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Final Exam Study Guide

by: Kendall Mansfield

Final Exam Study Guide BIOL 1020

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Kendall Mansfield

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Principles of Biology
Min Zhong
Study Guide
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This 41 page Study Guide was uploaded by Kendall Mansfield on Wednesday December 2, 2015. The Study Guide belongs to BIOL 1020 at Auburn University taught by Min Zhong in Fall 2015. Since its upload, it has received 164 views.

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Date Created: 12/02/15
Biology Final Exam Study Guide: Biology Test 1: Chapter 1 What is Science? A. Science is a way of learning about the natural world. B. Science does not prove anything absolutely -- all scientific ideas are open to revision in the light of new evidence. C. The process of science involves making educated guesses (hypotheses) that are then rigorously and repeatedly tested. D. Characteristics of science: 1. 2. 3. 4. 5. 6. 7. E. List of scientific sources best to worst 1. Peer reviewed journals. 2. Reviewed texts (your book) 3. Science books. 4. Science magazines. 5. Newspapers/TV 6. Internet II. What is Biology? A. Biology is the study of life and living organisms by using scientific methods III. Characteristics of Living Organisms 1. 2. 3. 4. 5. 6. 7. IV. Levels of Biological Organization A. The living and nonliving world is organized at many levels B. Life can be studied at different levels of organization Which organizations? V. Cell Theory – all living organisms are made up of cells A. Eukaryotic cells: B. Prokaryotic cells: VI. Genetic Information Transfer in Living Systems A. Information must be transferred from one generation to the next. 1. 2. 3. 4. 5. VII. Life Depends on a Continuous Input of Energy A. Energy flows through an ecosystem, usually entering as light and exiting as heat 1. Producers (autotrophs) manufacture their own food from simple materials 2. Consumers (heterotrophs) obtain energy by eating other organisms (ultimate source of food is producers); use food and oxygen, and release carbon dioxide and water 3. Decomposers obtain energy by breaking down the waste products, by products, and dead bodies of producers and consumers. Usually bacteria and fungi. VIII. Scientific Methods A. Procedure of scientific methods: 1. 2. 3. 4. 5. B. A systematic thought process. 1. Deductive reasoning: Summarize the information at hand and draw conclusions from that information; proceeds from the general to the specific. 2. Inductive reasoning: Drawing a generalization from several specific observations; proceeds from the specific to the general. Must be careful, because it is impossible to prove the accuracy of the generalization. Chapter 2: The Chemical Context of Life You must understand chemistry to understand life (and to pass this course)! I. Elements and Atoms A. Elements – substances that cannot be further broken down into other substances (at least by ordinary chemical reactions) • Unique chemical property. • Composed of atoms. 2. Every element has a chemical symbol (H for hydrogen, O for oxygen, etc.); this is most familiar from the periodic table 3. Essential elements: • E.g. 4. Trace element: • E.g. 5. E.g.: Carbon B. Atom: the smallest unit of an element that still retains the properties of that element 1. The smallest unit of a substance, but not smallest particles. 2. protons, neutrons, and electrons. 3. Electron Cloud model: 4. Atoms consist of subatomic particles • electron - contributes no significant mass to the atom, but carries a (- 1) electrical charge • proton - contributes a mass of approximately 1 mass unit, and carries a (+1) electrical charge • neutron - contributes a mass of approximately 1 mass unit, and carries no net electrical charge 5. atomic nucleus: 6. atomic number = ? 7. Atomic mass = ? 8. Important roles Atoms are electrically neutral: # positive protons = # negative electrons C. Protons and neutrons are usually equal weight, but not always. D. Isotopes: Atoms of the same element that differ in the # of neutrons. e.g.: E. Radioisotopes: an isotope that has an unstable nucleus – loss of neutrons from the nucleus. 1. atomic nuclei can undergo changes (decay) 2. decay rates are statistical averages, and are used for measuring time passage in many areas of science (carbon dating, etc.) F. Electron shell: electrons move within restricted three-dimensional spaces. 1. 1 shell: full with 2 electrons 2. the n shell: can hold up to 2n electrons. 3. energy level: shell is at the higher energy level as it goes farther from the nucleus. 4. Opposite roles of the nucleus and the electrons: 5. Valence shell: II. Molecules and Compounds A. Atoms combine to form molecules and compounds 1. What is molecule? Definition: • may be composed of one or more elements (examples: O , H O) 2 2 • not all substances are molecular (NaCl, table salt, isn’t) • if a substance is molecular, then an individual molecule is the smallest unit of the substance that exhibits the properties of the substance • thus, a molecule differs in its physical and chemical properties from the elements that make it up 2. what is compound ? Definition: • compounds have unique physical and chemical properties that differ from those of the elements used to make it • some compounds are held together by covalent bonds and are therefore molecular; some are held together by ionic bonds (defined later) e.g. B. chemists use two types of formulas to describe substances 1. chemical formula - a shorthand formula showing the number of atoms of each element present in a molecule 2. structural formula - shows the arrangement of atoms in a molecule e.g. III. Chemical Bonds Hold Molecules Together and Store Energy A. Two basic principles: 1. 2. B. Attractive force to hold atoms together to form molecules. Losing, gaining and sharing electrons in the valence shell. C. Three types of chemical bonds 1. covalent bonds - bonds in which atoms share valence electrons. • Covalent bonds are stronger than ionic bonds but vary in their • stability • Two types: Polar and Nonpolar E.g. • Free radicals and antioxidants 2. ionic bonds - Atoms bonded through attraction of oppositely charged particles (ions) - exchange electrons. E.g.: 3. Hydrogen bonds - Formed when partially positive hydrogen atom in a polar covalent bond is attracted to a partially neg. atom in another polar covalent bond E.g.: D. Chemical bonds hold molecules together and store energy. E. In aqueous systems (such as living organisms), the effective relative bond strengths are: ___________bond > __________ bond > _________ bond IV. Chemical Equations Describe Chemical Reactions A. Reactants are written on the left B. Products are written on the right C. an arrow ( ) is used to show the direction the reaction proceeds D. double arrows of equal lengths ( ) indicate equilibrium reactions (reactions proceeding simultaneously at equal rates in both directions) E. Sometimes, different lengths of double arrows are used to indicate which direction is favored V. Oxidation-Reduction Reactions (redox reactions) Are Common in Biological Systems A. Oxidation: B. reduction: C. oxidation and reduction are always paired (hence redox reactions) D. Oxygen is common oxidizing agent (hence “oxidation”) E. example: rusting 1. when iron rusts, iron oxide is formed by the oxidation of iron; this can be described by a chemical reaction as shown below: § 4 Fe + 3 O2 2 Fe2O 3 2. during the process iron atoms (Fe) become iron ions (Fe ): 3+ § 4 Fe 4 Fe + 12 e - 3. on the flip side, the oxygen atoms gain electrons; we can say that the oxygen is reduced in the reaction: § 3 O 2 + 12 e 6 O 2- F. Redox in biological systems, typically molecules are oxidized and reduced Chapter 3: Water and Life Overview: Life as we know it requires water. All organisms that we know of are made mostly of liquid water, and most of their metabolism requires an aqueous medium. In addition, many organisms live in liquid water or in an environment dominated by water in its various states (solid, liquid, or gas). Some numbers: • cells are typically 70% or more water by mass • about 75% of the Earth’s surface is covered by liquid water But then, just being common on the Earth doesn’t make something essential for life. A large percentage of the Earth’s crust is sand, but we don’t consider sand a requirement for life. What is it about water that makes it so special? Water molecules are polar nature. G. oxygen atoms are electron seeking (electronegative), especially compared to hydrogen; thus for an oxygen-hydrogen bond: H. The polar character of water allows water molecules to form many (up to 4) hydrogen bonds. What properties of water are important for life? I. Cohesion of water molecules 1. Cohesion: e.g.: 2. Adhesion: e.g.: 3. Surface tension: J. Ability to moderate temperature 1. The unusual specific heat of water leads to temperature stability • specific heat – • High specific heat of water à temp. stability § • 2. Evaporative cooling 3. Heat of vaporization: • • • A. Expansion upon freezing 1. Freezes at 0 degrees Celsius – ice 2. 3. 4. B. Versatility as a solvent 1. Solution - 2. Solute - 3. Solvent – • The highly polar character of water makes it an excellent solvent for other polar substances! 4. Hydrophilic substances –. 5. Hydrophobic substances –. VI. Acids and Bases A. An acid is any substance that increases the H concentration of a solution. B. Acids are proton donors 1. An acid is a substance that dissociates in solution to yield hydrogen ions (H ) 2. H = one proton C. A base is any substance that reduces the H concentration of a solution D. Bases are proton acceptors E. water tends to slightly dissociate into hydrogen and hydroxide ions (H and + OH ) HOH H + OH - F. the pH scale is a convenient short hand notation to express the proton concentration of a solution 1. the pH of a solution is defined as the reciprocal of the logarithm of the proton concentration in the solution, or -log[H ] + -7 2. pure water (having a proton concentration of 10 M) has pH = 7 3. pH scale of acid and base: acid: pH ______ 7; base: pH ______ 7. 4. the pH of most living cells is usually around 7.2 to 7.4 G. buffers minimize pH changes 1. what is buffer? How does it work? E.g.: Chapter 4: Carbon and the molecular diversity of life I. Organic Compounds A. Organic compounds: B. Inorganic: C. Carbon skeletons: D. Wide diversity in organic compounds 1. Carbon has diverse bonding patterns. H. • Carbon atomic structure • How many valence electrons in a carbon atom? • How many covalent bonds can a carbon atom maximum form? • Bonding patterns • Valence = ? 2. Different molecular shape: chains, branches, ring, etc. 3. Length difference. E. Hydrocarbons – e.g. II. Isomers are molecules that have the same molecular formula but different structures; there are two kinds of isomers A. structural isomers e.g.: B. stereoisomers - substances with the same arrangement of covalent bonds, but the order in which the atoms are arranged in space is different; two important types for our use 1. cis-trans isomers • • 2. enantiomers – • • • III. Functional groups determine most of the reactive properties (functions) of organic molecules A. functional groups are groups of atoms covalently bonded to a carbon backbone that give properties different from a C-H bond B. Active. C. the properties of the major classes of organic compounds (carbohydrates, lipids, proteins, and nucleic acids) are determined mostly by their functional groups D. learn these seven functional groups (note: X here stands for the “rest” of the molecule) – including names, structures, properties. 1. hydroxyl group (X-OH): 2. carbonyl group (X-C=O): 3. carboxyl group (X-COOH): 4. amino groups (X-NH ): 2 5. sulfhydryl groups (X-SH): 6. phosphate groups (X-PO H ):4 2 7. methyl groups (X-CH ): 3 Chapter 5: The structure and function of biological molecules. IV. Macromolecules A. Macromolecules – large polymers Polymers: Monomers: Examples: B. Dehydration synthesis (condensation) and Hydrolysis 1. Associate with water. 2. Typically requires an enzyme. • What are enzymes? Functions? 3. Dehydration synthesis – monomers are covalently linked to form polymers by removing water. 4. Hydrolysis – polymers are degraded into monomers by adding water. • How does water work during the process? C. The four major classes of biologically molecules are: V. carbohydrates include sugars, starches, and cellulose A. Carbohydrate composition 1. 2. B. Functions: C. Most small carbohydrates are water soluble. D. Construction 1. monosaccharides are simple sugars (a single monomer) • Classifications --The location of carbonyl group e.g. --The number of carbons e.g. • Linear or ring form? • Glucose (grape sugar)--(C H6O12 6 --Functional groups: –OH and –H --Usually found in a ring form in cells --Diabetes: glucose level • Fructose • Galactose • Ribose and deoxyribose 2. disaccharides • definition? • linkage: • e.g.: § maltose (malt sugar): § sucrose (table sugar): § lactose (milk sugar): • Uses: short-term energy storage 3. polysaccharides • number of subunits varies, typically thousands • Glycosidic linkage • some are for energy storage (examples: starch, glycogen); some are for structural components (example: cellulose) • Starch: § § • glycogen (polymer of glucose) § § § • Cellulose: § Found in the cell walls of plants § Indigestible for most animals due to orientation of bonds between glucoses § § • Chitin (polymer of modified glucose units) § insects, crabs, and spiders § cell walls of many fungi VI. lipids are fats and fat-like substances A. B. Characteristics --- --- --- C. Types --- --- --- D. Oil, fats (triacylglycerols) and waxes -- contain glycerol joined to three fatty acids 1. glycerol is a three carbon alcohol with 3 -OH groups 2. ester linkage: between a fatty acid and the glycerol 3. triacylglycerols (also called triglycerides) are the most abundant lipids, and are important sources of energy 4. a fatty acid is a long, unbranched hydrocarbon chain carboxyl group at one end • saturated fatty acids: • unsaturated fatty acids: 5. Waxes --Long hydrocarbon chains --Hydrophobic --Highly saturated and solid --Waterproofing E. phospholipids 1. structure: 2. property: 3. Function: F. Steroids 1. Structure: 2. Examples: 3. Functions: VII.proteins are macromolecules that are polymers formed from amino acids monomers linked together by peptide bonds A. Construction: --- --- --- B. roles: diversity [include enzyme catalysis, defense, transport, structure/support, motion, regulation; protein structure determines protein function] C. Protein structure determines its function. 1. Amino acids • Draw the structure: • there are 20 amino acids that commonly occur in proteins; pay attention to what makes an R group polar, nonpolar, or ionic (charged) and thus their hydrophobic or hydrophilic nature 2. the peptide bond joins the carboxyl group of one amino acid to the amino group of another; is formed by a condensation reaction D. the sequence of amino acids determine the structure (and thus the properties) of a protein E. proteins have 4 levels of organization or structure 1. primary structure (1°) : 2. secondary structure (2°) : 3. tertiary structure (3°): --hydrogen bonds -- ionic bonds -- hydrophobic interactions -- disulfide bridges 4. quaternary structure (4°): • when present, 4° structure is the final three-dimensional structure of the protein (the protein conformation) • example: hemoglobin has 4 polypeptide chains • not all proteins have 4° structure 5. protein conformation determines function 6. denaturation is unfolding of a protein, disrupting 2°, 3°, and 4° structure • Change in the environment (temperature, pH, or exposure to various chemicals) can change the shape of a protein = denature the protein • denatured proteins typically cannot perform their normal biological function • denaturation is generally irreversible F. Chaperonin and function: G. Protein denaturing and examples: · · · VIII. Nucleic acids transmit hereditary information by determining what proteins a cell makes A. Polymer: B. Monomer: C. Nucleotide structure: ·Phosphate group ·Five-carbon sugar : ·Nitrogen-containing base • purines : • pyrimidines : D. Be able to draw a nucleotide structure. E. phosphodiester bonds: link nucleotides together 1. the phosphate group of one nucleotide is fastened to the sugar of the adjacent nucleotide 2. the joining is yet another condensation reaction 3. the way that the are joined creates a polynucleotide strand with 5’ and 3’ ends F. Two types of nucleic acids 1. DNA: --- --- --- --- ---Antiparallel: ---Complementary base pairing role: 2. RNA: --- --- --- --- G. Adenosine triphosphate (ATP) is an important energy carrying compound in metabolism Biology Test 2: Fill in the missing definitions for the following terms Chapter 6: Cell Structure and Functions: - Know Cell theory and common features of cells Microscopy - Know the magnification and resolution for Light and Electron microscopes. Cell Fractionation: - Explain the Procedure: o Homogenization, centrifugation at a series of speed, and collection at those speeds Two Cell Types: - Prokaryotic and Eukaryotic o Know the differences and characteristics of each Tour of the Eukaryotic Cell: - Know Characteristics of these Organelles o Nucleus o Ribosome o Endomembrane system: Smooth and Rough ER ß know the differences o Vesicles o Golgi Apparatus o Lysosomes o Vacuoles: Food, contractile, and central - Energy Converting Organelles: o Mitochondria: include Cristae, and Matrix Space o Plastids: § Amyloplasts § Chromoplasts § Chloroplasts: where photosynthesis takes place • Stoma space and thylakoids Explain the Endosymbiotic Hypothesis for the Origin of Mitochondria and Chloroplasts - What is the Endosymbiotic Theory? Define: Peroxisomes – Oxidation: - Single membrane bound - Special metabolic compartment – What does it break down? Cytoskeleton - Define the Following Functions: o Cell shape and movement o Organelle Movement o Facilitation cell division - Define the Following Components o Microfilaments o Intermediate filaments o Microtubules Centrosomes - Microtubule - organizing centers (MTOCS) - Contains 2 centrioles Centrioles - Aids in cell division - 9+0 pattern Cilia and Flagella - Define the following: o Basal Body o Dynein Microfilaments: - Define the following o Contractile structures o Form cell extensions o Pinch in during cell division Motor Proteins: consume ATP Intermediate Filaments: support cell shape Extracellular Components: - ECM (extracellular matrix of animal cells) - Cell Junctions o Define the different types of cell junctions: o Plasmodesmata: § Tight junctions: § Desmosomes: § Gap junctions: Cell wall - Polysaccharides: cellulose Chapter 7: Cell Membrane - Plasma membrane and its functions: o What does it Isolate? o What does it regulate o How does it communicate o What does it create o What does it provide Fluid Mosaic Model: - Define o Fluid portion o Phospholipid bilayer (amphipathic nature) Fluidity of Membrane: - Define : o Homeoviscious adaption: Cholesterol in animal membranes: - How does it stabilize membranes and what are the ways it stabilizes them? Mosaics (membrane proteins) - Define: o Peripheral proteins o Integral proteins o Categories of membrane proteins: § Receptor, recognition, enzymatic, attachment, and transport Transport and Transfer Across Cell Membranes: - Diffusion in Fluids o Define the following § Diffusion § Concentration § Gradient - Transport across membranes o Passive Transport: no energy needed o Active Transport: energy needed, referred to as pumps - Simple Diffusion Through the Phospholipid Bilayer: o Doesn’t need proteins or energy - Diffusion Rate: o Higher temp à faster rate o Greater concentration gradient à faster rate § Concentration Gradient: drives simple and facilitated diffusion and osmosis o Cannot move molecules rapidly for a long distance - Osmosis: Diffusion of water across a selectively permeable membrane o Isotonic: same concentration on both sides of membrane – no net flow of water o Hypertonic: higher concentration of solutes – water moves towards cell o Hypotonic: lower concentration of solutes – moves water out of cell Define the following - Dialysis: - Facilitated Diffusion: - Aquaporins: - Co-Transport Endocytosis and Exocytosis: - Endocytosis: cells import substances o Define the following: § Pinocytosis § Receptor mediated endocytosis § Phagocytosis: § Amoeba: § White Blood Cell - Exocytosis: move material out of cell Chapter 8 Energy and Metabolism: - Define Energy: - Define Work: The Laws of Thermodynamics: - Define: o Thermodynamics: o Kinetic Energy: o Potential Energy: o ATP: § Hydrolysis of ATP o 1 Law of Thermodynamics: o 2 Law of Thermodynamics: o Entropy: o Metabolism: o What is the Ultimate Energy Source? o Catabolic pathways: o Anabolic pathways: Energy Flow in Chemical Reactions: - Define Chemical Reactions: Exergonic or Endergonic: - Define: o Free Energy: o Exergonic Reactions: o Endergonic Reactions: o Coupled Reactions: What are Phosphorylated Intermediates? Define: - ATP Regeneration: - Electron Carriers: Enzyme: - What is an Enzyme? Competitive Inhibitor and Drugs: Inhibitor: substance that interferes with an enzymes activity Cofactors: - Non-protein enzyme helpers - May be inorganic or organic - Coenzyme: organic cofactor Regulation of Enzyme Activity: - Define: o Allosteric Regulation: o Activators: o Inhibitors: Chapter 9 How Do Cells Obtain Energy? – Photosynthesis, Glucose Breakdown, Redox Reactions, Aerobic Respiration. - Define: o Photosynthesis: § Equation: o Glucose Breakdown: § 3 main parts: • Aerobic Respiration: o Define the four stages: § Glycolysis: • What are the 2 phases and what do they produce? § Pyruvate Oxidation: forms . § The Krebs Cycle: § Oxidative Phosphorylation: • Chemiosmosis: • Anaerobic Respiration: • Fermentation: o Two types: § Lactic Acid: § Alcohol: o Products: o Redox Reactions: § Oxidized: § Reduced: - Aerobic Respiration: o Enzyme-Catalyzed Reactions: § Substrate Level Phosphorylation: § Dehydrogenation Reactions: § Decarboxylation Reactions: § Preparation Reactions: - Coenzymes: o NAD and FAD accept and to the and become: and . - ETC: Versatility of Catabolism: - Proteins o What are proteins composed of? o Define Deamination: - Lipids: o Glycerol: o Fatty Acids: - Regulation – Feedback Inhibition: o Define Phosphofructokinase: § Inhibitors: § Activator: Chapter 10 Photosynthesis is the ability to capture and convert it to in complex organic molecules, releasing as a by-product. What are 5 Photoautotrophs? 1. 2. 3. 4. 5. Adaptions for Photosynthesis: - Define: o Leaf Structure: o Leaf Coat: o Stomata: o Thylakoids: o Light Reactions: o Grana: o Stroma: Chloroplasts contain and accessory . Define: - The Calvin Cycle: o Where does it take place: o Is light necessary? o 3 phases: § Carbon fixation: § Carbon reduction: § RuBP regeneration: o What are the 3 steps of the cycle? - Energy in Visible Light: - Photons: Light Captured by Pigments: - Action of light-capturing pigments: - What happens when: - 1. Certain wavelengths are absorbed: - 2. Certain wavelengths are reflected: - 3. Certain wavelengths are transmitted: Define Pigments: - What common pigments are found in Chloroplasts? o These pigments absorb all wavelengths of light except: Define Accessory Pigments: - Cartenoids: What is a Photosystem? - What are the two types and how do they differ? - PS I - PS II Electron Flow: - Define: - Linear Electron Flow - What does it produce? - Cyclic Electron Flow: Where does Light Reactions take place? What type of Reactions do light reactions drive? Define Glucose Synthesis: What is Photorespiration? What is the C4 Pathway? - Mesophyll Cells - Bundle-sheath Cells Define CAM Plants: What does CAM stand for? Biology Test 3: Cell Cycle: intracellular activity between one cell division to the next Cell Division: process by which a parent cell divides into 2 or more daughter cells 3 types: - Prokaryotic cell, Eukaryote somatic cell, and Eukaryotic gamete cell Prokaryotic Cell Division: - Binary Fission - Generation time Eukaryote Somatic Cell Division: - Mitosis: Asexual reproduction; one round of DNA duplication and one round of division à 2 diploid daughter cells Eukaryotic Gamete Cell Division: - Meiosis: Sexual reproduction; one round of DNA duplication and two rounds of division à 4 haploid daughter cells Key Terms: - Nucleotide: “genetic code” – made up of a sugar, a base, and a phosphate - Nucleic Acid: Chain of nucleotides - DNA: double helix with hydrogen bonds between strands - Chromatin: o Combination of DNA and protein molecules o Less condensed - Chromosome: o Formed when chromatin coils up when it is about to divide o More condensed - Centromere: Middle region where two sister chromatids come into contact - Sister Chromatid: Formed prior to mitosis by DNA replication - Homologous Chromosome: o Pairs during Meiosis o Genes for the same biological features § Different sources: 1 from mom and 1 from dad Eukaryotic Cell Cycle: 3types: - Generation Time, Mitosis, and Meiosis Generation Time: Interphase: Chromosomes duplicate G1 Phase: Gap; recovery S Phase: DNA synthesis to form sister chromatids G2 Phase: Gap, prepare, chromosomes condensed, and centrioles replicate M – Phase: When cell division occurs in Mitosis and Cytokinesis - M – Phase Mitosis: Nuclear division - M – Phase Cytokinesis: Cytoplasmic division 4 Stages of Mitosis: - Prophase: o Chromosomes condense o Mitotic Spindle forms § Mitotic Spindle: Organizes between the two poles of the cell; each pole has an MTOC; Nuclear envelope dissolves and chromosomes are captured by the spindle • MTOC: microtubule organizing center; contains centrioles • Centrioles: plants do not have them - Aster: short microtubules extended from chromosomes - Metaphase: o Spindle microtubules pull to the chromosomes to align them at the center of a cell § Metaphase Plate: imaginary plate through the center of a cell where the chromosomes align - Anaphase: o Removal of cohesion proteins causes the centromeres to separate o Microtubules pull the sister chromatids towards the poles o Cell elongates o Sister chromatids separate - Telophase: o Mitotic spindle breaks down o Two daughter cell’s nuclear envelopes form o Chromosomes begin to uncoil o Nucleolus reappears in each nucleus o Cytokinesis occurs - Cytokinesis: cytoplasmic division o Cytoplasmic Division: § Late anaphase to the end of telophase § 2 mechanisms: cell plate and cleave furrow • Cell Plate: (plants) - Golgi Vesicles line up and fuse and the cell splits in two • Cleavage Furrow: (animals) – microfilaments (Actin) ring contracts and pinches the cell apart - Mitosis/ Cytokinesis Outcome: - 1 parent cell à 2 identical daughter cells - Chromosome # remains the same from one generation to the next - Presence of Centrioles: animal vs. plant cells o Animal Cell: present o Plant Cell: absent Cell Cycle Regulation: - 3 checkpoints: G1, G2, and Mitosis - Go ahead or stop signal - Key Regulatory Components: Cyclins and cyclin dependent protein kinases (CDKS) - CDKS: cyclin dependent kinases – protein kinases phosphorylate proteins to activate or inactivate them Cancer Cells: - Uncontrolled cell growth - Divide excessively and can invade other tissues and displaces normal cells - Metastasis: growth of cancer cells beyond the original site - Cancer cells may travel through the circulatory system Tumors: Abnormal mass of cells 2 types: - Benign: tumors that do not spread - Malignant: cancerous; these tumors can spread Cancer Treatment – 3 Kinds: - Radiotherapy: o High energy radiation is used to destroy cells that are dying o Targets cancer cells but can destroy normal cells - Chemotherapy: drugs that disrupt cell division - Surgery Asexual Reproduction: - Offspring are genetically identical to the parents cells (clones) - Mitotic cell division - Split, bud, fragment - Rapid and efficient Sexual Reproduction: - Gametes fuse to form a single cell called a zygote - Meiosis - Offspring are not genetically identical to their parent cell or to each other - Genetic recombination Diploid Cells: have 2 complete sets of homologous chromosomes; 2n Haploid Cells: has one complete set of homologous chromosomes; n Polyploid Cells: extra sets of homologous chromosomes; 3n or more - Common in plants; usually rare and fatal in animals Meiosis: - Eukaryotic reproductive cells - Produces haploid gametes - Reduces # of chromosomes - One round of DNA duplication followed by 2 rounds of nuclear divisions - 2 stages: o Meiosis I o Meiosis II Meiosis I: - Meiotic Prophase I: o Homologous chromosomes pair up (synapsis and tetrad) o Crossing over occurs and creates chromosomes with new allele combinations § Crossing Over: genetic recombination; exchange of genetic material; causes genetic variation § Chiasmata: where crossing over occurs o Spindle microtubules assemble and capture chromosomes - Meiotic Metaphase I: o Homologous chromosome pairs randomly line up 2-abreast o Line up in different ways which causes genetic variation - Meiotic Anaphase I: o Homologous chromosome pairs separate and move to opposite poles - Meiotic Telophase I: o Spindle microtubules disappear o Cytokinesis occurs o Nuclear envelopes may reappear o Chromosomes usually remain condensed Interkinesis: Between Meiosis I and Meiosis II; varies in length and distinctiveness; differs from interphase because there is no S Phase (DNA replication); typically brief – some cells skip it altogether - Meiotic Prophase II: o Spindle microtubules reform and capture duplicated chromosomes - Meiotic Metaphase II: o Duplicated chromosomes line up singly, perpendicular to the spindle - Meiotic Anaphase II: o Sister chromatids separate - Meiotic Telophase II: o Cytokinesis occurs o Spindle microtubules disappear o Nuclear membranes reform o Chromosomes relax Overview of Meiosis I and Meiosis II: - Phases have the same names as equivalent Mitotic phases followed by a I or II to distinguish the 2 nuclear divisions in Meiosis - Prophase I – crossing over - Anaphase – homologous chromosomes separate - Anaphase II – sister chromatids separate Fertilization: - Combines two chromosome sets to produce diploid zygotes (2n) - Fusion of haploid gametes o Haploid Gametes: § Eggs § Sperm DNA Replication: - Mitosis: occurs during interphase before mitosis occurs - Meiosis: occurs during interphase before Meiosis I begins Number of Divisions: - Mitosis: one division including prophase, metaphase, anaphase, and telophase - Meiosis: two divisions including prophase, metaphase, anaphase, and telophase Synapsis of Homologous Chromosomes - Mitosis: does not occur - Meiosis: occurs during prophase I along with crossing over between non-sister chromatids; resulting chiasmata hold pairs together due to sister chromatid cohesion Number of Daughter Cells/ Genetics: - Mitosis: two, each diploid (2n) and genetically identical to parent cell - Meiosis: four, each haploid (n) containing ½ as many chromosomes as the parent cell and genetically different than the parent cell and each other Role in the Animal Body: - Mitosis: enables multicellular adult to arise from a zygote; produces cells for growth, repair, and in some cells sexual reproduction - Meiosis: produces gametes; reduces # of chromosomes by ½ and introduces genetic variability among gametes Synapsis and Tetrads in Prophase I: - Homologous chromosomes physically connect and exchange genetic information o Tetrads: paired homologous chromosomes at the metaphase plate § Instead of individual replicated chromosomes Genetic Variation: - Independent assortment of chromosomes: o Randomized line up and separation of homologous chromosomes in Meiotic Metaphase I and Anaphase I increase variation o # of possible combinations is 2^n à n = # of homologous pairs o In humans possible combinations in one gamete = ~8 million - Crossing over - Random fertilization: o Fusion of gametes from 2 individuals further increases the possible 2n combinations o Gametes from 2 different humans could produce ~ 64 trillion combinations o Each zygote has a unique genetic identity Inheritance: Process by which characteristics/ traits are passed on Key Terms: - Gene: o Heritable factor o Unit of heredity o Encodes characteristics that determine the phenotype - Allele: o Alternate versions of the same gene at the same locus point (in homologous pairs) – gene forums o Each trait is determined by a gene with 2 alleles o One allele on each homologous chromosome - Locus: o Location of a particular gene on a chromosome - Phenotype: o Appearance/characteristics of an organism = physical traits o Ex: yellow seeds - Genotype: o Genetic makeup of an organism o Determines the phenotype § Ex: Yy - Dominant: allele that dominates over the others in determining phenotype (capitalized letter) - Recessive: allele whose phenotype expression is hidden when a dominant allele is present (lowercase letter) - Homozygous: both chromosomes carry the same allele at a given locus (YY or yy) - Heterozygous: two chromosomes carry different alleles at a given locus (Yy) - Hybrid: offspring from a cross breeding - Monohybrid: evaluate the inheritance pattern of 1 trait - Dihybrid: evaluate 2 traits - P1 Generation: parental generation - F1 Generation: first generation offspring - F2 Generation: second generation offspring (offspring of F1 generation) Law of Segregation: - Two alleles separate to each other during meiosis - Random separation Genetic Linkage: - Independent assortment doesn’t always occur - Genes on same chromosome tend to be inherited together Genetic Mapping: Placement of a gene into a position in a linkage group - Map Unit: Distance between genes o One map unit = 1% recombination Linkage Group: - All genes on a particular chromosome tend to be linked together Non-Mendelian Inheritance Patterns: - Incomplete dominance: o Combined phenotypes o The phenotype of F1 hybrids is somewhere between the phenotypes of the parental varieties - Complete Dominance: o Occurs when phenotypes of the heterozygote and dominant homozygote are identical - Co-Dominance: o Two different alleles affect the phenotype in separate, distinguishable ways - Multiple Alleles: o A species may have more than 2 alleles for a given trait o Each individual trait still carries 2 alleles for the trait § Ex: human ABO blood types • 3 types: IA, IB, and ii • Blood type AB: codominance - Pleiotrophy: - Alleles at a single locus may have effects on 2 or more traits - Ex: Albinism - Epistasis: - One gene influences the phenotype that a second gene usually controls - masking any effects of alleles at the second gene - Ex: Mice coat color Polygenic Inheritance: Polygenic Traits: - Traits affected by interaction of 2 or more genes - Results in population variation o Ex: human skin color Environmental Impact: - Phenotypes are a combination of genetics and environment Norm of Reaction: - The phenotypic range of a genotype influenced by the environment Sex Chromosomes: - Female: XX - Male: XY - Autosomes: non-sex chromosomes Sex Determination: - Human sex ratio is approximately 1:1 Different Sex Determination System: - X-Y System: 2 types of sex chromosomes - X-O System: 1 type of sex chromosome - Z-W System: Sex determined by female - Haplo-Diploid: no sex chromosome Sex-Linked Genes: - Carried on a sex chromosome Sex-Linked Disorder: - Some disorders caused by recessive alleles on the X-Chromosome - Color Blindness - Duchene Muscular Dystrophy - Hemophilia Pedigree: - Family tree that describes the interrelationships of parents and children across generations - Reveal inheritance pattern of a trait Autosomal Recessive Disorders: - Albinism - Cystic Fibrosis: o Defective or absent chloride transport channels in plasma membranes - Sickle Cell Anemia: o Abnormal hemoglobin synthesis o Heterozygous are less susceptible to the malaria parasite Autosomal Dominant Disorders: - Achondroplastia - Huntington’s Disease: o Nervous system disease o No obvious phenotype effects until the individual is 35-40 years old - Marfan Syndrome - Polydactyly - Progeria - Hemophilia Sex Linked Disorders: - Red-green color blindness Multifactorial Disorders: - Many disorders such as: o Heart Disease o Diabetes o Mental Illness o Alcoholism o Cancer - Have genetic and environmental components Abnormal Chromosome Number: - Polyploidy - Aneuploidy Aneuploidy: - missing one copy or have an extra copy of a single chromosome - Trisomy - Monosomy Trisomy: 3 copies of a chromosome Monosomy: one copy of a chromosome Non-Disjunction: - incorrect separation of chromosomes of chromatids in Meiosis - Mistake Meiotic Anaphases Abnormal Number of Autosomes: - Down Syndrome - Trisomy 21: 3 copies of chromosome 21 Abnormal Number of Sex Chromosomes: - Turner Syndrome: sterile, woman with only one x chromosome; XO - Trisomy X: a fertile ‘normal’ woman with an extra X chromosome; XXX - Kleinfelter Syndrome: infertile man with an extra X chromosome; XXY - Jacob Syndrome: a tall man with an extra Y chromosome and a low IQ; XYY Chromosomal Rearrangement: - Translocations - Inversions - Deletions - Duplications Eukaryote Chromosome: Linear DNA, large amount of protein Bacterial Chromosome: circular; small amount of protein Cell Aging: caused by the absence of telomerase Telomerase: catalyzes the lengthening of telomeres in: - Germ cells - Cancer cells Telomere: - End region of chromosomes - 5’ end RNA primer cant be replaced with DNA causing 5’ en to be shorter than the parental strand - doesn’t occur in prokaryotes Complimentary Base Pairing: - A à T - G à C - Ex: Parent - TAGCCA - New – ATCGGT DNA Ligase: joins fragments on lagging strand Leading Strand: continuous Lagging Strand: discontinuous; okazaki fragments DNA Polymerase I: replace RNA primer with DNA DNA Polymerase: - Synthesize daughter strand - Synthesis can only occur in the 5 -> 3 direction - Proofread newly made DNA replacing any incorrect nucleotides Primase: starts new strand by making an RNA primer Topoisomerases: break and rejoin DNA strands Single Strand Proteins: keep separation created by Helicase open DNA Helicase: separate strands of DNA in replication Replication Fork: Y-shaped region where new DNA strands are elongating at each end of the replication bubble - Replication bubble: o Origins of replication o Beginning site – 2 DNA strands are separated § Bacteria: one origin § Eukaryotes: Several origins Phosphodiester Linkage: results in the 3’ and 5’ end of each strand DNA Backbone: Nucleotides are linked by the 3’-5’ phosphodiester linkage Watson Crick Model: - 2 strands of nucleotides - double helix - bases protrude inward Chargaff’s Rule: - A – T - G – C 4 nitrogen containing bases: - Adenine - Thymine - Cytosine - Guanine Nucleotide: - phosphate group - 5 carbon sugar - nitrogen containing base DNA Structure: Polymerase if Nucleotides DNA: deoxyribosenucleic acid Chromosomes: fit into the nucleus through an elaborate multilevel system of packing Chromatin: a complex of DNA and Proteins found in the nucleus of Eukaryotic cells DNA Replication: - Strands are separated - Each parent strand remains intact as template - Single strand binding proteins keep it open Nucleosomes: 8 Histones with DNA thread Linker DNA: String between nucleosomes Histones: - Positively charged - Associated with negatively charged phosphates of DNA - Further Packaging: - Histone H1 and scaffolding proteins - H1: one type of histone - Associate with linker DNA regions - 30nm Fiber Non-Scaffolding Proteins: non- histone proteins Condensed Chromatin: 700 nm Fiber Biology Final: Chapter 20: Biotechnology I. General outline of genetic engineering A. DNA recombination B. Cloning of the recombinant DNA C. DNA library D. PCR and gel Electrophoresis E. Sequencing II. Genetic Engineering A. Genetic engineering refers to the modification of genetic material to achieve specific goals B. Major goals of genetic engineering 1. Learn more about mechanisms. 2. Better understand and treat diseases 3. Generate economic and social benefits for agriculture III. Common techniques in biotechnology A. Recombinant DNA 1. Genetic engineering utilizes recombinant DNA technology • Splicing of genes from different organisms 2. Recombinant DNA can be transferred to plants and animals • Transgenic or genetically modified (GM) organisms 3. Recombination in Nature • Crossing over in Sexual Reproduction • Transformation: Bacteria can naturally take up DNA from the environment (transformation) and integrate the new genes into the genome (recombination) § Directly pick up DNA § Plasmid: Small circular DNA molecules • Viral Transfer of DNA: use virus as a vector § Viruses may package some genes from host cell into viral particles during assembly § Infection of new host cell injects genes from previous host, allowing for recombination 4. Developed Biotechniques • Bacterial Transformation: use plasmid to carry new genes • Transfection: deliberately introduce DNA into cells § Chemical-based methods § Particle-based methods i. Gene gun § Viral methods 5. Restriction enzymes: molecular scissors with a twist • Restriction enzymes, also called restriction endonucleases, are enzymes that cut DNA molecules in specific places. § E.g. EcoRI: palindromic sequence • Some can create staggered cuts with “sticky ends” are the most useful in gene cloning, others leave “blunt ends”. • Can • DNA ligase is an enzyme that seals the bonds between restriction fragments • Restriction enzymes are mostly from bacteria, and their natural role is to destroy DNA from invading viruses B. Cloning 1. Cloning refers to the development of offspring that are genetically identical to their parent. 2. Clone the desired gene • Purpose: Study for the gene structure, functions. • Steps: § Isolate the desired gene (by PCR or restiction enzyme) § Insert the gene into plasmid (cloning vector). i. Plasmids are small, circular DNA molecules with at least one replication origin most bacterial cells contain several plasmids some eukaryotic cells commonly have plasmids (such as the yeast Saccharomyces cerevisiae) § Transform plasimds into bacteria. 3. Clone an organism • Examples: C. DNA library 1. A collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning. • Genomic library: formed by genomic DNA § Break raw genomic DNA into fragments § Link DNA pieces into vectors and then the transform vectors into host cells § cells lines are maintained for each library piece (often, the whole genome is represented multiple times in the library for completeness) • cDNA library (complementary DNA library): formed from reverse- transcribed RNA. § Based on coding regions of DNA. § Procedure: § Isolate mRNA § Reverse transcriptase: convert mRNA back to cDNA. § Insert into vectors. 2. Screening • To find the DNA of interest. • DNA probe: complementary to part of the interested gene. D. PCR and gel Electrophoresis 1. Polymerase Chain Reaction (PCR) • Used to amplify a specific region of a DNA strand (the DNA target). • Replicate target DNA region in a test tube • What we need for PCR? • Four steps of PCR in thermocycler machine: control diff. temperatures. § § § § • PCR product: exponential increase as the cycle number goes up. • Applications of PCR § cloning, genetic engineering, sequencing § Forensic scientists PCR the short tandem repeats (STRs) in human genome 2. Gel Electrophoresis • Used to spread out different-length DNA fragments in a mixture. • Short DNA fragments move through the 3D meshwork of fibers between the gel. § DNA is negatively-charged § Short DNA fragments migrate farther than long ones • The invisible bands of DNA are made visible using stains or DNA probes • What we need to run a gel: § Sample: DNA mixtures § Agarose gel § An electric current. E. DNA sequencing 1. Uses special nucleotides and DNA gel electrophoresis • ddNTPs : (dideoxyribonucleotide triphosphates) fluorescent labeled § When a ddNTP is incorporated into a growing DNA strand, it prevents further elongation of the DNA strand i. No 3’-OH on which to add the next nucleotide, so the strand stops • Gel running: separated fragments by size • Can be read from the spectrogram. 2. the Human Genome IV. Uses and applications of genetic engineering (some examples) A. Transgenic organism - any organism with a foreign gene(s) incorporated in it B. Biotechnology in Agriculture 1. Examples: C. Biotechnology in Medicine 1. GM (genetically modified) Plants • Examples: 2. GM animals • Biomedical research § Examples: • Organ transplant § Examples: D. Gene therapy 1. Gene therapy is an experimental technique that uses genes to treat or prevent disease. 2. Methods: — Replace defective genes by insertion of a healthy copy. — Deliver novel genes that can destruct cancer cells. E. Safety guidelines 1. Potential misuses (both intentional and accidental) are a concern 2. Stringent guidelines are in place to prevent such things as producing and releasing a “super virus,” “super bacteria,” or “super weed” that would become a serious medical and/or ecological disaster 3. Genetically engineered organisms that are released into the environment in some way are closely monitored on a case-by-case basis – example of Bt corn 4. Much concern over genetic engineering exists in the general public (especially in Europe), so things such as labeling of genetically modified foods is a controversial issue. Chapter 22: Evolution The great evolutionary geneticist Theodosius Dobzhansky once remarked, “Nothing in biology makes sense except in the light of evolution”. I. Evolution and Darwin A. What is evolution? § Evolution – the inherited traits in populations of living things change over time – can result in new species. B. Darwin’s voyage II. Darwin’s Theory and Natural Selection A. Darwin’s theory: evolution occurs by natural selection 1. Observation #1: Members of a population often vary in their inherited traits 2. Observation #2: All species can produce more offspring than the environment can support, and many of these offspring fail to survive and reproduce 3. Natural selection • • • • • Evidence: § • • Natural selection can only increase or decrease heritable traits that vary in a population • Adaptations vary with different environments • Natural selection does not create new traits, but edits or selects for traits already present in the population • The local environment determines which traits will be selected for or selected against in any specific population 4. Two major branches: microevolution, or changes of a population over time, and macroevolution, or the formation of species III. Evidence supporting the theory of evolution A. The fossil record 1. Fossils: 2. Fossils provide direct evidence that life had changed over time 3. fossils most commonly form in sedimentary rocks in aquatic environments 4. the fossil record is biased toward organisms with hard parts that lived in aquatic or arid environments, where decay is slow and incorporation in rocks can occur with reasonable speed • organisms that lived in places of rapid decay are thus biased against in the fossil record B. Comparative morphology 1. Morphology – 2. Homologous features – • E.g.: 3. Analogous features: • E.g.:


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