Biochemistry Final Exam prep Flashcards
Synthesis of Acetyl CoA requires three enzymes and five coenzymes.
What are the three enzymes and their Abbreviation code?
Pyruvate dehydrogenase component (E1) Dihydrolipoyl transacetylase (E2) Dihydrolipoyl dehydrogenase (E3)
There are five coenzymes needed in the synthesis of Acetyl CoA…
What are the three catalytic coenzymes?
What are the two stoichiometric coenzymes?
Catalytic coenzymes: TPP, lipoamide and FAD
Stoichiometric coenzymes: CoA and NAD+
What is the Prosthetic group of E1, E2, and E3
E1 is TPP
E2 is Lipoamide/lipoic acid
E3 FAD
In the Synthesis of Acetyl CoA, what is the reaction catalyzed by Pyruvate dehydrogenase component (E1)?
Oxidative decarboxylation of pyruvate
In the Synthesis of Acetyl CoA, what is the reaction catalyzed by Dihydrolipoyl transacetylase (E2)?
Transfer of acetyl group to CoA
In the Synthesis of Acetyl CoA, what is the reaction catalyzed by Dihydrolipoyl dehydrogenase E3?
Regeneration of the oxidized form of lipoamide
The conversion of pyruvate to acetyl CoA involves three
reactions:
- Decarboxylation
- Oxidation and
- Transfer of acetyl group
What Coenzyme is Derived from vitamin B1?
TPP
Where does the Conversion of Pyruvate to acetyl CoA occur in eukaryotes?
In mitochondrial matrix.
What are the functional chemical groups common to any amino acid?
α carbon, carboxyl, and amino groups
What is the precursor for all nucleotide synthesis?
Pyrophosphate (PRPP)
Name 4 characteristics of Michaelis-Menten Enzymes:
1) Catalytic activity is not regulated
2) activity is controlled by mass action,
3) lack quaternary structure
4) enzyme kinetics plot is hyperbolic
Name characteristics of Allosteric enzymes: , usually have quaternary structure with multiple active sites in each enzyme (some could be monomeric and lack quaternary structures).
1) Catalytic activity regulated by environmental signals (regulatory molecules and end products in the pathway)
2) kinetics more complex than Michaelis-Menten enzymes
3) kinetics plot is sigmoidal
4) USUALLY have quaternary structure with multiple active sites in each enzyme
4) could be monomeric and lack quaternary structures).
Functions of Enzymes:
Enhance rates of reactions (applies to all enzymes) Information sensors (applies only to allosteric enzymes)
Enzyme Kinetics is:
Study of the rates of enzyme-catalyzed chemical reactions
Enzyme kinetics reaction V= k[A], what does each letter mean?
V= rate/velocity of the reaction k= rate constant [A] = substrate concentration
Where is the Electron Transport chain is located in eukaryotes and bacteria
eukaryotes: inner membrane of mitochondria
bacteria: located in the plasma membrane.
Michaelis-Menten model describes the kinetics of enzymes and is based on the premise:
that a specific ES complex is a necessary intermediate in catalysis.
When is Vmax attained?
ONLY when all enzymes (total enzyme or Et) are saturated/bound to substrate [S]
What does Km stand for and what are 3 characteristics of Km?
Km stands for Michaelis constant
1) KM is unique to each enzyme,
2) is independent of enzyme concentration
3) depends on specific substrate and environmental conditions.
What is a compilation of rate constants?
Km, or Michaelis Constant
How do you find the Km, or Michaelis Constant?
Km= (K-1 + K2) / K1
Is Vmax directly or indirectly dependent on enzyme concentration?
Directly dependent
When is Km equal to the substrate concentration?
When the reaction velocity is half its maximal value.
At very low substrate concentrations, what happens when the Substrate (S) is much less than the value of Km?
The velocity will be directly proportional to the substrate concentration.
What happens when the substrate is much greater than Km?
When Substrate is greater than Km, Vo= (Vmax/Km)[S]
Velocity will be maximal and independent of substrate concentration
Allosteric sites
1) always catalyze the committed steps of metabolic pathway.
2) Binds regulatory molecule (activators or inhibitors)
3) often have a shape different from the substrate molecule.
4) substrate binding site and allosteric site communicates with each other by conformational change of the protein.
5) regulated by products of the pathways under their control.
Concerted model (Monod, Wyman and Chaneaux model)
show that allosteric enzymes depend on changes in the quaternary structure and is built on four premises.
What is the rate of catalysis symbol?
Kcat (or aka K2) is equal to the rate constant, or rate of Catalysis
What is the definition of Vmax (maximum velocity)
Is the turnover number of an enzyme which is the number of substrate molecules that an enzyme can convert into product per unit time when the enzyme is fully saturated with substrate.
What is the specificity constant or catalytic efficiency?
Kcat/Km = measures the catalytic efficiency because it takes into account both the rate of catalysis with a particular substrate (Kcat) and the nature of the enzyme-substrate interaction (Km)
What are the four stages of Cellular Respiration?
1) Glycolysis 2) Pyruvate oxidation 3) Citric acid cycle
4) Oxidative phosphorylation
What happens in Glycolysis?
a six carbon is transformed into molecules of pyruvate, a three carbon organic molecule. ATP is made, NAD+ is reduced to NADH
What happens in Pyruvate oxidation?
Each pyruvate from glycolysis enters the mitochondrial matrix (innermost compartment of mitochondria) where it is converted to Coenzyme A, or acetyl CoA. CO2 is released and NADH is generated
What happens in the Citric acid cycle?
The acetyl CoA combines with a 4 carbon molecule to produce citrate (in the presence of Oxalacetate). At the end, regenerating a 4 carbon molecule, ATP, NADH and FADH2 and CO2 is released.
What happens in Oxidative phosphorylation?
The NADH and FADH2 that were made in the other sets, deposit their electrons in the electron transport chain (ETC) converting back to their oxidized forms (NAD+ and FAD). As Electrons move down the chain, energy is released and used to pump protons out of the matrix creating a gradient. Protons flow back into the matrix through a port called ATP synthase, making ATP. At the end to eh chain, Oxygen accepts electrons and takes up protons to form water
What is substrate-level phosphorylation?
a phosphate group is transferred from a pathway intermediate straight to ADP
What is a kinase?
an enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates.
What is phosphorylation?
high-energy ATP molecule donates a phosphate group to the substrate molecule
What are the two enzymes that are involved in the substrate level phosphorylation in glycolysis?
Phosphoglycerate kinase and pyruvate kinase
what is oxidative phosphorylation?
When the H+ flows back down the gradient from the electron transport chain. As the H+ passes through the ATP synthase, it drives the synthesis of ATP
What is cellular respiration?
When glucose is broken down using an electron transport chain, the breakdown is called cellular respiration
What does the mnemonic “LEO goes GER”?
Lose Electrons, Oxidized; Gain Electrons, Reduced.
what is a redox reaction?
When one molecule loses electrons and is oxidized, while another molecule gains electrons (the ones lost by the first molecule) and is reduced.
What is the electron transport chain?
series of 4 membrane embedded proteins and organic molecules found in the inner membrane of the mitochondria. Electrons are passed from one member of the transport chain to another in a series of redox reactions. Energy is released in the downhill electron transfers and is used to pump protons from mitochondrial matrix to intermembrane space to create the gradient.
What is chemiosmosis?
Any process in which energy stored in a proton gradient is used to do work. Energy released from the ETC reactions is captured as a proton gradient, which is then used to make ATP.
What are the two most important functions of ETC?
Regenerates electron carriers (NADH and FADH2) pass electrons to the ETC turning back into NAD+ and FAD (Oxidized forms are used in Glycolysis and the Citric Acid Cycle and are needed to keep processes running
Makes a proton gradient with higher H+ concentration in intermembrane space and lower concentration in matrix.
What are the Complexes I, III, IV of the ETC?
Proton pumps capture the H+ ions from released as the electrons flow through the chain to pump H+ ions from the matrix to the intermediate space.