Lecture 1 and 2 - Bonding, charges and non-covalent interaction

Question 1

The main 6 atoms involved in biochemistry

Answer 1

Hydrogen, Carbon, Oxygen, Nitrogen, Phosphorus, and Sulfur

Question 2

Functional groups:
Hydroxyl group

Answer 2

O-H

Question 3

Functional groups:
Aldehyde group

Answer 3

R-C=O
⠀⠀\H

Question 4

Functional groups:
Ketone group

Answer 4

R-C=O
⠀⠀\R’

Question 5

Functional groups:
Carboxyl group

Answer 5

R-C=O
⠀⠀\O-H

Question 6

Functional groups:
Carboxylate group

Answer 6

R-C=O
⠀⠀\O⁻

Question 7

Functional groups:
Carbonyl group

Answer 7

R-C=O
⠀⠀\R’

Question 8

Functional groups:
Sulfhyrdyl (thiol) group

Answer 8

R-S-H

Question 9

Functional groups:
Amino group

Answer 9

R-N-H₂
R-N-H₃⁺

Question 10

Functional groups:
Phosphoryl group

Answer 10

R-P=O
⠀⠀(OH)₂

R - P=O
O⁻/\ O⁻

Question 11

Functional groups:
Esters

Answer 11

R-C=O
⠀⠀\O-R’

R-O-P=O
⠀ ⠀⠀(OH)₂

Question 12

Functional groups:
Ethers

Answer 12

R-O-R’

Question 13

Bonds in organic chemistry:
Anhydrous bonds

Answer 13

R-OH + HO-R -> R-O-R’ + H₂O

Question 14

Bonds in organic chemistry:
Phosphodiester bonds

Answer 14

R-O-P=O
⠀O⁻/\O-R’

Found in linked bases

Question 15

Bonds in organic chemistry:
peptide bond

Answer 15

H₂N-CH-C=O + HN-CH-C=O -> H₂N-CH-C-NH-CH-CO⁻
⠀⠀\R ⠀\OH⠀H/ ⠀\R ⠀\O⁻⠀⠀ ⠀⠀ ⠀ ⠀\O ⠀⠀ ⠀\O

Found between amino acids
Also called a condensation reaction

Question 16

Bonds in organic chemistry:
Glycosidic bond

Answer 16

R(sugar)-O-R’(sugar)

Question 17

Bonds in organic chemistry:
Hemiacetal bond

Answer 17

R-O-CH-OH
⠀⠀ ⠀\R

A combo of an ether and hydroxyl group
Found in a sugar
Less stable than an acetal bond

Question 18

Bonds in organic chemistry:
Acetal bond

Answer 18

R-O-CH-O-R’’
⠀⠀⠀\R’

A combo of two ether groups
Found between two sugars
More stable than a hemiacetal bond

Question 19

Bonds in organic chemistry:
Disulfide bonds

Answer 19

S-S

Found between amino acids (cystine & methionine)

Question 20

The strength of covalent/noncovalent bonds

Answer 20

Covalent bonds - strong (200-800kJ/mol)

Non-covalent bonds - weak (<30kJ/mol)

Question 21

Hydrogen bonds: what are they and how strong are they?

Answer 21

Weak, noncovalent bonds between nearby hydrogen atoms and oxygen/nitrogen atoms

30kJ/mol - one of the strongest non-covalent type of bond

Question 22

Charge-charge interactions

Answer 22

Electrostatic interactions between opposite charges

Stronger than H-bond

• Can extend over greater distances than other noncovalent interactions
• Ion pairs buried within the hydrophobic interior of the protein are more stable

Question 23

What determines how hydrophobic something is?

Answer 23

How non-polar it is

If molecules are more polar, they are more hydrophilic