Biology II Unit 3

Evolution is essentially

Changes in a populations allele frequency over time

genotype

The organisms genetic info/code

phenotype

The physical traits in action

Within a double helix strand of DNA

There are coding regions and non coding regions that exist in the gene

Exons

protein coding sequence

Intron

Non coding protein sequence

START RNA codon

AUG

STOP RNA codons

• UAA

• UAG

• UGG

redundancy occurs in genetic code

Not all changes in the DNA sequence particularly happens when converted into RNA

Single nucleotide changes

• AKA point mutations

• Are considered neutral and don’t change the amino acid

If DNA codon AGA would make UCU codon ser, but mutates and UCC ser is made instead, is this change detrimental?

No, it is synonymous and no actual change in the code occurs

non-synonymous change

If DNA codon AGT becomes UCA Ser, but instead becomes codon GCA, this is _______ and causes a difference in the code

Non-coding

coding that happens after the stop codon, so nothing really affects the strand

Indel (insertion or deletion)

could be a rame shift or non-frame shift

Non-frame shift

The insertion or deletion happens in three, so the codons stay in place and changes are not as extreme

Frame shift

• when the insertion or deletion doesn’t happen in a group of three, so codons are all bumped and moved and everything is a new codon

Homology

All similar due to common ancestry

Orthologous genes

shared genes in different species that arrive by speciation

speciation

When a species split up but their future generations will all share some similiarities

paralogous genes

shared gene in different species that arise by gene duplication

synonymous

doesn’t change the amino acid/protein sequence, just neutral

homology

similarity due to common ancestry

Orthologous genes (orthologs)

genes that are shared in different species and came from a common ancestor

paralogous genes (paralogs)

shared gene in different species or within that came from gene duplication

Gene duplication

• a major mechanism driving biological novelty

• most common through eukaryotes

Where are coding sequences in the genome?

• in the introns and extrons, which are located in the genes/genic region

Transportable elements (TE)

• Short seuencs of DNA that occur in lots of cpies in the genome

• They’re not there to do a job for the organism, just use the genome to make copies of themselves

• bums

The 2 classes of TE’s

• retrotransposon (class 1)

• DNA Transposons

retrotransposon

Transcribed into RNA as an intermediate, then gets reinserted into the hosts genome

DNA Trasposons

Move around the genome on its own, jumps in, leaves its mark, and leaves

Horizontal Gene Transfer

Exhange of genes between species without reproduction

Horizontal gene transfer is more prominent in

Prokaryotic, bacterial organisms

How can we measure selection on the genome?

• Look at protein coding regions as land marks

Selection theory

All its mutations affect fitness

natural selection disfavors

deleterious mutations

natural selection favors

beneficial mutations

for selection theory, natural selection is the dominant driver of

evolutionary change in DNA sequences

Neutral mutations are

much more prevalent than beneficial mutations

what is the dominant driving force for evolutionary cange in DNA sequences

random genetic drift

Three types of molecular evolution

• selection theory

• neutral theory'

• nearly neutral theory

nearly neutral mutations

• have a slight/tiny beneficial or deleterious effect

• effect depends on population size

harmful mutation example

• Loss of protective coloration in squirrel coats

beneficial mutation example

• antibiotic resistence in bacteria

negative selection ______ The number of these mutants that live to breed, become rarer in future generations

reduces

Positive selection ______ The survival of these mutants over others, become more common in future generations

favors

How are neutral mutations decided to continue on or be reduced

• Entirely through random samplings

DNA to RNA transcription for A

—> U

DNA to RNA transcription for G

—> C

DNA to RNA transcription for T

—> A

DNA to RNA transcription for C

—> G

synonymous vs non-synonymous changes

• synonymous means the change was completely neutral

• Non-synonymous tells us the change had an affect on the protein function, whether positive or negative

The dN/ds or Ka/Ks ratio is

The rate of protein evolution relative to the neutral rate

dN/ds or Ka/Ks formula

# of non-synonymous substitutions per site / # of synonymous substitutions per site

dN/ds or Ka/Ks > 1

• postive selection

• More amino acid changes than neutral changes

dN/ds or Ka/Ks = 1

• neutral selection

• Amino acid changes happening at same rate as neutral change

dN/ds or Ka/Ks < 1

• negative/purifying selection

• fewer amino acid changes than neutral changes