DNA and Genotyping methods

Question 1

DNA organisation

Answer 1

23 chromosomes in humans. Each CSM contains single long molecule of DNA, wrapped up in proteins (histones) = Cromatin super coiled into chromatids.

Question 2

DNA organisation

Answer 2

23 chromosomes in humans. Each CSM contains single long molecule of DNA, wrapped up in proteins (histones) = Cromatin super coiled into chromatids.
Sugar and phosphate attached to each nucleotide - Adenin, Guanine, Thyin and Cytosine.
3 billion nucleotides in genome.

Question 3

Genes

Answer 3

there are non-coding regions of DNA.

Question 4

Genotyping

Answer 4

Processing of determining sequences of DNA and how that changes a phenotype.
Identify pathogens and mutations in bacterias. Paternity tests. Forensic science.

Question 5

Genetic variatiion

Answer 5

Variation in the DNA sequence - mutations and polymorphisms.

Question 6

Genetic variation causes - origins

Answer 6

Mutation = Problem in cell division and replication. Recombination changes.
Natural selection.

Question 7

Genetic variation causes - origins

Answer 7

Mutation = Problem in cell division and replication. Recombination changes.
Natural selection.
Population size - genetic drift (changes in diversity), bottleneck and founder effect.

Question 8

Genetic variation causes - origins

Answer 8

Mutation = Problem in cell division and replication. Recombination changes.
Natural selection.
Population size - genetic drift (changes in diversity), bottleneck and founder effect.
Gene flow - migration. Mix allels of DNA and increase variability.
Sexual reproduction - gene combination.

Question 9

Genetic variatiion

Answer 9

Variation in the DNA sequence - mutations and polymorphisms.

Can trace back mutations by looking at DNA and would increase in occurrence over time. Can check how old mutation is.

Question 10

Mutations and polymorphisms

Answer 10

A point or change in a section of DNA that varies between individuals.
Can directly influence traits/cause diseases.
Located in coding and non-coding DNA.
PM >1% population.
Mutation very rare. less than 1% of pop.

Question 11

Somatic genetic mutations

Answer 11

Sun bathing. Over time you have changes to your DNA. Not passed through generations - Lung and skin cancer.

Question 12

Germline mutations

Answer 12

Inherited from parent to child from Gametes into embryo.

Some types of cancer and present throughout life.

Question 13

De Novo

Answer 13

Not inherited - occur after fertilisation. Can be passed on. Some forms of cancer

Question 14

Genetic polymorphisms

Answer 14

1. Sequence repeats
2. Copy number variants
3. Positional variants
4. Single Nucleotide Polymorphisms (SNPs).

Question 15

Sequence repeats

Answer 15

Small segments of DNA repeated. Variable tandem repeats (VTR).
Minisatalites (10-50bp repeats)
Microsatalites (shorter than 0.1 kb)

Question 16

Sequence repeats (genetic polymorphism)

Answer 16

Small segments of DNA repeated. Variable tandem repeats (VTR).
Minisatalites (10-50bp repeats)
Microsatalites (shorter than 0.1 kb)

Question 17

Example of Sequence repeats - M = Huntington’s Disease

Answer 17

Repeats of CAG.
Increased number of repeats and depending where they are is can change course of disease. more than 40 copies = more severe.
Atrophy of basal ganglia.

Question 18

Copy number variants (CNV - genetic polymorphisms)

Answer 18

Changes from 1 kb TO SEVERAL MEGA BASES. Structural variation - abnormal nuber of copies in one of more sections of genome.
Can encompass entire genes including important regulatory elements.
Accounts for 12% human genomic DNA.. Can be inherited or de novo. Associsated with susceptibility or resistance of disease.
Example = autism or schizophrenia.

Question 19

Poly variants (genetic polymorphisms)

Answer 19

Inversion - Breakage during miosis where changes order of DNA. Gtes inverted and can make gene faulty.
Translocation - Breakage of DNA from two different chromosomes that can swap.
Example - downsyndrome. -

Question 20

Single Nucleotide Polymorphisms (genetic polymorphism)

Answer 20

1 SNP in every 300 bases - 10M. 
TT (homozygous)
TG/GT (heterozygous)
GG (homozygous)
Silent (No amino acid change)
Missense (replacement of one amino acid)
Nonsense (premature stop codon)

Question 21

Linkage Disequilibrium

Answer 21

Non-random association of alleles at two or more loci - individuals who have one allele tend to have the second allele as well.

Question 22

Linkage Disequilibrium

Answer 22

Non-random association of alleles at two or more loci - individuals who have one allele tend to have the second allele as well.
Always go close to each other.

Question 23

Haplotyope blocks

Answer 23

In genome recombination happening all the time. different areas different amounts of recombination.
Haplotype blocks are a set of closely linked alleles on a chromosome that tend to be inherited togethr over time.
High level of recomb = many HAP blocks and low Linkage disequilibrium.
Low level of recombination = few HAP blocks and high linkage disequilibrium.

Question 24

How do we but linkage disequilibrium in genotyping?

Answer 24

Tag SNPs.
I DONT GET THIS.
Capture variation across a whole gene using a limited number of SNPs by identifying blocks of DNA that co-segregate (HAP blocks).