Bio 211 Midterm 1 Study Guide With Diagrams
Bio 211 Midterm 1 Study Guide With Diagrams Biology 211
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This 16 page Study Guide was uploaded by Melissa on Friday January 29, 2016. The Study Guide belongs to Biology 211 at University of Oregon taught by Jana Prikryl in Fall 2015. Since its upload, it has received 71 views. For similar materials see Gen Biol I: Cells in Biology at University of Oregon.
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Date Created: 01/29/16
Orientation of the protein as it moves through the cell Progress of an enzymatic Reaction: Enzyme energy connection with ATP Energy pathways for diﬀerent organisms Redox Reactions Energy harvest reactions 1. Glycolysis: 2. Pryruvate processing 3. Kreb's Cycle 4. Electron transport Fermentation: Biology 211 Midterm 1 Study Guide: Jana Prikryl Quizlet: Biology Midterm 1 : https://quizlet.com/_1xtv88 Password to open: bio211 Macromolecules • Subunit: part of a larger molecule • Monomer: item that can be formed to make a polymer • Polymers made through hydrolysis and dehydration reactions o Monomers connected by condensation (dehydration) reactions o Polymers broken into monomers by hydrolysis • Carbohydrates o Polar because they are able to dissolve in water o Monomers: Monosaccharides o Polymers: Polysaccharides o Ratio of Carbon-Hydrogen-Oxygen § 1:2:1 o Typically form alpha or beta ring structures § Both have a hydroxyl group on the left; § On the right side • Alpha: hydroxyl is below hydrogen • Beta: Hydrogen is below the hydroxyl § Beta is more abundant because it is more stable o Functional groups § Hydroxyl and carbonyl o Condensation reaction between two hydroxyl groups forms a glycosidiclinkage § Alpha links point in the same direction while beta points in opposite § Alpha: used in energy storage • Have high free energy because of the Electronegativity on Hydrogen and Carbon § Beta: Used in structuring; resistant to enzyme break down • Cellulose o Functions § Energy storage § Structural § Cell-cell signaling o Monosaccharaides are polar (hydrophilic) • Lipids o Made mostly of carbon and hydrogen o Don’t dissolve in water o Don’t form polymers o Fatty acids § Have a carbocyclic acid on end which is polar but because the tail of the fatty acid is so large and non-polar, the entire molecule is considered non-polar § Saturated: No C-C double bonds and are saturated with hydrogen § Unsaturated: Some C-C double bonds • Appears as if there is a kink in the tail § Typically made up of Hydrocarbon chain and a carbocyclic acid o Steroid § Small hydroxyl group and hydrocarbon chain § Rings that stick together § Hydrophobic § Ex. Cholesterol o Phospholipid § Phosphate group, glycerol, and 2 fatty acids • Phosphate group is hydrophilic while the fatty acids are hydrophobic o Amphipathic § Important for structural purposes § When there are multiple, they form a lipid bilayer o Triglyceride § 3 fatty acids and glycerol § Linked by ester links o Glycolipid: sugar and a lipid § Ex. Glucocerbroside • People with Gaucher’s disease have too many of these molecules because the body is unable to break them down because it is missing the enzyme, glucocerbrosidease • Proteins o Monomer: amino acid o Polymer: polypeptides o Amino acids are protonated at a PH of 7 o Amino acids are the building blocks of proteins; they are NOT specifically proteins o As the PH becomes more basic, the molecule loses protons o Amino acids have high affinity for protons o Amino acids can have polar, nonpolar, or uncharged side chains § Nonpolar: amino acids are buried in the protein where they interact with each other or they are found on outside of the trans membrane where they are exposed to hydrophobic parts of the phospholipid bilayers § Polar: Have partial charges and found on exposed surfaces of proteins where they can interact with polar environments o Polypeptide chains are amino acids linked by peptide bonds § Parts • 8 amino acids • N-terminus • C terminus • Side groups • Polypeptide backbone o Four levels of protein structure § Primary: flat § Secondary: where it folds • Alpha helix and beta sheets • Stabilized by H bonding because Hydrogen acts as a bond and an acceptor • Shape comes from hydrogen forming between the backbone components • Non-covalent interactions § Tertiary • 3 dimensional shape • How the alpha helices and beta sheets come together • Interactions between the side chains o H bonds o Hydrophobic interactions o Covalent bonds o Charged base interactions • Where glucoerebrosidease is usually found § Quaternary • When multiple polypeptides are needed • Hemoglobin o Functions: Pretty much everything o Proteins found in the cell membrane § Receptor, transport, and signal proteins • Nucleic Acids o Monomer: nucleotide o Polymer: nucleic acid o Genetic material storage and processing of DNA and RNA o Made up of a phosphate group, sugar, and a nitrogenous base o DNA is packaged into chromosomes and the functional units are genes Cell Structure and Function • DNA uses polymerase to transcript RNA and RNA uses ribosomes for translation • Phagocytosis: o Plasma membrane detects a particle o Membrane stretches forming a phagosome o Fuses with the lysosome where particle is digested • Prokaryotic Cells o Bacteria § No nucleus and few organelles § Ribosomes § Cell wall § No chloroplasts § Single celled § Some photosynthesis o Achaea § No nucleus and few organelles § Ribosomes § Cell wall § No chloroplasts § Single celled § Some photosynthesis o DNA moves freely o Makes up 90% of our cells-mainly in our small intestine • Eukaryotic Cells: membrane bound nucleus o Protista § Single-celled § Some chloroplasts § Cell walls § Live in water o Fungi § Multi-celled § No photosynthesis § Cell wall o Plantae § Multi-celled § Chloroplasts § Cell wall o Animalia § Multi-celled § No photosynthesis § No cell wall • Cytoskeleton o Protein fibers that provide shape and allow for movement in the cell § Actin filaments • Cell shape and important in cell division and moving things within the cell § Intermediate filaments: cell shape and anchorage § Microtubules • Helps with the movement of chromosomes and other organelles; directs growth of the cell wall • Lysosome o Digestive enzyme • Mitochondria o Harvest energy from organic molecules o Takes products generated through the breakdown of glucose and uses them to make ATP o Pyruvate processing, Krebs Cycle, ETC, and Chemiosmosis take place here • Nucleus o Nucleolus: Ribosomes made here o Has a double bilayer made of phospholipids • Ribosomes: made of RNA and protein o Free in the cytoplasm or in the RER o If found in the cytoplasm, the reason they are unable to enter the RER is because of the differences with hydrophilic and hydrophobic parts • Smooth ER o Synthesizes membranes o Lipids are made and assembled into membranes o Where the glucocerebroside begins • Golgi apparatus: the sorting organelle o Modifies newly made proteins, lipids, and carbs and tags them for transport • Vesicles: how things move through the endomembrane system • Gives the protein modifications that act as tags to let the cells know where to send the protein • Sugars are added to lipids or proteins in the ER and the Golgi How do cells work? ENERGY! • Gibbs Free Energy o In a spontaneous reaction, the free energy decreases! o Exergonic: energy releasing; negative o Endergonic: Energy absorbing; positive o The portion of a system’s potential energy that can be used to perform work • Enzymes o Speed up the favorable reacti ons; negative Delta G § Otherwise the molecules react very slowly because they go through a transition state with a combination of old and new bonds o Couple favorable reactions with unfavorable reactions § This provides the “oomph” to make the energy absorbing reactions work o NOT used up during reactions o Lower the activation energy required o How does catalysis occur? § Stress bonds between substrates and they put substrates in their proper orientation o Form and function are related: lock and key model § Active site: site on enzymes where reaction takes place § Substrate: reagent that is going to be converted to a product by the enzyme § Enzyme-substrate complex: complex that forms when substrate and enzyme come together § Have a hydrogen bonding ability § When it catalyzes, it breaks into the products and the active site § Allows substrates to reach transition state more often o Factors that affect them § Substrate concentration, temperature, PH, and other chemicals o Progression of catalysis § Enzyme binds do to the substrate § Enzyme affinity: how well the enzyme binds which changes depending on cellular conditions § Then converts to product § Limited by concentration of substance § Releases the product § Products have lower affinity so this happens rapidly o How does substrate concentration affec t reaction rate? § After the concentration reaches a certain point, the reaction rate is limited by how fast the enzymes can convert the reactants to products • Graph flattens out § Low concentration, rate is limited by how quickly the enzyme can find and bind the substrate § As it increases, the enzyme can more easily find a new substrate molecule after finishing the previous reaction: saturating • When it is saturated, adding more substrate wont increase rate of reaction o How does temperature affect reaction rate? § As temperature increases, substrate molecules collide with the active sites more frequently • Due to putting in heat so there is more energy for products § However, if it gets too hot, the reaction rate declines rapidly because the proteins begin to unfold and cease working properly (They denature) • Mitochondria is used to generate energy and pumps ions • When you convert something that is not very stable to something very stable, a lot of energy is released • Reasons for binding: opposite charges and the shapes fit ATP: energy currency of the cell • Hydrolysis releases the energy which is used to do work o Energy released is used to catalyze the unfavorable reaction • Breaking the bond is favorable • Requires a lot of energy to break the bond • Energy removed from the reacta nt to form a product: Negative • Energy added to make a product: Positive • ATP contains a phosphate group, ribose and adenine (nitrogenous base) o Phosphates are negative and when the bonds are broken they release a lot of energy • Cells must regenerate this mol ecules from ADP and Pi to continue functioning • Why do organisms need food? o Ingest the macromolecules o Digestive System breaks them into subunits which are used in anabolism and catabolism in form of ATP • 2 Pathways for obtaining energy o Aerobic and Anaerobic • Molecules that make the best food have lots of PE! o Electrons are not held tightly and are shared equally between two atoms • Energy released that is used to make ATP is through a process called phosphorylation o Addition of a phosphate group to a molecule and requires both an electron acceptor and an electron donor o Energy comes from oxidation of high energy molecules in oxidative phosphorylation Redox Reactions • OIL RIG o Oxidation is Loss; Reduction is gain • If one molecule is being reduced, the other is being oxidized • In cellular respiration and fermentation, glucose is oxidized and energy released is used to make ATP o Glucose undergoes oxidation but is reduced while carbon is oxidized and therefore is undergoing reduction • Oxygen is a terminal electron acceptor to make H20 Energy Harvest Glycolysis • First step for both aerobic and anaerobic pathways; takes place in cytoplasm • First step in oxidation of glucose o Steps § 2 ATP are invested to make ADP: energy investment phase § Makes 2 G3P which each use NAD+ to make NADH and 2 ADP each release 2 ATP, resulting in two pyruvate • IN: 4 ADP, 2 NAD+, 2 ATP • Out: 4 ATP, 2 NADH, 2 pyruvate • Pyruvate then transported to mitochondria for Pyruvate Processing if oxygen is present Aerobic Pathway • If oxygen is available to act as a terminal electron acceptor, aerobic pathway is used to reduce glucose and make ATP • NAD+ is oxidized so it accepts 2 electrons during energy harvest • NADH is reduced so it carries electrons to the next reactant • Oxidation of NADH to NAD+ happens at the beginning of the electron transport chain o Steps § Pyruvate Processing • Pyruvate reacts with CoA-SH to make Acetyl Co A o Carbon is oxidized to CO2 and NAD+ is reduced to NADH • IN: 2 NAD+, 2 CoA, 2 pyruvate • Out: 2 CO2, 2 NADH, 2 Acetyl-CoA § Krebs Cycle • Energy is released by Acetyl CoA which begins the cycle • Undergoes 2 cycles for every glucose molecule • Regulated by feedback • Acetyl CoA is oxidized to produce 3 molecules of NADH, one FADH2 and 1 ATP • IN: 2 Acetyl CoA • Out, per cycle: 2 CO2, 3 NADH, 1 FADH2 and 1 ATP o CO2 is disposed of as waste § Electron Transport Chain • When electrons are passed from one molecule to another, energy released by redox reactions is used to move protons across the inner membrane • CoQ is found in the mitochondria and is lipid soluble so it moves efficiently throughout the hydrophobic interior o Shuttles electrons from one side of the membrane to another and allows electrons to proceed through the chain while protons contribute to the electrochemical gradient o Drops off electrons at Complex 3 and the accompanying protons into the intermebrane space • Cytochrome C acts as a shuttle that transfers electrons between the complexes; delivers to complex 4 • When oxygen accepts electrons to form H20, oxidation of glucose is complete • Complex 1 and 4 use PE from redox reactions to pump protons from matrix to intermembrane space • IN: 2 NADH, 2 FADH2 • OUT: 2 NAD+, 2 FAD • Oxygen is the terminal electron acceptor in aerobic pathways which allows for the production of H20 o Transfer of electrons provides the energy to transport H+ from matrix to the intermembrane space against the concentration gradient, creating the proton motive force • As electrons move through the ETC, each complex and carrier gets reduced when an electron is passed to it and oxidized when it passes the electron • Protons are only pumped in Complex 1 not complex 2 • Free energy decreases as you move through the chain because electrons are transferred to more and more EN molecules until they reach Oxygen § Chemiosmosis • After proton gradient is established, enzyme in inner membrane synthesizes the ATP from ADP and Pi o When protons move through the synthase, the protein spins and generates ATP o Releases around 30-36ATP • ATP production depends on the proton motive force which is based on the proton electrochemical gradient • Uncoupler proteins cause the reaction to speed up and produce more heat because it is not producing ATP • Allows the proteins to move into the matrix without using the ATP synthase o Occurred in the case of Kristine because complex 3 was unable to pass the electrons so complex 1 remained in its reduced state § To fix this, used Menadione and Vitamin C which allowed electrons to bypass complex 2 and go straight into cytochrome C • ATP can cause feedback inhibition • Each process produces heat Anaerobic Pathway • Oxygen is not available and thus electrons breakdown products of glucose o Pyruvate and Acetelhyde o Products are lactic acid or ethanol o Regenerates NAD+ by oxidizing NADH o In cells that have stopped functioning, fermentation is a backup that allows glycolysis to continue producing ATP even when ETC is not working • 2 steps o Glycolysis § Makes ATP and then NADH through the reduction of NAD+ § ATP comes from here in fermentation processes o Fermentation § Doesn’t make ATP § Oxidizes NADH back to NAD+ so that glycolysis can continue § Lactic Acid Fermentation • Regenerates NAD+ by forming lactate o Causes an increase in breathing and heart rate which creates more O2 so ETC can begin again • IN: 2 pyruvate • Out: 2 lactate and 2 NAD+ § Alcohol fermentation • NADHàacetylahyde which gives off CO2àaccepts electrons from NADH which gives off NAD+ which allows glycolysis to continue • Ethanol becomes a waste product • Out: 2 ethanol, 2 CO2, and 2 NAD+ o Anaerobic organisms typically grow much slower because they produce much less ATP **In Glycolysis: • Glucoseà 2 pyruvate: OXIDATION • Coupled with NAD+à 2 NADH: REDUCTION **In Fermentation • 2 pyruvateà 2 lactate: REDUCTION • Coupled with 2 NADHà 2 NAD+: OXIDATION Substrate Level Phosphorylation • ATP made through enzymatic reaction where phosphate added to ATP comes from high energy molecule Oxidative Phosphorylation • ATP made through the use of the PMF • Where ATP can develop negative feedback loop o Only makes the ATP when needed o If there is too much ATP, ATP molecule inhibits one of the first steps of glycolysis which stops the entire process of cellular respiration which causes the anaerobic process to cease as well because glycolysis is needed for both Gaucher’s Disease • Autosomal disease (2copies) • Symptoms o Large abnormal blood cells o Large spleen o Fragile bones o Anemia • Gaucher’s cells typically found in bone marrow • Phagocytosis does not work properly • Treatments for Gaucher Disease o Enzyme Replacement Therapy in which M6P is inserted § M6P is key targeting signal for digestive enzymes that are destined for the lysosomes o Cell transplantatio n and Gene therapy § In gene therapy: isolate the bone marrow where the Gaucher cells are located and infect with modified viruses o Drug Therapy § Drug regulates the expression of proteins that cause the mutation How do some glycoproteins end up inside the memb rane while others are found outside? • Polarity is primary cause o Amino acids exposed to the lipid portion of membrane are no polar which makes the protein stick permanently in the membrane while the tail appears on the outside of the vesicle that pinch off t o form part of the Golgi o Once in the Golgi, protein has sugars that are added to it by enzymes that reside in the Golgi and thus the sugars are on side of the protein that is exposed to the outside of the cell o Once the vesicle breaks off from the Golgi, t he side with the sugars is exposed to the outside of the cell while the protein is located on the inside of the plasma How do ribosomes end up being modified in the rough endoplasmic reticulum? • Have a specific sequence of amino acids and are brought to th e rough ER and are translated into the lumen of the ER • Protein then folds up
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