BCH-Week 6 Flashcards
What are some characteristics for binding
binding is essential for interactions, binding is saturable, it is reversible for noncovalent but irreversible for covalent binding
What are some characteristics of enzymes
they are present in smaller amount than their subtrate, they are unchanged after reacting with subtrate, are biological catalysts that stabalize transition state to lower activation energy to what can be biological possible
What is a zymogen and how is related to cleavage for activation
zymogen is the inactive precursor of an enzyme that gets activated when needed and to get activated it has to undergo proteolytic cleavage which is changing in the zymogen’s tructure to activate it
What is enzymatic kinetics and what can it tells us
enzyme kinetics is when enzyme converts the subtrate to products, it is the rate of reaction to convert teh subtrate to product, known as velocity ( V naught) and measuring it will tells us about the binding affinity and specifity
how does the subtrate concentration relate to rate of reaction
at low [ ], the enzymes aren’t saturated so the speed will be dependent on K[S]
at high [ ], when there is more than enough subtrates so the enzymes are saturated, that means rate is approaching Vmax
What is the Michaelis Menten kinetics equation used for
to describe the rate for simpel reactions and has two assumptions: 1- that the initial concentrations are of [S]»[P]
2- that rate of ES formation=rate of ES breakdown
What is the michaelis constant
Km, which describe the interaction between enzyme and specific subtrate, aka defines binding affinity
What is a special characteristics about the Km in simpel reactions
Km=[S] at 1/2 Vmax, so when half of active sites are bound by subtrate
lower Km and Kd indicates tighter binding
Km is independent of amount of enzyme present
What is the turnover number and how can it be obtained
Kcat, which is the rate constant when 100% of enzyme has been saturated
Kcat= Vmax/[E]total
larger Kcat= fster production of product
What is the Lineweaver-Burk Plot
the double reciprocal of Michaelis Menten equation to help us obtain a linear representation which will be used to find the Vmax and Km
Vmax obtained from y-intercept=1/Vmx
Km obtained from x-intercept=-1/Km
What is the reaction catalyzed by oxidoreductase
oxidation-reduction reactions involving NADH, FADH2, O2, NADPH
what is teh reaction catalyzed by transferase
functional group transfer between molecules
what is teh reaction catalyzed by hydrolases
a hydrolysis reaction where water is involved
what is the reaction catalyzed by lyases
adding/cleavinf reactions where it involves double bonds and/or cyclization
What is the reaction catalyzed by isomerases
a group transfer within molecules
what is teh reaction catalyzed by ligases
joins 2 molecules using nucleotides, involves ATP/GTP
what is the reaction catalyzed by translocase
movement of ions or molecules across membrane
What are some ways to regulate the function of proteins and enzymes
using structural changes mediated by cleavage, noncovalent or covalent interactions like phosphorylation/methylation/etc
How does phosphorylation inhibit teh enzyme and how does dephosphorylation re-activate it
phosphorylation by kinase will transfer phosphate group from ATP to the enzyme causing conformational change that inactivate its
dephosphorylation will be by phosphatases that re-activate the enzyme due to changes in structure
What is teh only way to overcome irreversible inhibition
since this type of inhibition is due to covalent bonding, the only way to overcoem it is by synthesis of new enzyme
What are teh three types of simple reversibel inhibitions
competitive- inhibitor bind active site
noncompetitive- inhibitor bind enzyme or ES complex
uncompetitive- inhibitor binds ER complex
What happens to Km and Vmax under competitive inhibition
Km= increases since more subtrate will be needed to outcompete the inhibitor for that active site
Vmax= will stay the same since the enzymes will be bound by either inhibitor or subtrate
What happens to Km and Vmax under uncompetitive inhibition
Km= decreases
Vmax= decreases
that is because of inhibitor binding the ES compelx and preventing the making of products so the reaction will be pushed to the right toward the E+S which will increase teh subtrate affinity for that enzyme’s active site
What happens to Km and Vmax during noncompetitive inhibition
Km= stays the same since teh inhibitor even if it binds, its binds on another site
Vmax= decreases because the binding of inhibitor to free enzyme or to ES complex will slow the formation of products
What are unique characteristics of allosteric regulation
occurs in quaternary structured proteins that are regulated by bidning of allosteric sites distant from active site and the bidning of allosteric site can be either stimulatory or inhibatory by causing conformational change in other subunits that affect binding of ligand
What are teh two conformations that the binding of allosteric site can cause
Taut (T) which means the enzyme won’t bind
Relaxed (R) which means the enzyme will bind
What does the S shaped, sigmoidal, kinetics indicates
this display is by teh allosteric enzymes which means there is cooperativity of binding of subtrates to adjacent active site
What is an example of allosteric regulator of hemoglobin
2,3-BPG which binds to deoxyhemoglobin and stabilize the T state and facilitate release of O2 and prevent rebidninh
