Cellular Biology
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| Hydrogen Bond | Strong cohesive forces between water molecules. Forces "squeeze" hydrophobic molecules away from water, and cause them to aggregate.
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| Water | Solvent in which chemical reactions of living cells take place-often acts as a product or a reactant-water molecules surround (solvate) a hydrophilic molecule, seperating it from the group
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| Hydrolysis | Breaks apart most macromolecules of living cells by adding an H2O molecule
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| Dehydration Synthesis | Forms macromolecules of living cells by removing an H2O molecule
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| Lipid | Biological molecule that has low solubility in water and high solubility in nonpolar organic solvents; Hydrophobic. Types: fatty acids, triacylglycerols, phospholipids, glycolipds, steroids, terpenes
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| Fatty Acids | Building blocks for most complex lipids. Long chains of carbons truncated at one end by a carboxylic acid. Saturated or unsaturated. Most fats reach the cell in the form of fatty acids. Oxidation liberates large amounts of chemical energy
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| Saturated Fatty Acids | Possess only SINGLE carbon-carbon bonds
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| Unsaturated Fatty Acids | Contain one or more carbon-carbon DOUBLE bonds
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| Triacylclycerols; triglycerides | Store metabolic energy in cell, provide insulation. Fats and oils. Constructed by 3 carbon backbone (glycerol) attached to 3 fatty acids. Ex: Adipocytes (fat cells)
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| Phospholypids | Ideal for membrane structural component. Built from glycerol backbone, with polar phosphate group replacing one of the fatty acids. Polar at phosphate end and nonpolar at fatty acid end (amphipathic)
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| Steroids | Regulate metabolic activities-Four ringed structures.Some hormones, vitamin D, cholesterol
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| Lipoproteins | Transport lipids in the blood.Lipid core surrounded by phospholipids and apoproteins. Greater ration of lipid to protein, the lower the density-chylomocirons, very low density lipoproteins (VLDL), low density (LDL), high density (HDL)
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| Proteins; Polypeptides | Built from chain of amino acids linked together by peptide bonds.Usually built from same alpha amino acids.Amine is attached to the carbon in the alpha position to the carbonyl
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| Amino acids | Differ from each other only by their side chains, known as R group; attached to the alpha carbon-Digested proteins reach cells as single amino acids. In solution always carry one or more charges; position and nature of charges depend solution's pH
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| Primary Structure | The number and sequence of amino acids.All proteins have primary structure
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| Secondary Structure | After primary structure forms, the single chain can twist into alpa helix or lie along side itself and form beta-pleated sheet (parallel or antiparallel).Contribute to the conformation of the protein.Most proteins have secondary structure
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| Tertiary Structure | Three dimensional shapre formed when peptide chain curves and folds (bending). Larger proteins may have tertiary structure
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| Quaternary Structure | When two or more polypeptide chains bind together
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| Five forces that create tertiary and quaternary structure | Covalent disulfide bonds between cysteine amino acids on different parts of chain. Electrostatic interactions. Hydrogen bonds. Van der Waals forces. Hydrophobic side chains pushed away from water toward center of protein
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| Denatured protein | When the conformation has been disrupted.Ex: Urea, salt, change in pH, mercaptoethanol, organic solvents, heat
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| Carbohydrates; Sugars; Saccharides | Made from carbon and water. Empirical formula: C(H2O).
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| Glucose | Six carbon carbohydrate. Liver or enterocytes convert digested carbohydrates into glucose. Animals eat alpha linkages, but only bacteria break the beta linkages.
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| Oxidation of Glucose | Transfers chemical energy to ATP. If cell has enough ATP, glucose is polymerized to the polysaccharide glycogen or converted to fat.
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| Liver | Regulates the blood glucose level; liver cells can reform glucose from glycogen and release it back into the blood stream.
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| Glucose Absorption | Usually through facilitated diffusion. Only some epithelial cells in digestive tract and kidney can absorb glucose against concentration gradient through a secondary active transport mechanism down the concentration gradient of sodium.
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| Insulin | Increases the rate of facilitated diffusion for glucose and other monosaccharides.
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| Plants and Glucose | Plants form starch and cellulose from glucose.
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| Nucleotides | Composed of three parts: a five carbon (pentose) sugar, a nitrogenous base and phosphate group. Includes: polymers to form DNA and RNA, ATP, cyclic AMP, NADH, FADH2
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| Nucleic Acids | DNA and RNA. Nucleotides joined together by phosphodiester bonds between the phosphate group of one nucleotide and the 3rd carbon of the pentose sugar of the other nucleotide; written 5'->3'
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| DNA | Two strands are joined by hydrogen bonds to make double helix structure. Top strand runs 5'->3' and bottom runs 3'->5'
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| Minerals | Dissolved inorganic ions inside and outside of cell; assist in cellular transport; give strength to matrix; cofactors in enzyme/protein function
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| Enzymes as catalysts | Usually globular proteins; govern virtually all biological reactions. Increase reaction rates; not consumed or altered by rxn, don't alter equilibrium rxn.
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| Enzyme-substrate complex | Substrates are reactants upon which an enzyme works; binding to a substrate's active site with numerous noncovalent bonds
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| Enzyme specificity | Usually enzymes are designed to work only on a specific substrate or group of closely related substrates. Ex: lock and key theory, induced fit model
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| Lock and key theory | The active site of enzyme has specific shape like a lock that only fits a specific substrate, the key. Explains some but not all enzymes.
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| Induced fit model | The shape of both the enzyme and the substrate are altered upon binding. Alteration increases specificity and helps reaction to proceed. If more than one substrate, enzyme may orient them and create optimal conditions for rxn to proceed
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| Enzymes and saturation kinetics | As the relative concentration of substrate increases, the rate of the reaction also increases, but to a lesser and lesser degree until maximum rate has been achieved. As more substrate is added, individual substrates must wait in line for free enzyme.
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| Enzymes and temperature | Initially, as the temperature increases, the reaction rate goes up, but at some point, the enzyme denatures and the rate of the reaction drops off. In human body, the optimal temperature is 37 C or 98.6 F.
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| Enzymes and pH | Enzymes function within specific pH ranges, with optimal pH varying depending on enzyme. Pepsin (stomach) prefers pH under 2, with trypsin (small intestine) works best with pH between 6 and 7.
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| Enzyme cofactor | To reach optimal activity, many enzymes require a non-protein component called a cofactor. Cofactors can be coenzymes or metal ions. Coenzymes are vitamins or their derivatives.
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| Enzymes: Irreversible inhibitors | Usually bind covalently to enzymes and disrupt their fuctions. Tend to be highly toxic. Ex: Penicillin binds to bacterial enzyme that assists in the manufacturing of peptidoglycan cell walls.
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| Enzymes: Competitive inhibitors | Compete with the substrate by binding reversibly with noncovealent bonds to the active site. Typically for only fraction of a second, they block substrate from binding during that time. Raise the substrate concentration without changing maximum rate.
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| Enzymes: Noncompetitive inhibitors | Bind noncovalently to an enzyme at a spot OTHER THAN the active site and change the conformation of the enzyme. Do not prevent the substrate from binding. Lower the maximum rate, but substrate concentration stays the same.
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| Negative feedback; feedback inhibition | When one of the products downstream in a reaction series comes back and inhibits the enzymatic activity in an early reaction. Provides shutdown mechanism when a sufficient amount of product has been produced.
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| Positive feedback | When the product returns to activate the enzyme. Occurs less often than negative feedback.
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| Metabolism Stage 1 | Macromolecules are broken down into constituent parts releasing little or no energy
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| Metabolism Stage 2 | Constituent parts are oxidized to acetyl CoA, pyruvate or other metabolites forming some ATP and reduced coenzymes (NADH and FADH2) in a process that does not directly utilize oxygen
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| Metabolism Stage 3 | With oxygen use,metabolites go into the citric acid cycle and oxidative phosphorylation to form large amounts of energy (more NADH, FADH2, or ATP) otherwise coenzyme NAD+ and other byproducts are either recycled or expelled as waste
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| Respiration | Second and third stages (energy acquiring stages). Aerobic: if oxygen is used. Anaerobic: if oxygen is not used.
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| Glycolysis | First stage of anaerobic and aerobic respiration. Series of reactions that breaks apart a 6-carbon glucose molecule into two 3-carbon molecules of pyruvate, 2 molecules of ATP from ADP, inorganic phosphate, water, 2 molecules of NADH from NAD+ reduction
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| Fermentation | Anaerobic respiration. Includes glycolysis, the reduction of pyrucate to ethanol (yeast) or lactic acid(human muscle cells), and the oxidation of the NADH recycled back to NAD+.
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| Glycolysis 6-carbon stage | Expends two ATPs to phosphorylate the molecule, like "priming a pump"
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| Glycolysis 3-carbon stage | Synthesizes two ATP with each carbon molecule
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| Substrate-level phosphorylation | Formation of ATP from ADP and inorganic phosphate using the energy released from the decay of high energy phosphorylated compounds as opposed to using the energy from diffusion. Occurs in Krebs cycle.
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| Aerobic respiration | Requires oxygen; the products of glycolysis (pyruvate and NADH) will move into the matrix of mitochondrion. Pyruvate is then converted to acetyl CoA, producing NADH and CO2. Produces 36 net ATPs.
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| Krebs cycle; citric acid cycle | Each turn produces 1 ATP, 3 NADH, and 1 FADH2. 1 NADH brings back 2-3 ATPs and 1 FADH2 brings back about 2 ATPs.
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| Electron transport chain (ETC) | Series of proteins, including cytochromes with heme, in the inner membrane of the mitochondrion.
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| Aerobic Respiration Reaction | Glucose+O2->CO2+H2O; Combustion reaction. Final electron receptor is oxygen.
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