Lecture 2: Intramolecular and Intermolecular Forces

Question 1

What are intramolecular forces

Answer 1

forces between atoms within/holding a molecule together

Question 2

What are intermolecular forces

Answer 2

Forces holding molecules together

Question 3

What bond creates strong forces

Answer 3

covalent bonds (100-900KJ/mol)

Question 4

What bonds/interactions are considered weak

Answer 4

Van der Waals forces (0.4-4 KJ/mol)
H bonds (12-30 KJ/mol)
Ionic interactions (20 KJ/mol)
Hydrophobic interactions (<40 KJ/mol)

Question 5

What are Van der Waals forces

Answer 5

result of induced electrical interactions between closely approaching atoms or molecules as their negatively-charged electron clouds fluctuate instantly in time

Form hydrogen bonds, dispersion forces, and dipole-dipole interactions

Question 6

Where/how do hydrogen bonds form

Answer 6

between a H atom covalently bonded to an electronegative atom (O, N) and a second electronegative atom that serves as the hydrogen bond acceptor

Question 7

Where/how do ionic interactions occur

Answer 7

Result of attraction forces between two oppositely charged groups (e.g., -tive carboxyl groups and +tive amino groups)

Question 8

Where/how do hydrophobic interactions occur?

Answer 8

In solution. Due to strong tendency of water to water to exclude non-polar groups/molecules

Question 9

What is the structure of DNA

Answer 9

Amino group - R group - carboxyl group

Question 10

What is the Ramachandran Plot

Answer 10

A standard way of defining the standard geometry of a give amino acid in a polypeptide chain

Shows the regions for which a amino acid residue can and cannot reside due to other nearby residues

Question 11

What is a dihedral angle and what are the two dihedral angles

What range of degree can it poses

Answer 11

The angle between two intersecting planes/half-planes where both of which pass through the same bond

Phi and Psi = two dihedral angles

-180 to +180 degrees

Question 12

where does the Phi angle form

Answer 12

between the alpha carbon to nitrogen

Question 13

where does the Psy angle form

Answer 13

between the alpha carbon to the carbonyl

Question 14

What are the steps in calculating phi/psy angles

Answer 14

1. look down the alpha carbon
2. place the N or C=O at noon (depending on whether phi or psy)
3. if the other N or carbonyl is between ‘12 and 6’ = positive angle, if the other N or carbonyl is between ‘6 and 12’ = negative angle

Question 15

What is the Helical Wheel Model

Answer 15

Gives the ability to determine the nature of an alpha helix based on the amino acid sequence

Question 16

What are coiled coils

Answer 16

Where two alpha helices from two proteins stick side by side

Question 17

What is the hydrophobic nature of coiled coils

Answer 17

form a hydrophobic streak down the joining region and an outer hydrophilic region

Question 18

What is a beta sheet composed of

Answer 18

beta strands

Question 19

what is the stability of beta strands and sheets

Answer 19

A single beta strand has low stability, so is required to from a beta sheet to be stable

Question 20

How are beta strands held together?

Answer 20

Hydrogen bonds

Question 21

What are the two types of beta sheets

Answer 21

anti-parallel and parallel

Question 22

how many beta strands in a beta sheet

Answer 22

<5 beta strands in a sheet is rare due to the instability and distortion of the hydrogen bonding

Question 23

Where do disulphide bonds form?
Are they long or short range?
What environment do they require?
What do they do?

Answer 23

covalent bonding between two cystines
long rage
require an oxidative environment
stabilise the protein structure

Question 24

What is the common structure of a DNA binding protein

Answer 24

Helix-turn-helix

Question 25

Where do DNA proteins often bind?

Answer 25

Major groove