SH EXAM 2 Flashcards
Describe: Lock & Key
Explain: Why enzymes don’t like it
- Binding of site of protein is a perfect fit for the substrate -The perfect fit creates many favorable interactions between the substrate and the enzyme. So there is no driving force to break the interactions to make product
Kd=[E][S]/[ES]
- The KD would increase
- phosphate backbone of DNA has a negative charge
- alanine is a nonpolar AA so it’s presence would decrease the amount of favorable interactions and decrease the amount of [ES].
is transverse diffusion of lipids fast or slower than lateral diffusion. WHy?
- Transverse diffusion is slower than lateral diffusion
- It is unfavorable due to the movement of the polar hydrophilic head group of the lipid through the hydrophobic membrane interior. This is thermodynamically unfavorable
- 2,3 BPG stabilizes the T state.
- When hemaglobin is in the T state, there is a large basic hole at the interface of all four subunits.
- 2,3 BPG binds to this hole due to it’s negative charge.
- Because 2,3 BPG is in this hole, it prevents the hole from closing to turn the hemaglobin into the R state, thus stabilizing the T state.
Describe why transition state analogs are often potent competitivte inhibitors of enzyme
transition state analogs are often potent competitivte inhibitors of enzymes because it mimics the transition state. The enzyme has the most favoarable interactions with the transition state to lower the energy of the transitions state. Because the enzyme has more favorable interactions with the analog compared to the substrate, the analog will out compete the substrate. Once bound, the analog inhibits the protein by blocking the active sit and not undergoing a chemical rxn
Triacylglycerols shape prevents it form forming bilayers. Bilayers need lipids that are square. The cone shape of Triacylglycerols, due to its tail group being wider than the head group, will cause the Triacylglycerols on the other side of the membrane to be bent. When the membrane is formed, it will make a sphere.
Would you expect an abundance of cardiolipins to be higher or lower in lipid rafts relative to a typical membrane (slide 27)
Cardiolipin highers in lipid rafts. characteristics of lipid rafts are that the lipids in the raft have reduced moement and stay close together. Cardiolipins structure contains two phospholipis covalently attached. This would contribute to the structure of lipid rafts by reducing the movement of the lipids in the rafts stay more associated
CO bind to O2 binding sites?
- [CO] increase
- Hemaglobin has a higher affinity for CO compared to O2. CO binds to hemaglobin in the R state, stabilizing it. Hemaglobin in the R state has a increased affinity for O2. CO binding would decrease hemaglobins ability to deliver O2.
HbH+ + 02= HbO2 + H+
A decrease in the ph cause the [H+] to increase. This shifts the eq to the left, increasing [HbH+]. H+ binds to hemaglobin in the T state, thus stabilzing it. T state hemaglobin has a lower afinity for O2. The T state stabilization would increase hemaglobins ability to deliver O2.
Which fatty acids have lower melting points? (2)
Unsaturated- dbs make kinks, kinks reduce stacking ability.
Shorter- decreased ability to make favorable interactions
At physiological pH.
Serine (-)
Choline (nuetral)
Ethanolamine (nuetral)
-Talk about net charge interactions at physio PH*****
- Rnase A is most active when His 12 is most active..
- His 12 is most active in catalyzing this reaction when the pH is near its pka.
- When the PH is close to the pka, his 12 can function as an ACID and a BASE.
- This is necessary for acid base catalysis.
AA composition/ structure
- silk is composed of extended antiparallel B sheets with alternateranting alanine and glycine
how structure is linked to properties
- Does not stretch easily because structure is fully extended
- Flexible due to Weak non covalent interactions between the betasheet layers
- _Proximity, orientation, entropy reduction *biding of the substrate peptide into the active site_
- Specificity pocket helps align the substrate peptide*
- Docking of molecule in serine protease active sit by side chain recognition.
- The amide bond that is to be broken is position adjacent to the activated
- Transition state stabilization
- Stabilization of the tetrahedral intermediate in the oxyanion hole* (hb bonds)
- Acid base catalysis
- Histidine acts as a acid and base in different steps*
- Base: Histidine deprotonates H2O to activate it
- Acid: Histidine donates a proton back to serine when the final product leaves the active site.
- _Covalent catalysis*_
- Serine acts as a nucleophile to form a covalently attached acyl enzyme intermediate*
Carbonic anhydrase
Catalytic water is activated by Zn2+ whIch generates a nucleophilic OH-. The OH- attacks CO2. The catalytic site is regenerated by binding and ionization of another H2O
No. The change in sterochemistry from L to D would prevent lysine from binding correctly in the binding pocket of trypsin
- What is the specific deficit
- Scurvy is caused by the lack of Vitamin C
- What is the impact on enzyme activity
- The enzymes that modifies proline to hydroxyproline needs Vitamin C to function. without hydroxyproline the structure of collagen is weaker because hydroxy proline is necessary for collagen’s tripple helix structure.
- Treatment
- Eat a lot of fruits and vegetables because they are high in vitamin C
