Exam 2 Review Flashcards
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
Binding pockets?
Chymotrypsin: aromatic
Elastase: small
Trypsin: basic
Competitive inhibitor?
Inhibitor binds to enzyme at same spot as substrate.
Increasing [S] outcompetes
Raises Km, no effect on V max
Hyperbola plot/ all intercept on Y axis on lineweaver plot
Y intercept is 1/ Vmax
Slope is alpha*Km/Vmax
X intercept is -1/alpha*Km
Uncompetitive inhibitor?
Inhibitor binds to enzyme-substrate complex.
Hard to overcome
Lowers Km, lowers V max
Parallel, linear plot lineweaver plot
Y intercept is alpha’/Vmax
Slope is Km/Vmax
X intercept is -alpha’/Km
Mixed inhibitor
Lowers Vmax while increasing or decreasing Km.
Allosteric enzyme regulation?
Ligand binds reversibly at a site other than the active site:
- causes conformational change and change in Km, Vmax
- can be cooperative
Ki?
Ki= [E][i]/[Ei]
5’ end and 3’ end nucleotide?
5’= phosphate
3’= hydroxyl
DNA read which way?
5-3
Why is DNA more stable?
Lack of reactive hydroxyl group
Which DNA form
Is most common?
B form
Which bases pair in double helix?
DNA= G:C and A:T
RNA= G:C and A:U
Pyrimidines vs purines
Purines: A and G
Pyrimidines: C, U, T
DNA nucleoside names?
Deoxyguanisine
Deoxyadenosine
Deoxythymidine
Deoxycytidine
DNA nucleotide names?
Deoxyguanylate
Deoxyadenylate
Deoxycytidylate
Deoxythymidylate
RNA nucleoside names?
Adenosine
Guanosine
Cytidine
Uridine
RNA nucleotide names?
Adenylate
Guanylate
Cytidylate
Uridylate
Base charge?
Bases uncharged between pH 5-9
Subunit definition?
Smallest unit of a protein with 4ry structure that can be removed without disrupting covalent interactions
Trypsin vs chymotrypsin cleavage?
Trypsin cleaves on c-terminal side of basic a.a.’s
Chymotrypsin cleaves on c-term side of aromatic a.a’s
Trypsin vs chymotrypsin cleavage?
Trypsin cleaves on c-terminal side of basic a.a.’s
Chymotrypsin cleaves on c-term side of aromatic a.a’s
