Lecture 2: Intramolecular and Intermolecular Forces Flashcards
What are intramolecular forces
forces between atoms within/holding a molecule together
What are intermolecular forces
Forces holding molecules together
What bond creates strong forces
covalent bonds (100-900KJ/mol)
What bonds/interactions are considered weak
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)
What are Van der Waals forces
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
Where/how do hydrogen bonds form
between a H atom covalently bonded to an electronegative atom (O, N) and a second electronegative atom that serves as the hydrogen bond acceptor
Where/how do ionic interactions occur
Result of attraction forces between two oppositely charged groups (e.g., -tive carboxyl groups and +tive amino groups)
Where/how do hydrophobic interactions occur?
In solution. Due to strong tendency of water to water to exclude non-polar groups/molecules
What is the structure of DNA
Amino group - R group - carboxyl group
What is the Ramachandran Plot
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
What is a dihedral angle and what are the two dihedral angles
What range of degree can it poses
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
where does the Phi angle form
between the alpha carbon to nitrogen
where does the Psy angle form
between the alpha carbon to the carbonyl
What are the steps in calculating phi/psy angles
- look down the alpha carbon
- place the N or C=O at noon (depending on whether phi or psy)
- 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
What is the Helical Wheel Model
Gives the ability to determine the nature of an alpha helix based on the amino acid sequence
What are coiled coils
Where two alpha helices from two proteins stick side by side
What is the hydrophobic nature of coiled coils
form a hydrophobic streak down the joining region and an outer hydrophilic region
What is a beta sheet composed of
beta strands
what is the stability of beta strands and sheets
A single beta strand has low stability, so is required to from a beta sheet to be stable
How are beta strands held together?
Hydrogen bonds
What are the two types of beta sheets
anti-parallel and parallel
how many beta strands in a beta sheet
<5 beta strands in a sheet is rare due to the instability and distortion of the hydrogen bonding
Where do disulphide bonds form?
Are they long or short range?
What environment do they require?
What do they do?
covalent bonding between two cystines
long rage
require an oxidative environment
stabilise the protein structure
What is the common structure of a DNA binding protein
Helix-turn-helix
Where do DNA proteins often bind?
Major groove
