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Date Created: 08/25/15
BIOLOGY 201 STUDY GUIDE Cells A Cells come in variety of shapes and sizes Smallest unit of life Small because it allows for greater surface to volume ratio Larger cells are usually longer or atter Genome is the genetic material of a cell Proteome is the expression of the proteins which gives each cell a speci c function B Cell theory 1 Cells are the smallest unit of life 2 All organisms are composed of one or more cells 3 Cells arise by division from previously living cells 4 Louis Pasteur disproved spontaneous generation of microorganisms C Prokaryotes vs Eukaryotes 1 All cells have DNA ribosomes cytoskeleton cytosol and plasma membrane 2 Prokaryotic cells archaea and bacteria do NOT have membrane bound nucleus or organelles D Life is characterized by the ability to 1 Maintain an organized structure 2 Metabolize 3 Grow reproduce and die 4 Respond to their environment and maintain homeostasis E Levels of organization 1 AtomsD MoleculesD Cells DTissuesl Organsljl Organismljl Population evolution happens here D Community D Ecosystemljl Biosphere wewwe Chemistry A Atoms 1 Protons Positive charge 0 Determine element 0 Determine atomic number 0 Found in atomic nucleus 2 Electrons Negative charge 0 Determine chemical relativity due to con guration of valence electrons Orbit the nucleus in a cloud 3 Neutrons No charge 0 Determine isotope elements that differ in atomic masses 0 Stable isotopes do not lose subatomic particles 0 Unstable or radioactive isotopes decay spontaneously emitting particles and energy o Added with protons to determine atomic mass 0 Found in atomic nucleus B Chemical Bonds 1 Covalent Shared valence electrons Polar covalent bond shared electrons reside closer to more electronegative atom resulting in partial charges on atoms dipole moment Nonpolar covalent bond electrons are shared evenly and electronegativity of atoms cancel out 2 lonic attraction of oppositely charged ions 3 Hydrogen between hydrogen atom in a polar molecule and another electronegative atom Dynamic constantly made broken and reformed Weak individually but strong and important for the 3D shape of molecules when there are many 0 Hydrogen bonding of water 0 Moderates temperature Speci c heat 0 Displays cohesion adhesion and is responsible for capillary actions 0 Expands when frozen 0 Readily dissolves polar moleculesSolution solvent solute and aqueous solution 0 Dissociates into H30 and OH 0 Hydrophilic polar molecules 0 Hydrophobic nonpolar molecules 4 Carbon 0 Four valence electrons Bonds with variety of atoms and to generate diverse molecules including hydrocarbons by bonding with hydrogen or more complex molecules by bonding with functional groups C Hydrolysis and Dehydration 1 Hydrolysis breaks down large molecules by the addition of water Hydrolysis of ATP to ADP and phosphate is highly exergonic A G 73 kcalmol and when coupled with an endergonic reaction it creates a net release of free energy making the overall reaction spontaneous 2 Dehydration reactions build large molecules by the removal of water 0 2 monosaccharides to form disaccharide D Acids and Bases 1 Acids increase the concentration of the H30 and decrease pH 2 Bases decrease the concentration of H30 and increase the pH 3 Buffers are substances that minimize changes in pH in a solution 4 The pH scale is negative logarithmic Macromolecules A Carbohydrates 1 Energy source molecules WM 4 U1 Structural support Monosaccharides Carbohydrate monomer containing 36 carbons Glyceraldehydemetabolic intermediate 3 carbons Ribosedeoxyribose Components of RNADNA 5 carbons Glucose primary source of energy found in most living organisms6 carbons Fructose simple sugar found in plants 6 carbons Galactose simple sugar found in dairy products 6 carbons Disaccharides two monosaccharides joined covalently by a dehydration reaction with a gylcosidic bond Sucrose table sugar composed of fructose and glucose Lactose milk sugar composed of galactose and glucose Maltose malt sugar composed of two glucoses Polysaccharides composed of hundreds to thousands of monosaccharides joined by gylcosidic bonds Starch and glycogen are used for storage Cellulosemade of glucose and Chitin are used for structural support B Lipids Macromolecules but not really polymers 1 Great for energy storage because of hydrocarbon bonds Insoluble and hydrophobic in water due to nonpolar bonds 3 Three main types 2 C Nucleic Acid Fats triacylglycero 1 glycerol and 3 fatty acid molecules joined by ester bond 0 Saturated single bonded and solid at room temperature 0 Unsaturated Double bonded and liquid at room temperature Phospholipids 1 glycerol 2 fatty acids and 1 phosphate group with a choline o Amphipathic polar heads and nonpolar tails essential for biological membranes this enhances the uidity of cellular membranes and resists solidi cation at colder temperatures 0 Spontaneously organize in AQUEOUS solutions Steroids lipids with a carbon skeleton containing four fused rings vary by functional group attached 0 Include cholesterol and sex hormones 0 Cholesterol is a temperature buffer in cellular membranes 1 Deoxyribonucleic Acid DNAstorage of hereditary information 2 Ribonucleic Acid RNA expression of hereditary information 3 Polymers of nucleotides Pentose sugar ribose or deoxyribose Nitrogenous base cytosine guanine adenosine thymine and uracil Phosphate group makes DNA acidic Linked together by phosphodiester bonds D Proteins 1 Proteins are 1 polypeptides folded into 3D structures Polypeptides are made of amino acids and linked by peptide bonds 0 20 common amino acids carbon covalently attached to and amino group carboxyl group hydrogen and a R group 2 Functions Catalysis Support 0 Defense 0 Transport 0 Motion 0 Regulation 0 Storage 3 Structure 0 Primary Structure linear sequence of amino acids in a protein 0 Secondary structure regions of folds and coils due to hydrogen bonding beta pleated sheets and alpha helices Tertiary Structure 3D shape of a protein determined by interactions among various side chains R groups 0 Hydrogen bonds disul de bridges ionic bonds hydrophobic effects van der Waals forces Quaternary structure overall shape of a protein due to association of multiple polypeptide subunits 4 Conformation of proteins Denaturation loss of proteins conformation and usually makes it inache 0 pH 0 Temperature 0 Salt concentrations Chaperone proteins help newly formed proteins fold properly and may help x proteins that are denatured Organelles and Their Functions A Cellular Membrane 1 Phospholipid bilayer with embedded proteins Semi uid lateral and rotational movements are spontaneous but movement across lea ets requires the enzyme ippase Lea et is one half of the bilayer Integral proteins are embedded in membrane o transmembranecomposed of nonpolarhydrophobic amino acids 0 lipidanchored Peripheral proteins attach to integral proteins 2 Functions of membrane proteins 0 Transport molecules 0 Enzymatic activity 0 Signal transduction Cellcell recognition lntracellularjunctions Attachment 3 Glycosylation extracellular portion covalent attachment of carbohydrates to lipids or proteins 0 Important recognition signals and cell surface markers Allows membranes to have internal and external surfaces 4 Gradients Across Membranes Membranes are selectively permeable Passive transport requires no energy occurs spontaneous moves down the concentration gradient diffusion or osmosis sometimes requires transport protein facilitated diffusion o Hypertonic high concentration 0 Hypotonic low concentration 0 lsotonic solute concentrations are at equilibrium 0 Active transport solutes move up concentration gradient requires input of energy ATP movement across membrane requires transport protein 0 Transport proteins 0 Facilitated Diffusion channels which are gated proteins and carriers uniporters undergo a conformational change both quotassistquot diffusion while aquaporins allow water across cell membrane 0 Active transport pumps preform primary active transport to establish concentration gradient by using ATP hydrolysis to transport molecules like the proton pump and coupled transporters perform secondary active transport by using the established concentration gradient to drive solutes against it anitporters two solutes move in opposite directions symporter two solutes move in same direction 5 Bulk transport movement of large macromolecules and particles across the plasma membrane via vesicles Endocytosis involves the transport of particles into the cell by either phagocytosis pinocytosis or receptor mediated endocytosis Exocytosis involves the transport of particles out of the cell by fusion of transport vesicles with the cell membrane B Nucleus 1 Functions Contains DNA in chromosomes that are made up of chromatin DNA and protein Synthesizes RNA in the nucleolus Gives orders to cell 2 Structure Nuclear pores proteins that lead to be passageways in nuclear envelope Nuclear envelope two phospholipid bilayer membranes inner and outer Nuclear matrix lls interior of nucleus Nuclear lamina intermediate laments A c9511 Chromatin in nucleus r 9 7 7 I Nucleus 1 V internal nuclear matrix l 4 3 393 2 m 39 p Inner membrane 1 Nuclear envelope Nuclear 539 L r 39 Outer membrane pore 39 7 I 7 7 7 complex Nuclear lamln proteins Cytosol C Endoplasmic Reticulum ER 1 Phospholipid bilayer the space enclosed is called lumen or cisternae 2 Rough ER Continuous with nuclear envelope Ribosomessynthesize proteins attach to the cytoplasmic face and give it its rough look Proteins for secretion or association with plasma membrane are synthesized on surface of rough ER and sent to the Golgi apparatus 3 Smooth ER Continuous with rough ER but not associated with ribosomes Synthesis of phospholipids including steroid hormones Carbohydrate metabolism Storing intracellular calcium ions Detoxi cation D Golgi Apparatus 1 Collects processes and directs the traf c of proteins 2 Stack of attened membranes with 3 compartments Cis protein receiving side Medial processing usually involves glycosylation and occurs here Trans protein shipping side 3 Turns proteins to hormones adds proteins to carbs packages proteins into vesicles which travels to plasma membrane puts nishing touches on lysosomes E Lysosomes 1 Contain enzymes that degrade proteins lipids nucleic acids and carbs 2 Important for breakdown of macromolecules and even organelles 3 Turn waste into building material F Peroxisomes 1 Important for metabolism of fatty acids and breakdown of reactive peroxides 2 Contain the enzyme catalasebreakdown of hydrogen peroxide to water and oxygen G Vacuoles 1 Stores water pigments inorganic and organic molecules 2 Serves diverse functions H Mitochondria 1 Semiautonomous membrane bound growreproduce depend on cell and endosymbiosis 2 Metabolic centers energy is changed from one form to another 3 Site of cellular respiration found in both plant and animal cells I Chloroplasts 1 Semiautonomous 2 Metabolic Center 3 Site of photosynthesis only in plant cells 4 Contains chlorophyll why leaves are green Outer membrane Intermernbrarle space 1 539 7 o I e a uter Inner 7 V 7 membrane membrane 5 139 j 7 quot F Inner membrane Mitochondrial 39 Thylakoid matrix membrane 7 1 cabal i n 4 I Thylakoud 1 3 e 2 5 Ll 3R lumen stack of th ylakoids J Cytoskeleton 1 Organization anchoring organelles 2 Support cell shape 3 Motility transport of materials and cell locomotion 4 Micro laments actin 0 Maintain cell shape 0 Form cleavage furrow during cell division 0 Provide cell motility 0 Muscle contractions pseudopodia and cytoplasmic streaming 5 Intermediate laments Maintain cell shape 0 Anchor nucleus and organelles Form nuclear lamina 6 Microtubules Maintain cell shape 0 Move material within cell Organize movement of chromosomes during cell division Mitotic spindles Provide cell motility Flagella and cilia 7 Motor Proteins Interact with micro laments and microtubules to promote movement 0 3 domains head tail and hinge Myosin associated with actin micro laments Kinesin and dynein are associated with microtubules K Cytoplasm 1 Contains all organelles 2 Cytosol intracellular uid and site of many important events 0 Water ions dissolved molecules 0 Metabolic processes signal transduction and protein synthesis Energy Enzymes and Metabolism A Energy the ability to do work 1 Kinetic energy is doing work while potential energy is the amount of energy capable 2 First law of thermodynamics Energy can be transformed from one form to another not created or destroyed 3 Second law of thermodynamics Every energy transformation increases the entropy of that system 0 Results in a loss of energy that is usable for work 4 Chemical reactions a process in which one or more substances is changed into other substances Direction determined by laws of thermodynamics changes in free energy 0 AG A H T A S Henthapy Sentropy and Gusabe energy 0 If negative exergonic products have less free energy than reactants energy is released and reactions are spontaneous sometimes requires activation energy 0 If positive endergonic products of reaction have more energy and reactants energy is required 0 If it equals 0 then the reaction is at equilibrium 0 Rate determined by presence of biological catalysts in cell 0 Enzymes and ribozymes B Enzymes 1 Do 0 Lower activation energy 0 Strain reactantsBring reactants together Recognizes their substrate with high speci city Undergo conformational changes that promote catalysis 2 Do NOT Alter the change in free energy 0 Get consumed in the reaction elaciiy Firm utilisetkund i TUBE A ll 2 ll 3 Factors that effect enzymes mm 1 1am 1m 1m Cofactors enhance enzyme activity 5 353 mm mm mm mm I quot lime o Nonprotein usually 53131333 at High gar inorgainic metallic ions or organic small molecules derived from vitamins like NADH or coenzyme A 0 Typically function at the enzyme site but also may act at allosteric sites sites distinct from active site Inhibitors reduce enzyme activity 0 Competitive inhibitors bind to active site 0 Noncompetitive inhibitors bind to an allosteric site 0 Physical factors that affect enzyme activity different optimal conditions for each enzyme and extreme conditions may denaturedecrease activity 0 Temperature 0 pH 0 ionic conditions 39I HM ll iufnefraiel C Metabolism 1 Sum of chemical reactions occurring within a cell 2 Catabolic breaking down macromolecules giving off energy 3 Anabolic synthesizing macromolecules requiring energy input 4 Metabolic pathways Organize chemical reactions in to sequences in which the product of one reaction provides the substrate for the next Often occur in discrete locations within the cell 0 Allow feedback inhibition as a mechanism for regulation Enzyme1 7 Enzyme2 EnzymeS Reaction 1 Reaction 2 7 Reaction 3 Starting Product molecule 0 The similarity of metabolic pathways among diverse organisms suggest that these pathways are essential ef cient and share a common evolutionary origin Disruptions can lead to disease Cellular Respiration C6H1206 6 02 gt 6 C02 6 H20 Energy ATP A Redox reaction 1 Chemical reactions that result in rearrangements in electrons between reactants are called reductionoxidation reactions or redox reactions OILRIG 2 Oxidation substance loses electrons or is oxidized 3 In reduction a substance gains electrons or is RumADP RimADP reduced Reduntion 4 In cellular respiration glucose is broken down to 9Y0 a H o XIdatIon C02 H NHZ H H NHZ Glucose is oxidized and 02 is reduced WH2e NADH B Glycolysis 1 Breaks down glucose into two pyruvate molecules 2 Occurs in the cytoplasm 3 3 major phases 0 Energy investment phase requires 2 APT 0 Hexokinase is regulated inhibited by glucose 6 phosphate 0 Phosphofructokinase is regulated through allosteric regulation inhibited by ATP Cleavage splitting phase 0 Energy payoff phase generates 4 ATP and 2 NADH o Pyruvate kinase is regulated through allosteric regulation inhibited by ATP and alanine 4 ATP is formed through substrate level phosphorylation 5 Fermentation produces ATP through glycolysis and reactions that regenerate NAD Alcohol fermentation NAD is regenerated by reducing acetaldehyde to ethanol Lactic acid fermentation NAD is regenerated by reducing Energy investment phase Cleavage phase Energy liberation phase Step 4 Step 5 G 0 Step 6 Step 39339 Step 3 Step 9 Step 10 G 0 Step 1 Step 2 Step 3 as OCHQ I O CHEO l 7 39 H 39139 7 HQ OH 3 OH H Glucose Fructose ll 6 bisplhosphate NADH Two molecules 01 a l V V glyceraldehyde Two molecules 3 phosphate of pyruvate pyruvate to lactate C Pyruvate translocation and conversion to Acetyl CoA 1 Translocation phase Hydrogen ionpyruvate cotransporter transports pyruvate into mitochondria 2 Conversion phase pyruvate dehydrogenase enzyme complex catalyzes the removal of C02 and addition of coenzyme A to form acetyl CoA 3 Transitions respiration into mitochondria and links glycolysis to the Citric acid cycle D Citric acid cycle 1 Metabolic cycles involving reactions that consume and then regenerate metabolites oxaloacetate 2 3 phases 0 Phase 1 step 1 citrate 6Carbon molecule is generated by adding oxaloacetate to acetylCoA Phase 2 steps 25 citrate is rearranged and oxidized to generate NADH and ATP 0 Phase 3 steps 68 oxaloacetate is regenerated and also forms FADH2 and NADH 3 Acetyl Co A enters cycle and C02 exits 4 NADH and FADH2 produced by cycle shuttle electrons extracted from food to the electron transport chain E Oxidative Phosphorylation 1 Starts with 10 NADH 2 FADH2 and 02 and produces a lot of ATP 34 2 Occurs across the inner mitochondrial membrane cristae 3 Two phases 0 Electron transport chain ETCproduces a proton gradient across the inner mitochondrial membrane and produces no ATP 0 Composed of a group of four protein complexes MW and two small organic molecules that are mobile electron carriers ubiquinone and cytochrome c Complexes I III and IV are also proton pumps cynide blocks complex IV The energy released in these electron transfers powers these pumps Protons move against their concentration gradient into the intermembrane space 02 is the nal electron acceptor aerobic respiration is aerobic because it requires oxygen as nal acceptor in ETC Anerobic respiration uses an electron transport chain with an electron acceptor other than 02 Function of ETC is to break down the large free energy amount from food to 02 into smaller steps that release energy in manageable amounts 0 ATP synthase uses the proton gradient to produce ATP 0 O O Protons move back across the membrane passing through channels in ATP synthase Uses exergonic ow of protons to drive phosphorylation of ATP Chemiosmosis is the use of energy stored in a proton gradient to do work F Cellular Respiration is Regulated 1 2 3 Respiration speeds up if ATP concentration begins to drop and vice versa ATP and key intermediates act as metabolic indicators and regulate respiration at multiple steps Regulation occurs at strategic points in the pathway Photosynthesis A Compared to cellular respiration 1 weww Photosynthesis is endergonic reaction that reduces C02 to glucose while H20 is oxidized Pathway by which energy enters the biosphere Generates 02 Pathway for carbon xation Takes place in chloroplasts B Light Reactions 1 Absorption of light by pigments Photons are little packets of light energy Pigments absorb different wavelengths and those that are not absorbed are re ected Absorption spectrum is a pigments light absorption vs wavelength Chlorophyll a is the main photosynthetic pigment absorbing purple and red light best Chlorophyll b and carotenoid are accessory pigments they broaden the spectrum used for photosynthesis action spectrum 2 Photosystems Chlorophyll molecules are arranged in complexes called photosystems o Resonance energy in electrons is transferred to nearby pigment molecules 0 Reductionoxidationelectron is transferred to a new molecule PS and PSI are connected by an electron transport chain 0 PSI donates electrons to NADP reductase C Calvin Cycle
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