Exam 2 Review Flashcards
(44 cards)
Peptide bond structure
Polar; Resonance hybrid allows cis and trans formations
99% are trans with the exception of proline (90% trans)
Resonance allows les reactivity
- rigidity and nearly planar
4 levels of protein structure
Primary= amino acid sequence
Secondary= alpha helix, beta sheet
Tertiary= 3D structure and interactions
Quaternary= 2 or more polyp. chains.
Alpha helix properties
H bonds stabilize within same polypeptide chain
- between carbonyl residue (Hacceptor) and amide NH (Hdonor) 4 molecules away
- most helices are right handed
How many residues per alpha helix turn?
3.6 residues per turn
Distance between alpha helix turn?
5.4 Angstrom per turn
Distance from one alpha C to another alpha C in an alpha helix?
1.54 Angstroms
Stability of Alpha helix?
H bonds are interior.
-Only stable in absence of water
Amphipathic alpha helices found on:
- protein surfaces (nonpolar towards interior)
- membrane surfaces (nonpolar towards lipids)
Beta helix properties?
H bonds between different poly. P. Strands.
Can be parallel or anti parallel.
-both occur in nature but anti parallel is more common and stabler due to linearity of H bond.
Side chains are above and below the plane of sheet.
B turns
Caused by proline in position 2 or glycine in position 3.
Stabilized by a h bond from carbonyl oxygen to amide three residues down.
Cause anti-parallel
Type 1 and 2 turns
Type 1 Beta turn
4 residues, hydrogen bonds
Proline at position 2
Type 2 Beta turn
Glycine at position 3
Peptide bond rotation?
Peptide bonds can not rotate, the bonds on either side can.
Phi bond: C-N bond
Psi bond: C-CO bond
Protein domain?
Region of a polypeptide chain that folds into a 3D unit
folds and is stable independently
Structure is conserved
Myoglobin?
Myoglobin: main oxygen storage protein
- 1 polypeptide chain
- mostly alpha helix
- 1 spot for binding oxygen
- structurally similar to hemoglobin subunits
- higher affinity for oxygen than hemoglobin
Kd?
The concentration of ligand when half of the protein is bound.
Lower Kd = higher affinity
Hemoglobin?
Has a lower affinity for oxygen, easier to release it than myoglobin.
Is cooperative: binding of one ligand changes affinity for binding or another at a different site
Tense state has lower affinity for O2
Quarternary
Fractional occupancy equation?
Theta= [L] / (Kd + [L])
Allostery?
- When something binding to one site affects the affinity for ligand/substrate at another site
- can be the same ligand or different
Cooperative molecule binding curve vs non-coop?
Cooperative: sigmoidal curve
Non-coop: rectangular hyperbol
Induced fit vs lock-and-key models of ligand binding?
Induced fit: binding site only had approximate match to substrate shape; changes to match it
Lock & key: substrate binds with negligible conformation change
Both are true
Enzymes?
- increase rxn rate by stabilizing high energy transition state
- don’t change delta g
- enzymes lower delta G double cross, meaning speeds up rxn
- decrease reactant mobility for good fit
Reaction coordinate diagram?
Hump is transition state,
Size of hump is activation energy
Michaelis-menten equation
v=(Vmax[s])/((alpha*Km)+[s])
Higher Km means less binding
As substrate concentration is increased velocity is up to a saturation point
Which A.A’s are good enzymes?
- Hydroxyl groups
- Sulfhydryl groups
- Amino groups
- Histidine
