Chapter 2 Flashcards
Enzymes
Biological catalysts (don’t impact thermodynamis but help reaction proceed at faster rate by lowering activation energy)
* Lower activation energy (make it easier for substrate to reach transition state)
* Increase rate of reaction
* Don’t alter equilibrium constant
* Appear in reactants and products (not used up in reactions)
* Are pH and temperature sensitive (optimal activity in certain ranges)
* Ideal temperature is lower with catalyst than without (need higher temperature without catalyst to lead to better chance of completing)
* Don’t affect overall ∆G of reaction
Enzyme Specificity
- Given enzyme will only catalyze a certain reaction or type of reaction
Oxidoreductases
- Catalyze oxidation-reduction reactions (transfer of electrons between biological molecules)
- Have cofactor that acts as electron carrier (ex: NADP+)
- Reductant: electron donor
- Oxidant: electron acceptor
- Usually have dehydrogenase or reductase in name
Transferases
- Catalyze movement of functional group from one molecule to another
- Straightforwardly named
- Kinases are also transferases
- Kinases: catalyze transfer of phosphate group (usually from ATP) to another molecule
Hydrolases
- Catalyze breaking of compound into two molecules by adding water
- Common uses, named only for substrate
- Ex: phosphatase (cleaves phosphate group), peptidases (break down proteins), nucleases (break down nucleic acids), lipases (break down lipids)
Lyases
- Catalyze clevage of single molecule into two products
- Don’t require water and don’t act as oxidoreductases
- Catalyze synthesis of two small organic molecules into single molecule (synthases)
Isomerases
- Catalyze rearrangement of bonds within molecule
- Catalyze reactions between stereoisomers and constitutional isomers
Ligases
- Catalyze addition/synthesis reactions (usually large similar molecules and require ATP)
- Synthesis reactions with smaller molecules
- Likely with nucleic acid synthesis
Endergonic Reaction
Requires energy input
∆G > 0
endo in
Exergonic Reaction
Energy given off
∆G < 0
exo out
Kinetics
- Largely effected by enzyme
- By lowering activation energy, equilibrium is achieved faster BUT equilibrium position doesn’t change
Substrate
The molecule that an enzyme acts on
Enzyme-Substrate Complex
Physical interaction between enzyme and substrate
Active site
Location within enzyme where substrate is held during chemical reaction
Lock and Key Theory
Enzyme’s active site (lock) is already in appropriate shape for substrate (key) to bind
* No changes needed
* Less accurate
Induced Fit Model
Active site of enzyme molds itself around substrate when it is present
* Tertiary/quaternary structure modified for enzyme to function
* More accurate
* Endergonic (requires energy)
Releasing substrate is exergonic reaction (releases energy)
Return to original shape once substrate releases
Cofactors/Coenzymes
- Activators of enzymes (conformational change in enzyme promoting its activity)
- Small so can bind to active site
- Participate in catalysis of reaction by carrying charge through ionization, protonation, deprotonation
- Usually in low concentrations
- Attach in many ways (weak noncovalent to strong covalent)
Apoenzymes
Enzymes without their cofactors
Holoenzymes
Enzymes containing their cofactors
Prosthetic Groups
- Tightly bound cofactors/coenzymes needed for enzyme function
Cofactor
- Inorganic molecules
- Metal ions
- Ingested in dietary minerals
Coenzyme
- Small organic groups
- Mainly vitamins/derivatives of vitamins
- Water-soluble vitamins (B vitamins and ascorbic acid)
Increasing [S] Substrate
- Substrate concentration low: proportional increase in enzyme activity
- Substrate concentration high: when enzyme is saturated increasing substrate has no affect because vmax already attained
Increasing [E] Enzyme
- Will always increase vmax regardless of starting concentration of enzyme
Michaelis-Menten Equation
How rate of reactin depends of concentration of enzyme and susbtrate which forms product
Velocity of Enzyme to Substrate Concentration
- Enzyme concentration constant
Reaction rate is half of vmax
Km is Michaelis constanst
Lineweaver-Burk Plot
- Double reciprocal graph of Michaelis-Menten equation
- X intercept: -1/Km
- Y intercept: 1/Vmax
Enzyme Cooperativity
- Interactions between subunits in a multisubunit enzyme/protein
- Binding of substrate to one subunit causes change in other subunit from T (tense) state to R (relaxed) state that encourage binding of substrate to other subunits
- In reverse direction, unbinding of substrate from one subunit cause change from R to T in remaining subunits promoting unbinding of substrate from remaining subunits
Michaelis-Menten vs Lineweaver-Burk Plots
Similarities:
* Account for values of Km and Vmax under various conditions
* Simple graphical interpretations and derived from Michaelis-Menten equation
Differences:
* Axes and visual representation
* Michaelis-Menten is v vs [S] (hyperbolic curve for monomeric enzymes)
* Lineweaver-Burk Plot is 1/v vs 1/[S] (Straight line)
Km (Michaelis Constant)
- Measure of an enzyme’s affinity for its substrate
- Substrate concentration where an enzyme is function at 1/2 its maximal velocity
- Enzyme with higher Km has lower affinity for its substrate (requires higher substrate concentration to be half saturated)
Temperature Effect on Enzymes
- Double in velocity for every 10˚C increase in temperature until optimum temperature is reached
- At body temperature, activity falls off and enzyme denatures at higher temperature
- Some enzymes regain function if cooled
- Ideal: 37˚C = 98.6˚ F = 310 K
pH Effect on Enzymes
- pH affects ionization of active site
- pH can lead to denaturation of enzyme
- Ideal blood ph is 7.4
- acidemia: blood pH < 7.35 (more acidic than physiologically neutral)
- Exceptions are digestive tract (ex: pepsin)
- Ideal (MOST): 7.4
- Ideal (gastric): 2
- Ideal (pancreatic): 8.5
Salinity Effect on Enzymes
- Altering concentration of salt can change enzyme activity in vitro (disrupting bonds)
- Causes disruption of tertiary/quaternary structure leading to loss of enzyme function
Feedback Inhibition/Negative Feedback
Product of an enzymatic pathway when produced in excess turns off enzyme that start the pathway
* Helps maintain homeostasis
Reversible Inhibition
- Competitive
- Noncompetitive
- Mixed
- Uncompetitive
Competitive Inhibition
- Binding site: Active site
- Substrates can’t access enzyme binding sites if inhibitors in the way
- Impact on Km (bonding affinity): Increase
- Impact on vmax (amount of enzyme available to react): Unchanged
- Overcome by adding more substrate to make ratio higher
Noncompetitive Inhibition
- Binding site: Allosteric site
- Bind to allosteric site and change shape so normal molecules can’t bind
- Can’t be overcome by adding more substrate
- Impact on Km: Unchnaged
- Impact on vmax: Decreases
Mixed Inhibition
- Binding site: Allosteric site
- Inhibitor can bind to enzyme or enzyme-substrate complex with different affinity for each
- Impact on Km: if inhibitor binds to enzyme-substrate complext lowers Km, if inhibitor binds to enzyme increases Km
- Impact on vmax: Decreases
Uncompetitive Inhibition
- Binding site: Allosteric site
- Bind only to enzyme-substrate complex and lock substrate in enzyme preventing release
- Impact on Km: Decreases
- Impact on vmax: Decreases
Irreversible Inhibition
Prolonged/permanent inactivation of an enzyme so that it can’t be easily renatured to regain function
* Ex: aspirin
* Common in drugs
Allosteric/Transient Enzymes
Enzymes with multiple bonding sites (active site and at least one other)
* Examples: Allosteric activation (makes active site more available for binding to substrate), allosteric inhibition (makes active site less available)
Covalently Modified Enzymes
- Phosphorylation/dephosphorylation (can’t tell if will activate without experiments)
- Glycosylation (covalent attachment of sugar moieties)
Zymogens
- Precursors of active enzyme
- Critical that some enzymes (ex: digestive) remain inactive until arriving to desired location
Metabolic Reactions
- Cofactors/coenzymes usually small (metal/organic)
- Can usually carry a charge
- Include oxidation-reduction reactions and movement of functional groups
