Pedigree Analysis and Sex Linkage

Pedigree Analysis

• Pedigree analysis diagrams the inheritance of traits or health conditions through generations.
• Phenylketonurics (PKU) was an early application of pedigree analysis.
• Genes carry information passed from one generation to the next.
• An allele is a variant form of a gene and can be dominant or recessive.
• A genotype is the allele combination (e.g., Bb, BB, bb).
• A phenotype is the observable physical trait (e.g., purple, blue, white).
• The law of segregation states that two alleles for a heritable character separate during gamete formation and end up in different gametes, represented in a Punnett square with 4 boxes.
• The law of independent assortment states that a pair of factors segregates independently, with all possible combinations occurring, represented in a Punnett square with 16 boxes.

Sex Linkage

• Sex-linked traits are determined by genes located on sex chromosomes.
• Types of sex-linked traits include:
  • X-linked traits, where the trait is only shown on the X chromosome (e.g., X^bY).
  • Y-linked traits, located on the Y chromosome.
• Females have XX chromosomes, while males have XY chromosomes.
• Sex-influenced traits are influenced by an individual's biological sex and are more prevalent in one sex, often involving autosomal traits.
• Sex-limited traits are expressed in diploid organisms but limited to one biological sex.
• Beard development in males, barred coloring in chickens for roosters, and patterns of secondary hormonal development are examples of sex-limited traits.

Non-Mendelian Genetics

• Co-dominance occurs when two versions (alleles) of the same gene are separately and equally expressed to show different traits in an individual, with both traits being present.
• Incomplete dominance involves gene interaction where both alleles at a locus are partially expressed, resulting in an intermediate or different phenotype, creating a mixed outcome.
• Multiple alleles involve more than two types of alleles for a given locus/trait, leading to more than two kinds of phenotypes and more variants of phenotypes.
• Mendelian inheritance involves genes and their corresponding traits being passed from parents to offspring through dominant and recessive alleles, with complete dominance as an example.
• Non-Mendelian inheritance includes patterns where two alleles are neither dominant nor recessive, such as co-dominance, incomplete dominance, and multiple alleles.

Structure of DNA, RNA, and Proteins

• Biological molecules include lipids, nucleic acids, carbohydrates, and proteins.
• Polymers are long-chain molecules made of repeating monomer patterns.
• Two types of nucleic acids:
  • DNA (Deoxyribonucleic Acid):
    • Double-stranded.
    • Contains Deoxyribose sugar.
    • Its nucleotide bases are Adenine, Guanine, Cytosine, and Thymine (AGCT).
    • Stores RNA and encodes information.
  • RNA (Ribonucleic Acid):
    • Single-stranded.
    • Contains Ribose sugar.
    • Its nucleotide bases are Adenine, Guanine, Cytosine, and Uracil (AGCU).
    • Carries protein-encoding information, makes proteins, and catalyzes reactions.
• The nucleotide is the monomer of polynucleotides.
• Components of a nucleotide include a nitrogenous base, a pentose sugar, and a phosphate group.
• DNA consists of 2 strands of polynucleotides in a double helix with an antiparallel orientation.
• Two strands of DNA are linked together by hydrogen bonds (ACGT).
• Purine and pyrimidine pairing results in a uniformed diameter for the helical shape of DNA.
• Types of proteins:
  • Enzymatic: Catalyzes selective acceleration of chemical reactions.
  • Defensive: Provides protection against disease.
  • Storage: Stores amino acids.
  • Transport: Transports substances.
  • Hormonal: coordinates organism’s activities.
  • Receptor: Responds to chemical stimuli.
  • Contractile and Motor: Facilitates movement.
  • Structural: Provides support.
• Protein structure:
  • Primary structure: Sequence of amino acids.
  • Secondary structure: Folded and aligned into alpha-helix and beta-pleated sheets, with random coils in non-repeating patterns.
  • Tertiary structure: 3D arrangement of polypeptide, including the interactions between side chains.
  • Quaternary structure: Overall protein structure from aggregation of polypeptide subunits (e.g., hemoglobin).
• Amino acids are molecules with both an amino and carboxyl group.
• There are 20 amino acids, with 11 non-essential and 9 essential for humans.
• The central dogma is DNA → RNA → Protein.
• DNA genes can directly synthesize RNA (mRNA).
• RNA molecules aid in the synthesis of polypeptides, which then form proteins.

DNA Replication

• DNA replication is the process of creating identical copies of DNA molecules.
• Base-pairing is maintained during DNA replication.
• Semi-conservative replication involves one of the two old DNA strands being conserved and present in each daughter molecule.
• DNA synthesis always proceeds in the 5' to 3' direction.
• Semi-discontinuous replication:
  • The leading strand (baba/down) is synthesized continuously in the 5'-3' direction.
  • The lagging strand (taas/up) is produced discontinuously in short stretches called Okazaki fragments.
• Steps of DNA replication:
  1. Helicase separates the DNA strands.
  2. Single-strand binding proteins prevent unwound strands from rejoining.
  3. Topoisomerase untwists the double helix.
  4. Primase makes short stretches of RNA on the DNA template.
  5. DNA polymerase adds DNA nucleotides to the RNA primer.
  6. The leading strand synthesizes continuously in the 5'-3' direction.
  7. Discontinuous synthesis of the lagging strand produces Okazaki fragments.
  8. After the RNA primer is replaced with DNA nucleotides, ligase seals the sugar-phosphate backbone.

Protein Synthesis

• Three types of RNA are needed for protein synthesis:
  • mRNA (messenger): Carries information that specifies a protein.
  • rRNA (ribosomal): Forms the ribosome, where protein synthesis occurs.
  • tRNA (transfer): Carries amino acids to the ribosome.
• Transcription is the process where a gene's DNA sequence is copied and transcribed into an RNA molecule.
• Transcription occurs in the nucleus.
• Cytosine (C) pairs with Guanine (G), and Uracil (U) pairs with Adenine (A).
• Steps of transcription:
  1. Initiation: a. RNA polymerase binds to a promoter region of the DNA. b. DNA unwinds, exposing nucleotides so RNA polymerase can read and make a complementary sequence.
  2. Elongation: a. RNA polymerase adds RNA nucleotides in the 5' - 3' direction.
  3. Termination: a. RNA polymerase reaches a terminator gene, signaling the release of the new mRNA strand and the removal of the enzyme from the DNA template.
• Processing mRNA involves:
  1. Addition of a 5' cap to the beginning of the RNA.
  2. Addition of a poly-A tail to the end of the RNA.
  3. Chopping out introns (junk sequences) and pasting together remaining good sequences (exons).
• A codon is a triplet code.
• Each genetic word in mRNA is 3 bases long.
• Given DNA strands translate to complementary mRNA, which is then checked for the corresponding amino acid.
• Translation is the process where the genetic code in mRNA is read to make a protein, which occurs in the cytoplasm.
• Translation requires mRNA, rRNA, tRNA, amino acids, and enzymes.
• Three tRNA-binding sites on the ribosome:
  • A (aminoacyl) site: Binds the tRNA with the new amino acid to be added.
  • P (peptidyl) site: Holds the tRNA with the nascent polypeptide chain.
  • E (exit) site: Binds the deacetylated tRNA before its ejection from the ribosome.
• Steps of translation:
  1. Initiation: Attaches to mRNA.
  2. Elongation: Increases in length, one amino acid at a time.
  3. Termination: A stop codon appears in the A site, a protein complex (release factor) binds to the stop codon, and cleaves the polypeptide from last tRNA.

Genetic Engineering

• Selective breeding involves artificial selection to develop new organisms with desirable characteristics.
• Classic breeding involves interbreeding or crossing closely or distantly related individuals to produce new varieties or lines with desirable properties.
• Genetic engineering uses molecular techniques to modify the traits of a target organism.
• Biotechnology involves manipulating organisms or components to make useful products.
• Recombinant DNA technology is the technology involving molecules containing DNA from two different sources.
• A transgenic organism is an individual that receives recombinant DNA.
• How to make recombinant DNA (rDNA):
  1. Vector: A carrier molecule, often a plasmid.
  2. Cut plasmid: Use a restriction enzyme to cut the plasmid DNA.
  3. Seal foreign DNA: Seal a foreign piece of DNA into the plasmid using DNA ligase.
  4. Return plasmid: Return the plasmid into the bacterial cell.
  5. Bacterial cell reproduction: The bacterial cell reproduces, replicating the desirable gene (gene cloning).
  6. Isolate copies: Researchers isolate copies of the cloned gene from the bacteria.
• Heat shock treatment involves heating bacteria to 42 degrees and then rapidly cooling to 4 degrees, opening pore sizes for entry of plasmid DNA.
• Electroporation involves expanding membrane pores through electric shock for insertion of genes into mammalian cells.
• Gel electrophoresis is a technique used to separate DNA fragments according to size.
• Polymerase chain reaction (PCR) creates multiple copies of a DNA segment, and amplification of the expected product confirms the presence of a gene within samples.

Hardy-Weinberg Equilibrium

• Wilhelm Weinberg was a German physician, and Godfrey Harold Hardy was a British mathematician.
• Hardy-Weinberg Equilibrium compares allele frequencies in a given population over a period of time.
• A population of alleles must meet 5 criteria to be considered "in equilibrium," although this never occurs in nature.
• This state is an ideal scenario for measuring gene evolution.
• Five principles/conditions for Hardy-Weinberg equilibrium:
  1. No gene mutations occur; allele changes do not occur.
  2. No migration of individuals occurs (either into or out of the population).
  3. Random mating must occur (individuals mate by chance).
  4. No genetic drift occurs (chance changes in allele frequencies).
  5. No natural selection occurs (changes in allele frequency due to environment).
• The Hardy-Weinberg equations:
  • p + q = 1
  • p² + 2pq + q² = 1
• Where:
  • p = dominant allele frequency
  • q = recessive allele frequency
  • p^2 = homozygous dominant genotype frequency
  • 2pq = heterozygous genotype frequency
  • q^2 = homozygous recessive genotype frequency.

History of Evolutionary Thought

• Georges-Louis Leclerc:
  • A French naturalist, he worked on a 44-volume natural history covering plants and animals.
  • Discussed evidence of evolution, and various causes.
• Erasmus Darwin:
  • A British physician and naturalist, was one of the first to develop formal theories on evolution in "Zoonomia."
  • Drew conclusions on changes in animals during development, animal breeding by humans, and the presence of vestigial structures.
• Georges Cuvier:
  • A French zoologist who advanced the sciences of comparative anatomy and paleontology.
  • Introduced the theory of catastrophism, suggesting that animal and plant species were destroyed time and again by natural catastrophes, with new species evolving afterward.
• James Hutton and Charles Lyell:
  • Developed the concept of uniformitarianism.
  • They argued that Earth’s landscapes (mountains and oceans) were formed over long periods by gradual processes.
• Jean Baptiste Lamarck:
  • A French biologist, best known for Lamarckism.
  • His theory was mainly based on two principles: the law of use and disuse and the inheritance of acquired characteristics.
  • Proposed that the environment can induce physical changes in an organism that can be inherited by the next generation.
• Thomas Malthus:
  • An English economist, who wrote "An Essay on the Principle of Population".
  • He postulated that the size of human populations is limited by the available resources to support them.
  • Charles Darwin used Malthus's principle to formulate his idea of natural selection.
• Charles Darwin:
  • An English naturalist who developed the scientific theory of evolution by natural selection, which became the foundation of modern evolutionary studies.
  • Documented the voyage on the HMS Beagle through his book “On the Origin of Species.”
  • Studied geology and fossils: He acknowledged geological changes and collected fossil specimens that differed somewhat from modern species, (e.g., Glyptodon (armadillo) and Mylodon darwinii).
  • He made biogeographical observations: noting similar environments that had similar-looking plants and animals but differed regionally (e.g. Patagonian hares in South America).
  • He also observed distinct characteristics like the Galapagos tortoises (short-necked in moist regions, long-necked in dry ones) and finches with variation in beak size and shape.
  • Presented at the Linnaean Society of London
• Neo-Darwinian Theory:
  • Genes are responsible for hereditary characteristics.
  • Populations, not individuals, evolve due to natural selection and genetic drift.
  • Speciation results from the accumulation of small genetic changes.

Microevolution

• Evolution is defined as a change in the frequency of a gene in a population.
• Microevolution refers to evolutionary change within populations.
• Causes of microevolution:
  • Natural selection:
    • Requires variation (members of a population differ from one another.)
    • Necessitates increased fitness (better adaptation to the environment leading to more reproduction.)
    • Demands inheritance (genetic differences must be heritable).
    • Types of selection: Directional, Diversifying, Stabilizing, Sexual.
  • Mutation: Random changes to the DNA sequence are a source of new genetic variation.
    • However, not all mutations affect the genetic equilibrium of a population.
  • Gene Flow: Gene flow brings new or rare alleles into a population, changing the allele frequency in the next generation.
  • Genetic Drift:
    • Genetic drift includes changes in the allele frequencies of the gene pool due to chance events.
    • It may eliminate individuals or genes, altering the population at random, without any regard for individual genotypes or phenotypes.
    • Two main types include:
    • Bottleneck effect: results in a loss of genetic diversity due to natural disasters.
    • Founder effect: genetic variation is lost when a few individuals break away from a larger group to found a new population.
  • Non-Random Mating:
    • Alleles in a gene pool assort into genotypes.
    • In assortative mating, similar types of individuals mate more frequently with each other than with dissimilar types.
    • In disassortative mating, dissimilar types of individuals mate more frequently with each other than with similar types.

Macroevolution

• Macroevolution refers to the patterns and processes associated with evolutionary changes at and above the species level.
• Speciation, or the formation of new species, is a key process.
• Patterns of macroevolution:
  • Divergent evolution: Interbreeding species diverging into two or more evolutionary groups.
  • Convergent evolution: Different species becoming more similar in structure and function.
  • Parallel evolution: Two species descended from a common ancestor develop the same traits due to similar environmental pressures.
  • Co-evolution: One species changes, and the other changes in response.
• Processes that Isolate Reproduction via:
  • Pre-zygotic isolation (occurs before the formation of a zygote to prevent attempts at reproduction): - Habitat isolation: Two species occupy different habitats and do not interact or produce offspring - Temporal isolation: Two species live in the same locale but reproduce at different times. - Behavioral isolation: Species have differing courtship patterns. - Mechanical isolation: Species have incompatible genitals or floral structures. - Gametic isolation: Gametes from two different species meet but fail to form a zygote.
  • Post-zygotic isolation (occurs after the formation of a zygote to prevent hybrid offspring): - Hybrid sterility: The hybrid zygote develops into a sterile adult, which can't produce normal gametes (e.g., a mule — a cross between a horse and a donkey. - Hyprid breakdown: If hybrids do reproduce their offspring will be feeble or sterile. - Hybrid inviabilty: The hybrid may lack necessary physiological structure, so they die before birth or can’t survive long.
• Modes of speciation:
  • Allopatric speciation: New species form when geographical barrier physically separates populations of the same species.
  • Parapatric speciation: Two populations live in neighboring areas but has a border zone
  • Sympatric speciation: Develops 2 or more reproductively isolated groups without prior geographic isolation

Evidence of Evolution

• Fossil Records:
  • Fossils are the remains or traces of organisms that lived long ago.
  • Layers of sedimentary rock contain these remains.
• Processes related to how fossils form:
  • Compression (compress)
  • Petrifaction (dead body turns to stone)
  • Impression (imprint of anatomical details / impression that stays on mud that turns into rock)
  • Cast
  • Intact preservation (preserved in tree resin)
  • Transitional fossils indicate traits that resemble 2 groups of the same species.
• Why fossil records are incomplete: - No trace of fossil - Plates are constantly moving - Hard to discover
• Biological evidence:

  • Biogeography = geographical distribution of fossils and living organisms

  • Wallace’s line = Alfred russel wallace → malay archipelago → distinct patterns of animal life on either side of imaginary boundary

• Anatomical evidence: - Homologous structures are the structures with same set of bones that evolved from common ancestor but may appear different with varied functions. - Analogous structures are structures with a similar function, but diff embryological developments / or a set of structures like bones - Vetigial structures features w/ anatomical features that were fully developed on oe species, reduced and nonfunctional in other similar species. - Evidence from molecular biology (RNA, DNA, PROTEINS similar of organisms)

Taxonomy

• Linnaean Taxonomy:

  • Carolus Linnaeus (KARL VON LINNE) is famous for inventing → SCIENTIFIC NAME TO EACH ORGANISM
  • He created the Linnaean system of classification (Did King Philip Come Over For Good Soup):
    • Domain
    • Kingdom
    • Phylum
    • Class
    • Order
    • Family
    • Genus
    • Species
  • Features:
    • Archaea, bacteria, and eukarya are most inclusive levels
    • Domain divided into kingdoms → divides into phyla → classes, orders, families, genera, and species
    • Taxon group at any rank
    • the more features two organisms share, the more taxonomic levels they share

• Binomial nomenclature: two-part format of its scientific name in latin that refers to both the genus & species

• Dichotomous key - Method of identification through categorizations of organisms repeated.

Phylogeny

• Phylogeny charts evolutionary history of a species / group of species.
• Cladistics defines groups into:
  • Ancestral (inherited attributes that resemble those of ancestor group).
  • Derived (attributes that are different from those found in ancestory group).
• A cladogram is a diagram of treelike structure built using shared derived characteristics.
• Root = Initial ancestor that is common to all organisms
• Node = Common ancestor speciated to give rise to 2 or more daughter taxa
• Outgroup = Distantly related species and functions as reference grp
• Clades = Common ancestor and all of its descendants
• Monophyletic = Single common ancestor and all of its descendants
• Paraphyletic = Common ancestor and some of its descendants
• Polyphyletic = Grouping w/ no recent common ancestor:

Respiration System - Gas Exchange

• Gas exchange involves the uptake of O2 from the environment and the discharge of CO2 into the environment.
• Respiration:
  • External: involves the gas exchange of air and blood within the lungs.
  • Internal: involves the gas exchange of blood and interstitial fluid.
• Respiratory surfaces include:
  • Thin and moist membranes.
  • With a large surface area to volume ratio.
  • The rate of diffusion varies in air and in water.
• Invertebrates:
  • Hydras: The outer layer that is in contact with the external environment, inner layer exchanges gases with water in gastrovascular cavity.
  • Earthworms: The body surface or skin is used for respiration, and capillaries are used close to the surface for oxygen exchange
  • Insects: Oxygen with help of Traeae, a system of air tubes with oxygen, and the aid of spirae with tracheae connecting to atmosphere
• Vertebrates, Lungs with air sack as the respiratory system, which circulates the blood

Aquatic- The Gills extract oxygen from watery oxygen

• Environmental substance exchanges gases with animal substance

• Ventilation - air moving and flowing into - (inhilation) or in reverse - (exhalation)

• Positive - The moving of the air thru is forced by body reactions- contraction

• One -way flow -negative - A suction caused lower of atmosphere creating the suction and the flow that results

CIRCULATORY SYSTEM

• The flowing of water in both xyelm to the enviroment. The losing of h2o is a function of evaportaion fromthe leave
• Adhesion - the h2o wanting to bond, creates a linked flow to the tree

The blood has its pathway A close and open system with cells in a liquid flowing to the orgamism and tissues Vertebrates Two chambers with circulation , and oxygen that moves on its own.

• Pulonary
• and Systmeic flows

1- RIGHT ventricle pumps into the blood 2,- Capalaries flow o2 and load blood and unloads 3- Blood flows from artery from heart into artery 4- two venae from and drains two vessels