Cell Chemistry and Protein Structure

Vocabulary flashcards covering cellular chemistry, protein structural organization, amino acid classification, protein folding, interaction networks, and protein misfolding conditions.

Keratin

A structural protein that makes up biological structures such as hair and nails.

Primary Structure

The specific linear sequence of amino acids in a polypeptide chain that determines a protein's ultimate three-dimensional shape.

Secondary Structure

Local folded structures within a polypeptide formed by hydrogen bonding along the protein backbone, including ̑\alpha-helices and $\beta$-pleated sheets.

$\alpha$-helix

A coiled secondary protein structure maintained by backbone hydrogen bonds, featuring $3.6$ amino acid residues per turn.

$\beta$-pleated sheet

A pleated secondary protein structure stabilized by hydrogen bonds between adjacent polypeptide strands, with a repeating distance of $7.0\,\text{\AA}$.

Tertiary Structure

The overall three-dimensional folded conformation of a single polypeptide chain, driven by interactions among side chain (R) groups.

Quaternary Structure

The spatial arrangement and noncovalent or covalent interactions between multiple polypeptide subunits in a multi-subunit protein complex.

Ionic Bond

A noncovalent electrostatic attraction occurring between full positive and negative charges on amino acid side chains or ions.

Hydrogen Bond

A noncovalent interaction between partial positive charges on hydrogen atoms and partial negative charges on electronegative atoms like oxygen or nitrogen.

Hydrophobic Interactions

The aggregation of nonpolar side chains in aqueous environments to minimize exposure to polar water molecules.

van der Waals Forces

Weak attractive forces between nonpolar atoms or molecules that operate when atoms come into very close proximity.

Polar Charged Amino Acids

Amino acids with side chains that carry a full charge at physiological $\text{pH} = 7$, including Glutamic acid (Glu), Aspartic acid (Asp), Lysine (Lys), Arginine (Arg), and Histidine (His).

Polar Uncharged Amino Acids

Hydrophilic amino acids whose side chains can form hydrogen bonds but do not carry a net charge at physiological $\text{pH}$, including Serine (Ser), Threonine (Thr), Glutamine (Gln), Asparagine (Asn), and Tyrosine (Tyr).

Nonpolar Amino Acids

Hydrophobic amino acids with nonpolar side chains that participate in hydrophobic interactions and van der Waals forces, including Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Methionine (Met), Phenylalanine (Phe), and Tryptophan (Trp).

Glycine

The smallest amino acid whose R group is a single hydrogen atom, allowing it to fit into tight spaces and accommodate sharp turns in polypeptide chains.

Proline

A hydrophobic amino acid containing a cyclic side chain structure that introduces sharp kinks or bends into a polypeptide chain.

Cysteine

An amino acid bearing a reactive sulfhydryl ($\text{-SH}$) group capable of undergoing oxidation to form covalent disulfide bonds.

Disulfide Bond

A covalent bond ($\text{-S-S-}$) formed oxidationally between the sulfhydryl groups of two cysteine residues, stabilizing protein conformation in oxidizing environments.

Soluble Proteins

Proteins dissolved in aqueous cellular compartments that typically present hydrophilic side chains on their exterior surface and hydrophobic residues within their core.

X-ray Crystallography

An experimental technique used to resolve high-resolution 3D tertiary protein structures by analyzing diffracted X-rays passed through a protein crystal.

Nuclear Magnetic Resonance (NMR) Spectroscopy

A structural biology method that determines dynamic, solution-state three-dimensional protein structures without requiring crystallization.

Protein Domain

A distinct, independently folding structural module within a polypeptide that performs a specific function and can be evolutionary shuffled.

SH3 Domain

A protein interaction module present in more than $200$ signaling proteins that binds specifically to proline-rich sequences.

Hub Proteins

Highly connected proteins in interactome networks that bind to multiple different protein partners.

Denaturation

The unfolding and loss of a protein's functional native tertiary or secondary structure caused by disruption of noncovalent bonds and disulfide bridges.

Renaturation

The refolding of a denatured protein back into its native, biologically active conformation upon removal of denaturing chemicals.

Urea

A chemical denaturing agent that interferes with hydrogen bonds and noncovalent interactions in proteins, causing them to unfold.

Mercaptoethanol

A chemical reducing agent used to cleave covalent disulfide bonds in proteins by reducing them to sulfhydryl groups.

Amyloid Precursor Protein (APP)

A membrane protein cleaved by $\beta$-secretase and $\gamma$-secretase to produce $A\beta 40$ and $A\beta 42$ peptides, the latter of which misfolds and aggregates into amyloid plaques in Alzheimer's disease.

Sickle Cell Anemia

A condition caused by a single amino acid substitution in hemoglobin from a polar glutamic acid to a nonpolar valine, leading to hydrophobic aggregation and sickle-shaped red blood cells.