Cell Biology: Unit 1 Review Flashcards

Comprehensive vocabulary flashcards generated from Cell Biology Unit 1 lecture notes covering protein structure, function, methods, and lipid membrane principles.

Central dogma of molecular biology

The core framework describing the flow of genetic information within a biological system: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$.

Translation

The cellular process in which mRNA sequences are decoded by ribosomes to synthesize specific amino acid chains.

Enzymes

Specialized proteins that accelerate chemical reactions by lowering activation energy, catalyzing covalent bond breakage or formation to convert substrates into products.

Alpha-carbon ($C_{\alpha}$)

The central carbon atom of an amino acid covalently bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group).

Peptide bond

A covalent chemical bond formed between the carboxyl group of one amino acid and the amino group of another through a condensation (dehydration) reaction that removes a water molecule.

Nonpolar amino acids

Hydrophobic amino acids whose side chains lack polar covalent bonds or charges, causing them to aggregate within protein interiors (e.g., Glycine, Alanine, Methionine).

Polar uncharged amino acids

Hydrophilic amino acids possessing side chains with polar groups that frequently reside on the outer surface of folded proteins (e.g., Serine, Threonine, Asparagine).

Polar acidic amino acids

Amino acids with side chains containing carboxyl groups that carry a net negative charge at physiological pH (e.g., Aspartic acid, Glutamic acid).

Polar basic amino acids

Amino acids with side chains containing nitrogenous bases that carry a net positive charge at physiological pH (e.g., Lysine, Arginine, Histidine).

Sickle cell disease

A genetic disease caused by a single nucleotide point mutation in the HBB gene, substituting Glutamic acid with Valine at position 6 of the $\beta$-globin chain.

Huntington's disease

A neurodegenerative disorder caused by an unstable expansion of 36 or more CAG trinucleotide repeats within the HTT gene, resulting in an expanded polyglutamine tract.

Noncovalent attractions in protein folding

Weak non-covalent interactions—including electrostatic attractions, hydrogen bonds, and van der Waals forces—that collectively stabilize folded protein conformations.

Urea denaturation

The unfolding of a native protein structure caused by high concentrations of urea disrupting noncovalent hydrogen bonds; removing urea permits spontaneous refolding.

Chaperone proteins

Specialized helper proteins that bind to exposed hydrophobic segments of newly synthesized or partially folded polypeptides to prevent misfolding and aggregation.

Alpha helix

A common secondary structure element stabilized by backbone hydrogen bonds between every N-H group and the C=O group located four residues prior, featuring a pitch of $0.54\,\text{nm}$ per turn ($3.6$ amino acids per turn).

Transmembrane alpha helix

An alpha-helical protein domain composed of 20–30 nonpolar, hydrophobic amino acids whose side chains interact favorably with the lipid bilayer interior.

Coiled-coil domain

A structural motif in which two or three alpha helices twist around one another to bury their hydrophobic side chain stripes away from the surrounding aqueous solution.

Beta sheet

A secondary structure formed by hydrogen bonds between peptide backbones in adjacent linear strands, arranged in either parallel or antiparallel orientations.

Amyloid fibrils

Insoluble, highly stable protein aggregates formed by misfolded beta sheet segments that accumulate and contribute to neurodegenerative pathologies.

Protein domain

A compact, independently folding unit or modular segment of a polypeptide chain that confers a distinct biochemical function.

Green Fluorescent Protein (GFP)

A reporter protein from Aequorea victoria featuring an 11-stranded beta-barrel cylinder enclosing a central alpha helix with a light-emitting fluorophore.

Intrinsically unstructured regions (IURs)

Flexible polypeptide loops lacking fixed secondary or tertiary structure that link domains, enhance binding collisions, and scaffold protein complexes.

Protein families

Groups of evolutionarily related proteins that share similar amino acid sequences, three-dimensional backbone structures, and catalytic or biochemical mechanisms.

Serine proteases

A protein family including elastase and chymotrypsin that maintain nearly identical 3D backbone folds but differ in cleavage specificity due to distinct binding pocket side chains.

Hemoglobin

A heterotetrameric oxygen-transport protein composed of two $\alpha$-globin and two $\beta$-globin subunits, each containing an iron-bound heme prosthetic group.

Disulfide bonds

Covalent sulfur-sulfur linkage staples formed by the oxidation of sulfhydryl (-SH) groups on cysteine residues to reinforce extracellular protein structures.

Ligand

Any atom, ion, small organic molecule, or macromolecule that is specifically bound by a protein's active or binding site.

Antibodies

Y-shaped immunoglobulins produced by B lymphocytes consisting of two identical heavy chains and two identical light chains held together by interchain disulfide bonds.

Michaelis Constant ($K_M$)

The substrate concentration at which an enzyme-catalyzed reaction achieves half of its maximum velocity ($V_{\max}$), serving as an inverse measure of substrate affinity.

Competitive inhibitor

A regulatory molecule that directly competes with the substrate for binding to an enzyme's active site, physically obstructing substrate access.

Allosteric regulation

The control of protein activity resulting from the binding of a regulatory molecule to an allosteric site separate from the active site, inducing a conformational shift.

Post-translational modifications (PTMs)

Covalent modifications made to specific amino acid side chains after translation that modulate protein activity, localization, stability, and macromolecular interactions.

Protein kinases

Enzymes that catalyze the transfer of a high-energy terminal phosphate group from ATP to specific hydroxyl groups on target amino acids (Serine, Threonine, Tyrosine).

Protein phosphatases

Enzymes that reverse phosphorylation by hydrolytically removing phosphate groups from target proteins.

GTPases

Molecular switch proteins that cycle between an active GTP-bound conformation and an inactive GDP-bound state via GTP hydrolysis.

Differential centrifugation

A subcellular fractionation technique that separates components in cell homogenates through sequential centrifugations at increasing rotational speeds and centrifugal forces.

Velocity sedimentation

A separation technique that fractionates subcellular components across a sucrose gradient based on their size and rate of sedimentation.

Equilibrium sedimentation

A high-speed centrifugation method that isolates cell components based strictly on their buoyant density within a steep density gradient, independent of size or shape.

Ion-exchange chromatography

A column chromatography method that separates proteins based on surface charge differences using charged matrix beads.

Gel-filtration chromatography

A chromatographic separation method based on molecular size that uses porous beads to retard smaller molecules while larger molecules pass through uninhibited.

Affinity chromatography

A high-purity protein purification technique that relies on matrix beads coupled with specific ligands to selectively capture target proteins.

SDS-PAGE

An electrophoretic technique that uses sodium dodecyl sulfate to denature proteins and impart a uniform negative charge, separating them exclusively by molecular weight.

Isoelectric focusing (IEF)

An electrophoretic method that separates proteins along a pH gradient to the point where their net electrical charge becomes zero ($pI$).

Western blotting

An analytical method combining SDS-PAGE separation, transfer to a membrane, and antibody probing to identify specific target proteins.

Cryo-Electron Microscopy (Cryo-EM)

A structural biology method in which vitrified, rapidly frozen protein samples are imaged using transmission electron beams to yield 3D density maps.

Phospholipids

Amphipathic membrane lipids consisting of a hydrophilic polar head group linked via glycerol to two hydrophobic fatty acid tails.

Cholesterol

A rigid membrane sterol that intercalates between phospholipids to stiffen the outer bilayer region, reducing permeability and fluidity.