Exam: Term Test 2 Study Guide

Cycle 1

Viruses, Viroids, and Prions

1. Understanding viruses is important bc it can help us deal with virus outbreaks and tracking global migration to improve quality of life and prevent illnesses
2. Viruses aren’t always bad; we can use viruses’ properties for our own purposes (e.g. gene therapy)
3. Viruses aren’t considered to be living organisms because they lack many of the properties of life, and are infectious biological particles
4. Can’t reproduce on their own
5. No metabolic system to provide energy
6. Structure of virus is bare minimum to transmit genome: 1+ nucleic acid molecules, surrounded by a protein capsid, may have an envelope surrounding it
7. Can evolve, but isn’t a cell: no cytoplasm with plasma membrane (all other known living things do)
8. Viral genome: can be RNA or DNA, single or double stranded, a few to a hundred genes
9. Genes encode coat proteins, envelope proteins (if it’s an enveloped virus), regulation of transcription, may have virus-specific enzymes for replication
10. Two basic structural forms:
11. Helical: capsid proteins in a rod-like spiral around genome, often infects plants
12. Polyhedral: capsid proteins form triangular units that form a polyhedron, may have protein spikes (for cell recognition) from vertices
13. Bacteriophage is a complex polyhedral virus
14. Both helicals and polyhedrals can be enveloped in a membrane made from host’s membrane 
15. In enveloped viruses, proteins synthesized from viral genome in host cell are transported and embedded in membrane before leaving the cell (for cell recognition)
16. Classified into order, family, family, genera, species
17. Based on size, structure, genome structure (RNA or DNA, single or double stranded), how nucleic acid is replicated
18. We classified >4000 viruses into >80 families (21 include viruses causing human disease)
19. Family names end in -viridae, named after disease/place discovered/structure (e.g. Coronaviridae for crown of protein spikes on capsid)
20. Every living organism is prob permanently infected by 1+ kinds of viruses
21. Usually infects a single or a few closely related species, and possibly only one organ system/tissue
22. Some can infect unrelated species naturally or after mutating

1. May be deadly, bothersome, or helpful (can protect against other viruses’ replication)
2. Ex: bacteria don’t take over the planet bc of bacteriophages (phagein = eat)
3. Vital in ecosystems: affect nutrient cycling through effects on prokaryotic organisms (kills them to release nutrients), also keeps their photosynthesis going (has genes for a protein in photosystem II that needs to be replaced often: ‘selfish’ bc it’s to make sure the virus can reproduce but net result is good)
4. Viruses move randomly until they contact the surface of a host cell, virus/viral genome enters host cell, viral genes are expressed, viral genome reproduced, progeny viruses assembled, virions releases (often ruptures host cell)
5. Viruses infecting animal cells:
6. Genome and viral coat enter (envelope doesn’t enter) cell by endocytosis 
7. If no envelope, binds by recognition proteins to the plasma membrane. If envelope, the envelope fuses with cell membrane
8. Genome usually directs synthesis of additional viral particles the same as bacterial viruses
9. Regulated phage gene expression produces proteins and enzymes for phage → Phage DNA replicated in host cell by a phage encoded DNA polymerase → Viral units synthesized → Assembly → Phage directs synthesis of a lysozyme which ruptures the cell wall and releases 100+ progeny phages
10. Sometimes, replication is complex (e.g. HIV)
11. Has 2 copies of RNA and reverse transcriptase in the capsid → transcriptase makes a complementary DNA strand from viral RNA → second DNA strand made from first → DNA integrates into host cell as a provirus → transcribed and translated to make new virus parts → released
12. Most asymptomatic bc causing disease has no benefit to virus
13. But some cause issues: massive cell death, cell contents are released (and inflammation occurs, e.g. influenza), alters gene function (e.g. cancer)
14. May have a latent phase (e.g. herpes) and then act up in a period of stress
15. No fossil record of viruses (too small), but there are remains of viruses in the DNA of things it infected such as us
16. We think that viruses have been around as long as life has (bc it can infect all life), and evolved alongside/before earliest cells
17. Paleovirology based on genomics (of hosts)
18. DNA of virus can become integrated in DNA of host, can stay there indefinitely if doesn’t affect it, and if in gametes, can be passed down (and preserved p well, bc DNA’s mutation rate is relatively v low)
19. If bits are found in several animals, they must have a common ancestor, so virus is at least as old as the ancestor
20. E.g. circoviruses (dog stomach issues) found to be >68 MYO (found in dogs, cats, pandas)
21. Oldest: bracoviruses (in wasps) could be as old as insects, in the Carboniferous Period 310 MYA
22. Mammal gene CGIN1 seems to be from a retrovirus from 125-180 MYA
23. 8% of human genome includes sequences from viruses
24. Virus-first model: since they’re simpler, they evolved first
25. Escape hypothesis: viruses evolved after cells did, from DNA that escaped
26. Regressive model: based on discovery of giant viruses (e.g. mimicking microbe Mimivirus) that affect amoeba and can make protein
27. Life: reproduce, make energy for itself, maintain a stable environment within its cells, can evolve, etc
28. Viruses not alive bc: can’t reproduce by themselves, no energy metabolism, can’t respond to stimuli

Evolution In Action: HIV

1. HIV part of our population since 1981, was considered as a death sentence (causes AIDS, no treatment so immune system is weakened)
2. Until 1995, rate of new HIV infections increased and then started decreasing
3. Deaths from HIV peaked in 2005 and rate of death went down (bc treatment is better now)
4. Stats
5. In 2019: 38M ppl living with HIV, 1.7M newly infected, 770K died from related illnesses
6. Since 1981: 77.5M infected, 32.7M died
7. AIDS-related mortality decreased by 39% since 2010
8. Most ppl in Africa, then Asia + Pacific, then Europe and North America
9. Zoonotic disease: 75% of new infectious diseases, have ‘spilled over’ from other species (usually closely related), usually more harmful in new host than original reservoir species
10.  HIV: single stranded RNA virus called a retrovirus
11. Retrovirus: subset of viruses, single-stranded RNA has genetic material
12. SIV (Simian [primates] immunodeficiency virus): long history of infecting nonhuman primates, has spilled over to humans several times and those are called HIV
13. HIV’s RNA undergoes reverse transcription to synthesize a DNA strand which is integrated into into our genome using integrase, and then new virions can be made
14. Mutations (mistakes) may occur during the reverse transcriptase’s activity
15. AZT: first drug to treat HIV; a nucleoside analog (almost like thymine, but an OH on the 3-sugar is a N3)
16. When a thymidine is needed, the reverse transcriptase may take the AZT-triphosphate and then the rest of the strand can’t form 
17. AZT worked for a while, but after just a few months HIV was resistant to it
18. A mutation of just two bases in the reverse transcriptase gene (POL gene) on the HIV genome allowed a proof-reading ability so it could remove the AZT
19. Evolution of AZT resistance: random mistakes in copying the HIV genome results in mutations (may or may not give resistance to AZT) in progeny viruses in a person, AZT kills off the viruses that aren’t resistant, so the ones that are left are drug-resistant
20. High error rate for reverse transcriptase → variation in viral population’s ability to proof-read
21. Using antivirals provides an advantage to drug-resistant variants: mutations are always occurring randomly and the environment helps determine which variants can reproduce and pass on their genes, resulting in the viral population changing over time
22. Variation + heritability + non-random survival = evolution (by natural selection)
23. HIV is no longer a fatal disease; can live a pretty long life
24. Treatment is using many drugs that attack life cycle at diff points: resistance to many drugs is way less likely
25. Hard to make a vaccine bc high mutation rate and so many variants (e.g. ones that change the structure of the virus so it can evade the immune system)

Scientific Theories and Falsifiability

1. Scientific definition of a theory + a fact, theory of evolution + empirical evidence
2. Theory: a coherent set of testable hypotheses that attempt to explain facts about the natural world (i.e. not just an assumption based on limited knowledge)
3. Fact: an assertion for which there is so much evidence that it would be perverse to deny it (-Gould)
4. Test a theory by attempting to falsify it; theories graduate to “fact-hood” after repeated testing fails to falsify it
5. Unfalsifiable assertions are not scientific

Development of the Theory of Evolution

1. Bacterial antibiotic resistance is one of Canada’s top health issues
2. Penicillin (discovered by Fleming, 1928) used to be able to kill most infections by inhibiting the function of an enzyme required for cell wall biosynthesis and was used widely in the 1950s+ but now is basically resistant 
3. Resistance increased because of overuse/misuse of antibiotics, and their inclusion in animal feed
4. Rate of developing new antibiotics doesn’t keep up with the rate that bacteria are becoming resistant
5. Evolution: species change over time
6. Plays a central role in our understanding of life (common features, diversity, changes, etc)
7. Evolution is variational and not transformational
8. Early view: life is unchanging
9. Aristotle: Scala Naturae (non-living, cells, fungi, algae, plants, invertebrates, vertebrates, humans, God)
10. Organisms specially created by God, species don’t change or go extinct, new species can’t arise
11. 14th century: Biological research was dominated by natural theology 
12. Linnaeus (18th century): tried to classify all organisms, binomial species classification system (similar-looking organisms groups together and then sorted)
13. Didn’t credit the similarities between organisms to anything other than God
14. Lamarck: challenged idea that organisms can never change
15. Inheritance of acquired characteristics (is false)
16. Proposed “perfecting principle”: simple organisms evolved into more complex ones (up Scala Naturae) and simple life came from non-living organisms
17. Darwin: on HMS Beagle around the world, was well educated but not v experienced (probably a good thing: had no pressure to conform to popular ideas), was v observant, took objective notes and took lots of specimens to ship back to England
18. Wasn’t the first to propose that organisms changed, but he arrived at how evolution might occur
19. His major insights came from geology and fossil record, geographic distribution of species, comparative morphology of species  
20. Geology + fossil record
21. Read Lyell’s “Principles of Geology,” who supported Hutton’s ideas that Earth’s surface was constantly changing due to natural events (e.g. earthquakes, volcanoes, etc) vs ancient/supernatural events (e.g. Noah’s flood)
22. Witnessed a powerful earthquake in 1835 Chile (Concepcion) and the changes that followed
23. Found marine fossils in Andes Mountains at h = 4000 m → confirmed this
24. Set Darwin to think that life may also change slowly over time 
25. Was aware that fossils of things that didn’t look like living species have been discovered
26. Living armadillos and fossilized glyptodonts had similar armour but why weren’t there any glyptodonts living? → Armadillos are descendants of them
27. Geographic distribution of species: 
28. Biogeography: why are some species spread out and some not, why some species far away from each other are so different and why some are similar 
29. Observed that none of the oceanic islands he visited had land mammals (only flying mammals), and species in islands were similar to species on nearby continents
30. Galapagos islands: many animals, looked slightly diff on diff islands, resembled animals in South America → they’re related but changed over time
31. Comparative morphology: 
32. Example: human arm, flippers of seals, foreleg of pigs, bat wings look very different but share an underlying structure 
33. Natural theologians can’t explain body parts w no apparent function
34. Buffon said that some animals changed since creation; they had a purpose in ancestral organisms and now don’t (but didn’t know how it happened)
35. Darwin explained vestigial structures using the idea of common ancestors
36. Homology: similarity due to a shared ancestor between organisms in different taxa
37. Wallace was also doing careful research and came to similar ideas about natural selection → sent his findings to Darwin → Darwin didn’t want Wallace to publish before him → published On the Origin of Species by Means of Natural Selection 
38. Malthus: influenced both Darwin and Wallace
39. Wrote An Essay on the Principle of Population: humanity is destined for disaster (population>>>food)
40. Clarified to Darwin how population and food are related (not all offspring grow up: “struggle for existence”)
41. Selective breeding/artificial selection 
42. Darwin realized that individual organisms don’t change over lifetime, but populations change
43. Natural selection
44. Organisms have a large capacity to reproduce but limiting resources constrain size of population → individuals within population compete for resources
45. Individuals differ in certain traits (e.g. size, colour, behaviour) that are inherited → organisms with traits that help them get the resources can reproduce more
46. Darwin’s mockingbirds: descent with modification
47. One species of mockingbird came from South America and colonized the islands, and specific traits became more common in diff islands as they adapted to the diff food sources, microclimates, etc
48. Study of this was complemented by his finch studies
49. Impact of Darwin’s study: generalized evolution to everything, underlying homology indicated that there’s a common ancestor
50. Fitness: describes an individual’s reproductive success
51. A relative concept (you only have to be better than other ppl to be fit)
52. A trait is only valuable if it increases fitness
53. The traits that increase fitness might change over time
54.  Gregor Mendel published his pea plant research around the same time as Darwin’s paper
55. 50 years later, Morgan discerned that genes are carried on chromosomes
56. Helped scientists form the modern synthesis of evolution (genetics + natural selection)
57. Random mutations causes variation in a population (i.e. natural selection directs which mutations survive)
58. Natural selection is a theory of evolution: heritable variation leads to differential survival and reproduction; supported by experimental and observational science
59. Note: natural selection acts on the phenotype, not the genotype
60. Examples
61. Peppered moth (Biston betularia) during industrial revolution: carbonaria (black) and typica (light) 
62. Stickleback (Gasterosteus aculeatus): freshwater ones have no spines and bony plates (less predators, prevents dragonflies to attack young sticklebacks, don’t need to bear the metabolic costs of having them)
63. Expression of Pitx1 gene is absent in the embryonic buds where fins develop (mutation to a regulatory gene)
64. Occurs very slowly in bigger animals due to generation time (average difference in age between parent and offspring)
65. Short generation time organisms (e.g. bacteria) can be used to study evolution
66. E. coli adapting to temperatures
67. Darwin said that we should look exclusively at an animal’s direct (lineal) ancestors, but it’s hardly ever acc possible
68. Natural selection is not the same as evolution: natural selection is a major mechanism (not the only one) that causes evolution
69. Homologous structures: similarity suggests common ancestor
70. Analogous structures: similar structures in unrelated organisms

Why Evolution is True

1. Humans are still evolving: increasing protection against malaria, lactose intolerance, etc 
2. Do ppl think evolution is true?
3. Difficult for some ppl to reconcile this theory with their beliefs on the origins on humans
4. Over time, more ppl are thinking that evolution occurred without God
5. Theory of evolution (populations of organisms change over time, and all organisms are related)
6. Evolution considered as a scientific theory but not creationism/intelligent design 
7. Theory of evolution is testable, falsifiable (can be contradicted by evidence)
8. Historical and continued evidence supports the validity of the theory of evolution
9. Falsifiable theory/conjecture:
10. Is able to be measured
11. Open to the possibility that it is wrong (e.g. there is no tiny teapot in outer space)
12. Points to hypotheses that need testing and evidence
13. Falsification starts a critical discussion (leads to more ideas abt how things work, forming a revised theory)
14. Not falsifiable if it needs an exhaustive search of all possibilities to disprove it (e.g. a tiny teapot is in outer space)
15. A falsifiable statement needs just one observation to disprove it
16. Evidence for evolution
17. Biogeography: similar species are found in distant places
18. 3 different types of flightless birds only live in South America, Africa, and Australia. Supports evolution bc if there was going to be a form of flightless bird, there’d only be one form, but there are 3+ species
19. Comparative morphology: 
20. Pig leg, dolphin flipper, bat wing: have different functions, but similar bone structures. Supports evolution bc it indicates a common ancestor 
21. Addresses vestigial structures (e.g. pigs have toes that don’t touch the ground): organisms are not perfect, structure must have had a function in an ancestral organism
22. Geology: changes in geology are slow and gradual (over billions of years)
23. If we acknowledge that the changes on the Earth have been going on for billions of years, there’s lots of time for evolution to have happened
24. Fossils: evidence that life on Earth today is different from the past
25. Lamarck proposed an idea for how evolution happens: inheritance of acquired characteristics (individuals change through lifetime and pass these changes on to offspring)
26. Charles Darwin (published “On The Origin of Species” in 1859):Natural selection (“descent with modification” from a common ancestor) is a mechanism to explain evolution
27. There is variation for traits in a population
28. Individuals whose traits allow them to survive better (higher fitness) leave more offspring who inherit these traits
29. Over time, individuals with these favourable traits become more common in the population (adaptation)
30. Evolution is variational, not transformational: individuals differ in phenotype, and success so populations change (instead of individuals changing and passing on these changes to offspring)
31. Gradualism: takes many generations to produce large evolutionary changes (i.e. many transitional forms)
32. Selection is not directed towards any specific goal; a population cannot “want” to evolve
33. Adaptations didn’t evolve on purpose even though they can be well suited to an environment
34. Living things aren’t always perfectly suited to the environment (environment can change, limited genetic variation in population, compromise between competing demands)
35. Example (environment): snowshoe hare in a non-snowy landscape isn’t camouflaged
36. Example (competing demands): some male birds are bright and showy are good to attract a mate and reproduce, but also call attention to themselves from predators
37. All life is related through common ancestry: LUCA (Last Universal Common Ancestor), a primitive entity who lived more than 3.5 billion years ago
38. New species form when an ancestral lineage divides into daughter lineages

cycle 2

Cell Cycles

1. Cell division occurs bc of: DNA replication, a dynamic cytoskeleton, and cell cycle checkpoints
2. Prokaryotic/simple eukaryotic cell division can give us clues abt ancestral cell division
3. Early 1900s: scientists know all life on Earth made of cells + cell products, all cells come from pre-existing cells
4. New progeny cells needed for increasing population of single-celled organisms, multicellular tissue growth, asexual reproduction, replacement of lost cells (e.g. shedding skin, virus infection)
5. Many cells in multicellular organisms have long lifespans and may not even ever divide
6. About 2 m of DNA in a cell before mitosis
7. Prokaryotic cell division (binary fission)
8. All bacteria/archaea use DNA, most have it in a single circular chromosome in the nucleoid
9. B period (growth), C period (chromosomes replicated and on opposite sides of cell), D period (membrane pinches between them to form two daughter cells)
10. In rapidly dividing prokaryotic cells, no B period bc growth is quick enough to be done when DNA is replicated (population can double in 20 mins)
11.  Chromosome replication begins at origin of replication (ori) where enzymes for DNA are located, and then the two new origins move to opposite poles and replication continues
12. Plasma membrane grown inward to produce two daughter cells (binary fission)
13. Central innovation of evolution of mitosis: two chromatids are held together after replication (to keep track of long chromosomes and orient them properly wrt cytoskeleton)
14. Components needed for this were present in ancestral prokaryotic cells
15. In high level eukaryotes, nuclear membrane disintegrates as chromosomes are being distributed, then reform later in daughter cells
16. Mitosis divides replicated DNA equally and precisely because of:
17. A program of molecular checks + balances to ensure orderly and timely progression
18. DNA replication to make two copies
19. Structural and mechanical web of cytoskeleton ‘cables’ and ‘motors’ to separate DNA molecules into daughter cells (clones)
20. Hereditary info in nucleus is stored in chromosomes with proteins to stabilize it, assist in packaging it during cell division, and influence expression of individual genes
21. Most eukaryotes have 2 copies of each type in nuclei: humans have 23 different pairs of chromosomes for a diploid number of 46
22. Replication of DNA in a chromosome yields sister chromatids that are held together along their length by cohesins (which are removed during mitosis)
23. Chromosome segregation: equal distribution of daughter chromosomes 
24. Rare mutations during replication cause the cells of a clone to have few slight differences 
25. Interphase: from end of one mitosis to beginning of next
26. G₁ phase: cell carries out function (e.g. transcription → RNA, proteins), may grow as well
27. Many cells stop dividing here: shift into G₀ phase (may begin re-dividing after going back into G1)
28. S phase: DNA replication and chromosome duplication
29. Most mammalian cells take 10-12 hours
30. G₂ phase: gap in cell cycle; growth continues and cell prepares for mitosis
31. Most mammalian cells take 4-6 hours for G₂, then <1 hr for mitosis
32. Chromosomes organized but loosely packaged within nucleus
33. Internal regulatory controls trigger phases of cell cycle when ready + regulate number of cycles a cell goes through
34. Affected by external influences (e.g. other cells, viruses, hormones, growth factors, death signals)
35. Steps of mitosis
36. Prophase: chromosomes condenses by forming nucleosomes (winding double helix twice around a complex of small positively charged histone proteins) 
37. 2 molecules each of four different histones make up nucleosome core
38. Linker (short segment of DNA) extends between nucleosomes, looks like beads on a string: called 10 nm chromatin fibre 
39. Fifth histone H1 binds to both nucleosomes and linker DNA: called 30 nm chromatin fibre, or solenoid (start to become visible as it coils)
40. Nucleolus becomes smaller and (in most species) disappears, stopping all RNA synthesis
41. Mitotic spindle begins to form between the two centrosomes as they move to form spindle poles, and bundles of microtubules radiate from poles
42. Prometaphase:
43. Nuclear envelope breaks down
44. Spindle microtubules grow from centrosomes (poles) towards cell center
45. Kinetochore formed on each sister chromatid at centromere (microtubules start to attach to chromosomes: determine which daughter cell it goes to)
46. Metaphase: 
47. Sister chromatids align
48. Chromosomes align at metaphase plate, spindle reaches its final form → chromatids can separate
49. Karyotype: all the condensed chromosomes arranged by size/shape, can identify species form it
50. Anaphase:
51. Separase cleaves cohesin ring holding chromosomes together
52. Kinetochores move first, then daughter chromosomes move to opposite poles (chromosome segregation)
53. Telophase: chromosomes at poles decondense, nucleolus reappears, RNA transcription resumes, new nuclear envelopes form, spindle disassembles and cytoskeleton goes back to normal interphase tasks
54. Now, each chromosome has one double helix (each chromosome was made up of two after DNA replication); two daughter cells receive 2n chromosomes even though there were only 2n in the original cell 
55. Cell has two nuclei
56. Cytokinesis: division of cytoplasm; not part of mitosis; begins during telophase or anaphase
57. Animals, protists, most fungi: furrow deepens until it cuts cell in two
58. Layer of microtubules that stay at former spindle midpoint expands laterally until it stretches across the whole thing
59. A band of microfilaments forms just inside plasma membrane and forms a belt following inside boundary of cell in the microtubule plane; motor proteins cause the microfilaments to slide together and constrict the cell to form a groove that eventually cuts cell in two
60. Plants: cell plate (new cell wall) forms and grows laterally until it divides the cytoplasm
61. Plane of cell division is v important for growth and morphology bc cell wall is what gives structur

Cell Cycling (Mitosis and Meiosis)

1. DNA can be used to learn about life: it’s not the master regulator, but it’s the program for life
2. Germ cell (which came from mitosis) undergo meiosis to become n, then sperm and egg couple to form a zygote (2n) → cell divides to form organism
3. Cell life cycle: interphase (G1, S, G0 or G2), mitosis (PMAT)
4. During embryogenesis, all cells are cycling, and after that, some cells, once differentiated, don’t cycle anymore (e.g. muscle cells, neurons)
5. Tissues that require growth/repair/regeneration: go from G0 to G1 (e.g. liver cells, adult stem cells)
6. Prokaryotic cells (bacteria, archaea) don’t have organelles or nuclear membrane, and DNA floats around
7. Divide by binary fission 
8. Eukaryotic cells divide by mitosis
9. Centromere splits in mitosis (and meiosis II), unlike in meiosis I where two sister chromatids are pulled to each pole
10. Why do we have 35 trillion cells when there are only 250 types of cells? Why do cells undergo mitosis so much?
11. Larger cells are harder to maintain: want a high surface area to volume ratio
12. Main checkpoints in cell cycle: at G1/S (biggest one), G2/M (accurate chromosome replication), metaphase (spindles properly attached, chromosomes lined up properly)
13. DNA is in nucleus, chloroplast, mitochondria in plants
14. Chloroplast and mitochondria have prokaryotic circular DNA from endosymbiosis and reproduce separately
15. Nucleus has eukaryotic DNA
16. Genome: all of the DNA sequence in one copy of an organism’s chromosomes
17. n = a copy (“set”) of all nuclear chromosomes; number of unique chromosomes; represents ploidy number
18. Humans have 2 copies: 2n = 46
19. Coefficient: number of copies of set of unique chromosomes
20. C = amount of DNA in one set of nuclear chromosomes (measured in number of copies; in picograms or base pairs); genome size
21. Coefficient: number of copies of genome (we have 2C: one copy from each parent)
22. Chromatid vs chromosome
23. Chromatids: (nearly) identical DNA molecules attached at centromere
24. Chromosome: made of two sister chromatids
25. Human karyotype (taken during metaphase): 23 pairs of homologous chromosomes; 46 pairs of sister chromatids held together by 23 centromeres (each X is actually two Xs)
26. During S phase, replication occurs to give two times the normal number of copies of DNA

DNA 

1. After DNA was found to be hereditary molecule, there was a competitive scientific race to find structure of DNA
2. DNA has four different types of nucleotides, 
3. Nucleotide: has deoxyribose (5 carbon sugar), phosphate group, one of four nitrogenous bases (A, C, T, G)
4. Purines (A, G): fused rings of carbon and nitrogen atoms
5. Pyrimidines (C, T): single carbon ring
6. Chargaff’s rules: equal numbers of A and T, and C and G
7. Sugar-phosphate backbone (phosphodiester bond): phosphate group bridges the 3’ carbon of one sugar and the 5’ carbon of the next one
8. Phosphate is at 5’ end, and a hydroxyl is at 3’ end
9. Watson and Crick used Rosalind Franklin and Maurice Wilkins’ x-ray diffraction data to find structure: published in Nature journal in 1953
10. Watson and Crick tested scale models until they found double stranded model structure (fits Chargaff and Franklin’s discoveries) where polynucleotide chains twist around in a right handed way
11. Complementary base pairing: one purine and one pyrimidine (A/T, C/G) fit together perfectly and are strengthened by hydrogen bonds 
12. Technically, each of the sugar-phosphate backbones are a molecule each because they are connected by hydrogen bonds (not covalent bonds)
13. Each base pair takes up 0.34 nm of length in double helix, and 10 base pairs are in one full turn (34 nm for one full turn)
14. Polynucleotide chains are antiparallel (3’ ends are on diff sides for each): important for replication
15. Genetic info stored in the sequence of nucleotides held by strong covalent bonds
16. Watson and Crick inferred replication from structure: hydrogen bonds break, and each strand is a template for the synthesis of its partner (semiconservative replication: half of each new strand is from the old strand)
17. Conservative replication model: each of the two strands is a template, and a whole new DNA strand is formed
18. Dispersive replication model: neither parental molecule is intact; both new DNA strands contain some of the original
19. Meselson and Stahl: showed replication is semiconservative
20. Bacteria grown with heavy nitrogen (15N) so it was in the DNA, then transferred to a light (14N) medium
21. DNA polymerases add deoxyribonucleoside triphosphates (nitrogenous base linked to sugar linked to three phosphate groups - similar structure to ATP except not w ribose)
22. dNTP forms a complementary base pair to template strand, then DNA polymerase catalyzes a phosphodiester bond between 3’ -OH and innermost 5’ phosphate → other two phosphates are released as pyrophosphate
23. DNA polymerase structure: made of polypeptides resembling a human right hand 
24. Palm domain is evolutionarily related among polymerases in bacteria, archaea, eukaryotes (but fingers and thumb part are different)
25. Template DNA lies in a groove created by “fingers” and “thumb”
26. Template strand and 3’ -OH of new strand meet at active site for polymerization in the palm domain, nucleotide is added when a complementary dNTP enters active site
27. Sliding DNA clamp: a protein that encircles DNA and binds to end of polymerase to tether it to template strand (so many more polymerizations can occur before it detaches → faster rate of polymerization)
28. DNA unwinding starts at a specific sequence called origin of replication (ori)
29. DNA helicase: binds to ori with the help of other proteins, unwinds DNA to form a replication fork
30. Single stranded binding proteins (SSBs): coat exposed single stranded DNA to prevent it from rejoining; are displaced when new polynucleotide chains are formed
31. Topoisomerase: prevents twisting of DNA when unwinding by cutting the DNA ahead of the replication fork, untwisting it, then rejoining the strands
32. Primase: makes an RNA primer when there’s no existing strand, RNA primer is removed and replaced with DNA later 
33. Can only elongate DNA 5’ to 3’: leading strand has continuous replication, lagging strand has discontinuous replication (Okazaki fragments) 
34. Overall, DNA replication is semi-discontinuous
35. RNA primer is needed for each Okazaki fragment
36. DNA polymerase III (main polymerase): adds nucleotides after RNA primer 
37. DNA polymerase I: replaces RNA primer from 5’ end of previous Okazaki fragment with DNA, and also from the beginning of leading strand 
38. Exonuclease activity of enzyme is used to digest the primer from 5’ to 3’
39. Detaches when it sees the first DNA nucleotide
40. DNA ligase: forms covalent bond in the nick (lack of bond) between adjacent Okazaki fragments after DNA polymerase I switched the RNA to DNA
41. Enzymes assemble at the fork and the strands pass through the assembly
42. Replication rate: 50-100 per second in eukaryotes, 500-1000 per second in bacteria
43. Researchers found these enzymes out through experiments with bacteria and eukaryotes and viruses that infect them both
44. Replisome: a complex with the key proteins and enzymes, sits stationary at fork and DNA moves through, optimizes speed of accuracy
45. Lagging strand loops out so 3’ end of single stranded DNA can be primed with RNA primer so DNA polymerase III can work on the bottom part of the loop
46. Loop becomes smaller as replication proceeds, and a larger loop forms again for next Okazaki fragment
47. In eukaryotes, replisomes are attached to specific places in nuclear matrix 
48. Replisome factories: an assembly of replisomes 
49. DNA replication is bidirectional: unwinding at an ori produces two replication forks that form a replication bubble, the two forks replicate in opposite directions
50. Any particular strand has continuous replication at one fork and discontinuous replication at the other fork 
51. Only one ori in small circular genomes (e.g. in E. coli)
52. Hundreds of origins of replications along eukaryotic chromosomes (so it’s sometimes faster than bacteria’s smaller genomes), replication forks extend until they meet to form fully replicated chromosomes
53. Linear chromosomes of eukaryotes get shorter each time they replicate: RNA primer is needed to start DNA synthesis and gaps are fixed by DNA Polymerase I, but not at the very beginning (no chain that can be elongated)
54. Will eventually be lethal for cell
55. Telomeres: noncoding “buffer” regions near the ends of chromosomes, 5’-TTAGGG-3’ repeating hundreds of thousands of times; buffering only fails when telomere is all gone
56. Telomerase: adds DNA to end of chromosome
57. After original RNA primer is taken off, there’s a 3’ end sticking out
58. Telomerase carries its own template strand and elongates the 3’ using the RNA as a template, DNA Polymerase can make the other strand normally
59. Telomerase not active in most somatic cells in multicellular organisms (can only divide a certain number of times)
60. Cancer: telomerase reactivated → rapid division becomes uncontrolled

Inheritance of “Sameness”

1. Genome: all of the DNA sequence in one copy of an organism’s chromosomes
2. n: one copy of all an organisms’s nuclear chromosomes (all the different ones)
3. Humans: n=23, we are diploid (2n), coefficient of n is the ploidy
4. C: the amount of DNA in one set of an organism’s nuclear chromosomes (genome)
5. Coefficient of C: copies of genome
6. C-Value Paradox: less complicated organisms can have larger genomes than most complicated organisms
7. Flowering plants and amphibians have the largest genomes (mammals have less, about 3B base pairs vs a flower that has 150B base pairs)
8. A larger genome doesn’t necessarily mean more genes
9. Karyotypes are made during metaphase
10. Repair enzymes proofread: if base pairs aren’t matched well it can see
11. Distinct 3’ and 5’ ends gives positional polarity to DNA backbones 
12. 3’ has a free -OH, 5’ has a free phosphate
13. DNA polymerase adds to a free 3’ -OH
14. Molecules can’t do some things bc they were restricted by evolutionary paths 
15. Replisomes replicate one strand continuously and one discontinuously
16. Bases always from 5’ to 3’, RNA primer first (U instead of T)
17. Template is filled from 3’ to 5’
18. Replication bubble forms from two forks
19. First bases that go on a strand: the ones in leading strand
20. Polymerase Chain Reaction: amplifies DNA (increases number of copies exponentially)
21. Copies just a selected region of DNA
22. Short DNA primers are single stranded and complementary to ends of strand to be copied (on the insides)
23. DNA + primers + DNA Polymerase + dNTPs in a thermocyclers (to control tube)
24. Heated to 95C, so strands separate (melt) 
25. Lowered to 60C, hydrogen bonds can reform (primers can anneal)
26. Raised to 72C, DNA Polymerase extends primer (warmer = faster) using dNTPs

CYCLE 3

Repair of Damage in DNA

1. Not all changes to DNA are mutations: mutations are double-stranded changes
2. Changes in only one strand are DNA damage: includes replication errors resulting in wrong base pairs, chemical reactions that add chemical groups to bases
3. 3 types of repair mechanisms:
4. Proofreading: for errors by DNA polymerase
5. Mismatch repair: for errors made during replication that escape proofreading
6. Excision repair: for various kinds of DNA damage (chemicals, radiation, etc)
7. Correction of errors: recognize error and remove it, replace removed DNA using a repair DNA repair polymerase, seal new DNA to old DNA using DNA ligase
8. Base pair mismatch corrected by a proof-reading mechanism in DNA polymerase during replication, or a DNA repair mechanism after replication
9. DNA polymerase: makes very few errors, usually base-pair mismatches
10. Has a proofreading mechanism: if nucleotide is mismatched, it can use a built-in 3’ to 5’ exonuclease activity to erase the mistake, and it can then continue
11. Major DNA polymerases of replication proofread their work 
12. E. coli’s PolIII is fully functional → error rate of 1 in 1 million
13. Proofreading function inhibited → error rate of 1 in 1000-10,000
14. Similar results for eukaryotes
15. Mismatch repair mechanism corrects about 99% of the 1 in 107 errors left by DNA polymerase → only leaves 1 in 109 errors
16. Evolutionary conservation in bacteria, yeast, humans, etc → ancient, vital
17. Important to prevent cancer
18. A type of colon cancer is caused by a mutation in a gene for a mismatch repair protein
19. Excision repair mechanisms: correct various types of damage
20. Non-bulky damage: may occur in chemical modification of bases, or the loss of purine bases
21. Base-excision repair: removes erroneous base and replaces it with the correct one
22. After proofreading, is the most important correcting mechanism
23. Bulky distortions: due to UV light (causes thymine dimers to form: adjacent T’s bond)
24. Can have serious consequences bc DNA polymerase can’t continue synthesis past the distortion → cell death
25. Nucleotide-excision repair: similar mechanism to other repairs; specific proteins recognize the bulky distortion and remove part of it containing the thymine dimer → repair DNA polymerase and DNA ligase replace and seal it to the rest of the DNA
26. Many other kinds of bulky and non-bulky damage; are repaired as well 
27. After proofreading and repair, there are very few mismatches (will be mutations/double-stranded changes)

Origin of Variation

1. Last replication bubble at the end of chromosomes (only applies to linear DNA, not in circular DNA like in bacteria): shortening of new strand
2. Primer is removed at 5’ end, so there’s a 3’ end sticking out. Can’t add more because there’s no template to add a primer and then fill with nucleotides
3. Newly synthesized strand starts to decrease in length, will eventually affect genes
4. Cells evolved to protect genes from shortening due to DNA replication: telomeres
5. Repeat of TTAGGG: buffers ends of chromosomes (doesn’t code for anything), but isn’t endless
6. Cell senescence (irreversible cell cycle arrest) occurs when cell reaches its Hayflick limit (# of times a cell divides before cell division stops)
7. Cancer cells, germ cells, stem cells keep replicating bc they have active telomerase
8. Telomerase restores length of telomeres; we need to restore the 5’ end  
9. Telomerase will extend the 3’ end to make more template for the replisome to act (primer, PolIII, etc)
10. Telomerase brings its own RNA template to make the DNA template strand 
11. Telomerase always acts in lagging strand
12. Mechanisms to ensure inheritance of sameness (prevent mistakes - but note that mutations aren’t always bad)
13. Proofreading by DNA Polymerase during S phase: for base pairs that are a mismatch 
14. Excision repair enzymes when proofreading fails: detects mistake, cuts newly synthesized strand and removes bad piece, and then DNA polymerase III can resynthesize from 3’ hang and ligase will seal gap (at 3' end of new strand) 
15. Our molecules are designed to ensure sameness
16. Complementary base pairing means that we can check for errors using shape
17. Semi-conservative replication means that DNA polymerase needs a template
18. Sources of DNA damage: 
19. Exogenous factors (from outside cell): UV light, chemicals, ionizing radiation (gamma rays, x-rays)
20. Endogenous factors (from inside cell): DNA replication errors, mitochondria (produce reactive oxygen species [ROS]: produce free radicals, highly reactive)
21. DNA Polymerase III makes a mistake 1 in 106, would be 1 in 1000 if no proofreading: but 3.2 B base pairs, so 3000+ errors in each
22. Mutation is a double-stranded change (one-sided change is just damage)
23. After DNA damage (e.g. wrong base pair), the second round of replication can result in a point mutation when changed base pair gets its complement
24. Thymine dimer: two adjacent T form covalent bonds when UV light absorbed
25. Can be repaired by photolyase (an enzyme) and white light

Doesn't work in humans anymore

1. Humans use excision repair enzymes (lost photolyase through evolution)
2. Melanoma: mutation in repair enzyme, so thymine dimers accumulate to cause skin cancer
3. Double-strand break: repair is during G1 during non-homologous end joining by ligase (just joins ends), may lose nucleotides that fell off, can result in mutation
4. Human Genome Project: sequence of the entire genome
5. 2000: Working draft compiled of DNA from several anonymous donors
6. Mid 2000’s: Individual sequences of Craig Ventor and James Watson (cost $100M at the time)
7. 2010: Individual sequences of Han Chinese, Korean, Yoruba, Bantu (Desmond Tutu), Neanderthal, unborn fetus, etc
8. 2015: 1000 Genomes Project reported
9. People thought they could find the cure to everything from the genome, but the genome was sequenced to do better science more efficiently (look at DNA as a whole and not as individual genes)
10. Goal is to figure out role of DNA in actual diseases
11. DNA sequence: 
12. 25% unknown (probably junk)
13. 10% essential (2% code for proteins)
14. 10% intron (junk)
15. 55% transposons, viruses, and “dead genes” (junk)

Genetic Variation due to Mutation

1. Mutations are not always bad, it leads to evolution
2. Type of mutation is one thing, but location is what affects whether or not there’s a change that affects the organism
3. Ways to get genetic diversity: independent assortment, recombination, mutation
4. Human variation: took 2504 genomes from 26 diff populations, and 0.14% was found to be different from the reference genome (made based on all of them)
5. Chimps have a 1.4% difference
6. Vast majority of variations between people are SNPs (single nucleotide polymorphisms)
7. This is what’s analyzed in DNA analysis: look at specific areas for differences
8. There are abt 12000 variants in coding regions, and abt 100 de novo (not in parents) variants, abt 30 variants are associated with diseases 
9. Mutations are more complicated than just good = helpful, bad = disease
10. Some types of mutations: substitution (point mutation), deletion, insertion, inversion (backwards)
11. Result of point mutations: silent (no change), nonsense (stop code), missense (change in amino acid: conservative if similar structure, nonconservative if not similar structure)
12. Single nucleotide polymorphisms (SNPs): occur in pairs (bc it’s a mutation), most common type of genetic variation among people, can occur anywhere in genome (usually between genes), most have no effect on health/development
13. InDel mutations (insertion/deletion): due to DNA Polymerase slippage, not SNPs
14. Insertion: slippage of new strand, repetitive sequences more prone to slippage
15. Deletion: slippage of template strand, so new strand has one less set of 3 bases
16. Tautomers: spontaneous tautomeric shifts (tautomerization) change base pairing partners
17. Common forms: A and T are normally in keto form, C and G are normally in amino form
18. Rare forms: A/T can switch to enol form, and C and G can switch to imino form
19. They switch partners: not a mismatch; the structures line up so repair enzymes don’t recognize the change
20. If a rare form of a nucleotide comes and pairs in the replication of a parental DNA, the first mutant shows up in second generation of parental DNA (bc tautomerization switches and goes back to normal form in the next round of replication)
21. Mismatch repair can introduce a mutation
22. Can happen if during the repair process, there is tautomerization (so it favours non-Watson/Crick pairing)
23. Can happen bc repair enzymes can cut template strand instead of newly synthesized strand instead 
24. Some mutagens are tautomerically unstable base “analogues” 
25. Ex. 5-bromouracil looks like thymine (has a Br instead of a CH3 on 5’ carbon)
26. 5BU gets put instead of T (is in keto form and favours A), but switches to enol form and favours G
27. After second round of replication, there are two normal strands, one with a mutagen/damage (not a mutation bc it still matches, but may undergo apoptosis), and one with a transition mutation (purine → purine)
28. Transition mutation: purine to purine and pyrimidine to pyrimidine
29. Transversion mutation: purine to pyrimidine or pyrimidine to purine 
30. Transposable elements (jumping genes): regions of DNA that move around
31. Discovered by Barbara McClintock in 1940s in maize: no one believed her, thought genome is stable (and she was a woman)
32. Kernels were spotted bc a TE (transposable element) came in the genes for pigmentation in some cells so pigmentation wouldn’t occur
33. Found in Drosophilia in 1950s, bacteria in 1960s, and humans in 1970s
34. Contain a region that codes for transposase enzyme (does the cutting/copying and pasting)
35. (Don’t need to know about diff types of TEs and mechanism of transposition)
36. Most common in plants, which is why their genomes are so big
37. 85% of barley’s genome is transposable elements
38. 50% of human genome has TEs, 70-80% of human genes contain TEs (up to 1000 per gene)
39. Most TEs don’t move due to inactivating mutations
40. Active TEs have evolved to be in “safe havens” where they don’t interfere with cell’s actions
41. We also have a mechanism to silence/inactivate TEs, if it doesn’t work → cancer

cycle 4

Genetic recombination

1. Many types of reproduction
2. Octopi: reproduction is occasional, preceded by courtship involving intermingling tentacles
3. Slipper limpet: reproduction is a lifelong group activity
4. Both genetic alikeness and difference are necessary for evolution
5. Mutation is the main source of genetic diversity: usually from errors in DNA replication, need more diversity so other mechanisms (e.g. genetic recombination) exist
6. Genetic recombination: widespread in nature; part of meiosis
7. Needs two double DNA helices, and a mechanism for bringing the strands close, enzymes to cut/exchange/paste DNA back together 
8. Recombination usually occurs between homologous regions
9. Enzymes break hydrogen bonds of one double helix and allow bases to reassociate with complementary bases in a homologous chromosome. DNA backbone is also cut, and then rearranged by nuclease enzymes

Recombination

1. List of mechanisms to generate genomic diversity
2. Meiosis: independent assortment, homologous recombination (not covered yet)
3. Transposons, slippage, tautomerization (during repair process), DNA fidelity (Polymerase adds a wrong base and fails to proofread), non-homologous end joining
4. Radiation exposure: radon, medical, internal, cosmic, terrestrial, consumer products
5. Ionizing radiation creates ROS (reactive oxygen species) from water that damages DNA
6. Oxygen is unstable because e- was taken from it so it’s very reactive (e.g. hydrogen peroxide, hydroxyl radical, etc)
7. Comes from decay of radioactive iodine (t1/2 = 1 week) and cesium (t1/2 = 30 yrs)
8. Repairing double stranded breaks can create rearrangements (e.g. non-homologous end joining)
9. Causes deletion, duplication, inversion, translocation (one chromosome to a different one)
10. Example: translocation of c-myc one gene (involved in cell cycling) from chromosome 8 → 14 results in Burkitt lymphoma (deregulates a cancer gene)
11. Promoter for this gene is usually turned off, but when translocation occurs, c-myc ends up next to a promoter for antibody production (very active)
12.  De novo mutations are only passed on to the next generation if they affect germ cells
13. Unequal recombination can generate copy number variations (CNV)
14. Crossing over normally occurs between alleles of homologous chromosomes during prophase I at the same point on each homolog
15. Unequal crossing over occurs when chromosomes aren’t aligned properly (one chromatid will have more genes and one will have less)
16. Copy number variations contributes to organism complexity
17. We have way more CNVs than simpler organisms
18. Zygotes bring DNA from two different parents into the same cell to contribute to diversity of population (is an organism’s purpose of life, from a biological perspective)
19. Homologous chromosomes carry the same genes but different alleles
20. Variation between humans’ genomes is about 14%
21. Recombination during meiosis cuts and pastes DNA backbones
22. Technically, recombination is a mutation bc it’s a double stranded change in the sequence
23. Meiosis (important):
24. Ploidy change (2n → n) at the end of meiosis I
25. Homologous pairs (not centromeres) split up
26. No ploidy change in meiosis II; equational phase
27. Homologous recombination is in prophase I
28. After meiosis II, we get one genome per haploid cell (gamete)
29. Won’t survive if you get more than one set
30. Life cycles (diploid, haploid phases; how are gametes produced and what are they called’ n and C values) of animals, plants, and fungi (NEED TO KNOW)
31. Animal life cycle: animal (2n) produces gametes (n) → fertilize to form animal
32. Plant life cycle: produce spores (n) which undergo mitosis to produce a gametophyte (n) and male/female gametes (n), which fertilize to make a zygote (2n) and a sporophyte (2n) which undergoes meiosis to produce spores
33. Some fungi/algae: gametophyte (n) undergoes mitosis to produce male and female gametes (n), which fertilize to form zygote (2n), which undergoes meiosis to form a spore (n), which divides to produce gametophyte

Meiosis

1. Life cycles of animals, plants, fungi: what process produces gametes (mitosis/meiosis), what are the gametes called
2. Animals: gametes formed by meiosis
3. Plants: gametes formed by mitosis, spores are formed by meiosis
4. Alteration of generations (multicellular organisms exist both in diploid and haploid)
5. Fern: sporophyte (2n) does photosynthesis; is dominant form for fern. Spores are in sporangium. 
6. Gametophyte have male and female organs (where male and female gametes are made, respectively): hermaphroditic
7. In flowering plants, female is carpal (includes ovary) and male is stamens (includes anther)
8. Some fungi/algae: gametes formed by mitosis, zygote divides by meiosis to form spore
9. Majority of life is as a gametophyte (n)
10. Diversity generated during meiosis: independent assortment in meiosis I, homologous recombination in prophase I
11. Increases randomness + possibilities of distribution of alleles
12. Differences between alleles of same genes: SNPs, InDel mutations, etc
13. Cytoskeleton: centromeres are part of chromosomes, kinetochores are attached to chromosomes and attach to spindle fibers to pull sister chromatids apart towards spindle pole, microtubules made of a polymer of tubulin proteins
14. Higher chance of recombination between farther genes bc there’s more possible space for recombination to occur (genes located close to each other are linked)
15. Aneuploidy: abnormal number of chromosomes; results from a single partitioning error
16. Occurs more when regulation is bad; spindle fibers don’t attach in right direction
17. Some chromosomes/sister chromatids end up in wrong cell
18. Nondisjunction during meiosis I: two final cells are n+1, two are n-1
19. Nondisjunction during meiosis II: two normal (n) cells, one is n+1, one is n-1
20. Examples of aneuploidy
21. Trisomy 21: Down’s syndrome
22. As age of mother increases, risk of kid having Down syndrome increases (different for men: they produce sperm every day so spindle fibers are fresh)
23. Trisomy 13: Patau Syndrome
24. Trisomy 18: Edwards Syndrome
25. Trisomy 8
26. Turner syndrome: OX (1 in 5000)
27. Klinefelter syndrome: XXY (1 in 2000)
28. Triple X syndrome: XXX (1 in 1000)

cycle 5

The Chromosomal Basis of Mendelian Inheritance

1. Gregor Mendel (1860s): used traits in generations of garden peas to study pattern of inheritance 
2. Shows how rigorous scientific work is done: observation, hypotheses, experiments
3. His techniques and conclusions were so advanced for the time that they weren’t appreciated until later: chromosomes and meiosis were yet to be discovered 
4. Was also lucky that the characters he analyzed all segregate independently (none are near each other on the chromosomes)
5. Blending theory of inheritance: scientists thought this was true until 1900s
6. Hereditary traits from parents blend evenly in offspring 
7. Doesn’t explain why extremes (e.g. very tall, very short) remain, and why blue-eyes kids show up in offspring of brown-eyes parents
8. Mendel studied characters (heritable characteristics)
9. Established that characters are passed to offspring in discrete hereditary factors
10. Used garden pea (Pisum sativum) that was true-breeding/pure-breeding: when self-fertilized (selfed), it passed traits without change from one generation to the next
11. Male gametes (pollen) made in anthers, and female gametes (eggs) are in ovary at bottom of carpel
12. He prevented self-fertilization by cutting anthers off → forces cross-pollination where he could put pollen from one flower onto another
13. Cross-fertilized plants produces seeds (were analyzed for seed traits such as wrinkly/round) that were grown into adult plants (white or purple)
14. Selected seven characters of study: flower colour, seed shape, seed colour, pod shape, pod colour, flower position, stem length
15. Alternative forms could be seen visually
16. Results: same pattern seen in all characters
17. P generation (parental): one purple parent and one white parent (both genders tested)
18. F1 generation (filial): all purple, no evidence of blending → was allowed to self
19. F2 generation: about 75% purple and 25% white
20. Definite, predictable proportion that showed up every time
21. Mendel’s hypotheses
22. Adult plants carry a pair of factors that govern the inheritance of each character
23. Modern terms: factors are genes, different version of genes are alleles, diploid organisms have two copies of each gene
24. If genes consist of different alleles, one is dominant and the other is recessive
25. Dominant allele determines phenotype, but do not directly inhibit recessive alleles
26. Ex: round seeds contain amylopectin (a branched starch) but wrinkled ones don’t; mutant (wrinkled) allele codes for a nonfunctional enzyme that doesn’t produce amylopectin, but if there’s a functional allele then there’s enough to make it round
27. Pairs of alleles separate when gametes are formed: half the gametes have one allele and half have the other (Principle of Segregation)
28. Fertilization occurs in fusion of gametes from parents → zygote has two alleles
29. True-breeding organisms are homozygotes: homozygous for allele in question (PP or pp)
30. Capital letter used for dominant and lowercase for recessive: e.g. P and p for purple and white 
31. F1 plants were all heterozygous (Pp): monohybrid (an offspring of parents with different traits wrt one gene)
32. Half their gametes are P and half are p, crossing two heterozygous organisms is a monohybrid cross 
33. Was allowed to self to produce the F2 generation
34. F2 plants:  
35. Genotype (genetic constitution): ¼ homozygous dominant, ½ heterozygous, ¼ homozygous recessive
36. Phenotype (expressed traits): ¾ dominant trait (purple), ¼ recessive trait (white)
37. This experiment supported Mendel’s 3 hypotheses
38. Testcross: a cross between an organism with dominant phenotype and a homozygous recessive individual
39. Mendel tested independence of different genes by crossing parents which had differences in two hereditary characters (e.g. seed shape + colour: Rr Yy)
40. Already found that each character was controlled by a pair of alleles
41. Dihybrid: a zygote from a cross involving two characters
42. Found ratio of 9 round yellow: 3 round green: 3 wrinkled yellow: 1 wrinkled green
43. Data consistent with previous findings; added a new hypothesis (independent assortment)
44. Principle of Independent Assortment: which allele is chosen for one trait has no influence on which allele is chosen for another trait
45. Testcross confirmed this: crossing the dihybrid with a rryy resulted in equal for round yellow, round green, wrinkled yellow, wrinkled green
46. Mendel’s results rediscovered in early 1900s (meiosis was understood), then Walter Sutton (a genetics student) saw the parallels and made chromosome theory of inheritance
47. Chromosomes (and thus alleles) are in pairs in sexually reproducing diploid organisms
48. Chromosomes (and thus alleles) in each pair are separated and one is given to each gamete
49. Separation + distribution in gametes of any pair of chromosomes is independent of separation of other pairs
50. One of each chromosome is from male parent and one is from female parent
51. Locus (plural loci): the site on a chromosome where a gene is located; usually encodes a protein/RNA product that causes the phenotype → alleles caused by small differences in DNA sequences that cause functional differences in protein/RNA 
52. Examples of recessive alleles: albinism, webbed fingers, achondroplasia (a type of dwarfism), cystic fibrosis
53. Incomplete dominance: effects of recessive alleles can be detected
54. Ex. true-breeding red and white snapdragons are crossed → F1 has pink flowers
55. Sickle cell anemia: occurs when homozygous for a recessive allele (produces defective hemoglobin), but heterozygous people have sickle cell trait (milder form bc some normal hemoglobin is made)
56. Familial hypercholesterolemia: gene that codes for LDL receptor (removes cholesterol from blood); homozygous recessive people have a severe form and are prone to atherosclerosis; heterozygous people have a less severe form 
57. Many alleles we think are dominant are actually incompletely dominant at molecular level
58. People heterozygous for an allele that causes Tay-Sachs have no symptoms, but there is a slightly reduced breakdown of gangliosides (this is much greater in people that are homozygous)
59. Codominance: both alleles have significant effects so heterozygotes can be detected
60. Human blood types (not ABO): M, MN, and N
61. L^ML^M gives type M, L^NL^N gives type N, L^ML^N gives type MN
62. Little medical importance, but used in paternity tests an din tracking evolution (bc genotype can be found directly from phenotype)
63. Inheritance type is essentially same as incomplete dominance bc each genotype has a different phenotype (can’t distinguish them just from offspring/crosses)
64. Multiple alleles: more than 2 alleles may be present in a population
65. More than 200 alleles of a gene that plays a role in the accepting/rejection of organ transplants in humans
66. Each diploid organism still only has two alleles (can still trace gametes/crosses)
67. Human ABO blood groups: Landsteiner found that only certain combinations of four blood types (A, B, O, AB) can be mixed safely
68. Three alleles: IA, IB, i
69. IA and IB are codominant to each other and dominant to i 
70. Epistasis: genes at different loci interact
71. We think epistasis is important for susceptibility to common human diseases (e.g. insulin resistance)
72. Polygenic inheritance: a more continuous distribution of phenotype (quantitative traits); when multiple different genes contribute to the same character
73. Distribution should be a bell curve (can use classes of variation: e.g. height in 180s)
74. May support the old idea of parents’ traits “blending,” but analysis shows that offspring actually ranges over a bell-shaped continuum (so kids might be shorter/taller than both parents)
75. Expression of genetic phenotype is also affected by environment
76. Pleiotropy: multiple characteristics affected by a single gene
77. Sickle cell disease: affects hemoglobin, so RBCs take a sickle shape in low oxygen. More common in Africa/Asia where malaria was endemic 
78. Other patterns of inheritance extend Mendel’s fundamental principles

Mendelian Inheritance

1. 1800s: people thought the F1 generation would be blended (mix of phenotypes of parents); often true irl but it’s because they’re polygenic
2. Mendel (1850s) didn’t even know DNA but just used experimental data
3. Wanted distinct, independent traits: round/shriveled peas, green/yellow peas
4. Careful experimentation with controlled crosses (cut off anthers) and quantitative analysis
5. Source of all this is DNA → base pair changes cause phenotype differences
6. Blood type is codominant (a type of non-Mendelian genetics)
7. Mendel’s explanatory model
8. Variation in traits is due to different alleles
9. Alleles segregate randomly into gametes
10. Organisms inherit two alleles for each trait
11. Appearance of heterozygotes is determined by dominant alleles
12. X-linked recessive, X-linked dominant
13. It matters whether the mutation is in mother or father
14. X-linked recessive: needs 2 copies in females, only one in males
15. RRYY and rryy cross → F1: RrYy and RrYy (dihybrid cross) → F2: 9:3:3:1 ratio
16. Sex linkage: illustrated in Drosophila eye colour
17. Wild type (normal, red) is w+, mutant type is w
18. Progeny is different when you cross a homozygous w+ female and w male, than a homozygous w female and w+ male (reciprocal cross: switch whether male or female is mutant)
19. Also see different progenies when selfing each of the reciprocal crossed F1 generations
20. Colour blindness is X-linked recessive
21. Note that males cannot be carriers for X-linked
22. Polygenic traits: show continuous variation in a population
23. Epistasis: 2 genes affect the same trait; non-Mendelian genetics (one gene interferes with expression of another)
24. Labrador retriever colours
25. Dominant alleles aren’t necessarily the most evolutionarily “fit,” or the most common

cycle 6

Microevolution Pt. 1

1. Microevolution: change in a population’s genetic makeup from one generation to the next
2. Phenotypic variation: differences in appearance or function (weight, physiology, etc)
3. Heritable variation is a driver of natural selection
4. Quantitative variation: individuals differ in small + incremental ways
5. Qualitative variation: polymorphism (exist in 2+ discrete states and intermediate forms are absent)
6. Phenotypic variation can be due to genotypic variation and/or environmental factors that each individual experiences, can also be an interaction between both
7. Under certain circumstances, the same genotype can cause different phenotype (or different genotypes can cause the same phenotype)
8. Knowing cause of phenotypic variation is important
9. Only genetically based variation is inherited
10. Can test this by manipulating environmental variables and measure effects on genetically similar subjects
11. Population genetics: focuses on genetic variation in populations + how it changes bc of evolution, and predicting how different factors affect it (describe genetic structure of population, then test hypotheses using mathematical models)
12. Caused by four processes: mutation, genetic drift, gene flow, natural selection
13. Each acting alone or in combination
14. Genetic variation is because individuals have different alleles of same genes
15. Locus: location of a gene on chromosome
16. Gene pool: all the alleles at the gene loci(us) of interest in all individuals in the population
17. Polymorphism: differences in nucleotide sequence (alleles) of a given gene in individuals
18. Technology advances makes DNA sequencing easier + cheaper --> we know a lot about sequences of entire genomes
19. Lots of variation in both coding and noncoding regions
20. Lots of variation between the two copies of a given gene in heterozygous ppl, between individuals in a given population, and within different populations/species
21. SNPs: account for ~90% of variation in humans
22. Genetic variation: raw material for evolutionary change
23. Can come from production of new alleles: mostly due to processes that cause mutations
24. Can come from rearrangement of existing alleles into new combinations: from meiosis (crossing over, independent assortment of chromosomes, and random fertilization between sperm and eggs)
25. Can be hard to determine genotype from phenotype: some traits involve many genes, traits are often influenced by environment
26. Snapdragon (a diploid plant): flower colour is controlled by a single gene and shows incomplete dominance so it's easy to determine frequencies of each genotype and use it to study microevolution

Variation in Populations Pt. 1

1. Mendelian genetics: inheritance of traits due to single gene characteristics; can discover principles of genetic inheritance through controlled crosses
2. Phenotype selection based on different alleles has differing effects on allele frequencies
3. Selection against dominant phenotype
4. Recessive trait becomes fixed
5. Selection against recessive phenotype
6. Recessive allele is not fully eliminated
7. Selection for heterozygotes (heterozygote advantage):
8. Frequencies of each allele goes to around 0.5
9. Selection against heterozygotes (heterozygote disadvantage)
10. Allele which starts off more common goes to fixation, less common allele goes to frequency 0
11. Populations usually don't show clean "Mendelian" ratios of phenotypes or genotypes, but knowing the distribution of parental genotypes in a population lets us predict next generation
12. Need to know what no evolution looks like (null model)
13. No selection, population mating randomly
14. Given allele frequencies p and q, can make a Punnett square with probabilities to find expected genotype frequencies
15. Hardy-Weinberg equilibrium (HWE): allele + genotype frequencies don't change over time
16. Requirements
17. No selection (all equally likely to reproduce)
18. No mutation
19. No gene flow (immigration/migration)
20. No genetic drift (assume infinite population)
21. Random mating
22. Can check if a population might be in HWE at a certain locus by seeing if expected genotype frequencies matches observed genotype frequencies: use p, q values obtained form observed to calculate expected and see if it matches

Microevolution Pt. 2

1. Hardy-Weinberg principle: mathematical model that specifies conditions needed for genetic equilibrium (no change in phenotype and genotype frequencies)
2. No migration/immigration
3. Population infinite in size
4. No mutations
5. All genotypes survive and reproduce equally well
6. Individuals mate randomly with respect to genotype
7. Agents of microevolution:
8. Gene flow: introduces new alleles from other populations, violates condition 1
9. Effects depend on differences between the populations and the rate of gene flow
10. Can alter a population's fitness, and decrease genetic difference between populations
11. Genetic drift: allele frequencies change between generations due to chance, violates condition 2
12. Founder effect: a few individuals leave and start a new population
13. Population bottleneck: large reduction in population size --> decrease in size of gene pool, and genetic diversity
14. Can be due to disease, starvation, hunting, etc
15. Mutation: a change to double-stranded DNA, violates condition 3
16. The only microevolutionary process that gives rise to genetic novelty
17. Can be caused by radiation (e.g. UV light) which can damage nucleotides, hazardous chemicals which can mess with replication
18. Usually caused by normal cellular processes: replication errors, transposons, etc
19. Mutations have to be in germ-line cells to alter allele frequencies in a population
20. Mutations are random and spontaneous: can't predict them, are not directed by selective pressures
21. Natural selection: shapes genetic variability by favouring some traits, violates condition 4
22. Measured by tracking changes in mean and variability of traits
23. 3 modes of natural selection:
24. Directional selection: mean shifted towards favoured extreme, variability may be reduced
25. Stabilizing selection: reduces genotype and phenotype variability, most common mode of natural selection
26. Disruptive selection: extreme phenotypes have higher fitness than intermediate ones, less common,
27. Non-random mating: mates selected because they have similar genotype
28. Inbreeding: reduces heterozygosity (everyone mates with their own genotype so homozygous increases)
29. Has negative effects on fitness (inbreeding depression): deleterious alleles tend to be recessive so there are more [homozygous] cases, can be fixed by outbreeding (introduce individuals from other populations, so new alleles will come)
30. Most human societies discourage it, but some (e.g. Amish, royal families) marry within the community
31. Sexual selection: favours individuals with traits that enhance ability to mate
32. Can experimentally test this by changing physical properties of animals and observing intersexual and intrasexual interaction changes
33. Intersexual selection: based on interactions between males and females, likely the cause of sexual dimorphism
34. Intrasexual selection: based on interactions between individuals of same sex
35. Diploidy maintains genetic variation by preserving recessive alleles from natural selection (in large enough populations)
36. Balancing selection: more than one allele actively maintained in a population
37. Heterozygote advantage ("hybrid vigour"): when an allele is may be harmful when homozygous for it, but gives a benefit when heterozygous
38. Sickle (HbS) allele: point mutation that codes for a defective, sickling hemoglobin
39. When heterozygotes get malaria, infected RBCs take sickle shape and lose potassium, killing the parasites and preventing spread in the body
40. Allele is more common in areas where malaria is prevalent
41. Frequency-dependent selection: rarity of a phenotype affects how useful it is

Variation in Populations Pt. 2

1. Fitness: the degree to which an individual contributes offspring (alleles) to future generations
2. Absolute fitness (W): a measurable quantity (e.g. average lifespan, number of eggs)
3. Relative fitness (w): an individual's absolute fitness divided by absolute fitness of most successful genotype in population
4. Heterozygote advantage: selection for heterozygotes/against homozygotes
5. Example: heterozygous corn is larger
6. Allele frequencies will approach approximately half-half as the population approaches all heterozygotes (rarer allele increases, more common allele decreases)
7. Maintains genetic variation because it keeps alleles in population
8. Heterozygote disadvantage: selection for homozygotes/against heterozygotes
9. Frequency of more common allele goes to 1, and frequency of less common one goes to 0 (because less common alleles are lost through heterozygotes)
10. Reduces genetic variation because there are fewer alleles
11. Gene flow: movement of individuals or genetic material from one population to another
12. Genetic drift: changes in allele frequencies due to chance
13. Chance events determine which individuals reproduce, and phenotype doesn't affect this
14. Bottleneck effect and founder effect: change in allele frequency due to random sampling of a small number of individuals (survivors/founders), results in reduced variation
15. Rare (beneficial) alleles are more likely to be lost
16. Increased frequency of deleterious alleles
17. Leads to inbreeding --> increased homozygosity of bad alleles
18. Example: bulldogs have shorter (8.4 years) lifespan, cataracts, heart valve problems, dermatitis, slipped disks, hip dysplasia, increased risk of cancer
19. Non-random mating: individuals select mates based on phenotype; departure from HWE occurs but no evolution bc allele frequencies don't change
20. Assortative mating: mating with similar phenotypes
21. Number of heterozygotes will half with each generation --> increased homozygosity
22. Inbreeding: mating with similar genotypes (genome-wide), a type of assortative mating
23. Inbreeding depression: increased prevalence of harmful phenotypes
24. Disassortative mating: mating with opposite phenotypes
25. Can result in hybrid vigour
26. Inbreeding avoidance (called out-crossing in plants): mating between unrelated individuals (genome-wide), a type of disassortative mating

cycle 7

Sexual Selection Pt. 1

1. Sexual selection is caused by drive to reproduce, competition for mates, mate choices
2. Sexual dimorphism: one gender is larger and more colourful than the other, may be due to sexual selection
3. Males often compete for females: larger, may have ornaments and weapons (horns, antlers, tail feathers, etc) for attracting females and fighting rival males (may be both at the same time)
4. Exaggerated structures are to show to females that the male is healthy, can harvest resources efficiently, has managed to survive to an advanced age, may have large/rich territories
5. Degree to which females actively choose genetically superior males varies among species
6. Northern elephant seals: female choice is passive; males locate clusters of females and fight violently to mate with many females
7. Sage grouse: female choice is more active; males defends a small territory in leks, females wander around and each will choose a male
8. Peafowl: peahens prefer males who have tails with many ornamental eyespots

All About (Biological) Sex

1. Sexual reproduction: cells fuse and combine genetic materials, results in new combinations of alleles in offspring
2. Sex: the exchange of genetic material (e.g. fusion of gametes)
3. Offspring's allele combinations are different from parents because of sex and recombination
4. Humans can have more than 10600 allele combinations
5. Usually different (two) sexes are involved for sexual reproduction
6. Dioecious: individuals are one sex or the other, most animals are this
7. Monoecious (called hermaphrodites in animals): individuals are both sexes; have female and male reproductive organs
8. Simultaneous hermaphrodite: male and female at the same time
9. Sequential hermaphrodites: different sexes at different points in life
10. Size-advantage model of sex change: reproductive success depends on size
11. Protogyny: transition from female to male (proto = first, gyny = female)
12. Reproductive success increases with size (for both sexes)
13. At low size, females have more reproductive success but at big size, males do
14. So, start off as female when younger (smaller) and then turn into a male when bigger
15. Protandry: transition from male to female
16. Other eukaryotes: can have 2+ mating types, gametes of different mating types fuse to exchange nuclei
17. Example: protists (single celled eukaryotes), fungi (has a and alpha mating types), ciliates
18. Not all reproduction is sexual: may be obligately sexual (most animals), facultatively sexual (many plants and protists), or obligately asexual (bacteria and archaea)
19. Parthenogenesis: a type of asexual reproduction in animals
20. Occurs in aphids, whiptail lizards, hammerhead sharks
21. Females produce offspring from unfertilized diploid eggs (no sex)
22. Asexual reproduction in plants: new individuals may grow from tubers or runners
23. Asexual reproduction in unicellular organisms: cell divides to form genetically identical offspring (clones)
24. Binary fission for bacteria and archaea
25. Mitosis for unicellular eukaryotes
26. Sex in bacteria and archaea: conjugation allows for plasmids (small circular bits of chromosome) to be exchanged, results in genetic exchange between individuals
27. Origins and history of sex:
28. 3.5 billion years ago: life evolved, LUCA was a prokaryote so reproduced asexually but likely also exchanged genes (conjugation, transduction)
29. 1.2 billion years ago: eukaryotes evolved, evolution of meiosis + fusion of gametes, most eukaryotes can reproduce sexually
30. Now: most animals must reproduce sexually, asexual animals are rare and are more prone to extinction
31. Sex is not always a good idea (but it still evolved, meaning that benefits outweighed the costs):
32. Risky: time-consuming, takes resources to find a mate, increased exposure to predation, increased exposure to STDs
33. Costly: two-fold cost of sex (only half of genetic material is inherited)
34. Inefficient: producing males reduces reproductive output, and asexual populations grow faster
35. Evolutionary benefits of sex:
36. Generates variation (new allele combinations) that can't occur with asexual reproduction
37. Offspring are genetically different from either parent and each other
38. "Lottery model": shows how more diverse populations (sexual populations) have a greater chance of some offspring having favourable phenotypes and surviving in a changing environment
39. Can make better combinations of alleles more quickly through sex and recombination
40. Makes it easier to remove bad alleles

 Sexual Selection Pt. 2

1. Natural selection: struggle for existence; traits that increase fitness are favoured
2. Sexual selection (particularly in animals): struggle for mates; traits that increase mating success are favoured
3. May evolve exaggerated structures that can reduce survival
4. Males: reproduction is limited by access to females, individual fitness can vary widely
5. Females: have limited gametes and need to spend time growing + rearing offspring
6. Intersexual selection: one sex chooses a mate from the opposite sex
7. Sex that invests more in parental care (has fewer contributions to next generation) is the chooser --> need to be selective to ensure quality offspring
8. Can involve courtship displays/calls, ornamentation, males compete for attention, etc
9. Intrasexual selection: individuals of one sex compete against each other for mates
10. Sperm competition: swimming speed (fastest to get to egg), scrapers (males have structures that scrape out sperm deposited by other males), mating plugs (males leave a plug in females after mating to prevent other males from mating with her)
11. Females also compete: for territory, access to males, resources, etc
12. Males have a higher potential fitness [possible number of offspring] than females
13. Average fitness of both sexes is the same
14. Benefits of choosing a mate wisely:
15. Direct benefits: attractive individuals are good parents, may have resources (food, territory, protection for offspring)
16. Indirect benefits: attractive individuals have good alleles
17. Survival: may have better genes for immunity
18. Improve attractiveness (and thus reproductive success) of offspring: "Sexy son hypothesis"
19. Sexual dimorphism: genders have a distinct difference in size/appearance
20. Relative role in parental care affects the degree of sexual dimorphism
21. Females provide most of parental care --> males under stronger sexual selection
22. E.g. Burrower bugs, grizzly bears
23. Males provide most of parental care --> females under stronger sexual selection
24. E.g. Seahorses, red phalaropes
25. Biparental care: both sexes invest heavily in parental care --> sexual selection acts on both
26. Little to no dimorphism

All the best on your test! :)