Genetics: Key Terms and Concepts

Genetics Overview

• Genetics studies genes, which transmit information across generations.

Key Genetics Terms

• Allele: A gene variant at a specific chromosome location.
• Chromosomes: Humans have 23 pairs; the first 22 are autosomal, and the last pair determines sex.
• Dominant allele: Expressed when present in the genotype, effectively overruling a recessive allele.
• Recessive allele: Expression is masked by a dominant allele.
• Genotype: An individual's allele combination for a particular gene (e.g., AA, Aa, aa).
• Homozygous: Possessing identical alleles of a gene.
• Heterozygous: Possessing different alleles of a gene.
• Phenotype: An observable characteristic resulting from the genotype.
• True-breeding: Homozygous organisms that produce offspring identical to themselves through self-fertilization.
• Hybrid: Heterozygous organisms that produce offspring with mixed genotypes and phenotypes through self-fertilization.
• Proband: The first person diagnosed with a disorder seeking treatment, called prepositus (male) or preposita (female).

Laws of Inheritance

• Law of Dominance (1st law): A dominant gene will be expressed in a pair of alleles if present.
• Law of Segregation (3rd law): Each parent contributes one gene from each pair of alleles.
• During gamete formation, alleles for a heritable character segregate and end up in different gametes.
• Law of Independent Assortment (2nd law): Each pair of factors segregates independently of other pairs during gamete formation.
• Dihybrid crosses utilize independent assortment.
• Genotypic ratio: 1 DD: 1 dd: 2 Dd = 100% (25% per box).
• Phenotype ratio (example: Brown eyes dominant over blue): 75% brown eyes, 25% blue eyes.

Sex Linkage and Recombination

• Sex-linked trait: Gene determining a character is located on a sex chromosome.
• X-linked trait: Gene or allele is found on the X chromosome.
• Y-linked trait: Gene or allele is found on the Y chromosome.
• Sex-influenced trait: Expression is affected by an individual's biological sex, occurring more frequently in one sex.
• Sex-limited trait: Expression is limited to one biological sex.
• Hemophilia is an inherited blood disorder causing less clotting and increased bleeding risk.
• Females are XX, males are XY; the father determines sex.
• For X-linked traits, the allele on the X chromosome is shown as a letter attached to the X chromosome.
• Example: XB = normal vision, Xb = color blindness.
• Sex-influenced traits are autosomal but expressed differently in sexes.
• These act as dominant in one sex and recessive in the other due to hormonal or physiological differences.
• Example traits: male pattern baldness, finger length, body hair, muscle mass.
• Baldness example: BB (bald male, normal female), Bb (bald male, normal carrier female), bb (normal male, bald female).
• Sex-limited traits occur in both sexes (autosomes) but are expressed in only one sex with the appropriate hormonal determiner.
• Example: milk yield in dairy cattle, beard in males, barred coloring in chickens.

Modifications to Mendel’s Ratios (Non-Mendelian)

• Co-dominance: Both alleles are expressed separately, yielding different traits in an individual (e.g., two different colors).
• Incomplete dominance: Alleles are partially expressed, resulting in an intermediate phenotype (e.g., blending of colors).
• Multiple alleles: More than two allele types for a given locus result in more than two possible phenotypes.

Mendelian vs. Non-Mendelian Genetics

• Mendelian inheritance passes traits from parents to offspring through dominant and recessive alleles (e.g., complete dominance).
• Non-Mendelian inheritance involves patterns where alleles are neither dominant nor recessive (e.g., co-dominance, incomplete dominance, multiple alleles).

Blood Type

• Human blood types follow a co-dominance pattern with two dominant alleles (IA and IB) and one recessive allele (i).

Molecular Structure of DNA, RNA, and Proteins

• Biological molecules include lipids (long-term energy), nucleic acids (genetic information), carbohydrates (immediate energy), and proteins (biochemical reactions via enzymes).
• Polymer: A long chain of molecules with repeating monomers.

DNA vs. RNA

• DNA is double-stranded, RNA is generally single-stranded.
• DNA contains deoxyribose sugar, RNA contains ribose sugar.
• DNA has nucleotide bases A, G, C, T; RNA has A, G, C, U.
• DNA stores information and transfers it to the next cell generation.
• RNA carries protein-encoding information, helps make proteins, and catalyzes reactions.

Nucleic Acid Structure

• Nucleotides consist of a nitrogenous base, a pentose sugar, and a phosphate group.
• Nucleotides are bonded by hydrogen bonds.
• Pyrimidines: Cytosine, Thymine, and Uracil.
• Purines: Adenine and Guanine.
• Phosphodiester bonds link the phosphate group of one nucleotide to the sugar of another.
• DNA has two polynucleotide strands forming a double helix in an antiparallel orientation.
• Base pairing links DNA strands, purine with pyrimidine, maintaining a uniform diameter.
• Codon: A set of three nucleotides (e.g., AAT) corresponding to a single amino acid.

Proteins

• Enzymatic proteins: Accelerate chemical reactions (e.g., digestive enzymes).
• Defensive proteins: Protect against disease (e.g., antibodies).
• Storage proteins: Store amino acids (e.g., casein in milk).
• Transport proteins: Transport substances (e.g., hemoglobin).
• Hormonal proteins: Coordinate activities (e.g., insulin).
• Receptor proteins: Respond to chemical stimuli.
• Contractile proteins: Enable movement (e.g., actin and myosin).
• Structural proteins: Provide support (e.g., keratin, collagen).
• Amino acids are the monomers of proteins, with 20 types in the human body.

Protein Structures

• Primary structure: Amino acid sequence (e.g., Transthyretin composed of 127 amino acids).
• Secondary structure: Folding into α-helix and β-pleated sheets.
• Tertiary structure: Overall 3D shape of a polypeptide.
• Quaternary structure: Overall protein structure from the aggregation of polypeptide subunits (e.g., hemoglobin).
• Example: Sickle cell disease results from a valine substitution for glutamic acid in hemoglobin.
• Genetic information flow: DNA → RNA → Protein.
• mRNA carries information to ribosomes.
• tRNA transfers amino acids to mRNA.

DNA Replication

• DNA replication makes an identical copy of a DNA molecule.
• Cell cycle includes interphase (G1, S, G2 phases) and M phase (prophase, metaphase, anaphase, telophase).
• Base pairing rules: Adenine (A) with Thymine (T), Guanine (G) with Cytosine (C).
• Semi-conservative replication: Each daughter molecule has one old and one new DNA strand.

DNA Elongation

• Nucleotides add only to the 3' carbon end of a strand.
• DNA synthesis proceeds in the 5' to 3' direction.
• Leading strand is continuous, lagging strand is discontinuous.
• Okazaki fragments are located in the lagging strand.
• DNA replication is semi-discontinuous: leading strand is synthesized continuously, lagging strand discontinuously.

Steps in DNA Replication

• Helicase separates DNA strands by breaking hydrogen bonds.
• Single-strand binding proteins (SSBP) prevent strands from rejoining.
• Topoisomerase untwists the double helix.
• Primase makes an RNA primer on the DNA template.
• DNA Polymerase adds DNA nucleotides to the RNA primer to lengthen the sequence.
• Leading strand synthesis continues in a 5' to 3' direction.
• Lagging strand synthesis produces Okazaki fragments discontinuously.
• Ligase seals the sugar-phosphate backbone after RNA primer replacement.

Protein Synthesis

• DNA → RNA → PROTEIN
• Genes on DNA direct RNA (mRNA) synthesis.
• RNA aids in polypeptide (protein) production.
• mRNA: Carries protein information.
• rRNA: Forms ribosomes for protein synthesis.
• tRNA: Transfers amino acids to the ribosome.
• mRNA contains codons, tRNA contains anticodons.

Transcription

• Transcription copies a gene's DNA sequence to make an RNA molecule, occurring in the nucleus.
• Cytosine (C) pairs with Guanine (G), Uracil (U) pairs with Adenine (A)
• Steps:
  • Initiation: RNA polymerase binds to the promoter region of a gene; DNA unwinds.
  • Elongation: RNA polymerase adds RNA nucleotides in a 5’ to 3’ direction.
  • Termination: RNA polymerase reaches a terminator gene, releasing the mRNA strand and enzyme.
• mRNA Processing:
  • Addition of a 5’ cap to the RNA beginning.
  • Poly-A tail added at the RNA end.
  • Introns (junk sequences) are removed; exons are pasted together.
• Codon: Each three-base sequence in mRNA codes for a particular amino acid.

Translation

• Translation converts genetic code in mRNA to make a protein, occurring in the cytoplasm (ribosomes).
• Requires mRNA, rRNA, tRNA, amino acids, and enzymes.
• tRNA Anticodon: A set of three nucleotides binds to a matching mRNA codon via base pairing, carrying the amino acid specified by the codon.
• Ribosome Sites:
  • E site (Exit) is where the empty tRNA exits after amino acid transfer.
  • P site (peptidyl) holds the tRNA with the growing polypeptide chain, usually the first site of entry..
  • A site (Aminoacyl) holds the incoming tRNA carrying an amino acid.
• Steps:
  • Initiation: Small ribosomal subunit attaches to mRNA near the start codon (AUG); tRNA (UAC anticodon) carries methionine.
  • Elongation: Polypeptide chain grows one amino acid at a time; tRNA from P site transfers its amino acid to the tRNA in the A site, then the ribosome moves forward.
  • Termination: Stop codon appears at the A site; a release factor binds to the stop codon, cleaving the polypeptide.
• Stop codons: UAG, UAA, UGA

Hardy-Weinberg Equilibrium

• Hardy-Weinberg equilibrium compares allele frequencies in a population over time.
• Principles:
  • No gene mutations.
  • No migration.
  • Random mating.
  • No genetic drift.
  • No natural selection.
• Allele frequencies: p + q = 1 (p = dominant, q = recessive).
• Genotype frequencies: p2 + 2pq + q2 = 1 (p2 = homozygous dominant, 2pq = heterozygous, q2 = homozygous recessive).

Microevolution

• Microevolution: Evolutionary change within populations.
• Macroevolution: Transformation of one species into another.
• Causes: natural selection, mutation, gene flow, genetic drift, and non-random mating.
• Natural Selection:
• Variation: Population members differ.
• Increased fitness: Better-adapted individuals reproduce more.
• Inheritance: Genetic differences are heritable.
• Types:
• Directional: One extreme phenotype is favored.
• Disruptive: Two or more extreme phenotypes are favored over an intermediate phenotype.
• Stabilizing: Intermediate phenotype is favored over extreme phenotypes.
• Sexual: Adaptive changes increase mating ability; Includes Intrasexual selection (competition within one sex) and Intersexual selection (one sex chooses mates)
• Mutation: Random DNA sequence change.
• Gene Flow: Allele movement between populations (migration).
• Genetic Drift: Allele frequency changes due to chance, including bottleneck effect (loss of diversity due to disasters) and founder effect (loss of variation with few founders).
• Non-Random Mating: Affects allele assortment into genotypes, including Assortative mating (similar types mate) and Dissortative mating (dissimilar types mate)

Macroevolution

• Macroevolution: Evolutionary change at and above the species level, often resulting in speciation.
• Speciation: Some population members can no longer interbreed.
• Patterns:
• Divergent: Interbreeding species diverge into two or more groups due to environment.
• Convergent: Distinct species become similar due to similar environments.
• Parallel: Species from common ancestors develop similar traits via adapting to similar environments.
• Coevolution: One species changes, prompting changes in another.

Reproductive Isolating Mechanisms

• Prezygotic Isolation: Occurs before zygote formation, preventing reproductive attempts.
  • Habitat Isolation: Species in different habitats are less likely to mate.
  • Temporal Isolation: Species reproduce at different times.
  • Behavioral Isolation: Unique courtship patterns.
  • Mechanical Isolation: Incompatible genitalia or floral structures.
  • Gametic Isolation: Gametes do not fuse.
• Postzygotic Isolation: Occurs after zygote formation, preventing hybrid offspring development or breeding.
  • Hybrid Inviability: Genes of parent species impair hybrid development.
  • Hybrid Sterility: Hybrids are sterile due to chromosome differences.
  • Hybrid Breakdown: First-generation hybrids are viable, but later generations are feeble or sterile.

Modes of Speciation

• Allopatric Speciation: A geographical barrier separates a population into non-interbreeding groups.
• Parapatric Speciation: Populations live in neighboring areas but share a border zone.
• Sympatric Speciation: A population develops into reproductively isolated groups without geographic isolation.

Systematics

• Phylogeny: Determining evolutionary relationships.
• Taxonomy: Classifying organisms.

Linnaean Taxonomy

• Hierarchical classification scheme with consistent scientific names.
• Hierarchy (most to least inclusive): Domain, kingdom, phylum, class, order, family, genus, and species.
• A taxon is a group at any rank.

Binomial Nomenclature

• Two-part scientific name (genus and species).

Dichotomous Key

• A method of identification that repeatedly divides organisms into two categories.

History of Evolutionary Thought

• Georges-Louis Leclerc: Provided evidence of evolution and proposed various causes.
• Carolus Linnaeus: Developed binomial nomenclature and a classification system, believed in scala naturae and fixity of species.
• Erasmus Darwin: Formulated early formal theories on evolution.
• Georges Cuvier: Established comparative anatomy and paleontology, proposing the theory of catastrophism.
• James Hutton & Charles Lyell: Developed uniformitarianism.
• Jean-Baptiste Lamarck: Proposed inheritance of acquired characteristics (Lamarckism).
• Thomas Malthus: Size of human populations is limited by resources, which influenced Darwin.
• Charles Darwin: Proposed theory of evolution by natural selection.

Darwin's Theory of Evolution

• Darwin's observations led him to natural selection and evolution theories.
• Noticed Galapagos Islands' finches exhibiting significant variance in beak size, believing a mainland finch was the common ancestor of all types on the islands.

Wallace

• Russel Wallace collected and identified thousands of species in the Malay Archipelago for 8 years.

Modern Synthesis (New-Darwinian Theory)

• Unifies ideas about DNA, mutations, inheritance, and natural selection.
• Genes are responsible for hereditary characteristics
• Populations, not individuals, evolve due to natural selection and genetic drift.
• Speciation occurs due to accumulation of small genetic changes.

Hardy-Weinberg Principle

• A population is in genetic equilibrium if allele frequencies do not change over time (stable, non-evolving state).

Evidence of Evolution

• Fossil Record: Remains or traces of organisms from long ago, found in sedimentary rock layers.
• Biogeographical Evidence: Study of the geographical distribution of fossils and organisms (Wallace’s Line).
• Anatomical Evidence:
  • Homologous Structures: Same set of bones evolved from a common ancestor with varied functions.
  • Analogous Structures: Same function but different embryological development.
  • Vestigial Structures: Fully developed in one group, reduced and nonfunctional in others.
• Evidence from Embryology: Study of organismal development from embryo to adult.
• Evidence from Molecular Biology: Similar molecules suggest descent from a common ancestor.

The Circulatory System: Transport and Circulation in Plants

• Water Transport in Xylem:
  • Transpiration: Water loss to the environment through leaf stomata.
  • Cohesion: Water's ability to stay linked in a chain.
  • Adhesion: Water's ability to stick to the inside of a xylem tube.
• Sugar Transport in Phloem:
  • Source (Leaves): Location where sugar is made or stored.
  • Sink (Roots): Location where sugar will be used.

Transport & Circulation in Animals (Animal Circulatory Systems)

• Open Circulatory System: Fluid bathes tissues directly.
• Closed Circulatory System: Heart pumps blood through a continuous system of vessels.
• One Circuit Circulatory Pathway (Fishes): Blood pumps to the gills
• Two-Circuit Circulatory Pathways:
  • Pulmonary Circuit (to lungs).
  • Systematic Circuit (to tissues).

Transport & Circulation in Humans (Human Heart)

• Septum: Separates each side of a heart.
• Atrium: Receives blood.
• Ventricle: Pumps blood.
• Valves: Keeps blood moving in the correct direction.
• Arteries: Move blood away from the heart.
• Veins: Move blood towards the heart.
• Two Major Circular Pathways:
  • Pulmonary Circuit: Carries O2-poor blood from the heart through the pulmonary arteries and to the capillaries (Lungs).
  • Systematic Circuit: Carries oxygenated blood from the heart out the aorta, through branching arteries and to capillaries throughout the body.

Flow of Human Digestive System

1. . Digestion Begins in the Mouth

• Mechanical Digestion → Chewing of food using the teeth into smaller pieces
• Chemical Digestion → Digestive enzyme called salivary amylase (saliva) break down carbohydrates

2. Pharynx and Swallowing Tongue → Mixes chewed food with saliva to form bolus in preparation for swallowing Epiglottis → Flap or tissue that covers the glottis to prevent food from entering the trachea
3. Swallowing When swallowing, the soft palate closes the pharynx, and the epiglottis covers the glottis
4. Peristalsis Waves of smooth muscle contraction push food along the esophagus and the rest of the digestive tract
5. . The Stomach Stores, Digests, Churns Food Stomach → Receives food from the esophagus, stores food, and starts the digestion of proteins, both mechanical and chemical digestion. Contains 3 muscle layers, separated by 2 sphincters
6. Small Intestine Digests and Absorbs Nutrients Small Intestine → Completes digestion and absorbs nutrients and water. Duodenum: Secrete mucus Jejunum: Absorbs carbohydrates and proteins Ileum: Absorbs water, fats, vitamins, and minerals
7. Role of Accessory Organs Pancreas→ Produce the hormone insulin and glucagon that regulates blood glucose levels. Secretes pancreatic juice into the small intestine that digests carbohydrates, proteins, fats and nucleic acids Liver → Produces bile Bile → Greenish-yellow fluid that breaks down fat into droplets Gallbladder → Stores bile
8. Large Intestine Completes Nutrient and Water Absorption Large Intestine → Absorb water and salts and eliminates waste.

The Respiratory System

• Gas Exchange: Uptake of molecular O2 and discharge of CO2.
  • External Respiration: Gas exchange between air and blood in the lungs.
  • Internal Respiration: Gas exchange between blood and interstitial fluid.
• External Respiration vs Internal Respiration:
• Between the Air and Blood
• Between the Blood and Intersititial Fluid
• Respiratory Surfaces: Thin, moist membrane with a large surface area.

Gas Exchange in Animals

• Hydra (Invertebrates): the outer layer of cells in contact with the external environment.
• Hydra (Invertebrates): the inner layer can exchange gases with the water in the gastrovascular cavity.
• Earthworms (Invertebrates)* Use their body surface (skin) for respiration (Bodies itself serve as the area of respiration)
• Insects (Invertebrates)* Have a system of air tubes called tracheae delivers oxygen directly to the cells without entering the blood.
• Aquatic Animals (Vertebrates): have gills that extract oxygen.
• Aquatic Animals (Vertebrates):Gills are out-foldings of the body surface that are suspended in the water.* Mammals (Vertebrates): Vertebrate lungs have a moist internal respiratory surface + Circulatory System aids in gas exchange
• Respiratory Medium The environmental substance either be AIR OR WATER
• Fish Kil Sudden and unexpected death of aquatic animals in a short period
• Ventilation: air flowing into the lungs and out of the lungs