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IMBRSea - Semester 1 > Genomics > Flashcards

Genomics Flashcards

1
Q

PCR

A

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.

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2
Q

Microsatellites

A

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

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3
Q

RFLP and AFLP

A

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.

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4
Q

Sanger Sequencing

A

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

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5
Q

Single Nucleotide Polymorphisms

A

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.

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6
Q

Genome

A

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

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7
Q

Allele

A

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

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8
Q

Homozygous allele

A

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

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9
Q

Heterozygous allele

A

Two different alleles (Tt)

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10
Q

Phenotype

A

Physical manifestation of a genotype

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11
Q

Genotype

A

The two alleles a person has for a given gene

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12
Q

Genetic Markers

A

Polymorphic regions of the genome

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13
Q

Allozymes

A

Enzymes coded by different alleles of the same gene

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14
Q

Locus

A

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

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15
Q

Recombination

A

Random mixing of the DNA of two creatures

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16
Q

Mutation

A

Random changes in DNA or “copying errors”

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17
Q

Microevolution

A

Change below the level of species

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18
Q

Macroevolution

A

Change above the level of species

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19
Q

Intron

A

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.

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20
Q

Exon

A

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

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21
Q

Synonymous mutation

A

The codon codes for the same protein

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22
Q

Missense mutation

A

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

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23
Q

Nonsense mutation

A

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

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24
Q

Evolution

A

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

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25
Q

Transitions

A

C to T or G to A

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26
Q

Transversions

A

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

27
Q

Fixation

A

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

28
Q

Homoplasy

A

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

29
Q

Saturation

A

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

30
Q

Degenerate positions

A

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.

31
Q

Substitution rate

A

r=K/2T

32
Q

Jukes-Cantor

A

?

33
Q

Kimura-2 p

A

?

34
Q

Pseudogenes

A

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

35
Q

Phylogenetics

A

Study of evolutionary relationship

36
Q

Nodes

A

Taxonomic units

37
Q

Indel

A

Insertion-deletion gaps

38
Q

Homology

A

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.

39
Q

Ortholog

A

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

40
Q

Paralog

A

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

41
Q

Xenolog

A

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

42
Q

Homolog

A

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

43
Q

Neutral evolutionary forces

A

Selection
Migration (gene flow)
Mutation
Genetic drift

44
Q

Hardy-Weinberg equilibrium

A

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
45
Q

Population

A

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

46
Q

F_is = 0

A

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

47
Q

F_is > 0

A

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

48
Q

F_is < 0

A

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

49
Q

Genetic drift

A

Random evolution of allele frequencies from generation to generation

50
Q

Bottleneck effect

A

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)

51
Q

Founder effect

A

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

52
Q

Metapopulation

A

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

53
Q

Fitness

A

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

54
Q

Directional selection

A

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

55
Q

Stabilizing selection

A

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

56
Q

Disruptive selection

A

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

57
Q

Balancing selection

A

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

58
Q

Wrights F Statistics

A

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.

59
Q

Gene flow

A

Exchange of genetic material between populations

60
Q

Migration

A

Exchange of individuals between populations

61
Q

Population genetic structure depends on:

A

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

62
Q

Panmixia

A

Random mating within a breeding population

63
Q

Polymorphic

A

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.

IMBRSea - Semester 1 (7 decks)

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