UWorld Biochemistry: Amino Acids Quiz #2

• At pH 7, amino acids are assumed to be in their zwitterionic form.
• Western blots employ SDS-PAGE to denature proteins, ensuring separation solely based on size.
• Increased pH that activates an ion channel often means a deprotonated negatively charged molecule triggers the opening.
• Ionizable molecules possess a pKa and can either gain or lose a proton based on pH.
• Solution pH affects a protein's charge acquisition or loss, without altering its pI.
• Kinases catalyze phosphate group transfers from nucleotide triphosphates (ATP, GTP) to other molecules or between phosphorylated molecules and nucleotide diphosphates (ADP, GDP).
• Negatively charged ionizable residues like aspartate and glutamate decrease pI, while positively charged ones like lysine and arginine increase it.
• Proline disrupts α-helices by forming a ring with the backbone nitrogen, inhibiting hydrogen bond donation, unlike bulky amino acids such as tryptophan.
• Proline and glycine disrupt α-helices and are not commonly found within them.
• Protein folding is essential for function; heat and urea disrupt noncovalent interactions, leading to denaturation.
• At a pH higher than an amino acid’s pKa, most side chains are deprotonated and neutral, but a small percentage remain protonated and positively charged if the protonated form carries a positive charge (e.g., His, Lys, Arg)
• Peptide bond nitrogen atoms are trigonal planar due to resonance with the carbonyl, flattening the geometry.
• Only amino acids with ionizable side chains, like glutamate or lysine, contribute to pH-dependent charge changes—so when calculating pH ranges using the Henderson-Hasselbalch equation, focus only on those with ionizable R groups.
• Secondary amino acids like proline have a unique ring structure that connects back to the backbone, making them ideal for rigid turns or fixed positioning between other amino acids.
• Proline is the only secondary amino acid, and its ring structure makes it rigid and less flexible compared to other amino acids.

Protein structures

• Secondary structures, such as α-helices or β-sheets, are formed by nearby residues.
• Tertiary structure: The overall 3D folding results from interactions between distant amino acid side chains and secondary structures.
• Tertiary structure is maintained by noncovalent bonds between side chains, but can include disulfide bonds.
• Ternary complexes consist of three molecules bound together, usually including a protein, which may assemble in a specific or random order.
• Binding to pre-existing complex suggests an ordered mechanism.
• SDS-PAGE denatures proteins, coats them with a negative charge for size-based separation; reducing agents break disulfide bonds.
• Multimeric proteins analyzed by reducing SDS-PAGE lose quaternary structure and run as monomers.
• Similar amino acid sequences result in similar tertiary structures due to their influence on protein folding.
• Refolding can occur as long as the primary structure (amino acid sequence) is still intact because it contains all the information needed to rebuild the protein’s correct shape.
• Tertiary structure is about how distant regions of a protein fold and interact.
• Monomeric proteins only go up to tertiary structure.
• Multimeric proteins can have quaternary structure (interaction between subunits).

Geometry

• Tetrahedral geometry occurs when an atom has four electron domains (bonding pairs or lone pairs) arranged as far apart as possible in 3D space (e.g., sp³ hybridized carbon atoms).
• Trigonal pyramidal geometry occurs when an atom has three bonding pairs and one lone pair that is not involved in resonance (e.g., nitrogen in NH₃).
• T-shaped geometry results from five electron domains around an atom, with three bonding pairs and two lone pairs (common in some halogen compounds).

Techniques

• High-performance liquid chromatography (HPLC) is a good technique for separating and quantifying small organic molecules such as amino acids and peptides.
• Spectrophotometry measures how much light a substance absorbs at a specific wavelength, but it cannot distinguish between different molecules that absorb at the same wavelength.

Binding Affinity

• Small Kd indicates high affinity via a low tendency to break apart the complex.
• Larger Kd = Lower Affinity
• Smaller Kd = Higher Affinity
• Porphyrin rings consist of four pyrrole rings, forming a stable, flat structure that holds a metal ion like iron in heme.
• Hydrophobic interactions primarily drive tertiary structure, pulling nonpolar side chains to the core; disrupting these interactions causes unfolding.
• Alpha helices are classified as secondary structure but are included within the tertiary structure's overall shape.
• Positive ΔG indicates a non-spontaneous reaction, weak binding, and high Kd.
• Negative ΔG indicates a spontaneous reaction, strong binding, and low Kd.
• Large Kd means weak binding and corresponds to a positive ΔG.
• Small Kd means strong binding and corresponds to a negative ΔG.
• A molecule that stays intact despite a spontaneous reaction being possible is doing so because the reaction is kinetically slow, not because it's thermodynamically unfavorable.
• Equilibrium membrane potential depends on the concentration gradient of ions across the membrane.
• Allosteric regulation is a molecule binding to one site on a protein and causing a functional change at a different site.
• More negative side chains → lower pI
• More positive side chains → higher pI
• Unbound + open = highest ΔG (least stable)
• Bound + open = lower ΔG
• Bound + closed (desensitized) = lowest ΔG (most stable)

Signaling

• Cells communicate through chemical signals called hormones. Hydrophilic molecules such as peptide hormones cannot cross the cell membrane and require second messengers.
• Steroid hormones are hydrophobic molecules derived from cholesterol that share a characteristic structure of four fused rings—three 6-membered and one 5-membered—and can cross the cell membrane to signal without the need for second messengers.
• Positive regulators enhance protein function by increasing activity, such as boosting ion flow through channels, which is reflected by a higher electric current.

Miscellaneous

• Permeant refers to ions capable of passing through a channel.
• Impermeant refers to ions incapable of passing through a channel.
• Glutamine and asparagine both have amide groups and can release ammonia through deamidation in the urea cycle.
• Hydrophobic residues often drive protein-protein binding by avoiding water.
• Enzymes only work when they are properly folded so more folded = more active = higher reaction rate

Cell cycle:

• G₀ (Resting phase): Cell is not dividing.
• G₁ (Growth 1): Cell grows and produces proteins
• S (Synthesis): Cell replicates its DNA.
• G₂ (Growth 2): Cell checks DNA and prepares to divide.
• M (Mitosis): Cell divides into two cells.
• Ubiquitination involves attaching ubiquitin to a protein, typically at a lysine residue, signaling its degradation by the proteasome.
• Peptide bond nitrogen atoms are trigonal planar due to resonance with the carbonyl, reducing the lone pair to part of a pi bond and flattening the geometry.