Biomolecules - Amino Acids and Proteins

Question 1

How does epigenetic change gene expression?

Answer 1

methylation and histone modification

Question 2

How is a peptide bond formed?

Answer 2

nucleophilic addition substitution between the C terminus of one AA and the N terminus of another

Question 3

How are peptide bonds stabilized?

Answer 3

delocalization across the O and N on either side of the peptide bond

Question 4

What is an AA in a polypeptide called?

Answer 4

residue

Question 5

The N terminus is the?

Answer 5

amino group at the beginning

Question 6

The C terminus is the?

Answer 6

carboxyl group at the end

Question 7

What is pKa?

Answer 7

shows acid strength, lower the pKa the higher the acidity

Question 8

Why is histidine useful to have an active sites?

Answer 8

Its side chain has a pKa of ~6.5 which is close to the physiological pH of ~7.4

Sensitive to pH change so it can stabilize or destabilize a substrate

Question 9

pH < pKa

Answer 9

AA is protonated (+)

Question 10

pH = pKa

Answer 10

mix of +/- AAs

Question 11

pH > pKa

Answer 11

AA is deprotonated (-)

Question 12

What’s weird about proline?

Answer 12

It has a 2* alpha amino group (side chain doubles back to bond with the N again)

This disrupts the alpha helix because the 2* alpha amino group causes kinks

Question 13

What’s weird about glycine?

Answer 13

The simplest AA with side chain -H

Alpha carbon is no longer chiral (only nonchiral AA)

Disrupts the alpha helix because -H is so small which makes the molecule very flexible which causes kinks

Question 14

What’s weird about cysteine?

Answer 14

Forms disulfide bridges if 2 get too close

Question 15

CystEine vs cystine

Answer 15

Has the E if its reduced (SH)

No E if oxidized (S-)

Question 16

Where are cysteine vs cystine?

Answer 16

extracellular = oxidizing = cystine

intracellular = reducing because of antioxidants = reduced = cystEine

Question 17

How to determine L vs D AA?

Answer 17

With COOH at the top and R at the bottom

If the amino group is on the Left = L

Question 18

Isoelectric point (pI)

Answer 18

the pH point where a molecule is net neutral

Question 19

How to find pI

Answer 19

take the average of pKas of all functional groups

Question 20

pH < pI

Answer 20

Everything is protonated = net +

Question 21

pH = pI

Answer 21

zwitterion = net neutral

Question 22

pH > pI

Answer 22

Everything is deprotonated = net -

Question 23

How are proteins 3* structure stabilized?

Answer 23

H bonding, Van der Waals forces, disulfide bridges, and hydrophobic packing

Question 24

solvation shell

Answer 24

the layer of solvent surrounding a protein which helps to stabilize (or destabilize) the outer layer