental pressure. THis suggests that with a number of different cultures, if all cells are exposed to phage at the same time then each culture should have mutation occuring at the same time. Each culrue should have about the same number of reistant cells - adaptive model
found that 10 cultures had a wide variety of resistant cultures. Indicates the mutation is spontaneous. Reffered to as the fluctuation test.

Additional work has been down to show that mutation is primarily spontaneous. There are rare occasions when mutation is adaptive.

(23:00) How to classify mutations

Spontaneous vs. induced.

Spontaneous mutation arises naturally in a spontaneous fashion. No exposure that led to the mutation.
Induced mutation: some envionmental exposure leads to a mutation. EX: Smoke two packs a day and you develop a mutation --> lung cancer.

(27:10) Somatic mutations vs gametic mutations

somatic mutations arise in somatic cells. A somatic cell mutation typically leads to a small population of cells with that mutation.
Gametic mutations - mutations in gametes. A gametic mutation in a gamete involved in a fertilization, that offspring will have that mutation in every cell.

(32:20) Broad categories of mutation

morphological mutation. A mutation which alters the structure of a all organisms.
Nutritional mutation: Lack the ability to synthesize an amino acid vitamin or a mutation that prevents you from breaking down some compound.
Behavioural mutation: any mutation which alters the behaviour of an organism. EX. Fruitflies - beating of wings is important in mating. A mutation that impacts the ability of a fruit fly to Beat its wings will have behavioral consequences.
(38:00) Regulatroy mutations: mutations in genes which produce proteins that regulate the expression of other genes. Alter the way the regulated gene is expressed.
(40:10) Lethal Mutation: any mutation which kills an organism
Conditional mutation: only seen under certain conditions.

EX temperature sensitive mutation: a mutation that is scene at a particular temperature.

Genetics