Protein Structure and Function Flashcards

Vocabulary practice flashcards covering fundamental biochemistry concepts including amino acid properties, protein structure, folding mechanics, enzyme kinetics, and regulatory mechanisms.

Proteins

Linear polymers of $\alpha$-amino acids joined by peptide bonds, synthesized from the N-terminus to the C-terminus.

$\alpha$-Amino Acid

An amino acid in which both the amino group and carboxylic acid group are attached to the same carbon atom.

Zwitterion

A dipolar molecule containing both positively and negatively charged functional groups that cancel each other out, such as an amino acid at pH $7$.

Hydrophobic Effect

The entropically driven exclusion of non-polar solutes from aqueous media, serving as a primary driver of protein folding.

Chaperone Proteins

Proteins that assist in the proper folding of newly synthesized or partially folded proteins to prevent misfolding.

Christian Anfinsen

Biochemist who demonstrated using Ribonuclease A and urea that a protein's primary structure contains all the information required for proper folding.

Native State

The lowest energy, single stable functional conformation into which a protein folds.

$\alpha$-Helix

A common secondary structure motif containing $3.6$ residues per turn with side chains pointing outward, stabilized by hydrogen bonding between NH and carbonyl CO groups $4$ positions away.

$\beta$-Pleated Sheet

A secondary structure consisting of parallel or anti-parallel strands stabilized by hydrogen bonding between peptide backbones.

Linus Pauling

Biochemist known as the Father of Structural Biochemistry who proposed the $\alpha$-helix and $\beta$-sheet secondary structures of proteins.

Hydrophobic $\alpha$-Helix

An $\alpha$-helical segment of $18\text{--}22$ amino acids sufficient to traverse the lipid bilayer of the plasma membrane.

Coiled-Coil

A structural motif formed between $\alpha$-helices featuring heptad repeats with aligned hydrophobic side chains facing inwards.

Protein Domain

A stable region of a protein consisting of $\alpha$-helices and $\beta$-sheets that can fold independently into a functional unit.

Immunoglobulin Fold

A structural fold consisting of two $\beta$-sheets (one with $5$ strands and another with $3$) connected by disulfide bridges.

GEF (Guanine Nucleotide Exchange Factor)

A regulatory protein that turns ON G-proteins/small GTPases by stimulating the exchange of GDP for GTP.

GAP (GTPase-Activating Protein)

A regulatory protein that turns OFF G-proteins/small GTPases by facilitating the hydrolysis of bound GTP to GDP.

Elongation Factor Tu (EF-Tu)

A prokaryotic GTPase switch protein that escorts aminoacyl-tRNA to the A site of the ribosome.

SH3 Domain

A protein domain that binds proline-rich sequences, inducing a kink in the target protein structure.

Prions

Infectious misfolded proteins that assemble into stacked $\beta$-sheet amyloid fibers and cause cytotoxicity.

hsp70

A heat shock chaperone protein that binds to exposed non-polar amino acid residues to prevent misfolding and aggregation.

Ubiquitin

A $76$-amino acid protein covalently attached to the $\varepsilon$-amino group of lysine residues to target proteins for degradation.

Aspartate Carbamoyltransferase

An enzyme controlled by negative allosteric feedback regulation that governs pyrimidine biosynthesis.

Lineweaver-Burk Plot

A double-reciprocal plot of enzyme kinetics where the y-intercept corresponds to $\frac{1}{V_{\max}}$ and the x-intercept corresponds to $-\frac{1}{K_M}$.