Lecture 2 - Proteins

Question 1

How are amino acids classified?

Answer 1

• polar (uncharged)
• nonpolar
• basic (+)
• acidic (-)

Question 2

Peptide bonds

Answer 2

• carboxyl carbon of one aa shares electrons w/ nitrogen of amino group from another aa
• loss of H2O (condensation rxn)
• strong, covalent bonds

Question 3

What kind of interactions and/or noncovalent bonds help proteins fold?

Answer 3

• noncovalent: hydrogen bonds, electrostatic, van deer Waals
• hydrophobic clustering force

Question 4

Common folding motifs of proteins

Answer 4

• α helix: N-H of a peptide bond is hydrogen bonded to CO 4 residues away
• β sheet: hydrogen bonding between different strands hold it together, aa in each strand project above and below the plane alternately

Question 5

Why does a protein spontaneously refold after the denaturing agent is removed?

Answer 5

Because all the information needed for the 3D protein structure is found within the amino acid sequence

Question 6

What are protein domains?

Answer 6

• modular units from which larger proteins are built from
• structural unit that folds mostly independently

Question 7

How does a coiled-coil form?

Answer 7

When 2+ of the α helices have the hydrophobic region on one side of the strand –> wrap together and hydrophobic regions are on the inside of the coiled-coil

Question 8

What is the SH2 domain?

Answer 8

A protein structure that responds to cell signals to cause selected proteins to bind to each other –> alter cell behavior

Question 9

Domains of the Src protein

Src protein - functions in signaling pathways

Answer 9

• SH2 and SH3 domains: regulatory functions (respond to signals turning the kinase on/off)
• C terminal domain: gives kinase activity

idea = different domains have different functions

Question 10

What do disulfide bonds do for a protein?

Example

Answer 10

Strengthens/reinforces the most favored conformation of the protein

acts as staples

Lysozymes retain their antibacterial activity for a long time due to disulfide bonds (cross-linkages)

Question 11

What prevents insulin from being able to reform efficiently?

Answer 11

Interrupting their disulfide bonds because denaturation loses part of proinsulin
- proinsulin = assembly factor that has the info for insulin to reform spontaneously

Question 12

What does the ability for a protein binding to a ligand with high affinity depend on?

Answer 12

The formation of a set of weak noncovalent bonds
- allows ligand + binding site to fit precisely together

Question 13

How does a protein binding site form noncovalent bonds only with certain ligands?

Answer 13

the folding of a polypeptide chain creates crevices/cavities (binding site)
- contains set of aa that are specific for certain ligands (to form noncovalent bonds)

Question 14

What are scaffold proteins?

Answer 14

Proteins w/ binding sites for multiple proteins or RNA molecules

Question 15

What is the function of scaffold proteins?

Answer 15

Multiple binding sites = link together specific sets of interacting macromolecules and hold them in place

can also enhance the rate of reactions

Question 16

Biomolecular condensates

Answer 16

Cellular structures built from proteins and often RNA that are held together by weak, changing interactions

Question 17

Why are biomolecular condensates multivalent?

Answer 17

They have 1+ scaffold proteins that make multiple independent interactions w/ self or other macromolecules

Question 18

Liquid-liquid phase separation

or liquid-liquid demixing

Answer 18

The process of biomolecular condensate formation
- fluctuating interactions (weak interactions are constantly forming and breaking) make it act like a liquid

Question 19

Why is it important for domains to be low complexity and disordered to form a biomolecular condensate?

Answer 19

Because it mediates the weak reactions which ultimately form the condensate