Biology 1001: Essential Outcomes

Principles underlying evolution by natural selection

• Mutations arise in a population randomly
  • Recombination in sexual reproduction during meiosis (crossing over)
• If a mutation is favorable, the organism will survive and reproduce to pass on the allele
• Over time, the frequency of this allele will rise in the population = evolution

Evidence supporting descent with modification from a common ancestor

• Historical Biogeography
  • Studies of the world distribution of plants and animals
• Comparative Morphology
  • Comparing anatomical structures of organisms (vestigial structures) and embryonic development similarities
• Geology
  • Looking at fossils representing organisms

Characteristics of a scientific theory and the importance of falsifiability

• Theories are testable hypotheses about the natural world
• Must be falsifiable to be considered scientific
• Must be objective, not mythical, cannot be a definition, can't be faith-based, and must be reasonably possible to test

Changes in amount of DNA throughout the cell cycle

• G1: One copy of DNA
• S: DNA is copied
• G2: Two copies of DNA
• M: prophase-metaphase (n=2, c=4) anaphase-telophase (n=2, c=2)

Main features of each stage of mitosis with respect to the cytoskeleton and the chromatin

• Prophase
  • Chromatin condenses, nucleolus disappears, spindle (microtubules) begin forming and moving to poles, nuclear membrane breaks down
• Pro-metaphase
  • Microtubules grow from centrosomes towards cell center, spindles attach to chromosome kinetochores
• Metaphase
  • Spindle microtubules move chromosomes into alignment, chromosomes complete condensation
• Anaphase
  • Sister chromatids separate and move along spindles using kinetochore motor, some spindles push each other and some pull chromosomes
• Telophase
  • Spindle disassembles, nucleolus and nuclear envelope reappear

Cytokinesis

• Cleavage furrow
  • Layer of microtubules stretches across spindle midpoint
  • A band of microfilaments (actin) forms in plasma membrane and tightens to squeeze off cell into two
• Cell Plate
  • Layer of microtubules in the middle is covered in vesicles across the entire cell
  • Vesicles fuse together to make a new cell wall splitting the cell in half

Structure of a replication bubble

• Origin of replication is in the middle
• Replication fork unzips from this point in opposite directions
• Leading strand (one RNA primer extended) and lagging strand (multiple RNA primers added in Okazaki fragments) for each side of the bubble
• Linear chromosomes have many simultaneous bubbles, circular chromosomes have only one at a time

Relationship between DNA replication and metaphase chromosome structure

• DNA has been replicated in Interphase and stays together as two sister chromatids up until Metaphase
• Each chromosome in Metaphase contains two double helixes (extremely condensed and attached at a centromere)

Difference between DNA damage and mutation

• Damage is a single-stranded change in the DNA
• Mutations are any double-stranded change in the DNA sequence
• Mutations may arise from initial damage and can be good or bad, but are necessary for evolution

Origin of various types of genomic variation

• SNP's (Single Nucleotide Polymorphisms)
  • Caused by replication errors and tautomeric shifts
• CNV's (Copy Number Variations)
  • Caused by uneven crossing over
• In/Del
  • Caused by "slippage" when many of the same nitrogen base are next to each other in a sequence
• Duplication, Inversion, Translocation, and Large Deletions
  • May occur due to ionizing radiation that creates reactive O2 that steal electrons and break chromosomes
  • Non-homologous end joining pastes the end back together and is highly mutagenic
• Mobile elements
  • Insertion sequences, transposons, retrotransposons, and retroviruses exist and move throughout the genome
  • Cut and paste or copy and paste mechanisms without the enzyme transposase
  • Increase genetic variability

Main differences between meiosis and mitosis

• Mitosis
  • Somatic cells
  • One cell division
  • Creates two identical diploid daughter cells
  • No crossing over/recombination
• Meiosis
  • Gametes
  • Two cell divisions
  • Creates four genetically different daughter cells
  • Crossing over occurs in prophase I
  • Homologous pairs are separated in the first anaphase and chromatids are separated in the second anaphase

Products of meiosis in animals vs. plants, fungi, and algae

• Animals
  • Meiosis makes haploid gametes, which fuse together at fertilization and grow into diploid organisms through mitosis
• Plants
  • Diploid sporophytes make haploid spores using meiosis
  • Spores divide by mitosis to create gametophytes, which make gametes by mitosis
  • Gametes fuse together at fertilization to make a diploid zygote, which undergoes mitosis to return to the sporophyte stage
• Fungi and algae
  • Diploid zygotes create haploid spores by meiosis
  • Spores divide by mitosis to make a gametophyte, which makes gametes by mitosis
  • Gametes fuse together at fertilization to return to a diploid zygote

Characteristics of homologous chromosomes

• Carry the same genes
• Centromeres are in the same place
• Carry the same genes in the same place
• Different distribution of SNP's and different types of alleles
• Inherited from different parents

Mechanism by which recombination creates new combinations of alleles

• Recombination occurs when homologous pairs line up one on top of the other and switch out pieces of their chromosomes at a chiasmata
• Cutting all four backbones and pasting them to the other chromosome

Various mechanisms by which meiosis generates variation

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• Recombination:
  • Crossing over of the tetrads at the chiasmata creates new combinations of alleles during Prophase I.
• Random Segregation:
  • Homologous pairs separate at Anaphase I, creating random combinations of maternal and paternal alleles.
  • Sister chromatids also separate randomly during Anaphase II.
• Random joining of male and female gametes.
• Segregation of various alleles during meiosis in monohybrid, dihybrid, and sex-linked situations.
• Random Segregation:
  • Alleles segregate randomly into different haploid gametes.
• Independent Assortment:
  • Applies to dihybrid crosses.
  • Different traits combine with each other randomly to produce combinations.
• Sex-linked traits:
  • Linked to the X or Y chromosome.
  • Distributed differently based on offspring sex.
  • Males who inherit one X with the trait are called homozygous and express the trait.
  • Females must inherit two recessive or one dominant allele on an X to express the trait.
• Other non-Mendelian inheritance patterns:
  • Incomplete dominance, Codominance, Epistasis, Polygenic inheritance, Pleiotropy, inactivation of one X chromosome, etc.

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• Conditions under which allele frequencies in a population will not change.
• If a population is in Hardy-Weinberg equilibrium:
  • Allele frequencies in a population will not change.
• Heterozygous advantage:
  • Allele frequencies have already leveled out.
• Assortative mating:
  • Allele frequencies have already leveled out.
• Hardy-Weinberg equilibrium assumptions:
  • No mutations occurring.
  • Population is closed to migration.
  • Infinite population size.
  • All genotypes are equally fit.
  • Random mating for the trait being considered.

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• How the dominance status of alleles affects their response to selection.
• Selection against dominance:
  • Dominant allele disappears entirely.
• Selection against recessive:
  • Recessive allele decreases in frequency but never completely disappears.
  • It stays hidden in the heterozygotes.
• Heterozygote advantage:
  • Allele frequencies stabilize at 0.5, maintaining both alleles in the population.
  • Rare alleles will increase in frequency until they are no longer rare.
• Homozygote advantage:
  • Rare alleles completely disappear.
  • Common allele goes to fixation.
  • Rare alleles are found mostly in heterozygotes, whereas common alleles are found mostly in homozygotes.

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• Relationship between selection and evolution.
• Selection without evolution:
  • Occurs in heterozygote advantage after allele frequencies level out.
• Evolution without selection:
  • Attributed to genetic drift and random mutations.
• Calculate relative fitness from absolute fitness:
  • Absolute fitness is the average number of surviving offspring.
  • Relative fitness is calculated by dividing the absolute fitness of the genotype in question by the absolute fitness of the most successful genotype.
  • Relative fitness should be between 0 and 1.

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• How different types of selection and other evolutionary processes affect levels of heritable variation in a population.
• Increases variation:
  • Gene flow, mutations.
• Decreases variation:
  • Heterozygote disadvantage, genetic drift, selection against dominant and recessive alleles, assortative mating.
• Maintains variation:
  • Heterozygote advantage, disassortative mating.
• Whether or not a population is at genetic equilibrium (Hardy-Weinberg equilibrium), given observed genotype frequencies.
• Calculate allele frequencies:
  • (# of homozygotes x 2 + # of heterozygotes) / number of organisms x 2.
  • The other allele frequency is 1 minus the calculated allele frequencies.
  • Plug the calculated allele frequencies into p^2, 2pq, and q^2.
  • If they create the same ratio of offspring, the population is in equilibrium.

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• Which assumptions of Hardy-Weinberg equilibrium have likely been violated, given an observed set of genotype or phenotype frequencies.
• If lots of homozygotes, there was likely assortative mating.
• Costs and benefits of reproducing sexually as opposed to asexually.
• Cost of sexually reproducing:
  • Need to find a mate (could be dangerous).
  • Intrasexual selection causes males to decrease their survival fitness.
  • Males waste energy on sexual dimorphic traits.
  • Only pass on 0.5 of your alleles.
• Cost of asexually reproducing:
  • More at risk for extinction.
  • Don't get the short-term benefits of sexual reproduction (genetic variability).
  • Fall behind in evolutionary arms race.

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• Why males usually compete for access to females (rather than vice versa), and why in some species this pattern is reversed.
• Who is choosy and who competes depends on parental investment and potential fitness.
• In most species, females have higher parental investment and lower potential fitness than males.
• Females increase their potential fitness through quality offspring, while males increase their fitness through quantity of offspring.
• Kin selection theory explains the persistence of helpful behavior.
• Kin selection theory:
  • We help others that are related to us.
  • Our alleles continue to be passed on and our inclusive fitness increases.
• Situations in which kin selection does or does not favor helping non-descendant relatives.
• According to Hamilton's rule, kin selection favors helping non-descendant relatives when their relatedness to you multiplied by the benefit to them is greater than the cost to you (rb > c).
• How asymmetries in relatedness can generate conflict between relatives.
• Differences in opinion arise on when you should offer help based on the relatedness of other family members to the person in need.
• Conditions that favor or disfavor cooperation between non-relatives.
• Repeat interactions and the ability to recognize individuals who cooperate or cheated in the past favor cooperation.
• One-time interactions or knowing the number of interactions favor selfishness.
• Most recent common ancestor (MRCA) for a given group(s), given a phylogenetic tree.
• The closest branching point shared between two groups is the MRCA.
• Why some traditional groupings of organisms do not reflect evolutionary relationships.
• Traditional groupings were made using morphological similarities without considering evolutionary history.
• Relatively close and relatively distant relatives, given a phylogenetic tree.
• Relatedness on a phylogenetic tree is determined by looking at the most recent common ancestor.

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• Monophyletic and non-monophyletic groupings in phylogenetic trees
  • Monophyletic groups (clades) include the MRCA and all descendants
  • Non-monophyletic groups include species from different lineages (polyphyletic) or include the ancestor but not all descendants (paraphyletic)
• Parsimony in phylogenetic trees
  • The most parsimonious phylogeny has the least number of evolutionary changes
  • Considered correct until falsified
• Distinction between homology and homoplasy
  • Homology: similarities due to common ancestry
  • Homoplasy: misleading similarity or dissimilarity due to convergent or divergent evolution
• Determining the most likely phylogenetic tree
  • Look for synapomorphies (derived and shared traits)
  • Order species based on similarities to the out-group and to each other
• Criteria used by different species concepts to define species
  • Morphological: based on physical appearance
  • Biological: based on ability to interbreed and produce fertile offspring
  • Phylogenetic: based on shared derived characteristics and evolutionary trees
• Weaknesses/limitations of different species concepts
  • Morphological: not reliable alone, variation within species and convergent evolution
  • Biological: not applicable to asexual or extinct organisms, geographic separation
  • Phylogenetic: limited by unknown evolutionary history, may rely on morphological features

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• Species concept used in 'real world' examples
  • Morphological species concept used in field guides and for fossilized species
• Why improving equipment for survival does not always lead to winning an evolutionary arms race
  • As one species evolves, the other species evolves in response
  • Improvement is necessary for survival, but not necessarily for surpassing the other species
• Costs and benefits of being highly virulent for parasites
  • Cost: host dies sooner, unfavorable for transmission in low population density or direct contact
  • Benefit: quicker reproduction using host machinery, enhanced transmission in dense populations or indirect contact
• How trade-offs, rapid environmental change, and arms races affect human susceptibility to disease
  • Arms race with parasites: parasites evolve quickly due to large population size and short generation times
  • Rapid environmental change: diseases of civilization, decrease in infectious diseases but increase in autoimmune disorders
  • Antagonistic pleiotropy: trade-offs between different aspects of fitness, harmful alleles kept through heterozygous advantage

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• Examples of proximate and ultimate explanations
  • Proximate explanation: physical and biochemical mechanisms underlying a trait
  • Ultimate explanation: role of natural selection, arms races, history, and chance in creating or continuing a trait
• Costs and possible advantages of large brains
  • Cost: 2% of mass, 20% of energy
  • Possible advantages: utility hypothesis (survival-related skills) favored by natural selection, mating mind hypothesis (mating-related skills) favored by sexual selection

Skill Development Outcomes:

1. Deep Learning

• Making connections, understanding, and applying knowledge
• Excludes memorization

1. Serial Dilutions

• Calculation of CFU/mL using dilution factor and volume of culture plate
• Dilution factor calculated by dividing final volume by sample volume and multiplying by the denominator of serial dilution fractions

1. Role of cyclin in the cell cycle

• Cyclin regulates the rate of cell division and is important in cell cycle checkpoints

1. Microscope calibration

• Formula for measuring objects using stage divisions and ocular divisions
• Calculation of magnification using ocular lens and objective lens

1. Chi squared statistical analysis

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• Null Hypothesis and Alternate Hypothesis
  • Null Hypothesis states no effect/correlation/will be no change
  • Alternate Hypothesis states there is an effect/correlation/will be a change
• Chi squared analysis
  • Determines if data is significant enough to support the alternate hypothesis
  • Compares observed values (collected in the study) with expected values (calculated based on null hypothesis)
  • Calculation: x^2 = sum of ((O-E)^2/E)
• Degrees of freedom and critical value
  • Critical value is compared to chi-square value for statistical significance
  • Can be found on a chart or provided
• Primary vs secondary scientific articles
  • Primary articles: original data and ideas from scientific investigations reported by scientists
  • Published in journals and contain sections like Abstract, Introduction, Methods, Results, Discussion, References
  • Secondary articles: review and analyze primary sources in more depth

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• FST Population Genetics
  • FST = 1 - (average heterozygosity expected within populations / heterozygosity expected across total population)
  • HS = (2p1q1 + 2p2q2)/2
  • HT = 2pTqT
  • Use Hardy-Weinberg to calculate p and q values for individual populations, then add population numbers together and recalculate for the total
  • Interpretation of FST values:
    • FST = 0: no disturbance
    • FST > 0.25: significant disturbance
    • FST = 1: complete separation of populations

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• Allozyme Electrophoresis for genetic variability calculation
  • Takes advantage of the fact that organisms produce allelic variants of enzymes called allozymes
  • Each allozyme has a slightly different amino acid sequence and is the product of a unique allele
  • Genotype at a gene locus coding for an enzyme can be inferred from the number and position of spots observed on gels
  • Genetic variation in a population is the average frequency of heterozygous individuals per locus
  • Calculated by determining the frequency of heterozygotes at each locus and averaging these frequencies over all loci

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• Creating phylogenetic trees using DNA sequencing
  • Phylogenies can be estimated by looking at differences in DNA sequence
  • Species with the most differences is the out-group
  • If no differences, it is the same species and should be drawn on the same vertical line
  • Length of horizontal lines may indicate the