biology 2

What is Biology?

• Biology is the science of how life works.
• We understand life from multiple levels:
  • Molecular mechanisms within the cell
  • Integrated actions of cells within an organ or individual
  • Interactions among different organisms in nature
• Reference: Ch. 1.1

The Scientific Approach in Biology

• There is no single, stepwise pathway to new knowledge about the world.
• To understand biology, we need to understand what science is (Ch. 1.1).
• Observations lead to questions, which lead to hypotheses.
• Hypothesis: a tentative explanation or educated guess that makes testable predictions (Ch. 1.1).
• Predictions from predictions can be tested through experiments.
• Design and conduct experiments to test hypotheses.
• Based on results, we can support or not support a hypothesis; we cannot prove it correct/incorrect.

Hypothesis vs Theory

• A hypothesis is a testable tentative explanation (correct option: B).
• In everyday language, "theory" is often used like a guess, but in science:
  • A theory is supported by many hypotheses that have withstood testing and come from a large body of evidence.
  • A theory explains a broad array of natural phenomena and can generate many hypotheses.
  • A good theory also generates predictions that can be tested.
• Examples of theories (Ch. 1.1):
  • Theory of evolution by natural selection
  • Cell theory
  • Atomic theory
  • Big Bang theory
  • Theory of Quantum Mechanics
  • Theory of Relativity
  • Theory of Plate Tectonics

Evolution: Pattern and Process

• Biological systems are dynamic and change over time.
  • Changes can occur within individuals over their lifetimes or in populations over generations.
• Evolution = descent with modification: organisms descend from others, and over generations accumulate unique traits.
• Understanding evolution requires genetics and phenotype concepts (Ch. 1.4, 20.3).
• Important distinction:
  • The pattern of evolution is observable (not a theory).
  • The process that explains the pattern is a theory (e.g., natural selection as mechanism).
• Reference: Evolution by natural selection is a theory for the mechanism driving evolutionary patterns.

Genes, Alleles, Genotypes, and Phenotypes

• Genes are the units of heredity; they exist as DNA sequences and code for traits (phenotypes).
• Alleles are genetic variants resulting from differences in DNA sequence.
• In diploid organisms, we have more than one allele per gene; all alleles for a phenotype constitute an individual’s genotype.
• Genotype: the specific alleles present in an individual for a given gene.
• Phenotype: the expressed trait resulting from the genotype and environmental influence.

Key Genetic Concepts (Review Questions)

• Genes: choose all that apply
  • A) Are only found in gametes — False
  • B) Can be passed down from parents to offspring — True
  • C) Are comprised of DNA sequences — True
  • D) Always produce identical proteins — False
  • E) Always found in a particular location on a chromosome — Generally True (locus is defined)
  • Correct: B, C, E
• Alleles: choose all that apply
  • A) Are variants of a gene — True
  • B) Can be passed down from parents to offspring — True
  • C) Are comprised of DNA sequences — True
  • D) Always produce identical proteins — False
  • E) Always found in a particular location on a chromosome — True
  • Correct: A, B, C, E
• A genotype is…
  • A) all the alleles in a population — False (gene pool)
  • B) all the genes of a chromosome — False
  • C) An individual’s set of alleles — True
  • D) An individual’s trait — False
  • E) The entire genome — False
  • Correct: C
• A phenotype is…
  • A) all the alleles in a population — False
  • B) influenced by the environment and DNA — True
  • C) An individual’s set of alleles — False
  • D) An individual’s trait — True
  • E) The entire genome — False
  • Correct: B, D

DNA, Alleles, and Variation

• All organisms possess DNA, which stores and transmits information.
• DNA stores genetic material; some DNA segments code for phenotypes (genes).
• Alleles are variant forms of a gene.
• Expression of genes is regulated and influenced by the environment.
• References: Ch. 1.3; Ch. 13.1; Ch. 1.3 (BIOL1107)

Alleles and Genotypes: Examples

• Alleles: genetic variants from DNA sequence differences.
• In diploids, two alleles per gene (for a given phenotype) can be present; all alleles for a phenotype form the genotype.
• Dominant vs Recessive examples (conceptual):
  • Dominant allele (B) masks recessive (b) in phenotype when present in at least one copy.
  • Genotypes: BB (homozygous dominant), Bb (heterozygous), bb (homozygous recessive).
• Example: Purple (dominant) vs White (recessive) flower trait.

Beta Hemoglobin and Sickle Cell Example

• S allele (sickle cell) and A allele (wild-type) on chromosome 11 (beta hemoglobin gene).
• Genotypes: AA (wild-type, no sickling), AS (sickle cell trait), SS (sickle cell disease).
• Phenotypes: AA = normal; AS = trait; SS = disease.
• Reference: Ch. 13.1; Ch. 20.4

Mutation and Recombination: Sources of Variation

• Mutation: changes to the DNA sequence; ultimate source of new alleles.
• Mutations are inherited only if they occur in reproductive cells.
• Recombinations during meiosis shuffle DNA sequences, creating new allele combinations.
• Independent assortment of chromosomes leads to genetically unique gametes.
• Combined, genetic variation arises from mutations and recombination.
• References: Ch. 13.1; Ch. 14.1; Ch. 20.1; Ch. 14.1; Fig. 14.2; Ch. 20.1
• The S allele in the beta hemoglobin gene originated via mutation (not present from the start of the population).

Gene Pools and Population Genetics

• A gene pool is all the alleles present across all individuals in a population.
• To understand molecular evolution, consider allele frequencies and genotype frequencies within a population, and how these change over generations.
• Allele frequencies can increase, decrease, or stay the same depending on phenotype effects, environment, and chance.
• Novel alleles can be harmful, beneficial, or neutral to survival and reproductive success.
• References: Ch. 20.1

Population-Level Sickle Cell Example: Calculations

• Population of 1000 people with:
  • AA = 890
  • AS = 100
  • SS = 10
• Allele frequencies in this population:
  • S allele frequency: $f(S) = \frac{2\cdot N<em>{SS} + N</em>{AS}}{2N} = \frac{2\cdot 10 + 100}{2\cdot 1000} = \frac{120}{2000} = 0.06$
  • A allele frequency: $f(A) = 1 - f(S) = 0.94$
• Genotype frequencies:
  • $f(AA) = \frac{890}{1000} = 0.890$
  • $f(AS) = \frac{100}{1000} = 0.100$
  • $f(SS) = \frac{10}{1000} = 0.010$
• Alleles in the population:
  • Total alleles = $2N = 2\cdot 1000 = 2000$
• Practice question: If population becomes 2000 with 1580 AA, 350 AS, 70 SS:
  • S allele count = $2\cdot N<em>{SS} + N</em>{AS} = 2\cdot 70 + 350 = 490$
  • Total alleles = $2\cdot 2000 = 4000$
  • Allele frequency for S: $f(S) = \frac{490}{4000} = 0.1225$
  • Allele frequency for A: $f(A) = 1 - f(S) = 0.8775$
  • Genotype frequencies: $f(AA) = \frac{1580}{2000} = 0.79\;, \; f(AS) = \frac{350}{2000} = 0.175\;, \; f(SS) = \frac{70}{2000} = 0.035$
• Practice questions also show how to compute genotype frequencies from allele frequencies using Hardy-Weinberg expectations (see below).

Hardy–Weinberg Equilibrium (HWE)

• HWE describes a non-evolving population for a single gene with two alleles, with random mating in a diploid species.
• Null hypothesis for evolutionary change: a population is not evolving with respect to the studied gene.
• Conditions for HWE (Ch. 20.3):
  • 1) No selection: no differences in survival and reproduction among genotypes.
  • 2) No mutations: the gene is not mutating.
  • 3) No migration: population size is unaffected by movement of individuals.
  • 4) Large population: no genetic drift (sampling errors are negligible).
  • 5) Random mating: individuals pair by chance.
• If these conditions hold, genotype frequencies follow: $p^2, 2pq, q^2$ where $p = f(A)$ and $q = f(a)$, with $p + q = 1$.
• The beta hemoglobin example (S vs A) does not meet HWE, so the population evolves with respect to this trait.
• Practical use: Deviations from HWE serve as a baseline to explore evolutionary mechanisms.

Evolutionary Implications: Selection and Maintenance of Alleles

• If a harmful allele reduces survival to adulthood, its frequency is expected to decline over generations (Ch. 13.1, Ch. 20.3-20.4).
• Why is a harmful allele like S still present in some populations?
  • Possible explanations include heterozygote advantage (sickle cell trait provides malaria resistance in some environments; AS individuals have a survival advantage in malaria-endemic regions).
  • Other forces include mutation, migration, genetic drift, and balancing selection.

Calculating Allele Frequencies: Classic Examples

• Example 1: Mendel’s pea colors (AA yellow, Aa yellow, aa green). If every plant is green (phenotype aa), what are allele frequencies?

  • If all are aa, then f(a) = 1, f(A) = 0.
  • General approach: use counts to compute allele totals and divide by twice the number of individuals.

• Example 2: Population with genotype frequencies: 50% aa, 25% Aa, 25% AA in a population of 100 individuals.

  • Allele frequency for a:$f(a) = \frac{2\cdot f(aa) + f(Aa)}{2} = \frac{2\cdot 0.50 + 0.25}{2} = \frac{1.25}{2} = 0.625$
  • Allele frequency for A: $f(A) = 1 - f(a) = 0.375$

Measuring Genotype/Allele Frequencies: DNA Sequencing Example

• DNA sequencing can detect all genetic variation in a gene.
• Example: For a gene position in 50 diploid individuals, if 70 alleles are A and 30 alleles are G at a position:
  • Allele frequency for A: $f(A) = \frac{70}{100} = 0.70$
  • Allele frequency for G: $f(G) = \frac{30}{100} = 0.30$
• Note: Protein-level analyses may miss silent mutations; sequencing reveals DNA-level variation.

Practical Takeaways for Exam Preparation

• Distinguish between pattern (observable) versus process (theory-driven mechanism) in evolution.
• Be able to define and apply the following terms: gene, allele, genotype, phenotype, mutation, recombination, gene pool, allele frequency, genotype frequency.
• Be able to compute allele frequencies from genotype counts using the formula: $f(A) = \frac{2N<em>{AA} + N</em>{Aa}}{2N}$ and to compute genotype frequencies from counts: $f(AA) = \frac{N<em>{AA}}{N}, \; f(Aa) = \frac{N</em>{Aa}}{N}, \; f(aa) = \frac{N_{aa}}{N}$.
• Understand Hardy–Weinberg principles, including the conditions and the expected genotype frequencies $p^2, 2pq, q^2$ with $p+q=1$.
• Practice with real numbers from the transcript (beta hemoglobin example, pea example, and the sequencing example) to solidify intuition.

Homework and Assessments (Overview)

• Due: 29th Aug at 12 pm
• Tasks:
  • Who are you? (Discussion)
  • Syllabus quiz
  • Time management activity
  • Intro survey (check Assessment document for point breakdown and policies)
• Grade distribution (illustrative):
  • Introductory activities: 5–10 points
  • Intro post, Surveys, Time management: variable points totaling 30
  • Individual activities and quizzes: ~130–400 points
  • In-class U1–U4 activities: 20 points each
  • Graded writing (GR writing 1 & 2): 25 points each
  • Unit exams and Final: ~100 + 200 points
  • Total possible points: 1000