Quiz 5 Flashcards
(23 cards)
5 general mechanisms of catalysis that follow substrate binding
- acid-base (dotted lines)
- covalent catalysis (solid line)
- metal ion
- induced fit binding (substrate change structure in TS)
- approximation (multiple substrates)
3 covalent catalysis proteases and where they cleave the protein
- chymotrypsin (FYWM)
- trypsin (KR)
- elastase (AS)
4 proteases and the amino acids apart of the active site
serine - A, H, S
cysteine - C, H
aspartyl - 2 A
metalloprotease - Q, H20, Zn2+, 2H, x
Coenzyme to know
(vitamin-coenzyme-reactions)
vitamin = Niacin (vitamin B3)
coenzyme = Nicotinamide adenine dinucleotide (NAD)
reaction = oxidation-reduction
Enzyme regulation strats (5)
- allostery (S bind E, feedback inhibition)
- multiple forms (isoenzymes)
- reverse covalent (kinase, phosphorylase)
- proteolytic activation (zymogen)
- transcriptional control (
ATCase feedback inhibition
- ATCase make CTP
- CTP is a heteroallostery bind to ATCase
- promote T-state
- if CTP binds to R state, change bond direction, close active site
Allosteric constant
L=T/R
Isoenzymes in the body
- which 2
- what area
- what make
- close to open angle change
hexokinase 2 = muscles
- energy (glycolysis)
- low glucose
- 12º conformational change
hexokinase 4 = liver
- storage (glycogen/triglycerides)
- high glucose
- 99º conformational change
Roles of kinase and phosphatase
kinase - add phosphate
phosphatase - remove phosphate
Why is non-coding RNA less constrained than DNA?
- more building blocks
- unconventional base pairing (wobble)
Two types of wobble
G-U
A-C
Diversification of bases (draw out)
- guanosine
- uridine
- N,N-dimethylguanosine
- N4-isopentenyladenosine
- dihydrouridine
- 4-thiouridine
- 2-thiouridine
- pseudouridine
- 2’O-methyluridine
find ss
Definition of junctions
3 joints of ssDNA
Difference between a bulge and an internal loop
bulge - additional residue on one side
internal loop - unpaired nucleotides on both sides
Hairpin loop motif
GNRA
guanosine-any base-any purine-adenosine
- base pair + pi-stacking stabilization
The difference between the RNA non-coding vs protein backbone stabilization
RNA = negative charge
protein = H-bonds
RNA tertiary structures
= ssDNA-ssDNA
= ssDNA-dsDNA
= dsDNA-dsDNA
ss-ss = pseudoknot
- coaxial helical stack of two discontinuous helices
ds-ss = base-triples
- hoogsteen, A-minor motif
ds-ds = coaxial base stacking
- two helical elements stack end-to-end
Key differences between the building blocks of RNA and proteins that make their folding process very different
- RNA less building blocks = lower info density
- RNA no use hydrophobic collapse
- RNA more stable secondary base-pairing = deep energy wells
- RNA high anionic backbone makes folding onto itself challenging
3 general metal ion interactions with RNA
find ss
- diffuse interaction (lots of water in-between = lowest ∆H, highest ∆S)
- outer-sphere coordination (charge-charge, me, medium ∆H, medium ∆S)
- inner-sphere coordination (direct metal-ion, high ∆H, low ∆S(ion), high ∆S(solvent)
Metal-ion interactions with RNA
- ∆G(binding) =
∆G(hyd) + ∆G(ion-diffuse) + ∆G(ion-RNA)
hyd = removing water from the ion surface (∆G>0)
ion-diffuse = interrupt bound ions with diffuse ions (∆G>0)
ion-RNA = electrostatic interaction between ion and RNA (∆G<0)
Any _____ charged ions can promote RNA folding, although _____ are more efficient than ______. Why better?
- positively
- divalent cations (Mg2+, Ca2+)
- monovalent cations (Na+, Zn+)
- higher charge density
How is RNA folding a cooperative operation?
- first counterions binding = neutalize the bakcbone to bend onto itself = higher charge density = attract more counterions
RNA folds through which pathway?
multi-state
- fast to get to native to ensure that high activation needed for misfolded
