Chapter 1 Flashcards
(14 cards)
What is an alpha helix?
An alpha helix is a rodlike structure in which the peptide chain coils clockwise around a central axis. 3.6 residues per turn, H bonds every ten atoms
What is a beta pleated sheet?
A beta pleated sheet is a structure in which peptide chains lie alongside one another, forming rows.
Describe the special role played by proline in secondary structure
Proline’s rigid ring structure makes it unsuitable for inclusion in the middle of alpha helices and beta pleated sheets. When introduced into the middle of these structures, proline produces kinks in the secondary structure. However, proline’s rigidity makes it useful at the start of alpha helices and in the turns taken by beta pleated sheets. These are the two locations one is likely to find proline.
What is Cystine?
Cystine is the name used to refer to the disulfide bond made between two cysteine’s in a protein.
What is denaturation?
Denaturation is the process by which a protein loses its tertiary structure. This is usually accomplished through disruption of the bonds that hold tertiary structure together.
What is a solvation layer?
A solvation layer is a layer formed around a molecule by nearby solvent molecules. These result as a consequence of electrostatic interactions.
Why is the pushing of nonpolar amino acids into the core of a protein spontaneous?
When there are nonpolar amino acids on the outside of the protein, water cannot hydrogen bind with the protein, which means it can only hydrogen bind with itself. This reduces water’s options, which lowers its entropy, which makes this process unfavorable.
On the other hand, if water can hydrogen bind with the outside of the protein (polar AA’s on the exterior), that gives water more options and lowers the entropy of the system, which is favorable.
What roles can the formation of quaternary structure serve?
- Quaternary structure can stabilize a protein
- Quaternary structure can reduce the amount of DNA needed to encode a protein complex
- Quaternary structure can bring catalytic sites together, which allows intermediates to be shuttled directly to the next step.
- Quaternary structure can induce cooperativity, also known as allosteric effects.
What is a conjugated protein?
A conjugated protein is a protein that derives part of its function from the presence of proesthetic groups.
What is a prosthetic group?
A prosthetic group is a covalently attached molecule that allows a protein to function. Prosthetic groups can be organic molecules such as vitamins or metal ions, like iron.
What is a lipoproptein?
A lipoprotein is a protein with a lipid based prosthetic group.
What is a glycoprotein?
A glycoprotein is a protein with a carbohydrate based prosthetic group.
What is a nucleoprotein?
A nucleoprotein is a protein with a nucleotide based prosthetic group.
What are common ways to denature a protein?
- Heat. As temp increases, hydrogen bonds and salt bridges destabilize.
- Solutes such as urea and beta mercaptoethanol can disrupt disulfide bridges, causing denaturation.
- Detergents can solubilize proteins, which disrupts noncovalent bonds and therefore promotes denaturation.
