BIO 114 Lecture Notes Vocabulary

Scientific Method

• Observation: Initial step; involves noticing phenomena and gathering information.

• Hypothesis: A testable explanation for the observed phenomena; an educated guess.

• Experimental design:

  • Control: A group that does not receive the experimental treatment; used as a baseline for comparison. Contains everything EXCEPT the experimental variable.

  • Experimental variable(s): The factor being tested or changed in the experiment. Controlled and manipulated by the researcher.

• Results:

  • Statistics: Mathematical analyses of the data collected to determine significance.

  • Graphs: Visual representations of data to show trends and relationships.

• Discussion: Interpretation of the results in the context of the hypothesis. Comparison with existing knowledge and literature.

• Conclusion:

  • Hypothesis is true/supported/confirmed: Indicates that the data supports the initial hypothesis.

  • Hypothesis is not correct: Indicates that the data does not support the initial hypothesis, requiring a revised hypothesis (back to the drawing board!)

• Bias: Scientific prejudice. Systematic errors in the experimental design or interpretation of data.

• Scientific fraud: Doctoring the data. Intentional manipulation or falsification of research data.

Molecules

• Organic Molecules:

  • Contain Carbon (C) and Hydrogen (H). Fundamental building blocks of living organisms.

  • Covalent bonding: Involves sharing of valence or outer-shell electrons, following the octet rule to achieve stability.

• Inorganic Molecules:

  • Examples: NH3, H2O, CO2, HCl, H3PO4, H2SO_4

• Bonding:

  • Covalent Bonding: Sharing of electrons between atoms.

  • Ionic Bonding: Attraction between positive and negative ions, resulting in electron transfer.

  • Non-bonding Associations:

  • Hydrogen bonding: Between H and an electronegative element (e.g., water). Weak but crucial for stabilizing biological molecules.

  • Dipole-dipole interaction: Molecule has positive and negative ends, leading to electrostatic attraction.

  • Van der Waals: Weaker interactions due to temporary fluctuations in electron distribution.

Functional Groups

• Examples: -CH3 (methyl), -OH (hydroxyl), O=C- (carbonyl), -NH2 (amino), -PO_4H (phosphate), -COOH (carboxyl)

Dehydration and Hydrolysis

• Dehydration: Removing water to make a bond (anabolic/synthesis of larger molecules). Results in the formation of a covalent bond.

• Hydrolysis: Breaking a bond with water (polymer + H_2O -> monomers; catabolic -> breakdown of larger molecules). Reverses dehydration.

Carbohydrates

• Monomer: Glucose (monosaccharide). Simple sugar; primary energy source for cells.

• Polysaccharides: Glycogen (in animals), starch (in plants). Polymers of glucose; storage forms of energy.

• Function: Storing energy, structure (cellulose, chitin). Structural components in cell walls (cellulose) and exoskeletons (chitin).

Lipids

• Characteristics: Do not dissolve in water. Hydrophobic nature.

• Components: Fatty acids and glycerol. Building blocks of lipids.

• Functions: Stored form of energy, phospholipids (membrane), cholesterol, steroids (hormones). Diverse functions in energy storage, membrane structure, and cell signaling.

• Structure:

  • Hydrocarbon tail (non-polar) -> Hydrophobic: Repels water.

  • Polar head (contains O, N, P) -> Hydrophilic: Attracts water.

Proteins

• Monomers: 20 amino acids. Building blocks of proteins; each with a unique side chain.

• Polymers:

  • Four levels of structure:

  • Primary: Specific amino acid sequence. Linear chain of amino acids.

  • Secondary: Alpha helix, beta-pleated sheet. Local folding patterns stabilized by hydrogen bonds.

  • Tertiary: 3-D shape/folding into a functional polypeptide. Overall shape determined by various interactions.

  • Quaternary: Two or more polypeptides in association (collagen, hemoglobin). Multiple polypeptide subunits combine to form a functional protein.

• Function: Enzyme, support, actin, myosin, antibody. Diverse roles including catalyzing reactions, structural support, muscle contraction, and immune defense.

Nucleic Acids

• DNA: Double-stranded, deoxyribose sugar, ATCG. Contains blueprints to make polypeptides. Stores genetic information.

• RNA: Single-stranded, ribose sugar, AUCG. Types: mRNA, tRNA (carries an amino acid), rRNA (made in the nucleolus). Involved in protein synthesis and gene regulation.

Saturated vs. Unsaturated Lipids

• Saturated Lipids: All carbon molecules with single bonds; animal origin. Solid at room temperature because their straight structure allows them to pack tightly.

• Unsaturated Lipids: Carbons bonded with double/triple bonds; plant origin (olive, sunflower). Liquid at room temperature due to kinks in the fatty acid chains.

Denaturation

• Breakdown of polypeptide/protein structure; likely non-functional. Disrupts the native conformation of the protein.

• Causes: Heat, light, salt, acid, base (e.g., egg white). Disrupts the bonds that maintain secondary and tertiary structures.

Cell Structure (Eukaryotes)

• Golgi apparatus: Packaging/deployment, vesicle formation (secretory and transitory vesicles). Modifies, sorts, and packages proteins and lipids.

• Nucleus: Double membrane, nuclear pores, contains genetic material. Control center of the cell; contains DNA.

• Rough Endoplasmic Reticulum (RER): Protein synthesis. Ribosomes attached for synthesizing and modifying proteins.

• Smooth Endoplasmic Reticulum (SER): Lipid synthesis. Involved in lipid and steroid hormone synthesis; detoxification.

• Ribosomes: Site of protein synthesis (70% protein, 30% rRNA). Translate mRNA into proteins.

• Mitochondrion: Double-membraned, produces energy. Powerhouse of the cell; site of cellular respiration.

• Lysosomes: Digestive enzymes/housekeepers. Break down cellular waste and debris.

• Peroxisomes: Break down peroxides. Detoxify harmful substances.

• Chloroplasts: Double-membraned, photosynthesis; grana (thylakoid membranes), stroma, lamellae. Site of photosynthesis in plant cells.

• Cytoskeleton: Filaments: actin (microfilaments), intermediate, microtubules. Provides structural support, cell shape, and movement.

• Centrioles: 9 triplets microtubule arrangement + 0. Involved in cell division.

• Flagellum: 9 doublets + 2; mobility. Long, whip-like structure for cell movement.

• Cilia: 9 doublets + 2; mobility (paramecium), stereocilia. Short, hair-like structures for movement or sensory functions.

• Basal body: 9 + 0. Anchors flagella and cilia.

• Cell wall: Plants. Provides rigid support and protection.

Fluid Mosaic Model of Plasma Membrane

• Phospholipid bilayer with embedded proteins.

  • Fluid: Phospholipid bilayer. Allows lateral movement of lipids and proteins.

  • Mosaic: Embedded proteins. Proteins are dispersed throughout the lipid bilayer.

• Hydrophilic portion: Likes water. Polar heads of phospholipids.

• Hydrophobic portion: Fears water. Non-polar tails of phospholipids.

• Semi-permeable membrane/selectivity. Controls the movement of substances in and out of the cell.

• Plasma membrane = cytomembrane = cytolemma. Outer boundary of the cell.

Types of Embedded Proteins

• Channel: Facilitates transport. Forms a pore for ions or molecules to pass through.

• Cell recognition: Histocompatibility. Identifies cells as self or non-self.

• Carrier: Facilitates transport. Binds to specific molecules and transports them across the membrane.

• Receptor: Combines with molecules based on shape, size. Triggers cellular responses upon binding.

• Enzymes: ATP synthetase. Catalyzes reactions at the membrane surface.

• Signal transduction. Transmits external signals into the cell.

• Sodium-potassium pump: Active transport. Maintains ion gradients across the membrane.

Solutions

• Solvent: Liquid that dissolves a solute. Typically water in biological systems.

• Solute: Substance dissolved by the solvent. E.g., Salt or sugar.

• Solution: Homogeneous mixture of solvent and solute. Uniform composition throughout.

• Isotonic Solution: Equilibrium; no overt change in cell volume. Solute concentration is the same inside and outside the cell.

• Hypotonic Solution: Less salt outside the cell; cell swells, may lyse. Water enters the cell, causing it to swell.

• Hypertonic Solution: More salt outside the cell; cell releases water, shrivels, may undergo apoptosis (programmed cell death). Water leaves the cell, causing it to shrink.

• Dialysis membrane: Size constraints determine what passes through. Allows separation of molecules based on size.

Transport Processes

• Active process: Needs energy (ATP); e.g., sodium-potassium pump. Moves substances against their concentration gradient.

• Passive process: No energy expended:

  • Diffusion: High to low concentration. Movement of molecules from an area of high concentration to low concentration.

  • Facilitated transport: Across membrane. Requires carrier proteins or channels.

  • Osmosis: Diffusion of water. Movement of water across a semi-permeable membrane.

• Exocytosis: Large molecules secreted via secretory vesicles. Releases substances from the cell.

• Endocytosis: Small ions/molecules taken in via vesicle formation:

  • Pinocytosis: Cell drinking. Uptake of small droplets of fluid.

  • Phagocytosis: Cell eating. Uptake of large particles or cells.

• Diffusion: Movement from high to low concentrations (gradient). Driven by the concentration gradient.

• Osmosis: Movement of water from high to low water concentration. Water moves to equalize solute concentrations.

Cell Junctions

• Gap: Flow of ions. Allows direct communication between cells.

• Anchor/Intermediate: Tissue formation. Provides mechanical stability.

• Tight Junction: Prevent leakage. Seals cells together to prevent passage of molecules.

• Plants: Plasmodesmata (channels). Allows transport and communication between plant cells.

Metabolism

• Catabolism: Break down (digestive processes). Releases energy.

• Anabolism: Synthesis. Requires energy.

Enzymes

• Substrate: Reactant/metabolite that becomes a product: S + E -> E-S complex -> P + E. The substance upon which an enzyme acts.

• Enzyme: Protein catalyst; lock and key theory. Speeds up biochemical reactions.

• Active Site: Where substrate binds and is converted to product.

  • Competitive inhibition: Chemical resembles substrate, binds to active site. Blocks substrate binding.

  • Non-competitive inhibition: Chemical binds elsewhere (allo), changes enzyme shape; feedback inhibition (A -> B -> C -> D -> E). Alters enzyme conformation, reducing activity.

• Coenzyme: Organic molecules. Assists enzyme function.

• Cofactors: Ions and coenzymes. Non-protein components that help enzymes.

Thermodynamics

• First law: Cannot create or destroy energy; total energy is constant; law of conservation of energy. Energy can be converted from one form to another.

• Second law: Energy transformation is not 100% efficient. Some energy is lost as heat, increasing entropy.

Oxidation and Reduction

• Oxidation: Lose electrons (lose H ion): NADH -> NAD^+ + 2e- + H^+. Loss of electrons or increase in oxidation state.

• Reduction: Gain electrons (gain H ion). Gain of electrons or decrease in oxidation state.

Energy Changes

• Exergonic: Release of energy (-ΔG -> spontaneous). Reactions release free energy.

• Endergonic: Need energy (+ΔG -> non-spontaneous). Reactions require an input of energy.

• Exothermic: Release heat (-ΔH). Reactions release heat.

• Endothermic: Require heat (+ΔH, ENTHALPY). Reactions absorb heat.

Enzyme Activity

• Factors affecting: Temperature (T), pH, [S] (substrate concentration), heavy metals (inhibit). Influences enzyme activity and reaction rates.

• Optimal T, optimal pH, optimal [S]. Bell-shaped curve. Enzymes have specific conditions for maximal activity.

ATP

• Structure: Adenine, sugar, 3 phosphates. Energy currency of the cell.

• Function: Provides energy. Powers cellular processes.

• Coupled reactions: Cycles, exchange of electrons/energy. Energy from exergonic reactions drives endergonic reactions.

Photosynthesis

• Fixing carbon: Light reactions (PSI: make NADPH, ATP; PSII: make ATP) and dark reactions (Calvin Cycle). Conversion of light energy into chemical energy.

• CO_2 ----> make sugar!!! Synthesis of glucose from carbon dioxide and water.

• Components: Water, electrons, sunlight, chlorophyll, NADP^+, hydrogen ions, CO2, O2, PGAL, RuBP, glucose. Key players in photosynthesis.

• Light dependent: PSI and PSII. Converts light energy into chemical energy (ATP and NADPH).

• Light independent: Calvin cycle – formation of PGAL (ATP and NADPH used) in stroma. Uses ATP and NADPH to fix carbon and produce sugars.

Cellular Respiration

• Aerobic respiration: Oxygen IS involved. Breakdown of glucose to produce ATP with oxygen.

• Anaerobic respiration: Oxygen NOT involved (e.g., glycolysis). Breakdown of glucose without oxygen.

• Fermentation: Lactic acid, ethanol. Produces ATP in the absence of oxygen.

Reactions of Cellular Respiration

• Glycolysis: 2ATP and 2NADH (in cellular cytoplasm). Breakdown of glucose into pyruvate.

• Krebs Cycle (TCA cycle): 2ATP, 6NADH, 2 FADH_2 (in matrix of mitochondria). Oxidizes acetyl-CoA to produce energy carriers.

• Electron Transport: 34 ATP (cytochromes in inner mitochondrial membrane). Uses energy carriers to produce ATP.

• Fats and proteins: Feed into glycolytic pathways. Can be used as alternative energy sources.

Mitosis

• Asexual reproduction: Parent cell into two genetically identical daughter cells. Produces identical copies of cells.

• Somatic cells: Growth of multicellular organism. Non-reproductive cells.

• Human somatic cells: 46 chromosomes; daughter cells also have 46 chromosomes, diploid to diploid. Maintains chromosome number.

• Cell Cycle

Phases of Mitosis/Cell Cycle

• Interphase (Go): Chromosomes not visible. Cell grows and prepares for division.

• Prophase: Nuclear envelope breaks down, see condensed chromatin (chromosomes). Chromosomes become visible.

• Metaphase: Chromosomes line up. Chromosomes align at the metaphase plate.

• Anaphase: Chromosomes move across the cell. Sister chromatids separate and move to opposite poles.

• Telophase: Formation of nuclear envelopes, cleavage furrow (animal cell)/cell plate (plant cell) forming; followed by cytokinesis. Cell divides into two daughter cells.

Meiosis

• Sexual reproduction: Gametes/diploid to haploid. Produces genetically diverse gametes.

• Meiosis I: Reduction division, diploid->haploid; Prophase I: tetrad formation, recombination possible. Homologous chromosomes separate.

• Meiosis II: Similar to mitosis (haploid to haploid). Sister chromatids separate.

Oogenesis

• Oogonia (diploid) -> primary oocytes (diploid, 46) ->MI-> secondary oocyte (haploid, 23)->MII-> ovum (haploid, 23) + 3 polar bodies…conservation of the cytoplasm in the final egg

Spermatogenesis

• Spermatogonia (diploid, 46) -> primary spermatocytes(diploid, 46)-> MI->secondary spermatocytes (haploid, 23) ->MII ->spermatids (haploid, 23) -> mature sperm cells (head, neck and flagella) (metamorphosis)

Prophase I of Meiosis I

• Homologous chromosomes form the tetrad (synapsis). Pairing of homologous chromosomes.

• Recombination is possible -> genetic variability. Exchange of genetic material between homologous chromosomes.

Gametes v Somatic Cells

• Gamete (mature egg and mature sperm have 23 chromosomes )

• Somatic Cells (46 chromosomes in humans)

Zygote

• Fertilized egg.

• Zygote will start to reproduce via MITOSIS =====

Alleles, Genes, and Locus

• Allele: Form of a gene: dominant allele -> uppercase letter; recessive allele -> lowercase letter

• Gene: Carries the code to form a polypeptide.

• Locus: Location of the gene/allele (on the chromosome).

Mendelian Inheritance

• Follow Mendel’s Laws:

  • Law of Probability (0.5).

  • Law of Independent assortment (alleles randomly sorted in formation of gametes).

  • Law of Segregation (alleles separate upon formation of the gametes).

  • Monohybrid (1 trait) versus Dihybrid (2 traits)

• Dominant allele: Always seen in the majority of the population; only need one dominant allele to exhibit the dominant phenotype

• Recessive allele: Seen less in the population; need both recessive alleles to exhibit the recessive phenotype [Phenotype: physical expression; Genotype: genetic makeup]

• Homozygous dominant (DD), heterozygous (Dd) – considered a carrier, homozygous recessive (dd)

• Mating DD with dd - > All phenotypes with dominant trait (Dd); DD x dd

• Mate Dd with Dd -> 3:1 ratio of dom to rec (Phenotypic ratio) versus genotypic of 1:2:1 Dd x Dd

Punnett Squares

• Use Punnett square for a one-trait and a two-trait cross

• Two Trait (DiHybrid) Cross:

  • Parental AABB x aabb

  • F1 AaBb x AaBb

  • F2 : Phenotypic ratio: 9:3:3:1

  • 9 AB : 3 Abb: 3 aaB : 1 aabb

  • AaBb -> gametes will be: AB, Ab, aB, ab

Non-Mendelian Inheritance

• Pink Flower: incomplete dominance (another example: sickle cell trait); Recessive allele is not as masked, and starts to be expressed

• Codominance: both alleles are expressed (type AB blood).

• Polygenic Inheritance (think skin types) (think the sisters) [AaBBcc] (2 or more genes -> 1 trait)

• Pleiotropy (1 gene –Many traits) – King George III. Sickle cell anemia

• Environment (temperature and sex; habitat)

Non-disjunction

• Separation of the chromosomes was not perfect

  • May occur in Meiosis I or Meiosis II

  • 2n-1 (monosomy – Turner’s Syndrome), 2n+1 (trisomy – Down’s Syndrome)

Chromosome mutations/aberration

*   Deletion – chromosome gets shorter
*   Translocation – two different chromosomes exchange part of their structure
*   Replication – chromosome gets longer
*   Inversion – flip of a segment of chromosome (180 degree) resulting in a different arrangement of the genes
*   Formation of Rings

Linkage

• Gene Linkage (thank you Dr. Thomas H. Morgan):

• Will be observed in phenotypic ratios of the offspring that DOES NOT FOLLOW THE MENDELIAN 9:3:3:1 ratio

• Tightly linked -> distance between the alleles on the chromosome-> short

• Loosely linked -> distance between the alleles on the chromosome -> longer

• Mapping -> Frequencies of the phenotypes correlated to mapping distance

Sex-linked Genes

• color blindness in males, hemophilia (Queen Victoria), MD

• X^HX^h x X^HY -> X^HX^H, X^HX^h, X^HY, X^hY

Molecular Basis of Inheritance

• Structure of dna (Deoxyribose sugar, phosphate – sugar phosphate backbone, ATCG); direction ( strand pairing with 5’-----3’)

• Complementary base pairing: A with T, C with G Purine (2 rings) (A, G) hydrogen bonding with a pyrimidine (1 ring) (T, C)

• DNA and RNA replication: initiation, elongation, termination

• DNA replication is semi-conservative

• Triplet Codon, Triplet anti-code (transfer RNA); codon codes for an amino acid

• Genetic code – 64 possible combinations (4^3): redundant, non-ambiguous, universal, start and stop

• Transcription occurs in the nucleus (eukaryotic organism) Primary mRna -> CAP AND TAIL ->SPLICEOSOMES (cut Introns)->mature mRNA (ALL EXONS)

• Translation occurs in the cytoplasm (eukaryotic – endoplasmic reticulum, mitochondria, prokaryotic – cytoplasmic ribosomes/polyribosomes): mRNA, tRNA, rRNA

Protein Synthesis

• Diagram of Protein Synthesis

  • Parent DNA strand 3’-AAA-CGC-ATA-GAT-ACA-5’

  • Other parent strand for DNA 5’-TTT-GCG-TAT-CTA-TGT-3’

  • mRna 3’-AAA-CGC-AUA-GAU-ACA-5’

  • tRNA UUU GCG UAU CUA UGU (anticodon)

  • polypeptide Lys-Arg-Ile-Asp-Thr (from the mRNA)

• DNA Synthesis -> leading strand and the lagging strand (Okazaki fragments -> DNA Ligase)

• Helicase, DNA Polymerase, RNA primer, DNA Ligase

Biotechnology

• Transformation – involves introduction of foreign DNA, such the receiving organism is a recombinant and a transgenic organism

• How to introduce foreign DNA into a plasmid or into viral DNA to give recombinant DNA

• Gene therapy: in vivo and ex vivo

Darwin and Natural Selection

• Darwin and the Five Assumptions for Natural Selection

• Supportive Evidence: Fossils, Biogeography

Comparative Anatomy

• Homologous structures

• Analogous structures

Microevolution

• Hardy-Weinberg Statistics – 1-mutations, 2-Gene Flow (migration – snake example), 3-Non-random mating, 4-genetic drift (founder’s effect, bottleneck), 5-Natural Selection (reproductive fitness)

• Industrial melanism (white moth v black moth:

  • white dominant

  • black recessive;

  • but when trees turned dark -> population shift -> more black moths survived than white moths; as soon as pollution was abated, then shift back to more white moths over black moths)

Macroevolution

• formation of a species

Natural Selection Types

• Natural Selection:

  • 1) Stabilizing -

  • 2-Disruptive -

  • 3-Directional

Speciation

• Allopatric (geographical) speciation

• Sympatric (ecological) speciation

Origin of Life

• Origin of Life – Oparin’s Hypothesis, Miller & Urey experiment, protocells

• Abiotic synthesis

Earth

• Age of earth: 4.5 Billion years

Taxonomy

• Domain-> Kingdom -> Phylum -> Class -> Order -> Family -> Genus -> Species

Biomes

• Biomes: desert, tundra, grasslands (prairie and savanna), scrubland, taiga (Coniferous Forest), temperate (Deciduous Forest), Tropical Rain Forest

Succession

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Here are the definitions of in vivo and ex vivo gene therapy:

• In vivo: Gene therapy where genetic material is transferred directly into cells within the body.

• Ex vivo: Gene therapy involving modification of cells outside the body before transplanting them back in.