Biology 243 Final Exam Notes

Themes 1 and 2 Evolution: A Brief History

Jean-Baptiste Lamarck o Believed that species changed over time o Lamarckism Acquired traits can be inherited Thomas Malthus o Principle of Populations human population can increase faster than food supply, and therefore this leads to competition and survival of the fittest Alfred Russell Wallace o Cam up with theory of natural selection independently of Darwin Charles Darwin o Voyage of the Beagle Described and collected plant and animal specimens and found interesting patterns regarding distribution of species o The Origin of Species Provides evidence for the evolution of species Idea of descent with modification Describes natural selection as the mechanism for evolutionary change o The Galapagos Islands Endemics Animals live there that are found nowhere else on earth Limited gene flow between islands and mainland Darwins 4 Postulates for Evolution via Natural Selection o Individuals VARY o More offspring are produced than can survive and/or reproduce o Survival and reproduction is not random o Some variation is passed to offspring (Heritable) Evolution o A change in the frequency of an allele o Evolution can occur quickly enough to observe within a matter of seasons o Evolutionary change can be very small scale

Theme 3 Topic 1 DNA as an Information Molecule

Genotype Entire DNA sequence (genome) that is inherited from parents to progeny and contains all the biological information needed to build and maintain a living organism The full set of genes inherited by an organism Turning on genes produces RNA and proteins

Phenotype: body plan, behaviour, metabolism, & much more Proteins determine phenotype, as proteins ultimately control every reaction in the cell o Enzymes, structural proteins, signalling proteins, etc.

Establishing DNA as the Hereditary Molecule Griffith Transformation Principle o The conversion of a cells hereditary makeup by the uptake of DNA from another cell o Injected mice with the bacteria to understand how infection takes place Avery et al. Identifying the Chemical Nature of the Transformation Principle o Determined whether it was DNA, RNA, or protein that allowed for transformation principle to take place o Found that DNA was the transformation molecule Hershey and Chase The Blender Experiment o Determined that the nature of genetic material in the bacteriophages was DNA, not proteins o Tagged bacteriophage DNA and proteins with radioactive isotopes 32P and 35S respectively

Topic 2 Structure of DNA

Components of DNA DNA consists of equal parts of o Pentose Sugar (Ribose for RNA, Deoxyribose for DNA) o Phosphate o Nitrogenous Bases

Purines
Guanine Adenine
-

Pyrimidine s
Uracil Thymine

Cytosine

Pentose Sugars o Carbon atoms are labeled for orientation o Absence of the 2 hydroxyl group in deoxyribose increases mechanical flexibility in DNA compared to RNA

Purines Double-Ringed Structure Adenine Amine Guanine Amine + oxygen

Pyrimidines Single-Ringed Structure Cytosine Amine + oxygen Thymine Methyl + 2 oxygen Uracil 2 Amine + 2 oxygen

Deoxynucleotides (dNTPs) are the building blocks of DNA They form by the removal of water

Polynucleotides The polymerization of nucleotide monomers Covalent bonds form phosphodiester back bone Polynucleotide has directionality and polarity Type of nucleic acid depends on sugar (DNA = deoxyribose, RNA = ribose) present Upstream = towards 5 PO43- end Downstream = towards 3 OH- end Synthesized in 5 to 3 direction

Chargaffs Rule

%A = %T and %C = %G
States % purines = % pyrimidines Franklins X-Ray Diffraction Revealed the structure of DNA Significant patterns in arrangement of atoms viewed in repeating intervals It was discovered that DNA was cylindrical, and ultimately helical

Watson and Crick Created a scale model of DNA Two sugar-phosphate backbones running antiparallel to one another They discovered the backbone to be hydrophilic, and the bases to be hydrophobic Purines always paired with pyrimidines complimentary base pairing o Purine-purine base pairing is too wide o Pyrimidine-pyrimidine base pairing is too narrow Hydrogen bonds hold the nucleotides and the two strands together

Watson and Crick decided that genetic information must be coded in the nucleotide sequences of DNA

Watson and Cricks Model of DNA Replication Parental strands act as templates for replication through complimentary base pairing Parental strands unwind by breaking hydrogen bonds Semiconservative replication where new double helix contains one parental and one newly synthesized strand

DNA Organization Can be circular or linear Prokaryotes o Typically have one chromosome (usually circular) o Also have other small independent circular DNA called plasmids in the cytoplasm Eukaryotes o Linear and enclosed in nucleotides o Compacted in DNA to fit in cell nucleus o Chromosomal structure protects DNA from damage o Chromosomes can easily be separated during cell division

Essential Components of Eukaryotic Chromosomes 1) Origin of Replication o The attraction of multiple proteins to initiate DNA replication 2) Centromere o DNA sequences required for correct segregation of chromosomes after DNA replication 3) Telomeres o DNA sequences located at the ends of the chromosome that attracted proteins preventing degradation and allow for proper replication of chromosomal ends Histones Positively charged proteins that DNA wind around Histone H1: Binds DNA to nucleosomes to form chromatin fibre Prokaryotes DO NOT have histones since bacterial chromosomes need not be compacted

Chromatin Heterochromatin o Regions of higher DNA compaction o Where transcription is turned off o Found in telomeres and centromeres o Barr Body an X chromosome becomes inactive by the block of heterochromatin Euchromatin o Regions of less DNA compaction o High levels of gene expression

Note: More complex organisms typically have lower gene density an organisms complexity is not directly proportional to genome size

Topic 3 DNA Replication

Three Putative Models of DNA Replication 1) Semiconservative Complimentary base pairing allows for parental strands to act as templates for replication Parental strands unwind through breaking of H-bonds 2) Conservative After replication, both daughter strands pair up 3) Dispersion Daughter strands will have a mixture of parental and newly-synthesized DNA

Meselson and Stahl Experiment Distinguished between old and new DNA to determine how replication occurred DNA labelled with isotopes 15N and 14N and isotopes incorporated into DNA molecules via nitrogenous bases Tracking of parental and newly synthesized DNA strands over many generations analyzed Discovered that semiconservative model was correct

DNA Polymerases Synthesizes the new strand in the 5-3 direction, with new nucleotides added to the new strand at the 3 OH end Requires an RNA primer to begin synthesis Contains a single active site that can catalyze four different reactions and requires optimum confirmation of site for incoming nucleotide to add to correct base pair

DNA Replication in Prokaryotes 1) Initiation Unwinding and separation of the two template DNA strands, forming two replication forks 2) Elongation Simultaneous synthesis of the two new DNA strands from the template strands by DNA polymerase 3) Termination When forks meet at opposite side of circular DNA, replication stops and protein complex of DNA polymerase drops off from DNA

Replication Forks One strand continuously synthesized (leading strand) Other strand synthesized discontinuously (lagging strand) The small fragments (Okazaki fragments) are linked together

DNA Replication Enzymes The Replisome is the complex of enzymes that replicate DNA

Enzyme Helicase Primase Single-Strand Binding Protein DNA Topoisomerase/Gyrase DNA Polymerase III DNA Polymerase I DNA Ligase

Function Unwinds the double helix by breaking hydrogen bonds Synthesizes RNA primers for DNA polymerase Stabilizes ssDNA before replication by preventing reannealing so that the strands can serve as template Removes super coils that form ahead of the replication fork, relieves torque/tension of mainly circular DNA Synthesizes DNA by adding nucleotides to the new DNA strand Removes RNA primer and fills the gaps with DNA Joins the ends of DNA segments by forming phosphodiester bonds

DNA Replication Steps 1) Helicase unwinds the DNA and Primase synthesizes RNA primers

2) RNA primers used as starting points for addition of nucleotides by DNA Polymerase

3) DNA unwinding, leading strand synthesized continuously, lagging strand discontinuously

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4) DNA Polymerase I removes RNA primer, replaces with DNA, leaving a nick

5) DNA Ligase closes the nick

6) DNA continues to unwind and synthesis cycle repeats

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Plasmid Replication Occurs by the process of rolling circle replication Fertility plasmids contain genes for conjugation

DNA Replication in Eukaryotes There are multiple origins along chromosomes so DNA replication can be completed in time during S phase End Replication Problem o When RNA primer is removed, DNA Polymerase I can elongate 3 end of Okazaki fragment o At the very end of chromosome, no such fragment is present on 3 end o Therefore there is additive loss at chromosomal ends after each replication o Genes can become deleted leading to organismal death o Telomeres solve this problem

Telomeres Genes protected by a buffer of non-coding DNA added to the 3 end of chromosomes by Telomerase Telomerase adds additional telomere repeats to the end of the template strand prior to replication Approximately 10000 bp long Can be worn away after each replication, and when completely gone, cell stops dividing

Proofreading Activities of DNA Polymerases 3 exonuclease activity to remove the most recent mismatched nucleotides

Photoreactivation: repair of UV-Induced DNA Damage DNA absorbs photonic energy resulting in fusing of adjacent thymines Photolyase recognizes this and uses light energy to separate the fused thymines (photoreactivation)

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Topic 4 Central Dogma

Central Dogma: The universal flow from DNA to protein in order to convert genotype to phenotype Gene The basic physical and functional unit of heredity Made up of DNA and act as instruction to make proteins Genes encode for: o Coding RNA (mRNA): codes for a protein o Noncoding RNA (tRNA, rRNA, snRNA, microRNA): does not code for a protein

Beadle and Tatum Hypothesized that genes encode enzymes that function at each step of a biochemical pathway needed to make an essential nutrient Believed that mutating a gene that coded for an enzyme would interrupt metabolic pathway and the organism would no longer be able to synthesize needed nutrient They showed the direct relationship between gene and enzyme

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The Genetic Code Nonsense/Stop Codons o Three codons that do not specify amino acids Redundancy/Degeneracy o Synonyms for same amino acid There are no commas in the genetic code, and therefore there is only one correct reading frame

Topic 5 Transcription
Transcription in Prokaryotes 1) Initiation RNA Polymerase binds to promoter DNA unwound freeing the template strand (transcription bubble) Ribonucleotides added de novo 2) Elongation RNA Polymerase moves along template DNA unwinding DNA in front, and reannealing DNA behind 3) Termination Sequences located at the 3 end of the new RNA molecule causes dissociation of the RNA and RNA polymerase from DNA template RNA Polymerase Binds to promoter region to initiate transcription Does not need a primer Unwinds and rewinds DNA helix during RNA synthesis The promoter specifies where the RNA Polymerase will begin transcription

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Prokaryotic Promoter Located immediately upstream (towards 5) of transcriptional start point (+1) A specialized DNA sequence where transcription determines which gene is turned on or off

Promoter strength determines how well the RNA polymerase binds and initiates transcription Pribnow Box - The sequence TATAAT and serves as the location of transcription initiation Prokaryotic Elongation RNA is created in the 5 to 3 direction Uses the 3 to 5 DNA strand as a template RNA Polymerase breaks the complimentary base pairs by breaking hydrogen bonds Behind the enzyme, DNA strands reforms a double helix Transcription continues until the end of the gene Another RNA polymerase can start creating another RNA transcript as soon as there is room at the promoter

Prokaryotic Termination The completed RNA molecule is released from template DNA Double helix of DNA reforms In prokaryotes, transcription is terminated in two ways: o Rho-Independent Termination Terminator sequence in mRNA base pairs with itself to form GC hairpin Causes RNA polymerase to stall and dissociate o Rho-Dependent Termination Terminator sequence in mRNA is recognized and bound to the Rho helicase enzyme which unwinds the RNA from the template DNA and RNA polymerase
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Features of the Prokaryotic Gene Operon o Cluster of prokaryotic genes and the DNA sequences involved in their regulation Promoter o Transcription initiation

Note: Prokaryotic mRNA is polycistronic a single mRNA encodes for multiple peptides usually involved in the same function Comparing RNA Transcription and DNA Replication

Transcription in Eukaryotes Three types of RNA polymerases I, II, III which make rRNA, mRNA, and tRNA respectively Several general transcription factors (GTFs) are necessary to recruit RNA polymerase to the promoter mRNA termination mediated by a polyadenylation signal Eukaryotic mRNA is monocistronic

Eukaryotic Initiation RNA pol I and III non-protein coding genes (rRNA, tRNA) RNA pol II protein-coding genes RNA pol does not recognize promoter
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A key element in protein-coding genes = TATA Box Transcription factors recognize and bind to TATA Box RNA pol II recognizes multiRegulatory protein complex and bind to it Gene(s)

Promoter DNA TATA Box

-

Transcription Unit

Exon Intron Exon Intron Exon 5 UTR 3 UTR

Transcription initiation mediated by binding of DNA-binding proteins to specific regions on gene General Transcription Factors bind to promoter and recruit RNA polymerase II for initiation (basal or normalized rate transcription) TFI

TFIID, A, B, F, E, H (GTFs) and RNA Pol II

Activator Transcription Factors bind to promoter proximal regions and enhancer regions to cause o Enhancer binding proteins increase transcription rate by stimulating initiation of RNA polymerase o Enhancers and associated proteins are brought close to the promoter by DNA looping

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Chromatin Remodelling During Initiation Transcription initiation inhibited by dense arrays of nucleosomes Access of promoter to RNA polymerase and GTFs requires reorganization of nucleosomes Activator proteins displace nucleosomes from promoter regions Activator proteins recruit histone acetyltransferase that add acetyl groups to histones loosening DNA binding

mRNA Processing in Eukaryotes Precursor-mRNA contains transcribed introns and exons Pre-mRNA undergoes processing in the nucleus to produce mature translatable mRNA A 5 Cap (modified guanosine triphosphate) added by a capping enzyme following transcription initiation o Functions as a binding site during translation Transcription termination controlled by a polyadenylation signal in the 3 sequence o Protects mRNA from RNA digesting enzymes

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Eukaryotic Transcriptional Termination Termination is linked to polyadenylation CPSF (Cleavage and Polyadenylation Specificity Factor) cleaves mRNA after transcription passes the poly-A signal The poly-A tail is added to the 3 end of mRNA by poly-A polymerase Poly-A-tail prevents digestion of mRNA

mRNA Splicing: pre-mRNA to RNA pre-mRNA contains exons and introns (exons being coding segments, introns being noncoding segments) Introns are removed from the pre-mRNA and exons spliced together to form mature mRNA

Splicing is carried out by the spliceosome which is made up of non-coding mRNAs called snRNPs or Small Ribonucleoprotein Particles After introns are removed, they are degraded and snRNPs are free to be reused

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Alternative mRNA Splicing Joining different exons can amount to different protein diversity Several related protein products (isoforms) or the same mRNA molecule can be formed by making different combination of mRNAs Alternative splicing dramatically increases the number and variety of proteins that can be encoded by the genome The most highly expressed genes had only SHORT INTRONS

Transcriptional and Posttranscriptional Regulation in Eukaryotes 5 cap, 3 polyadenylation tail, splicing, and microRNAs Half-life of mRNA can vary significantly and depends upon regulation of mRNA after transcription Removal of the poly-A tail or 5 cap results in mRNA degradation by exoribonucleases MicroRNAs as a regulator: o Noncoding RNA located within genes are transcribed by RNA polymerase II o Hairpin miRNA cleaved to 21-23 bp by Dicer Rnase o Silencing RNAs (siRNAs) are unwound and one of the strands functions as a template in RISC (RNA induced silencing complex) to guide cleavage of complimentary mRNA and inhibit translation

Reverse Transcription Found in viruses with RNA genomes Even if viral genome is RNA, a DNA template must be made to produce mRNA

Topic 6 Translation
The Genetic Codes Consists of 64 sense codons and the amino acids specified by these codons Codons are written 5 to 3as they appear in the mRNA AUG (methionine) an initiation (start) codon UAA, UAG, UGA = termination codons and do not code for amino acids o The tRNA does not bind to these codons Codons are non-overlapping and contain no gaps

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Type

Amino Acids Contain an amino acid and carboxyl group bonded to a central carbon with a hydrogen and R functional group R group determines uniqueness of amino acid Amino acids joined together by a covalent peptide bond Polypeptides are chains of amino acids linked by peptide bonds Nonpolar amino acids (R groups contain CH2 or -CH3) Uncharged polar amino acids (R groups usually contain OH) Charged amino acids (R groups that contain acids/bases that can ionize) Aromatic amino acids (R groups contain benzene ring)

Non-Polar

Uncharged Polar Acidic Basic

Name Alanine Valine Leucine Isoleucine Glycine Cysteine Phenylalanine Tryptophan Methionine Proline Serine Threonine Tyrosine Asparagine Glutamine Aspartic Acid Glutamic Acid Lysine Arginine Histidine

The Ribosome A complex molecule made of rRNA molecules form a factor for protein synthesis in cells Composed of two subunits o Large 50S subunit o Small 30S subunit Each subunit exists separately in the cytoplasm, but the two join together on the mRNA molecule The ribosomal subunits contain proteins and specialized RNA molecules ribosomal rRNA and transfer RNA (tRNA)

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3 binding sites (A, P, E) o Aminoacyl (A) site: binds to aminoacyl-tRNA o Peptidyl (P) site: for the aminoacyl-tRNA carrying the growing polypeptide chain o Exit (E) site

tRNA Molecules tRNAs bring amino acids to the ribosome o Small RNAs (75-90 nucleotides) o Act as an adaptor between codons and amino acids Aminoacyl-tRNA (charging): tRNA + amino acid o Aminoacyl-tRNA synthetase adds correct amino acid to the acceptor stem of correct tRNA tRNA and the Wobble Effect o The complete set of 61 codons can be read by FEWER than 61 tRNAs o This is because of the pairing properties in the bases of anticodons o Pairing of anticodon with first 2 nucleotides is precise, but the third has more flexibility o Third position can wobble

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Phases of Translation The beginning of mRNA is not translated during initiation Untranslated region (UTR) is located between the first nucleotide that is transcribed and one before the start codon (AUG) region o Does not affect the sequence of amino acids in a protein

Initiation 5 UTR contains the ribosomal binding site Initiation occurs with the interaction of certain key proteins of 5 cap Small ribosomal subunit binds to 5 UTR Methionine charged tRNA binds to the AUG start codon, completing the initiation complex Large ribosomal subunit joins initiation complex Met-tRNA now occupies P site establishing the reading frame

Elongation Elongation factor G - a protein that allows the ribosome to move along mRNA in the 5 to 3 direction (translocation) The tRNA for second codon can then bind to the A site tRNA molecule enters E site and is released into cytoplasm to pick up another amino acid SRPs guide ribosome to ER membrane and bind with SRP receptor and protein can be released into ER

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Termination Termination codons are not recognized by tRNAs In place of a tRNA, a termination factor binds and facilitates release of mRNA from the ribosome and causes the separation of the ribosome

Post-translational Modification of Polypeptides Eukaryotic proteins inactive when released from ribosome Post-translational modification is necessary protein biosynthesis Enzymes may remove amino acids from the amino end of the protein Methionine is usually taken off during post-translational modification

Topics 7 & 8 Changes in DNA Sequences and Spontaneous Mutations

Mutation: A change in the physical structure or in the nucleic acid sequence, resulting in an error in the transmission of genetic information Occurs in DNA and RNA Occurs in somatic or germ line cells Can result in change to the amino acid sequence resulting in phenotypic variation Effects can be neutral, deleterious, or beneficial

Types of Mutations Somatic: o Occur in any of the body cells except gamete cells o Therefore, these mutations are NOT heritable Germ Line: o These types of mutations are of evolutionary significance o Mutation is the only process that is both necessary for evolution and sufficient by itself to cause evolution Small Scale locus specific o Point mutations (missense, nonsense, silent) o Insertions/deletions (frameshift) Large Scale - chromosomal o Gene duplications/deletions o Translocations/inversions

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Point Mutations Substitution of a single pair of nucleotide bases with another pair Substitution of purine for purine or pyrimidine for pyrimidine is 2x as common as a pyrimidine for purine substitution Can have discrete effects on the amino acid sequence o Missense codes for different amino acid o Nonsense new codon is a STOP codon causing premature termination o Silent (Synonymous) no change in amino acid sequence

Insertion/Deletion/Frameshift A shift in reading frame, affecting translation of other codons in coding DNA

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Large Scale Mutations Chromosomal Duplication/Deletion

Entire chromosomes can also change An individual with an abnormal set of chromosomes is an aneuploid Aneuploidy occurs mainly through non-disjunction o ex) Downs Syndrome (trisomy 21)

Copy Number Variation (CNV) Large regions of the genome that have been deleted or duplicated Variation accounts for ~12% of human genomic DNA

Spontaneous Mutations (Natural) Naturally occurring as a result of errors in DNA replication o ex) Deamination and depurination of nitrogenous bases Slippage Mutations o Causes an increase and decrease in the number of sequences o Common in repetitive sequences of DNA o Occurs only in DNA replication Microsatellites o Short tandem repeats (STR) of DNA o Mutations can lead to a new number of repeats (due to replication slippage, and thus new alleles) Spontaneous mutation rates vary with organism, and with tissue type in organism

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Induced Mutations Mutagens o Induce mutations by replacing a base o Alters a base causing a mispair with another base o Damages bases so no pairing is possible Base Analogs o Mimic bases and incorporates into DNA (can cause mispairing during DNA replication) Chemicals that alter base structure Damage to bases through UV radiation exposure

Note: Not all types of mutations occur with equal probability and therefore are not truly random occur randomly with respect to whether their effects are beneficial or deleterious RNA Mutations Very high rates of mutations in RNA viruses Viral RNA polymerases lack proof-reading ability of DNA polymerases

Mutant Alleles Wild Type Allele o Normal form of the gene found in nature of the standard laboratory strains of a model organism Amorphs/Null Alleles o No gene function, usually entire gene is deleted (recessive mutation) Hypomorphs o Reduced gene function relative to wild type (recessive mutation in gene that partially affects gene function) Hypermorphs o Enhanced gene function relative to wild type (dominant gain-of-function mutation)

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Topic 9 Inheritance
Cell Division in Prokaryotes Binary Fission o Prokaryotes undergo a cycle of cytoplasmic growth, DNA replication, and cell division o Replication begins at ori o Replicated origins migrate to ends of poles o Inward growth of plasma membrane and partition assembly of new cell wall, dividing replicated DNA producing two daughter cells o Effective method since only one chromosome

Eukaryotic Cell Cycle Interphase Gap 0 (G0) Phase o A resting phase where the cell has left the cycle and has stopped dividing Gap 1 (G1) Phase o Initial period of cytoplasmic growth o Synthesis of enzymes required for S phase, mainly those needed for DNA replication and structural proteins Synthesis (S) Phase o Rapid duplication of DNA and chromosomal proteins Gap 2 (G2) Phase o Period of cell growth o End of G2 signifies the end of interphase G2/M Checkpoint o A DNA damage checkpoint o An arrest of the cell in G2 prior to mitotic entry in response to genotoxic stress such as: UV radiation Oxidative stress DNA intercalating agents

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Mitosis Prophase o Chromatin condenses into chromosome o Nucleolus disappears RNA synthesis ENDS o Chromosomes bounds together at centromere o Centrosomes nucleate microtubules to form spindle by polymerizing tubulin o Molecular motor proteins push centrosomes to create spindle poles Prometaphase o Nuclear membrane breakdown o Spindle microtubules have direct access to chromosomes o Each kinetochore of sister chromatids attached to spindle microtubules o Chromosomes move to equator of cell o Microtubules connect to each chromosome at its kinetochore, a complex of proteins positioned at the centromere Metaphase o Chromosomes align along cell equator o Kinetochore microtubules attach the chromosomes to the spindle pole Anaphase o Sister chromatids separate, moving to opposite poles becoming independent chromosomes o Enzymatic breakdown of cohesin linked the sister chromatids together during prophase o Chromosomes walk themselves along stationary microtubules, using motor proteins in their kinetochores Telophase o Chromosome arrive at poles o Mitotic spindle disassembles o Formation of new nuclear membrane around each group of chromosomes Cytokinesis o Physical process that splits the parent cell into two identical daughter cells with cytoplasm dividing by furrowing o Cell membrane pinches in at the cell equator, forming cleavage furrow o Position of furrow dependant on position of astral and interpolar microtubules
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Regulation of the Eukaryotic Cell Cycle G1/S Control Point o Initiation of DNA synthesis G2/M Control Point o Regulation of mitotic entry Progression past these points depends upon activation of CDK (cyclic dependent kinase) bound to its regulatory cyclin subunit prompting cell to proceed into next cell cycle phase o CDK allows cycle to proceed past control points, telling cell to proceed to next step of cell cycle Cyclins are expressed in specific phases of the cell cycle which determines when a CDK is active Cell Size Checkpoint o Must attain a certain size at START, and G2/M checkpoints o The cells must be twice as big as daughter cells at G2/M checkpoint

Mother cell (larger) G1 Budding yeast

START

Daughter cell spends a longer time in G1 phase as it must take more time to grow

START

G1 Daughter cell (smaller)

When Cell Cycle Regulation Goes Wrong Cancer o Uncontrolled cell division o Altered expression of multiple genes due to mutations Oncogenes o Positive regulators (gain of function) in the cell cycle Tumor Suppressor Genes o Loss of function at checkpoint genes o Mutation prevents there from being division regulation

These mutated genes implicate cancer

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Cell Division Senescence (When cells become very old) Infinite division of cells impossible o Due to damage, defective telomeres, etc. Genes affecting cellular again we first found to be tumor supressors Division arrest followed by either Genetic recombination o Apoptosis (cell suicide) o Senescence (stopping cell division)

Genetic Recombination At the level of population, variation is necessary for evolution by natural selection Ultimate source of variation is mutation Diversity increases through genetic recombination

Asexual - Offspring are clones of parents - Inheritance of ALL parental genes in offspring - Transformation/transduction provide addition of sources of DNA for recombination

Sexual - Gametic union - Dependant on meiosis - Inheritance of alleles from each parent - Offspring not likely to be like parent/sibling

Genetic Recombination in Bacteria F-factor and conjugation bridge necessary for genetic material transfer Bacterial conjugation is equivalent of mating as genetic material is exchanged Bacteria have a conjugative plasmid integrated into genomic DNA called F-factor o Attempts to transfer entire DNA through the mating bridge o Since F-factor transfers itself during conjugation, the rest of genome is dragged along with it

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F+ cell
F+ and F- cell differ in alleles o F+ = a+, b+, c+, d+ o F- = a-, b-, c-, dRecombination occurs between donor chromosome and recipients chromosome Crossover produces a b+ recombinant (F-: a-, b+, c-, d-)

F- cell

Strategic Sex Evolution of recombination had to have happened in presence of asexuals Sex is expensive o Cost of finding a mate o Ecological o Mechanical

Comparing Mitosis and Meiosis

Mitosis

Meiosis

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Fertilization (aka Syngamy) Haploid gametes come together to create a diploid zygote through fusion Resulting in a zygote with a maternal and paternal cell

Introduction to Meiosis Reduction Division (Meiosis I) Equational Division (Meiosis II) G1, S, G2 and M still occur DNA replicated in S phase o Each chromosome copied (now there is a pair of sister chromatids refer to diagram)

Meiosis 1 Prophase 1 o Synapsis occurs (homologous chromosomes pair up) o Chromosomes have sequences that act as signals for pairing and alignment o Fully paired chromosomes are called tetrads when there are four chromatids together o Genetic recombination/crossing over physical exchange mixing alleles of the homologous chromosomes Occurs between any two chromatids in tetrad structure Visualized in structures called chiasmata Cells not forming chiasmata may cause aneuploidy in gametes Recombination results in different allele combinations

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Prometaphase I o Nuclear envelope breaks down spindles enter Metaphase/Anaphase I o Alignment of tetrads and separation of chromosomes of each homologous pair Telophase I and Interkinesis o No synthesis, reassembly of microtubules for 2nd division

Meiosis II There is no preceding S phase so meiosis II is not exactly like mitosis o Chromosomal behaviour is however like mitosis

How Germ Cells are Affected by Environment Male germ cells o Meiosis occurs after puberty o Mutation rates are higher in males due to the meiotic rate Female germ cells o Meiosis occurs within fetal ovary and all eggs are arrested in meiotic prophase until maturity

Nondisjunction Failure of homologous chromosomes to separate in meiosis I Failure of sister chromatids to separate in meiosis II Imbalance of chromosomes (aneuploidy) o Monosomy Loss of chromosome (2n-1) o Trisomy Gaining an extra chromosome

Meiosis and Diversity Variation increases chance that some offspring in a population have favorable combinations of alleles to survive Different combinations of maternal/paternal chromosomes during segregation o Random o Independent Assortment

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Spindle connections are random, not distinguishing between maternal and paternal chromosomes Each chromosome carries one recombinant and one non-recombinant chromatid Random fertilization occurs between gametes providing multiple combinations of zygotes too

Theme 4 Mendels Experiments, Genes, and Alleles

3 Hypotheses 1) All plants carry a pair of factors (genes) governing inheritance of a character 2) A pair of genes consists of different alleles, with one allele dominant over the other 3) Alleles that control a character separate as gametes separate Mendels Principle of Segregation Each organism is diploid: has two alleles Homozygous: two alleles are the same Heterozygous: two alleles are different Parental Cross: Cross of true breeding lines (homozygous) F1 Generation: First Filial Generation A recessive allele is only expressed if two copies of recessive allele is present

Testcrosses Cross an individual with a dominant phenotype to a homozygous recessive phenotype If offspring ratio is 1:1 dominant to recessive, tested individual is heterozygous If offspring ratio is all expressing dominant phenotype, tested individual is homozygous dominant

Determining Dominance in Mutant Alleles Cross homozygous mutant with homozygous wild-type individual o If heterozygote shows mutant phenotype, allele is dominant o If heterozygote shows wild type phenotype, allele is recessive Loss of Function mutant alleles are recessive (amorphs/hypomorphs) Gain of Function mutant alleles are dominant (hypermorphs)
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Incomplete Dominance One allele is not completely dominant to the other allele Superscripts used to label the alleles instead of uppercase and lower case letters o (Red Flowers)x(White Flowers) = Pink Flowers (blend of the colors)

Co-Dominance The heterozygote for the allele exhibits both homozygote phenotypes The offspring will exhibit both of the phenotypes because the alleles co-exist with one another and work together to express the phenotype o Ex) (Red Flowers)x(White Flowers) = Flowers that each show red and white coloring

Theme 5 Population Genetics and Selection

Darwins Four Postulates for Evolution by Natural Selection 1. 2. 3. 4. Individuals within a species VARY Variation is HERITABLE More offspring produced than can survive (SURPLUS) Survival and reproduction not random, but due to phenotypic variation

Important Things to know about Natural Selection Things that Prevent Evolution by Natural Selection o No variation o No heritability of variation o Variation heritable, BUT there is no fitness consequence that improves fitness of new generation Natural selection does not act directly on genes Acts upon phenotypes, is non-random, and does not produce perfection It does not act for the good of a species, but rather selects on the individuals

Inheritance Blending Inheritance Theory - problematic o Offspring have traits that are intermediate to parents Inheritance of Acquired Characters - problematic o Idea that only favorable traits acquired by parents were passed onto offspring

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Hardy Weinberg Equilibrium (HWE) Assumptions for HWE o Infinitely large population (to expect minimal genetic drift) o No evolutionary forces (no mutation, no selection, no migration) o Random mating to ensure normalized distribution of gene frequencies Predictions o Allele frequencies remain constant o Genotype frequencies remain constant o Equilibrium genotype frequencies reached in ONE generation of random mating

p + 2pq + q
-

p+q=1

It is important to never take the square root of either p2 or q2 to determine p or q (respectively) if you arent sure that the population is in HWE

Theme 6 Variations and Consequences

Selection Differential propagation of different genotypes Aspects of the environment that influence survival and reproduction o Mutations too Effects of selection include: o Fixation (when allele has reached 1.00 in frequency) of one allele ultimately resulting in the loss of genetic variation for another allele o Maintenance of genetic variation

Natural Selection Direction Selection: Individuals of one extreme phenotype favored Stabilizing Selection: Individuals with intermediate phenotype favored; Extreme phenotypes selected against Disruptive Selection: Both extreme phenotypes favored; intermediate phenotypes selected against

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Directional Selection There is DIRECTION in the trend towards left or right extrema

Disruptive Selection Multiple peaks = disruptive curve in graph Offspring that are larger or smaller in body length (for example) are selected for in this type of pattern

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Stabilizing Selection The intermediate phenotype is selected for, while extreme phenotypes are selected against More commonly found in nature

We can sometimes infer that there is a heterozygote advantage Example: Sickle Cell Anemia and Malaria o Single amino acid substitution leads to crystallization of hemoglobin at low oxygen concentrations o Two alleles are co-dominant A = normal S = sickle AS = mild condition present SS = often dont survive o Malaria also infect red blood cells, therefore AA individuals at sickle cell locus are seriously affected by malaria, and heterozygotes for sickle cell are less effected o Survival: AA < AS > SS

Types of Selection Viability Selection: Differences in survival Fecundity Selection: Differences in reproductive success

Defining Differences between Males and Females Gametes o Males: Produce large numbers of energetically cheap and motile sperm
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o Females: Produce smaller numbers of energetically expensive (less motile) o Hermaphrodites: Can produces both types of gametes Sexual Monomorphism o When females and males dont have significantly different defining phenotypic characteristics Sexual Dimorphism o When females and males have noticeably different phenotypic characteristics Reproductive Success = Fecundity + Mating Success

Sexual Selection: Favors traits that increase the individuals ability to obtain a mate Fecundity: The number of gametes produced by an individual (governed by natural selection) Parental Investments o Gamete Production Eggs are expensive, sperm is cheap In any species, more sperm than eggs are produced o Parental Care Cost of bearing (pregnancy) & raising offspring Usually greater in females, but exceptions exist

Batemans Principle If females invest more in offspring, they are more limited by resources Males are limited instead by access to females, and should exhibit o A stronger correlation between mate number and offspring number in males o A greater variance in mate (and offspring) number Notice the graph on the right and how there is not such a strong correlation between numbers in mates and number of offspring since they are ultimately limited to the resources available

Limits on Reproductive Success If females are limited by RESOURCES, then males are limited by ACCESS to females We expect males and females to use different strategies to maximize their reproductive success o Males compete for females o Females can afford to be choosy (quality not quantity)
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Most importantly, total numbers of matings doesnt differ between sexes Non-random variance in mating success matters to evolution by sexual selection o Highly successful males father disproportionally more offspring

Sexual Dimorphism Polygynous = one male mates with MANY females Males are 3x the weight of females Males larger variance in reproductive success than females The larger the male is to the female = greater polygyny occurs When female:male size ratio is close, monogamy usually is the case = increased parental care

Inbreeding A special case of non-random mating (this is an example of the violation of HWE assumptions) Causes for inbreeding are o Small populations (absolute, geographical, cultural) o Mating system (mating with relatives, such as cousins)

An example is self-fertilization of plants: AA (p2) Aa (2pq) aa (q2) 250 500 250 Generation 0 375 250 375 Generation 1 437.5 125 437.5 Generation 2 468.75 62.5 468.75 Generation 3 Ratio of heterozygotes to homozygotes decreases because gametes produced by heterozygotic plant causes some homozygotes to be produced of AA or aa. Genotype # individuals

freq A = a = 0.5 Genotype frequencies change, allele frequencies dont!

Effect of Homozygosity Usually related to evolution because the result is typically something that selection can act upon For some flowers, inbreeding can result in less success through germination of seeds due to less fitness, and some inbred plants can be smaller and produce fewer flowers suggesting fitness can suffer as a result of homozygosity (associated with a deleterious mutation = decline in fitness)

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In inbreeding, a greater proportion of offspring are homozygous than proportion of individuals that outcross o Non-random mating changes genotype ratios Depending on the amount of genetic variation this could produce homozygous recessives at many loci in offspring If a significant proportion of mutation are deleterious, these will be expressed o A greater proportion of your offspring will have lower fitness than offspring from outcrosses.

Genetic Drift A completely random process Changes in allele frequency due to chance in finite population, especially very small populations Contrast with inbreeding o Inbreeding does not change allele frequencies o Is not necessarily a random process (mate choice can be involved) Drift in a small population: survival and reproduction involves sometimes just being at the right place at the right time Effects o Random change in allele frequency o Gradual loss of genetic variation o Differentiation among populations Populations can get stuck in an extinction vortex (allele effect)

Darwinian Fitness Contribution an individual makes to the gene pool of the next generation relative to the contribution of others A value of 1 is assigned to the phenotype with highest representation Other phenotypes are assigned based on the reproductive success relative to the dominant type

The type of selection occurring in the fitness value example was Disruptive Selection Because the female mimic phenotype does affect the frequency vs. trait curve due to the mating strategies of the female mimic phenotype.

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Speciation The process by which new species arise Major categories of species concepts o Morphological individuals that look alike o Reproductive ability to produce offspring o Phlyogenetic/Genetic shared evolutionary history

Morphological Species Concept organisms defined by unique reliable morphological character Most traditional concept, practical and simple to use No clear genetic of evolutionary justification choice of characters may be arbitrary

Biological Species Concept (BSC) defines two populations as being two different species if reproductively isolated from one another Most commonly used concept Clear and biologically relevant lack of gene exchange between populations Applies only to sexual and contemporary populations Gene flow presents an issue for this concept

Process of Speciation Starts with one species (interbreeding organisms) Genetic Variant spreads through a small amount of species bearers of this variant my mate only with other bearers of same variant Two phenotypically variant species form, and further behavioural/ecological differences may evolve

Reproductive Isolation Mechanisms Maintaining genetic diversity between 2+ similar species Prezygotic Mechanisms o Prevent mating or fertilization o Barriers of this type of mechanism include: Habitat Behavioural
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Temporal Mechanical when physical components of reproduction dont fit Gametic zygotes dont form some incompatibility with systems in plants Postzygotic Mechanisms o Prevent zygote development or reproduction o Barriers of this type include Reduced hybrid viability (low survivorship sometimes embryonic development fails early in development) Reduced hybrid fertility Hybrid breakdown (hybrids are made, but are not very successful) Three Outcomes Indicative of Successful/Unsuccessful Speciation 1. When individuals hybridize readily = no speciation has therefore occured 2. When individuals do not hybridize at all = full speciation has occurred since hybrids cant form 3. Individual hybridize but have reduced fitness = speciation in progress selection for evolution of strong reproductive barriers

Allopatric Speciation - initiated by a geographical barrier Provided sufficient time has elapsed such that significant divergence has taken place If barrier is removed and populations come back into contact, the may remain distinct Interbreeding prevented by pre and/or postzygotic mechanisms Causes of allopatric speciation include: o Glaciation, geological processes, continental drift Genetic Divergence the accumulation of genetic differences between two populations Founder Effect o Small non-random number of individuals perform long distance dispersal and found a new population

Sympatric Speciation - takes place in a single geographical area Autopolyploidization example of taking place in same geo-area o Can cause sudden speciation o When a 2n gamete is fertilized with another 2n gamete o Autopolyploids can only mate with other autopolyploids (reproductive isolation) o Allopolyploidization is similar but involves first the mating between two closely related species

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o Polyploidization ultimately can occur regardless of geographical barriers o Initial state of sympatric speciation is polymorphism (that affects fitness)

Theme 7 Phylogeny and Diversity

Phylogenetic Trees / Phylogenies A branching diagram that shows the relationships between species according to the recency of their common ancestors

Nodes indicate that there was some common ancestor, yet we really dont know what that organism at the node was Closely related taxa are called sister taxa Species A and B share a more recent common ancestor with each other than either species shares with any other species in diagram below You must physically trace back through branches to understand ancestral relationships Trees can rotate in 3 dimensial space To determine the correct phylogenetic tree, inference is used rather than actual oberservations by analyzing the following shared characteristics of species: o Morphological (ex. Wing patterns, prescence or absence of a structure) o Chromosomal (ex. Number of chromosomes) o Molecular (ex. Chloroplast DNA sequences)
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Morphological Characters Refers broadly to the observable characters of the whole organism A number of discrete character states are examined o Ex) Flower color Blue vs. Yellow A Sample Data Matrix o Lists different types of characters showing presence (+) or absence (-)

Homologous Characters Shared Because of Common Ancestry Shared Ancestral Characters o Evolved in a distant ancestor and are shared by many descendant taxa in addition to the taxa under consideration NOT phylogenetically informative Shared Derived Characters o Evolved in the common ancestor of 2 taxa They ARE phylogenetically informative o Can simply occur through mutation and arent found in the shared common ancestor

Analogous Characters (Homoplasies) When different characters point to different phylogenies, at least some of the characters are misleading A set of species has only one phylogeny If two characters suggest incompatible phylogenies, something is wrong with at least one of them These traits are misleading in building phylogenetic trees Convergent evolution more than one group evolves the same trait independently (similar function) o Ex) Wings in different species, thorns in roses vs. cacti These traits can be recognized by o Structural Similarity Spines of roses and cacti only superficially similar Relations between parts How thorns are connected to the stem Embryonic development When the spines develop during growth Using fossil records can give us some direct info of whether a trait was common in the common ancestry

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Molecular Data Each nucleotide in the DNA sequence can act as a trait Amino acid sequence (alanine, leucine, etc) of proteins can work in the same way Underlying logic of phylogenetic inference is identical for morphological and molecular characteristics

Principle of Parsimony The phylogeny requiring the fewest evolutionary changes is the best estimate of the true phylogeny Reasoning: Most mutation are deleterious, thus evolution of new traits is rare If ancestor of modern species both have same state of character assume that intermediates also possessed same state Maximum parisomy to find the maximum parsimonious tree, calculate # of changes on all possible trees and find one with the lowest number of changes o Ex) Tree on left is possible, but the tree on the right is the tree with the least number of evolutionary changes and therefore the more likely phylogeny o The tree on the left has more evolutionary transitions and is therefore less likely and therefore, by the principle of parsimony, the tree on the right is the most parsimonious tree

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Outgroup Comparisons An example Did the presences of seeds evolve from a nonseedy state or were seeds the ancestral condition? Pines and oaks have seeds The outgroups or older groups to pines and oak are the ferns and ferns lack seeds Conclusion: Applying the principle of parsimony would indicate that seeds evolved once and is therefore the more derived condition Inferring traits of the outgroup can often be confirmed by examining a fossil Outgroup = the older groups

King Phillip Came

Phylogeny and Taxonomy -

Over Linnaeus classification developed a rough set of phylogenies The Phylogenetic Tree of Life: Archaea, Bacteria, Eukaryotes For Monophyletic Group o Classification based upon evolution history Great o Includes all descendants from a common ancestor Sex o Relates back to some classification group that a more traditional taxonomist created Ex) Order Carnivora Group is monophyletic because we can go back and look at all of the descendants of the species and see that they branch back to a common ancestor, forming a group Paraphyletic Group o Includes some of the descendants from a common ancestor o Ex) Reptiles group assemblage birds share a more recent common ancestor with crocodiles Polyphyletic Group o An assemblage with members from separated evolutionary lines o Ex) Vultures assemblage new world vultures descend from stork-like birds, whereas old world vultures descend from birds of prey
Most important to recognize monophyletic group, and NON-monophyletic group
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Theme 8 History of Life

Age of the Earth Earth is 4.5 billion years old Unicellular prokaryotes by 3.5 billion Multicellular life by 2.1 billion years ago Complex multicellular animals by 650 million years ago

Rock Types Igneous: Form from molten rock Metamorphic: Form from other rock types exposed tpo high heat and pressure Sedimentary Rocks: Form from chemical precipitation or deposited from particles of other eroded rocks o Where fossils typically found due to parts being best preserved with lack of high heat and pressure

Determining Age of Fossils Aging of organisms comes from the relative position of fossils in sedimentary rock o Strata closer to earth = older layers Examining fossil assemblages o Certain types of fossils are grouped together In certain strata and therefore newly found fossils can easily be aged according to known data Radiometeric Dating o Can only be used for igneous and metamorphic rocks because the actual composition of atoms is effected by heats/pressure these act as clock resets that allow rocks to be dated from the moment they were in liquid form o Half-life: amount of time needed for half of reactant to be converted to daughter molecules

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o Radioactive isotopes spontaneously decay into daughter products o Useable range of radioactive isotope dating depends on half-life of isotope o A comparable ratio of daughter to parent components o Every different isotope has a different half-life Magnetic Fields o Analyzing bands of igneous rocks in geographical plates can tell us where the plates were oriented in certain points of time

The Origin of Life Early Earth Atmosphere o Originally little oxygen o Thought to include water, methane, ammonia, and hydrogen as major components o Input of energy (lightning) would transform this compounds into a primordial soup o Further modification of compounds in environment Miller-Urey Apparatus o Determined if life could self-assemble by assuming early atmosphere had reducing properties o Injections of high energy used to see if assemblage of sugars and polypeptides would spontaneously form o After 1 week, 10-15% of the carbon in the system was in organic compounds o 2% of carbon was in amino acids o Glycine was most abundant o Subsequent experiments added HCN and CH2O and fatty acids, nucleotide sugars, and phospholipids formed o Revisiting of experiment in 2008 used steam to simulate volcanic eruptions, and found that many more compounds were discovered that werent before Criticisms of Miller-Urey Apparatus o Suggested that ocean atmosphere might not have been reducing o However, there exist today a number of pockets of reducing environments in the deep oceans sulfur bacteria, etc. o Suggested that deep ocean vent communities provided evolutionary model Clay particles may have catalyzed the polymerization of basic monomers produced in initial stages of earthly development
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Ribozymes Molecules of ribonucleotides that simply cause the RNA to self-replicate This idea of self-replication leads to the possibility of mutations Mutations ultimately can change the protein formed and the change could be beneficial

Vesicles from Phospholipids Contribute to Cell Formation Compartmentalization within some type of cellular structure Phospholipids were found in Urey-Miller experiment and the phospholipids have the ability to self-assemble into a lipid bilayer Ribozymes were able to be compartmentalized within these cells and were ultimately protected from the rest of the environment

Extinction The concept was first described by Cuvier in 1796 Important to understanding evolutionary patterns For widespread species, stress must be very rare to cause extinction of these cosmopolitan species that live everywhere all over the world o Ex) On Hawaiian islands, extinction could readily occur due to concentration of species geographically Little evidence that extinction was selective Extinctions over many years have seemed to have certain periodicity

Mass Extinction Normal background rate of extinction varies but usually less than or equal to rate of speciation over time Some periods of time when the rate of extinction greatly exceeds rate of speciation and extinction rate peaks o Mass extinction = more than 75% of known species in a geologically short interval o These mass extinction are periodic (the Big 5)

Causes of Mass Extinction Extensive flood-basalt volcanism o Permian-Triassic o Cretaceous-Palaeogene Seal level fall o All Big 5 mass extinctions
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Ocean Anoxia o Permian-Triassic o Triassic-Jurassic o Ordovician-Silurian o Late Devonian Asteroid impact o Cretaceous-Palaeogene None of these things really explain periodicity Press vs. Pulse Theory of Explaining Mass Extinction o Press: long term o Pulse: short term Some marine fossil records show recovery of certain species over 10 million years after a mass extinction

Importance of Mass Extinction on Evolution Clears out niches and makes ecological opportunities available Low diversity remnants of once diverse lineages

Archaean Proterozoic (4 billion 510 million years ago) First Prokaryotes o Oldest known specimens are from 3.2 3.4 billion years old o Many found in stromatolites where cyanobacteria form a biofilm trapping layers of sediment o Some of these prokaryotes were important because they produced oxygen o Carbonaceous microstructures in thin section are removed from rocks by acid maceration o Photo to the right shows how the stromatolites are like columns that elevate due to cyanobacterial mats formed from sediment

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o Cyanobacteria had evolved the ability to combine sunlight, water and CO2 to create sugar so build new cells in the process of photosynthesis releasing O2 and changing the chemistry of the oceans and rest of earth Eukaryotes o First appear in fossil records 2.7 billion years ago o First well preserved body fossils of eukaryotes are multicellular alga o They are much larger than prokaryotes o They are nucleated o They contain organelles, which are bound by membranes o The Endosymbiont Hypothesis Eukaryotes engulfed prokaryotes and this resulted in the usage of them as cell organelles

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o Losing the rather strong cell wall resulted in a flexible plasma membrane critical component to evolution of eukaryotes o Endosymbiosis resulted in chloroplast formation o No digestion occurred of cell after endosymbiosis o Evidence of Endosymbiosis Organelles bound by membrane Organelle ribosomes are like those of prokaryotes Organelles have own DNA separate from DNA in nucleus Mitochondrial DNA sequences similar to a group of bacteria Chloroplast DNA sequences similar to those of cyanobacteria Origin of Multicellularity o Multicellularity allows for the division of labour o Most important division is between soma (body) and germ (seed) When these types of cells can team up and operate together, many more advantages in terms of reproductive success were available Great Oxygenation Event

o Free oxygen begins to accumulate in the atmosphere probably of biological origin from cyanobacteria about 2.5 billion years ago o Evidence includes the observation of banded iron formations o Major changes in number of rock types formed after this event like hydrated and oxidized minerals o The reasoning for why there was a long gap before O2 seen includes Probably a long period of anoxygenic photosynthesis
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Free oxygen reacted with ocean chemistry immediately, not released into atmosphere long time to accumulate sufficient gas Ediacaran Fauna (635-542 million years ago) o Soft bodied fossils, clearly of complex metazoans with tubular structures o High diversity o Exhibited different types of symmetry in structure (bilateral, for example) that gives rise to increased diversification in the Cambrian explosion

Paleozoic Era Cambrian Explosion (530 mya) o Complex morphologies observed o Exponential growth in diversity with tons of new types of species in the Cambrian o Rapid appearance of many groups of organisms o Preceded by appearance of small shell parts o Unusually high number of sites with soft-body preservation o Includes evidence of arthropods, echinoderms, and a large number of extinct forms o Features of many modern groups appear Heads, mouths, eyes, legs o Causes for explosion of diversity are Genetic diversity already present Increasing O2 levels from eukaryotic algae Diversified in terms of nourishment for organisms in terms of trophic levels Shift in ocean chemistry favoring calcium carbonate and the creation of cell parts from this chemical compound Invasion of Land (450 mya) o Spores of vascular plants appeared Vascular tissue added physical support but also allowed water to be channelled from lower to high parts in land plants o Atmospheric oxygen increases rapidly o Arthropods follow when plants are there to be consumed o Earliest body fossils in Silurian age (428 mya) o Insects first appear in the Devonian (400 mya) o Tetrapods first appear (395 mya)

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Mesozoic Era Radiation of dinosaurs, marine reptiles Appearance of birds, mammals, and angiosperms

Cenozoic Radiation of modern mammals and birds Evolution and spread of grasses Climatic changes and glaciations Evolution of humans o Evidence suggests humans had an impact on extinction early on

Denisovans Fragmentary fossil material from caves dated 40000 BP DNA well-preserved because of cold conditions in cave DNA sequences indicates remains of new hominin species with most recent ancestry with modern humans 1 million years ago

Macroevolutionary Patterns Adaptive Radiations o The rapid evolution of new species occupying new niches (a one million year time frame would be considered rapid) o The speed at which speciation has occurred o The Cambrian Explosion could be considered adaptive radiation o Ex) The Galapagos Finches Their varying morphologies can be explained by the evolutionary dynamics bursts of speciation were rapid Anagenesis o The gradual rate at which some single species evolves o Intraspecific evolutionary change o Slow and gradual species formation without branching of the evolutionary line of descent Cladogenesis o The species appear to show up rather suddenly o The act of producing an entirely different species

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Phyletic Gradualism and Punctuated Equilibrium o In the 1970s an argument whether pace of evolutionary change was gradual of punctuated was investigated o Some paleontologists argues punctuated pattern was much more common o Both are found in fossil record, and neither dominates currently, but studies continue to determine which pattern prevails

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Hardy-Weinberg Equilibrium Example

Question: Wing coloration in a moth. Coloration in the species has been previously shown to behave as a single-locus, two-allele system with incomplete dominance. Data for 1612 individuals is shown White spotted (AA) = 1469 Intermediate (Aa) = 138 Little Spotting (aa) = 5 AA 1469/1612 = 0.911 p2 = (0.954)2 = 0.910 O>E (O~E) Selection for the genotype Aa 138/1612 = 0.086 2pq = 2(0.954)(0.046) = 0.088 E>O (O~E) Selection against the genotype aa 5/1612 = 0.003 q2 = (0.046)2 = 0.002 O>E (O~E) Selection for the genotype

Observed Expected Difference Interpretation

Freq(A) = p2 + 0.5(2pq) = 0.911 + 0.5(0.086) = 0.954 Freq(a) = q2 + 0.5(2pq) = 0.003 + 0.5(0.086) = 0.046 This spotted trait is not under selection because the observed frequency is rather close to expected frequency. These values are close enough (expected and observed) to conclude that the population is in HW Equilibrium.

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Geological Data

Complex Multicellular Organisms

Humans Grasslands (20 mya)

Birds (200 mya)

Multicellular Organisms

Dinosaurs (250 mya)

Reptile and Mammal Ancestors Amniotes/Synapsids (375 mya) First Seed Plants Insects First Appear (400 mya) Tetrapods (395 mya) Earliest Body Fossils (428 mya) Arthropods Vascular Plants Plants Colonize Land (450 mya)

Prokaryotes

First Vertebrates Cambrian Explosion (530 mya)

(We currently live in the quaternary period of the Cenozoic Era)

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Important Experiments
Griffith: Transformation Principle discovery injection of mice to determine how infection takes place Avery et al: Determined if it was DNA, RNA, or Protein allowing for Transformation Principle to take place Hershey and Chase: Blender Experiment determined genetic material contained in DNA, not proteins by tagging phosphorus and sulphur separately Franklin: X-ray diffraction used to discover helical structure of DNA Watson and Crick: Determined the semi-conservative model of DNA replication Beadle and Tatum: Showed relationship between genes and enzymes believed mutating a gene coding for an enzyme would interrupt metabolic pathway Meselson and Stahl: Proved that semi-conservative model of DNA replication was correct Miller-Urey: Attempted to prove whether or not life could self-assemble under the reducing properties of the atmosphere and how these conditions could contribute to the development of life-providing chemical compounds

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Critical Terms and Definitions

Activator Transcription Factors (ATFs): Binds to proximal regions and enhancer regions to cause eukaryotic maximal transcription enhancers and activator proteins brought close to one another through DNA looping Adaptation: Any characteristic that improves the survival or reproductive success of an organism, and is often the result of natural selection causing successive generations of organisms to closely match their environment Adaptive Radiations: The rapid evolution of new species occupying new niches (a one million year time frame would be considered rapid) an example of this could be the Cambrian Explosion Allopatric Speciation: Speciation that occurs when biological populations of the same species become isolated due to geographical changes Aminoacyl-tRNA: The tRNA molecules containing an amino acid formed by the addition of the correct amino acid to the tRNA molecule by aminoacyl-tRNA synthetase Amorph/Null Alleles: No gene function, usually with an entire gene deleted (recessive mutation) Anagenesis/Phyletic Gradualism: Slow and gradual species formation without branching of the evolutionary line of descent Analogous Characters (Homoplasies): Misleading characteristics when building a phylogenetic tree, and can be recognized by structural similarity (for instance, thorns in different types of flowers) Aneuploid: An individual with an abnormal number of chromosomes Anticodon: Codon sequence present on the incoming tRNA molecule containing the amino acid required by the mRNA chain complimentary to codon on mRNA chain Apoptosis: Cell suicide typically due to cell senescence Bateman's Principle: The theory that females almost always invest more energy into producing offspring than males invest, and therefore in most species females are a limiting resource over which the other sex will compete Biological Species Concept (BSC): Defines two populations as being two different species if reproductively isolated from one another (i.e. Little to no gene flow between populations)
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Central Dogma: The universal flow from DNA to protein in order to convert genotype to phenotype Centromere: DNA sequences required for correct segregation of chromosomes after replication Chargaffs Rule: % Purines = % Pyrimidines Cladogenesis/Punctuated Equilibrium: The formation of a new group of organisms or higher taxon by evolutionary divergence from an ancestral form speciation occurs Co-Dominance: Heterozygote for allele exhibits both homozygote phenotypes (red and white spots on a flower crosses from parental white and parental red flowers of single color) Cohesin: Broken down enzymatically during anaphase held the sister chromatids together Conservative Replication: After replication, both daughter strands pair up Continuous Traits: Display a range of phenotypes (height in humans) led to the development of quantitative genetics studies CPSF (Cleavage and Polyadenylation Specificity Factor): Cleaves mRNA after transcription passes the poly-A-signal Cyclins: Interact with stages of the cell cycle and are promoted when cell grows to a sufficient size, ultimately signalling the cell to continue through the cell cycle Discrete (Mendelian) Traits: Does not have a range of phenotypes but rather only one or the other (red eyes in a fly vs. black eyes no blending of phenotypes) led to the development of population genetics studies Dispersion Replication: Daughter strands will have a mixture of parental and newly made DNA DNA Polymerase I: Removes RNA primer and fills the gaps with DNA DNA Polymerase III: Synthesizes DNA by adding nucleotides to DNA strand DNA Topoisomerase: Removes supercoils and relieves torque in circular DNA Elongation Factor: Protein that allows ribosome to move along mRNA (translocation) End Replication Problem: Associated with the fact that gene deletion can occur after every replication of DNA at the ends of chromosomes problem solved with telomeres Endemics: Something being unique to a specific geographical location in the world

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Equational Division: Occurs in Meiosis II, and implies that the same amount of chromosomes is present after Meiosis II since the sister chromatids are separating Euchromatin (Regular Chromatin): Regions of less DNA compaction and high levels of gene expression Evolution: A change in the frequency of an allele Evolutionary/Darwinian Fitness: An individuals contribution of genes to the next generation Exons: Segments of mRNA coding for specific proteins Fecundity: The number of gametes produced by an individual (governed by natural selection) Fertilization (Syngamy): When haploid gametes come together to create a diploid zygote through fusion Founder Effect: When a small non-random number of individuals perform long distance dispersal and found a new population Frameshift Mutation: An insertion or deletion of a single nucleotide pair causing a change in reading frame for translation Gene: Code for coding RNA (mRNA), and code for noncoding RNA (tRNA, rRNA, etc) and also known as a unit of heredity composed of DNA and found at a specific locus on a chromosome and can contain different alleles for that one gene General Transcription Factors (GTFs): Bind to promoter region (TATA) and recruit RNA polymerase II for initiation of eukaryotic basal transcription (gene non-specific) Genetic Divergence: The accumulation of genetic differences between two populations Genotype: The full set of genes inherited by an organism from parents to progeny Helicase: Unwinds DNA double helix Heterochromatin (Different Chromatin): Regions of higher DNA compaction where transcription is turned off found on telomeres and centromeres Histone Acetyltransferase: Adds acetyl groups to histones to loosen DNA binding in chromatin to allow for transcription during initiation Histones: Positively charged proteins DNA wraps around forming chromatin fibre absent in prokaryotes due to DNA simplicity

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Hypermorph: Increased gene function relative to wild type alleles (dominant gain of function mutation) Hypomorphs: Reduced gene function relative to wild type alleles (recessive mutation) Incomplete Dominance: One allele is not completely dominant to the other (blending of phenotypes) Introns: Segments of mRNA that are non-coding regions Kinetochore: A region on chromatids where the spindle fibres attach during cell division Ligase: Forms phosphodiester bonds between fragments of DNA in lagging strand Mass Extinction: When ~75% of known species at a given time become extinct in a geologically short period of time MicroRNAs: A small, single-stranded RNA molecule that binds to a complementary sequence in mRNA molecules and directs associated proteins to degrade or prevent translation of the target mRNA Miller-Urey Apparatus: Attempted to prove whether or not life could self-assemble under the reducing properties of the atmosphere and how these conditions could contribute to the development of life-providing chemical compounds Monocistronic mRNA: When the mRNA only codes for the formation of one polypeptide as mRNA does in eukaryotes Morphological Characters: Refers broadly to the observable characters of the whole organism Morphological Species Concept: Organisms defined by unique reliable morphological character Mutation: A change in the physical structure or in the nucleic acid sequence resulting in an error in the transmission of genetic information Nonsense/Stop Codons: Do not specify for an amino acid result in translational termination Nucleosome: The combined tight loop of DNA and protein in compaction multiple nucleosomes coil together and stack together forming chromatin Operon: A cluster of prokaryotic genes and the DNA sequences involved in their regulation Phenotype: Body plan, behaviour, metabolism, etc; determined by proteins that control reactions in cells

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Photolyase: Recognizes the fusing of adjacent thymines as a result of UV-induced damage and uses light energy to separate fused thymines through photoreactivation Pleiotrophy: A gene that may show multiple phenotypes Point Mutation: Substitution of a single pair of nucleotide bases with another pair resulting in missense, nonsense, or silent/synonymous mutations Polyadenylation Signal (AAAA): Protects mRNA from RNA digesting enzymes and is added to 3 end of mRNA by Poly (A) Polymerase Polycistronic mRNA: When the mRNA has open reading frames and can code for multiple types of polypeptides as it typically does in prokaryotes Polygynous: One male mates with MANY females Pre-mRNA: Contains transcribed introns that need to be cleaved from mRNA during mRNA processing stages Press and Pulse Theory of Mass Extinctions: Believed that mass extinctions require two factors a press (long-term pressure such as sea level fall or volcanism) and a pulse (short-term such as an asteroid impact) Pribnow Box (TATAAT): Sequence especially important within promoter region for transcriptional initiation in bacteria Primase: Synthesizes RNA primers for DNA polymerase Principle of Parsimony: The phylogeny requiring the fewest evolutionary changes is the best estimate of the true phylogeny Promoter: Region on RNA where RNA polymerase binds, indicting where transcription shall occur (upstream from promoter towards 5 end of DNA sense strand) strength of promoter determines how well RNA polymerase can bind to it Reduction Division: Occurs in Meiosis I when the cells become haploid after the first division in Meiosis I (diploid reduced to haploid) Redundancy/Degeneracy: Synonyms for same amino acids from different combinations of ribonucleotides Replisome: A complex of enzymes (polymerase, primase, ligase, etc) used for DNA replication

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Rho-Dependent Termination: Terminator sequence in mRNA recognized and bound to Rho helicase unwinding RNA from the template DNA and RNA polymerase in prokaryotes Rho-Independent Termination: GC hairpin forms in mRNA basepairs causing RNA polymerase to stall and dissociate in prokaryotes Ribosome: Molecule made of two subunits (50s and 30s) that join together on mRNA molecule to perform translation made up of rRNA molecules RNA Polymerase: Binds to promoter region of DNA to initiate transcription and doesnt require a primer also unwinds DNA helix whilst adding ribonucleotides in sequence Rolling Circle Replication: Process by which plasmid replication occurs Semiconservative Replication: New double helix contains one parental and one newly synthesised strand Sexual Dimorphism: When females and males DO have significant phenotypic differences Sexual Monomorphism: When females and males DO NOT have significant phenotypic differences Sexual Selection: Favors traits that increase the individuals ability to obtain a mate Shared Ancestral Characters: Evolved in a distant ancestor and are shared by many descendant taxa in addition to the taxa under consideration NOT phylogenetically informative Shared Derived Characters: Evolved in the common ancestor of 2 taxa These ARE phylogenetically informative Single-Strand Binding Protein: Stabilizes ssDNA before replication by preventing reannealing to strands act as a template Spliceosome: made up of non-coding mRNAs called snRNPs (Small Ribonucleoprotein Particles) that carry out the splicing of introns from the pre-mRNA by looping out the intron and cleaving it form the sequence Spontaneous Mutations: Naturally occurring mutations such as slippage (common in repetitive sequences where deletion occurs), and microsatellites (leads to a new number of repeats) Sympatric Speciation: The process through which new species evolve from a single ancestral species while inhabiting the same geographic region

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Synapsis: Occurs when homologous chromosomes pair up in prophase I, forming tetrads that allow for the crossing over of genetic material through recombination TATA Box: Used in eukaryotic initiation for transcription transcription factors bind to TATA where RNA Polymerase II recognizes and binds to the protein complex starting transcription Telomerase: Adds telomere repeats to the end of the template strand prior to replicationrepeats can be worn away after a while, leading to the end of cell division Telomeres: Prevent chromosomal degradation and allow for replication of chromosome ends by acting as a non-coding DNA buffer of about 10000 bp in length Termination Factor: Binds to stop codon in place of a tRNA molecule causing the release of mRNA from ribosome and the release of the protein chain as well The Wobble Effect: Gives rise to the redundancy of the genetic code since the third base in the anticodon of a tRNA does not need to be precise, while the first two do need to be precise with the third being able to wobble, the same amino acid can be coded for by different codons Transformation Principle: The conversion of a cells genetic makeup by uptake of DNA from another cell (Griffith experiment) Tubulin: Polymerized by centrosomes to form the spindle fibres UTR Regions of mRNA (Untranslated Regions): Area on mRNA not translated does not affect amino acids in proteins Wild Type Allele: Normal form of a gene found in a model organism X-ray Diffraction: Revealed structure of DNA 5 Cap: Added by a capping enzyme to the 5 end of mRNA following initiation of transcription

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