Lecture #3

Question 1

Allele

Answer 1

the DNA sequence(s) at a locus of one of the two homologous chromosome

Question 2

Genotype

Answer 2

the combination of alleles at the same locus of the homologous chromosomes in a genome/cell

Question 3

Homozygote

Answer 3

when an individual has a pair of identical alleles at the locus, the genotype is homozygous

Question 4

Heterozygote

Answer 4

two different alleles at the same locus, the genotype is heterozygous

Question 5

Hemizygous/hemizygote

Answer 5

one allele presents, while another allele is missing
hemizygous genotype is also heterozygous

Question 6

Nature of a genotype: Mendel’s law

Answer 6

each of the parents passes a randomly selected allele (one of the two homologous chromosomes) to the offspring (law of segregation

Question 7

Single nucleotide polymorphism (SNP)

Answer 7

a single nucleotide is changed to another
the most common DNA sequence variation account for >90% of all genetic variations
occurs 1 SNP/~300-750bp in the genome
a total of 55M SNPs deposited in the SNP databse
most PGx polymorphisms are SNPs

Question 8

SNP in the coding region (cNSP)

Answer 8

non-synonymous: changing amino acid in the protein - missense SNP: amino acid substitution (could lead to gain or loss of function for the protein depending on what amino acid it changes to), nonsense SNP: amino acid changes to a stop codon (normally leads to loss of function)
synonymous SNP: does not change amino acids, usually does not change gene/protein function - silent SNP: no amino acid change

Question 9

cannot determine _____ just by knowing it’s missense SNP

Answer 9

gain or loss of function

Question 10

Noncoding region SNPs

Answer 10

intronic SNP, SNPs in the gene flanking regions and intergenic regions, SNPs in the UTR region

Question 11

Copy number variation

Answer 11

a DNA region (many contain a part of even or or more entire genes) has 0-n copies in a population
structural variation
1kb-severl Mb
making each chromosome longer or shorter

Question 12

Insertion/deletion

Answer 12

nucleotides present or absent from a locus: 0 or 1 copy
can be 1 to N nucleotides
single nucleotide indel is a specific form of SNP
large ones are actually CNVs

Question 13

Insertion and deletion, other than 3 nucleotides often causes

Answer 13

frameshift of the open reading frame leading to truncated protein for degradation

Question 14

Truncated protein

Answer 14

loss of function

Question 15

Nomenclature

Answer 15

this type of nomenclature is widely used in clinical setting by doctors and pharmacists
gene/allele name: italic
protein name: regular