BIO NMDCAT

Protein function depends on proper folding into the native three-dimensional structure.

The oxidizing environment of the endoplasmic reticulum promotes the formation of disulfide bonds in secreted and membrane proteins.

The Val-6 substitution creates a hydrophobic patch on deoxyhemoglobin, leading to polymerization and sickling of red blood cells.

Domains are independently folded regions within a single polypeptide and are part of tertiary structure.

Resonance restricts rotation around the peptide bond, making these six atoms coplanar.

The C-peptide connects the A and B chains in proinsulin and is removed to form mature insulin.

The φ (phi) and ψ (psi) angles define backbone conformation in proteins.

These repetitive sequences allow close packing of antiparallel β-sheets.

Binding of oxygen to one subunit increases affinity of the remaining subunits.

Collagen contains the repeating sequence Gly-X-Y. Glycine occurs every third residue, allowing tight packing of the triple helix.

The α-carbon of 19 of the 20 standard amino acids is attached to four different groups, making it a chiral center. With very rare exceptions, ribosomes exclusively incorporate amino acids with the L-configuration into proteins. Glycine has two hydrogens and is thus achiral.

At the isoelectric point (pI), the amino group is protonated (-NH₃⁺) and the carboxyl group is deprotonated (-COO⁻). The molecule carries equal positive and negative charges, making it electrically neutral overall, termed a zwitterion.

The pI is the pH where the net charge on the amino acid is zero. At this pH, the molecule is a zwitterion and will not move towards either the anode or cathode during electrophoresis. For neutral amino acids, pI is the average of pKₐ₁ and pKₐ₂.

A carbon atom must be bonded to four different groups to be chiral. The α-carbon of glycine is bonded to an amino group, a carboxyl group, and two hydrogen atoms. Since two substituents are identical, it is not a chiral center, and glycine is optically inactive.

The thiol (-SH) group of cysteine's side chain can be oxidized to form a covalent disulfide bond (-S-S-) with another cysteine residue. This bond is critical for stabilizing the tertiary structure of secreted proteins like insulin and immunoglobulins. Methionine contains sulfur but cannot form disulfide bridges.

In proline, the R-group forms a pyrrolidine ring by bonding back to the amide nitrogen. This cyclization eliminates the amide hydrogen needed for H-bonding in an α-helix and imposes a rigid, fixed kink in the polypeptide backbone, disrupting the regular helical conformation.

Complete acid hydrolysis (e.g., 6M HCl at 110°C for 24 hours) cleaves all peptide bonds in a protein, releasing the constituent free amino acids. Partial hydrolysis yields smaller peptides (di-, tri-, and oligopeptides).

Primary structure is the linear, genetically determined sequence of amino acids in a polypeptide chain, held together by covalent peptide bonds. This sequence dictates all higher levels of protein structure.

Peptide bond formation is a dehydration synthesis. The carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH₂) of another, releasing a water molecule (H₂O) and forming a covalent amide linkage (-CO-NH-).