4 Proteins structure and function

Question 1

Protein functions

Answer 1

Catalysis / structure / transport / signalling / storage / movement / immunity / control / buffer

Question 2

Peptide bond

Answer 2

Planar character (almost always trans isomer)

Question 3

Peptide sequence - primary structure

Answer 3

N-terminus, C-terminus

Have the NH2 unbound side at the start

Conventional

Direction

Question 4

Secondary structure

Answer 4

Function of the backbone rather than the side chains

Alpha helixes have hydrogen bonding within the coils

Question 5

Secondary structure - When does the stretch of alpha helix come to an end

Answer 5

When a proline is present

Question 6

Secondary structure - glycine and alpha helix

Answer 6

Glycine fits well in the alpha helix however it also provides an oppurtunity for the alpha helix to kink as its very flexible so provides extra motion

Question 7

Secondary structure - beta sheets

Answer 7

Can form both parallel (short linker) and anti parallel (longer linker needed)

Question 8

Tertiary structre

Answer 8

Most important is packing of hydrophobic (non-polar) side chains to exclude water

Question 9

Tertiary structure - hydrophobic effect

Answer 9

Water is rather ordered on the surface of hydrophobic molecules and crowding of these molecules excludes water resulting in the entropy of the water increasing

Question 10

Tertiary structure - disulphide bonds

Answer 10

During an oxidation reaction of 2 cysteine AAs in close proximity, a cystine is formed

Disulphide bonds occur in extracellular protiens (eg. Insulin and antibodies)

Question 11

Quaternary

Answer 11

Non covalent interactions

Question 12

Protein folding

Answer 12

Most proteins will fold by themselves (structure is entirely dependant on the sequence)

Rossman folds - same folds occur

Proteins aren’t necessarily a single monolithic fold —> eg. Pyruvate kinase has 3 main domains that fold independently of eachother (same polypeptide but 3 different domains)

Question 13

Structure determination - protein purification

Answer 13

Chemical methods can purify proteins based on charge, size and other properties - purification followed by SDS polyacrylamide gel (electrophoresis method that allows protein separation by mass)

Question 14

Structure determination - X-ray crystallography

Answer 14

take a protein and allow to crystallise, order in the crystal as all proteins in same orientation, then take the crystal and shine x-ray light —> small spots show up = pattern of reflection from this you can work out where all the electrons are (if you know protein sequence then you try to match it up to electron arrangement)

Problems - requires crystals (not all proteins can make crystals) / static image = no dynamics

1957 - John Kendrew (myoglobin)

Question 15

Structure determination - cryo-electron microscopy

Answer 15

samples rapidly frozen in ice then use electron micrograph and superimpose a very large number of images and then maps of the proteins can be made

Advatages - works on proteins that wont crystallise (doesn’t require crystal samples) / works on large proteins / used for membrane proteins —> larger

Question 16

Structure determination - AI Alpha Fold

Answer 16

artificial intelligence - uses existing 3D data and sequences, can deduce sequences based on likeliness of certain sequences being near eachother - not entirely accurate but very closely reproduced an existing known protein structure just based on sequence

Now have structures of all theoretical proteins / not good with protein components (eg. If it has a haem group)

Question 17

Additional functionality

Answer 17

Co-enzymes or prosthetic groups —> non-protein components of proteins, especially enxymes, providing chemistry that amino acids cant. They can be covalently or non-covalently bound to the protein

Pyridoxal phosphate - 4% of all enzyme activities use thise

Question 18

Post-translational modification

Answer 18

Covalent attachment of other chemical entities to proteins —> provide additional functionality or change behaviour