Biochemistry Exam 1 Review: Molecular Interactions, Protein Structure, Function, Trafficking, and Chromatin Remodeling

Vocabulary practice flashcards covering fundamental biochemistry concepts including chemical bonding, protein folding and structure, biochemical techniques, intracellular protein trafficking, and chromatin remodeling.

Covalent Bond

A strong chemical bond formed when atoms share one or more pairs of electrons to achieve greater atomic stability.

Non-covalent Bond

A category of weak electrostatic interactions between atoms or molecules, including hydrogen bonds, ionic bonds, and dispersion forces, that do not involve sharing electrons.

London Dispersion Forces

Weak electrostatic attractive forces that arise when temporary, opposing dipoles created through the random distribution of electrons around atomic nuclei interact.

Hydrogen Bond

A non-covalent interaction occurring between a hydrogen atom covalently bound to a highly electronegative atom like oxygen ($O$) or nitrogen ($N$) and another electronegative atom with a negative partial dipole.

Ion-Dipole Interaction

An electrostatic attraction occurring between an atom or functional group with a full ionic charge and a nearby atom or molecule possessing an opposing permanent partial charge.

Peptide Bond Resonance

The partial double-bond character of the peptide bond resulting from electron resonance, which restricts rotation around the $C-N$ bond and constrains backbone geometry.

Helix Breakers

Amino acids, specifically Glycine and Proline, that disrupt regular $\alpha$-helical backbone hydrogen bonding due to excessive conformational flexibility (Glycine) or extreme conformational rigidity (Proline).

Amphipathic $\alpha$-Helix

An $\alpha$-helical secondary structure characterized by having hydrophobic amino acid residues localized on one face and hydrophilic or charged residues on the opposite face.

Ramachandran Plot

A two-dimensional plot of backbone torsion angles Phi ($\phi$) versus Psi ($\psi$) that indicates allowed and forbidden conformational spaces for amino acid residues in proteins.

Protein Domain

A distinct, compact, and independently folded structural unit within a single polypeptide chain that can fold and function autonomously.

Hydrophobic Effect

The major thermodynamic driving force of protein folding in aqueous solution, where non-polar side chains aggregate inward to exclude water, increasing the net entropy ($\Delta S$) of the solvent.

Prions ($PrP^{Sc}$)

Misfolded, disease-causing protein conformers that template the conversion of normal cellular prion proteins ($PrP^C$) into pathological, aggregate-forming structures.

Molecular Chaperone

A protein, such as Hsp70, that binds to exposed hydrophobic regions of unfolded or misfolded proteins to prevent inappropriate aggregation and facilitate correct folding.

Dissociation Constant ($K_D$)

An equilibrium constant measuring the affinity between a protein and its ligand; a smaller $K_D$ value corresponds to a higher binding affinity.

Affinity Chromatography

A protein purification technique that separates a specific target protein from a complex lysate using immobilized ligands or antibodies that selectively bind the protein non-covalently.

SDS-PAGE

Sodium dodecyl sulfate-polyacrylamide gel electrophoresis, a denaturing technique where SDS coats proteins with a uniform negative charge-to-mass ratio, enabling separation purely by molecular weight.

Reducing SDS-PAGE vs Native-PAGE

Techniques used in combination to analyze protein quaternary structure, where Native-PAGE maintains intact multi-subunit complexes and reducing SDS-PAGE denatures subunits and breaks disulfide bonds to reveal individual polypeptide chains.

Loading Control

A ubiquitous, consistently expressed protein like $\beta$-actin analyzed in Western blotting to confirm equal sample loading across all gel lanes.

Post-translational Modification

Covalent chemical modifications made to a protein after ribosomal translation, including glycosylation, phosphorylation, and disulfide bond formation.

Secretory Pathway

The intracellular route for secreted and membrane proteins, traversing from cytosol to ribosome, ER lumen, Golgi apparatus, secretory vesicles, and the plasma membrane.

Ran GTPase

A monomeric GTP-binding protein that regulates nuclear transport; its GTP-bound state in the nucleus promotes importin-cargo dissociation and exportin-cargo binding.

Ran-GEF

Guanine nucleotide exchange factor localized in the nucleus that activates Ran by promoting the exchange of bound GDP for GTP.

Ran-GAP

GTPase-activating protein localized in the cytoplasm that inactivates Ran by stimulating GTP hydrolysis to GDP.

Nuclear Localization Signal (NLS)

A sequence rich in basic amino acids displayed on the surface of a folded protein that targets it for nuclear import via importin transport receptors.

Signal Recognition Particle (SRP)

A cytosolic ribonucleoprotein complex that binds an N-terminal ER signal sequence emerging from the ribosome, temporarily halting translation to deliver the complex to the Sec61 translocon on the ER membrane.

Sec61 Translocator

A transmembrane protein channel in the ER membrane through which nascent polypeptides are translocated into the ER lumen or integrated into the lipid bilayer.

Multipass Transmembrane Protein Topology

The spatial arrangement of a protein spanning the membrane multiple times via hydrophobic $\alpha$-helices, oriented according to charged flanking residues that dictate cytosolic or lumenal location.

Chromatin

The complex of genomic linear DNA, histone octamers, and non-histone proteins packaged within the nucleus of eukaryotic cells.

Euchromatin

A transcriptionally active, loosely packed form of chromatin where DNA is accessible to transcription factors and RNA polymerase.

Heterochromatin

A highly condensed, transcriptionally silent form of chromatin where tightly packed nucleosomes prevent gene expression.

Nucleosome

The basic repeating unit of chromatin structure, consisting of approximately $1.5$ turns of double-stranded DNA wrapped around a core octamer of histone proteins.

Histone Acetyltransferase (HAT)

An enzyme that adds acetyl groups to lysine residues on histone N-terminal tails, neutralizing their positive charge and promoting euchromatin formation.

Histone Deacetylase (HDAC)

An enzyme that removes acetyl groups from lysine residues on histone tails, restoring their positive charge and encouraging heterochromatin formation.

Histone Methyltransferase (HMT)

An enzyme that transfers methyl groups to specific lysine or arginine residues on histone tails, modulating gene expression depending on the specific residue modified.

DNA Methyltransferase

An enzyme that covalently transfers methyl groups directly to cytosine bases in DNA, typically leading to gene silencing when occurring in promoter regions.