unit 2 biochem

Vocabulary flashcards for enzyme basics, covering myoglobin, hemoglobin, enzyme kinetics, free energy, electron transport chain, and enzyme regulation.

Homologous proteins (Myoglobin and Hemoglobin)

Proteins with similar primary sequences and functions that both bind oxygen and contain a heme ring stabilized by histidine.

Hemoglobin

Transports oxygen in the blood within red blood cells to deliver oxygen to tissues.

Myoglobin

Remains in the heart and skeletal muscle cells to bind oxygen released by hemoglobin.

Apoprotein

A protein missing its ligand or ligands; example: hemoglobin lacking heme.

Holoprotein

A protein with its ligand, enabling it to function; example: hemoglobin bound to heme.

Myoglobin structure

Monomer with 8 α-helices linked by α-turns, containing a hydrophobic pocket with heme and a ferrous iron atom (Fe2+) for oxygen binding.

Fe2+ in Myoglobin

Binds to a histidine R-group of the α-helix in myoglobin, stabilizing the reduced state of iron when it binds to oxygen.

Prosthetic group (Heme)

Tightly bound to the globin in myoglobin and hemoglobin.

Hyperbolic binding

The type of binding exhibited by Myoglobin.

Hemoglobin (Hb) structure

Heterotetramer composed of 2 α and 2 β subunits, each with its own heme, capable of binding 4 oxygen molecules.

Cooperativity

When an enzyme (such as hemoglobin) is altered by the substrate, affecting the conformation of other subunits.

Sigmoidal binding curve

The manner which Hemoglobin does not bind oxygen as strongly as myglobin.

vi

The component of the Michaelis-Menten equation that represents the initial velocity.

Vmax

The component of the Michaelis-Menten equation that is the maximal velocity (rate) a reaction can achieve at an infinite concentration of substrate.

Km

The substrate concentration at which the reaction rate is at half-maximum.

Small Km

Indicates a high affinity, meaning that the rate will approach Vmax at lower concentrations of substrate.

[S]

The component of the Michaelis-Menten equation that is the substrate concentration.

No impact on DeltaG

The impact of an enzyme on overall energy.

Oxidation

The loss of electrons.

Reduction

The gain of electrons.

Competitive inhibitor

Binds in the active site of an enzyme and increases Km while Vmax remains the same.

Total energy remains constant

The first law of thermodynamics.

In all spontaneous reactions, entropy always increases when both the system and environment are taken into account

The second law of thermodynamics.

Entropy

Disorder or randomness of a system.

Enthalpy

Internal energy of a system.

Endergonic

A reaction that requires the absorption of energy.

Exergonic

A reaction that gives off energy to its surroundings.

DeltaG

Change in free energy, denoted as ΔG.

Endergonic reaction

Reaction requires energy to proceed; positive ΔG.

Exergonic reaction

Reaction is spontaneous; negative ΔG.

Coupling reactions

Allows for a system to organize reactions such that energy released from one reaction can be used to move the subsequent reaction forward.

Additive

The overall ΔG of a series of reactions.

ATP

Used as an energy carrier in the cell.

Phosphodiester bonds

Where energy is stored in ATP.

Complex II

Not required for oxidative phosphorylation because it does not span the mitochondrial membrane; accepts succinate and is coupled with FADH2 oxidation.

CoQ

Not membrane-bound and can move freely along the membrane in the electron transport chain.

Quinol

Fully reduced form of CoQ containing 2 electrons and 2 protons.

Quinone

Fully oxidized form of CoQ.

Semiquinone

Reduced form of CoQ containing 1 electron.

Cytochrome c

Mobile component in the electron transport chain.

Inhibitors of ETC

Block oxidation and reduce both ATP generation and oxygen consumption

Uncouplers of ETC

Disrupt the mitochondrial membrane and reduce ATP product but increase oxygen consumption.

ETC location

Located in the mitochondrial membrane.

Oxygen

Final electron acceptor in the electron transport chain.

NADH or FADH2 generated in the cytosol

Must be transported actively into the mitochondria, because they do not freely cross the membrane.

Glycerophosphate shuttle

Moves reducing equivalents of NADH from the cytosol to an FAD in the mitochondrion.

FAD

Required cofactor for glycerol-3 phosphate dehydrogenase in the glycerophosphate shuttle.

Oxaloacetate

Does not move across the mitochondrial membrane in the malate-aspartate shuttle.

Oxaloacetate

Is REDUCED to malate by cytosolic malate dehydrogenase in the cytosol to start Malate-Aspartate Shuttle.

Malate

Can be OXIDIZED back to oxaloacetate by mitochondrial malate dehydrogenase in the mitochondria.

Transamination reaction

The reaction undergone by oxaloacetate with glutamate, generating alpha-ketoglutarate and aspartate.

2.5

The number of ATP molecules generated for each NADH equivalent in the malate-aspartate shuttle.

Noncompetitive inhibitor

Binds in an alternative location to the active site, decreasing Vmax while Km remains the same.

Enzyme quanitity

Can impact reaction rates by regulating protein turnover.

Transcriptional regulation

Increase in transcription leads to increase in enzyme production and increase in the product formed.

Allosteric effectors

Bind to a site that is NOT the active site and enhance or inhibit an enzyme reaction.

Allosteric activators or positive allosteric effectors

Enhance an enzyme reaction and stabilize a conformation of the protein that increases binding of substrate and reaction rate (R-state).

Allosteric inhibitors or negative allosteric effectors or modulators

Inhibit the enzyme reaction and stabilize a conformation of the protein that decreases binding of substrate and reaction rate (T state).

Phosphorylation

Modified by a kinase can change the conformation and the activity of a protein or charge.

Kinases

Phosphorylate serine/threonine residues.

Protein phosphatases

Are enzymes that hydrolyze the phospho-ester bonds of phosphor-seryl and phosphor- tyrosyl residues (R-groups).

Methylation

Nucleotide modification that can alter DNA. Typical on C or G nucleotides.

Acetylation

Will alter the condensation of the DNA. Increase histone acetylation will result in a decreased histone:DNA interaction allowing for transcriptional accessibility

Cleavage

Often required for activation, ensuring a protein is active in the correct tissue or cellular compartment.

Feedback inhibition

Suppression of the activity of an enzyme participating in a sequence of reactions when the product accumulates beyond an optimal amount.

Feedforward activation

The control of a metabolic pathway by a metabolite that acts in the same direction as the metabolic flux, increasing the rate of a downstream reaction.

T (tense) state

State where Hb has a low affinity for O2 and is stabilized by allosteric inhibitors.

R (relaxed) state

State where Hb has a high affinity for O2 and is stabilized by allosteric activators.

Bohr effect

The impact of pH on oxygen binding hemoglobin; a decrease in pH decreases hemoglobin saturation.

Substrate specificity

The ability of an enzyme to select one or a few substrates from a group of similar substrates.

Active site of an enzyme

Contain functional groups that participate in the reaction.

Enzymes as catalysts

Increase the rate of the reaction by decreasing the activation energy, i.e., stabilizing the transition state.

Oxidoreductases

Catalyze oxidation reduction reactions.

Transferases

Catalyze group transfer reactions - the transfer of a functional group from one molecule to another.

Hydrolases

Cleave C-O, C-N, and C-S bonds by addition of H2O in the form of OH- and H+ to the atoms forming the bond.

Lyases

Cleave C-C, C-O, C-N, and C-S bonds by means other than hydrolysis or oxidation.

Isomerases

Rearrange the existing atoms of a molecule to create isomers of the starting material.

Ligases

Synthesize C-C, C-S, C-O, and C-N bonds in reactions coupled to the cleavage of high energy phosphate bonds in ATP or some other nucleotide.

Amylase

Involved in carbohydrate digestion; elevated levels indicate acute pancreatitis

Alanine aminotransferase (ALT)

Used to transfer amino groups from an amino acid to a ketoacid; elevated levels indicate viral hepatitis.

Lactate dehydrogenase

Anaerobic glycolysis to convert glucose to lactate; elevated levels indicate liver diseases/ skeletal muscle damage.

Lipase

Located on endothelial cells and hydrolyzes triacylglycerol into free fatty acids; elevated levels indicate acute pancreatitis.

β-Glucocerebrosidase

Involved in complex lipid metabolism; deficiency indicates Gaucher disease.

Troponin

Type of muscle found in the heart; not normally found in circulation; its presence in serum indicates a heart attack.

Transketolase

Participates in the nonoxidative portion of the Pentose phosphate pathway and requires thiamine as a cofactor; reduced activity indicates a thiamine deficiency

Coenzymes

Any organic cofactor that binds to the enzyme and is necessary for the reaction; usually inert when not bound to their respective enzyme.

Metal ions

Inorganic and may be incorporated as part of a prosthetic group (e.g., heme).

Prosthetic groups

Tightly bound within an enzyme through non-covalent mechanisms

NAD / FAD

Used in redox reactions.

Pantothenic acid (CoA)

Acyl group carriers.

Thiamine (thiamine pyrophosphate)

Decarboxylation reactions.

Pyridoxal phosphate

Transamination.

Biotin

Carboxylation reactions.

Cobalamin

Carbon transfers.

Heme

Required for oxygen carrying.

Lock and key model

Originally thought that a rigid substrate would slide into a rigid active site of the enzyme and a reaction would take place

Induced fit model

The enzyme changes its conformation when it binds to a substrate.

Transition State

State during an enzyme reaction when an intermediate that resembles both substrate and product, and contains the most free energy, exists.

Activation Energy

Energy necessary to achieve the transition state.

Acid-base catalysis

Activates the substrate by interaction with an acidic or basic amino acid R group to initiate a reaction