Biochemistry I: Amino Acid 2

What is the general structure of an amino acid?

An α-carbon bonded to an amino group, carboxyl group, hydrogen atom, and variable R group.

What is a zwitterion?

A molecule with both positive and negative charges; amino acids usually have NH₃⁺ and COO⁻ near neutral pH.

What determines the chemical properties of amino acids?

Their variable R groups, which differ in polarity, charge, size, and structure.

What are the four major amino acid side-chain categories?

Nonpolar, polar uncharged, acidic (negatively charged), and basic (positively charged).

Which amino acids have predominantly nonpolar side chains?

Glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, and tryptophan.

Which amino acids have polar, usually uncharged side chains?

Serine, threonine, asparagine, glutamine, cysteine, and tyrosine.

Which amino acids have acidic side chains?

Aspartate (Asp, D) and glutamate (Glu, E); usually negatively charged at pH 7.

Which amino acids have basic side chains?

Lysine (Lys, K), arginine (Arg, R), and histidine (His, H).

Which amino acids contain hydroxyl groups?

Serine, threonine, and tyrosine.

Which amino acids contain amide side chains?

Asparagine and glutamine.

Which amino acids contain aromatic rings?

Phenylalanine, tyrosine, and tryptophan.

Which amino acids have branched aliphatic side chains?

Valine, leucine, and isoleucine.

What makes glycine unique?

Its R group is H, making it the smallest, achiral, and highly flexible amino acid.

What makes proline unique?

Its cyclic side chain restricts backbone flexibility.

What are selenocysteine and pyrrolysine?

Additional genetically encoded amino acids incorporated using specialized translation machinery.

How does pH relative to pKa determine protonation?

When pH < pKa, the group is predominantly protonated; when pH > pKa, predominantly deprotonated.

What is the approximate side-chain pKa of aspartate?

3.9; its carboxyl side chain is usually deprotonated and negatively charged at pH 7.

What is the approximate side-chain pKa of glutamate?

4.1; its carboxyl side chain is usually deprotonated and negatively charged at pH 7.

What is the approximate side-chain pKa of lysine?

10.5; its amino side chain is usually protonated and positively charged at pH 7.

What is the approximate side-chain pKa of arginine?

12.5; its guanidinium side chain is usually positively charged at pH 7.

What is the approximate side-chain pKa of histidine?

6.0; its imidazole group can accept or donate H⁺ near physiological pH.

Why is histidine important in enzyme catalysis?

Its imidazole group can act as an acid or base by donating or accepting H⁺.

What are the approximate side-chain pKa values of cysteine and tyrosine?

Cysteine ≈ 8.3 and tyrosine ≈ 10; both are mostly neutral near pH 7.

How do disulfide bonds form?

Oxidation of two cysteine thiol (–SH) groups produces a covalent –S–S– bond.

What is cystine?

Two cysteine residues joined by a disulfide bond.

What is the function of disulfide bonds in proteins?

They stabilize tertiary or quaternary protein structure through covalent cross-links.

Where are disulfide bonds especially common?

Secreted and extracellular proteins and the oxidizing environment of the ER lumen.

Why are disulfide bonds less common in the cytosol?

The reducing cytosolic environment favors cysteine's free –SH groups.

How are amino acid side-chain carbons labeled?

Starting from Cα, successive side-chain carbons are Cβ, Cγ, Cδ, Cε, etc.

What is the usual R/S configuration of L-amino acids?

Most L-amino acids have S configuration at the α-carbon.

Which L-amino acid has R configuration instead of S?

L-cysteine, because its sulfur-containing side chain has higher CIP priority than its carboxyl group.

Why can enantiomers have different biological activities?

Enzymes and receptors are chiral, so enantiomers can differ in binding, activity, metabolism, and toxicity.

Which ibuprofen enantiomer has greater COX-inhibitory activity?

S-ibuprofen; R-ibuprofen is much less active at COX, although some R converts to S in the body.

What are post-translational modifications (PTMs)?

Covalent chemical modifications made to amino acid residues after their incorporation into proteins.

What is the purpose of post-translational modifications?

To expand protein chemical diversity and regulate protein activity, stability, structure, or interactions.

What is phosphorylation?

Addition of a phosphate group to an amino acid residue, often acting as a regulatory switch.

What is lysine acetylation?

Addition of an acetyl group to lysine, modifying its chemical properties and potentially regulating protein function.

What is hydroxyproline and why is it important?

A modified proline residue important for collagen structure; its formation requires vitamin C.

What is γ-carboxyglutamate?

A modified glutamate residue formed through a vitamin K-dependent process that promotes Ca²⁺ binding.

What is GFP?

Green fluorescent protein; its internal chromophore absorbs excitation light and emits green fluorescence.

Which amino acid residues form the GFP chromophore?

Ser65, Tyr66, and Gly67 undergo cyclization, dehydration, and oxidation after protein folding.

What is GFP used for?

Visualizing gene expression and protein localization in living cells.

What neurotransmitter is derived from glutamate?

GABA (γ-aminobutyric acid), an inhibitory neurotransmitter.

What signaling molecule is derived from histidine?

Histamine, involved in inflammation and gastric secretion.

What biologically active molecules are derived from tyrosine?

Dopamine, norepinephrine, epinephrine, and thyroxine (T₄).

What is the pathway from tyrosine to dopamine?

Tyrosine → L-DOPA → dopamine; dopamine can also be converted to norepinephrine and epinephrine.

What is glutathione (GSH)?

A tripeptide composed of glutamate, cysteine, and glycine that functions as a cellular redox buffer.

What is the amino acid sequence of glutathione?

γ-Glu–Cys–Gly; glutamate is linked through its γ-carboxyl group rather than its α-carboxyl group.

What is the main function of glutathione?

Maintaining a reducing intracellular environment and protecting cells from oxidative damage.

What is the difference between GSH and GSSG?

GSH is reduced glutathione; GSSG is oxidized glutathione formed when two GSH molecules form a disulfide bond.

Which glutathione residue is responsible for its redox activity?

Cysteine, because its thiol (–SH) group can undergo reversible oxidation.

How is oxidized glutathione (GSSG) converted back to GSH?

Glutathione reductase uses NADPH to reduce GSSG into two GSH molecules.

Why is the GSH/GSSG system important?

It helps maintain cellular redox balance and protects against reactive oxidizing agents.

What is a polypeptide?

A linear chain of amino acid residues joined by peptide bonds.

What is the primary structure of a protein?

The linear sequence of amino acid residues in its polypeptide chain.

What is a peptide bond?

A covalent amide linkage between the α-carboxyl group of one amino acid and the α-amino group of another.

What type of reaction does peptide bond formation formally represent?

A condensation reaction with a net loss of H₂O.

How are peptide bonds formed inside cells?

On ribosomes using activated amino acids attached to tRNAs, rather than direct condensation of free amino acids.

In what direction are peptide sequences written?

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

What is the N-terminus of a polypeptide?

The end containing the free α-amino group of the first amino acid residue.

What is the C-terminus of a polypeptide?

The end containing the free α-carboxyl group of the final amino acid residue.

How are amino acid residues named within a peptide?

All residues except the C-terminal residue use the suffix -yl; the final residue retains its full name.

How would the sequence Ala–Tyr–Asp–Gly be named?

Alanyl–tyrosyl–aspartyl–glycine.

What is the difference between a polypeptide and a functional protein?

A polypeptide is an amino acid chain; a functional protein consists of one or more folded polypeptide chains.

How many polypeptide chains are present in mature insulin?

Two chains: the A chain with 21 residues and the B chain with 30 residues.

How many disulfide bonds are present in mature insulin?

Three total: two interchain bonds and one intrachain bond.

What is the difference between interchain and intrachain disulfide bonds?

Interchain bonds connect different polypeptide chains; intrachain bonds connect residues within the same chain.

What is the role of disulfide bonds in insulin?

They stabilize insulin's functional three-dimensional structure and connect its two chains.

How is insulin initially synthesized?

As a single precursor polypeptide that is processed to form mature insulin.

What is myoglobin?

A small, single-chain protein containing approximately 153 amino acid residues and weighing about 17 kDa.

What is hemoglobin?

A protein containing four subunits, approximately 574 total residues, and a mass of about 62 kDa.

What is titin?

An enormous single-chain multidomain protein containing approximately 35,000 residues and weighing about 3.9 MDa.

How can the approximate molecular mass of a protein be calculated?

Multiply the number of amino acid residues by approximately 110 Da per residue.

Why is protein molecular mass estimated using 110 Da per residue?

110 Da is the approximate average mass of an amino acid residue within a polypeptide.

Does amino acid sequence length alone determine protein architecture?

No. Proteins can contain one or multiple chains and differ greatly in folding, domains, and functional organization.