Sources of Variation: Genetics Review Mutation Recombination

DNA, RNA, and Proteins A. Proteins 1. Amino Acids

DNA, RNA, and Proteins A. Proteins 1. Amino Acids 2. Polymerization

DNA, RNA, and Proteins A. Proteins 1. Amino Acids 2. Polymerization 3. Levels of Structure

DNA, RNA, and Proteins A. Proteins 1. Amino Acids 2. Polymerization 3. Levels of Structure 4. Functions

Structural - actin (cytoskeleton, muscle) - elastin - collagen Enzymatic Trypsin Salivary amylase DNA polymerase II Responsible for making all other types of biomolecules Transport Protein channels in membranes Hemoglobin Immunity - Antibodies Communication - Hormones (insulin) Regulatory - Transcription Factors

DNA, RNA, and Proteins B. DNA 1. Nucleotides

DNA, RNA, and Proteins B. DNA 1. Nucleotides 2. Polymerization

5’ 3’

DNA, RNA, and Proteins B. DNA 1. Nucleotides 2. Polymerization 3. Double Helix and Genes

Antiparallel Complementary Purine Pyrimidine

“Split-gene” structure of eukaryotic genes

DNA, RNA, and Proteins B. DNA 1. Nucleotides 2. Polymerization 3. Double Helix 4. Eukaryotic Chromosome

1.2 % of human genome codes for proteins

DNA, RNA, and Proteins B. DNA 1. Nucleotides 2. Polymerization 3. Double Helix 4. Eukaryotic Chromosome 5. Chromosomes, sister chromatids, homologous chromosomes

A a A A a a

DNA, RNA, and Proteins B. DNA 1. Nucleotides 2. Polymerization 3. Double Helix 4. Eukaryotic Chromosome 5. Chromosomes, sister chromatids, homologous chromosomes 6. Genomes

Ophioglossum vulgarum 1024 chromosomes

DNA, RNA, and Proteins C. RNA 1. Nucleotides – 2 diff’s with DNA

DNA, RNA, and Proteins C. RNA 1. Nucleotides

DNA, RNA, and Proteins C. RNA 1. Nucleotides – 2 diff’s with DNA 2. Types and Functions

TRANSCRIPTION

DNA, RNA, and Proteins D. Gene Regulation

Regulation of Transcription TATA Binding Proteins bind to Promoter – enhance binding of Polymerase Activators (transc. factors) bind to enhancers – increase expression Repressors – bind to silencers, activators, promoters and decrease expression

Regulation of RNA Processing

Regulation of Translation Micro-RNA’s block translation of other m-RNA’s… turns gene expression ‘off’

DNA, RNA, and Proteins II. Mutation: A change in the genome of a cell A. Types:

Loss or gain of a chromosome

DNA, RNA, and Proteins II. Mutation: A change in the genome of a cell A. Types: B. Effects

Can affect the timing of gene action, the quantity of protein product, and/or the type of protein produced…. or not!

DNA, RNA, and Proteins II. Mutation: A change in the genome of a cell A. Types: B. Effects C. Frequency

Point mutations are rare (1/million cell divisions), but with 6 billion base pairs in the human genome, they are actually abundant. But mutations that affect whole chromosomes, while very rare, affect more base pairs when they happen.

DNA, RNA, and Proteins II. Mutation: A change in the genome of a cell A. Types: B. Effects: C. Somatic vs. Germ Line Somatic affect body tissues (like cancers) Germ Line (affect egg or sperm) - heritable

DNA, RNA, and Proteins II. Mutation: A change in the genome of a cell A. Types: B. Effects: C. Somatic vs. Germ Line D. Causes

Point Mutations, Insertions, Deletions: DNA Replication Errors

Gene Duplication and Inversions: Error in Crossing-Over: Unequal crossing over leads to gene duplication and deletion A B a b

Gene Duplication and Inversions: Error in Crossing-Over: b B

Gene Duplication and Inversions: Error in Crossing-Over: b B

deletions are usually bad – reveal deleterious recessives i. Unequal Crossing-Over a. process: b. effects: - can be bad: deletions are usually bad – reveal deleterious recessives additions can be bad – change protein concentration

deletions are usually bad – reveal deleterious recessives i. Unequal Crossing-Over a. process: b. effects: - can be bad: deletions are usually bad – reveal deleterious recessives additions can be bad – change protein concentration - can be good: more of a single protein could be advantageous (r-RNA genes, melanin genes, etc.)

deletions are usually bad – reveal deleterious recessives i. Unequal Crossing-Over a. process: b. effects: - can be bad: deletions are usually bad – reveal deleterious recessives additions can be bad – change protein concentration - can be good: more of a single protein could be advantageous (r-RNA genes, melanin genes, etc.) source of evolutionary novelty (Ohno hypothesis - 1970) where do new genes (new genetic information) come from?

Gene A Duplicated A generations Mutation – may even render the protein non-functional But this organism is not selected against, relative to others in the population that lack the duplication, because it still has the original, functional, gene.

Gene A Duplicated A generations Mutation – may even render the protein non-functional Mutation – other mutations may render the protein functional in a new way So, now we have a genome that can do all the ‘old stuff’ (with the original gene), but it can now do something NEW. Selection may favor these organisms.

If so, then we’d expect many different neighboring genes to have similar sequences. And non-functional pseudogenes (duplicates that had been turned off by mutation). These occur – Gene Families

And, if we can measure the rate of mutation in these genes, then we can determine how much time must have elapsed since the duplication event… Gene family trees…

Gene Duplication and Inversions: Error in Crossing-Over: Inversions occur when a chromosome crosses-over with itself:

Loss or gain of a chromosome occurs by Error in Meiosis: non-disjunction

Fusion occurs by translocation:

Genome duplication (polyploidy) occurs by failure of meiosis or failure of mitosis in tissues that produce gametes:

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: a. Autopolyploidy: production of a diploid gamete used in reproduction within a species. Failure of meiosis I or II 2n gamete 3n zygote Correct meiosis in other parent 1n gamete

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: a. Autopolyploidy: production of a diploid gamete used in reproduction within a species. Errors in mitosis can also contribute, in hermaphroditic species

2n 1) Consider a bud cell in the flower bud of a plant.

2n 4n 1) Consider a bud cell in the flower bud of a plant. 2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell.

2n 4n 1) Consider a bud cell in the flower bud of a plant. 2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell. 3) A tetraploid flower develops from this tetraploid cell; eventually producing 2n SPERM and 2n EGG

2n 1) Consider a bud cell in the flower bud of a plant. 4n 2) It replicates it’s DNA but fails to divide... Now it is a tetraploid bud cell. 3) A tetraploid flower develops from this tetraploid cell; eventually producing 2n SPERM and 2n EGG 4) If it is self-compatible, it can mate with itself, producing 4n zygotes that develop into a new 4n species. Why is it a new species?

How do we define ‘species’? “A group of organisms that reproduce with one another and are reproductively isolated from other such groups” (E. Mayr – ‘biological species concept’)

How do we define ‘species’? Here, the tetraploid population is even reproductively isolated from its own parent species…So speciation can be an instantaneous genetic event… 4n 2n Gametes Zygote 1n 3n Triploid is a dead-end… so species are separate

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: a. Autopolyploidy: production of a diploid gamete used in reproduction within a species. b. Allopolyploidy: fusion of gametes from different species (hybridization). These are usually sterile because the chromosomes are not homologous and can’t pair during gamete formation. BUT… if the chromosomes replicate and separate without cytokinesis, they create their own homologs and sexual reproduction is then possible.

X Spartina alterniflora from NA colonized Europe Spartina maritima native to Europe Sterile hybrid – Spartina x townsendii Allopolyploidy – 1890’s Spartina anglica – an allopolyploid and a worldwide invasive outcompeting native species

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: Polyploidy is common in plants; 50% of angiosperm species may be the product of polyploid speciation events.

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: Polyploidy is common in plants; 50% of angiosperm species may be the product of polyploid speciation events. In vertebrates, polyploidy decreases in frequency from fish to amphibians to reptiles, and is undocumented in birds. There is one tetraploid mammal. (Red viscacha rat).

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism:

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: - when the sexes are separate, the rare, random mutation of producing a diploid gamete is UNLIKELY to occur in two parents simultaneously. So, the rare diploid gamete made by one parent (karyokinesis without cytokinesis doubling chromosome number in a cell) will probably fertilize a normal haploid gamete. This produces a TRIPLOID… which may live, but would be incapable of sexual reproduction. 2n 3n 1n

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: - unless…. the new organism could ALSO produce eggs without reduction..clonally… and these are the rare animals that we see – triploid ‘species’ that are composed of females that reproduce asexually. (Some may still mate with their diploid ‘sibling’ species so that the sperm stimulated the egg to develop – but without incorporation of sperm DNA.) Like this Blue-spotted Salamander A. laterale, which has a triploid sister species, A. tremblayi

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: SO! Polyploidy may be more frequent in plants because they are hermaphroditic more often than animals; especially vertebrates. Most cases of polyploidy in animals is usually where triploid females survive and reproduce asexually. Also, simpler development in plants means they may tolerate imbalances better.

Mutations I: Changes in Chromosome Number and Structure A. Polyploidy 1. Mechanisms: 2. Frequency: 3. The effect of hermaphrodism: 4. Evolutionary Importance: - obviously can be an instant speciation event - polyploidy is also a mechanism for “genome doubling” or “whole genome duplication” - this duplication allows for divergence of copied gene function and evolutionary innovation. Eventually, the copies may be so different that they don’t really represent duplicates any more… resulting in “diploidization”.

DNA, RNA, and Proteins II. Mutation: A change in the genome of a cell Sources of Variation: A. Mutation - change to the genome B. Recombination - new genes

Recombination can produce new genes Crossing over WITHIN a gene, in introns, can recombine exons within a gene, producing new alleles. EXON 1a EXON 2a EXON 3a Allele “a” EXON 1A EXON 2A EXON 3A Allele “A” Allele “α” Allele “ά”

DNA, RNA, and Proteins II. Mutation: A change in the genome of a cell Sources of Variation: A. Mutation - change to the genome B. Recombination - new genes - new genotypes

Without crossing over: 2n = 4, gametes = 4 2n = 6, gametes = 8 n = x, gametes = 2x 2n = 46, gametes = 8,388,608

70 trillion combinations Without crossing over: 2n = 4, gametes = 4 2n = 6, gametes = 8 n = x, gametes = 2x 2n = 46, gametes = 8,388,608 Two reproducing humans: Any of the 8 million sperm could fertilize any of the 8 million types of eggs, creating: 70 trillion combinations

“Hey!! That solves my dilemma about how new variation is produced each generation!! Too bad I’m dead!

DNA, RNA, and Proteins II. Mutation: A change in the genome of a cell Sources of Variation: A. Mutation - change to the genome B. Recombination – new genes and genotypes C. The environment