Biochemistry II – AI Notes

A comprehensive set of vocabulary flashcards covering key terms from biological membranes, transport mechanisms, signal transduction, carbohydrate metabolism, glycogen regulation, and cellular respiration.

Micelle

Spherical aggregate of amphipathic lipids in water; hydrophobic tails inside, polar heads outside.

Lipid Bilayer

Two lipid leaflets forming a planar, amphipathic sheet that is the basic structure of biological membranes.

Vesicle (Liposome)

Closed, spherical bilayer enclosing an aqueous compartment; useful for transport and drug delivery.

Liquid-ordered (Lo) state

Gel-like membrane phase in which lipid motions are highly constrained.

Liquid-disordered (Ld) state

Fluid membrane phase with rapid lateral and rotational movement of lipids.

Membrane Fluidity

Degree of lipid and protein mobility within a membrane; affected by temperature, FA saturation and cholesterol.

Cholesterol

Sterol that buffers membrane fluidity—rigidifying at high T and fluidizing at low T.

Lipid Raft

Cholesterol- and sphingolipid-rich microdomain that is thicker and more ordered than surrounding membrane.

Flippase

ATP-dependent enzyme that moves phospholipids from the outer to inner leaflet.

Floppase

ATP-dependent enzyme that transfers lipids from the inner to outer leaflet.

Scramblase

Ca²⁺-activated enzyme that equilibrates lipids between leaflets without ATP.

SNARE protein

Cytosolic membrane proteins that mediate vesicle docking and fusion (v-SNARE & t-SNARE).

Endocytosis

Uptake of extracellular material by vesicle invagination of the plasma membrane.

Exocytosis

Fusion of intracellular vesicles with the plasma membrane to release contents outside the cell.

Peripheral Membrane Protein

Protein loosely associated with the membrane via electrostatic or H-bond interactions; removed by mild treatments.

Integral Membrane Protein

Protein embedded within the lipid bilayer; requires detergents to remove.

Monotopic Protein

Integral protein that contacts only one leaflet and does not span the bilayer.

Bitopic Protein

Single-pass transmembrane protein crossing the bilayer once.

Polytopic Protein

Integral protein with multiple transmembrane helices crossing the bilayer several times.

Transmembrane Segment

~20-residue hydrophobic α-helix or β-strand that spans a lipid bilayer.

Positive-Inside Rule

Cytosolic loops of membrane proteins are enriched in Lys/Arg residues.

Hydropathy Index

ΔG for transferring an amino acid side chain from hydrophobic to aqueous environment; positive = hydrophobic.

Hydropathy Plot

Graph of average hydropathy versus residue number to predict membrane-spanning segments.

Lipid Anchor

Covalent attachment of a lipid (e.g., prenyl, myristoyl, GPI) that tethers a protein to a membrane.

GPI-anchored Protein

Protein linked to membrane via glycosyl-phosphatidylinositol moiety on the outer leaflet.

Ion Channel

Membrane protein that forms a pore allowing passive, selective ion flow down an electrochemical gradient.

Transporter (Carrier)

Membrane protein that binds specific solutes and undergoes conformational cycling to move them across bilayers.

Simple Diffusion

Unassisted movement of small, non-polar molecules across a membrane down their concentration gradient.

Facilitated Diffusion

Passive transport of molecules down a gradient via channels or transporters; saturable and selective.

Active Transport

Energy-requiring movement of solute against a gradient; driven by ATP, light, or another gradient.

Secondary Active Transport

Coupled transport where uphill movement of one solute is powered by downhill flow of another.

Electrochemical Gradient

Combined chemical (ΔC) and electrical (Δψ) potential driving ion movement.

Uniport

Transporter moving a single substrate in one direction.

Symport

Cotransporter that moves two substrates in the same direction.

Antiport

Cotransporter exchanging two substrates in opposite directions.

GLUT1

Ubiquitous facilitative glucose transporter with Km ≈ 3 mM for basal uptake.

Selectivity Filter

Ion channel region whose backbone carbonyls or side chains confer size and charge selectivity (e.g., K⁺ channel).

Aquaporin

Tetrameric water channel with Asn and Arg residues that prevent proton passage.

P-type ATPase

Primary active transporter forming a phosphorylated Asp intermediate (e.g., Na⁺/K⁺ pump, SERCA).

SERCA Pump

Sarco/endoplasmic reticulum Ca²⁺ ATPase that transports 2 Ca²⁺ per ATP into the ER lumen.

Na⁺/K⁺ ATPase

P-type pump exporting 3 Na⁺ and importing 2 K⁺ per ATP, creating membrane potential.

ABC Transporter

ATP-Binding Cassette pump that exports diverse substrates; two NBDs + two TMDs.

MDR1

Multidrug resistance ABC transporter that expels anticancer drugs, causing chemotherapy failure.

CFTR

Chloride channel ABC protein; mutation causes cystic fibrosis.

GPCR

G-protein-coupled receptor with 7 transmembrane helices activating heterotrimeric G proteins.

G Protein

Heterotrimer (αβγ) that binds GDP/GTP; transduces signal from GPCRs to effectors.

Ligand

Molecule that specifically binds a receptor to initiate signaling (e.g., hormone, neurotransmitter).

Second Messenger

Small intracellular signal molecule (cAMP, Ca²⁺, IP₃, DAG) that propagates receptor activation.

Effector Enzyme

Downstream enzyme regulated by activated G protein (e.g., adenylyl cyclase, phospholipase C).

GEF (Guanine-nucleotide Exchange Factor)

Protein that promotes GDP→GTP exchange to activate a G-protein.

Adenylyl Cyclase

Membrane enzyme converting ATP to cyclic AMP (cAMP).

cAMP

Cyclic nucleotide second messenger activating protein kinase A.

Protein Kinase A (PKA)

cAMP-dependent Ser/Thr kinase regulating metabolism and transcription.

Intrinsic GTPase Activity

Autohydrolysis of GTP to GDP by G-protein α-subunit, terminating signaling.

Signal Amplification

Cascade in which one receptor activates many effectors, greatly increasing response.

Signal Specificity

Selective receptor-ligand pairing ensuring distinct cellular responses.

Desensitization

Adaptive reduction in receptor responsiveness during continued stimulation.

RTK (Receptor Tyrosine Kinase)

Single-pass transmembrane receptor with cytosolic Tyr-kinase domain activated by dimerization.

Autophosphorylation

Self-phosphorylation on Tyr residues that activates RTKs.

SH2 Domain

Protein module that binds phosphorylated tyrosines in signaling complexes.

Grb2

Adaptor protein with SH2/SH3 domains linking RTKs to Sos.

Sos

GEF that activates Ras by promoting GDP release.

Ras

Monomeric GTPase initiating MAPK signaling; oncogenic when mutated.

MAPK Cascade

Sequential activation of Raf→MEK→ERK kinases leading to gene regulation.

Voltage-Gated Channel

Ion channel that opens in response to changes in membrane potential (e.g., Na⁺ channel).

Ligand-Gated Channel

Ion channel opened by binding of a chemical messenger (e.g., acetylcholine receptor).

Hormone Response Element (HRE)

DNA sequence bound by nuclear hormone receptor to alter transcription.

Nuclear Hormone Receptor

Intracellular receptor that, upon binding lipid-soluble ligand, regulates gene expression.

Glycolysis

Cytosolic pathway converting glucose to 2 pyruvate, generating net 2 ATP and 2 NADH.

Hexokinase

High-affinity enzyme phosphorylating glucose to glucose-6-P; inhibited by product.

Glucokinase

Liver isozyme with high Km and Vmax; not product-inhibited and acts as glucose sensor.

PFK-1

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

Fructose-2,6-bisphosphate

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

Pyruvate Kinase

Enzyme forming pyruvate and ATP from PEP; inhibited by ATP and phosphorylation (liver).

Warburg Effect

Preference of cancer cells for aerobic glycolysis producing lactate even with O₂ present.

Cori Cycle

Liver conversion of lactate from muscle back to glucose via gluconeogenesis.

Glucose-Alanine Cycle

Transport of alanine from muscle to liver for gluconeogenic conversion to glucose.

Pyruvate Carboxylase

Biotin-dependent mitochondrial enzyme converting pyruvate to oxaloacetate in gluconeogenesis.

PEPCK

Phosphoenolpyruvate carboxykinase generating PEP from oxaloacetate; uses GTP.

FBPase-1

Fructose-1,6-bisphosphatase removing phosphate to form fructose-6-P; inhibited by AMP & F-2,6-BP.

Glucose-6-phosphatase

ER-membrane enzyme converting glucose-6-P to free glucose in liver and kidney.

Pentose Phosphate Pathway (PPP)

Cytosolic route generating NADPH and ribose-5-P; has oxidative and non-oxidative phases.

NADPH

Reducing cofactor for biosynthesis and antioxidant defense; produced by PPP.

Glucose-6-phosphate Dehydrogenase (G6PD)

Rate-limiting PPP enzyme; deficiency leads to hemolytic anemia.

Glycogen

Branched polymer of glucose (α1→4 with α1→6 branches) serving as animal storage carbohydrate.

Glycogenolysis

Breakdown of glycogen to glucose-1-P by glycogen phosphorylase and debranching enzyme.

Glycogenesis

Synthesis of glycogen from UDP-glucose via glycogen synthase and branching enzyme.

Glycogen Phosphorylase

Enzyme releasing glucose-1-P from non-reducing ends; activated by phosphorylation and AMP.

Debranching Enzyme

Transfers trisaccharide to main chain and hydrolyzes α1→6 branch point glucose.

UDP-Glucose

Activated glucose donor for glycogen synthesis.

Glycogen Synthase

Key enzyme forming α1→4 linkages; active (a) when dephosphorylated.

Branching Enzyme

Amylo-(1→4)→(1→6) transglycosylase that introduces glycogen branches.

Glycogenin

Self-glucosylating protein primer on which glycogen chains are built.

GSK-3

Glycogen synthase kinase-3 that phosphorylates and inactivates glycogen synthase.

PP1

Protein phosphatase-1 that dephosphorylates and activates glycogen synthase while inactivating phosphorylase.

Pyruvate Dehydrogenase Complex (PDH)

Mitochondrial multienzyme complex converting pyruvate to acetyl-CoA, CO₂ and NADH.

Thiamine Pyrophosphate (TPP)

Vitamin-derived cofactor on E1 that stabilizes carbanion intermediates in PDH.

Lipoic Acid

Swinging arm cofactor on E2 that transfers acyl groups and electrons in PDH and α-KGDH.

Acetyl-CoA

High-energy thioester entering the citric acid cycle or fatty acid synthesis.

Citrate Synthase

First TCA enzyme condensing acetyl-CoA with oxaloacetate to form citrate.