ACS Biochemistry Exam Flashcards

Henderson-Hasselbach Equation

• pH = pKa + log ([A-] / [HA]) helps relate pH to the concentrations of acids and their conjugate bases in solution.

FMOC Chemical Synthesis

• FMOC is a protecting group used in the synthesis of amino acids on a polystyrene bead to facilitate chain elongation.

Salting Out (Purification)

• A purification technique that precipitates proteins from a solution by matching their charges to those in the solution.

Size-Exclusion Chromatography

• Technique that separates molecules by size, allowing larger molecules to elute first while smaller ones take longer.

Ion-Exchange Chromatography

• Method for separating proteins based on charge, where negatively charged DEAE and positively charged CM attract oppositely charged proteins.

Hydrophobic/Reverse Phase Chromatography

• Utilizes beads coated with carbon chains, favoring the binding of hydrophobic proteins and eluting them with non-hydrogen bonding solvents.

Affinity Chromatography

• Involves attaching a ligand to beads that binds specifically to a target protein, with the potential to elute by using harsh chemicals.

SDS-PAGE

• Utilizes SDS to denature proteins for separation based on mass in a polyacrylamide gel, visualized using Coomassie blue dye.

Sodium Dodecyl Sulfate (SDS)

• A detergent that unfolds proteins and imparts a uniform negative charge, aiding their separation during electrophoresis.

Isoelectric Focusing

• A gel electrophoresis variant where proteins migrate to their isoelectric point (pI), where they are neutral and stop moving.

FDNB (1-fluoro-2,3-dinitrobenzene)

• Reacts with N-terminus of proteins to label the first amino acid residue, enabling sequential analysis of amino acid composition.

DTT (dithiothreitol)

• A reducing agent that breaks disulfide bonds, often used in protein studies.

Iodoacetate

• Reagents that add a carboxymethyl group to free thiol (-SH) groups, effectively blocking disulfide bond formation.

Homologs, Orthologs, Paralogs

• Homologs share 25% identity between genes; orthologs are similar genes found in different organisms; paralogs are related genes within the same organism.

Ramachandran Plot

• Illustrates favorable phi-psi angle pairs in protein structures, featuring distinct regions for α-helices and β-sheets.

Glycine and Proline Ramachandran Plots

• Glycine allows for more flexibility in angle variety; proline has restricted angles due to its cyclic nature.

α-helices

• Common α-helix features include Ala prevalence, interaction every 3-4 residues, and a helical turn every 3.6 residues.

Helix Dipole

• The helix's dipolar nature arises from hydrogen bonds, with the N-terminus having a partial positive charge and the C-terminus a partial negative charge.

β-sheets

• Can be either parallel or anti-parallel; anti-parallel sheets are characterized by straight H-bonds, while parallel sheets have angled H-bonds.

β-turns

• Characterized by tight u-turns and specific phi-psi angles, often involving glycine or proline.

Circular Dichroism

• A spectroscopy method that utilizes UV light to analyze the secondary structure of proteins, indicating structural stability.

Disulfide Bonds

• Form between two thiol groups, playing a critical role in stabilizing protein secondary and tertiary structures.

α-keratin and Collagen

• α-keratin forms from coiled α-helices, while collagen consists of a repeating Gly-X-Pro sequence, forming a triple helical structure.

Hemoglobin Structure

• Hemoglobin is a tetramer (α2β2) with a cooperative binding mechanism leading to a sigmoidal oxygen binding curve.

Cooperative Protein Folding

• Characterized by sharp folding transitions, allowing proteins to revert to native states more readily.

Protein-Protein Interfaces

• Comprise a hydrophobic core and a hydrophilic fringe, aiding in protein interactions.

Binding and Regulation

• Includes concepts of homotropic and heterotropic regulation where the substrate also acts as a regulator or other factors are involved.

Michaelis-Menton Equation

• Describes enzyme kinetics with V0 = (Vmax[S])/(Km + [S]), providing insights into substrate concentration effects.

Types of Inhibition

• Competitive inhibition decreases Km while maintaining Vmax; uncompetitive decreases both; mixed inhibition alters both independently.

Ion Transport

• Ionophores facilitate the movement of ions across membranes, disrupting concentration gradients.

Carbohydrates

• Starch and glycogen serve as polysaccharide energy stores, differing in branching frequency; cellulose forms strong sheets due to β-1,4 linkages.

Nucleic Acids and Chargaff's Rule

• DNA contains a double helix structure with complementary base pairing, where the ratio of A:T and G:C is approximately equal.

DNA Forms

• A-form DNA is condensed; B-form is the standard Watson-Crick model; Z-form is a left-handed helix with distinct structural properties.