Pre Knowledge (Chapters 2, 5, 12) Flashcards
(2) Proteins are polymers consisting of ..
amino acids
Proteins contain a wide range of … like alcohols, thiols, thioethers, carboxylic groups, amines and basic groups like amines
Functional groups
Components amino acid
central a carbon
R group (side chain)
amino group (NH2)
carboxyl group
Amino acids are chiral: explain
Mirror isomers: L isomer and D isomer.
Only L isomers are found in proteins
Zwitterions
Amino acids in solution at physiological pH have a dipolar form (NH3+ and COO-)
Hydrophobic / nonpolar amino acids
-Glycine, Gly, G
-Alanine, Ala, A
-Proline, Pro, P
- Valine, Val, V
- Leucine, Leu, L
- Isoleucine, Ile, I
- Methionine, Met, M
- Tryptophan, Trp, W
- Phenylalanine, Phe, F
polar uncharged amino acids
- Serine, Ser, S
- Threonine, Thr, T
- Tyrosine, Tyr, Y
- Asparagine, Asn, N
- Glutamine, Gln, Q
- Cysteine, Cys, C
- Histidine, His, H
Polar positive amino acids
- Lysine Lys, K
- Arginine, Arg, R
Polar, negative amino acids
- Aspartate, Asp, D
- Glutamate, Glu, E
Peptide bond
C=O - NH
Most common cross-ink within the linear polypeptide chain
Disulfide bonds
Most peptide bonds have the … configuration
trans
> Steric repulsion, two atoms closer tha Van der Waals contact distance > opposing force
The alpha helix is stabilized by intrachain …
hydrogen bonds
Characteristics of globular proteins: enzymes, signaling molecules, regulatory proteins
-Lack of symmetry
-Solubility in water
Which motif is found in many DNA binding proteins
Helix-turn-helix
(2) motifs
Secondary structures frequently present in proteins
(5) Catalytically active RNA molecules
Ribozymes
Properties of enzymes are speed and specificity. Which enzymes catalyze proteolysis of peptide bonds?
Proteases
The six major classes of enzymes
- Oxidoreductases: oxidation-reduction
- Transferases: group transfer
- Hydrolases: hydrolysis reactions (transfer of funcional groups of water)
- Lyases: addition or removal of groups to form double bonds
- Isomerases: isomerization (intramolecular group transfer)
- Ligases: ligation of two substrates at the expense of ATP hydrolysis
Ester bond
C=O
-O
Kinase and phosphatase function
Kinase: phosphorylation
Phosphatase: de phosphorylation
Molecules which regulate activity of the enzyme
Cofactor
Groups of cofactors
-Coenzymes (small organic molecules)
-Metals
Tightly bound coenzymes which are unchanged in the overall chemical reaction
Prostethic groups
> loosly associated coenzymes often behave like second substrates (cosubstrates) > bound by enzyme, changed and released.