Foundations of Biology Unit 3

Forward genetics

An approach that begins with an interesting phenotype, finds the gene(s) underlying it, and then determines as much as possible about those genes

Reverse genetics definition

An approach that begins with a gene and attempts to determine its function, often by examining what happens when the gene is knocked out

What does reverse genetics do?

Uses the genetic code to predict the amino acid sequence of the protein, computational methods to predict protein structure and function, and experimental methods to mutate the gene and see the effect on the organism.

Sanger method

Uses chemically modified nucleosides (ddNTPS) in combination with normal nucleosides (dNTPS). Synthesis stops when a ddNTP is added by DNA polymerase to a polynucleotide chain because ddNTP has no hydroxyl group at the 3' end. The sequence is determined by detecting the terminal (3') base (A, C, G, or T) at each position in the DNA.

Components of sequencing methods:

DNA polymerase, short (18-22 bases) primer complementary to template strand, all 2' deoxynucleoside triphosphates (dNTPs), all 2' and 3' dideoxynucleoside triphosphates (ddNTPs); labeled uniquely so that each can be detected, template DNA

T or F: the ratio between dNTPs and ddNTPS in DNA sequences is important

True

Human Genone Project

A publicly and privately funded research effort, successfully completed in 2003, to produce a complete DNA sequence for the entire human genome

High-throughput sequencing

Rapid DNA sequencing on a microscale in which many fragments of DNA are sequenced in parallel; involves physical binding of DNA to a solid surface or to microbeads and amplification of DNA templates by PCR; Thousands or millions of sequencing reactions are run at once

Transcriptome

The subset of the genome that is expressed as RNA in a particular cell or tissue at a particular time

RNA sequencing (RNA-seq)

The sequencing of all of the complementary DNA in a sample, obtained from the RNA by reverse transcription

Functional genomics

The assignment of functional roles to the proteins encoded by the genes identified by sequencing entire genomes

Genome annotation

Identifying the various functional regions of the genome

Open reading frames

Sequences of DNA within genes that begin with a start codon and end with a stop codon; can help biologists find a protein-coding gene

Comparative genomics

Computer-aided comparison of DNA sequences between different organisms to reveal genes with related functions

Proteomics

The study of the proteome

Proteome

The set of proteins that can be made by an organism. Because of alternative splicing of pre-mRNA, the number of proteins that can be made is usually much larger than the number of protein-coding genes present in the organism's genome

Ways a proteome can be measured

1. Gel electrophoresis
2. Mass spectrometry
3. Antibodies

Metabolomics

The study of the metabolome as it relates to the physiological state of a cell, tissue, or organism

Metabolome

The quantitative description of all the small molecules in a cell, tissue, or organism

Primary metabolites

Involved in normal cellular processes, such as intermediates in pathways such as glycolysis. Also includes hormones and other signal molecules

Secondary metabolites

Are often unique to particular organisms or groups of organisms. They are often involved in special responses to the environment. Examples are alkaloids (morphine, cocaine, caffeine), Terpenoids (Taxol), Phenols (salicylic acid), and antibotics (penicillin)

Key features of prokaryotic genomes

Relatively small, usually one circular chromosome
Compact--mostly protein-coding regions and RNA genes
Most genes do not have introns
Often carry plasmids--small circular DNA molecules

Core genome

Genes common to all strains of a species; only in prokaryotes

Pan genome

All genes found in a species across all strains

What is CRISPR-Cas9?

A new way of knocking out genes that is more specific

Pseudogene

A nonfunctional copy of a gene

Paralogs

Genes that arise via duplication

Gene family

Two or more paralogs in a genome

Two common types of common genetic variation

SNPS and STRs

Single Nucleotide Polymorphisms (SNPs)

Inherited variations involving a single base-- originating by point mutations

Short Tandem Repeats (STRs)

Short repetitive sequences occurring side by side on chromosomes, usually in noncoding regions

Restriction Fragment Length Polymorphisms (RFLPs)

Mutations at restriction sites that change the ability of the enzyme to cut; observed as bands on an electrophoresis gel following digestion of PCR-amplified target or hybridization of digested DNA with probe

Natural selection

Slight variations among individuals that affect the chances of surviving and producing offspring

Artifical selection

Selective breeding of animals and plants by humans similarly produced changes in characteristics of those breeds

Coyne's 6 elements of evolutionary theory

Evolution, Common Ancestry, Gradualism, Natural Selection, Speciation, and Nonselective Mechanisms

Fitness

Reproductive contribution of a phenotype to subsequent generations relative to other phenotypes; determined by the rate (or amount) of survival and reproduction of individuals with that phenotype relative to other phenotypes

Sexual selection

Acts on characters that determine reproductive success; favors traits that increase the chances of reproduction

Intrasexual selection

Traits such as bright colors, long horns, and elaborate courtship displays that may improve ability to compete for mates

Intersexual selection

Traits that make an organism more attractive to the opposite sex that improves chances of mating

Three kinds of natural selection

Stabilizing, directional, and disruptive

Stabilizing selection

Preserves average phenotype; often called purifying selection

Directional selection

Favors individuals that vary in one direction; also called positive selection

Disruptive selection

Favors individuals that vary in opposite directions from the mean

Frequency of an allele (A for example but also works for a)

[(2 x # of AA individuals) + # of Aa individuals] / 2 x total

Hardy-Weinberg Equilibrium

A model population in which allele and genotype frequencies do not change

Requirements for a Hardy-Weinberg population

No mutations, No gene flow, Infinite population size, random mating, and no natural selection

Short-term deviations from the Hardy-Weinberg equilibrium

Nonrandom mating and gene flow

Long-term deviations from the Hardy-Weinberg equilibrium

Mutation, genetic drift, natural selection

Selfing (self-fertilization)

A way that certain plants reproduce by themselves; reduces the frequency of heterozygotes and increases the frequency of homozygotes, but does not change allele frequencies in the population

Genetic drift

Changes in allele frequencies that results from chance (is random)

T or F: Size of population and strength of genetic drift are positively correlated

False; there is a larger # of changes in smaller populations and a smaller # of changes in larger populations

Bottleneck effect

A temporary reduction in population size in which much of the genetic variation of the population is lost

Founders effect

Equivalent to a population bottleneck, but applies to small populations that colonize a new region; the small colonizing population is likely to contain only a subset of genetic variation, and descendant generations will exhibit elevated frequencies of the alleles present in founder individuals

T or F: Random genetic drift decreases genetic variation

True

Neutral allele

An allele that does not affect fitness; they increase in frequency by genetic drift

Positive selection

Natural selection acts to increase the frequency of an allele that increases individual fitness; the rate of increase depends on fitness of the heterozygote; ex. Lactase persistence

Balancing selection

Natural selection acts to maintain intermediate frequencies of alleles at the locus, because heterozygotes are favored; ex. Sickle-Cell anemia

Phylogeny

The evolutionary history of relationships among organisms or their genes

Convergent evolution

Independently evolved traits subjected to similar selection pressures may become superficially similar

Homoplasies

Similar traits generated by convergent evolution and evolutionary reversals; no common ancestor!

Homologous

Features shared by two or more species that were inherited from a common ancestor

Ancestral traits

A characteristic of a homologous trait that was present in the common ancestor of the group

Derived traits

A characteristic of a homologous trait found in a descendant that differs from the ancestral trait; specific to the group

Synapomorphies

Derived characteristics of homologous traits shared among a group that are viewed as evidence of the common ancestry of the group

Parsimony principle

The simplest explanation of observed data is the preffered explanation

Occam's razor

The best explanation fits the data with the fewest assumptions

Taxon order

Species, genus, family, order, class, phylum, kingdom, and domain

Monophyletic

One taxon contains an ancestor, and all descendants are of that ancestor, and no other organisms

Paraphyletic

A group that does not include all descendants of a common ancestor

Polyphyletic

A group that does not include its common ancestor

Molecular clock hypothesis

Rates of molecular change are constant enough to predict timing of evolutionary divergence

Molecular clock

Uses the average rate at which a given gene or protein accumulates changes to gauge the timing of divergences; must be calibrated using independent data, such as the fossil record, known divergences, or biogeographic dates

Neutral theory of molecular evolution

The majority of mutations are neutral, and may fix in populations through genetic drift

T or F: the rate of fixation is equal to the neutral mutation rate

True

Substitution

Loss of the ancestral allele

Probability of fixation=

1/2N (N= population size)

Rate of fixation=

2Nu(1/2N)=u (N= population size) (u=neutral mutation rate per gamete per generation)

Molecular evolution

Study of the mechanisms and consequences of the evolution of macromolecules, the relationships between the structure of genes and proteins and organism function, and using molecular variation to reconstruct evolutionary history

Synonymous/silent substitutions

A substitution that does not change the amino acid that is specified and therefore has no effect on the protein coded

Nonsynonymous/missense substitutions

A substitution that changes the amino acid that is specified and effects the protein; often deleterious

If an amino acid position is under positive selection for change, the rate of nonsynonymous substitutions can be ________ than synonymous

Much higher

If an amino acid is position is under purifying selection, the rate of synonymous substitutions is ______ than nonsynonymous

Much higher

What happens with the two genes after one is duplicated?

One copy becomes nonfunctional from accumulation of deleterious substitutions and becomes a pseudogene, both genes retain original function but expression diverges in different tissues or at different times, and one copy accumulates substitutions that allow it to perform a new function

Maternal effect genes

Regulates expression of segmentation genes in Drosophilia

Segmentation genes

Define segment number and orientation of each segment in Drosophilia

Types of segmentation genes

Gap genes, pair rule genes, segment polarity genes

Gap genes

1st segmentation gene to act; organzies broad areas

Pair rule genes

2nd segmentation gene to act; divides embryo into units of two segments each

Segment polarity genes

3rd segmentation gene to act; determines boundaries and anterior-posterior organization in individual segments

Hox genes

Expressed in different combinations along the length of the embryo. Their expression determines the morphology of each segment; in two segments, ordered the same as their spatial expression in the embryo

Homeotic mutants

Mutants with mis-regulation of gene expression

Genetic toolkit

The regulatory genes that govern developmental processes that have been highly conserved throughout evolution

What does the Ubx Hox gene do?

It is involved in producing morphological differences in thoracic and abdominal appendages

Heterometry

Altered quantity of gene expression of a developmental gene

Heterochrony

Altered timing of gene expression of a developmental gene

Heterotopy

Altered spatial pattern of gene expression of a developmental gene

Species

Groups of organisms that mate with one another and can produce fertile offspring

Types of species concepts

Biological, lineage, and morphological

Biological species concept

Groups of actually or potentially interbreeding populations which are reproductively isolated from other such groups are defined as a species; does not apply to organisms that reproduce asexually

Lineage species concept

Species are terminal monophyletic branches on the tree of life; each species has a history that starts at a speciation event and ends at extinction or another speciation event