Biochemistry: Enzymes, Proteins, and Lipids

Vocabulary flashcards covering key definitions, classifications, models, structures, and properties of enzymes, proteins, and lipids.

Biocatalyst

A biological catalyst synthesized by living cells that increases the velocity or rate of a chemical reaction without undergoing any overall change in the process.

Ribozymes

A group of ribonucleic acid (RNA) molecules that function as biological catalysts, regarded as non-protein enzymes, discovered by Altman and his coworkers in 1983.

Holoenzyme

A complete, catalytically active enzyme composed of an apoenzyme (protein portion) combined with its cofactor or coenzyme.

Apoenzyme

The inactive protein portion of an enzyme that requires an inorganic cofactor or coenzyme to form an active holoenzyme.

Cofactor

A non-protein chemical component or inorganic metal ion (such as $\text{Mg}^{2+}$ or $\text{Fe}^{2+}$) required by an enzyme for catalytic activity.

Coenzyme

A specific organic cofactor, often derived from vitamins (such as $\text{NAD}^+$), that binds loosely to an enzyme and transfers functional groups during catalysis.

Oxidoreductases

A class of enzymes that catalyze oxidation-reduction reactions involving substrate molecules, including subclasses like oxidases, reductases, and dehydrogenases.

Transferases

A class of enzymes that catalyze the transfer of functional groups (such as amino or phosphate groups) between two substrates.

Hydrolases

A class of enzymes that catalyze substrate hydrolysis reactions by adding a water molecule to break a chemical bond.

Lyases

A class of enzymes that catalyze the addition of a group to a double bond or the removal of a group to create a double bond in a manner that does not involve hydrolysis.

Isomerases

A class of enzymes that catalyze the conversion of a substrate into another compound that is isomeric with it.

Ligases

A class of enzymes that catalyze the bonding together of two substrate molecules coupled with the participation of ATP.

Active Site

The specific portion of an enzyme that participates in binding and interacting with a substrate during a chemical reaction.

Lock-and-Key Model

A model of enzyme action proposed by Emile Fischer in 1894 stating that the active site of an enzyme has a fixed, rigid conformation.

Induced-Fit Model

A model of enzyme action proposed by Daniel Koshland in 1958 stating that the conformation of the active site is flexible and adapts upon substrate binding.

Constitutive Enzymes

Housekeeping enzymes with a short half-life whose concentration in cells remains fairly constant regardless of metabolic demand.

Adaptive Enzymes

Enzymes whose cellular concentrations increase or decrease according to the body's specific physiological needs.

Irreversible Inhibitors

Substances that bind covalently to an enzyme and permanently destroy its catalytic activity, often acting as toxic poisons.

Reversible Inhibitors

Inhibitors that bind to an enzyme through weak non-covalent interactions and can readily dissociate from the enzyme.

Protein

The most abundant (~15% of cell mass) and versatile biomolecule, composed of amino acids, coined by Gerard Johann Mulder in 1838 from the Greek word proteios ('first of rank').

$\alpha$-Amino Acid

An organic compound containing a basic amino group ($-\text{NH}_2$) and an acidic carboxyl group ($-\text{COOH}$) attached to the same central alpha-carbon ($\text{C}_\alpha$).

Zwitterion

A dipolar hybrid molecule containing equal positive and negative ionic charges, resulting in a net charge of zero at its isoelectric pH.

Isoelectric Point (pI)

The characteristic pH at which an amino acid or protein carries no net electrical charge and exists as a zwitterion.

Ampholytes

Molecules containing both acidic ($-\text{COOH}$) and basic ($-\text{NH}_2$) groups that can act as either proton donors or proton acceptors.

Essential Amino Acids

Ten indispensable amino acids (Arg, Val, His, Ile, Leu, Lys, Met, Phe, Thr, Trp) that cannot be synthesized by the human body and must be supplied through the diet.

Non-Essential Amino Acids

Ten dispensable amino acids (Gly, Ala, Ser, Cys, Asp, Asn, Glu, Gln, Tyr, Pro) that can be synthesized internally by human metabolic pathways.

Peptide Bond

A strong covalent amide linkage formed when the carboxyl group of one amino acid reacts with the amino group of another.

Primary Structure

The linear sequence of amino acid residues forming the backbone of a polypeptide chain, linked together by covalent peptide bonds.

Secondary Structure

The spatial arrangement formed by the localized twisting or folding of a polypeptide chain, such as an $\alpha$-helix or $\beta$-pleated sheet, stabilized by hydrogen bonds.

$\alpha$-Helix

A common spiral secondary protein structure proposed by Pauling and Corey (1951) containing 3.6 amino acids per turn and a distance/pitch of $0.54\,\text{nm}$.

$\beta$-Pleated Sheet

A secondary protein structure proposed by Pauling and Corey consisting of two or more fully extended polypeptide segments aligned in parallel or antiparallel orientation and held by neighboring hydrogen bonds.

Tertiary Structure

The overall three-dimensional folded conformation of a functional single polypeptide chain, stabilized by interactions among side chains.

Quaternary Structure

The spatial arrangement and association of two or more individual polypeptide chains (subunits) forming a functional protein complex.

Denaturation

The process wherein a protein loses its native 3D structure and biological activity due to the disruption of secondary, tertiary, and quaternary stabilizing forces.

Simple Proteins

Proteins that yield only amino acids upon complete hydrolysis, classified into globular proteins and scleroproteins.

Conjugated Proteins

Proteins consisting of a protein portion combined with a non-protein prosthetic group (such as carbohydrates, lipids, nucleic acids, or metal ions).

Lipids

Non-polar (hydrophobic) biomolecules containing fatty acids or a steroid nucleus, named from the Greek word lipos ('fat'), insoluble in water but soluble in organic solvents.

Fatty Acid

A carboxylic acid featuring a long nonpolar hydrocarbon chain, representing the simplest structural unit of lipids.

Saturated Fatty Acid

A fatty acid possessing only single carbon-carbon bonds in its hydrocarbon chain, leading to close molecular packing and high melting points.

Unsaturated Fatty Acid

A fatty acid containing one or more carbon-carbon double bonds, creating kinks in the chain that prevent close packing and lower the melting point.

Triacylglycerol

A complex ester lipid formed when glycerol reacts with three fatty acid molecules, serving as the main form of stored energy in body tissues.

Waxes

Simple ester lipids composed of saturated fatty acids bonded to long-chain alcohols, providing water-repellent coatings.

Saponification

The base-catalyzed hydrolysis of a triacylglycerol with a strong base (such as $\text{NaOH}$ or $\text{KOH}$) to yield glycerol and fatty acid salts (soaps).

Prostaglandins

Eicosanoid lipids containing 20 carbon atoms with a 5-carbon cyclopentane ring, produced by injured tissues to mediate pain, fever, and inflammation.

Glycerophospholipid

The most abundant cell membrane lipid, consisting of glycerol esterified to two nonpolar fatty acids, a phosphate group, and an amino alcohol.

Sphingolipid

A class of membrane lipids built on an 18-carbon unsaturated amino alcohol backbone called sphingosine.

Sphingomyelin

A sphingolipid found abundantly in nerve cell myelin sheaths, containing sphingosine linked to a fatty acid via an amide bond, plus phosphate and choline.

Gangliosides

Glycosphingolipids containing two or more monosaccharide units attached to sphingosine; accumulation of $\text{GM}_2$ causes Tay-Sachs disease.

Steroid Nucleus

A rigid polycyclic structure consisting of three 6-membered cyclohexane rings and one 5-membered cyclopentane ring fused together.

Cholesterol

The most abundant steroid in animal tissues, synthesized in the liver and required for cell membrane structure, steroid hormones, bile salts, and Vitamin D.

Bile Salts

Steroid derivatives synthesized in the liver from cholesterol and stored in the gallbladder that emulsify dietary fats in the small intestine.

Low-Density Lipoprotein (LDL)

A plasma lipoprotein that carries cholesterol from the liver to cells and deposits excess cholesterol in arterial walls as plaque.

High-Density Lipoprotein (HDL)

A plasma lipoprotein that collects excess cholesterol from tissues and transports it back to the liver for elimination.

Fluid Mosaic Model

A cell membrane structural model describing a dynamic lipid bilayer embedded with fluidly moving proteins, carbohydrates, and cholesterol.

Active Transport

The energy-dependent transport of molecules or ions across a cell membrane against a concentration gradient using ATP.