Lecture_5_notes_Protein_Structure_BCH400_Spring_2025_v2

What is the role of enolase in cellular metabolism?

Enolase acts as a catalyst in the glycolytic pathway.

What is the function of hemoglobin?

Hemoglobin transports O2 in the blood.

Which protein regulates blood pressure by stimulating contractions of smooth muscles?

Vasopressin.

What is the significance of vitamin C in the activity of PAM enzyme system?

Vitamin C is a necessary vitamin cofactor for the production of oxytocin.

What causes the rigidity and partial double bond character in peptide bonds?

The resonance structure of the peptide bond.

How do peptide bonds influence protein structure?

They exhibit rigidity and restrict rotation due to their partial double bond character.

What does a Ramachandran plot represent?

It shows the distribution of Φ and Ψ dihedral angles found in a protein.

What is AlphaFold and its significance in biology?

AlphaFold is an AI algorithm that predicts protein structures from sequences.

How does the α helix stabilize its structure?

Hydrogen bonds between backbone amides of the n and n + 4 amino acids.

What distinguishes parallel and antiparallel β sheets?

Parallel strands are oriented in the same direction; antiparallel strands are oriented in opposite directions.

What is a protein's tertiary structure?

The three-dimensional shape of a protein formed by interactions among amino acid side chains.

What stabilizes protein structures?

Hydrophobic effects, hydrogen bonds, van der Waals interactions, electrostatic interactions, and cystine bridges.

What is the role of chaperones in protein folding?

They promote correct protein folding and prevent misfolding and aggregation.

What is the defining feature of a protein's quaternary structure?

It is formed by the assembly of multiple polypeptides into a larger complex.

What happens during protein denaturation?

Loss of structural integrity leads to loss of activity.

Which amino acids are common in beta turns?

Proline and glycine.

How does hydroxyproline function in collagen?

It stabilizes the collagen triple helix through additional hydrogen bonding.

What is the impact of vitamin C deficiency on collagen?

It can lead to scurvy due to impaired collagen stability.

What kind of interactions stabilize the α helix structure?

Hydrogen bonds between the backbone amides.

How many residues are in a single turn of the α helix?

3.6 residues per turn.

What is the consequence of misfolded proteins?

They can induce misfolding and aggregation of additional proteins.

What does the peptide bond feature in terms of reactivity?

Peptide bonds are less reactive compared to esters.

What are motifs in protein structure?

Recognizable regions of structure that represent specific arrangements of secondary elements.

What contributes to the thermal stability of collagen?

The presence of hydroxyproline helps stabilize the triple helix.

Which technique is used to study protein structures like hemoglobin?

Quaternary structure analysis.

What is responsible for the strength of collagen fibers?

The triple helix structure of collagen provides high tensile strength.

What role does cysteine play in protein structure?

Cysteine forms disulfide bonds that stabilize protein structure.

Name two common secondary structure arrangements in proteins.

α helix and β sheet.

What is the function of ribonuclease?

It catalyzes the degradation of RNA.

How do proteins regain activity after denaturation?

By spontaneous refolding, re-establishing disulfide bonds and the correct conformation.

What can break disulfide bonds in proteins?

Reducing agents like beta-mercaptoethanol (BME).

Why are large volumes of protein conformations problematic?

They make the search for the native structure extremely time-consuming.

What factors can lead to protein misfolding diseases?

Protein aggregation and self-assembly of misfolded proteins.

What is the usual consequence of amyloid-β fibrillation?

Neuronal damage and synaptic dysfunction.

Name an example of an AI application in protein design.

The creation of toxin-targeting proteins from scratch.

What is the role of peptide bonds regarding rotation?

Rotation around peptide bonds is restricted due to their double-bond character.

How does proline affect the structure of proteins?

Proline can introduce kinks or bends due to its cyclic structure.

What are the implications of studying protein misfolding in Alzheimer's disease?

Understanding misfolding can aid in developing drugs to inhibit aggregation.

What are the three example of protein misfolding problems?

Alzehimer’s, Parkinson’s, & Huntington’s