L4 - Covalent And Non-covalent Bonding Flashcards
What is ionic bonding?
The electrostatic interaction of the differently charged species
NaCl as an example of ionic bonding
- 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
What is covalent bonding?
The chemical bond that involved the sharing of pairs of electrons between atoms
How do covalent bonds form?
Bring two atoms close together, the 2 atomic orbitals now merge into a single bond orbital that contains both electrons
What are important points about covalent bonds?
- 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
What is bond dissociation energy?
The energy needed to break the bond that was formed
A measure of how strong the bond is
What is hydrogen bonding?
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
What does the strength of the hydrogen bond depend on?
The donor and acceptor atoms and their environments and geometries
What are the consequences of H bonding in small molecules?
Increase in melting point, boiling point, solubility and viscosity
What are Van der Waals forces?
Relatively weak forces that attract neutral molecules to one another
What are the three soureces that VdW arise from?
- 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
What is pi-stacking?
Attractive, non covalent interactions between aromatic rings
What are the 3 recognised arrangements?
- sandwhich
- t shaped
- parallel; displaced
What is the evidence for pi stacking?
- 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
What are hydrophobic interactions?
Describes the segregation of water and non-polar substances
What feature does water have that affects mixtures?
- strong network of hydrogen bonds
= non polar molecules cannot form hydrogen bonds
What are amphiphiles?
Molecules both hydrophobic and hydrophilic domains
What are amphiphilic molecules arranged like in micelles?
The hydrophilic head is found on the outside and the hydrophobic tails reside inside
What are proteins? And give examples of amino acids with hydrophobic elements
Macromolecules
- glycine
- alanine
- valine
- leucine
- phenylalanine
- tryptophan
- methionine
Why are charged and polar residues found on the outside?
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
What are the protein structures?
- primary
- secondary
- tertiary
- quaternary
What is the primary protein structure?
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
What is the secondary protein structure?
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
What is the tertiary protein structure?
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
What is the primary structure started by?
The amino-terminal (N) end
How are beta pleated sheets held?
Hydrogen bonds
- carbonyl of residue n interacts with the amide proton of residue n+4
How many residues do alpha and beta need in the secondary structure?
Alpha - 5.4
Beta - 3.6
How are tertiary and quaternary structure?
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
