Biology 243 Final Exam Notes

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Themes 1 and 2 – Evolution: A Brief History

- Jean-Baptiste Lamarcko Believed that species changed over timeo “Lamarckism” – Acquired traits can be inherited

- Thomas Malthuso “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 specieso “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

- Darwin’s 4 Postulates for Evolution via Natural Selectiono Individuals VARY o More offspring are produced than can survive and/or reproduceo Survival and reproduction is not randomo Some variation is passed to offspring (Heritable)

- Evolutiono A change in the frequency of an alleleo Evolution can occur quickly enough to observe within a matter of seasonso Evolutionary change can be very small scale

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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 cello Enzymes, structural proteins, signalling proteins, etc.

Establishing DNA as the Hereditary Molecule

- Griffith – Transformation Principleo The conversion of a cell’s hereditary makeup by the uptake of DNA from another

cello Injected mice with the bacteria to understand how infection takes place

- Avery et al. – Identifying the Chemical Nature of the Transformation Principleo 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” Experimento Determined that the nature of genetic material

in the bacteriophages was DNA, not proteinso Tagged bacteriophage DNA and proteins with

radioactive isotopes 32P and 35S respectively

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Topic 2 – Structure of DNA

Components of DNA

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

- Pentose Sugarso Carbon atoms are labeled for orientationo 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 – ½ Amine + 2 oxygen

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

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Purines PyrimidinesGuanine Cytosine

Uracil ThymineAdenine

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’ PO4

3- end- “Downstream” = towards 3’ OH- end - Synthesized in 5’ to 3’ direction

Chargaff’s Rule

- States % purines = % pyrimidines

Franklin’s 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 wideo Pyrimidine-pyrimidine base pairing is too narrow

- Hydrogen bonds hold the nucleotides and the two strands together

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%A = %T and %C = %G

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

Watson and Crick’s 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

- Eukaryoteso Linear and enclosed in nucleotideso Compacted in DNA to fit in cell nucleuso Chromosomal structure protects DNA from damageo Chromosomes can easily be separated during cell division

Essential Components of Eukaryotic Chromosomes

1) Origin of Replicationo The attraction of multiple proteins to initiate DNA replication

2) Centromereo DNA sequences required for correct segregation of chromosomes after DNA

replication3) 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

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Chromatin

- Heterochromatino Regions of higher DNA compactiono Where transcription is turned offo Found in telomeres and centromereso Barr Body – an X chromosome becomes inactive by the block of heterochromatin

- Euchromatino Regions of less DNA compactiono 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

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1 2 3

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 forks2) Elongation

Simultaneous synthesis of the two new DNA strands from the template strands by DNA polymerase

3) Termination

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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 FunctionHelicase Unwinds the double helix by breaking hydrogen bondsPrimase Synthesizes RNA primers for DNA polymeraseSingle-Strand Binding Protein

Stabilizes ssDNA before replication by preventing reannealing so that the strands can serve as template

DNA Topoisomerase/Gyrase

Removes super coils that form ahead of the replication fork, relieves torque/tension of mainly circular DNA

DNA Polymerase III Synthesizes DNA by adding nucleotides to the new DNA strandDNA Polymerase I Removes RNA primer and fills the gaps with DNADNA Ligase Joins the ends of DNA segments by forming phosphodiester

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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

fragmento At the very end of chromosome, no such fragment is present on 3’ endo Therefore there is additive loss at chromosomal ends after each replicationo Genes can become deleted leading to organismal deatho 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 proteino 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

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- They showed the direct relationship between gene and enzyme

The Genetic Code

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Nonsense/Stop Codonso Three codons that do not specify amino acids

- Redundancy/Degeneracyo 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 behind3) 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

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- Does not need a primer- Unwinds and rewinds DNA helix during RNA synthesis- The promoter specifies where the RNA Polymerase will begin transcription

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:

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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

Features of the Prokaryotic Gene

- Operono Cluster of prokaryotic genes and the DNA sequences involved in their regulation

- Promotero 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

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- 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- A key element in protein-coding genes = TATA Box- Transcription factors recognize and bind to TATA Box RNA pol II recognizes multi-

protein complex and bind to it

- 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)

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

TFIID

- 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

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 initiationo Functions as a binding site during translation

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- Transcription termination controlled by a polyadenylation signal in the 3’ sequenceo Protects mRNA from RNA digesting enzymes

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 non-coding 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 IIo Hairpin miRNA cleaved to 21-23 bp by Dicer Rnaseo 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

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- Consists of 64 sense codons and the amino acids specified by these codons- Codons are written 5’ to 3’as 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

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)

The Ribosome

- A complex molecule made of rRNA molecules form a factor for protein synthesis in cells- Composed of two subunits

o Large 50S subunito 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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Type Name

Non-Polar

AlanineValine

LeucineIsoleucine

GlycineCysteine

PhenylalanineTryptophanMethionine

Proline

UnchargedPolar

SerineThreonineTyrosine

AsparagineGlutamine

Acidic Aspartic AcidGlutamic Acid

BasicLysine

ArginineHistidine

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

tRNA Molecules

- tRNAs bring amino acids to the ribosomeo Small RNAs (75-90 nucleotides)o Act as an adaptor between codons and amino acids

- Aminoacyl-tRNA (charging): tRNA + amino acid

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o Aminoacyl-tRNA synthetase adds correct amino acid to the acceptor stem of correct tRNA

- tRNA and the Wobble Effecto The complete set of 61 codons can be read by FEWER than 61 tRNAso This is because of the pairing properties in the bases of anticodonso Pairing of anticodon with first 2 nucleotides is precise, but the third has more

flexibilityo Third position can wobble

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) regiono 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

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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

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 cellso Therefore, these mutations are NOT heritable

- Germ Line:

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o These types of mutations are of evolutionary significanceo 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 - chromosomalo Gene duplications/deletionso Translocations/inversions

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 acido Nonsense – new codon is a STOP codon causing premature terminationo Silent (Synonymous) – no change in amino acid sequence

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Insertion/Deletion/Frameshift

- A shift in reading frame, affecting translation of other codons in coding DNA

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) Down’s 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

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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 DNAo Occurs only in DNA replication

- Microsatelliteso Short tandem repeats (STR) of DNAo 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

Induced Mutations

- Mutagenso Induce mutations by replacing a baseo Alters a base causing a mispair with another baseo Damages bases so no pairing is possible

- Base Analogso 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 Alleleo 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)

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- Hypermorphso Enhanced gene function relative to wild type (dominant gain-of-function

mutation)

Topic 9 – Inheritance

Cell Division in Prokaryotes

- Binary Fissiono Prokaryotes undergo a cycle of cytoplasmic growth,

DNA replication, and cell divisiono Replication begins at orio Replicated origins migrate to ends of poleso 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) Phaseo A resting phase where the cell has “left the cycle” and has

stopped dividing- Gap 1 (G1) Phase

o Initial period of cytoplasmic growtho Synthesis of enzymes required for S

phase, mainly those needed for DNA replication and structural proteins

- Synthesis (S) Phase

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o Rapid duplication of DNA and chromosomal proteins- Gap 2 (G2) Phase

o Period of cell growtho End of G2 signifies the end of interphase

- G2/M “Checkpoint”o A DNA damage checkpointo 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

Mitosis

- Prophaseo Chromatin condenses into chromosomeo Nucleolus disappears RNA synthesis ENDSo Chromosomes bounds together at centromereo Centrosomes nucleate microtubules to form spindle by polymerizing tubulino Molecular motor proteins push centrosomes to create spindle poles

- Prometaphaseo Nuclear membrane breakdown o Spindle microtubules have direct access to chromosomeso Each kinetochore of sister chromatids attached to spindle microtubuleso Chromosomes move to equator of cello Microtubules connect to each

chromosome at its kinetochore, a complex of proteins positioned at the centromere

- Metaphaseo Chromosomes align along cell equatoro Kinetochore microtubules attach the

chromosomes to the spindle pole- Anaphase

o Sister chromatids separate, moving to opposite poles becoming independent chromosomes

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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

- Telophaseo Chromosome arrive at poleso Mitotic spindle disassembleso Formation of new nuclear membrane around each group of chromosomes

- Cytokinesiso Physical process that splits the parent cell into two identical daughter cells with

cytoplasm dividing by furrowingo Cell membrane pinches in at the cell equator, forming cleavage furrowo Position of furrow dependant on position of astral and interpolar microtubules

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Regulation of the Eukaryotic Cell Cycle

- G1/S Control Pointo Initiation of DNA synthesis

- G2/M Control Pointo 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 Checkpointo Must attain a certain size at START, and G2/M checkpointso The cells must be twice as big as daughter cells at G2/M checkpoint

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

When Cell Cycle Regulation Goes Wrong

- Cancero Uncontrolled cell divisiono Altered expression of multiple genes due to mutations

- Oncogeneso Positive regulators (gain of function) in the cell cycle

- Tumor Suppressor Geneso Loss of function at checkpoint geneso Mutation prevents there from being division regulation

Cell Division Senescence (When cells become very old)

- Infinite division of cells impossibleo Due to damage, defective telomeres, etc.

- Genes affecting cellular again we first found to be tumor supressors- Division arrest followed by either

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

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These mutated genes implicate

cancer

Genetic recombination

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 bridgeo Since F-factor transfers itself during conjugation, the rest of genome is “dragged”

along with it

- - F+ and F- cell differ in alleleso F+ = a+, b+, c+, d+o F- = a-, b-, c-, d-

- Recombination occurs between donor chromosome and recipients chromosome- “Crossover” produces a b+ recombinant (F-: a-, b+, c-, d-)

“Strategic Sex”

- Evolution of recombination had to have happened in presence of asexuals- Sex is “expensive”

o Cost of finding a mate

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F+ cell F- cellAsexual Sexual- Offspring are clones of parents- Inheritance of ALL parental genes in offspring- Transformation/transduction provide addition of sources of DNA for recombination

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

o Ecologicalo Mechanical

Comparing Mitosis and Meiosis

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

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Meiosis

Mitosis

o Each chromosome copied (now there is a pair of sister chromatids – refer to diagram)

Meiosis 1

- Prophase 1o Synapsis occurs (homologous chromosomes pair up)o Chromosomes have sequences that act as signals for pairing and alignmento Fully paired chromosomes are called tetrads when there are four chromatids

togethero 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

- Prometaphase Io Nuclear envelope breaks down – spindles

enter- Metaphase/Anaphase I

o Alignment of tetrads and separation of chromosomes of each homologous pair

- Telophase I and Interkinesiso No synthesis, reassembly of microtubules for 2nd division

Meiosis II

- There is no preceding S phase so meiosis II is not exactly like mitosis

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o Chromosomal behaviour is however like mitosis

How Germ Cells are Affected by Environment

- Male germ cellso Meiosis occurs after pubertyo Mutation rates are higher in males due to the meiotic rate

- Female germ cellso 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 Randomo “Independent Assortment”

- 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 – Mendel’s Experiments, Genes, and Alleles

3 Hypotheses

1) All plants carry a pair of factors (genes) governing inheritance of a character2) A pair of genes consists of different alleles, with one allele dominant over the other

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3) Alleles that control a character separate as gametes separate

Mendel’s 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 individualo If heterozygote shows mutant phenotype, allele is dominanto 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)

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

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o Ex) (Red Flowers)x(White Flowers) = Flowers that each show red and white coloring

Theme 5 – Population Genetics and Selection

Darwin’s Four Postulates for Evolution by Natural Selection

1. Individuals within a species VARY2. Variation is HERITABLE3. More offspring produced than can survive (SURPLUS)4. Survival and reproduction not random, but due to phenotypic variation

Important Things to know about Natural Selection

- Things that Prevent Evolution by Natural Selectiono No variationo No heritability of variationo 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 - problematico Offspring have traits that are intermediate to parents

- Inheritance of Acquired Characters - problematico Idea that only favorable traits acquired by parents were passed onto offspring

Hardy Weinberg Equilibrium (HWE)

- Assumptions for HWEo 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

- Predictionso Allele frequencies remain constanto Genotype frequencies remain constant

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o Equilibrium genotype frequencies reached in ONE generation of random mating

- It is important to never take the square root of either p2 or q2 to determine p or q (respectively) if you aren’t 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

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

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p2 + 2pq + q2

p + q = 1

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

Stabilizing Selection

- The intermediate phenotype is selected for, while extreme phenotypes are selected against

- More commonly found in nature

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- 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 don’t 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

- Gameteso Males: Produce large numbers of energetically cheap and motile spermo Females: Produce smaller numbers of energetically expensive (less motile)o Hermaphrodites: Can produces both types of gametes

- Sexual Monomorphismo When females and males don’t have significantly different defining phenotypic

characteristics- Sexual Dimorphism

o When females and males have noticeably different phenotypic characteristics

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Reproductive Success = Fecundity + Mating Success

- Sexual Selection: Favors traits that increase the individual’s 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

Bateman’s 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 maleso 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

successo Males compete for femaleso Females can afford to be “choosy” (quality not quantity)

- Most importantly, total numbers of matings doesn’t 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

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- 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 areo Small populations (absolute, geographical, cultural)o Mating system (mating with relatives, such as cousins)

An example is self-fertilization of plants:

Genotype AA (p2) Aa (2pq) aa (q2)# individuals 250 500 250 Generation 0

375 250 375 Generation 1437.5 125 437.5 Generation 2468.75 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.

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)

- 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.

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freq A = a = 0.5Genotype frequencies change, allele frequencies don’t!

Genetic Drift – A completely random process

- Changes in allele frequency due to chance in finite population, especially very small populations

- Contrast with inbreedingo Inbreeding does not change allele frequencieso 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

- Effectso Random change in allele frequencyo Gradual loss of genetic variationo 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.

Speciation

- The process by which new species arise- Major categories of species concepts

o Morphological – individuals that look alikeo Reproductive – ability to produce offspringo Phlyogenetic/Genetic – shared evolutionary history

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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

- Prezygotic Mechanismso Prevent mating or fertilizationo Barriers of this type of mechanism include:

Habitat Behavioural Temporal Mechanical – when physical components of reproduction don’t “fit” Gametic – zygotes don’t form – some incompatibility with systems in

plants- Postzygotic Mechanisms

o Prevent zygote development or reproductiono Barriers of this type include

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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 Speciation1. When individuals hybridize readily = no speciation has therefore occured2. When individuals do not hybridize at all = full speciation has occurred since

hybrids can’t form3. 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-areao Can cause sudden speciationo When a 2n gamete is fertilized with another 2n gameteo Autopolyploids can only mate with other autopolyploids

(reproductive isolation)o “Allopolyploidization” is similar but involves first the mating

between two closely related specieso 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

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- A branching diagram that shows the relationships between species according to the recency of their common ancestors

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- Nodes indicate that there was some common ancestor, yet we really don’t 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)

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 Characterso 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 aren’t 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

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- 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 byo 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

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 changeso 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 phylogenyo 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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King

Phillip

Came

Over

For

Great

Sex

Outgroup Comparisons – An example

- Did the presences of “seeds” evolve from a “non-seedy” 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

Phylogeny and Taxonomy

- Linnaeus’ classification developed a rough set of phylogenies- The Phylogenetic Tree of Life: Archaea, Bacteria, Eukaryotes- Monophyletic Group

o Classification based upon evolution historyo Includes all descendants from a common ancestoro 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

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o Includes some of the descendants from a common ancestoro 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

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 rockso 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 rocko Strata closer to earth = older layers

- Examining fossil assemblageso 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

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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

o Radioactive isotopes spontaneously decay into daughter productso Useable range of radioactive isotope dating depends on half-life of isotopeo A comparable ratio of daughter to parent components o Every different isotope has a different half-life

- Magnetic Fieldso 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 Atmosphereo Originally little oxygeno Thought to include water, methane, ammonia, and hydrogen as major

components

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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 acidso Glycine was most abundanto 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 weren’t before

- Criticisms of Miller-Urey Apparatuso Suggested that ocean atmosphere might not have been reducingo 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

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

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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 worldo 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 volcanismo Permian-Triassico Cretaceous-Palaeogene

- Seal level fallo All Big 5 mass extinctions

- Ocean Anoxiao Permian-Triassico Triassic-Jurassico Ordovician-Siluriano Late Devonian

- Asteroid impacto Cretaceous-Palaeogene

- None of these things really explain periodicity- Press vs. Pulse Theory of Explaining Mass Extinction

o Press: long termo Pulse: short term

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- 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 Prokaryoteso Oldest known specimens are from 3.2 – 3.4 billion years oldo Many found in stromatolites where cyanobacteria form a biofilm trapping layers

of sedimento Some of these prokaryotes were important because they produced oxygeno Carbonaceous microstructures in thin section

are removed from rocks by acid macerationo Photo to the right shows how the stromatolites

are like “columns” that elevate due to cyanobacterial mats formed from sediment

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

- Eukaryoteso First appear in fossil records 2.7 billion years agoo First well preserved body fossils of eukaryotes are multicellular algao They are much larger than prokaryoteso They are nucleatedo They contain organelles, which are bound by membraneso The Endosymbiont Hypothesis

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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 formationo No digestion occurred of cell after endosymbiosiso 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 Multicellularityo Multicellularity allows for the division of labouro 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

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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 formationso Major changes in number of rock types formed after this event like hydrated and

oxidized mineralso The reasoning for why there was a long gap before O2 seen includes

Probably a long period of anoxygenic photosynthesis 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 structureso High diversityo 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 observedo Exponential growth in diversity with tons of new types of species in the

Cambriano Rapid appearance of many groups of organismso Preceded by appearance of small shell partso Unusually high number of sites with soft-body preservationo Includes evidence of arthropods, echinoderms, and a large number of extinct

formso Features of many modern groups appear

Heads, mouths, eyes, legso Causes for explosion of diversity are

Genetic diversity already present Increasing O2 levels from eukaryotic algae

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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 rapidlyo Arthropods follow when plants are there to be consumedo Earliest body fossils in Silurian age (428 mya)o Insects first appear in the Devonian (400 mya)o Tetrapods first appear (395 mya)

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

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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 occurredo The Cambrian Explosion could be considered adaptive radiationo Ex) The Galapagos Finches

Their varying morphologies can be explained by the evolutionary dynamics – bursts of speciation were rapid

- Anagenesiso The gradual rate at which some single species evolveso Intraspecific evolutionary changeo Slow and gradual species formation without branching of the evolutionary line of

descent- Cladogenesis

o The species appear to show up rather suddenlyo The act of producing an entirely different species

- Phyletic Gradualism and Punctuated Equilibrium

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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 commono Both are found in fossil record, and neither dominates currently, but studies

continue to determine which pattern prevails

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 Aa aaObserved 1469/1612 = 0.911 138/1612 = 0.086 5/1612 = 0.003Expected p2 = (0.954)2 = 0.910 2pq = 2(0.954)(0.046)

= 0.088q2 = (0.046)2 = 0.002

Difference O>E (O~E) E>O (O~E) O>E (O~E)Interpretation Selection for the

genotypeSelection against the genotype

Selection for the genotype

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

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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.

Geological Data

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Complex Multicellular Organisms

Multicellular Organisms

ProkaryotesEarliest Body Fossils (428 mya)

Insects First Appear (400 mya)

Arthropods

Tetrapods (395 mya)

First Seed Plants

Reptile and Mammal Ancestors

Dinosaurs (250 mya)

Amniotes/Synapsids (375 mya)

Birds (200 mya)

Grasslands (20 mya)Humans

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

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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Cambrian Explosion (530 mya)

Plants Colonize Land (450 mya)Vascular Plants

First Vertebrates

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)

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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)

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

Chargaff’s 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

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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

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 individual’s 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

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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

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

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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

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

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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

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 doesn’t 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

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Sexual Monomorphism: When females and males DO NOT have significant phenotypic differences

Sexual Selection: Favors traits that increase the individual’s 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

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 replication- repeats 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 –

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with the third being able to “wobble”, the same amino acid can be coded for by different codons

Transformation Principle: The conversion of a cell’s 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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