Chapter 2: Reproduction Types

• Chapter 2

Sexual vs. Asexual Reproduction

• Sexual Reproduction involves the fusion of gametes from two parents
• Benefits include genetic diversity and adaptability
• Drawbacks include energy-intensive and slower processes
• Asexual Reproduction produces clones from a single parent
• Benefits include speed and efficiency
• Drawbacks include lack of genetic diversity, making populations vulnerable to environmental changes

Binary Fission vs. Mitosis

• Binary Fission is found in prokaryotes, and involves simple division like in bacteria with a single circular chromosome without a nucleus
• Mitosis occurs in eukaryotic cells with multiple linear chromosomes in a nucleus, ensuring chromosomal alignment and segregation
• Key Difference: Eukaryotes require spindle formation due to chromosomal complexity and process organization, while prokaryotes do not

Sister Chromatids vs. Homologous Chromosomes

• Sister Chromatids are identical copies of a single chromosome connected at the centromere, formed during DNA replication
• Homologous Chromosomes are pairs of chromosomes, one from each parent, that have the same genes but potentially different alleles

Steps of the Eukaryotic Cell Cycle

• The cell cycle includes Interphase, Mitosis and Cytokinesis
• Interphase includes the G1 phase (cell growth), S phase (DNA replication), and G2 phase (preparation for division)
• Mitosis includes Prophase, Metaphase, Anaphase, and Telophase
• Cytokinesis is division of the cytoplasm

Mitosis vs. Meiosis

• Mitosis is a single division that produces two genetically identical diploid cells, for growth/repair
• Meiosis includes two rounds of division that yield four genetically diverse haploid gametes for sexual reproduction

Crossing Over (Holliday & Double Strand Break Models)

• The Holliday Model proposes homologous recombination initiated by single-strand nicks
• The Double Strand Break Model initiates recombination through double-strand breaks, providing greater accuracy in gene exchange

Genetic Variation in Meiosis

• Crossing Over involves the exchange of genetic material between homologous chromosomes
• Independent Assortment is the random alignment of chromosomes during metaphase I
• Random Fertilization adds further variability post-meiosis

Spermatogenesis vs. Oogenesis

• Spermatogenesis is the continuous production of sperm, yielding four sperm per meiosis

• Oogenesis produces one mature ovum and polar bodies, starting prenatally and completing upon fertilization

• Similarity: Both involve meiosis and gamete formation

• Difference: Timing and cytoplasmic division

• Chapter 3

Characteristics of Mendel's Experiments

• Ideal Traits: Studied traits with clear, contrasting forms (e.g., tall vs. short plants)
• Used pea plants, had short life cycles, and could self-pollinate or cross-pollinate
• Collected large sample sizes, ensuring statistically meaningful results
• Followed traits across multiple generations for detailed patterns
• Why: These traits allowed Mendel to identify patterns of inheritance, such as dominant and recessive behaviors, that were predictable and reproducible

Mendel's Laws (Simplified)

• The Law of Dominance states that in a heterozygous pair, the dominant allele masks the effect of the recessive one
• The Law of Segregation states that during gamete formation, alleles for a gene separate, so each gamete carries only one allele
• The Law of Independent Assortment states that genes for different traits assort independently if they are on different chromosomes

Biological Processes Behind Segregation & Independent Assortment

• Segregation happens during anaphase I of meiosis, where homologous chromosomes are pulled apart
• Independent Assortment occurs during metaphase I of meiosis, when homologous chromosome pairs align randomly along the equatorial plate

Punnett Square

• Definition: A grid used to predict the genotype and phenotype ratios of offspring in genetic crosses
• Use: Helps visualize how alleles combine from parents
• Reveals: Probabilities for inheritance patterns, such as monohybrid and dihybrid crosses

Product Rule

• Definition: The probability of two independent events occurring together is the product of their individual probabilities
• Use: Helps calculate the likelihood of inheriting combinations of traits in multifactor crosses

Solving Inheritance Problems

• Practice predicting outcomes for monohybrid crosses (one trait), dihybrid crosses (two traits), and trihybrid crosses (three traits)
• Example: Apply the Product Rule to simplify complex probabilities

Pedigree Symbols

• Squares represent males
• Circles represent females
• Shaded shapes indicates individuals expressing the trait
• Half-shaded shapes indicate carriers of a trait (if applicable)
• Lines: Horizontal indicates mating, vertical indicates offspring

Predicting Inheritance with Pedigrees

• Use: Analyze family history to determine the mode of inheritance (e.g., autosomal dominant, autosomal recessive, X-linked)
• Helps Predict carrier status and risk of passing traits to offspring

Chi-Squared Analysis

• Goal: Tests if observed genetic data align with expected inheritance patterns

• Steps:

  • Calculate expected ratios based on Mendelian principles

• Use the formula: $$\chi^2 = \sum \frac{(O - E)^2}{E}$$ (O = observed, E = expected)

• Compare the result to a critical value in a chi-squared distribution table

• Chapter 5

Inheritance Pattern

• Simple Mendelian inheritance is where traits follow Mendel's laws of dominance, segregation, and independent assortment

  • The possible cause is single-gene traits with dominant/recessive alleles
  • The effects on Mendel's Ratios includes consistent 3:1 (phenotype) and 1:2:1 (genotype) ratios

• Incomplete penetrance is where not all individuals with a genotype express the phenotype

  • Possible causes include modifier genes, environment, or stochastic effects
  • Effects on Mendel's Ratios reduces phenotypic ratios and some carriers appear unaffected

• Variable expressivity is variation in the degree or intensity of phenotype among individuals

  • Possible causes include genetic background, epigenetics, or environment
  • Effects on Mendel's ratios shows ratios may remain Mendelian but phenotype intensities vary

• Incomplete dominance is were heterozygotes exhibit an intermediate phenotype between the two homozygotes

  • The possible cause is intermediate allele expression
  • The effect on Mendel's ratios alters ratios to 1:2:1 for both genotype and phenotype

• Overdominance is where heterozygotes have a phenotype that is more favorable or distinct than either homozygote

  • Possible causes include heterozygote advantage in certain environments
  • The effect on Mendel's ratios can distort observed fitness advantages but ratios hold

• Codominance is where both alleles in a heterozygote are fully expressed simultaneously

  • The possible cause is equally dominant alleles
  • The effect on Mendel's ratios is the phenotypic ratio matches the genotype ratio (1:2:1)

• Sex-influenced inheritance is where expression differs between sexes due to hormonal or physiological differences

  • The possible cause is the influence of sex hormones on allele expression
  • The effect on Mendel's ratios alters phenotypic ratios depending on the sex of offspring

• Sex-limited inheritance is where trait expression is restricted to one sex, even though both sexes carry the genes

  • The possible cause is hormonal differences or sex-specific regulatory pathways
  • The effect on Mendel's ratios alters phenotypic ratios based on sex (e.g., traits expressed only in males or females)

• Sex-linked inheritance is where traits are associated with genes located on the sex chromosomes (X or Y)

  • The possible cause is X or Y-linked gene mutations
  • The effect on Mendel's ratios deviates from Mendelian ratios, with patterns differing between males and females (e.g., X-linked recessive traits)

• Lethal alleles are where alleles that result in death when present in a specific genotype

  • The possible cause is essential gene mutations or dominant/recessive effects
  • The effect on Mendel's ratios alters ratios by removing certain genotypes entirely (e.g., 2:1 instead of 3:1 when homozygous lethal alleles are involved)

• Pleiotropy is where one gene influences multiple, seemingly unrelated traits

  • The possible cause is a single gene impacts different biological pathways
  • The effect on Mendel's does not directly alter Mendelian ratios but complicates interpretation due to multiple trait effects

• Epistasis is the interaction between genes where one gene masks or modifies the effect of another

  • The possible cause is gene interaction affecting trait expression
  • The effect on Mendel's ratios distorts expected ratios, such as 9:3:3:1 in dihybrid crosses altering to 9:7 or 12:3:1

• Complementation is where two defective genes from different loci combine to produce a normal phenotype

  • The possible cause is interaction between genes at separate loci
  • The effect on Mendel's ratios restores a wild-type phenotype, masking the expected mutant ratios

• Gene redundancy is where multiple genes perform the same function, so loss of one does not affect the phenotype

  • The possible cause is backup functional genes
  • The effect on Mendel's ratios obscures expected phenotypic ratios due to compensatory genetic functions

• Chapter 4

Genetic Methods of Sex Determination

• XY System is found in mammals, with males as XY (heterogametic) and females as XX (homogametic)
• XO System is found in some insects (e.g., grasshoppers), with females as XX and males having a single X (XO)
• ZW System is found in birds and some reptiles, with females as ZW (heterogametic) and males as ZZ (homogametic)
• Haplodiploidy is found in bees and ants, where females develop from fertilized (diploid) eggs and males develop from unfertilized (haploid) eggs
• Environmental Determination is where some reptiles (e.g., turtles) determine sex based on environmental cues, like temperature during development

Comparing XY, XO, and ZW Systems

• Differences:
  • XY: Males are heterogametic (XY), females homogametic (XX)
  • XO: Males have a single sex chromosome (XO), while females have two (XX)
  • ZW: Females are heterogametic (ZW), males homogametic (ZZ)
• Similarities: All involve chromosomal differences that determine sex and rely on specific gene activation for sexual development

Dosage Compensation

• Definition: A mechanism ensuring equal expression of X-linked genes between males (one X) and females (two Xs)
• Necessity: Prevents imbalances in gene expression that could disrupt cellular and developmental processes

X-Inactivation in Humans

• Process: One of the two X chromosomes in female cells is randomly inactivated during early embryonic development, forming a compact structure called a Barr body
• Complication for X-Linked Inheritance: Heterozygous females may have a mosaic expression of X-linked traits, due to random inactivation

Dosage Compensation in Humans, Flies, and Nematodes

• Humans: X-inactivation equalizes X-linked gene expression between sexes
• Flies (Drosophila): Male X chromosome expression is doubled to match females' two X chromosomes
• Nematodes (C. elegans): Both X chromosomes in hermaphrodites are partially downregulated

Patterns of X-Linked, Y-Linked, and Pseudoautosomal Inheritance

• X-Linked:
  • Traits are carried on the X chromosome
  • Males are hemizygous (have only one X), so traits manifest if they inherit the allele
  • Females can be carriers or express the trait if homozygous
• Y-Linked:
  • Traits are passed strictly from father to son since only males inherit the Y chromosome
  • Rare due to the small number of genes on the Y chromosome
• Pseudoautosomal:
  • Regions on X and Y chromosomes where recombination occurs during meiosis
  • Inheritance patterns mimic autosomal traits
• Why Differences Exist: X and Y chromosomes have distinct roles in sex determination, while pseudoautosomal regions are shared to maintain pairing during meiosis

Predicting X-Linked Inheritance

• Define steps for solving problems

• Chapter 7

Syntenic vs. Linked Genes

• Syntenic genes are located on the same chromosome
• Linked genes are syntenic genes that is Inherited together more often than expected by independent assortment
• The key difference is that while all linked genes are syntenic, not all syntenic genes are linked. Syntenic genes can assort independently if they are far apart on the chromosome, due to frequent crossing over

Why Are All Syntenic Genes Not Linked?

• Reason: Crossing over during meiosis can separate syntenic genes located far apart on a chromosome
• Independent Assortment: Genes behave as if they are on different chromosomes, when crossing over occurs frequently

Determining Gene Linkage

• Method: Perform a test cross and examine the offspring ratios
• Explanation: Offspring phenotypes deviate significantly from expected Mendelian ratios indicates linkage and a chi-squared test can confirm statistical significance

Recombinant vs. Nonrecombinant Phenotypes

• Recombinant Phenotypes: Traits in offspring resulting from crossing over between homologous chromosomes (new allele combinations)
• Nonrecombinant Phenotypes: Traits that are identical to those in the parental generation

Two Ways Recombinant Phenotypes Occur

• Crossing Over: Exchange of genetic material between homologous chromosomes during prophase I of meiosis
• Independent Assortment: Occurs when genes are on different chromosomes or far apart on the same chromosome

How Are Linkage Maps Constructed?

• Steps:
  • Calculate recombination frequencies between pairs of genes, using experimental cross data
  • Convert recombination frequencies into map units (1% recombination = 1 map unit or centimorgan)
  • Arrange genes in order based on calculated distances to build the map
• Principle: The farther apart two genes are, the higher the recombination frequency

Using Experimental Data to Determine Linkage

• Approach:
  • Analyze phenotypic ratios from genetic crosses
  • Compare observed data to expected independent assortment ratios
  • Perform a chi-squared analysis to test for significant deviations
  • If the observed recombination frequency is below 50%, genes are likely linked

Constructing a Linkage Map from Data

• Procedure:
  • Identify parental and recombinant phenotypes from experimental cross results
• Calculate recombination frequencies between gene pairs: $$ \text{Recombination Frequency} = \frac{\text{Number of Recombinants}}{\text{Total Offspring}} \times 100 $$
  • Use recombination frequencies to determine the relative distances between genes
  • Organize genes based on calculated distances to construct the map