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BIOL 219 Exam #1 Study Guide

by: Sophia Valla

BIOL 219 Exam #1 Study Guide Bio 219

Marketplace > West Virginia University > Biology > Bio 219 > BIOL 219 Exam 1 Study Guide
Sophia Valla
GPA 3.5

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Things to expect to see on the exam
The Living Cell
Lima Huebert
Study Guide
Biology, Molecular
50 ?




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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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