Unit 1 MCB FINAL (Part1)

entropy driven

carbonic acid-bicarbonate buffer system
- controls blood pH (7.4)
dihydrogen phophate-hydrogen phosphate system
- intercellular buffer
proteins
- histidine - imadazole side chain

Absorbs light at 280 nm

serine, threonine, tyrosine

- non-chiral and found in surface of proteins
- imino acid and found in surface of proteins

The pathway for the synthesis of aromatic amino acids in plants and microorganisms. This pathway is not present in humans.

blocks part of the shikimate pathway and ends in death of the plant/micro-organism

vitamin C

1. shorter bond length
2. NO free rotation on peptide bond
3. 6 atoms on same plane
4. partial double bond feature because C-N is shorter than typical

2 pI = pKcooh + pKnh3+

N-C
C-C

- very restricted due to side chain
- very flexible

type of backbone; h bond formed btwn -C=O of residue i and -NH of residue i + 4

Proline - phi angle - does not have -NH group

Ile, Thr, Val, Ser, Asp, Asn, Gly

branching. Leucine is compatible because branching occurs on gamma carbon

Polar group side chain; competes with main chain for hydrogen binding

- h bonds are not unifromally distrubuted
- VERY STRONG h bonds because they are collinear

- h bonds are uniformly distributed
- weak h bonds because they are not collinear

1. Purify proteins of protein complex: >2mg (5-30mg/ml)
2. Grow crystals of the protein that diffract well (can take a long time)
3. Obtain X-ray diffraction data
4. Compute electron density maps
5. Fitting/ refinement

- 4 disulfide bonds (2 cysteine)
- If you remove beta-mercaptoethanol before the urea, the protein won’t refold correctly

- incorrect disulfide bonds
- proline residues
- clustering of intermediates bc of hydrophobic groups

- enzymes that assist formation of proper disulfide bonds during folding
- Incorrect disulfide bonds are on protein surface

- Enzymes that catalyzes trans to cis changes in selected (any amino acid)-Proline peptide
- Cis proline very essential
- PPI speed up slow process of trans --> cis

Ubiquitin: protein that acts as a tag for targeting other proteins for degradation
Proteasome: large protein complex that degrades proteins

1. Ubiquitin Activating Enzyme
- ATP, thioester bond Cys + Cterminal
2. Ubiquitin Conjugating Enzyme
- Transferring the activated ubiquitin from E1 to its own Cys residue
3. Ubiquitin Ligase
- lysine residue

- proteins that prevent and reverse any inappropriate interactions
- most are ATPases
- known as "heat shock" proteins

HSP 70, Chaperonin, HSP90, Nucleoplasmins

- early life of proteins (ribosomes)

- acts when protein is fully synthesized
- form large barrel shape complex