Protein Structures and Amino Acids – Flashcards (Lectures 2.2 & 2.3)

Flashcards covering amino acid structure, classification, pI, protein folding forces, misfolding diseases, and the four levels of protein structure, including collagen, myoglobin, and hemoglobin to prepare for exam questions.

What are the core components of an alpha-amino acid's structure?

An alpha-carbon (sp3, tetrahedral), a carboxyl group, an amino group, a hydrogen, and a distinctive side chain (R).

Which amino acid is the simplest and is not chiral?

Glycine, whose side chain is just a hydrogen atom.

Which enantiomer is predominantly used by living organisms?

The L-enantiomer (L-amino acids).

List the nonpolar, hydrophobic amino acids mentioned.

Glycine, Alanine, Proline, Valine, Leucine, Isoleucine, and Methionine.

Name the aromatic amino acids and a notable property of Tyrosine.

Phenylalanine, Tyrosine, Tryptophan; Tyrosine has an OH group that can form phosphotyrosine, affecting protein structure/function. Aromatic residues absorb UV light around 275–280 nm.

What wavelengths do the aromatic amino acids absorb UV light, and why?

Around 275–280 nm due to their aromatic rings (Phe, Tyr, Trp). This absorption contributes to protein UV absorbance.

Name the polar, uncharged amino acids and a key property they share.

Serine, Threonine, Cysteine, Asparagine, Glutamine; they can form hydrogen bonds, and cysteine can form disulfide bonds.

Which amino acids are positively charged and can be found in their ionized form?

Lysine, Arginine, Histidine.

Which amino acids are negatively charged?

Aspartate and Glutamate.

What are the possible ionization forms of amino acids as pH changes?

Cation form, Zwitterion (net charge 0, pI), and Anion form.

How do you calculate the pI when a side chain is ionizable?

Identify the zwitterion; identify the two relevant pKa values (acid strength and base strength) that define the zwitterion; average those two pKa values to obtain the pI.

What forces stabilize protein structure besides hydrogen bonds?

Hydrophobic interactions, salt bridges (electrostatic), Van der Waals forces, and disulfide bonds (covalent).

Which neurodegenerative diseases are associated with protein misfolding?

Alzheimer’s disease (beta-amyloid and TAU aggregates) and Parkinson’s disease (alpha-synuclein aggregates).

What are the four levels of protein structure?

Primary, Secondary, Tertiary, and Quaternary structures.

Describe primary structure.

The amino acid sequence bound by peptidic (covalent) bonds; linear; N-terminus and C-terminus; rotation is allowed around the alpha-carbon, not the peptide bond; condensation requires energy.

What characterizes the secondary structure and its main forms?

Alpha-helix and beta-sheets; alpha-helix stabilized by hydrogen bonds; proline disrupts helices.

Describe beta-sheets and their types.

Beta-sheets are extended, zig-zag backbones with R groups protruding outward; parallel and antiparallel forms; held by hydrogen bonds; antiparallel is typically more stable; keratin is rich in parallel beta-sheets.

What is prion disease and an example mentioned?

Diseases caused by misfolded proteins; Creutzfeldt–Jakob disease is an example.

Describe tertiary structure.

The overall 3D arrangement of a protein; stabilized by hydrophobic interactions, hydrogen bonds, salt bridges, van der Waals forces, and disulfide bridges; contains motifs and domains that confer function.

What are motifs and domains in protein structure?

Motifs are recurring interactions between segments with functional roles; a domain is a region with a specific conformation enabling a particular function (e.g., Troponin C has two domains).

Explain collagen structure and the role of Vitamin C.

Collagen chains are rich in glycine and proline, forming a superhelical triple helix with high tensile strength; Vitamin C enables proline hydroxylation to 4-hydroxyproline, which increases hydrogen bonding; vitamin C deficiency causes scurvy.

Describe myoglobin and its prosthetic group.

Myoglobin stores O2 in muscle; it contains a heme group (iron) as a prosthetic group, buried in the hydrophobic core to prevent iron oxidation and enable oxygen binding.

What is the quaternary structure and provide an example?

Interaction of multiple polypeptide chains; example: hemoglobin, which binds O2 in the lungs and releases it in tissues.

How can protein conformation be modified according to exam cues?

By altering phi and psi rotational angles; to induce conformational changes, change the Cα–C and Cα–N bond angles.

Are all amino acids chiral?

All except glycine are chiral; living organisms predominantly use the L-enantiomer.

What is a zwitterion in amino acids?

A neutral form with positively charged amino group and negatively charged carboxyl group, resulting in a net zero charge at the isoelectric point (pI).