Enzyme catalysis and vocabulary

Chapter 6 Vocabulary

• Enzyme catalysis involves the acceleration of a reaction by a biological molecule.
• Activation energy (Eᴀ) is the energy required to reach the transition state.
• Transition state is an intermediate state during a reaction.
• A metastable state is relatively stable but not at the lowest energy level.
• A catalyst lowers the activation energy and increases reaction rate, but is not consumed. Enzymes are protein catalysts.
• Ribozymes are RNA molecules with catalytic activity.
• Active Site is the specific region of an enzyme where substrate binding and catalysis occur.
• Prosthetic groups are non-amino acid components that contribute to protein structure and function.
• Coenzymes are organic, non-protein molecules that assist enzymes in carrying out reactions.
• Substrate specificity is the ability of an enzyme to bind to one specific substrate.
• Hydrogenation is a chemical reaction involving the addition of hydrogen.
• Group specificity is the ability of an enzyme to act on a range of substrates with a particular functional group.
• The International Union of Biochemistry (IUB) Enzyme Commission (EC) developed a classification system of six major classes for enzymes.
• Homeotherms are organisms that maintain a stable internal body temperature.
• Denaturation is the process where proteins lose their structure, caused by heat, pH change or other factors.
• The lock-and-key model is a simplified model on how enzymes and substrates fit.
• The induced-fit model is a more accurate model that describes how the active site changes to bind to the substrate.
• Substrate activation is when a substrate gains energy to reach the transition state.
• There are three activation mechanisms like substrate binding, bond distortion and proton transfer.
• Enzyme kinetics studies the rate of enzyme-catalyzed reactions.
• Initial reaction velocity (v) is the rate of a reaction at the beginning, before much product has been formed.
• Saturation is when all enzyme active sites are occupied.
• Substrate concentration [S] is the molarity of the substrate.
• Michaelis constant (Kᴍ) is the concentration of substrate at which the reaction rate is half of Vmax.
• Maximum velocity (Vmax) is the highest possible rate of reaction when the enzyme is fully saturated with substrate.
• Michaelis-Menten equation describes the rate of enzymatic reactions relating reaction rate to substrate concentration.
• Turnover number (kcat) is the number of substrate molecules one enzyme molecule can convert per unit time.
• The Lineweaver-Burk equation is a double reciprocal of the Michaelis-Menten equation, allowing Vmax and Km to be more easily determined.
• Double-reciprocal plot helps visualize enzyme kinetics, and can be used to analyze different forms of inhibition.
• Substrate analogs are compounds that resemble the substrate and bind to the active site, inhibiting the enzyme.
• Allosteric effectors are molecules that bind to an enzyme somewhere, other than the active site, causing a change in its shape and affecting its activity.
• Reversible inhibitors bind non-covalently and can dissociate, restoring enzyme activity.
• Irreversible inhibitors bind covalently, permanently inactivating the enzyme.
• Competitive inhibitors bind to the active site, preventing the substrate from binding.
• Noncompetitive inhibitors bind to an allosteric site, changing the shape of the enzyme and reducing its activity.
• Feedback inhibition is when the end product of a metabolic pathway inhibits an earlier enzyme in the pathway.
• Substrate-level regulation is the direct control of enzyme activity by the levels of substrate and product.
• Allosteric enzymes have multiple binding sites, and their activity is modulated by allosteric effectors.
• Allosteric effectors bind to the other sites on the enzyme to change its activity.
• An allosteric site is a location on an enzyme away from the active site that can bind molecules and modulate the enzyme's activity.
• The active site is where the substrate binds and the chemical reaction occurs.
• An allosteric inhibitor binds to the allosteric site to decrease the enzyme's activity.
• An allosteric activator binds to the allosteric site to increase the enzyme's activity.
• Catalytic subunits are the parts of a multi-subunit enzyme that contain the active sites and carry out the catalytic reaction.
• Regulatory subunits bind regulatory molecules, or effectors, that modulate the catalytic activity of the enzyme.
• Cooperativity is when the binding of one substrate molecule to an enzyme makes it easier for subsequent substrate molecules to bind.
• Phosphorylation is the addition of a phosphate group to a molecule.
• Covalent modification involves the formation or breaking of covalent bonds on an enzyme.
• Protein kinase is an enzyme that adds phosphate groups to proteins.
• Protein phosphatase is an enzyme that removes phosphate groups from proteins.
• Dephosphorylation is the removal of a phosphate group from a molecule.
• Phosphorylase is an enzyme that catalyzes the addition of phosphate groups to glycogen to break it down, and exists in two forms: a is active and b is inactive.
• Phosphorylase kinase activates phosphorylase by phosphorylating it.
• phosphorylase phosphatase inactivates phosphorylase a by removing a phosphate.
• Glycogen synthase is an enzyme that catalyzes the conversion of glucose to glycogen.
• Proteolytic cleavage is the activation of an enzyme from an inactive proenzyme.
• Trypsinogen is an inactive precursor of trypsin, a digestive enzyme.
• Trypsin is a digestive enzyme that breaks down proteins in the small intestine.
• The pancreas is an organ that produces digestive enzymes and hormones.
• Duodenum is the first section of the small intestine where digestion occurs.
• Zymogen is an inactive enzyme precursor, requiring a biochemical change (such as hydrolysis) for it to become an active enzyme.
• Hexapeptide is a peptide composed of six amino acids.
• Enterokinase is an enzyme that converts trypsinogen into active trypsin.
• Ribosomes are molecular machines that use RNA and proteins to synthesize proteins.
• Ribozymes are RNA molecules that have catalytic activity.
• Peptidyl transferase is an enzymatic activity of the ribosome responsible for forming peptide bonds during translation.

Chapter 7 vocabulary

• The plasma membrane is a phospholipid bilayer that surrounds all cells, forming a selectively permeable barrier between the cell and its external environment.
• Membrane transport refers to the movement of substances across the cell membrane, which includes passive and active transport.
• Signal transduction is the process by which cells convert extracellular signals into intracellular responses.
• Receptors are proteins on the cell surface or within the cell that bind specific molecules to initiate cellular responses.
• The fluid mosaic model describes the structure of the plasma membrane as a dynamic arrangement of phospholipids and proteins.
• Lipophilic substances are soluble in lipids or non-polar solvents.
• Amphipathic molecules have both hydrophobic and hydrophilic regions.
• Erythrocytes are red blood cells that facilitate oxygen transport in the blood.
• A lipid bilayer is a thin polar membrane made of two layers of lipid molecules that form a continuous barrier around all cells.
• The Davson-Danielli model is an outdated model describing the plasma membrane as a lipid bilayer sandwiched between two layers of proteins.
• Polar pores are channels in the membrane that allow polar or charged molecules to pass through.
• Trilaminar staining pattern is a staining pattern observed under electron microscopy, indicating a three-layered structure that was initially interpreted as support for the Davson-Danielli model.
• Phospholipases are enzymes that hydrolyze phospholipids.
• Peripheral proteins are located on the surface of the membrane and are easily removed without disrupting the membrane's structure.
• Integral membrane proteins are permanently embedded within the lipid bilayer.
• Transmembrane segments are the segments of an integral membrane protein that span the lipid bilayer.
• Lipid-anchored proteins are located on the surface of the cell membrane that are covalently attached to lipid molecules embedded within the cell membrane.
• Phospholipids are lipids containing a phosphate group.
• Lipid rafts are cholesterol- and sphingolipid-enriched microdomains within the cell membrane.
• Sterols are lipids with a characteristic four-ring structure.
• Glycolipids consist of a carbohydrate attached to a lipid.
• Sphingolipids are a class of lipids derived from sphingosine.
• Phosphoglycerides are phospholipids with a glycerol backbone.
• Phytosterols are plant-derived sterols similar to cholesterol which are important components of plant cell membranes.
• Cholesterol is a key component of animal cell membranes that modulates their fluidity.
• Transverse diffusion or flip-flop is the movement of a lipid molecule from one layer to the other.
• Fatty acids are carboxylic acids with a long aliphatic tail.
• Membrane asymmetry refers to the unequal distribution of lipids and proteins between the two leaflets of a cell membrane.
• Rotation is the spinning or rotational movement of a lipid molecule within the plane of the membrane.
• Lateral diffusion refers to the movement of lipid molecules and proteins within the plane of the cell membrane.
• Flippases are enzymes that catalyze the movement of phospholipids from one leaflet to another.
• Photobleaching is the photochemical destruction of a fluorophore, resulting in loss of fluorescence.
• Fluorescence recovery is the return of fluorescence in a photobleached area due to the lateral movement of fluorescently labeled molecules.
• Phase transition is the change in the state of a membrane from a fluid to a more solid or gel-like state due to decreased temperature.
• Transition temperature (Tᴍ) is the specific temperature at which a membrane undergoes a phase transition.
• Cis- vs. trans- fats involve distinct configurations of fatty acids around a double bond. Cis have substituents on the same side, creating a bend, while trans have substituents on opposite sides, resulting in a more linear structure.
• Kinases are enzymes that phosphorylate molecules.
• Freeze fracturing is a technique used to study membrane structure by splitting the lipid bilayer and examining the internal faces.
• Integral membrane proteins are permanently embedded within the lipid bilayer.
• Transmembrane proteins are integral membrane proteins that span the entire lipid bilayer.
• Integral monotopic proteins are proteins that are bound to only one layer of the membrane.
• Multipass proteins are transmembrane proteins that cross the lipid bilayer multiple times.
• Singlepass proteins are transmembrane proteins that cross the lipid bilayer once.
• β barrel is a type of protein structure that consists of beta strands forming a hollow cylindrical structure.
• Multisubunit proteins are composed of multiple polypeptide chains.
• Hydropathic analysis is used to identify hydrophobic and hydrophilic regions in a protein sequence, which can predict transmembrane domains.
• Porins hydrophobicity plot is a plot that shows the hydrophobicity of amino acids along the protein sequence for porins.
• DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule.
• Liposomes are artificial vesicles made of lipid bilayers, used as models for cell membranes and drug delivery systems.
• Site-directed mutagenesis is a technique used to create specific alterations in the DNA sequence of a gene.
• Recombinant DNA is DNA that has been artificially combined from different sources.
• Glycoprotein is a protein with carbohydrate molecules attached.
• Epitope is the specific site on an antigen to which an antibody binds.
• N-linked glycosylation is the attachment of a carbohydrate to the nitrogen atom of asparagine (Asn) residue in a protein.
• Glycosylation is the process of adding carbohydrates to a molecule.
• Glycocalyx is the carbohydrate coat on the outer surface of a cell.
• O-linked glycosylation is the attachment of a carbohydrate to the oxygen atom of serine (Ser) or threonine (Thr) residue in a protein.
• Fluorescent antibodies are antibodies labeled with a fluorescent dye, used to visualize and detect specific antigens in cells or tissues.
• Cell fusion experiments are used to study membrane protein mobility and mixing by fusing two cells with different membrane markers.

Chapter 8 vocabulary

• Selective permeability is a property of cellular membranes that allows only certain molecules to enter or exit the cell.
• Secretion is the process by which cells release substances into the extracellular space.
• Membrane transport encompasses the various mechanisms by which molecules cross cellular membranes.
• Simple diffusion is the movement of molecules across a membrane down their concentration gradient without the aid of transport proteins.
• Transport proteins are membrane-spanning proteins that facilitate the movement of specific molecules across a membrane.
• Facilitated diffusion is the transport of molecules across a membrane down their concentration gradient with the aid of transport proteins.
• Active transport is the movement of molecules across a membrane against their concentration gradient, requiring energy input.
• A concentration gradient is the change in concentration of a substance from one area to another.
• Channels are transmembrane proteins that form pores through which specific ions or molecules can pass.
• The electrochemical potential is the driving force that determines the movement of ions across a membrane, considering both the concentration gradient and the electrical potential.
• Osmosis is the movement of water across a semipermeable membrane from an area of high water concentration to an area of low water concentration.
• Membrane potential (Vᴍ) is the difference in electrical potential between the interior and exterior of a cell.
• Osmolarity is the concentration of a solution expressed as the total number of solute particles per liter.
• A hypertonic solution has a higher solute concentration than another solution, causing cells to shrink as water moves out.
• An isotonic solution has the same solute concentration as another solution, resulting in no net movement of water across cell membranes.
• A hypotonic solution has a lower solute concentration than another solution, causing cells to swell as water moves in.
• Counter-ions are ions that accompany the movement of charged molecules to maintain electrical neutrality.
• Turgor pressure is the pressure exerted by the cell membrane against the cell wall in plant cells, resulting from the osmotic uptake of water.
• Plasmolysis is the contraction of the protoplast of a plant cell as a result of loss of water from the cell.
• A channel protein is a membrane protein that forms a hydrophilic pore through which specific molecules can pass.
• A carrier protein is a membrane protein that binds to a specific molecule and undergoes a conformational change to transport it across the membrane.
• The alternating conformation model suggests that carrier proteins undergo conformational changes to transport solutes across the membrane.
• porins are channel-forming proteins found in the outer membrane of mitochondria and some bacteria, allowing the diffusion of small molecules.
• A uniporter is a carrier protein that transports a single type of molecule across the membrane.
• Coupled transport is the simultaneous transport of two or more molecules across a membrane, linked by a single carrier protein.
• A symporter is a carrier protein that transports two different molecules across the membrane in the same direction.
• An antiporter is a carrier protein that transports two different molecules across the membrane in opposite directions.
• the anion exchange protein mediates the exchange of chloride and bicarbonate ions across the red blood cell membrane.
• the glucose transporter (GLUT) is a membrane protein that facilitates the transport of glucose across the cell membrane.
• Carbonic anhydrase is an enzyme that catalyzes the interconversion of carbon dioxide and water to bicarbonate and protons.
• the chloride-bicarbonate exchanger is a membrane protein that facilitates the exchange of chloride and bicarbonate ions across the cell membrane.
• Ion channels are membrane proteins that form pores allowing specific ions to pass through the membrane.
• Transmembrane channels are channels that span the entire cell membrane.
• β-barrel is a protein structure composed of beta strands that form a cylindrical channel through the membrane.
• Directionality refers to the ability of a transport process to move molecules in a specific direction across the membrane.
• Pumps (active transport) are transport proteins that use energy to move molecules against their concentration gradient.
• Aquaporins (AQPs) are channel proteins that facilitate the rapid transport of water across the cell membrane.
• Direct active transport uses ATP directly, while indirect active transport uses the movement of one molecule down its concentration gradient to power the movement of another.
• Cystic Fibrosis (CF) is an inherited disorder caused by a mutation in the CFTR gene, leading to mucus buildup in various organs.
• Lumen is the inside space of a tubular structure, such as the endoplasmic reticulum or the intestine.
• CF Transmembrane Conductance Regulator (CFTR) is a protein a chloride channel protein responsible for regulating the transport of chloride ions across epithelial cell membranes.
• ATPase pumps are enzymes that use the energy from ATP hydrolysis to transport ions or molecules across the membrane.
• Multidrug resistance (MDR) transport protein is a membrane protein that pumps various drugs out of cells, leading to drug resistance in cancer cells and bacteria.
• ATP synthase is an enzyme that synthesizes ATP from ADP and inorganic phosphate, using the proton gradient across the mitochondrial membrane.
• Na+/K+ ATPase (pump) is an enzyme that uses ATP energy to pump sodium ions out of the cell and potassium ions into the cell, maintaining the electrochemical gradient.
• Na+/glucose symporter is a membrane protein that transports both sodium ions and glucose across the membrane, using the sodium gradient as the driving force.
• Bacteriorhodopsin is a light-driven proton pump found in archaea.

Chapter 9 vocabulary

• Chemotrophs obtain energy by oxidizing chemical compounds.
• Phototrophs obtain energy from sunlight.
• Metabolism refers to the sum of all chemical reactions that occur within an organism.
• Metabolic pathways are a series of interconnected chemical reactions.
• Anabolic pathways are biosynthetic pathways that build complex molecules from simpler ones, requiring energy.
• Catabolic pathways break down complex molecules into simpler ones, releasing energy.
• Aerobic processes require the presence of oxygen.
• Anaerobic processes occur in the absence of oxygen.
• Energetic coupling is the process by which energy released from exergonic (energy-releasing) reactions is used to drive endergonic (energy-requiring) reactions.
• Adenosine triphosphate (ATP) is the primary energy currency of the cell.
• A phosphoester bond is a chemical bond that attaches a phosphate group to other molecules.
• A phosphoanhydride bond is formed when two phosphate groups are linked together.
• Adenosine is a nucleoside composed of adenine and ribose.
• Adenosine diphosphate (ADP) is a nucleotide composed of a nitrogenous base. two phosphate groups, and a sugar.
• Hydrolysis is the chemical breakdown of a compound due to reaction with water.
• Adenosine monophosphate (AMP) is a nucleotide that contains on phosphate group, adenine, and ribose sugar.
• Condensation is a chemical reaction in which two molecules combine to form a larger molecule, with the loss of a small molecule.
• Charge repulsion refers to the repulsion between negatively charged phosphate groups in ATP, which contributes to its high energy content.
• Resonance stabilization is the stabilization of a molecule due to the delocalization of electrons within its structure.
• Resonance hybrid is a molecule that is best described as the average of two or more Lewis structures.
• Oxidation is the loss of electrons from a molecule.
• Group transfere reactions involve the transfer of a functional group.
• Reduction is the gain of electrons by a molecule.
• Chemotrophic energy metabolism is the process of obtaining energy from chemical compounds.
• Dehydrogenation is the removal of hydrogen atoms from a molecule.
• Hydrogenation is the addition of hydrogen atoms to a molecule.
• Nicotinamide adenine dinucleotide (NAD+) is a coenzyme that functions as an electron carrier in redox reactions.
• Niacin is a vitamin that is a precursor to NAD+.
• The glucose aerobic respirat is the final electron acceptor in the electron transport chain.
• Anaerobic respiration uses a different electron acceptor other than oxygen.
• Fermentation is the metabolic process by which energy is extracted from glucose without oxygen.
• Lactate fermentation is a type of anaerobic respiration that produces lactic acid
• -alcohol fermentation is a type of anaerobic respiration that produces ethanol.
• Glycolysis is the breakdown of glucose into pyruvate, producing a small amount of ATP and NADH.
• Substrate-level phosphorylation is a metabolic reaction that results in the formation of ATP or GTP by the direct transfer of a phosphoryl group to ADP or GDP from another phosphrylated compound.
• Phosphoolysis is the cleavage of a bond by the addition of a phosphate group.
• Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors.
• Bypass reactions are reactions that are used to circumvent irreversible steps in a metabolic pathway.
• Sucrase is an enzyme that catalyzes the hydrolysis of sucrose into glucose and fructose.
• Sucrose is a disaccharide consisting of glucose and fructose units.
• Triacylglycerol is a fat molecule composed of three fatty acids attached to a glycerol backbone.