Bio 2 unit 3 exam

Pray

Genomics

study of whole genomes, including genes and their functions

Transcriptomics

All RNA

Proteomics

study of the structure and function of proteins

Metabolomics

metabolites

structural genomics

studying structure of genes

comparative genomics

comparing two or more complete genomes

What are the two sources of DNA in eukaryotes

Nucleus and mitochondria

How many base pairs in nuclear genome

3 million

How many protein

coding genes are in the human genome? How many RNA

transcripts and why?

There are 20,000 protein

Describe DNA in mitochondria

Fewer basepairs than the nucleus and circular chromosome

What do all omics have in common?

All study macromolecules

Microbiome

all of the microorganisms that live in a particular environment, such as a human body

metagenetics

study off all the organism in one sample

What is required for PCR

DSDNA template dNTPS DNA primer Taq Polymerase buffer solution

PCR process

1 Melting 2 Annealing 3 Extension

What happens during the melting stage

DSDNA template unwinds

What happens during the annealing phase

Primers bind to the unwound DNA

What happens at the extension phase

The dNTPS extend the DNA

GC content

% of seqeunce that is G or Cs

Sequencing

1 Cutting DNA into fragments 2 Denature into SSdna 3 Adaptor sequence
4 PCR to make copies

contigs

Overlapping segments of DNA that are pieced together by a tool called the gene assembler to reconstruct the original chromosome

Alignment

Aligning identical sequences of DNA to see what overlaps and what does not to piece together the original DNA sequence

de novo sequencing

Determination of a full genome sequence without using a known

reference organism

The first organism of that type that is sequenced becomes the reference organism which other organisms are compared to of the same type

Resequencing

sequencing the genome of an organism with a known genome

bacterial transformation

the ability of bacteria to alter their genetic makeup by uptaking foreign DNA from another bacterial cell and incorporating it into their own (For our purpose put a plasmid with altered genes into a bacteria to get what we want expressed)

Vector

vehicle of putting DNA segments into the host cell (Often times we take copies of DNA from PCR and throw it into the vector)

Plasmids

small circular DNA molecules that replicate separately from the bacterial chromosome The location where we put the foreign DNA which then goes into the bacteria

What is special about the plasmids we make in the lab?

They typically have antibiotic resistance and fast ORI to make the process easier

restriction enzymes

An enzyme that cuts DNA at a specific sequence of nucleotides multiple restriction enzymes can be used on the same chromosome (usually 4 or 6 base pairs long)

What type of bonds do restriction enzymes cut? Will be asked about on test

Covalent and Phosphodiester bonds (Hydrogen bonds just break naturally)

Blunt sites

When the restriction enzyme cuts straight down

overhang

when restriction enzyme does not cut straight but creates the two strands that overhang

restriction sites

sites where restriction enzymes cut DNA, they are subject to mutations and are palindromes

Evolution

In a biological sense evolution refers specifically to the change in the genetic makeup of a population over time HAPPENS IN POPULATIONS NOT INDIVIDUALS

Why are mutations important to evolution

They are the raw material for evolution

Somatic vs Gamatic mutations

Somatic mutations do not lead to evolution but gametic does

Allele

One or more versions of DNA sequence at a point

genotype

The written representation of alleles present Not all alleles contribute to phenotype

Change in any frequency of allele

Is evolution 1 of 1,000,000 alleles could change it would be evolution its just boring

natural selection

Beneficial alleles increase while bad ones are removed Usually from predation

artificial selection

Specific traits are artificially bred for An example is when humans make big dogs because people like them

Bottle neck

A random subset of organisms sharing alleles survive while the other with different alleles die off leaving the surviving to increase their alleles in the population

Genepool

All alleles of a gene of interest in a population or species

Genes and alleles in individuals

All individuals have the same genes but vary which alleles they have

immigraton

When organisms born in one place move to another and reproduce Arriving in the new place makes them an immigrant

Emmigration

When an organism leaves the place it was born to go to another place and reproduce Leaving the original location makes them an emigrant

sexual selection

One sex (usually) the female selects mates based on heritable phenotypes Unselected individuals don't pass down alleles while selected favored traits become more common

Size dimorphism

Typically, size is what is sexually selected for so this leads to a size discrepancy in males and females of a species

Traits that get sexually selected for

Ornaments, colors, songs, dances etc

genetic drift

Random mating causes the allele frequency to be random

Abundance

Quantity of specific alleles in a population

Relative frequency

Percentage of the population that is made up by a specific allele

Assumptions needed for Hardy Weinberg

1 No mutation2 No selection for any of the genotypes 3 Completely random mating 4 No migration 5 Large population size (technically infinite)

concensus sequence

Is a nucleotide or amino acid sequence in which each position represents the base most often found when many actual sequences are compared by aligning them

Genome assembly

The computer intensive process of putting sequenced fragments of DNA into their correct chromosomal positions

Bioinformatics

Using computers and math to sort large amounts of biological information

founder effect

When an isolated population is started by a very small number of pioneering individuals, the sample of genes carried by the few originators is usually less diverse, or otherwise unrepresentative of the gene pool of the base population

sticky ends

Single stranded ends of DNA left after cutting with enzymes

expression vector

A plasmid that contains all the necessary components to produce a protein in a host

how to find probability of off spring

multiplying the allele frequencies p^2+2(p*q)+ q^2\= 1

allele fixation

When an allele is either at 0% or 100% frequency

directional selection

When natural or artificial selection acts to increase or decrease allele frequency towards fixation

positive and negative selection

Positive is increasing allele frequency to 100% while negative is decreasing to 0% Keep in mind that as the frequency of one allele increases another one will decrease

phylogenetic tree

A family tree that shows the evolutionary relationships thought to exist among groups of organisms

root

The common ancestor

branch

One organism or taxa

Node

The split in the tree

sister species

two species that are each other's closest relatives

Clade

A group of species that includes an ancestral species and all its descendants

Taxnonomy

How organisms are named, grouped, and classified

Genus

A group of related species

subspecies

variations of a species that can not be considered different species

Order of classification

Domain Kingdom Phylum Class Order Family Genus Species

gene flow

movement of alleles from one population to another

Speciation

Formation of new species

What makes a clade

Shared derived characteristics

derived characteristics

A characteristic that all members of a clade share that only they have

homologous structures

Structures in different species that are similar because of common ancestry

analogous structures

structures that have the same function but independently evolved

Gnathostomes

Clade with shared derived characteristic of bony jaw

Apomorphy

shared derived character trait

Autapomorphy

unique derived trait to one taxa useless for making tree

Synapomorphy

Traits that are shared by multiple taxa on a tree

character matrix

an array of taxa (at left) and characters (at top) that contains the character states for the taxa 1\= present 0\= absent

Nested clade

A clade within a bigger clade

Plesiomorphies

ancestral traits all taxa share (red blood cells in vertebrates)

convergent evolution

When evolutionary distinct taxa arrive at same character state (warm

homoplasies

Structures that function similarly but arrived through convergent evolution or evolutionary reversal

evolutionary reversal

Characteristic or organism evolves to resemble its ancestral state

In L1014F what is the wildtype amino acid

Leucine

In L1014F what does the 1014 indicate

the amino acid that is mutated

repeated mutations

the same allele being created multiple independent times

unrooted phylogenetic tree

show relationships but not a common ancestor

For a given locus how many different character states can DNA take on

5
A,T,C,G and indel

Monophyletic

group of organism on a phylogenetic tree including the ancestor

Parsimony

The simplest way to write out a tree requires the fewest number of splits, reversals, and convergents. (Easier to assume mammals and birds developed warm-blooded than all reptiles were warm-blooded then each reptile developed cold-blooded)

Cladogenesis

Long-term phenomena of new clades forming creates new taxa. Also new types of organisms like plants and animals.

Species delineation

Process or defining/declaring 2 organisms are different species.