Protein Biochemistry and Proteomics - Flashcards

Flashcards covering key vocabulary and concepts from the lecture notes on protein biochemistry and proteomics.

Importance of Protein Properties and Structures:

Proteins play a critical role in all living organisms and are involved in numerous biological processes such as enzymatic catalysis, transport, and signaling.

Three Main Classes of Proteins:

Globular proteins, fibrous proteins, and membrane proteins.

Globular Proteins:

Spherical/round shape, polar amino acid side chains on the exterior surface, nonpolar amino acid side chains on the interior surface, water-soluble, function in catalysis, transport, and the immune system.

Membrane Proteins:

Shape depends on the function needed, amphiphilic polarity, low water solubility, function in communication, structure, transport, and signaling.

Fibrous Proteins:

Elongated shape, nonpolar in nature, insoluble in water, provide structure, connection, and protection.

Amino Acid Side Chains:

The side chains vary in size, charge, hydrophobicity, and polarity, influencing the chemical and physical properties of the amino acid.

Amino Acid Sequence:

The sequence of amino acids determines the final three-dimensional structure of the protein.

Size limits of Polypeptides:

Polypeptides must be at least 40 residues long to maintain a stable fold. Polypeptides with well over 1,000 residues approach the limits of efficiency for the protein synthetic machinery

Peptide Group:

Has a rigid planar structure due to its resonance interactions, giving the peptide bond 40% double bond characteristics.

Trans vs Cis Conformation:

Trans conformation is much more stable due to less steric hindrance between adjacent neighboring atoms. Proline amino acids reduce steric interference and 10% of Pro amino acids are cis.

Steric Interference in Polypeptide Backbone:

The rotation around the Cα¬N and Cα¬C bonds to form certain combinations of phi and psi angles will cause the amide hydrogen, the carbonyl oxygen, or the substituents of C of adjacent residues to collide.

Primary Structure:

The sequence of amino acids in a polypeptide.

Secondary Structure:

Local folding of the polypeptide chain, which results from hydrogen bonding between nearby amino acids.

Alpha Helices Properties:

α helices have 3.6 residues per turn, an H-bond between C=O and N-H of the (N+4)th residue, are right-handed, and have a pitch of 5.4 Å.

Beta Pleated Sheets:

Antiparallel sheets have dihedral angles (φ, ψ) of (–140°, 135°), while parallel sheets have dihedral angles (φ, ψ) of (–120°, 115°).

Collagen structure:

Forms a triple helix structure and is found in all multicellular animals. It is the most abundant protein in vertebrates and primary stress-bearing elements in connective tissues.

Tertiary Structure:

The overall three-dimensional structure of a polypeptide chain, determined by the interactions between amino acid side chains and the surrounding environment.

Interactions Determining Tertiary Structure:

Hydrophobic interactions, hydrogen bonds, disulfide bonding, ionic bonds, and van der Waals interactions.

Quaternary Structure:

The arrangement of multiple polypeptide chains, each with its own tertiary structure, into a multi-subunit protein.

Association of Subunits:

Subunits associate non-covalently, like single subunits, with non-polar residues on the inside, and stabilized by hydrogen bonds and, in some cases, disulfide bonds.

Factors Influencing Protein Stability:

The hydrophobic effect and electrostatic interactions.

Types of Membrane Proteins:

Integral membrane proteins, lipid-linked proteins, and peripheral membrane proteins.

Integral Membrane Proteins:

Contain a transmembrane structure consisting of α helices or a β barrel with a hydrophobic surface.

Lipid-Linked Proteins:

Have a covalently attached prenyl group, fatty acyl group, or glycosylphosphatidylinositol group.

Peripheral Membrane Proteins:

Interact noncovalently with proteins or lipids at the membrane surface.