L4 - Covalent And Non-covalent Bonding

Question 1

What is ionic bonding?

Answer 1

The electrostatic interaction of the differently charged species

Question 2

NaCl as an example of ionic bonding

Answer 2

• in order to reach stability of a filled shell, it can gain an e- from a suitable source
• when salt in solid form, ions are arranged in regular arrays
• energy of the electrostatic interactions is partly why it’s stable

Question 3

What is covalent bonding?

Answer 3

The chemical bond that involved the sharing of pairs of electrons between atoms

Question 4

How do covalent bonds form?

Answer 4

Bring two atoms close together, the 2 atomic orbitals now merge into a single bond orbital that contains both electrons

Question 5

What are important points about covalent bonds?

Answer 5

• electrons must have opposite spins, must be paired
• each electron is able to exist in any part of the bond orbital, belongs to both atomic nuclei

Question 6

What is bond dissociation energy?

Answer 6

The energy needed to break the bond that was formed

A measure of how strong the bond is

Question 7

What is hydrogen bonding?

Answer 7

A partially electrostatic attraction between a H which is bound to a more electronegative atom such as N,O,F and another adjacent atom bearing a lone pair of electrons

Question 8

What does the strength of the hydrogen bond depend on?

Answer 8

The donor and acceptor atoms and their environments and geometries

Question 9

What are the consequences of H bonding in small molecules?

Answer 9

Increase in melting point, boiling point, solubility and viscosity

Question 10

What are Van der Waals forces?

Answer 10

Relatively weak forces that attract neutral molecules to one another

Question 11

What are the three soureces that VdW arise from?

Answer 11

• electrically neutral molecules may exhibit permanent electric dipoles
• these dipoles have tendency to align = net attractive force
• permanent dipoles may temporarily distort the electric charge in a neraby molecule
• molecules with no permanent dipole temporarily dipoles from the random electron motion = london forces

Question 12

What is pi-stacking?

Answer 12

Attractive, non covalent interactions between aromatic rings

Question 13

What are the 3 recognised arrangements?

Answer 13

• sandwhich
• t shaped
• parallel; displaced

Question 14

What is the evidence for pi stacking?

Answer 14

• gas phase and low temp benzene forms a dimer, binding energy
• x-ray crystallography gives perpendicular and offset paraller configuartions in many simple aromatic compounds

Question 15

What are hydrophobic interactions?

Answer 15

Describes the segregation of water and non-polar substances

Question 16

What feature does water have that affects mixtures?

Answer 16

• strong network of hydrogen bonds
  = non polar molecules cannot form hydrogen bonds

Question 17

What are amphiphiles?

Answer 17

Molecules both hydrophobic and hydrophilic domains

Question 18

What are amphiphilic molecules arranged like in micelles?

Answer 18

The hydrophilic head is found on the outside and the hydrophobic tails reside inside

Question 19

What are proteins? And give examples of amino acids with hydrophobic elements

Answer 19

Macromolecules

• glycine
• alanine
• valine
• leucine
• phenylalanine
• tryptophan
• methionine

Question 20

Why are charged and polar residues found on the outside?

Answer 20

They can intereact with the surrounding water molecules

• minimises the number of hydrophobic side chains exposed to the water solvation sphere
  = the principle driving force behind the folding process

Question 21

What are the protein structures?

Answer 21

• primary
• secondary
• tertiary
• quaternary

Question 22

What is the primary protein structure?

Answer 22

Sequence of amino acids in the polypeptide chain
- held together by peptide bonds
- formed from the acid group of one and the amine group of another

Question 23

What is the secondary protein structure?

Answer 23

Highly regular sub-structures on the polypeptide backbone chain (alpha helix, beta pleated sheets)
- pattern defined by hydrogen bonds
- between the main-chain peptide groups

Question 24

What is the tertiary protein structure?

Answer 24

Overall 3D shape of the protein molecules, 2nd structure folded into a compact globular structure
- driven by the non-specific hydrophobic interactions
- interactions such as salt bridges, hydrogen bonds, tight packing of side chains and disulphide bonds

Question 25

What is the primary structure started by?

Answer 25

The amino-terminal (N) end

Question 26

How are beta pleated sheets held?

Answer 26

Hydrogen bonds
- carbonyl of residue n interacts with the amide proton of residue n+4

Question 27

How many residues do alpha and beta need in the secondary structure?

Answer 27

Alpha - 5.4
Beta - 3.6

Question 28

How are tertiary and quaternary structure?

Answer 28

Hydrophobic effect is the main driving force in the protein folding
- hydrophobic residues forced into core of the forming globular sturcture, hydrophilic remain at the surface
- energy gain = vdw in the hydrophobic region = stability of folded protein
+ pi-stacking, salt bridges and disulphide bonds