General amino acid formula
R group (amino acid side chain) Carboxyl group (- charge) Amino group (+ charge) C (a-carbon atom)
What happens to amino and carboxyl groups at pH 7?
They get ionized
Optical isomers
Optical isomers occur because the a-carbon is asymmetric, which creates 2 mirror images (stereoisomers L and D)
What is the optical isomers of proteins?
L-isomer
Peptide bond
amide linkage that joins 2 amino acids (C-N bond)
Why is there no rotation around the C-N bond?
peptide bonds form a rigid planar unit
How can amino acids be more flexible?
single bonds allow rotation
How are amino acid side chain properties grouped?
size, charge, polarity
Protein shape is determined by?
amino acid sequence
amino acid sequence referred to as?
primary structure
Name 3 noncovalent bonds that help proteins fold?
Electrostatic attractions, van der Waals attraction, hydrogen bonds
Common folding patterns of proteins
a helix b sheet
Secondary structure
regular local structure of protein backbone stabilized by intramolecular bonding
B-sheets can occur in what configurations?
Antiparallel vs parallel
alpha helices can form what superstructure?
coiled coil
Coiled-coil
In the helix, there are amino acids from a-g. The amino acids in a and d are often nonpolar. Proline breaks the helix.
How does coiled-coil superstructure minimize exposure of hydrophobic amino acid side chains to aqueous environment?
alpha helices wrap around each other. Specifically, the hydrophobic amino acids in the a and d position of the alpha helices are wrapping around each other
What is the structure of the Scr kinase?
SH2 and SH3 domains, ATP
tertiary structure
full 3D organization of polypetide chain
What stabilizes extracellular proteins?
covalent cross-linkage (disulfide bonds SH)
What do intrinsically disordered regions often contain?
few hydrophobic amino acids and are relatively highly charged
What are some functions of intrinsically disordered regions?
1) binding
2) signaling
3) tethering
4) diffusion barrier
What determines protein chemistry?
Surface Conformation
What are the 2 mechanisms to increase reactivity of active site?
Keep water out or cluster functional residues together
What are 3 ways that proteins can bind to other proteins?
1) Surface-string
2) helix-helix
3) surface-surface
equilibrium constant
measures binding strength (dissociation)
How do enzymes speed up reactions?
By selectively stabilizing transition states
Transition rate
Transition rate determines the activation energy, and is the most unstable intermediate in catalysis reactions.
Why do enzymes selectively stabilize transition states during catalysis?
When they are stable, enzymes have a higher affinity for transition states than substrates
Enzymes use acid and base catalysis simultaneously example
A) no catalysis
Enzyme mechanisms
1) precise substrate orientation
2) distortions of electron clouds
3) forcing substrate into transition state
Coenzymes are?
tightly bound small non-amino acid molecules that are often:
1) metal ions
2) small organic molecules
3) both in one molecule
ex retinal heme
Since enzymes are effective, many reactions in the cell are ____?
diffusion limited
3 Cellular mechanism for increasing metabolism?
1) use membranes to compartmentalize
2) enzymes are localized into the cell and group with enzymes that share the same pathway
3) form multi enzyme complex
Multi enzyme complexes increase?
metabolism rate
multi-enzyme complexes increase?
metabolism rate (fatty acid synthase)
Explain how fatty acid synthase works?
It has 5 enzyme domains, and the acyl carrier domain passes it off to each enzyme domain
Pathway nodes?
Enzymes compete for the same substrate
Enzyme regulation is achieved by?
1) expression regulation
2) regulation of subcellular distribution
3) PTM
4) enzyme degradation
5) small molecule binding
Feedback regulation
allostery, sometimes competition
Feedback inhibition
?
Example of feedback activation?
ADP activates enzymes for sugar catabolism
Allosteric enzymes have how many binding sites?
Allosteric enzymes have two or more interacting binding sites
symmetric protein assemblies produce?
cooperative allosteric transitions (ligand stabilizes the protein conformation it binds to)
phosphorylation can affect?
1) protein conformation 2) allow protein binding 3) mask binding site on protein
Which amino acid side chains can be phosphorylated?
Serine (S), Threonine (T), Tyrosine (Y)
PTMS and allosteric shape changes enable protein to function as?
microprocessor, assembly factor/scaffold/mechanic motor/ ion pump
Protein that functions like a microprocessor
Src protein
Src kinase mechanism
1) phosphate removal loosens structure
2) activating ligand binds to SH3 domain
3) kinase can now phosphorylate tyrosine to self-activate
molecular input-output device of Src kinase (micropressor)
inputs= has this phosphate been removed, has this binding been disrupted? has this phosphate been added
If yes to all three
Src-type protein kinase activity turns on
Proteins can be regulated by?
covalent addition of other proteins: Ubiquitin, SUMO (small ubiquitin-related modifier)
Covalent modification of proteins can direct proteins to?
Covalent modifications can direct proteins to specific cell sites
