Session #3 & 4: Amino Acids and Protein Structure; Protein Structure & Folding

The amino acids in hemoglobin (or any protein) uniformly have which of the following configurations? - D - R - L - S #KhanAcademy

Answer = *L* 😊 Configurations (either relative or absolute) in amino acids refers to the stereochemical configuration around the chiral carbon. Due to differences in the priority of different amino acid side chains, not all amino acids have the same "Absolute Configuration", which refers the R/S naming convention. Some amino acids are R, and some are S. However, all amino acids have the same "Relative Configuration", which refers to the D/L naming convention. *All biologically produced amino acids are in the L configuration.*

Which of the following properties of a protein is least likely to be affected by changes in pH? • Secondary structure • Net charge • Primary structure • Tertiary structure

Answer = *Primary Structure* will not be affected by pH changes! 😊 → Primary structure = the amino acid sequence of a protein plus the peptide bonds joining them together. → Change in pH are unlikely to alter amino acid sequence or break peptide bonds.

Which of the following amino acids has a net negative charge at physiologic pH (~7.4)? - Glutamic Acid - Histidine - Asparagine - Lysine

Answer = Glutamic Acid/Glutamate! • Amino acids with *acidic side groups* carry a net negative charge at physiologic pH. • Glutamate (glutamic acid) has a side group containing a carboxylic acid.

List all the hydrophobic amino acids! "A, V, L, I, M"

Remember, what is the reason for the hydrophobicity of these amino acids.

What are some aliphatic compounds?

There are so many: - methane (CH₃) - cycloheptane (C₇H₁₄) - propane (C₃H₈) etc.

A polypeptide with a net positive charge at physiologic pH (~7.4) most likely contains amino acids with R groups of what type? - Aromatic R groups - Basic R groups - Aliphatic R groups - Acidic R groups

• *Basic* R groups! • At physiologic pH, basic functional groups will be protonated, attaining a positive charge. • Thus, a polypeptide with a net positive charge at physiologic pH most likely has a basic R group.

The unique cyclic structure of which of the following amino acids plays a central role in the formation of alpha helices and beta sheets? - Lysine - Arginine - Valine - Proline

• *Proline!* • *Proline* plays a central role in the *formation* of alpha helices and beta sheets. While proline's unique structure may also disrupt both alpha helixes and beta sheets, it's ability to make sharp turns facilitates the *formation* of both structures, with proline commonly being found *at the beginning of alpha helices or at the turns in beta sheets*.

*Primary Structure* of a Protein

• A protein's primary structure is its sequence of amino acids, the sequence of amino acids in the polypeptide chain, held together by the peptide bonds.

Define '*zwitterion*.'

• A zwitterion is a neutral molecule with both positive (+) and negative (-) electrical charges. • (In some cases multiple positive and negative charges may be present)-- but the overall charge of the molecule is still neutral.

The alpha helix is an example of which of the following structural properties of proteins? • primary structure • quaternary structure • tertiary structure • secondary structure

• Alpha Helices are a part of *Secondary Structure*! • Secondary structure = 3D arrangement of polypeptides • α-Helix three dimensional arrangement of amino acids in a polypeptide, where the chain takes on a telephone-cord-like shape.

All hydrophobic amino acids (valine, leucine, isoleucine, etc.) share which of the following properties? • Basic R groups • Acidic R groups • Polar uncharged R groups • Nonpolar uncharged R groups

• Answer = All hydrophobic amino acids share *nonpolar uncharged R groups*. • Hydrophobic amino acids prefer to minimize their interactions with water molecules. • Polar, acidic, and basic R groups all share partial or full charges, which interact favorably with polar water molecules.

Another name for glutamate is __________________, and another name for aspartate is __________________.

• Glutamic Acid and Aspartamic Acid

Which amino acid is often found where: "a small side chain is required to allow polypeptide chains to come near each other, or allow a polypeptide to make a right turn?"

• Glycine! Glycine

What word/chemical characteristic is synonymous with 'aliphatic,' in terms of our amino acids? Explain.

• Hydrophobic! The 'aliphatic' and 'hydrophobic' groups are the same group, just different names (to describe essentially the same quality)!

What is physiological pH?

• Physiological pH = *7.4* or *~7* • This affects amino acids: their charge, whether they are zwitterionic, etc. • More on this later.

What is special about *proline*, the amino acid?

• Proline has a unique cyclic structure which differentiates it from the other common amino acids.

List the first *5* letters/symbols/names of the Greek alphabet.

• α = alpha • β = beta • γ = gamma • δ = delta • ε = epsilon