Amino Acids, Peptide Bonds, and Protein Structure & Stability

Comprehensive practice flashcards covering amino acid structures and ionization properties, titration curves, peptide bond formation, ribosomal protein translation, secondary structure geometry, Ramachandran diagrams, and the thermodynamic principles of protein stability and folding.

What are the four common substituents attached to the central chiral carbon in the general amino acid structure?

The central $\alpha$-carbon ($\text{C}_\alpha$) is covalently bonded to an $\alpha$-amino group, an $\alpha$-carboxyl group, a hydrogen atom, and a variable R-group (side chain) that confers unique chemical properties.

Which of the 20 standard amino acids contains an achiral $\alpha$-carbon?

Glycine ($\text{Gly}$, $\text{G}$), because its R-group is a second hydrogen atom ($\text{--H}$), making the $\alpha$-carbon symmetrical.

Which stereoisomeric configuration of amino acids is exclusively found in ribosomally synthesized proteins?

Only $\text{L}$-amino acids ($\text{L}$-enantiomers) are incorporated into proteins during translation.

How does a polarimeter distinguish between enantiomeric compounds?

It measures the rotation of plane-polarized light: molecules that rotate the light clockwise are dextrorotatory, while those that rotate it counterclockwise are levorotatory.

What reference molecule is used in the Fischer convention to assign $\text{D}$ and $\text{L}$ configurations to amino acids?

Glyceraldehyde (specifically comparing the spatial orientation of functional groups around the chiral center to $\text{L}$-glyceraldehyde and $\text{D}$-glyceraldehyde).

Why is proline referred to as a conformationally restricted amino acid and a secondary structure 'helix breaker'?

Proline's aliphatic side chain forms a covalent ring bonded back to its $\alpha$-amino nitrogen, creating a rigid cyclic structure that kinks the polypeptide chain and leaves no amide hydrogen available for backbone hydrogen bonding.

Why is methionine classified as a nonpolar amino acid despite containing an electronegative sulfur atom?

The electronegativity of the sulfur atom is masked by flanking hydrocarbon groups in a thioether linkage ($\text{--CH}_2\text{--CH}_2\text{--S--CH}_3$).

Why is histidine unique among basic polar amino acids at physiological $\text{pH}$ (~$7.0$)?

Histidine's imidazole side chain has a $\text{p}K_{\text{a}} \approx 6.0$, which is close to physiological $\text{pH}$, allowing it to exist in an active equilibrium of protonated (positively charged) and deprotonated (neutral) forms.

What are the approximate average $\text{p}K_{\text{a}}$ values for the $\alpha$-carboxyl and $\alpha$-amino groups of free amino acids?

The average $\alpha$-carboxyl group $\text{p}K_{\text{a}}$ is $\sim 2.2$, and the average $\alpha$-amino group $\text{p}K_{\text{a}}$ is $\sim 9.5$.

What is the ionization state and net charge of a simple neutral amino acid (e.g., alanine) at physiological $\text{pH}$ (~$7.0$)?

It exists as a zwitterion with a net charge of $0$: the $\alpha$-carboxyl group is deprotonated and negatively charged ($\text{--COO}^-$), while the $\alpha$-amino group is protonated and positively charged ($\text{--NH}_3^+$).

What is the Henderson-Hasselbalch equation, and what condition occurs at an inflection point (plateau) of a titration curve?

$\text{pH} = \text{p}K_{\text{a}} + \log\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)$; at the inflection point, half the weak acid is neutralized ($[\text{A}^-] = [\text{HA}]$), meaning $\log(1) = 0$ and $\text{pH} = \text{p}K_{\text{a}}$.

In the shown titration curve of glutamate, what does point 3 represent, and how is it related to net charge?

Point 3 represents the isoelectric point ($\text{pI}$) at $\text{pH} = 3.22$, where the molecule possesses an overall net charge of zero.

How is the isoelectric point ($\text{pI}$) calculated for an acidic amino acid with three ionizable groups, such as glutamate ($\text{p}K_1 = 2.19$, $\text{p}K_{\text{R}} = 4.25$, $\text{p}K_2 = 9.67$)?

It is calculated by averaging the two $\text{p}K_{\text{a}}$ values that border the zwitterionic (neutral) species: $\text{pI} = \frac{\text{p}K_1 + \text{p}K_{\text{R}}}{2} = \frac{2.19 + 4.25}{2} = 3.22$.

What reaction forms a peptide bond, and which functional groups are joined?

A dehydration (condensation) reaction that eliminates $\text{H}_2\text{O}$, joining the $\alpha$-carboxyl carbon of one amino acid to the $\alpha$-amino nitrogen of the incoming amino acid.

What gives the peptide bond its planar geometry and prevents free rotation about the $\text{C--N}$ bond?

Resonance delocalization between the carbonyl double bond and the amide nitrogen gives the peptide $\text{C--N}$ bond approximately $40\%$ double-bond character.

What are the structural features and bond lengths of the planar trans-peptide group shown?

Six atoms lie in the amide plane ($\text{C}_\alpha$, $\text{C}$, $\text{O}$, $\text{N}$, $\text{H}$, and the adjacent $\text{C}_\alpha$); the peptide $\text{C--N}$ bond length is $1.33\,\text{Å}$ and the carbonyl $\text{C=O}$ bond length is $1.24\,\text{Å}$.

What enzyme charges a tRNA with its specific amino acid, and what high-energy intermediate is formed?

Aminoacyl-tRNA synthetase; it hydrolyzes $\text{ATP}$ to form an aminoacyl-AMP intermediate before transferring the amino acid to the $3'$ CCA end of the tRNA.

What are the primary structural arms of the tRNA cloverleaf shown in the diagram?

The amino acid acceptor arm ($3'$ CCA end), the D arm (containing dihydrouridine residues), the anticodon arm (with the wobble position), the extra/variable arm, and the $\text{T}\psi\text{C}$ arm (containing thymidine, pseudouridine, and cytidine).

What catalyzes peptide bond synthesis within the ribosome during translation?

The peptidyl transferase activity of the ribosomal RNA (rRNA) in the large ribosomal subunit, functioning as a ribozyme.

How many GTP molecules are hydrolyzed per elongation cycle during ribosomal protein synthesis?

Two $\text{GTP}$ molecules: one by EF-Tu to promote binding of the aminoacyl-tRNA to the A site, and one by EF-G to facilitate ribosome translocation in the $5' \rightarrow 3'$ direction.

Which backbone torsion angles are represented by Phi ($\phi$) and Psi ($\psi$)?

Phi ($\phi$) is the torsion angle around the $\text{N}_\text{amide}\text{--C}_\alpha$ bond, and Psi ($\psi$) is the torsion angle around the $\text{C}_\alpha\text{--C}_\text{carbonyl}$ bond.

What fundamental constraint does the Ramachandran Principle describe regarding polypeptide conformations?

Steric collisions between non-bonded atoms prevent the backbone from adopting most combinations of $\phi$ and $\psi$ angles, leaving only small, specific allowed regions that correspond to regular secondary structures.

Why is the allowed conformational space for proline on a Ramachandran diagram restricted to a narrow vertical region around $\phi = -60^\circ$?

The covalent ring formed by the proline side chain with its $\alpha$-amino group restricts rotation about the $\text{N--C}_\alpha$ bond, locking $\phi$ to $-60^\circ \pm 25^\circ$.

What are the key repeating dimensional values and hydrogen-bonding scheme of a standard $\alpha$-helix?

An $\alpha$-helix has $3.6$ residues per turn, a translation pitch of $5.4\,\text{Å}$ per turn, and intrachain hydrogen bonds between the carbonyl oxygen of residue $n$ and the amide hydrogen of residue $n+4$.

Why does an $\alpha$-helix possess a significant macrodipole moment?

Each peptide bond has an individual dipole from resonance; because the intrastrand hydrogen bonds align all peptide units in the same orientation, their dipoles sum to create a partial positive charge ($\delta^+$) at the N-terminus and a partial negative charge ($\delta^-$) at the C-terminus.

How does an amphipathic $\alpha$-helix arise from an amino acid sequence?

Hydrophobic and hydrophilic residues alternate every $3$ to $4$ amino acids along the primary sequence, placing nonpolar side chains on one face of the cylinder and polar side chains on the opposite face.

How do parallel and antiparallel $\beta$-sheets differ in their interstrand hydrogen-bonding geometry?

In antiparallel $\beta$-sheets, adjacent strands run in opposite directions and hydrogen bonds are straight and perpendicular to the strands; in parallel $\beta$-sheets, strands run in the same direction and hydrogen bonds are slanted.

In the $\beta$-turn structures shown, why is glycine strongly favored at residue $i+2$ in a Type II turn?

In a Type II $\beta$-turn, any residue with an R-group larger than hydrogen at position $i+2$ would cause severe steric clash with the carbonyl oxygen of residue $i+1$.

How does a $3_{10}$-helix differ from a standard $\alpha$-helix?

A $3_{10}$-helix is a tighter, narrower spiral with $3.0$ residues per helical turn and $10$ atoms in the hydrogen-bonded ring ($n \rightarrow n+3$ hydrogen bonding), compared to $3.6$ residues and $13$ atoms in an $\alpha$-helix.

What is the primary thermodynamic driving force for tertiary folding of globular proteins in aqueous solutions?

The hydrophobic effect: nonpolar amino acid side chains collapse into the interior core to minimize the unfavorable ordering (loss of entropy) of water molecules in surrounding clathrate cages.

Why do ionic bonds (salt bridges) contribute relatively little net free energy to the stability of a folded protein?

The free energy gained by forming an internal ionic bond is largely offset by the loss of favorable hydration interactions that the charged side chains make with water in the unfolded state.

What are the three proposed theoretical models of protein folding pathways?

1. Hydrophobic collapse model (clustering of nonpolar side chains forms a core that drives secondary/tertiary structure). 2. Framework model (local secondary structures form independently before assembling). 3. Nucleation model (a localized correct tertiary structure acts as a seed for surrounding elements).

What is the definition of the protein melting temperature ($T_{\text{m}}$), and what is its value in the thermal denaturation curve shown?

$T_{\text{m}}$ is the midpoint of the thermal denaturation transition where $50\%$ ($0.50$ fraction) of the protein is unfolded; in the shown curve, $T_{\text{m}} \approx 30\,^\circ\text{C}$.

Why is protein denaturation described as a cooperative process?

Disruption of stabilizing interactions in one region destabilizes the rest of the structure, resulting in a sharp, all-or-none transition with virtually no stable partially folded intermediates.

How do molecular chaperones, such as the E. coli GroEL/GroES complex, facilitate protein folding?

They bind unfolded or misfolded polypeptides in a sheltered central cavity and use the energy of ATP binding and hydrolysis to allow folding without hydrophobic aggregation.

What is the structural difference between apomyoglobin and holomyoglobin shown in the figure?

Apomyoglobin is the polypeptide chain lacking its bound prosthetic group, whereas holomyoglobin is the fully assembled, functional complex containing both the globin protein and the bound iron-protoporphyrin IX (heme) group.

How do post-translational modifications (PTMs) impact cellular proteomic diversity relative to the genome?

While the human genome contains approximately $20{,}000\text{--}25{,}000$ genes and $\sim 100{,}000$ mRNA transcripts, diverse PTMs (e.g., phosphorylation, acetylation, carboxylation) expand the functional proteome to over $1{,}000{,}000$ unique proteins.