Biochemistry: Proteins and Lipids Reviewer

Comprehensive vocabulary flashcards covering protein structural hierarchy, biological classifications, and denaturation mechanics alongside lipid classifications, fatty acid properties, digestion pathways, and membrane lipid structures.

Proteins

Unbranched polymers built from $20$ standard L-α-amino acids linked together by condensation reaction-formed peptide bonds, whose identity, sequence, and spatial 3D conformation determine their biochemical specificity.

Peptide Bond Resonance

A phenomenon giving the C–N bond partial (~$40\%$) double-bond character, which prevents free rotation around the C–N bond, restricts the polypeptide backbone to planar units, and limits folding rotation to the α-carbon bonds (phi φ and psi ψ angles).

Primary ($1^\circ$) Structure

The unique linear sequence of amino acids from the N-terminus to the C-terminus, encoded directly by mRNA and stabilized exclusively by covalent peptide bonds (amide linkages).

Secondary ($2^\circ$) Structure

The local spatial arrangement of the polypeptide main chain without considering side-chain R-groups, stabilized exclusively by hydrogen bonds between the backbone carbonyl oxygen (C=O) and amide hydrogen (N-H).

α-Helix Motif

A rigid, right-handed coiled secondary structure stabilized by intrachain hydrogen bonds between the C=O of residue $i$ and the N-H of residue $i+4$, possessing $3.6$ amino acid residues per turn with R-groups projecting outward perpendicularly.

Helix Breakers

Specific amino acid residues that disrupt α-helical structure, notably Proline due to its rigid ring structure and Glycine due to its excessive conformational flexibility.

β-Pleated Sheet Motif

A secondary structure motif composed of fully extended polypeptide strands running side-by-side stabilized by interchain hydrogen bonds, with amino acid R-groups alternating above and below the sheet plane.

Antiparallel β-Sheets

β-pleated sheet arrangements where adjacent polypeptide strands run in opposite directions ($\text{N}\rightarrow\text{C}$ / $\text{C}\rightarrow\text{N}$), resulting in stronger, straight hydrogen bonds compared to the bent bonds of parallel sheets.

Tertiary ($3^\circ$) Structure

The overall 3D spatial conformation and functional native state of a single polypeptide chain, stabilized by R-group side-chain interactions including hydrophobic interactions, hydrogen bonds, salt bridges, disulfide bonds, and Van der Waals forces.

Hydrophobic Effect

The primary driving thermodynamic force of tertiary protein folding, in which water molecules increase overall entropy as nonpolar amino acid side chains bury into the interior protein core away from aqueous solvent.

Disulfide Linkage

A covalent bond formed between two cysteine residues to yield cystine via thiol oxidation ($-\text{SH} + -\text{SH} \rightarrow -\text{S}-\text{S}-$), essential for stabilizing extracellular proteins like insulin.

Salt Bridges

Electrostatic attractions between positively charged amino acid side chains (Lys, Arg, His) and negatively charged amino acid side chains (Asp, Glu) that stabilize protein tertiary and quaternary conformations.

Quaternary ($4^\circ$) Structure

The spatial organization of two or more independent polypeptide subunits held together by non-covalent side-chain interactions and occasional interchain disulfide bonds, enabling cooperativity and allosteric regulation.

Molecular Chaperones

Specialized proteins such as heat shock proteins (Hsp70, GroEL/GroES complex) that prevent the premature aggregation of exposed hydrophobic patches during protein synthesis and assist misfolded proteins in refolding into their native 3D state.

Myoglobin

A monomeric oxygen-storage protein found in muscle tissue that exhibits only tertiary structure, possesses high $O_2$ affinity, and generates a hyperbolic oxygen-binding curve.

Hemoglobin

A tetrameric oxygen-transport protein ($\alpha_2\beta_2$) with quaternary structure found in red blood cells that exhibits cooperative oxygen binding, a sigmoidal binding curve, and regulation by pH, $\text{CO}_2$, and 2,3-BPG.

Fibrous Proteins

Long, elongated, sheet- or rod-like structural proteins that are insoluble in water due to high concentrations of hydrophobic amino acids and provide mechanical strength (e.g., α-keratin, collagen, fibroin, elastin).

Globular Proteins

Compact, spherical, water-soluble proteins whose hydrophobic residues are buried inside and which execute dynamic cellular functions like catalysis, signaling, transport, and immunity (e.g., enzymes, immunoglobulins, serum albumin).

Protein Denaturation

The unfolding and loss of a protein's native secondary, tertiary, and quaternary conformations accompanied by the complete loss of biological activity, while leaving covalent peptide bonds (primary structure) intact.

Chaotropic Agents

Denaturing compounds such as urea and guanidinium HCl that disrupt water structure and non-covalent interactions, stabilizing the unfolded polypeptide backbone.

Anfinsen's Experiment

A biochemical experiment using Ribonuclease A denatured by urea and β-mercaptoethanol; upon removal of the agents, the protein spontaneously refolded into its active conformation, demonstrating that the primary amino acid sequence contains all necessary information for 3D folding.

Sickle Cell Anemia Mutation

A pathological non-conservative mutation swapping a charged Glutamate for a hydrophobic Valine on the exterior of the hemoglobin β-chain, generating an exposed hydrophobic patch that triggers fiber aggregation under low $O_2$ conditions.

Lipids

A heterogeneous group of organic molecules defined by their insolubility in water (hydrophobic) and high solubility in nonpolar organic solvents (e.g., ether, chloroform), consisting predominantly of carbon and hydrogen with few oxygen-containing groups.

Simple Lipids

Esters of fatty acids with various alcohols containing only carbon, hydrogen, and oxygen, including neutral fats/oils (triglycerides) and waxes (such as beeswax and carnauba wax).

Complex (Compound) Lipids

Amphipathic esters of fatty acids that contain non-lipid chemical groups attached to an alcohol backbone, such as phospholipids, glycolipids, and lipoproteins.

Derived & Precursor Lipids

Lipid-soluble substances produced by the hydrolysis of simple or complex lipids, or synthesized via repeating isoprene units, including free fatty acids, steroids, eicosanoids, and terpenes.

Saturated Fatty Acids

Hydrocarbon chains containing only single carbon-carbon bonds (C–C) fully saturated with hydrogen atoms, adopting straight linear conformations that pack tightly and remain solid or semi-solid at room temperature ($25\,^\circ\text{C}$).

Unsaturated Fatty Acids

Hydrocarbon chains containing one or more carbon-carbon double bonds (C=C); cis double bonds introduce a rigid $30^\circ$ bend/kink that impedes close packing and keeps them liquid at room temperature.

Trans Fatty Acids

Fatty acids produced via industrial partial hydrogenation where hydrogen atoms are on opposite sides of the double bond, creating a straight chain that packs like a saturated fat, increases LDL, decreases HDL, and raises coronary heart disease risk.

Essential Fatty Acids (EFAs)

Fatty acids that humans cannot synthesize de novo due to lacking desaturase enzymes for double bonds beyond Carbon-9, specifically Linoleic Acid ($18:2\,(\Delta^{9,12})$) and Alpha-Linolenic Acid ($18:3\,(\Delta^{9,12,15})$).

Triacylglycerols (TAGs)

Neutral, hydrophobic storage lipids composed of one glycerol molecule esterified to three fatty acid chains, storing energy anhydrously and yielding $9\,\text{kcal/g}$ compared to $4\,\text{kcal/g}$ for hydrated glycogen.

Saponification

The basic hydrolysis of triacylglycerols using a strong aqueous base (e.g., $\text{NaOH}$ or $\text{KOH}$) that cleaves ester bonds to yield free glycerol and three sodium/potassium fatty acid salts (soap).

Bile Salts

Biological detergents (glycocholate and taurocholate) synthesized from cholesterol and released by the gallbladder via CCK stimulation to emulsify dietary lipids into micro-droplets and maintain cholesterol solubility in bile.

Mixed Micelles

Tiny soluble clusters ($\sim 4\text{--}8\,\text{nm}$) formed by 2-monoacylglycerol, free fatty acids, free cholesterol, fat-soluble vitamins, and bile salts that transport lipids across the unstirred water layer to enterocytes.

Chylomicrons

Lipoprotein particles assembled in the enterocyte endoplasmic reticulum containing re-esterified TAGs, cholesteryl esters, phospholipids, and Apolipoprotein B-48 (Apo B-48), which are exocytosed into lacteals to enter lymphatic circulation.

Orlistat (Xenical)

An anti-obesity drug that inhibits gastric and pancreatic lipases, blocking the digestion and absorption of approximately $30\%$ of dietary fat and potentially causing steatorrhea.

Glycerophospholipids

The most abundant class of membrane lipids, composed of a glycerol-3-phosphate backbone esterified to two fatty acids and an alcohol-derived polar head group (e.g., choline, ethanolamine, serine, or inositol).

Sphingomyelin

A sphingophospholipid composed of a sphingosine backbone linked to a fatty acid via an amide bond (ceramide) and esterified to a phosphocholine head group, serving as a key structural component of nerve myelin sheaths.

Glycolipids (Sphingoglycolipids)

Membrane lipids built on a ceramide backbone linked directly to sugar residues without a phosphate group, located exclusively on the outer leaflet of the plasma membrane for cell recognition and ABO blood group determination.

Cerebrosides

Neutral glycosphingolipids composed of a ceramide backbone attached to a single monosaccharide unit, either glucose or galactose.

Gangliosides

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

Cholesterol (Membrane Sterol)

A rigid sterol featuring a four-fused carbon ring nucleus and a hydroxyl group that acts as a bidirectional membrane fluidity buffer by limiting excessive phospholipid mobility at high temperatures and hindering tight packing at low temperatures.

Cholelithiasis

The formation of gallstones resulting when the concentration of cholesterol in bile exceeds the solubilization capacity of available bile salts, causing cholesterol to precipitate and crystallize.

Steatorrhea

The excessive excretion of undigested fat in feces, occurring due to lipid malabsorption caused by pancreatic lipase deficiency, bile duct blockage, or pharmacological lipase inhibitors.