Lecture 21 Flashcards
(50 cards)
1
Q
Genomics
A
- the field that attempts to understand the content, organization, function and evolution of genetic information contained in whole genomes
2
Q
structural genomics
A
concerns the organization and sequence of genetic information within a genome and includes genetic and physical maps of chromosomes
3
Q
genetic maps
A
- based on recombination frequencies
- for linked genes, the rate of recombination is proportional to the physical distance between the loci
- distances measured in percent recombination cM or map units
- they may no accurately correspond to physical distances between genes because crossing over rates may vary in different parts of a chromosome.
4
Q
physical maps
A
- based on the direct analysis of DNA and they place genes in relation to distances measured in base pairs, kilo bases, or megabases
5
Q
restriction mapping
A
- technique for creating physical maps
- determines the position of restriction sites on DNA
6
Q
single-nucleotide polymorphism
A
- a site in the genome where individual members of a species differ in a single base pair
7
Q
haplotype
A
- the specific set of SNPs and other genetic variants observed on a single chromosome
- SNPs within a haplotype are physically linked and tend to be inherited together
8
Q
linkage disequilibrium
A
the nonrandom association between genetic variants within a haplotype
9
Q
Genome-wide association studies
A
- the use of numerous SNPs scattered across the genome to find genes of interest
- used to identify associations between genes and the incidence of major diseases, including CAD, Chron’s, RA, bipolar disorder, etc
10
Q
When a SNP is physically close to a disease-causing locus,
A
- it will tend to be inherited along with the disease-causing allele
11
Q
people with the disease will tend
A
to have different SNPs from those of healthy people
12
Q
a comparison of SNP haplotypes in people with a disease and in healthy people can reveal
A
the presence of genes that affect the disease
13
Q
nonrandom associations between SNPs and a disease suggest
A
that one or more genes that contribute to the disease are closely linked to the SNPs
14
Q
Bioinformatics
A
- develops methods and software tools for understanding biological data.
15
Q
functional genomics
A
- characterizes the function of genes.
- goal is to include the identification the transcriptome and proteome
16
Q
transcriptome
A
all of the RNA molecules transcribed by a genome
17
Q
proteome
A
the complete set of proteins found in a given cell
18
Q
microarrays
A
- knowing when and where genes are expressed.
- has allowed the expression of thousands of genes to monitored simultaneously
- can provide information about which genes are active in a particular tissue
- can also be used to monitor how gene expression changes in the course of a biological process such as development of a disease or disease progression.
19
Q
how microarrays work
A
- microarray costs of DNA probes fixed to a solid support, such as nylon membrane or glass side
- each spot has a different DNA probe
- RNA is extracted from cells and reverse transcription in the presence of a labeled nucleotide produces a cDNA molecule with a fluorescence tag
- the tagged cDNA will pair with any complementary probe
- after hybridization, the color of the dat indicates the relative amount of mRNA in the samples
- a microarray can be constructed with thousands of different DNA probes.
20
Q
proteomics
A
the study of the proteome
21
Q
biological evolution
A
- genetic change taking place in a group of organisms.
- allele frequencies change over time which can result in a new species.
22
Q
Two step process of biological evolution
A
- genetic variation arises through mutation which produces new alleles and recombination, which shuffles alleles into new combination. both processes are random and produce genetic variation continually
- the second step is the increase and decrease in the frequencies of genetic variants. Various evolutionary forces cause some alleles in the gene pool to increase in frequency and other alleys to decrease in frequency.
23
Q
Anagenesis
A
- evolution taking place in a single group (lineage)
- when enough mutations have accumulated and become stable in a population so that it is significantly differentiated from an ancestral population, a new species arises.
24
Q
Cladogenesis
A
- the splitting of one lineage into two
- when a lineage splits, the two branches no longer have a common gene pool and evolve independently
- usually occurs when a few organisms end up in new, often distant area or when environmental changes cause several extinctions, opening up new ecological niches for the survivors.
25
species
- kind or appearance
| - different kinds or types of living organism
26
biological species concept
- species as a group of organisms whose members are capable of interbreeding with one another but are reproductively isolated from the members of other species
- members of the same species have the biological potential to exchange genes, and members of different species cannot exchange genes.
- Because different species do not exchange genes, each species evolves independently.
27
reproductive isolation
- biological characteristics that prevent genes from being exchanged between different species
28
reproductive isolating mechanism
- any biological factor or mechanism that prevents gene exchange
29
allopatric speciation
arises when a geographic barrier first splits a population into two groups and blocks the exchange of genes between them.
30
sympatric speciation
- arises in the absence of any geographic barrier to gene flow
- reproductive isolating mechanisms arise within a single breeding population
- genetic differentiation is initiated by a strong
disruptive selection taking place in a single
population
31
phylogeny
the evolutionary relationships among a group of organisms
32
phylogenetic tree
- a graphical representation of a phylogeny
| - depict evolutionary relationships among different organisms
33
parts of a phylogenetic tree
nodes connected by branches
34
node
- represents the organisms being compared
35
terminal nodes
organisms for which data have been obtained
36
internal nodes
represent common ancestors that are inferred from the analysis
37
branches
represent evolutionary connections
38
rooted
when one internal node represents a common ancestor of all organisms in the tree
39
gene trees
- DNA sequence that helps base phylogenetic trees
40
types of prezygotic isolation
- BEFORE ZYGOTE FORMED
- ecological - differences in habitat; individuals don't meet
- temporal - reproduction at different times
- mechanical - anatomical differences prevent copulation
- behavioral - differences in mating behavior prevent mating
- gametic - gametes incompatible or not attracted to each other
41
types of post zygotic isolation
- AFTER ZYGOTE FORMED
- hybrid inviability - hybrid zygote does not survive to reproduction
- hybrid sterility - hybrid is sterile
- hybrid breakdown - F1 hybrids are viable and fertile, but F2 are inviable or sterile
42
alignment of homologous sequences
- identify homologous sequences and properly align their nucleotide bases
- assume base substitutions
- assume insertions or deletions
43
synonymous substitutions
- do not change the amino acid
| - rate higher than non synonymous
44
non synonymous substitutions
do change the amino acid
45
pseudogenes
- duplicated nonfunctional copies of genes that have acquired mutations
- high rates of substitution occur here
46
exons encode
discrete functional domains of proteins
47
exon shuffling
- exons of different genes are exchanged, creating genes that are mosaics of other genes.
48
gene duplication and divergence
- new genes have evolved through duplication of whole genes and their subsequent divergence.
- the extra copy is free to diverge and potentially take on a new function
- common fate is that the gene accumulates mutations that render it nonfunctional, leading to a pseudogene
49
multigene families
sets of genes that are similar in sequence but encode different products.
50
nucleotides substitution rate
- rate of evolutionary change in nucleotide sequence
