Download BCHM 270 Module 3 Test: Enzymes and Enzyme Kinetics and more Exams Biochemistry in PDF only on Docsity!
BCHM 270 Module 3 Test With
Correct Answers
Enzymes - ANSWER -Catalysts for chemical reactions in living things
- globular proteins
- they work by binding to a substrate, and lowering the energy needed to cause the chemical reaction to happen (known as the activation energY)
activation energy - ANSWER energy needed to start a chemical reaction
transition state - ANSWER - the activation energy is lowered by an enzyme to bring a molecule to transition state
- transition state is a molecule that has a structure between the substrate and product
naming enzymes - ANSWER end in "ase", the root of the word comes from the substrate which they act on
essential enzyme properties - ANSWER - active site
enzyme active site - ANSWER where the substrate binds
enzymes have specificity - ANSWER - they only catalyze for 1 type of reaction
6 classes of enzymes - ANSWER (grouped based on the reactions they catalyze)
- oxidoreductase (transfer electrons between molecules)
- lysase (add a functional group to double bonds or removes them to form a double bind)
- transferase (transfer functional groups between molecules)
- isomerase (move functional groups within a molecule)
- hydrolase (cut molecules by adding water)
- ligase (joins 2 molecules in a reaction powered by ATP hydrolysis)
enzyme complexes - ANSWER - some enzymes are inactive when alone (called apoenzymes)
- when a cofactor binds, the enzyme becomes active
- cofactor and enzyme complex is cooed holoenzyme (which is active)
cofactors - ANSWER nonprotein enzyme helpers
- include a metal ion
- include coenzymes (non-protein molecules that bind to the enzyme, when tightly bound, they can be considered a proesthetic group)
chemistry of an active site - ANSWER - active site is made up of the binding site and the catalytic site
- the active site aligns the substrates, and then reduced activation energy for
Enzyme reactions and reversibility - ANSWER - enzyme can catalyze the forward and backward reaction
- this helps reach equilibrium with the products and reactants
- (some enzymes do require a forward enzyme and a seperate reverse enzyme)
isoenzymes - ANSWER - different enzymes that catalyze same reaction
- found in different parts of the cell or body, and have different reaction rates or substrate specificity
enzymes in clinical diagnosis - ANSWER - many proteins or enzyme levels or increased or decreased in response to a disease, do by using ELISA, SDS-PAGe, or western blots, we can measure the levels of the enzyme in the body for a diagnosis
clinical application of isoenzymes - ANSWER - creatine kinase is an isoenzyme that has different combinations of B and M subunits.
- in the body, we know where the different enzyme subunit comibinations are located, so we can see where there is elevated levels of the different isoenzymes to see where the tissue damage is
Gibbs free energy - ANSWER - used by chemists to determine is a reaction is spontaneous or not (under constant pressure and temperature)
3 factors that affect Gibbs free energy direction - ANSWER - enthalpy (heat released or absorbed)
- entropy (disorder)
- temperature
(together they determine Gibbs free energy)
Gibbs free energy equation - ANSWER Δ G = Δ H - T Δ S
Gibbs free energy equation results - ANSWER - G is positive (the reaction requires additional energy)
- G is 0 (the reaction is at equilibrium)
- G is negative (the reaction is spontaneous
Changes of Gibbs Free energy on a graph - ANSWER
exergonic reaction - ANSWER - releases energy from the system to the surrounding
- Gibbs free energy is negative, so the reaction is spontaneous and has
pH - ANSWER - the ionization of the side chains of amino acids is affected by pH (which is crucial for folding)
- enzymes work within a specific pH range, for optimal results
substrate concentration on enzyme rates - ANSWER - the amount of available substrate has an effect on reaction rate
- unlimited substrate causes high velocity reaction rates
product inhibition (enzyme rate effect) - ANSWER - inhibitors can bind to the enzymes to prevent the forward reaction by stopping the substrate from binding
- if the reaction is not at equilibrium, and there is more product than reactant, the enzyme is inhibited to allow more substrate (brings it back to equilibrium
covalent modifications (effects enzyme rate) - ANSWER - phosphorylation, glycosyltaion, and adding a prosthetic group can affect enzyme activity
- ex. phosphorylation of an serine, tyrosine, and threonine is the most common example which may increase or decrease activity
allosteric enzymes regulate biochemical pathways - ANSWER - allosteric
enzymes are regulated by effectors which bind to allosteric sites
- allosteric enzymes are controlled in the body
- have an active site and a allosteric site
Micheal-Menten enzymes - ANSWER are not regulated in the cell, but just work if enzymes are present
homotropic effectors (on an allosteric enzyme) - ANSWER - are the substrate of the enzyme and positively affect the enzymes other active sites to bind substrates
- help the reaction progress because binding 1 homotropic effector allows the other active sites on the enzyme to more easily bind substrate
hetertopic effectors (on allosteric enzymes) - ANSWER - they are a downstream product of the reaction the enzyme is involved with (a product)
- they allow for negative feedback to control the concentration of reactants or products
- they can be negative or positive, by increasing reaction rate of slowing it
enzyme synthesis is degradation - ANSWER - controls how many enzymes are in a cell
- enzymes synthesis can be increased or decease by changing the amount of
Micheal-Menten equation : Vmax - ANSWER - the maximum reaction rate
- reached when all enzymes are saturated and increasing substrate will no long increase reaction rate
- Vmax is dependent on the enzyme concentration is the solution
- measured in mol/s
Micheal-Menten equation: Km - ANSWER - describes the enzyme affinity (how well an enzyme binds to) the substrate
- also the substrate concentration where half the enzymes are bound to substrate (0.5Vmax)
- enzymes with poor affinity have large km (more substrate is needed to half-saturate the enzyme)
- enzymes with high affinity have low Km (less substrate is needed half-saturate the enzyme)
Lineweaver-Burk Plot - ANSWER - Reciprocal of Michaelis-Menten equation
- allows for the km and Vmax to be determined quickly
- x-intercept is -1/Km and the y-intercept is 1/Vmax
Regulation of allosteric enzymes - ANSWER - they have a sigmoidal curve
and are more complex than the Micheal-menten equation
- use the hill equation
- effectors of allosteric enzymes can change the Km or the Vmax of the enzyme
- allosteric enzymes are more sensitive to substrate chain than Micheal-Menten enzymes
hill equation - ANSWER - n is the degree of cooperativity
(when there is positive cooperation, n >1, increases enzyme activity)
(when there is negative cooperation, n<1, decreases enzyme activity)
positive and negative effectors - ANSWER - positive effectors will increase enzyme activity by increasing Vmax or increasing affinity (lower Km)
- negative effectors will decrease Vmax and lower affinity (increase Km)
reversible inhibitors - ANSWER - noncompletative
- competative
- uncompetative
- mixed
(decreases enzyme activity)
- is similarly structured to the substrate and bind to the activite site to form a stable enzyme-inhibitor complex
energy requirements of the cell - ANSWER - enzymes an couple with the breakage of a high energy bond to make reactions more favourable
high energy molecules - ANSWER ATP, NADH, FADH
homeostasis - ANSWER - the balance of metabolic activities in the body and cell
3 mechanisms that regulate metabolism - ANSWER - the amount of enzymes
- the activity of these enzymes
- the accessibility of substrates
metabolic processes in the cell (parts of the cell) - ANSWER shown in next slides
nucleus - ANSWER DNA and RNA are made here
cytosol - ANSWER glycolysis, protein synthesis, fat synthesis occurs here
proteasome - ANSWER - in the cytosol, degrade damaged proteins into amino acids
mitochondria - ANSWER - the TCA cycle, ETC, oxidative phosphorylation
Golgi apparatus - ANSWER - glycoslyation occurs in the Golgi
Endoplasmic Reticulum - ANSWER - rough ER is site of protein synthesis
- smooth ER is site of long chain fatty-acid synthesis
lysosome - ANSWER - large structures are degraded by lysosomes
how high energy molecules are used in cellular metabolism - ANSWER - anabolism
anabolism - ANSWER - reactions that consume ATP to build large macromolecules
ATP - ANSWER adenosine triphosphate
- made of an adenosine molecule, a ribose sugar, and a chain of 3 phosphates
GTP - ANSWER guanosine triphosphate
- identical to ATP but has a guanosine instead of an adenosine
- used in specific-energy requiring enzymatic reactions
ATP bond energy - ANSWER - there is free energy (G) stored between the bonds of the 2nd and 3rd phosphates of ATP, making ATP a high energy molecule
- when ATP loses a phosphate, it because ADP and energy is formed
how does ATP work as energy "currency" - ANSWER - many reactions will use the stored energy in ATP (or other high energy molecules like GTP, NADH, FADH2) to drive them forward
coupling with an unfavourable reaction - ANSWER - an energy requiring reaction (endergonic) is coupled with an energy releasing reaction (exergonic, example hydrolysis of ATP) to share a common intermediate
ATP as an allosteric factor - ANSWER - allosteric factors are elements that bind to an enzyme outcome the active site to induce a conformational and functional change in the enzyme
- ATP can do this by binding the the enzyme, and can cause a conformational change. if the ATP turns into ADP, this can cause ANOTHER conformational change
- ex. Na/K pump
High energy Molecules: FAD - ANSWER - flavin adenine dinucleotide
- changed from its high energy from by adding to H ions and 2 electrons producing FADH
High energy Molecules: NAD - ANSWER - changed from its high energy form by the addition of 1 H and 2 electrons
NADP+ - ANSWER - another high energy molecule that is similar to NAD (just has an extra phosphate)
- the phosphate is affective ar changing the substrate binding od enzymes, so most enzymes can only take NAD or NADP
mitochondria introduction - ANSWER - the body needs 2000 kcal/day, which is recycled from ATP to ADP to ATP, etc. (called oxidative phosphorylation)
regulated
- it is activated when the energy state is low and inhibited by high energy state
step 1: formation of citrate - ANSWER - acetyl-coA and oxaloacetate are joined by CITRATE SYNTHASE to form citrate and release a CoA
step 3: formation of alpha-ketogluterate - ANSWER - isocitrate is decarboxylated (loses CO2) by ISOCITRATE DEHYDORGENASE to produce alpha-ketogluerate
- this is a rate limiting step of the TCA
- this step creates the first NADH and CO
citrate synthase - ANSWER - inhibited by citrate
isocitrate dehydrogenase - ANSWER - inhibited by ATP and NADH
- activated by ADP and Ca2+
step 4: oxidative decarboxylation of alpha-ketogluterate - ANSWER - a second molecule of CO2 is removed and a molecule of CoA is added, converting alpha-ketogluterate to succinyl-CoA
- this reaction is Catalysed by alpha-ketogluterate dehydrogenase
alpha-ketogluterate dehydrogenase - ANSWER - inhibited by its products (NADH and succinyl CoA)
energy generated by TCA - ANSWER - TCA produces 5 high energy molecules: 3 NADH, 1 FADH, and 1 GTP
step 5: Cleavage of Succinyl-CoA and GTP formation - ANSWER - succinate thiokinase couples with this cleavage of succinyl CoA to the phosphorylation of GDT to GTP
succinate thiokinase - ANSWER
Step 6: Formation of Fumarate - ANSWER - succinate is oxidized to form fumigate by SUCCINATE DEHYDROGENASE
- the first FADH2 is created
step *: formation of Oxaloacetate - ANSWER - MALATE DEHYDROGENASE turns L-malate into oxoacetate
