Lectures 18-25, Enzymes, regulation, Citric Acid Cycle, Glycolysis + Gluconeogenesis Flashcards
What is Sir Archibald Edward Garrod known for?
First to make a connection between
disease and fundamental errors in
biochemical reactions
• Coined term “inborn errors of
metabolism”
• Enzymes must be link
– Thus, mutations in enzymes can cause
disease by altering biochemical reactions
What: – Contains a unique microenvironment, usually void of water, and controls the proper
shape, pH and polarity for substrate binding and chemical reactivity
Active Site
Define: Transition state
– Intermediate structure that is not the substrate and not yet the product
• Unstable and highest free energy
Define: Apoenzyme
enzyme without its cofactor
Define: Haloenzyme
Cofactor bound and catalytically active
Coenzymes are small organic molecules often derived from _________
vitamins
When coenzymes are bound tightly they are called _______
prosthetic groups
Examples of cofactors
Metals [smallest cofactor], coenzymes (vitamins - Biotin)
Stabilize
In alcohol dehydrogenase:
______ is reduced to ______ in the conversion of ethanol to acetaldehyde
The cofactors _____ and _____ are in a specific arrangement for this catalysis
Slide 27 - hint hint might be on test with a couple of questions
NAD+, NADH
NAD+, Zinc
Which class of enzymes is associated with the this type of reaction:
Oxidation-reduction
- transfering electrons from one molecule to another
Oxidoreductases (ex. Lactate dehydrogenase)
ex. Alcohol dehydrogenase - converts alcohols to aldyhydes or ketones - Alcohol is oxidized and NAD+ is reduced
Which class of enzymes is associated with the this type of reaction:
Group transfer
Donor molecule required
Transferases (ex. nucleoside monophosphate kinase)
Coenzyme A transfering Acytl groups
Kinase receptors - phosphorylate proteins and themselves
Which class of enzymes is associated with the this type of reaction:
Hydrolysis reactions (transfer of functional groups to water)
Enzyme that catalyzes the hydrolysis of covalent bonds
transfer of functional groups to water
Hydrolases (ex. Chymotrypsin)
Ex. Disaccharidases - cleave double sugars to single sugars
Ex. defects in lactase - lactose intolerance
Which class of enzymes is associated with the this type of reaction:
Addition or removal of groups to form double bonds
Unique active site that can transfer electrons to active site and move them around on the product. Normally one substrate becoming two products with the formation of a double bond.
Lyases (ex. Fumarase)
Ex. Alsolase
Which class of enzymes is associated with the this type of reaction:
Isomerization (intramolecular group transfer)
Intramolecular oxidation-reduction reaction (group transfer)
Don’t lose any products, just move a double bond
Isomerases (ex. triose phosphate isomerase)
**making an isomer
Which class of enzymes is associated with the this type of reaction:
Ligation of two substrates at the expense of ATP hydrolysis
Creating the covalent linkage of two substrates
Ligases (Aminoacyl-tRNA synthetase)
Ex. DNA ligase - joining two DNA molecules, two phosphodiester bonds between the two molecules.
T/F: enzymes are biocatalysts that follow classical chemical laws. They speed up the rate at which a chemical reaction reaches equilibrium and alter the final concentrations of the reactants at equilibrium
False: they do not alter the final concentrations
What is enzyme kinetics?
Enzyme kinetics is the study of biochemical
reactions that are catalyzed by enzymes. The
focus of which is the reaction rates of these
enzymatic reactions.
Enzymes affect reaction rates by lowering the activation energy (ΔG‡) for the reaction.
Steady-state kinetics assumptions:
- ES is in rapid equilibrium with E and S
- Rate of ES formation = rate of ES breakdown
– Therefore [ES] is essentially constant - [S] >>> [E]
– Therefore [S] is essentially constant - Initial velocity of reaction is measured from
time = 0 (thus, V0)
KM is the substrate concentration that produces
______ for the catalyzed reaction.
½ Vmax
• KM has units of molarity (M)
• KM is independent of enzyme amount and purity
• KM is dependent on assay conditions such as pH,
presence of inhibitors or activators, temperature,
and ionic strength. This is because that KM is
constructed purely of rate constants.
Km is called Michaelis constant
____ is the maximum velocity - at which enzyme is
saturated with substrate.
Vmax
• Vmax has units of μmol/min
• Vmax is dependent on amount of enzyme used.
• Vmax is the highest reaction rate that can be
attained because all of the enzyme is
saturated with substrate.
kcat =
Vmax/[Etotal]
kcat is called either the catalytic constant or turnover number
• If kcat = 1000 sec-1, the enzyme can convert 1000 molecules of substrate into product each second at saturating [S]
**number of molecules that can be converted to product per second.
On a Lineweaver Burk Plot the y intercept =
1/Vmax
On a Lineweaver-Burk Plot the x-intercept =
-1/Km
On a lineweaver burk plot the slope =
Km/Vmax
A low Km means what about the affinity of the active site?
high affinity at active site.
What is the name of the concentration at which half the active sites are filled?
Km
What is the measure of catalytic efficiency?
kcat/Km
higher the kcat/Km value the more efficient te enzyme (limits - 10^9. Cannot be more efficient than standard diffusion)
How is the lineweaver burke plot derived?
it is the reciprocal of michaelis-menton
michaelis menton: Vo= Vmax*[S]/(Km+[S])
lineweaver burke: 1/Vo = Km/ (Vmax*[S]) + 1/Vmax
** Look at tables of Lineweaver Burke, be able to get Km and Vmax, etc.
What type of reaction:
All substrates bind to the enzyme before any product
is released
Sequential reactions
both substrates form some product. ex. NADH binds first, then creates better binding site for pyruvate, then lactate is formed and NAD+ is released
What type of reaction:
One of the products is released before a second
substrate binds
Double-displacement (ping-pong) reactions
One substate binds, a product is released, then a second substrate comes in and binds and a second product is released.
Where is Sirt1 found in the cell?
In the nucleus
Where is Sirt3 found in the cell?
in the mitochondria
Define: Reversible Inhibition
bind to enzymes with non-covalent interactions such as H+ bonds, hydrophobic interactions and ionic bonds and do not undergo chemical reactions when
bound to the enzyme and can be easily removed by dilution or dialysis.
Mimics the substrates
– EXAMPLE: HIV protease inhibitors: mimics the enzymes’ substrates
Define: Irreversible Inhibition
**covalently modifies an enzyme**, and **inhibition cannot therefore be reversed**. These inhibitors aregenerally specific for one class of enzyme and do not inactivate all proteins; they do not function by destroying protein structure but by specifically altering the active site of their target
“kills the enzyme”
– Example: FFR-CK (Phenlalanine-phenelalanine-arginine
chloromethylketone) covalently binds to the active site serine in
plasmin.
What are the Three kinds of Reversible Inhibition and what are their effects?
- Competetive - **Increase effective Km **(More substrate needed because active site are filled by inhibitors). Inhibits at the active site.
- Uncompetetive - Binds only to the enzyme-substrte complex. Both Km and Vmax are altered. DOES NOT inhibit at the active site.
- Non-competitive - Affects only the Vmax. can bind with both the enzyme and enzyme substrate complex.
LOOK AT GRAPHS FOR EACH!!!!! Be able to indentify!
How does pH effect enzyme activity?
pH can denature and change effectivness (kcat)
Changes in pH may denature enzymes by
altering the enzyme’s charge
altering the ionic bonds of the enzyme that
contribute to its functional shape
Enzymes have an optimal pH that helps
maintain their 3D shape
What two outcomes happen with Allosteric regulation?
allosteric inhibition stabilizes the enzyme in it’s low affinity form resulting in little or no activity
OR
stabilizes it in high affinity form, resulting in enzyme activity
Review slide 30
ATCase is what type of enzyme modification?
Transferase
condensation reaction joining two molecules with loss of a small molecule
ATCase is found in what two distinct conformational states?
textbook example of allosteric modification (products inhibit upstream reactions)
T state (less active - favored by CTP binding - inhibits the enzyme) and R state (more active - relaxed/open - ** Favored by substrate binding**)
Zinc is a cofactor in ATCase
Why do you have the multiphasic curve in the formation of N-carbamoylaspartate (ATCase)?
Combination of T and R state curves. - Sigmoidal curve
Serine proteases use what for the active site?
Use active site serine for peptide cleavage
Cleavage of peptide backbone in serine proteases occurs in which step?
3rd.
Go over slide 52
Acyl-anzyme intermediate created via the serine
Where is Pepsin synthesized?
Stomach
Where is Chymotrypsin, Trypsin, Carboxypeptidase, and Elastase synthesized?
Pancrease
Anabolic are:
those that require inputs of energy to proceed
____ Is the Universal Currency of Free Energy in
Biological Systems
ATP
In aerobic organisms, the ultimate electron acceptor in the
oxidation of carbon is ____
and the oxidation product is _____
.
O2, CO2
Which of the following has the most energy released during oxidation?
A. Methane
B. Methanol
C. Formaldehyde
D. Formic Acid
E. Carbon Dioxide
A. Methane
A->E is most to least amount of energy, Slide 10
Oxidation of 2-carbon units to produce
2 CO2 molecules
1 GTP
Electrons in the form of NADH and FADH2
3 ways metabolic processes are regulated:
1) Controlling the amounts of enzymes
Transcription/signaling
2) Controlling catalytic activity
Feedback inhibition – conformation/modification
3) Controlling the accessibility of substrates
Compartmentalization of pathway
Citric acid cycle general characteristics:
Take place in mitochondria matrix, etc…
Under anaerobic conditions pyruvate
is converted to __________
lactate or ethanol
State the Prosthetic group, Reaction catalyzed, and # of chains:
- E1
- E2
- E3
- 24 chains, TPP, Oxidative decarboxylation of pyruvate
- 24 chains, Lipoamide, Transfer of acetyl group to CoA
- 12 chains, FAD, Regeneration of the oxidized form of lipoamide
Slide 28 table
First step in Citric Acid cycle is what?
Generation of Acetyl CoA
Pyruvate is fromed via what process?
Glycolysis
Draw out and go over slide 39!!
T/F: Prosthetic groups are modified and put back into the origional form for each step of the reaction?
True
How can pyruvate dehydrogenase be regulated?
Allosterically and by reverse phosphorylation
Slide 47
high Acetyl CoA inhibits E2
Products also increase phosphorylation of PDH E2
Accumulation of ADP and pyruvate activate phosphatases
The citric acid cycle occurs under ______ conditions and
produces _____ energy from glucose than glycolysis
aerobic, more
What is the function of PDH?
Pyruvate dehydrogenase (PDH) links glycolysis to the citric acid cycle
PDH contains ___ enzymes and uses ____ cofactors to
generate acetyl CoA for entry into the citric acid cycle
3, 5