Protein Properties and Structure Lecture Notes

Flashcards covering protein classification, hierarchy of structure, stability factors, and specific membrane protein types based on the lecture transcript.

Primary structure

The simplest level of protein structure, defined as the precise sequence of amino acids in a polypeptide chain as dictated by the genetic code.

Secondary structure

Locally folded patterns of the polypeptide chain, such as alpha helices and beta sheets, resulting from hydrogen bonding between nearby amino acids.

Tertiary structure

The comprehensive three-dimensional conformation of an individual protein molecule, determined by interactions between amino acid side chains and the surrounding environment.

Quaternary structure

The spatial arrangement and organization of multiple protein molecules (subunits) into functional assemblies.

Fibrous proteins

Proteins generally composed of long, narrow strands with structural roles, such as keratin and collagen, providing connection and protection.

Globular proteins

Proteins with a compact, rounded shape and functional roles like catalysis or transport, typically having polar side chains on the exterior and nonpolar on the interior.

Membrane proteins

Proteins integrated into or associated with the cell membrane, including integral, transmembrane, lipid-linked, and peripheral types.

Peptide bond

A rigid, planar structure with $40\%$ double bond characteristics due to resonance interactions between amino acids.

Alpha helix

A right-handed coil secondary structure with $3.6$ residues per turn and a pitch of $5.4\,\text{\AA}$, stabilized by hydrogen bonds between the C=O group of one residue and the N-H group of the $(n+4)$ th residue.

Beta sheet

A secondary structure consisting of adjacent polypeptide strands (parallel or antiparallel) linked by hydrogen bonds, forming a pleated appearance.

Collagen

A triple-helix fibrous protein and the most abundant protein in vertebrates, serving as the primary stress-bearing element in connective tissues like bone and teeth.

Scurvy

A condition resulting from vitamin C deficiency, which prevents prolyl hydroxylase from converting proline to hydroxyproline, thus weakening collagen synthesis.

Hydrophobic effect

The major determinant of native protein structure and stability, where nonpolar side chains aggregate in the interior to minimize contact with water and increase solvent entropy.

Hydropathy

A measure of the combined hydrophobic and hydrophilic tendencies of amino acids, used to predict which portions of a polypeptide are buried or exposed.

Ion pair (salt bridge)

The electrostatic association between two protein groups of opposite charge, such as Lysine and Aspartic acid, typically found on the protein surface.

Zinc fingers

Small protein domains, often found in nucleic acid-binding proteins, that are stabilized by one or two $Zn^{2+}$ ions tetrahedrally coordinated by Cys, His, Asp, or Glu residues.

Chaotropic agents

Ions or small organic molecules like urea or guanidinium ion that increase the solubility of nonpolar substances in water and denature proteins by disrupting hydrophobic interactions.

Renaturation

The spontaneous refolding of a denatured protein into its native, enzymatically active conformation, as demonstrated by the RNase A experiment.

Integral membrane proteins

Amphiphilic proteins firmly bound to the membrane through hydrophobic interactions, often containing transmembrane alpha helices or beta barrels.

Peripheral membrane proteins

Extrinsic proteins that associate noncovalently with the membrane surface via electrostatic and hydrogen-bonding interactions and can be detached by gentle salt or pH changes.

Prenylated proteins

Lipid-linked proteins containing isoprene units, such as farnesyl ($C_{15}$) or geranylgeranyl ($C_{20}$), attached via a thioether linkage to a Cysteine sulfur atom.

Myristoylation

A stable, nonreversible modification where myristic acid is bonded to the N-terminal of an amino acid.

Palmitoylation

A reversible lipid modification (S-palmitoylation or O-palmitoylation) where palmitic acid is bonded to Cysteine, Serine, or Threonine residues.

GPI-linked proteins

Proteins located exclusively on the exterior face of the plasma membrane, anchored by a glycosylphosphatidylinositol structure consisting of mannose, glucosaminyl, and phosphoethanolamine.

Beta barrels

Transmembrane structures composed of 8 to 22 antiparallel beta strands, common in channel-forming proteins called porins found in Gram-negative bacteria.

Protomers

Identical subunits within a protein that has a quaternary structure consisting of multiple polypeptide chains.

Cis and Trans conformation

The two spatial arrangements of the peptide bond relative to alpha-carbon atoms; most bonds are trans to avoid steric hindrance, though $10\%$ of Proline residues may be cis.