Amino Acids, Peptides, and Protein Structure

Flashcards covering amino acid structures, pKa values, ionization states, peptide bonds, and protein properties.

Which amino acid is non-chiral because it lacks an R group side chain?

Glycine

What is the second smallest nonpolar aliphatic amino acid?

Alanine

Why is proline considered the most rigid amino acid?

Because of its cyclic structure.

What wavelength of UV light is typically absorbed by aromatic amino acid side chains?

$$\sim 280\,\text{nm}$$

How does the side chain of glutamine structurally compare to asparagine?

Glutamine is $1$ carbon longer than asparagine.

What is the $\text{p}K_a$ of the cysteine side chain thiol group?

$$8.4$$

What molecule is formed when two cysteine residues undergo oxidation to form a disulfide bond?

Cystine (along with $\text{H}_2\text{O}$)

What type of chemical agent converts a cystine disulfide bond back into two cysteine thiol groups?

A reducing agent

What structural protein in hair contains a high percentage of cysteine residues that allow shape modification via reduction and oxidation?

Keratin

What is the side chain $\text{p}K_a$ of aspartate (Asp, D)?

$$3.9$$

What is the side chain $\text{p}K_a$ of glutamate (Glu, E)?

$$4.1$$

In the titration curve of glutamate, what are the values of $\text{p}K_1$, $\text{p}K_R$, and $\text{p}K_2$?

$\text{p}K_1 = 2.19$, $\text{p}K_R = 4.25$, and $\text{p}K_2 = 9.67$

What is the side chain $\text{p}K_a$ of lysine (Lys, K)?

$$10.5$$

Why is lysine commonly found in proteins that interact with DNA?

Lysine is positively charged, whereas DNA is negatively charged.

What functional group is present in the side chain of arginine?

Guanidinium

What is the side chain $\text{p}K_a$ of arginine (Arg, R)?

$$12.5$$

What ring structure forms the side chain of histidine?

Imidazole

What is the side chain $\text{p}K_a$ of histidine (His, H)?

$$6.0$$

At physiological $\text{pH} = 7.0$, what proportion of histidine side chains are protonated versus neutral?

Approximately $10\%$ protonated and $90\%$ neutral.

What amino acids are referred to as the "21st" and "22nd" amino acids?

Selenocysteine (21st) and Pyrrolysine (22nd)

Which three amino acid residues are commonly modified by phosphorylation?

Tyrosine (pTyr), Serine (pSer), and Threonine (pThr)

Which amino acid side chain is modified by acetylation?

Lysine (Lys)

Which two amino acid side chains are modified by methylation?

Lysine (Lys) and Arginine (Arg)

What is the typical $\text{p}K_a$ of an amino acid's $\alpha$-carboxyl group?

$$\sim 2$$

What is the typical $\text{p}K_a$ of an amino acid's $\alpha$-amino group?

$$\sim 9.5$$

Why is the $\alpha$-carboxyl group of an amino acid more acidic than standard carboxylic acids?

The protonated amino group withdraws electrons from the carboxyl group, lowering its $\text{p}K_a$.

Why is the $\alpha$-amino group of an amino acid less basic than standard amines?

Electronegative oxygen atoms in the carboxyl group withdraw electrons from the amino group, lowering its $\text{p}K_a$.

What term describes a molecule bearing both a positively charged group and a negatively charged group, resulting in a net charge of zero at physiological pH?

Zwitterion

What is the definition of the isoelectric point (pI)?

The $\text{pH}$ where a molecule carries no net charge (equal number of positive and negative charges).

What is the formula to calculate the isoelectric point (pI) for a molecule with two ionizable transitions?

$$\text{pI} = \frac{1}{2}(\text{p}K_i + \text{p}K_j)$$

What happens to the net charge of an amino acid when the solution $\text{pH}$ is greater than its $\text{pI}$?

The net charge becomes negative.

What happens to the net charge of an amino acid when the solution $\text{pH}$ is less than its $\text{pI}$?

The net charge becomes positive.

How does placing a carboxylate group in a nonpolar/hydrophobic environment affect its protonation state?

A hydrophobic environment favors the uncharged neutral form ($\text{COO}^- \rightarrow \text{COOH}$).

Who analyzed albumins in 1838 and declared their minimal unit to be $\text{C}_{400}\text{H}_{620}\text{N}_{100}\text{O}_{120}$?

Gerrit Mulder

What molecular weight value is subtracted from the average amino acid molecular weight ($\sim 128\,\text{Da}$) to account for water loss during peptide bond formation?

$18\,\text{Da}$ (yielding an average residue molecular weight of $110\,\text{Da}$)

What formula is used to estimate the number of amino acid residues in a protein from its molecular weight?

$$\text{Number of residues} = \frac{\text{molecular weight}}{110}$$

What chemical property maintains the planarity of peptide (amide) bonds?

Partial double bond character due to electron delocalization.

Why is the trans conformation of a peptide bond energetically favored over the cis conformation?

Due to steric clash of the side chains in the cis conformation.

What percentage of peptide bonds preceding proline (X-Pro) exist in the cis conformation under unstrained conditions?

$$10\text{--}30\%$$

In what direction are peptide sequences conventionally written and numbered?

From the N-terminal residue (amino-terminal end) to the C-terminal residue (carboxyl-terminal end).

What is a conjugated protein?

A protein that contains permanently associated non-amino acid chemical components.

What is the non-amino acid part of a conjugated protein called?

A prosthetic group

What type of prosthetic group is contained in glycoproteins?

Carbohydrates (sugars)

What type of prosthetic group is contained in hemoproteins?

Heme (iron porphyrin)

What is an example of a metalloprotein containing zinc as a prosthetic component?

Alcohol dehydrogenase

Which amino acid is depicted in this ball-and-stick structural model?

Cysteine

Which amino acid's titration curve is represented in this figure?

Glutamate (Glutamic Acid)

What chemical process is depicted in this reaction diagram?

Oxidation of Cysteine to form Cystine (disulfide bond formation)

What is the charge state of an amino acid's ionizable groups when the solution $\text{pH}$ is lower than their $\text{p}K_a$ values?

Protonated

What type of bond covalently links amino acid monomers together to form a polypeptide polymer?

Peptide bond (amide bond)