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Final Exam Study Guide

by: Ally Bradfield

Final Exam Study Guide 1020

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These notes cover the material on the final exam.
Principles of Biology
Dr. Zanzot
Study Guide
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This 27 page Study Guide was uploaded by Ally Bradfield on Friday April 29, 2016. The Study Guide belongs to 1020 at Auburn University taught by Dr. Zanzot in Fall 2015. Since its upload, it has received 20 views. For similar materials see Principles of Biology in Biology at Auburn University.


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Date Created: 04/29/16
Biology Final Exam Study Guide UNIT 1 Evolution: the process of change that as transformed life on earth from its earliest beginnings to the diversity of organisms living today -accounts for the unity and diversity of life Biology: the scientific study of life Emergent properties: new properties that emerge with each step upward in the hierarchy of life -owed to arrangement and interactions of parts as complexity increases -elements and compounds Reductionism: reducing complex systems to simpler components that are more manageable to study by looking at a small part to reveal truth about the whole Systems biology: an approach to studying biology that aims to model the dynamic behavior of whole biological systems based on a study of interactions among the system’s parts Levels of Biological Organization 1. Biosphere: includes all living things on earth 2. Ecosystems: living and nonliving things in an environment, together with their interactions 3. Communities: entire array of organisms inhibiting a particular ecosystem 4. Populations: all of the individuals of a species living within the bounds of a specified area 5. Organisms: individual living things 6. Organs and organ systems: consist of two or more tissues, create teams that cooperate in a specific function (organ system) 7. Tissues: made up of a group of cells that work together to perform a specialized function 8. Cells: life’s fundamental unit of structure and function 9. Organelles: various functional compounds present in cells 10. Molecules: a chemical structure with two or more small chemical units (atoms) Interactions between organisms ultimately result in: the cycling of nutrients in ecosystems Global climate change: a change in the world’s climate Evolutionary adaptation: an accumulation of inherited characteristics that enhance organisms’ ability to survive and reproduce in specific environments -ex. Brown bears and polar bears Growth and development Baby>adult Egg>baby>adult Energy processing: organisms take in energy and transform it to perform all of life’s activities (characteristic of life) Regulation: helps regulate environment LIFE: -carbon based -requires water -has DNA based transfer of hereditary information -made up of cells -integrated with other organisms Life is organized by a hierarchy of biological organization Life requires: -energy transfer and transformation ex. Photosynthesis Structure and function are correlated at all levels The continuity of life -based on heritable info in DNA form Feedback mechanisms: regulate biological systems -negative feedback: accumulation of an end product of a process slows that process -positive feedback: an end product speeds up its production Not common, hard to control Eukaryotic cells: cells with a membrane-enclosed nucleus and other internal organelles Prokaryotic cells: cells lacking a membrane-enclosed nucleus and membrane-enclosed organelles (bacteria and archaea) Kingdoms and domains are the broadest units of classification Chordata: animals with backbones 3 levels of domain: -bacteria -archaea -eukarya Tree of life: common ancestor waded out to several niches Science: a way of knowing about the natural world by making observations and testing hypotheses Inquiry: a search for information and explanation with specific questions Data: recorded observations Qualitative data: information that describes physical characteristics Quantitative data: numerical data generally recorded as measurements Inductive reasoning: collecting and analyzing observations can lead to important conclusions based on a type of logic Hypothesis: tentative answer to a well framed question Deductive reasoning: reasoning from the general to the particular, or cause and effect Controlled experiment: designed to compare experimental group with a control group Theory: broad based framework for explaining natural phenomena generating testable hypotheses -must be supported by observational and experimental evidence Model organism: a species that is easy to grow in the lab and lends itself particularly well to the questions being investigated Matter: what organisms are composed of -consists of chemical elements in pure form and in compounds -takes up space -has mass -can exist as solid, liquid, or gas Element: substance that cannot be broken down by chemical means Compound: substance of two or more elements combined in a fixed ratio Elements that make up living matter: -O,C,H,N = 96.3% Trace elements: elements required by an organism but only in minute quantities Atoms: smallest unit of matter, indivisible by chemical means Nucleus: the central part of an atom Proton: nuclear particle with a positive charge Neutron: nuclear particle with no charge Subatomic particles: tiny bits of matter that atoms are composed of -neutrons, protons, and electrons electrons: atomic particle with negative charge 1 dalton = 1 amu (atomic mass unit) Location -protons: nucleus -neutrons: nucleus -electrons: clouds of negative charge John Dalton -developed atomic theory Atomic number: determined by number of protons Atomic mass: determined by number of protons plus neutrons Isotope: different versions of elements (same number of protons but different number of neutrons) Radioactive isotope: unstable, nucleus decays spontaneously and gives off particles of energy Chemical reactions make and break bonds -bonds: interactions between electrons -energy: the capacity to do work or effect change -potential energy: energy that matter possesses because of its location or structure Electrons have this because of arrangement in relation to the nucleus: negatively charged electrons are attracted to the positively charged nucleus, creating more potential energy as there is more distance between the nucleus and electron Electrons potential energy is determined by its energy level Electron shells: where electrons are found and each shell with a characteristic average distance and energy level Valence electrons: number of electrons in the outermost shell Valence shell: outermost electron shell Orbital: 3D space where electrons are found 90% of the time Chemical bonds: how molecules are formed -strong types: covalent, ionic -weak types: hydrogen bonds, vander waals Covalent bond: sharing a pair of valence electrons by 2 atoms -Nonpolar covalent: when electronegativity is equal between 2 of the same atoms -Polar covalent: when one atom is bonded to a more electronegative atom and the electrons of the bond are not shared equally, polarity varies Ionic bonds: one atom gives electron away in order to create full electron shells, when cations and anions attract Ions: charged atoms or molecules, protons don’t equal electrons Cation: + charged ion Anion: - charged ion Ionic compounds: compounds formed by ionic bonds (salts) Hydrogen bonds: noncovalent bond between a hydrogen and electronegative atom Van der waals attraction/interaction -typical in nonpolar molecules -asymmetry in charge distribution -large molecules packed together -weaker than hydrogen bonds ex. Gecko climbing walls Concentration of reactants affect the rate of reactions Chemical reactions: make and break bonds, reversible Equilibrium: rates of forward and reverse reactions are the same 4 Emergent properties of water 1. Cohesion of water molecules 2. Moderation of temperature by water 3. Ice floats 4. Water is the solution (at least the solvent) Cohesion: hydrogen bonds sticking together Adhesion: clinging of one substance to another Surface tension: a measure of how difficult it is to stretch or break the surface of a liquid Kinetic energy: the energy of motion Heat: form of energy, total kinetic energy (measured in calories) Temperature: a measure of heat intensity that represents the average kinetic energy of the molecules, regardless of volume Kilocalories: food calories Specific heat: the amount of heat required to change temperature Why does ice float? Lower density, hydrogen bonds cause ice to expand What happens when water begins to freeze? Molecules are moving too slow to break hydrogen bonds Solution: a uniform mix of 2 or more substances -aqueous: solution where water is the solvent Solvent: the liquid dissolving reagent in a solution Solute: the dissolved reagent in a solution Precipitate: undissolved solute which falls out of the solution Hydration shell: sphere of water molecules around dissolved ion in a solution, eventually dissolves all ions Hydrophilic substances: substances that attract water (ionic/polar) Hydrophobic substances: substances that repel water (nonpolar and nonionic) Molarity: number of moles solute per liter Molecular weight: sum of atomic weight Water can dissolve into ions H+ and OH- Acids: compounds that contribute H+ ions, pH less than 7 Bases: compounds that contribute OH- ions, pH greater than 7 pH = -log[H+] Buffers: act as acids or bases or both, are weakly ionizing Bicarbonate: important buffer in vertebre blood Metabolism: the totality of an organism’s chemical reactions, emergent property of life that arises from interactions between molecules within the cell Pathways -Metabolic pathway: begins with a specific molecule and ends with a product by enzymes catalyzing each step -Catabolic pathways: release energy by breaking down complex molecules into simpler compounds ex. Hydrolysis: adding water to break things down -Anabolic pathway: consume energy to build complex molecules from simpler ones ex. Synthesis of protein from amino acids Bioenergetics: study of how energy flows through living organisms Energy: the capacity to cause charge Thermodynamics: study of energy transoformations Isolated system: system isolated from its surroundings Ex. Thermos Open system: energy and matter can be transferred between the system and its surroundings Laws of Thermodynamics 1. (Principle of Conservation energy) energy can be transferred and transformed but it cannot be created or destroyed 2. Every energy transfer or transformation increases the entropy of the universe Entropy: a measure of disorder or randomness in the world Spontaneous processes: living cells unavoidable convert organized forms of energy to heat -occur without energy input -can happen at any rate Gibbs free energy: energy that can do work when temperature and pressure are uniform Free energy: a measure of a systems instability, tendency to change to a more stable state Reactions -Exergonic reaction: proceeds with a net release to free energy and spontaneous, puts energy out -Endergonic reaction: absorbs free energy from its surroundings and nonspontaneous Equilibrium in metabolism: state of maximum stability, never at equilibrium UNIT 2 Nucleus -contains most DNA and cell genes -makes eukaryotic cells eukaryotic Ribosomes -use info from DNA to make proteins -made of ribosomal RNA and a protein -carry out protein synthesis in two locations: cytosol & outside of ER Nuclear Envelope -encloses nucleus -separates nucleus from cytoplasm -has a double membrane and lipid bilayer Chromatin -has a protein and DNA -uncondensed and most nucleus contents Nuclear Lamina -referred to as the “sheet” -inside the nucleus in order to keep it from collapsing -makes up intermediate filaments Endoplasmic Reticulum -more than half of the total membrane -continuous with nuclear envelope in two regions: Smooth ER -synthesizes lipids -metabolizes carbohydrates -detoxifies drugs and poison -stores calcium ions Rough ER -has bound ribosomes -distributes transport vesicles -has a membrane factory for the cell Vesicles: have components that are continuous or are connected by transfer of it -transport vesicles: proteins surrounded by membranes -tiny little vessels of plasma membrane -move by motor protein along tubules to where it needs to be Glycoproteins: type of protein that covalently bonds to carbohydrates Endoplasmic system contains: -nuclear envelope -endoplasmic reticulum -golgi apparatus -lysosomes -vacuoles -plasma membrane Cisternae -flattened membrane sacs -folds of an inner membrane -maximizes surface area Golgi Apparatus -has cisternae -modifies products of the ER -manufactures some macromolecules -sorts and packages materials into transport vesicles Lysosome: membranous sac of hydraulic enzymes that can digest macromolecules -lysosomal enzyme hydrolyzes proteins, fats, polysaccharides, and nucleic acid, works best in acidic environments Autophagy: self eating Vacuole (in plant or fungal cells from ER) -Food: formed by phagocytosis -Contractile: in freshwater protists and pumps excess water out of cells -Central: in mature plant cells, holds organic compounds/water Pathogenic causes disease Eukaryotic cells are diverse in shape and multicellular Nucleic pores: let things in and out of nucleus Cytoskeleton -L: microtubules: where more vesicles need to go, tubes, resist compressions -M: intermediate filaments/fibers: only in animals, long lasting, make nuclear lamina, range in diameter, larget -S: microfilaments: made of active proteins, threadlike, solid rods, twisted double chain of actin, bear tension, make up core of microvilli intestines, on cerebral of the cell (outside) Protein dymers -referred to as “tubulin” -is alpha/beta -makes up lumen Cillia and flagellum -function based on interaction and is between microbuses and motor proteins Myosin -Active: moves right -Passive: moves left Cells -make up all organisms -simplest collection of matter considered to be living -structure based on function -size related to descent, metabolic requirements, and surface area: volume ratio Light microscope: light passes through specimen and through glass lens Magnification: ratio of object image size to real size Resolution: measures clarity or minimum distance of 2 distinguishable points Contrasts: visible differences in parts of the sample Amphipathic: hydrophilic and hydropathic Plasma membrane -has two types of molecules -boundary separating cell from outside -selectively permeable Fluid mosaic model: has various embedded proteins Proteins -Peripheral: bound to surface of membrane -Integral: penetrates hydrophobic core, hydrophobic region of integral proteins, stretches of nonpolar amino acids -Transmembrane: span of membrane -Transport: allows passage of hydrophilic substances across a membrane Transport enzymatic activity: anchors enzymes that have similar functions -Channel: hydrophilic channel that certain molecules/ions use as tunnel (aqauaporin), provides corridors that allow them to cross the membrane Single transduction: transmits a signal (stimuli) and the molecules interact with proteins (how neurons work) Diffusion: tendency for molecules to spread evenly, spontaneous, molecules move randomly, has dynamic equilibrium (when as many molecules cross in one direction as in the other) -Osmosis: diffusion of water over a selectively permeable membrane from a region of lower solute to a concentration that is higher Tonicity: has ability of surrounding solutions to cause cells to gain/lose water -Isotonic: when a solute concentration is the same as the inside of the cell, no movement -Hypertonic: when solute concentration is lower in cell, cell loses water -Hypotonic: when solute concentration is higher in cell, cell gains water Electron Microscopy: used to study sub cellular structures -Scanning: microscope focuses a beam of electrons onto surface (3D) -Transmission: focuses a beam of electrons through specimen, internal structure Cell fractionation: takes cells apart and separate the major organelles from one another and separates cells into component parts Basic features of Cells -plasma membrane -semi fluid substance -chromosomes -ribosomes Prokaryotes -no nucleus -unbound region -cytoplasm bounded by plasma membrane Eukaryotes -protists, fungi, animals, plants Functions of Plasma Membrane -selective barrier -allows passage of oxygen nutrients and waste -double layer of phospholipids Mitochondria -site of cellular respiration -the metabolic process that uses oxygen to generate ATP -in nearly all eukaryotic cells -has smooth outer membrane and inner membrane of cisternae Chloroplast -found in plants and algae -sites of photosynthesis Endoplasmic theory: idea that early ancestors of eukaryotic cells in prokaryotic cells and the eukaryotic cell and mitochondria merge into a single organism Chlorophyll -green pigment -found in leaves and other green organisms and in algae Peroxisomes -specialized metabolic compartments bounded by a single membrane -produces hydrogen peroxide and convert it to water -performs reactions with different functions Cytoskeleton -network of fibers extending through cytoplasm -organizes cell structure and activities -anchors organelles -supports cell -intact with motor proteins -vesicles travel along it -helps regulate biochemistry activity Centrosome: microtubule organization center that microtubules grow out of Cilia: controlled by microtubules and differ in beating pattern Flagella: core of microtubules sheathed by plasma membrane that has a basal body that anchors it Cell wall: extracellular structure, maintains shape, prevents uptake of water, has multiple layers, made of cellulose fibers imbedded in polysaccharides and proteins -Primary layer: thick and flexible -Middle layer: thin layer -Secondary layer: between plasma membrane and primary cell wall Extracellular matrix: made of glycoproteins and covers animal cells instead of cell walls -Integin: extracellular matrix in a plasma membrane Cell junction: neighboring cells in tissue/organ/organ system and acts through physical contact -tight: membranes of neighboring cells pressed together preventing leakage of fluid -gap: communicating junctions that provide cytoplasmic channels between adjacent cells Plasmodesmata: channels that perforate plant cell walls -water and small solutes can pass from cell to cell Desmosomes: anchor functions and fasten cells together in strong sheets Facilitated diffusion: transport proteins speed the passive movement of molecules across plasma membrane -can move solutes across concentration gradients Active transport: moves substances across concentration gradient Membrane potential: voltage difference across a membrane Electrochemical gradient 2 combined forces (chemical and electrical) -drives diffusion of ions across the membrane Exocytosis -transport vesicles migrate to membrane and fuse with it to release contents -secretory cells use this to export their products Endocytosis -cell takes macromolecules by forming vesicles from plasma membrane involves different proteins than exocytosis Metabolism: totality of an organism’s chemical reactions, emergent property of life, from interactions between molecules and cells -Metabolic pathway: catalyzed by a specific enzyme and begins with specific molecules and ends with a product -Catabolic pathway: release energy by breaking down complex molecules into simple -Anabolic pathway: building complex molecules from simpler ones Cellular respiration: breaking down glucose to make ATP Biogenetics: study of how organisms manage their energy sources Energy: capacity to cause change, converted from one to another type of energy Forms of energy -kinetic -heat -potential -chemical -light Thermodynamics: study of energy transformation, isolated system, open system Phospholipids: most abundant lipid in plasma membrane, amphipathic Osmoregulation: controls solute concentration and water balance Paramecium: hypertonic using contractile vacuole as a pump 3 Types of Endocytosis -Phagocytosis -Pinocytosis -Receptor Energy coupling: exergonic process to drive an endergonic one Catalyst: chemical agent that speeds up a reaction without being consumed by the reaction Enzyme: catalyst protein, catalyzes reactions by lowering Ea barrier -doesn’t affect the change in free energy -hasten reactions that occur eventually Activation energy: chemical reaction of bonds breaking and forming Substrate: reactant that an enzyme acts on Induced fit: brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction Cofactor: nonprotein enzyme helpers, inorganic Coenzyme: organic cofactor involving enzymes Enzyme Inhibitors -Competitive: binds to active site of enzyme competing with substrate -Noncompetitive: binds to another part of an enzyme to change shape Chemical chaos: cells metabolic pathways were not tightly regulated, cell turns genes on or off to encode enzymes or regulate activity of enzymes Allosteric regulation: occurs when regulating molecules bind to proteins at one site and affects the proteins function at another site, inhibit or stimulate enzyme activity -cooperatively: amplifies enzyme activity Feedback inhibition: end product of metabolic pathway shuts down the pathway -prevents cell from wasting chemical resources by synthesizing more product than needed Redox reactions: transfer of electrons during chemical reactions release energy stored in organic molecules, released energy ultimately used to synthesize ATP Reduction: when a substance gains electrons Anabolic respiration: uses electron transport chain with a final electron accepter other than O2 Fermentation: uses substrate level phosphorylation instead of an electron transport chain to generate ATP -consists of glycosides plus reactions that regenerate NAD+ -can be reused by glycolysis Obligate anaerobes -carry out fermentation or anaerobic respiration -cannot survive in presence of O2 Facultative anaerobes -yeast and many bacteria -survive using fermentation or cell respiration Pyruvate: fork in metabolic road that leads to two alternative catabolic routes UNIT 3 Cell division: parent cell divides into two or more daughter cells -prokaryotes go through binary fission Chromosomes replicate, a copy of the origin moves to the other end of the cell until replication is complete, the plasma membrane curves in and a cell wall is made to separate two daughter cells. -eukaryotes (somatic cells) go through mitosis & (gametes) go through meiosis Interphase: GI, S Phase (DNA synthesis/replication), G2 Prophase: Chromosomes condense, mitotic spindle begins to form, centrosomes move and the nucleolus disappears Pro-metaphase: Nuclear envelop fragments and spindle microtubules attach to kinetochores Metaphase: Mitotic spindle is complete, nuclear envelop is completely gone, and chromosomes align at metaphase plate Anaphase: Chromatids separate and resulting daughter chromosomes move to opposite poles of cell due to cohesion protein removal Telophase: Cytokinesis occurs, daughter nuclei form, and nuclear envelops form isolating each cell *** DNA replication does NOT occur in animals MAIN GOAL OF CELL DIVISION & REPRODUCTION OF CELLS: the continuity of life; repair, reproduction, development/growth Cell Cycle Regulation -Cyclins and cyclin-dependent kinases (CDKs) help control the cell cycle as regulatory proteins -Cyclin-CDK complex = Maturation Promoting Factor (MPF) enables G2 to go to M phase by phosphorylation -Cytoplasmic factor: chemical signals in cytoplasm ultimately drive cell cycle -Platelet-Derived Growth Factor (PDGF): regulates cell division through anchorage dependence (need for cell to attach to surface) and density dependence (need for cell to cover surface area through replication) Normal cell undertakes transformation to become a cancer cell -cancer cells make own growth factors and signals & continue to divide/grow -lose density and anchorage dependence -form tumors: masses of abnormal cells in normal tissue Benign tumors: remain at original site, harmless Malignant tumors: spread, harmful -Metastasis: spread of cancer through rapid proliferation and mestasizing (migrating to other parts of the body) Cancer Treatment -surgery -chemotherapy: targets cell division -radiotherapy/radiation: damages DNA Basics -DNA = sugar + phosphate + base (nucleotides) Nucleotide chain = nucleic acid Double helix with hydrogen bonds -DNA + proteins = chromatin Chromatin condenses into chromosomes Cleavage furrow: indention in cell surface where cytokinesis occurs Cell plate: basically the cleavage furrow in plant cells Reproduction -Asexual: mitotic division, producing genetically identical offspring (clone) -Sexual: gametes form zygote through fertilization, producing genetically different gamete offspring (gene recombination) Ploidy -n = one pair of homologous chromosomes -haploid: (n) ex. Somatic cells -diploid: (2n) ex. Zygote ***Polyploidy: having more than two pairs of chromosomes PURPOSE OF MEIOSIS: increase genetic variation -crossing over in Prophase I of homologous chromosomes -Independent Assortment allows alleles to be inherited without influence of others -Random fertilization Meiosis -> Produces 4 genetically different daughter cells -Interphase & M phase same as mitosis Interkinesis: no DNA replication Prophase II: spindle apparatus forms Metaphase II: chromosomes align at metaphase plate Anaphase II: sister chromatids separate to opposite poles Telophase II: cytokinesis, nuclear envelopes form Random/Independent Assortment -2^n when n = number of homologous pairs -> assortments -assortments^2 = number of combinations Basics Diploid cells -> haploid gametes -> fertilization -> diploid zygote ***Fungi go through meiosis AFTER fertilization Inheritance Hypothesis -Particulate: offspring are a combination of parents, variation is maintained over time, variation is maintained over time -Blending: offspring are a blend with new alleles, variation disappears over time Law of Segregation: alleles separate in meiosis randomly as parents are homozygous or heterozygous Benefits of the Pea-plant Experiment 1. Controlled mating & self fertilization of purebreds 2. Rapid reproduction producing a large number of offspring 3. Short generation time Crossing -Monohybrid cross: two individuals for one trait (heterozygous offspring) -Dihybrid cross: two individuals for two traits (heterozygous offspring for both) Genetic Linkage -Linked genes: inherited together since close to other on the same chromosomes -Genes on same chromosome usually inherited together til crossing over breaks linkage -Distance between linked genes =recombination frequency -Genetic Map: orders gene loci on chromosome -Linkage Map: genetic map based on recombination frequencies Dominance -Complete dominance: when phenotypes of heterozygous and homozygous are the same, the dominance allele covers up the recessive one completely -Incomplete dominance: new phenotype of F1 generation is between phenotypes -Codominance: phenotype shows both of parent phenotypes separately but included -Multiple alleles: when there are more than two alleles for a trait but only two are carried per person (ex. Blood type ABO) -Pleiotropy: one allele impacts multiple traits (ex. Albinism) -Epistasis: one gene influences phenotype of another (ex. Lab color) -Polygenic traits: traits that occur by gene interaction, leads to population variation -Norm of reaction: phenotype range of genotype influenced by environment Pedigrees Autosomal Dominant: equal likelihood for sexes, passed on, doesn’t skip generations, all kids have it when both parents do and half do if only one parent has it Autosomal Recessive: equal likelihood for sexes, skips generations, ¼ of offspring are affected if both parents are heterozygous for it, happens w/ consanquinity X-linked Dominant: more in females, doesn’t skip generations, daughters get it if one parent has it and sons get it if both parents have it, heterozygous mom dist. evenly X-linked Recessive: more in males, never passed from father to son, daughters of affected fathers are carriers Disorders -Autosomal dominant: Huntington’s, Achondropasia (dwarfism), Marfan syndrome (tissue formation) & polydactyly -Autosomal recessive: Ex. Albinism, cystic fibrosis, sickle-cell anemia -Sex linked: hemophilia, red/green color-blindness Multifactorial disorders: include environmental factors Ex. Heart disease, alcoholism, diabetes, etc. Nondisjunction: wrong number of chromosomes/chromatids separate Polyploidy: extra complete set of chromosomes (fatal) Aneuploidy: missing or extra copy of chromosome (trisomy vs. monosomy) Sex-linked Disorders -Down Syndrome: Trisomy 21 -Turner Syndrome: Sterile females (XO) -Trisomy X: females (XXX) -Kleinfelter syndrome: sterile males (XXY) -Jacob syndrome: low male IQ (XYY) Mendel: Law of Genetics- segregation & independent assortment Morgan: genetic material = genes & proteins Griffin: DNA genetically transforms bacteria Hershey-Chase: viruses inject DNA into bacteria DNA (deoxyribonucleicacid) 3 -> 5 -nucleotides: nitrogen base (ATCG), phosphate group, sugar -Chargraff’s rule: AT and CG pair -double helix (Watson Crick model) -two DNA & sugar phosphate backbone -antiparallel structure: A & T have 2 hydrogen bonds, C & G have 3 hydrogen bonds -A & G are purines and T & C are pyrimidines DNA Replication 1. Separate strands at origin site (replication bubble) 2. Helicase separates two strands 3. Single-strand binding proteins hold it open 4. Topoisomerases break and rejoin strands 5. Primase starts new strand with RNA primer 6. DNA polymerase replicates 5 -> 3 7. DNA polymerase replaces primer with DNA 8. Strands replicated 9. DNA ligase joins fragments on lagging strand 10. DNA polymerase proofreads nucleotides ***Telomerase lengthens telomeres (ends of chromosomes) in germ & cancer cells Replication fork -leading strand: continuous -lagging strand: fragmented (Okazaki fragments) DNA Packaging -DNA, nucleosome, packaged nucleosomes, looped domains, condensed chromatid, condensed chromosome -dNTPs are ATP but with deoxyribose instead of ribose -Prokaryotes elongate faster than eukaryotes Gene Expression (transcription & translation) DNA is transcribed -> mRNA -> polypeptide Beadle & Tatum: genes encode polypeptides GENETIC CODE -mRNA encode amino acids -triplet code: 1 amino acid has 3 nucleotides (codon) -stop codons: UAA, UAG, UGA -start codon: AUG -prokaryotes have simultaneous gene expression -eukaryotes separate gene expression by nuclear envelope Transcription: Synthesis of RNA Translation: Polypeptide Synthesis (in ribosomes) splicesomes: proteins see splice sites and sometimes splice ribozymes: RNA molecules splice tRNA: transfer amino acids to grow polypeptide aminoacytl-tRNA synthase: enzyme matches tRNA and amino acid Transcription & Translation Initiation -> Elongation -> Termination -prokaryotes terminate by terminator sequence -eukaryotes terminate by polyadenylation signal that caprs G at 5 and splices Mutations (caused by mutagens) -point mutation: affect one or few nucleotides, 1 base pair change Silent: no effect Missense: wrong codon Nonsense: nonfunctional, codon stops -frameshift mutation: insertion or deletion of nucleotides UNIT 4 Darwin challenged previous views of unchanging species. For example, Aristotle believed that all species were unchanging and ranked on a hierarchical ladder of perfected species. The Old Testament believes that God put every species on the Earth as already perfect and unchanging. Important people: Linnaeus created taxonomy: the naming and classifying of species into categories by genus and species. Cuvier created paleontology: the study of fossils. He also created catastrophism: the difference between strata is caused by catastrophe. Hutton and Lyell both had a very important impact on Darwin’s theory. Hutton created gradualism: geological changes over time. Lyell created uniformitarianism: geological processes haven’t changed. Lamarck believed in Use & Disuse: vestigial structures no longer being necessary in evolved species so those parts are thrown out or stored. He also believes in evolution by acquired characteristics. Malthus focused on population growth with the exponential model. Wallace introduced Darwin to natural selection and studied biogeography. Darwin’s Views: Wrote a book called the Origin of Species by Means of Natural Selection. Evolution: descent by modification Observations 1. Members of a population often vary in inherited traits. 2. All species can produce more offspring than the environment can support but many fail to survive/reproduce. Inferences 1. Individuals that inherit traits have a higher chance of survival/reproduction than others. 2. The unequal ability of survival/reproduction will lead to more favorable traits over generations. Homology: shared ancestors but varied functions, same/similar structures Comparative embryology: homologies are only present before birth Analogy: similar structure from convergent evolution (independent), no shared ancestry Microevolution Nonrandom factors: natural selection Random factors: genetic drift, gene flow *** IS NOT DRIVEN BY MICROEVOLUTION Macroevolution: patterns of evolutionary change above the species level Genetic variation enables evolution. Hardy-Weinburg Model/Equation Tests evolution in a population Gene maintained at HW equilibrium: 1. No mutations 2. Random mating 3. No gene flow 4. No genetic drift 5. No natural selection Natural selection: favorable inherited traits are more likely to survive/reproduce -leads to adaptive evolution by increasing the frequency of good alleles. Genetic Drift Founder Effect: population moves partially to a new location Genetic Bottleneck: population decreases by catastrophic event Most common in small populations. Leads to allele fixation (having only one allele for a gene) and loss in genetic diversity. Randomly changes allele frequencies. Gene Flow: spread of alleles within and to other populations, and random with different effects. ***NOT evidence for evolutkon Modes of Selection after Shift Directional: favors one extreme phenotypically Disruptive: favors both phenotypic extremes Stabilizing: favors middle variant Sexual selection -> mating success -> sexual dimorphism Diploidy (balancing selection) preserves genetic variation Speciation = new species = divergence of old species Biological species: group of populations that can interbreed and reproduce with each other not not successfully with other populations The Biological Species Concept (BSC) -> reproductive isolation, gene flow is required. Reproductive Isolation Pre-zygotic barriers: Habitat isolation- species live in a different place Temporal isolation- species breed at different times, seasons, etc. Gametic isolation- gametes come into contact but no fertilization takes place Behavioral isolation- species are capable of reproducing but don’t due to differences in mating techniques Mechanical isolation- incompatibility of structure of species to reproduce Post-zygotic barriers: Reduced hybrid variability Reduced hybrid fertility Hybrid breakdown Other concepts: morphological, ecological (species described by role in environment), and phylogenetic. Geographic Speciation Allopatic (other country, more common) Sympatric (same country) results from polyploidy, habitat differentiation, and sexual selection. The more barriers there are, the more biodiverse. Hybrid zones -> reproductive isolation Reinforcement of boundaries Stabilization of hybrid population Fusion of species Ecology: study of interactions between organisms and the environment Biological processes influence population density, dispersion, and demographics (how populations change in character, track survival/reproduction and sexual equality. Also can produce a survivorship curve). Survivorship Curves Type I: death rate starts low and increases later in life Type II: consistent death rates Type III: many offspring die at first, few live on Exponential Model Zero population growth: birth and death rates are equal Change in population = growth rate x initial population Logistic Model Population growth slows when half of the carrying capacity is reached. Allee effect: when a population is too small to effectively survive/reproduce Natural selection produces life history traits: 1. Age of first reproduction 2. Number of times an organism reproduces 3. How many offspring are produced at a time Semelparous species: reproduce once with lots of offspring, often occurs in an unstable environment Iteroparous species: reproduce several times with fewer offspring, often occurs in a stable environment K-selection: density dependent, favors few, more offspring r-selection: density independent Density Dependent Factors -disease -predation -territoriality -competition -toxic waste -intrinsic factors (hormones) Competition (-/-) species cannot coexist Predation (+/-) one kills another and eats it -predators develop claws, fangs, venom, etc. as adaptations -prey develop behavioral, mechanical, chemical, morphological, and physiological adaptations to avoid predation Herbivory (+/-) heterotroph kills and eats autotroph -autotrophs develop mechanical adaptations such as thorns, prickles, etc. and chemical adaptations such as toxic compounds Symbiosis: intimate, direct contact between species Parasitism (+/-) Mutualism (+/+) Commensalism (0/+) Facilitation (+/+) Mimickry -Batesian: harmless species mimics a harmful one -Mullerian: two harmful species mimic one another Character displacement: a tendency for characteristics to be more divergent in sympatric populations of two species than in allopatric populations of the same two species Niche: a species occupation using abiotic and biotic resources -fundamental (potential) vs. realized (actual) niches Competitive exclusion: two species competing for the same limited resource cannot coexist in the same habitat Resource partitioning: differentiation of ecological niches such that similar species may coexist in a community IMPORTANT INFORMATION Law of superposition: states that old rock is on the bottom and new rock is on the top Punctuated equilibrium: periods of apparent stasis marked by sudden change Gradual equilibrium: more gradual Viruses have the highest mutation rate (even over bacteria) Cline: gradual change in a trait along a geographical axis Hybrids usually suffer from alloploidy (different species) Autoploidy: own species Reinforcement: hybrids unequal to parent, low survival rate Fusion: fuses two species successfully Stability: hybrid is stable Random dispersion occurs in the absence of strong attractions or repulsion Clumped: attraction occurs Uniform: spread evenly Global -> Landscape -> Ecosystem -> Community


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