Cell Biology, Genetics, and Evolution: Key Concepts
Hypothesis: statement about observations. Prediction: quantifiable + specific. Characteristics: common chemical composition, cells, convert environment to bio, extract energy, homeostasis, genetic info: develop, maintain, function, reproduce, use genome to produce proteins, evolve. Major events: Formation of cells (prokaryote), Photosynthesis, Aerobic metabolism, Eukaryotic cells, Multicellularity and Specialization. Evidence: Cyanobacteria (prokaryote), Photosynthesis, Colonial, Stromatolites. Atoms, small molecules, large molecules, cells, organism, population, community, ecosystem, biosphere. Polar (hydrophilic): water, C-O, H-O, N-H, P-O, non-polar (hydrophobic): C-C, C-H, C-N. Hydrogen bonds from bond polarity. Ions are attracted to poles of water. Functional groups: Hydroxyl: R-OH (form H+ bonds with water), Aldehyde: R-C-H=O (reactive, energy releasing). Keto: R-C=O (Polar, energy reactions). Carboxyl R-C-OH=O (acidic, lose H+), Amino R-N-H-H (Basic), Phosphate R-O-P-O–-O–=O (negative charge), Sulfhydryl, R-SH (covalent bonds), methyl R-CH3 (non-polar, low reactive). Carbs: (monosaccharide, glycosidic link), aldehyde + hydroxyl. energy, structure, membrane connection/communication. Lipids: triglycerides (fatty acids + glycerol, ester link, unsaturated = bent, because double bond, Less H), many nonpolar CH, carboxyl, energy storage, cell membranes (Hydrophobic tail), energy capture, signaling, hormones and vitamins, Thermal + electrical insulation, Water repelling. Protein: (amino acids, peptide link) amino + carboxyl. Enzymes, Defense, Hormones, Receptors, Storage, Structural, Transport, Gene Regulation. Primary: Peptide + order of side chains = polypeptide. Secondary: between amino + carboxyl of another (hydrogen bonds). Tertiary: side chains, 3D, hydrogen bonds, hydrophobic interactions, ionic bonds, or disulfide bridges (covalent), folded polysaccharide. Quaternary: between polypeptides, same bonds as 3rd, weak interactions = easy change shape. Nucleic Acids: (Phosphodiester bonds, nucleotide = nucleoside + phosphate), code for protein primary. DNA -> RNA -> Polypeptide. Cell Membranes: More phospholipids with unsaturated fatty acid tails = more fluid membrane, Cholesterol stabilizes. Integral: partly embedded. Transmembrane: through both sides. Peripheral: in the heads. Carbs are tags/labels, Integrin “grabs” matrix, binds to cytoskeleton. Functions: Cell recognition + adhesion, Compartmentalization + organization, Energy transformation, Signaling/Communication. Passive Transport: along gradient, simple diffusion (no protein, small, non-polar, hydrophobic lipids, O2, CO2), diffusion through channel, facilitated diffusion (membrane proteins, Osmosis (aquaporins): Hypertonic= more solute). Active Transport: ATP hydrolysis/phosphorylation against gradient, coupled transporters, pumps (Ca+). Primary: ATP directly, phosphate changes pump shape, ions (Ka+) (Uniport: 1, Antiport: 2 opp direction). Secondary: energy to move from gradient by pump (Symport: 2 same direction). Vesicle (active): Endo/Exo-cytosis, Phagocytosis (eating bacteria), Pinocytosis (drinking). TEST 2: Signal Transduction: Signal-Receptor-Response, 1 receptor: 1 signal, Autocrine: in cell, Juxtracrine: cell to cell, Paracrine: cell to cell no touch, Endocrine: hormones, blood stream, specific receptor, Ligand = signal, signal changes shape of receptor because phosphorylation. Membrane receptors: Ion Channel: ion binds: receptor opens channel (Na+) Protein Kinase: phosphorylate proteins, PK cascades G Protein-linked: use G-proteins as an intermediate, Signal activates G-protein, GDP -> GTP -> effector protein produces second messenger (cellular response, back to GDP). Second Messengers: amplify signals, signal cascades. SA:V limits cell size, deal with by: add internal membranes, create cell membrane projects (villi), elongate/change cell shape, increase SA, but not cell V. SA directly related to rate of diffusion. SA doubles, V more than doubles. Cytoskeleton: provides structure + movement, composed of protein fibers, cell support, shape, movement, organelle position + movement, anchor cells. consists of microfilaments, intermediate filaments, microtubules. Microfilaments: help cell move and determine cell shape, Actin monomers, change length, attach or separate (dynamic instability), interact with other proteins. Intermediate Filaments: made of fibrous proteins, move/take up food, anchor organelles, various rope-like proteins, stable, permanent, shape/structure of cell, join different cells (desmosomes in animal cells). Microtubules: transportation, largest, form a dynamic internal skeleton and transportation network, tubulin dimers (α,β), form long, hollow tubes, change length, dynamic instability, form interior of cilia + flagella, important in movement. 9 doublets of microtubules, two single microtubules on inside, Interact with motor proteins. ATP phosphorylation, Dynein: Motor protein, slides microtubules past each other. Nexin (links microtubules) stops this (causes cilia to flex). Organelles move along microtubules using motor proteins, ATP phosphorylation, Kinesin (motor protein). Extracellular Matrix: made of fibers in a gel-like medium. Plant Cell Wall: support, limit volume, barrier to infection. Animal Cell: collagen, proteoglycans, hold together tissues, cell recognition, framework for skin, bone cartilage. Cell membrane proteins (Integrins) link extracellular matrix and cytoskeleton. Cell Junctions: connect cells, tight junctions (nothing gets through), Desmosomes (looser, keratin, intermediate filaments), gap junctions (small pores). Cells provide compartments for chemical reactions, all have cell membrane, cytoplasm, ribosomes. Ribosomes make proteins, made of rRNA + protein, assembled in nucleolus, protein synthesis, in cytoplasm (free) or on RER (bound). Nucleus, membrane bound, DNA and associated proteins, Nucleolus, site of transcription not translation. Endomembrane: plasma membrane, nuclear membrane, RER, SER, golgi, lysosomes, vesicles. ER: protein synthesis + chemical modification. SER: lipid synthesis, toxin modification, glycogen breakdown, calcium storage. RER: bound ribosomes, protein synthesis, protein modification, protein transport. Golgi: processes proteins and aids in secretion, cisternae, cis(same), trans(opp), vesicle. Lysosomes: derived from the Golgi, Primary: digestive enzymes (break down macromolecules), Secondary: fused with phagosome (food vesicle), autophagy. Mitochondria: transform chemical energy to ATP, fuel molecules (carbohydrates, proteins, lipids), membranes (outer, inner), cristae (folds), matrix (inner folds). Chloroplasts: light to sugar, membranes (outer, inner), stroma (cytoplasmish), thylakoid (pancake), granum (stack). Peroxisomes: accumulate, detoxify peroxides which could damage cells. Vacuoles: store and detoxify waste products, move water. Domains of Life: Eukarya (plants, animals, fungi, protists, nucleus). Bacteria + Archaea (cell wall, no DNA membrane). Chemical Reactions: 1st Law of Thermo: energy neither created or destroyed. 2nd Law: Energy is lost (entropy, increases with # of reactions). Anabolic: consume energy (+ΔG, -ΔS). Catabolic opposite (spontaneous). Catalysts increase the rate (how quickly products are produced) of reaction, do not cause reactions, lower activation energy. Enzymes: bind specific reactants at their active sites, specific, reusable. Cofactors: metal ions (non-protein), Coenzymes (not permanent), Prosthetic groups (permanent). Metabolic pathways: intermediate products, regulated by inhibition Inhibition: reversible, Competitive: bind to active site, Uncompetitive: block binding. Noncompetitive: binds elsewhere to stop (allosteric, enzyme changes shape). Pathways regulated by negative feedback.
Energy stored in covalent bonds is released by glycolysis and cellular respiration. Redox reactions: transfer energy, oxidation lowers the energy held by carbon. NAD+: electron carrier, used for redox reactions, (NAD+ (reduc)->NADH (oxi)-> NAD+) Cellular Respiration: Glycolysis (cytoplasm, 2 ATP): 2 pyruvate, 2NADH, 2H2O 2 ATP. Energy Investing (kinases): glucose used, ATP investment, phosphate transfer, 2G3P produced. Pyruvate Oxidation: (across m membrane, both): 2 NADH, 2 Acetyl CoA, 2 ATP, 2CO2 (waste). CAC (matrix, redox, last 4 C oxidized to CO2, NAD+ reduced by dehydrogenases, O’s oxidized, in: 1 Acetyl CoA, H2O, NAD+, FAD, GDP): 3NADH, FADH2, 2CO2, ATP Oxidative Phos (inner membrane): ETC: Respiratory chain, need oxygen to oxidize protein, energy from proton gradient from diffusion of protons through ATP synthase, substrate level: redox and kinase Chemiosmosis: protons pumped to make a gradient, coupled with ATP synthase, O2 is final electron acceptor. Fermentation: oxidize NADH so cells can use NAD+. Photosynthesis: 1Light Reactions (thylakoid membrane): Cyclic (across thyla mem): one photosystems(transmembrane proteins, NOT in outer membrane of chloroplast), no e- carrier, produces ATP, produces proton gradient in thylakoid interior. Non-cyclic (thylakoid membrane): electrons from water moved to NADP+ then reduced to NADPH, ATP. 2Carbon Fixation (dark, stroma): 2 photosystems, NADPH and ATP produced. 1Carbon fixation (ATP is used to bond CO2 to an organic molecule like sugar, carbon is reduced), 2Reduction of 3PG (sugars like 3PG donate their electrons to NADP+), Regeneration of the CO2 acceptor (ATP is consumed to recreate RuBP). Test 3:Nucleic Acids: complementary base pairs hydrogen bonded, 3′ OH of sugar to 5′ of next phosphate. Purines to pyrimidines(3 bonds), 3′ leading. DNA lacks OH on 2′, uniform diameter (Chargaff’s Rule A=T, C=G), antiparallel, right handed chirality, major and minor grooves (edges of N bases exposed, allows for binding) PCR: uses a DNA primer) Replication (origin of replication): How genome copied, condensation Separation: “ori” sequence, Helicase (ATP hydrolysis) Extension (starts with RNA primer, which is produced by primase): DNA polymerase adds nucleotides to free 3’OH. Leading Strand: continuously made, template/read 3′-5′, newly synthesized/made 5′-3′. Lagging: Okazaki fragments. DNA polymerase removes RNA primers and recently synthesized RNA fragments, DNA ligase patches new DNA. Division: G1 – Normal cellular function, S – DNA replication (two sister chromatids), G2 – Preparation for mitosis (build microtubules), Mitosis and cytokinesis. Checkpoint: cell health, DNA damage, bad replication, poor spindle attachment, means apoptosis. RB: stop (active, present). Cyclin-D-Kinase: phosphorylate RB to inactivate RB and activates E2F. CDK always present, not always active. Cyclin (expression triggered by growth factors): allosterically activates/opens site CDK, Cyclins inhibited by p21 which stops process, phosphorylation of p53 makes p21, p53 stops when mutagen. Transcription (RNA from DNA: mRNA, tRNA, rRNA, microRNA, snRNA, initiator/ terminator sites are in DNA. 1RNA polymerase recognizes a promotor. Elongation: extends RNA by phosphodiester binding with rNTPs, no proofreading. Termination: releases RNA and RNA polymerase. mRNA: modified after transcription, nucleus, Intron (NOT part of mature mRNA), Exon, Poly-A tail, 5′ Cap. Translation: NO promoter, start codon 5’AUG, stop codon not included in polypeptide. mRNA to proteins (need mRNA template, ribosomes (rRNA), tRNA (linked to amino acids). Code is redundant but not ambiguous. tRNA reads mRNA and determines amino acid, tRNA synthase uses ATP to add amino acid to the 3′ end of a tRNA. Initiation: 5′ cap, initation complex, small subunit, start codon (5’AUG). Elongation: joins amino acids. Termination: ends polypeptide chain, protein release factor. Proteins made in cytoplasm or ER. Test 4: Mutations: point mutations, deletions or additions, can produce incorrect proteins. Transition: purin:purin, transversion: purin:pyrim. Silent Mutations: no effect on translation. Missense: cause amino acid change. Nonsense: produce stop codon in mRNA early. Frameshift: shift entire reading frame. Chromosomal: Deletion (ABCD, ABD), Duplication (ABCDEFG,ABCDCDEFG), Inversion (ABCD,DBCA) Reciprocal (ABCD, ABEF). Spontaneous: Replication errors, Tautomers, Chemical reactions alter structure, Meiotic error. Induced: Nitrogenous base modification, Radiation. Sexual Reproduction: gametes, spores, meiosis, fertilization, zygote. Meiosis makes Haploid (N) from Diploid (2N). Segregation: pairs of alleles are separated when gametes are formed. Independent Assortment: pairs of alleles will be sorted independently of one another when gametes are formed. Meiosis I: homologous pairs separate. Meiosis II: sister chromatids split, 4 cells, haploid from diploid, no replication. Crossing-over: recombines genes within a homologous pair. Alleles: different forms of a gene, assort in Meiosis I, Homologous pairs separate (M1), Duplicates separate (M2). Sister chromatids with the same alleles segregate in M2. Law of Segregation: one of each allele in offspring. Law of Independent Assortment: which allele you get is random. Incomplete dominance: heterozygotes have a new different phenotype. Codominance: both alleles expressed. Sex-linked: like on X chromosome. Epistasis: one locus masks another locus. Evolution: biological change in populations over time. Hardy-Weinberg Equilibrium: null hypothesis, p^2+2pq+q^2=1 Random mating, No gene flow, No mutation, No genetic drift, No selection. Genetic drift: Founder effect: small number starts population, Bottleneck: drastic reduction in number. Natural selection occurs when individuals differ in their ability to survive or reproduce, acts on phenotype, specific to environment. Heritability: The amount of phenotypic variation in a trait that is due to genetic variability. Selection: Individual fitness and reproductive success, Some traits are advantageous, Change population frequency, Selection pressure, does NOT make new phenotypes. Stabilizing: No change in the mean, Loss of extremes., Less variation. Disruptive: Mean doesn’t change, Increases variance, Bimodal distribution. Species: Species can be morphologically different, distinct lineages, should be reproductively isolated. Isolation prevents exchange of genes between species. Allopatry, Reproductive barriers prevent gene flow, prezygotic, postzygotic. Habitat differences assortative mating, Breeding season temporal, behavioral traits, Physical characteristics mechanical, Sperm/egg characteristics gametic. Post-zygotic barriers act after fertilization, Hybrid sterility, Low hybrid fitness, Adults, Zygotes