Midterm III Flashcards
What is a coenzyme?
A small molecule that helps an enzyme work
Coenzyme A
Acetyl groups that are attached by a thioester bond (which has a very negative ∆G of hydrolysis); structure H-S-CoA
NAD+/NADH
Reducing power packets; many oxidation/reduction reactions in metabolism because it can transfer electrons from glucose (oxidized) to oxygen (reduced); it oxidizes other molecules and carries the electrons released; NAD+ can accept two electrons from compounds that have a higher electron transfer potential in the form of a “hydride” ion
ATP/ADP/AMP
All energy packets; hydrolyze with water to break phosphoanhydride bond of the phosphate group
Pi/PPi
Inorganic phosphate and inorganic pyrophosphate respectively - what is cleaved off in the hydrolysis of ATP
Vitamin
A small molecule needed for life that WE CANNOT SYNTHESIZE and thus require in our diet - often coenzymes or components of coenzymes
pathway
a set of enzymatic reactions in series
thioester bond
single bond from a carbonyl carbon to a sulfur atom; has relatively high ∆G of hydrolysis (~7.5 kcal/mol)
phosphoanhydride bond
the chemical bond between two adjacent phosphate groups; also relatively high standard free energy of hydrolysis (~7.3 kcal/mol or greater)
group transfer potential
the amount of energy released when a bond to a chemical group is hydrolyzed; a chemical group can be transferred from molec. with higher group transfer potential to one with lower group transfer potential to get ∆G < 0
electron transfer potential
energy released when a molecule is oxidized (transferring of electrons to another molecule)
coupled reactions
reactions that are forced by the enzymatic mechanisms of metabolism to occur together - one cannot occur without the other one also occurring
catabolic
metabolic reactions that break larger molecules into smaller ones
anabolic
metabolic reactions that build larger molecules from smaller ones
futile cycle
set of metabolic reactions that send molecules through series of intermediates and back to the original molecules without making anything useful - bulldozing through the energy source
regulation/integration
regulation to refer to mechanisms that control individual metabolic pathway; integration to refer to mechanisms that coordinate the regulation of different metabolic pathways
glycolysis
conversion of glucose to pyruvate
fermentation
anaerobic conversion of glucose to ethanol + CO2 (yeast) or lactate (humans)
kinase
an enzyme that catalyzes transfer of a phosphoryl group between ATP and another molecule
isomerase
an enzyme that rearranges a molecule without adding or removing any atoms
dehydrogenase
an enzyme that catalyzes transfer of a phosphoryl group between ATP and another molecule
aldol cleavage
a common reaction type in metabolism that breaks a carbon-carbon bond to generate alcohol and aldehyde groups at the two new ends generated from the cleaved bond
metabolic flux
the rate at which metabolites flow through a pathway
homeostasis
living organisms tend to maintain themselves in a constant state. In metabolism, this means that metabolites tend to be maintained at a constant concentration despite large changes in metabolic flux
energy charge
a measure of current ability of the cell to supply ATP - decrease in energy charge is typically sensed by an increase of [ADP] and/or [AMP], as these quantities increase substantially before large decreases in [ATP] occur
first committed step
the first non-equilibrium reaction unique to the metabolic pathway - think PFK! It is also usually used as the control point to regulate flux through the pathway
feedback inhibition
a regulatory strategy in which a metabolite inhibits activity of non-equilibrium enzyme that acts somewhere upstream - helps hold the concentration of the metabolite at a constant homeostatic concentration
feedforward activation
a regulatory strategy in which a metabolite activates the activity of a non-equilibrium enzyme that acts somewhere downstream in a pathway that consumes that metabolite
biotin
a coenzyme that carries activated carboxyl groups, often used by carboxylase enzymes
substrate cycle
a set of reactions that use one set of enzymes to convert metabolite A to B and different enzymes to convert B back to A
The Cori Cycle
Allows muscles in an animal to carry out a sprint for longer; gluconeogenesis in the liver recycles the lactate from anaerobic homolactic fermentation int he muscle back to glucose that is then returned to the muscle
Citric Acid Cycle
the pathway that oxidizes the acetyl group of acetyl CoA to 2 carbon dioxides, conserving the liberated free energy for ATP production
amphibolic
this describes a pathway that is used for both catabolic and anabolic purposes (such as the citric acid cycle)
prochiral
describes the asymmetry of a carbon atom that makes single bonds to four substituent chemical groups, two of which are identical. Enzymes have the ability to distinguish between the two identical substituents by recognizing the subtle asymmetry - think of citrate!
pyruvate dehydrogenase
a multi-enzyme complex found in mitochondria that catalyzes a 5-step reaction that bridges between glycolysis and the citric acid cycle
thiamine
a coenzyme used to decarboxylate a molecule and then transfer the remainder of the molecule onto an acceptor
lipoamide
a coenzyme in pyruvate dehydrogenase that accepts an acetyl group, and then transfers it to coenzyme A
FAD
Flavin adenine dinucleotide: an electron carrier that functions similarly to NAD+
glyoxylate cycle
a modified citric acid cycle that can occur in plants and bacteria that allows them to carry out the conversion of FATTY ACIDS to CARBOHYDRATES, something humans cannot do
oxidative phosphorylation
the process in which ATP is formed as a result of the transfer of electrons from NADH or FADH2 to O2 via a series of electron carriers
substrate level phosphorylation
the process in which enzymes directly transfer phosphoryl groups from substrates with high phosphoryl group transfer potential to ADP to generate ATP
mitochondrion
an organelle found in eukaryotic cells that carries the machinery of oxidative phosphorylation in a series of multienzyme complexes embedded in the inner of its two membranes
electron transport chain/respiratory chain
reactions carried out by complexes I through IV of oxidative phosphorylation in which electrons from NADH and succinate pass through a series of electron carriers to ultimately reduce O2 to H2O, with the free energy released by these oxidation/reduction reactions used to pump protons out of the mitochondrial matrix
electrochemical gradient
a proton gradient across the inner mitochondrial membrane that stores energy in both an electrical voltage across the membrane and in a chemical concentration gradient of protons across the membrane
proton motive force
the force pushing protons down their electrochemical gradient
reduction potential
a measure (in V) of the affinity of various molecules for electrons.. Oxidation/reduction reactions have a negative free energy when electrons pass from a molecule with a more negative reduction potential to one with a more positive reduction potential
Coenzyme Q
a lipid-soluble small molecule dissolved in they hydrophobic core of the inner mitochondrial membrane that ferries electrons from complexes I and II to complex III
Iron Sulfur Clusters
found in electron transport complexes; can accept and then give up one electron at a time
cytochromes
small proteins found in electron transport complexes, or existing as a separate protein (e.g., cytochrome c) that carry a heme group. The cytochrome can carry one electron by reducing the iron ion at the center of the heme, and can then give up the electron when the iron is reoxidized
The Q cycle
name of the mechanism used by complex III to transfer electrons from coenzyme Q to cytochrome c while using the free energy liberated to pump protons out of the mitochondrial matrix
phosphatase
enzyme that hydrolyzes inorganic phosphate group off essentially
