BIOL 219 Exam #1 Study Guide
BIOL 219 Exam #1 Study Guide Bio 219
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This 10 page Study Guide was uploaded by Sophia Valla on Sunday September 11, 2016. The Study Guide belongs to Bio 219 at West Virginia University taught by Lima Huebert in Summer 2016. Since its upload, it has received 16 views. For similar materials see The Living Cell in Biology at West Virginia University.
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Date Created: 09/11/16
BIOL 219 Study Guide # 1 Cell Theory 1. All organisms are made of 1 or more cells 2. Cells are the basic unit of life 3. All cells come from cell like themselves Cell Makeup ● Organelles (membrane bound) ● Membranes ● Macromolecules ● Ions ● Water Life is Composed of Chemistry ● Carbon 18% ● Hydrogen 10% ● Nitrogen 3% ● Oxygen 65% Bonds ? Atoms make bonds to become stable ? Most stable = lowest energy ? Make bond (exergonic) ? Break bond (endergonic) ● Ionic an atom gives an e to another atom ● Covalent shares equally ○ Nonpolar ○ Polar ● Hydrogen attraction from partial charges Protein Carbohydrates Nucleic Acids Lipids Macromolecule Synthesis ● Carrier molecules activates monomers (needs ATP)(directionality) ● Condensation rxn on initial monomer to form a dimer (doesn’t need ATP) ● W/ repeated polymerization condensation w/ activated monomers continues directionally until polymerization stops ○ Carrier is recycled Most macromol. Are polymers held together by covalent bonds Assemblers mediate covalent bonds Proteins → amino acids→ ribosomes Nucleic acids nucleotides DNA/RNA polymerase → → Polysaccharides→ monosaccharides → glycosyltransferase Lipids → glycerol→ fatty acid synthesis INTRAmolecular Assembly (noncovalent interactions) ● Protein folding by hydrophobic rxns ● RNA folding by hydrogen bonds between sugars of complete nucleotides INTERmolecular Assembly ● Membranes guided by hydrophobic rxns between lipids ● Mosaic by lipids and proteins ● Membranes are selectively permeable ● Chromosomes built through hydrogen bonds and ionic bonds in DNA and proteins Protein Structures ● Primary ? amino acid chain ? Covalent peptide bonds ? Condensation rxn possible through ribosomes ● Secondary ? α helix polypeptide chain (twisted) ● H bonds shielded w/ helix ● R group on the outside ? β sheets polypeptide chain (grooved) ● H bonds perpendicular to shielded between sheets ● High tensile strength ? H bonds between backbone ● Tertiary ? Domains, whole proteins ? Hydrophobic, H bonds, vdW, ionic, disulfide bonds ? Sidechainsidechain / sidechainbackbone ● Quaternary ? Multiple proteins ? Requires noncovalent interactions ◆ Hemoglobin tetramer binds to O2 using heme groups Membranes ● Makeup mostly lipids and proteins ● Amphipathic both hydrophobic and philic Lipids ● Polar heads phosphates Fatty Acids nonpolar ● Saturated no double bonds ● Unsaturated at least 1 double bond CIS Fat vs. TRANS fat Lipid Bilayer (stable and dynamic) ● Fluid ○ Lipids and proteins can move w/in the membrane ○ Fluidity ● Mosaic ○ Various molecules arranged in 2D Membrane Lipids ● Phospholipids, glycolipids, sterols ● Proportions can be determined by cell fractionation (TLC) Types of Movement Laterally Rotate Flex (fatty acids) closer or further Transverse Diffusion flip flop ● NOT likely ● Requires ATP (hydrolysis/lipases) Microscopy passes light through a sample absorbed/reflected magnify image ● Bright field light ● Phase contrast light ● Transmission EM ○ Passes electricity through s sample ○ High resolution ○ Kills cells ● Confocal fluorescence ○ Resolution ○ Live cells ○ Specificity ● FRAP Fluorescence Recovery After Photobleaching ○ Label, bleach, watch recovery Cholesterol decreases fluidity ● Saturated less fluid ○ Melts at higher temp ● Unsaturated more fluid ○ Melt at lower temp Membrane Transport ● Facilitated Diffusion ○ Proteins in the membrane help transport with the gradient Secondary structures can make membrane pores α helices and β sheets can form pores ● Channels specific holes ○ Specificity based on size and charge ● Gates ligands = gates Carriers open and close ● Binds solute, changes shape allostery ● Works in both directions (depends on conc) Active Transport endergonic / exergonic ● Direct ○ Energy provided by rxn that modifies transporter ■ Na+/K+ ATPase or Pump ● Indirect ○ Energy provided by the movement of other molecules and ions down the gradient ■ Na+/glucose symporter Laws of Thermodynamics 1. Energy isn’t created or destroyed 2. Chemical changes are spontaneous toward greater entropy Equilibrium ● Conc. not changing ● Le Chatelier's Principle add reactants or products until rxn shift toward equilibrium c d C❑ ∗D❑ K eq❑ = A ∗B❑ b ↔ aA+bB cC+dD ● −Δ G → more reactants than products ■ Exergonic spontaneous ● Δ G → more products than reactants ■ Endergonic NOT spontaneous Membrane Transport for UNCHARGED Molecules [Products] Δ G=R∗T∗ln [Reactants] Membrane Transport for CHARGED Molecules [Products] Δ G=ΔG❑ +RTln +nF❑ z [Reactants] ● Δ G❑ 0 = 0 ● R= 0.001987 kcal/mol*K ● T= 310 K ● n= moles ● F= 23.062 kmol/ mol*v ● z= #V Thermodynamics spontaneity does NOT EQUAL a high probability of rxn Kinetic Barriers ● HIGH activation energy ● Makes rxn regulatable ● Add an enzyme ○ Transcription/translation ○ Inactive → active ○ Localizing Enzymes 1. Substrate and enzyme come together (induced fit) a. Most enzymes are proteins (RNA) b. Binds at the active site i. Distortions of enzyme and substrate ii. Distorted substrate uncatalyzed transition state 1. Stabilized by NONcovalent bonds 2. Active site binds and activates substrate a. Substrate orientation i. Proper orientation & high local conc. activation energy lowers b. Substrate reactivity i. Charged amino acids donate/accept protons and e 1. Substrate is more reactive ii. Active site utilizes acidic/basic 1. Residue better than acid/base catalysis c. Induced strain on the substrate i. Twist or bend substrate 1. Weakens bonds 2. Lowers activation energy 3. Products released and enzyme returned to OG conformation S= substrate E= enzyme P= product S+E → SE → EP → E+P Initial Rxn Rates [S] > [P] k= rate constant for a reaction moving in a specific direction K1 K3 aA+bB ↔ ES ↔ cC+dD K2 K4 Michaelis Menten Plot ● Measures substrate consumption or product by spectrophotometry ○ Can determine initial velocities from the slope ○ Plot initial velocities against substrate conc Slopes ΔConcentration/Time Vmax = fastest rxn can go at energy Km= amount of substrate for peak efficiency (½ Vmax) Vmax(s) Velocity= Km+Substrate K= rate constant cat= catalytic Kcat= # molecules of substrate that an enzyme can convert to products per unit time Kcat=Vmax/Energytotal Speed up Rxn ● Change enzyme conc. Substrate conc Environment (temp., pH) Allostery Changes Rxn Velocity ● Changes confirmation of protein ● Has +/ effects on the enzyme ● Distort active site Reduce Rxn Velocity ● Irreversible inhibition ○ Enzyme is dead at the end of the rxn (Vmax=0) ● Reversible inhibition ○ Competitive binds to active site ○ Noncompetitive binds to allosteric site Competitive Noncompetitive Metabolism ● Catabolism break bonds for energy release energy ● Anabolism makes bonds for energy uses energy ATP is a Good Carrier Phosphoanhydride bonds Coupled to endergonic rxns by transfer of phosphates NADH is a Good Carrier Can be reduced/oxidized Has extra phosphate on ribosome photosynthesis Unstable = more energy (ATP) Stable = less energy (ADP) Methane most reduced CO2 most oxidized Sunlight + CO2 → ATP & Sugar Photosynthesis in Thylakoid and Stroma of Chloroplasts ● Light Rxn ○ Energy transductions ○ Harvests light, creates H+ gradient, ATP and NADPH synthesis Antenna pigments chlorophyll and accuracy (visible range) High energy = Low wavelength Low energy = High wavelength ● Dark Rxns ○ Carbon assimilation ○ CO2 to glucose ATP Synthesis ● Has 3 allosteric conformations that “ratchet” ● Most macromolecules are polymers that self assemble ○ Polysaccharides assemblers= glycosyl & transferase Dark Rxns uses CO2 in Calvin cycle to make sugars ● Rubisco ○ Links CO2 to 3 ribolase biphosphate ■ =6 3 Carbon molecule ○ 6 ATP hydrolyzed / 6 NADPH oxidized ○ 9 ATP & 6 NADPH for ½ sugar ○ 6 3 Carbon molecule for 1 sugar ○ Can use O2 and CO2 as a substrate C4 Plants ● Divides steps spatially ● CO2 & O2 in mesophyll ○ Makes 4 carbon molec. To bundle sheet ○ Keeps O2 away from rubisco CAM Plants ● Divides steps temporally ● Closes stomata no O2 or CO2 ○ Opens at night Carrier Molecules Made and Modified by Polysaccharides 1. Digestion a. Catabolism b. Neg. Δ G c. Induced fit d. Lowers temperature and activation energy e. Hydrolysis 2. Glycolysis a. Oxidizes glucose to CO2 b. NAD+ reduced to NADPH c. Makes 2 ATP ● Energy investment prepare glucose ● Return on investment redox ATP out ● Pyruvate formation, ATP generation ATP Kinase moves around phosphates Isomerase flips isomers Allostery ● Products = negative regulators ● Reactants = positive regulators ● Energy needs are met inhibition ● Energy products are needed activation ● Regulates at 3 points Aerobic Respiration (mitochondria) ● Requires O2 ● Krebs cycle and ETC Fermentation (cytosol) ● Yeast ethanol ● Humans lactic acid ● No O2 Gluconeogenesis Lactate from fermentation sent to liver built back to pyruvate the glucose Takes 6 ATP in liver to get 2 ATP in the muscles Mitochondria ● Synthesis of amino acids ● Heme groups ● Uptake and release ● Regulates cell death ● Stores own DNA ● Energy metabolism Acetyl CoA carrier Made from fatty acid and nucleotide Acetyl conds with CoA for thiosulfate bonds Krebs Cycle ● 1 ATP / 3 NADH / 1 FADH2 / Oxaloacetate regenerated ● Carbons from acetyl CoA added to oxalacetate ○ Lost as CO2 by decarboxylation Oxidative Phosphorylation ● Energy carried by redox of double bonds ○ Conjugated double bonds ○ Hemes NADH oxidized (exergonic) reduced H+ pushed across to generate proton gradient O2 reduced to water generates ATP (36) Light Cycle NADPH NADP Calvin cycle glucose digestion glycolysis pyruvate NAD+ NADH Krebs cycle person exhales CO2 back to plants
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