Mcat: Molecular Biology; Cellular Respiration

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Water

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Solvent in which the chemical reactinos of all living cells take place. Polar molecule that hydrogen bonds.

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Hydrophobic

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Dont like water.

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Hydrophilic

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Like water.

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Hydrolysis

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Use water to break macromolecules.

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Dehydration sythesis

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Releases water to form bonds.

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Lipid

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Is any biological molecule that has low solubility in water and high solubility in nonpolar organic solvents. Six major groups: Phospholipids, Steroids, Glycolipids, Terpenes, Triacylglycerols, and Fatty acids.

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Fatty acids

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Are the building blocks fo most, but not all, complex lipids. They are long chains of carbon truncated at one end by a carboxylic acid. Usually even number and can be unsaturated or saturated.

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Unsaturated Fatty Acids

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Contain one or more carbon-carbon double bonds.

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Saturated Fatty Acids

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Contain only carbon-carbon single bonds.

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Triacylglycerols, Triglycerides, Fats, Oils

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Constructed from a three carbon backbone called glycerol, which is attached to three fatty acids. They function to store energy, provide thermal insulation, and padding.

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Adipocytes

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Fat cells, are specialized cells whose cytoplasm contains almost nothing but triglycerides.

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Phospholipids

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Built from a glycerol backbone, but a polar phosphate group replaces one of the fatty acids. The phosphate group lies on the opposite side of the glycerol from the fatty acids making the phospholipid polar at the phosphate end and nonpolar at the fatty acid end. Major components of membranes.

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Amphipathic

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One end polar, one end nonpolar.

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Steroids

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Four ringed structures, that include some hormones, vitamin D, and cholesterol. Regulate metabolic activites.

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Proteins

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Are built from a chain of amino acids linked together by peptide bonds.

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Peptide bonds

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link amino acids together to form polypeptides

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Essential amino acids

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Cannot be generated by the human body therefore must be ingested.

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Amino acids

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Basic unit of protiens. Usually contains some charge in solution. The position and nature of the charges will be determined by the pH of the solution. Four groups: Nonpolar, polar, acidic, and basic.
R
|
NH2-C-COOH
|
H

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Primary Structure

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The number and sequence of amino acids in a polypeptide.

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Secondary Stucture

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The conformation of the protein. Alpha helices and Beta pleated sheets are reinforced by hydrogen bonds between the carbonyl oxygfen and the hydrogen on the amino group.

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Tertiary Structure

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Refers to the three dimensional shape formed when the peptide chain curls and folds (The bending of a polypeptide chain). Governed by five forces: Covalent disulfide bonds between two cysteine amino acids on different parts of the chain, elcetrostatic (ionic) interactions mostly between acidic and basic side chains, hydrogen bonds, van der Waals forces, and hydrophobic side cahns pushed away from water (toward the center of the protein).

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Quaternary Structure

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When two or more polypeptide chains bind together. Same five forces as tertiary structure work here.

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Denatured

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Protein has lost most of its secondary, tertiary, and quaternary structure.

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Carbohydrates

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Made from carbon an water. Emipircal formula C(H2O).

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Glucose

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The most commonly occuring six carbon carbohydrate. Accounts for 80% of the carbohydrates absorbed by humans.

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Anomers

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Glucose exist in aqueous solution primarily in the ring form not the chain form. Two glucose anomers, alpha and beta. In alpha glucose the hyrdoxyl group on the anomeric carbon (carbon number 1) and the methoxy group (carbon number 6) are on opposite sides of the carbon ring. In Beta Glucose the hydroxyl group and the methoxy group are on the same side of the carbon ring.

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Glycogen

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If cell has sufficient ATP then glucose converted to glycogen. Glycogen is a branched glucose polymer with alpha linkages. Mostly found in muscle and liver. Converted back to glucose in liver.

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Starch

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Formed by plants has alpha linkages. Can be digested by animals because has alpha linkages.

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Cellulose

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Formed by plants from glucose has beta linkages and cannot be digested by animals.

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Nucleotides

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Form ploymers to create the nucleic acids , DNA and RNA. Are composed of three components a five carbon sugar, a nitrogenous base, and a phosphate group. Some important nucleotides include ATP, cyclic AMP, NADH and FADH2.

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Phosphodiester Bonds

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Join nucleotides together between the phosphate group of one nucleotide and the 3rd carbon of the pentose of the other nucletide. Phosphate group attached to 5' end.

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Double helix

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Stucture created by two strands of nucleotide polymers joined together by hydrogen bonds. Adenine and thymine form two hydrogen bonds, while cytosine and guanine form three.

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Minerals

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Dissolved inorganic ions insdie and outside the cel. Create electrochemical gradinets assisting in transport inside and outside cell, combine to give strength to a matrix such as bone, and also act as cofactors.

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Enzymes

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Virtually all biological reactions are governed by enzymes. Are typically globualr proteins (some may be nucliec acids), act as a catalyst lowering energy of activation and therefore increasign the rate of the reaction.

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Substrates

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The reactant or reactants upon which the enzyme works.

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Active Site

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The position on the enzyme to where the substrate binds, usually with numerous noncovalent bonds.

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Enzyme Specificity

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Normally, enzymes are designed to work only on a specific substrate or group of closely related substrates.

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Lock and Key Theory

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Example of enzyme specificity. The Enzyme has particular shape like a lock that only fits a specific substrate, the key.

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Induced Fit

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The shape of both the enzyme and the substrate aer altered upon binding.

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Saturation Kinetics

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As the relative concentration of the substrate increases, the rate of the reaction also increases, but to a lesser and lesser degree until a maximum rate has been achieved.

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Cofactor

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May be required by enzymes to reach optimal activity. Can be coenzymes or metal ions.

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Coenzymes

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Vitamins or their derivatives.

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Irreversible Inhibitors

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Bind covalently to enzymes and disrupt their function. Example is Penicillin.

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Competative Inhibitors

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Compete with the substrate by binding reversibly with noncovalent bonds to the active site. This type of inhibition is overcome by increasing the concentration of substrate.

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Noncompetative Inhibitors

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bind noncovalently to an enzyme at a spot other than the acive site and change the conformation of the enzyme.

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Zymogen;Proenzyme

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Inactive form of an enzyme

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Allosteric interactions

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Allosteric regulation is the modification of the enzyme configuration resulting from the binding of an activator or inhibitor at the specific binding site on the enzyme.

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Negative Feedback or Feedback Inhibition

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Negative feedback provides a shut down mechanism for a series of enzymatic reactions when that series has produced a sufficient amount of product.

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Coopertivity

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Enzyme shape changes may cause other substrats to bind more easily (Positive Coopertivity) or not as easily (Negative Coopertiity).

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Enzyme Classiication

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-ase, Means enzyme. Once it is recongnized that chemical is enzyme, you know it contains a nitrogen and is subject to denaturation.

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Metabolism

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All cellular chemical reactions. Consist of Anabolism- molecular synthesis and Catabolism- molecular degradation.

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Respiration

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The energy aquiring stages. if oxygen is used then aerobic, if no oxygen then anaerobic.

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Anaerobic Respiration

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Respiration in which oxygen is not required.

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Glycolysis

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Is the series of reactions that breaks a 6-carbon glucose molecule into two 3-carbon molecules of pyruvate. Products are 2 ATP, 2 Pyruvate, and 2 NADH. Produces ATP via substrate level phosphorylation and occurs in cytosol (fluid portion) of the cell.

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Fermentation

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Anaerobic respiration. It includes glycolysis, the reduction of pyruvate to ethanol or lactic acid, and the oxidation of the NADH back to the NAD+.

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Aerobic Respiration

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Requires oxygen. The products of glycolysis travel to the Mitochondrial Matrix. Pyruvate travels via facilitated diffusion and is converted to Acetyl CoA while NADH requires energy from ATP.

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Substrate Level Phosphorylation

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Is the formation of ATP from ADP and inorganic phosphate using the energy released fromt the decay of high energy phosphorylated compounds as opposed to using energy from diffusion.

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Krebs Cycle or Citric Acid Cycle

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Occurs in the mitochondrial matrix, each turn produces 2 CO2, 1 ATP, 3 NADH, and 1 FADH2. The process of ATP production in Krebs Cycle is called substrate level phosphorylation.

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Electron Transport Chain

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Is a series of proteins, includng cytochromes with heme, in the inner mitochondrial membrane. Electrons are passed down the protein series and oxygen is the final electron acceptor. As electrons are moved protons are pumped into the inner mitochondrial space causing this area to be at a lower pH.

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Proton Motive Force

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Created by ETC proteins, propels protons through ATP sythase (located on the inner mitochondrial membrane) to manufacture ATP.