Protein Structure: Secondary Structures

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What type of bonding is responsible for the formation of secondary structures in a polypeptide?

Hydrogen bonding between the peptide backbone atoms (correct)

Van der Waals interactions between the alpha-helices

Covalent bonding between the R groups

Ionic bonding between side chains

In which type of structure do the R groups (side chains) point away from the helix?

Tertiary structure

Quaternary structure

Beta-pleated sheets

Alpha-helix (correct)

What type of structure is formed by the assembly of multiple polypeptides?

Alpha-helix

Secondary structure

Tertiary structure

Quaternary structure (correct)

What experimental technique is considered the gold standard for determining the 3D structure of proteins?

X-ray crystallography Signup and view all the answers

What does the Ramachandran plot show for amino acids in a protein?

Allowable torsion angles for forming certain secondary structures Signup and view all the answers

Which type of structure is held together by different chemical interactions between side chains or between a side chain and the peptide backbone atoms?

Tertiary structure Signup and view all the answers

What is the diameter order from smallest to largest for beta-turns, 310 helix, and pi-helix?

$\pi$-helix > $310$ helix > beta-turns Signup and view all the answers

Which type of protein is formed by 2 or more identical subunits or polypeptide chains?

$4$ different homo-multimeric proteins Signup and view all the answers

What holds together the tertiary structure of a protein?

Different chemical interactions between side chains or between a side chain and the peptide backbone atoms Signup and view all the answers

What is the formula for calculating dilution factor (DF)?

Target final volume / Initial concentration Signup and view all the answers

At what pH does the Coomassie Brilliant Blue G-250 dye have a blue color?

pH > 2 Signup and view all the answers

What stabilizes the anionic, blue form of the Coomassie Brilliant Blue G-250 dye?

Electron donation from the protein Signup and view all the answers

What is the wavelength of maximum absorption of the Coomassie Brilliant Blue G-250 dye when it is not yet bound to a protein?

$470-595$ nm Signup and view all the answers

What is used to prepare the Bradford reagent?

Methanol and glacial acetic acid Signup and view all the answers

How is the dilution factor (DF) calculated in the context of protein samples in the Bradford assay?

$4000 imes Final hinspace volume$ Signup and view all the answers

What is the concentration of the dilute solution if the concentration of the stock solution is 300 ug/uL and the dilution factor is 150?

$2$ ug/uL Signup and view all the answers

What is the traditional one-step preparation solute volume for a 400 uL solution at a dilution factor of 4000?

$0.1$ uL Signup and view all the answers

In step dilution, what are two smaller dilution factors used to achieve a target larger dilution factor of 40?

$4$ and $10$ Signup and view all the answers

What is the overall dilution factor (DF) with respect to stock solution when preparing a 400 uL solution at a 1:4000 dilution using step dilution with an intermediate solution?

$40$ Signup and view all the answers

What does the binding of dye to protein allow according to the text?

Enhances protein conformation change. Signup and view all the answers

Which combination will result in a green color for Coomassie Brilliant Blue G-250?

pH > 2 with no net charge of the dye. Signup and view all the answers