Biochemistry Review – Lipids, Metabolism & Protein Structure

Vocabulary flashcards covering lipids, diabetes, metabolic regulation, bioenergetics, amino acid chemistry, protein structure, and key enzymatic steps mentioned in the lecture notes.

Lipids

A broad class of hydrophobic biomolecules including fatty acids, triglycerides, phospholipids, steroids, and glycolipids.

Fatty Acid

Long-chain carboxylic acid; hydrophobic tail with a terminal carboxyl group.

Saturated Fatty Acid

Fatty acid containing no C=C double bonds; straight chains; solid at room temperature.

Unsaturated Fatty Acid

Fatty acid with one or more C=C double bonds; kinked chains; liquid at room temperature.

Phospholipid

Amphipathic lipid with glycerol backbone, two fatty acid tails, and a phosphate-containing head group (e.g., choline, serine).

Steroid

Lipid with four fused rings (three hexane + one pentane); largely hydrophobic but overall amphipathic.

Cholesterol

Amphipathic steroid with hydrophobic ring system and a single polar hydroxyl (–OH) group.

Glycolipid

Lipid covalently bonded to one or more sugars through a glycosidic linkage.

Type 1 Diabetes

Autoimmune destruction of pancreatic β-cells leading to absolute insulin deficiency.

Type 2 Diabetes

Metabolic disorder characterized by insulin resistance in target tissues.

Preproinsulin

Initial polypeptide precursor of insulin that contains a signal peptide for secretion.

Proinsulin

Insulin precursor after removal of signal peptide; contains connecting C-peptide.

Disulfide Bridge

Covalent –S–S– bond between two cysteine residues that stabilizes protein structure.

Chemotherapeutic Targeting

Strategy of inhibiting synthesis of specific, non-essential ribonucleotides to slow cancer cell growth.

ATP (Adenosine Triphosphate)

Universal energy currency; necessary for metabolism, RNA synthesis, and signaling.

GTP (Guanosine Triphosphate)

Nucleotide required for protein synthesis, signal transduction, and gluconeogenesis.

Electron Transport Chain (ETC)

Series of mitochondrial (or chloroplast) complexes that pump protons and produce electrochemical gradients.

pH Gradient

Difference in proton concentration across a membrane used to drive ATP synthesis.

ATP Synthase

Rotary enzyme that converts ADP + Pi to ATP using proton-motive force.

Thylakoid Lumen

Internal space of chloroplast thylakoids where photosynthetic proton accumulation occurs.

Mitochondrial Intermembrane Space

Compartment between inner and outer mitochondrial membranes where ETC pumps protons.

FADH₂

Reduced flavin nucleotide that donates electrons to Complex II of the ETC.

NADH

Reduced nicotinamide nucleotide that donates electrons to Complex I of the ETC.

Malate–Aspartate Shuttle

Mitochondrial transport system that moves cytosolic NADH equivalents into the matrix.

Tricarboxylic Acid (TCA) Cycle

Central metabolic pathway oxidizing acetyl-CoA to CO₂ while generating NADH and FADH₂.

Isocitrate Dehydrogenase

TCA enzyme converting isocitrate to α-ketoglutarate; allosterically activated by ADP and inhibited by ATP/NADH.

Transamination

Exchange of amino groups between an amino acid and α-keto acid, forming new amino/keto acids.

Urea Cycle

Hepatic pathway that converts toxic ammonia into urea; consumes ATP.

Fructose-2,6-Bisphosphate (F-2,6-BP)

Potent allosteric activator of PFK-1 and inhibitor of FBPase-1, coordinating glycolysis and gluconeogenesis.

Phosphofructokinase-1 (PFK-1)

Rate-limiting glycolytic enzyme converting F-6-P to F-1,6-BP; activated by F-2,6-BP and AMP.

Fructose-1,6-Bisphosphatase-1 (FBPase-1)

Gluconeogenic enzyme that hydrolyzes F-1,6-BP to F-6-P; inhibited by F-2,6-BP and AMP.

Essential Amino Acids

Amino acids that cannot be synthesized by humans and must be obtained from the diet (e.g., Lys, Leu, Phe).

Nonpolar Amino Acids

Hydrophobic amino acids such as Val, Leu, Ile, Phe, Met.

Polar Uncharged Amino Acids

Amino acids with polar side chains lacking net charge; Ser, Thr, Asn, Gln.

Acidic Amino Acids

Amino acids with negatively charged side chains at physiological pH; Asp, Glu.

Basic Amino Acids

Positively charged amino acids; Lys, Arg, His.

Titratable Side Chain

Amino acid side chain capable of gaining or losing protons within physiological pH range.

Henderson–Hasselbalch Equation

Formula relating pH, pKa, and ratio of protonated/deprotonated species.

Isoelectric Point (pI)

pH at which a molecule carries no net electrical charge.

Protein Denaturation

Loss of secondary, tertiary, and quaternary structure leading to functional inactivity.

Primary Structure

Linear sequence of amino acids in a protein; remains intact during denaturation.

Secondary Structure

Local α-helix or β-sheet formations stabilized by hydrogen bonds.

Tertiary Structure

Overall 3-D folding of a single polypeptide chain.

Quaternary Structure

Spatial arrangement of multiple polypeptide subunits.

Myoglobin

Monomeric oxygen-binding protein in muscle; contains heme stabilized by two histidines.

Hemoglobin

Tetrameric blood protein that transports oxygen; interacts with BPG to modulate O₂ affinity.

2,3-Bisphosphoglycerate (BPG)

Negatively charged glycolytic intermediate that lowers hemoglobin’s oxygen affinity by binding its central cavity.

Glyceraldehyde-3-Phosphate (G3P)

Three-carbon glycolysis intermediate produced by aldolase and consumed by GAPDH.

Fructose-1,6-Bisphosphate (F-1,6-BP)

Key glycolytic intermediate formed by PFK-1; later split into G3P and DHAP.

Lactate

Anaerobic reduction product of pyruvate that regenerates NAD⁺ in muscle and RBCs.

Ethanol (Fermentation)

Alcohol produced by yeast anaerobic metabolism of pyruvate, regenerating NAD⁺.

Hexokinase

Glycolytic enzyme phosphorylating glucose to G6P; inhibited by its product.

Glucokinase

Liver isoform of hexokinase with higher Km; active after meals.

Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH)

Glycolytic enzyme converting G3P to 1,3-BPG while producing NADH.

Pyruvate Kinase

Glycolytic enzyme converting phosphoenolpyruvate to pyruvate, yielding ATP; regulated by allostery and phosphorylation.

Glycogen

Highly branched α-1,4/α-1,6 glucose polymer serving as animal carbohydrate storage.

Starch

Plant glucose storage polymer composed of amylose and amylopectin with α-linkages.

Cellulose

Structural plant polysaccharide of β-1,4-linked glucose; indigestible to humans.

β-1,4 Glycosidic Bond

Linkage connecting glucose units in cellulose; confers rigidity and insolubility.

α-1,6 Branch Point

Glycosidic bond creating branches in glycogen and amylopectin.

Surface Amino Acids

Generally polar or charged residues (e.g., Ser, Glu) exposed to aqueous environment.

Interior Amino Acids

Hydrophobic residues (e.g., Val, Ile, Phe) buried within protein cores or membranes.

Enzyme–Substrate Complex (ES)

Transient association between enzyme and substrate during catalysis.

Km (Michaelis Constant)

Substrate concentration at which enzyme operates at half Vmax; reflects ES affinity.

Transmembrane Amphipathic Helix

Helical domain containing both hydrophobic and hydrophilic regions, allowing membrane anchoring.

Phosphoserine

Serine residue phosphorylated to carry two negative charges, altering protein interactions.

Proton-Motive Force

Electrochemical gradient of protons that drives ATP synthesis and transport processes.