Genomics

Question 1

PCR

Answer 1

Polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it to a large enough amount to study in detail.

Question 2

Microsatellites

Answer 2

A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism’s genome. https://www.youtube.com/watch?v=lQSi84xFsrY

Question 3

RFLP and AFLP

Answer 3

RFLP: In molecular biology, restriction fragment length polymorphism (RFLP) is a technique that exploits variations in homologous DNA sequences, known as polymorphisms, in order to distinguish individuals, populations, or species or to pinpoint the locations of genes within a sequence.

AFLP: Amplified fragment length polymorphism (AFLP) is a PCR-based technique that uses selective amplification of a subset of digested DNA fragments to generate and compare unique fingerprints for genomes of interest.

Question 4

Sanger Sequencing

Answer 4

Sanger sequencing, also known as the “chain termination method”, is a method for determining the nucleotide sequence of DNA.

Question 5

Single Nucleotide Polymorphisms

Answer 5

Single nucleotide polymorphisms, frequently called SNPs (pronounced “snips”), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide.

Question 6

Genome

Answer 6

The total DNA of an organism
(3.2 billion base pairs)
(20k genes - the unit of heredity)

Question 7

Allele

Answer 7

Different versions of the same gene (different nucleotide sequence) which codes for slightly different versions of a protein

Question 8

Homozygous allele

Answer 8

Two of the same alleles (Ex: TT or tt)

Question 9

Heterozygous allele

Answer 9

Two different alleles (Tt)

Question 10

Phenotype

Answer 10

Physical manifestation of a genotype

Question 11

Genotype

Answer 11

The two alleles a person has for a given gene

Question 12

Genetic Markers

Answer 12

Polymorphic regions of the genome

Question 13

Allozymes

Answer 13

Enzymes coded by different alleles of the same gene

Question 14

Locus

Answer 14

In genetics, a locus is a specific, fixed position on a chromosome where a particular gene or genetic marker is located.

Question 15

Recombination

Answer 15

Random mixing of the DNA of two creatures

Question 16

Mutation

Answer 16

Random changes in DNA or “copying errors”

Question 17

Microevolution

Answer 17

Change below the level of species

Question 18

Macroevolution

Answer 18

Change above the level of species

Question 19

Intron

Answer 19

Sequences that will not be part of the mature RNA but are primary transcripts synthesized by RNA polymerase. They are removed before the mature mRNA leaves the nucleus.

Question 20

Exon

Answer 20

The remaining regions of the transcript, which include the protein-coding regions. They are spliced together to produce the mature mRNA.

Question 21

Synonymous mutation

Answer 21

The codon codes for the same protein

Question 22

Missense mutation

Answer 22

The codon codes for a different protein which may change physical characteristics, function or genotype

Question 23

Nonsense mutation

Answer 23

The codon codes for a “termination codon”. Produces shortened final protein.

Question 24

Evolution

Answer 24

Change of the genetic composition of populations (change of allele frequencies over time)

Question 25

Transitions

Answer 25

C to T or G to A

Question 26

Transversions

Answer 26

C to G, C to A, T to G or T to A

Question 27

Fixation

Answer 27

Mutations fixed in a population substitute (replace) the former ones

Question 28

Homoplasy

Answer 28

When a trait is gained or lost independently in separate lineages (parallel, convergent, reversal evolution)

Question 29

Saturation

Answer 29

Genetic saturation is the result of multiple substitutions at the same site in a sequence, or identical substitutions in different sequences, such that the apparent sequence divergence rate is lower than the actual divergence that has occurred

Question 30

Degenerate positions

Answer 30

A position of a codon is said to be a twofold degenerate site if only two of four possible nucleotides at this position specify the same amino acid. For example, the third position of the glutamic acid codons (GAA, GAG) is a twofold degenerate site.

Question 31

Substitution rate

Answer 31

r=K/2T

Question 32

Jukes-Cantor

Answer 32

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Question 33

Kimura-2 p

Answer 33

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Question 34

Pseudogenes

Answer 34

Genes that have lost function, and are useful for studying substitution rates

Question 35

Phylogenetics

Answer 35

Study of evolutionary relationship

Question 36

Nodes

Answer 36

Taxonomic units

Question 37

Indel

Answer 37

Insertion-deletion gaps

Question 38

Homology

Answer 38

Homology means that two sequences descend from a common ancestor. Homology is all or nothing; two genes can't be 50% homologs.For molecular sequence data, homology means that two sequences or even two characters within sequences are descended from a common ancestor.

Question 39

Ortholog

Answer 39

Homologous genes that have diverged from each other after speciation events (e.g., human β- and chimp β-globin).

Question 40

Paralog

Answer 40

Homologous genes that have diverged from each other after gene duplication events (e.g., β- and γglobin)

Question 41

Xenolog

Answer 41

Homologous genes that have diverged from each other after lateral gene transfer events (e.g., antibiotic resistance genes in bacteria).

Question 42

Homolog

Answer 42

Genes that are descended from a common ancestor (e.g.,all globins).

Question 43

Neutral evolutionary forces

Answer 43

Selection Migration (gene flow) Mutation Genetic drift

Question 44

Hardy-Weinberg equilibrium

Answer 44

If allele frequencies do not change over time. Criteria 1. Population must be large 2. No mutations 3. No migrations 4. Mating must be random 5. No natural selection can occur

Question 45

Population

Answer 45

mono-specific group of individuals that reproduces randomly, and that shares the same space during at least one part of their life cycle

Question 46

F_is = 0

Answer 46

Population at Hardy-Weinberg Equilibrium (HWE) at a given locus

Question 47

F_is > 0

Answer 47

Deficiency in heterozygotes in comparison to HWE (less heterozygotes than expected according to HWE)

Question 48

F_is < 0

Answer 48

Excess in heterozygotes in comparison to HWE (more heterozygotes than expected)

Question 49

Genetic drift

Answer 49

Random evolution of allele frequencies from generation to generation

Question 50

Bottleneck effect

Answer 50

Reduction in genetic diversity due to strong genetic drift induced by a drastic decrease in the size of a population (ex: disease, natural disaster, overexploitation)

Question 51

Founder effect

Answer 51

Organisms that "founded" an area that did not represent the original population they came from

Question 52

Metapopulation

Answer 52

Group of spatially separated sub-populations, with independent dynamics, and interconnected by possible migration.

Question 53

Fitness

Answer 53

Fitness = Viability x Fertility Viability: Probability of reaching a reproductive age Fertility: Number of offspring reaching reproductive age

Question 54

Directional selection

Answer 54

Selection of the extreme value of a phenotypic trait (positive selection)

Question 55

Stabilizing selection

Answer 55

Selection against the extreme values of a phenotypic trait (purifying or negative selection)

Question 56

Disruptive selection

Answer 56

Selection against the intermediate values of a phenotypic trait (diversifying selection)

Question 57

Balancing selection

Answer 57

Selection pressure resulting in active maintenance of multiple alleles in the population.

Question 58

Wrights F Statistics

Answer 58

The correlation between genes drawn at different levels of a (hierarchically) subdivided population. The measures FIS, FST, and FIT are related to the amounts of heterozygosity at various levels of population structure. Together, they are called F-statistics, and are derived from F, the inbreeding coefficient.

Question 59

Gene flow

Answer 59

Exchange of genetic material between populations

Question 60

Migration

Answer 60

Exchange of individuals between populations

Question 61

Population genetic structure depends on:

Answer 61

-Population efficient size -Population divergence rate -Migration rate +Natural selection for some loci

Question 62

Panmixia

Answer 62

Random mating within a breeding population

Question 63

Polymorphic

Answer 63

A gene is said to be polymorphic if more than one allele occupies that gene's locus within a population. In addition to having more than one allele at a specific locus, each allele must also occur in the population at a rate of at least 1% to generally be considered polymorphic.