Protein Structure Quiz

Study Notes

Protein Structure

The peptide bond has partial double bond character, making it planar and unable to rotate.
Dihedral angles (phi and psi) allow for rotation around single bonds, resulting in different conformations.
Ramachandran plots show possible phi and psi angles for amino acids in proteins.
Common secondary structures include alpha helices and beta sheets.
Alpha helices are stabilized by hydrogen bonds between the carbonyl oxygen of one amino acid and the amide hydrogen of the amino acid four residues down the chain.
Right-handed helices have a rise (distance along the helix axis) of 1.5 Å per residue and a pitch (rise per turn) of 5.4 Å.
Proline and glycine often destabilize alpha helices.
Beta sheets are formed by hydrogen bonds between strands of polypeptide chains.
Beta sheets can be parallel or antiparallel (antiparallel sheets have stronger hydrogen bonds).
Beta turns are tight turns that connect strands of beta sheets.
Circular dichroism spectroscopy can be used to determine the secondary structure of proteins by measuring the absorption of circularly polarized light.
Tertiary structure is the overall 3D structure of a single polypeptide chain, including the arrangement of secondary structures.
Globular proteins are spherical and compact, while fibrous proteins are long and thread-like.
Collagen, keratin, and silk are examples of fibrous proteins.
Motifs (folds) are recurring structural patterns within a protein, while domains are functional units that can fold independently within a protein.
Intrinsically disordered proteins lack a fixed tertiary structure.
Multi-subunit proteins have quaternary structure, which describes the arrangement of multiple polypeptide chains.
Protein denaturation is the loss of a protein's 3D structure, often caused by heat, pH changes, detergents, or chaotropic agents.
Protein folding is a hierarchical process, beginning with the formation of secondary structures and culminating in the final tertiary structure.

Protein-Ligand Interactions

Protein-ligand interactions are crucial for protein function.
The dissociation constant (Kd) describes the affinity between a protein and its ligand.
The association constant (Ka) is the inverse of Kd.
For oxygen-binding proteins, P50 is the partial pressure of oxygen at which the protein is 50% saturated with oxygen.
Hemoglobin (Hb) and myoglobin (Mb) are oxygen-binding proteins with different structures and functions.
Hb is a tetrameric protein with two alpha subunits and two beta subunits, allowing for cooperativity in oxygen binding.
Hb has two states: the T state (low affinity for oxygen) and the R state (high affinity for oxygen).
Hb's affinity for oxygen is influenced by pH (Bohr effect), CO2 concentration, and 2,3-bisphosphoglycerate (BPG).
BPG binds to Hb and decreases its affinity for oxygen, aiding in oxygen release in tissues.
Hb is an allosteric protein, meaning its conformation can be altered by ligand binding.
Oxygen binding to Hb is cooperative: binding of one oxygen molecule increases the affinity of Hb for other oxygen molecules.
A Hill plot is used to visualize the cooperativity of ligand binding.
Sickle cell anemia is caused by a single amino acid change in Hb, leading to deformed red blood cells.
Heme, a porphyrin ring containing Fe2+, is the oxygen-binding site in Hb and Mb.
Globin chains contribute to oxygen binding by interacting with heme and stabilizing the Fe2+ ion.
Proximal histidine interacts directly with the Fe2+ ion in heme, while distal histidine is involved in oxygen binding.

Immunoglobulins

Antibodies (immunoglobulins) are proteins specific for antigens.
Five classes of immunoglobulins exist in humans: IgG, IgM, IgA, IgD, and IgE.
IgG is the most abundant immunoglobulin.
IgG has a Y shape with two antigen-binding sites.
An epitope is the specific region on an antigen that an antibody binds to.
ELISA and Western blotting are analytical techniques that use antibodies to detect and quantify antigens.

Description

Test your understanding of protein structure including peptide bonds, dihedral angles, and common secondary structures such as alpha helices and beta sheets. Dive into concepts like Ramachandran plots and the characteristics of proline and glycine in protein folding.