Medical Biochemistry: Biomolecules, Protein Structure, Enzymology, and Lipids

Comprehensive vocabulary flashcards covering carbohydrate chemistry, amino acids and protein structure-function relationships, enzyme mechanisms and kinetics, clinical enzymology, nucleotide chemistry, and lipid biology.

Carbohydrates

Aldehyde or ketone compounds containing multiple hydroxyl groups ($-\text{OH}$), having the general empirical formula $(CH_2O)_n$ where $n \ge 3$.

Aldose

A monosaccharide whose carbonyl group is an aldehyde ($-\text{CHO}$), conferring reducing properties to the sugar.

Ketose

A monosaccharide whose carbonyl group is a ketone ($\text{C}=\text{O}$) situated between two carbon groups.

Enantiomers (D- and L-Isomers)

Stereoisomers that are non-superimposable mirror images of each other; in sugars, the designation depends on whether the $-\text{OH}$ group on the asymmetric carbon farthest from the carbonyl group is on the right (D-form) or left (L-form).

Epimers

Carbohydrate isomers that differ in molecular configuration around only one specific asymmetric carbon atom (e.g., glucose and galactose at C-4; glucose and mannose at C-2).

Pyranose

A 6-membered cyclic hemiacetal carbohydrate ring structure consisting of five carbon atoms and one oxygen atom, derived from pyran.

Furanose

A 5-membered cyclic carbohydrate ring structure consisting of four carbon atoms and one oxygen atom, derived from furan.

Anomeric Carbon

The new chiral carbon atom generated upon ring closure of a monosaccharide, located at C-1 in aldoses and C-2 in ketoses, giving rise to $\alpha$ and $\beta$ anomers.

Glycosidic Bond

A covalent linkage formed between monosaccharides following a condensation or dehydration reaction that eliminates one molecule of water ($H_2O$).

Glycogen

A highly branched homopolysaccharide of glucose that serves as the major energy storage polymer in animal liver and skeletal muscle, containing $\alpha(1\rightarrow 4)$ backbone linkages and $\alpha(1\rightarrow 6)$ branch linkages.

Hyaluronate (Hyaluronic Acid)

An important glycosaminoglycan consisting of alternating glucuronate and N-acetylglucosamine residues, serving as a structural component of connective tissue, synovial fluid, and the vitreous humor.

$\alpha$-Amino Acid

A carboxylic acid containing a central chiral $\alpha$-carbon bonded to an amino group ($-\text{NH}_2$), a carboxyl group ($-\text{COOH}$), a hydrogen atom, and a distinctive side-chain (R group).

Zwitterion

A dipolar molecule carrying both a positive charge (protonated amino group, $-\text{NH}_3^+$) and a negative charge (dissociated carboxyl group, $-\text{COO}^-$) on different atoms, giving an overall net charge of zero at physiological $\text{pH } 7$.

Selenocysteine (Sec)

The 21st proteinogenic amino acid, structurally identical to cysteine except that a selenium atom replaces the sulfur atom, encoded by an alternate interpretation of the UGA stop codon.

Pyrrolysine

The 22nd genetically encoded amino acid, representing a modified form of lysine found exclusively in certain species of archaebacteria.

Essential Amino Acids

The eight amino acids that cannot be synthesized de novo by humans and must be acquired through the diet: lysine, isoleucine, leucine, valine, threonine, methionine, phenylalanine, and tryptophan.

Semi-essential Amino Acids

Amino acids whose endogenous synthesis is inadequate to support growth during periods of physiological demand: arginine and histidine.

Citrulline

A non-protein amino acid metabolite of arginine and a byproduct of nitric oxide synthase, an enzyme producing the vasoactive signaling molecule nitric oxide ($\text{NO}$).

Creatinine

A metabolic breakdown product derived from the non-enzymatic cyclization of muscle creatine, excreted in urine via the kidney in a relatively constant daily amount proportional to muscle mass.

Peptide Bond

A rigid, planar covalent amide linkage formed between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of another via dehydration, characterized by partial double-bond character that restricts backbone rotation.

Glutathione (GSH)

A biological tripeptide ($\text{Glu-Cys-Gly}$) that serves as the major intracellular antioxidant and maintains cysteine residues in proteins in a reduced state.

Protein Denaturation

The disruption of secondary, tertiary, and quaternary structural conformations of a protein caused by heat, extreme pH changes, detergents, heavy metals, or organic solvents, leading to unfolding and loss of biological activity.

Primary Structure

The linear sequence of amino acid residues in a polypeptide chain, read from the N-terminal end to the C-terminal end as determined by genetic sequence.

$\alpha$-Helix

A rod-like secondary protein structure in which the polypeptide backbone coils clockwise at $3.6$ residues per turn, stabilized by intramolecular hydrogen bonds between peptide amide hydrogens and carbonyl oxygens.

$\beta$-Pleated Sheet

A secondary protein structure formed by hydrogen bonding between peptide bonds of adjacent polypeptide chains, arranged in either parallel or antiparallel directions.

Tertiary Structure

The complete three-dimensional, biologically active folded conformation of a polypeptide chain, assembled into domains and stabilized by hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.

Quaternary Structure

The structural organization of a protein composed of two or more distinct polypeptide subunits held together by non-covalent or covalent interactions (e.g., adult hemoglobin, $\alpha_2\beta_2$).

Tropocollagen

The fundamental molecular unit of collagen consisting of three polypeptide chains wound into a tight triple helix, wherein every third residue is a glycine ($-\text{Gly-X-Y-}$).

Scurvy

A connective tissue disorder caused by dietary vitamin C (ascorbate) deficiency, impairing the prolyl and lysyl hydroxylase enzymes necessary for stabilizing the collagen triple helix.

Ehlers-Danlos Syndrome Type V

A collagen deficiency disease resulting from a defect in lysyl oxidase, clinically presenting with hypermobile joints and hyperextensible skin.

Osteogenesis Imperfecta

A genetic bone fragility disorder caused by mutations in Type I collagen genes that substitute cysteine for glycine residues, disrupting the collagen triple helix.

Myoglobin

A compact, monomeric globular heme protein found in skeletal and cardiac muscle that contains eight stretches of $\alpha$-helix and binds a single oxygen ($O_2$) molecule as an oxygen reservoir.

Hemoglobin A

A tetrameric ($\alpha_2\beta_2$) globular allosteric protein found exclusively in red blood cells that transports four oxygen ($O_2$) molecules from lungs to peripheral tissues, shifting from a low-affinity T (taut) state to a high-affinity R (relaxed) state upon oxygenation.

Chaperones

Specialized proteins (including Hsp70 and chaperonins) that interact with partially or improperly folded polypeptides, facilitating correct folding pathways and providing suitable microenvironments.

Amyloidosis

A pathological condition characterized by the deposition of insoluble, fibrillar, spontaneously aggregating protein filaments enriched in $\beta$-pleated sheets (e.g., $A\beta$ peptide in Alzheimer disease).

Prion Protein ($\text{PrP}^{\text{Sc}}$)

An infectious, insoluble, proteolysis-resistant conformational isomer of the normal cellular prion protein ($\text{PrP}^\text{C}$) in which $\alpha$-helices are replaced by $\beta$-sheets, acting as a template to seed spongiform encephalopathies like Creutzfeldt-Jakob Disease.

Oxidoreductases

Enzymes that catalyze oxidation-reduction reactions involving the transfer of electrons or hydrogen atoms (e.g., lactate dehydrogenase).

Transferases

Enzymes that catalyze the transfer of functional groups (such as amino, methyl, or phosphate groups) from one molecule to another (e.g., alanine aminotransferase).

Hydrolases

Enzymes that catalyze the hydrolytic cleavage of chemical bonds through the addition of water (e.g., urease).

Lyases

Enzymes that catalyze the non-hydrolytic cleavage of $\text{C-C}$, $\text{C-S}$, and certain $\text{C-N}$ bonds (e.g., pyruvate decarboxylase).

Isomerases

Enzymes that catalyze geometric or optical structural rearrangements and racemizations within a molecule (e.g., aconitase).

Ligases

Enzymes that catalyze the synthetic joining of two molecules coupled to the cleavage of a high-energy phosphate bond such as ATP (e.g., pyruvate carboxylase).

Induced-Fit Model

The enzyme catalytic model proposing that substrate binding induces conformational alterations in the enzyme that position catalytic residues to stabilize the transition state.

Apoenzyme

The inactive protein-only portion of an enzyme that requires an associated cofactor or coenzyme to become catalytically active.

Holoenzyme

A complete, catalytically functional enzyme complex composed of an apoenzyme combined with its necessary non-protein cofactor or coenzyme.

Prosthetic Group

A non-protein cofactor or metal ion that is tightly or covalently bound to an enzyme and remains associated throughout its catalytic cycle (e.g., heme).

Coenzyme

A non-protein organic helper molecule (frequently derived from water-soluble B vitamins) that participates in catalytic cycles by transferring chemical groups or electrons (e.g., $\text{NAD}^+$, $\text{FAD}$, $\text{CoA}$).

Activation Energy

The energy barrier required to transition reactants to the activated state; enzymes accelerate reaction rates by lowering this barrier without altering overall chemical equilibrium.

$K_m$ (Michaelis Constant)

The substrate concentration at which the enzymatic reaction velocity reaches half of maximal velocity ($\frac{1}{2}V_{\max}$), serving as an inverse measure of enzyme affinity for its substrate.

$$V_{\max}$$

The maximum theoretical rate of an enzyme-catalyzed reaction observed when all enzyme active sites are completely saturated with substrate.

Lineweaver-Burk Plot

A double-reciprocal linear plot of $\frac{1}{v}$ versus $\frac{1}{[S]}$ whose y-intercept represents $\frac{1}{V_{\max}}$, x-intercept represents $-\frac{1}{K_m}$, and slope represents $\frac{K_m}{V_{\max}}$.

Turnover Number ($k_{\text{cat}}$)

The number of substrate molecules converted to product per enzyme molecule per second when the enzyme is fully saturated with substrate.

Catalytic Perfection

The upper limit of catalytic efficiency where the specificity constant ($k_{\text{cat}}/K_m$) is diffusion-controlled, falling within the range of $10^8\text{ to }10^9\,\text{M}^{-1}\text{s}^{-1}$.

Competitive Inhibition

A form of reversible enzyme inhibition in which an inhibitor mimics the substrate and binds to the active site, increasing apparent $K_m$ without altering $V_{\max}$.

Non-competitive Inhibition

A form of reversible enzyme inhibition where the inhibitor binds to an allosteric site on both the free enzyme and the enzyme-substrate complex, lowering $V_{\max}$ while leaving $K_m$ unchanged.

Uncompetitive Inhibition

A form of reversible enzyme inhibition where the inhibitor binds exclusively to the enzyme-substrate ($\text{ES}$) complex, decreasing both apparent $V_{\max}$ and apparent $K_m$.

Organophosphorus Inhibitors

Irreversible neurotoxic enzyme inhibitors (e.g., Sarin, VX) that covalently bond to an active-site serine hydroxyl group in acetylcholinesterase, preventing acetylcholine degradation.

Suicide Inhibition (Mechanism-Based Inactivation)

Irreversible inhibition where the target enzyme converts an inhibitor analogue into a reactive intermediate that covalently binds and permanently inactivates the enzyme (e.g., allopurinol oxidized to oxypurinol by xanthine oxidase).

Limited Proteolysis

A post-translational regulatory mechanism in which an inactive proenzyme or zymogen is irreversibly converted into an active enzyme by selective cleavage of specific peptide bonds (e.g., enteropeptidase activating trypsinogen to trypsin).

Isozymes (Isoenzymes)

Physically distinct forms of an enzyme encoded by different genes that catalyze the same chemical reaction but differ in amino acid sequence, kinetic parameters ($K_m$, $V_{\max}$), and tissue distribution.

Lactate Dehydrogenase Isoenzymes

Five tetrameric isoenzymes ($\text{LDH}_1$ to $\text{LDH}_5$) formed by different combinations of Heart ($\text{H}$) and Muscle ($\text{M}$) subunits, used clinically to detect tissue-specific damage (e.g., an inverted $\text{LDH}_1 > \text{LDH}_2$ ratio after myocardial infarction).

Creatine Kinase (CK)

A dimeric diagnostic enzyme catalyzing the reversible phosphorylation of creatine by ATP, existing as three tissue-specific isoenzymes: CK-BB (CK1, brain), CK-MB (CK2, heart), and CK-MM (CK3, skeletal muscle).

Cardiac Biomarker Timeline

The sequential appearance of enzymes and proteins in serum following myocardial infarction, characterized by early peaking of CK-MB and AST followed by prolonged elevation of cardiac troponins T and I for up to 7–10 days.

Recombinant Human DNase

A therapeutic enzyme administered by inhalation in cystic fibrosis to degrade high molecular weight extracellular DNA from necrotic neutrophils, reducing sputum viscosity.

International Unit (U)

The standard measure of enzyme catalytic activity defined as the amount of enzyme that catalyzes the transformation of $1\,\mu\text{mol}$ of substrate into product per minute under specified conditions ($1\,\text{U} \approx 16.67\,\text{nkat}$).

Nucleotide

A monomeric unit of nucleic acids consisting of a purine or pyrimidine nitrogenous base, a five-carbon pentose sugar (ribose or deoxyribose), and one, two, or three phosphate groups.

Nucleoside

A structural compound consisting of a nitrogenous purine or pyrimidine base linked to a pentose sugar via an N-glycosidic bond, lacking phosphate groups.

Purines

Double-ring heterocyclic nitrogenous bases composed of a fused pyrimidine and imidazole ring; the principal purines found in DNA and RNA are adenine and guanine.

Pyrimidines

Single-ring six-membered heterocyclic nitrogenous bases; includes cytosine (found in DNA and RNA), thymine (DNA only), and uracil (RNA only).

Phosphodiester Bond

A covalent ester linkage connecting the $5^\prime$-phosphate group of one nucleotide to the $3^\prime$-hydroxyl group of the adjacent pentose ring, forming the backbone of DNA and RNA.

DNA Melting Temperature ($t_m$)

The temperature at which 50% of double-stranded DNA helical structure is thermally denatured into separate single strands, which increases in direct proportion to the percentage of $\text{G}\equiv\text{C}$ base pairs.

Lipids

A heterogeneous group of water-insoluble, non-polymeric biomolecules that are soluble in non-polar organic solvents (such as ether and chloroform), categorized into simple, compound, and derived lipids.

Fatty Acids

Hydrocarbon chains terminating in a carboxylic acid group ($-\text{COOH}$) that can be saturated (containing no double bonds) or unsaturated (containing one or more double bonds).

Triacylglycerols (Triglycerides)

Neutral simple lipids composed of three fatty acid molecules esterified to a single glycerol molecule, serving as the primary storage form of energy in adipose tissue.

Glycerophospholipids

Amphipathic compound lipids containing a glycerol backbone esterified to two fatty acid chains and a phosphate group linked to an alcohol head group (such as choline, ethanolamine, serine, or inositol).

Plasmalogens

Phospholipids containing a vinyl-ether bond at the sn-1 position and an ester bond at the sn-2 position of the glycerol backbone, providing membrane stability in lipid rafts.

Lysophospholipids

Monoacylphosphoglycerols produced when phospholipase $A_2$ removes a fatty acid from the C-2 position of a glycerophospholipid, acting as detergent-like agents capable of inducing hemolysis.

Sphingomyelin

A sphingophospholipid composed of a ceramide unit (sphingosine attached to a long-chain fatty acid via an amide bond) esterified to a phosphocholine head group, functioning as an essential electrical insulator in myelin sheaths.

Cerebrosides

Neutral glycosphingolipids composed of a ceramide unit linked to a single monosaccharide residue (either galactose or glucose), highly concentrated in brain and nervous tissue.

Gangliosides

Complex glycosphingolipids consisting of ceramide attached to an oligosaccharide chain that contains one or more residues of sialic acid (N-acetylneuraminic acid, NANA).

Cholesterol

The predominant animal sterol composed of a four-ring steroid nucleus and a C-3 hydroxyl group, serving as a structural regulator of membrane fluidity and the precursor to bile acids, steroid hormones, and vitamin D.

Lipoproteins

Macromolecular transport complexes comprising a hydrophobic core of non-polar triglycerides and cholesteryl esters surrounded by an amphipathic surface monolayer of phospholipids, unesterified cholesterol, and apolipoproteins.