Kavran_protein

Question 1

four classes of biological molecules

Answer 1

sugars, fatty acids, amino acids, nucleotides

Question 2

T/F. Double bonds in biological molecules have rotational freedom

Answer 2

F. Double bonds are barrier to rotation, whereas single bonds are free to rotate

Question 3

Sharing of electron forces that cause bound molecules to be coplanar

Answer 3

resonance

Question 4

what limits how close nuclei can get to one another?

Answer 4

van der waals radius

Question 5

what are dipoles and why do they form?

Answer 5

positive and negative charges separated by distance on same molecule, formed from unequal sharing of electrons between atoms in a polar molecule

Question 6

energy of a C-C covalent bond

Answer 6

85 kcal/mol

Question 7

types of noncovalent interactions (4)

Answer 7

hydrogen bonds, van der waals, ionic interactions and hydrophobic effect

Question 8

optimal H bond distances

Answer 8

2.2-2.5 Å as “strong, mostly covalent”, 2.5-3.2 Å as “moderate, mostly electrostatic”, and 3.2-4.0 Å as “weak, electrostatic”

Question 9

optimal salt bridge distance

Answer 9

2.7A, not angle dependent

Question 10

name six broad functions of proteins

Answer 10

structural, enzymatic, mechanical, replication, transport, signalling

Question 11

T/F. Proteins found in D form most commonly.

Answer 11

False, L isomer prevalent

Question 12

Direction of polypeptide chain orientation (ie names of two termini)

Answer 12

N+ (amino) ——> C- (carboxyl)

Question 13

T/F. Peptide bond is planar

Answer 13

True, H-N-C-O atoms lie in a plane from resonance, but side chains hooked to C-alpha are free to rotate

Question 14

primary structure

Answer 14

amino acid sequence, written N to C

Question 15

secondary structure

Answer 15

alpha helix, beta sheets, stabilized by H-bonds

Question 16

T/F. Beta sheets have alternating parallel and anti-parallel strands

Answer 16

True

Question 17

tertiary structure

Answer 17

3D arrangement of chemical groups, this level of structure tells you things about function

Question 18

quaternary structure

Answer 18

assembly of separately translated polypeptide chains into protein final form

Question 19

energy of hydrogen bonds

Answer 19

1-3 kcal/mol

Question 20

energy from an electrostatic interaction in salt bridges scales with this equation

Answer 20

1/r, where r=distance between two charged centers of atoms

Question 21

van der waals energy of interactions

Answer 21

less than 1 kcal/mol

Question 22

what molecule dominates interactions between all biological molecules

Answer 22

water