BIOL 4210 Lecture 03: Protein Structure and Function

Flashcards covering amino acids, protein structure, domains, folding, interactions, and covalent/post-translational modifications from Lecture 03 notes.

How are amino acids grouped by the properties of their side chains?

Uncharged polar, Nonpolar, Acidic, and Basic.

At physiological pH (~7), what form do amino acids commonly exist as?

Zwitterions with an NH3+ (protonated amino group) and a COO− (deprotonated carboxyl group).

Name a basic amino acid and its one-letter code.

Lysine (Lys, K) (also Arginine Arg, R and Histidine His, H are basic).

Name the acidic amino acids and their one-letter codes.

Aspartic acid (Asp, D) and Glutamic acid (Glu, E).

What type of bond can form between two cysteine residues to stabilize a protein?

Disulfide bond (S-S bond).

Where do nonpolar (hydrophobic) side chains tend to be located in a folded protein?

In the protein core, away from water.

Where do polar, hydrophilic side chains typically reside in a folded protein?

On the surface, interacting with water.

Which backbone dihedral angles allow rotation in a polypeptide, and what do they determine?

Phi (Φ) around N–Cα and Psi (ψ) around Cα–C; they determine the protein’s fold/shape.

Name the main types of noncovalent interactions that help proteins fold.

Electrostatic attractions, hydrogen bonds, and van der Waals interactions.

How do alpha helices and beta sheets differ in their hydrogen-bond patterns?

Alpha helices have intra-chain H-bonds; beta sheets have inter-strand H-bonds and can be parallel or antiparallel.

What structural motif involves two or more helices wrapping around each other to hide hydrophobic residues?

Coiled-coil.

What is the difference between protein domains and overall protein structure levels?

Domains are distinct, independently folding units within a protein; proteins can have multiple domains and domains can be shuffled to create new proteins.

Give two examples of protein domains mentioned in the notes.

SH2 and SH3 domains.

What is the role of disulfide bonds in cellular environments?

Stabilize protein structure in oxidative (extracellular) environments; cytosolic proteins are in a reducing environment and typically lack disulfides.

What is ubiquitin, and how is it attached to proteins?

Ubiquitin is a 76‑amino‑acid polypeptide; attached through a cascade of E1, E2, and E3 enzymes (ubiquitination).

List common covalent post-translational modifications and their typical targets.

Phosphorylation (Ser/Thr/Tyr); Methylation (Lys); Acetylation (Lys); Palmitoylation (Cys); N‑acetylglucosamine (Ser/Thr); Ubiquitination (Lys).

What is the regulatory concept of multisite covalent modifications?

A regulatory protein code where combinations of modifications direct different fates (localization, activity, interactions, degradation).

What is the general effect of protein phosphorylation on function and what enzymes regulate this?

Phosphorylation can activate or inhibit function; kinases add phosphates and phosphatases remove them.

What are GTP-binding proteins used for in signaling, and how do they function as switches?

GTPases act as molecular switches, toggling between active (GTP‑bound) and inactive (GDP‑bound) states; hydrolysis and regulators like GEFs and GAPs control timing.

What is a scaffold protein?

A protein that tethers multiple reactive proteins via structured domains and flexible linkers to increase collision probability and speed reactions.

What is allostery in proteins?

Conformational changes caused by binding at one site that regulate activity at a different site, enabling positive or negative regulation.

What determines a protein’s ligand-binding site and why is water often excluded?

The binding site is determined by amino acid composition, charge, folding, and PTMs; water is typically excluded to allow binding interactions.

What are three modes of protein binding described in the notes, and which is likened to a key-and-lock interaction?

Surface-surface binding (most like a key-and-lock interaction), domain-domain interactions, and other noncovalent modes; surface-surface binding is highlighted as key-and-lock-like.

What is a protein complex that performs a mechanical task called?

A protein machine (e.g., the ribosome).

What is a protein domain shuffling?

Recombination of distinct domains found in different proteins to create new proteins with novel functions.

What are some typical representations used to visualize a protein domain in structural biology?

Backbone, Ribbon, Wireframe (including R groups), and Space‑filling models.

What are examples of domains in proteins with multiple domains (domain architecture)?

Cytochrome b562 (single-domain), NAD-binding domain of lactate dehydrogenase, variable domain of immunoglobulin, SH2 domain.