Exam 2- Lecture 10: Enzyme Classification & Regulation

  1. What are enzymes: biological catalysts (protein or RNA)

   

  1. Catalyst: a substance that increases the rate of a chemical reaction by lowering the activation energy but does not change form at the end of the reactions
  2. How do you identify if something is an enzyme: The name always ends in “ase”
  3. What are enzymes named after: the substrate of the reaction it catalyzes.
    1. What are the various components of a biological reaction: enzyme, substrate, turnover number, cofactor, coenzyme, apoenzyme, holoenzyme, and an active site

   

  1. Substrate: the reactant of an enzyme catalyzed reaction
  2. Turnover number: the number of substrate molecules that are converted to product over a given time period
  3. CofactorCofactor: nonprotein substance that binds to the protein (enzyme) and is required for catalysis like copper, iron, manganese, magnesium, cobalt, and zinc since metal is important for active binding sites?????????????

       1. INORGANIC substance attached to the enzyme that helps complete reaction (without it, rxn would be really slow or completely fail)

          1. hemoglobin needs Fe for receiving oxygen

  1. CoenzymeCoenzyme: organic cofactors typically found in redox enzymes like vitamins (natural form of vitamin) and derivatives of vitamins (usable form of vitamin) ??????????

       1. ORGANIC version of cofactor

  1. ApoenzymeApoenzyme: Protein minus its cofactor/enzyme????????

       1. raw enzyme without the extra piece (coenzyme/cofactor) to complete the reaction so usually not enough to complete reaction

  1. Holoenzyme: Catalytically active enzyme containing the apoenzyme with its cofactor/coenzyme

       1. little piece plus big piece= complete piece

  1. Active site: Pocket in the enzyme where catalysis takes place like the mouth in the example from class
    1. What is the chemicalnatureofenzymeschemical nature of enzymes and their overall role in reactions: enzymes are either proteins or RNA and their role is to lower the activation energy needed to initiate an enzymatic reaction

   

  1. isn’tthisthesameasinfoabove??????shouldiaddanythingisn’t this the same as info above?????? should i add anything
    1. How do enzymes work as catalysts to speed up reactions: through the proximity effect, orientation effect, energy effect, or the catalytic affect

   

  1. proximity effect: bring reactants together
  2. orientation effect: hold reactants at the required distance and orientation for the reaction
  3. %%energy%% effect: lower activation %%energy%% by inducing (forcing) strain on the bonds of the substrate (reactant)
  4. catalytic effect: provide acidic, basic, and other types of functional groups (side chains of amino acids) that are required for catalysis

       1. the result of interactions in the active site 2. enzyme active site is chemically coded for specific type of substrate. so active site may require acidic amino acid

          1. acidicandbasicwhat?aminoacidsacidic and basic what? amino acids 2. whatfunctionalgroups?coenzymessometimeswhat functional groups? coenzymes sometimes

  1. What are the 6 classes of enzymes-Answer in terms of the general reactions they catalyze and their subclasses: oxidoreductase, transferase, hydrolase, isomerase, lyase, and ligase

   

  1. ^^oxidoreductase: catalyze oxidation-reduction (redox) reactions (catalyze the oxidation or reduction of a substrate) (look at picture example on slide 10)^^

       1. subclass: dehydrogenase which removes 2 hydrogen atoms from a substrate to form a double bond 2. doesitalwayshavetobeALCOHOLdehydrogenase?oristhatonlyrequiredforNADdoes it always have to be ALCOHOL dehydrogenase? or is that only required for NAD

          1. what does dehydrogenase require: it requires FAD or NAD+ as a coenzyme because it needs an electron transfer from the hydrogen atoms 2. what does FAD do:

            FAD removes H from 2 covalently bonded carbon atoms to form an alkene 3. what does NAD do:

            NAD removes H from the covalently bonded OH and C to form a carbonyl group (one H from OH and one H from C)

  1. ^^transferase: transfer of a functional group (amino or phosphoryl) between substrates (Catalyze the transfer of a functional group) (picture slide 11)^^

       1. subclasses: kinase and transaminase

          1. kinase: transfers a phosphoryl group (–PO3 2- ) between substrates 2. trans%%amin%%ase: transfers an %%amin%%o group (–NH3+) between substrates

  1. ^^hydrolase: catalyze hydrolysis (split bonds with water) of substrates (water lysis) (picture slide 13)^^

       1. subclasses: lipase, protease, nuclease, and amylase

          1. Lipase: hydrolyze ==ester== bonds in lipids 2. Proteases: hydrolyze ==peptide== bonds (backbone amides) 3. Nucleases: hydrolyze the ==phosphate ester== bonds in DNA/RNA 4. Amylases: hydrolyzes the 1,4 ==glycosidic bonds== in amylose

  1. ^^isomerase: catalyze the isomerization of substrate (rearranges bonds of the substrate) (^^Catalyze the rearrangement of atoms in a substrate to produce an isomer) (picture slide 14)

       1. isomer: same formula, different arrangement of atoms, different properties

  1. ^^lyase: catalyze the elimination of a functional group by forming a double bond or breaking a double bond (^^Catalyze the addition or removal of a small molecule to/from a double bond) (slide 16)

       1. subclasses: decarboxylase, dehydrase, deaminase, and synthase

          1. Decarboxylases - removal of CO2 2. Dehydrases - removal of H2O 3. Deaminases - removal of NH3 4. Synthases - addition of a small molecule to a double bond

  1. ^^ligase: catalyze bond formation couple with ATP hydrolysis (which provides the energy of the bond formation) (^^Catalyze the bonding of two molecules using ATP energy (coupled reactions))(slide 17)

       1. subclasses: synthetase, and carboxylase

          1. Synthetases: bond two substrate molecules together 2. Carboxylases: add CO2 to form carboxylate group

  1. What are the two types of enzyme specificities: highly specific enzyme, and nonspecific enzyme (slide 20)

   

  1. highly specific enzyme: active site catalyzes one type of reaction for a single substrate.
  2. nonspecificenzyme−catalyzesasinglereactionforagroupofsimilarsubstratesnonspecific enzyme - catalyzes a single reaction for a group of similar substrates

       1. whatismeantby“similarsubstrate”?????samechemicalcompatibility????what is meant by “similar substrate” ????? same chemical compatibility????

  1. which type or types of enzymes must have %%pockets%% that are %%chemically compatible%% with the substrate it reacts with: both highly specific and nonspecific enzymes require %%pocket chemical compatibility%%
  2. what does binding specificity depend on: it depends on the stereochemistry of the substrate (slide 22)

       1. don’tunderstandwhatshappeninginslide22withtheequationdon’t understand whats happening in slide 22 with the equation

  1. Whydoestheinducedfitmodelmoreaccuratelydescribesubstratebindingthanthelock−and−keymodel:becauseitshowshowthesubstratebindingtriggersaconformationalchangeintheenzyme(armsthat“catches”enzymetohelpitbind)asopposedtoastationaryholethatsimplywaitsforthesubstratetofallin.ThishappensinalloccasionsbutcanbeassimpleasasidechainmovementortheentiremovementofahexokinaseWhy does the induced fit model more accurately describe substrate binding than the lock-and-key model: because it shows how the substrate binding triggers a conformational change in the enzyme (arms that “catches” enzyme to help it bind) as opposed to a stationary hole that simply waits for the substrate to fall in. This happens in all occasions but can be as simple as a side chain movement or the entire movement of a hexokinase

   

  1. confirmationalchange:generalshapeofenzymeisdifferentconfirmational change: general shape of enzyme is different
  2. hexokinase:typeofenzymehexokinase: type of enzyme
    1. What atomic level processes affect enzyme activity: temperature, pH, enzyme concentration, and substrate concentration (slides 32-37)

   

  1. How does temperature affect enzyme activity:lowtemperaturesdecreasetherateofthereactionbecauseparticlesaremovingslowlywhilehightemperaturesalsodecreasetherateofthereactionbecausetheheatcausesproteinstodenature(breakapart)ivity: low temperatures decrease the rate of the reaction because particles are moving slowly while high temperatures also decrease the rate of the reaction because the heat causes proteins to denature (break apart)
  2. HowdoespHaffectenzymeactivity:lowpHalsocausesdenaturing?becauseofachangeinpronation?idkwhathighpHdoesHow does pH affect enzyme activity: low pH also causes denaturing? because of a change in pronation? idk what high pH does
  3. Howdoesenzymeconcentrationaffectenzymeactivity:asenzymeconcentrationincreasessteadily(withexcesssubstrate),therateofreactionincreasessteadilysoitcreatesadirectlyproportionalrelationship(diagonalline)How does enzyme concentration affect enzyme activity: as enzyme concentration increases steadily (with excess substrate), the rate of reaction increases steadily so it creates a directly proportional relationship (diagonal line)

       1. class example of enzyme concentration graph: as you invite more people to candy eating party, the rate of eating remains constant because everyone only eats one at a time and it is manageable

  1. How does substrate concentration affect enzyme activity: as substrate concentration increases steadily (with constant enzyme concentration), the rate of the reaction increases logarithmically??(soinitiallytherateincreasesdirectlywiththesubstrateconcentrationuntilitapproachesthemaximumreactionratespeedwhereitthenlevelsoffandbecomesconstant)logarithmically?? (so initially the rate increases directly with the substrate concentration until it approaches the maximum reaction rate speed where it then levels off and becomes constant)

       1. class example of substrate concentration graph: 8 students each 100 candies at once- initially eat fast but then mouths fill quickly and rate slows down