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43 Cards in this Set
- Front
- Back
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All 20 standard amino Acids are:
a: Alpha b: Beta c: Delta d: Gamma |
Alpha. This means they all have an amine group attached to the Alpha Carbon (First carbon away from the carboxylic acid).
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What does Zwitterionic mean?
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One formal positive charge and one formal negative charge on the molecule at the same time. This is true of all standard amino acids.
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How do amino acids cross the cell membrane?
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Transport Proteins.
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In what configuration do the 20 standard amino acids exist?
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L-configuration. The D is not found in humans.
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What are the different classifications of Amino Acids by Side Chains?
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1. Charged: Negative and Positive
2. Neutral : Polar, Aromatic, Non-polar or Aliphatic |
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What are the Negatively charged amino acids?
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Aspartic acid, Glutamic Acid
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What are the positively charged amino acids?
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Lysine, Histidine, Arginine
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What are the Neutral Polar Amino Acids?
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Serine, Cysteine, Threonine, Asparagine, Glutamine
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What are the 3 Aromatic Amino Acids?
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Phenylalanine, Tyrosine, Tryptohan
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What are the 7 Non-polar Amino Acids?
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Glycine, Alanine, Valine, Leucine, Methionine, Isoleucine, Proline
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Draw out the 7 non-polar aliphatic amino acids
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Do it
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Draw out the 3 aromatic amino acids
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Do it
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Draw out the 5 polar amino acids
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Do it
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Draw out the Charged (positive, negative) Amino Acids
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Do it
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What are the exceptions to the amino acid abbreviation first three letter rule?
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Asn=Asparagine
Gln=Glutamate Ile=Isoleucine Trp=Tryptophan |
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What is a peptide bond?
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Same as Amide bond, helps amino acid form polymers. Short amino acid polymers are called peptides or oligopeptides and long ones are proteins.
Peptide bonds form when amine of one amino acid reacts with the carboxylic acid of another. Peptide bonds are covalent bonds, but can be cleaved by hydrolysis. |
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What is a Disulfide Bond?
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A type of covalent bond found in proteins and peptides that forms between 2 thiol groups. Of the standard amino acids, disulfide bonds only occur between the side chains of two cysteines. Disulfide bonds are formed by oxidation, and are cleaved by reduction.
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Why must peptide and protein drugs be given by injection of IV?
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1. They are digested in the GI tract by peptide bond cleavage
2. Absorbed poorly through membranes Therefore, do not give these drugs orally fool. |
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What is an example of a peptide drug that cannot be ingested?
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Insulin is delivered by subcutaneous injection for type 1 diabetes.
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What is the isoelectric point (pl)?
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The pH at which a solution of amphoteric molecules having both acidic and basic groups will have a charge of Zero. NOTE: Not all molecules are equal charge. They are not uncharged, it just means that the zwitter dominates (80%) and the others cancel each other out.
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What happens when a ph that is above the isoelectic point or a ph below it?
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When pH is above the pl, the net charge will be negative and the peptide will migrate toward the positive terminal (Anode) in an electrical field.
At the ph below pl, the net charge will be positive and peptide will move toward the negative terminal in an electrical field. (cathode) |
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What is the significance of pl on solubility?
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Molecules are least soluble at the isoelectric point.
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What is a an Enzyme? What are its characteristics?
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Proteins that catalyze reactions, meaning they increase the rate at which a reaction will achieve equilibrium. Enzymes do NOT change Keq, only lower the energy barrier.
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What is Keq?
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Ratio of products to reactants after a reaction has achieved equilibrium. Keq does NOT tell how long it took. Enzyme will NOT affect whether products or reactants are favored at equilibrium.
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What is an "Active Site" of an enzyme?
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Where the substrate binds and catalysis takes place. Active sites are selective of certain sizes and shapes. Product is released from the active site following catalysis and another molecule of substrate can bind. Like all catalyst, enzymes can do many reaction in their lifetime.
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How can Proteins be denatured?
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Heat, pH extremes, Detergents, organic solvents (acetone, alcohols, etc)
This is not the same as digestion. |
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What are 2 cofactors and what are their characteristics?
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Coenzyme: an organic, loosely bound enzyme
Prosthetic group: Organic OR Inorganic that is tightly bound to the enzyme. |
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What are the mechanisms of Enzyme Regulation?
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Product inhibition
Allosteric Regulation Covalent modification Protein-Protein Regulation Zymogen Cleavage Enzyme synthesis and degradation |
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What is product inhibition?
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Reversible inhibition of an enzyme that occurs when reaction product competes with substrate for binding at the active site. Product is similar to the reactant.
Occurs when enough product builds up to compete with the substrate for the active site, inhibiting enzyme catalysis of more product. |
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What is Allosteric Regulation?
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Reversible inhibition OR activation from an enzyme binding somewhere other than the active site. You can have positive or negative allosteric inhibitors or activators.
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What is Covalent Modification?
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Reversible inhibition OR activation that occurs when a molecule is covalently attached to an enzyme.
A common type of covalent modification is phosphorylation: -Protein kinases covalent attachment of a phosphate molecule from ATP to alcohol-containing residues on the enzyme being regulated -Protein Phosphatases catalyze removal of a phosphate molecule from the enzyme being regulated Phosphorylation may increase or decrease an increase or decrease an enzymes activity, depending on the enzyme. |
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What are Protein-Protein interactions?
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Reversible activation OR inhibition of an enzyme that results when the enzyme that results when the enzyme is bound by another protein to form a complex.
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What is Zymogen cleavage?
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Irreversible activation of a zymogen by proteolytic cleavage.
Causes changes that expose enzyme active site. Digestive enzymes are often synthesized as zymogens, then activated as needed by other proteases. |
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What is Enzyme Synthesis/Enzyme Degradation?
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If more enzyme is synthesized, the reaction rate increases.
If the amount is reduced, reaction rate decreases. Enzyme synthesis and degradation takes longer than other forms of regulation, occurring over hours TO DAYS |
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What is the Michaelis-Mentin Equation?
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Mathematically describes the relationship between rate (v) and the substrate concentration (S) for an enzyme-catalyzed reaction. IN order for the equation to be true, certain assumptions must be true.
Only 1 substrate S>>E P is low (only initial rates are used) v=Vmax(S/Km+S) |
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What is Vmax?
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The maximal rate of reaction. The actual value of Vmax will depend on the specific enzyme and substrate, but it is proportional to enzyme concentration. More enzyme-higher Vmax.
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What are the two meanings of Km?
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Km is a type of equilibrium constant. Is reported in units of concentration.
One meaning for Km is that it is the substrate concentration at which of the total enzyme pool will be bound by substrate ("half-saturated") The second meaning for Km is that it is the substrate concentration at which the rate will be one half the maximal rate (1/2 Vmax) as shown on graph below. |
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What is better for enzyme reactions to speed up, low or high Km?
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Km should be low. Less enzyme is needed for catalyzation.
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What are the 3 types of enzyme inhibitors?
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Competitive, Noncompetitive, Irreversible.
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Explain Competitive inhibition. Give an example
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A competitive inhibitor competes with the substrate for the active site of the free enzyme. Competitive inhibitors have similar structures to the substrate.
THEY DO NOT AFFECT VMAX, they DO INCREASE KM NSAIDS or IBUPROFIN is a great example. |
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What is a Noncompetitive inhibitor and give an example.
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Bind the enzyme someplace other than the active site. Can do it whether substrate is bound or not.
Noncompetitive inhibitors LOWER VMAX, DO NOT CHANGE Km. Caspofungin is a noncompetitive inhibitor example |
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What is an Irrevesible Inhibitor and give an example.
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Poisons the enzyme by covalently binding to the free enzyme (usually at the active site).
Active enzyme is only regenerated by synthesizing more. If the concentration of irreversible inhibitor is less than the concentration of enzyme, an irreversible inhibbitor will NOT EFFECT Km and WILL LOWER Vmax. If the concentration of irreversible inhibitor is greater than the concentration of enzyme, no catalysis will occur-all the enzyme will be inactive. Aspirin adn most NSAIDS are good example. |
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What are the differences with Kinetics of Allosterically Regulated Enzymes
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They do not fit the Michealis-Menten equation. For this reason, K0.5 is used instead of Km to indicate the substrate concentration. An inhibitor shifts curve to the right K0.5, activator shifts left the sigmoidal curve by K0.5.
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