BCH-Week 6

Question 1

What are some characteristics for binding

Answer 1

binding is essential for interactions, binding is saturable, it is reversible for noncovalent but irreversible for covalent binding

Question 2

What are some characteristics of enzymes

Answer 2

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

Question 3

What is a zymogen and how is related to cleavage for activation

Answer 3

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

Question 4

What is enzymatic kinetics and what can it tells us

Answer 4

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

Question 5

how does the subtrate concentration relate to rate of reaction

Answer 5

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

Question 6

What is the Michaelis Menten kinetics equation used for

Answer 6

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

Question 7

What is the michaelis constant

Answer 7

Km, which describe the interaction between enzyme and specific subtrate, aka defines binding affinity

Question 8

What is a special characteristics about the Km in simpel reactions

Answer 8

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

Question 9

What is the turnover number and how can it be obtained

Answer 9

Kcat, which is the rate constant when 100% of enzyme has been saturated
Kcat= Vmax/[E]total
larger Kcat= fster production of product

Question 9

What is the Lineweaver-Burk Plot

Answer 9

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

Question 10

What is the reaction catalyzed by oxidoreductase

Answer 10

oxidation-reduction reactions involving NADH, FADH2, O2, NADPH

Question 11

what is teh reaction catalyzed by transferase

Answer 11

functional group transfer between molecules

Question 12

what is teh reaction catalyzed by hydrolases

Answer 12

a hydrolysis reaction where water is involved

Question 13

what is the reaction catalyzed by lyases

Answer 13

adding/cleavinf reactions where it involves double bonds and/or cyclization

Question 14

What is the reaction catalyzed by isomerases

Answer 14

a group transfer within molecules

Question 15

what is teh reaction catalyzed by ligases

Answer 15

joins 2 molecules using nucleotides, involves ATP/GTP

Question 16

what is the reaction catalyzed by translocase

Answer 16

movement of ions or molecules across membrane

Question 17

What are some ways to regulate the function of proteins and enzymes

Answer 17

using structural changes mediated by cleavage, noncovalent or covalent interactions like phosphorylation/methylation/etc

Question 18

How does phosphorylation inhibit teh enzyme and how does dephosphorylation re-activate it

Answer 18

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

Question 19

What is teh only way to overcome irreversible inhibition

Answer 19

since this type of inhibition is due to covalent bonding, the only way to overcoem it is by synthesis of new enzyme

Question 20

What are teh three types of simple reversibel inhibitions

Answer 20

competitive- inhibitor bind active site
noncompetitive- inhibitor bind enzyme or ES complex
uncompetitive- inhibitor binds ER complex

Question 21

What happens to Km and Vmax under competitive inhibition

Answer 21

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

Question 22

What happens to Km and Vmax under uncompetitive inhibition

Answer 22

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

Question 23

What happens to Km and Vmax during noncompetitive inhibition

Answer 23

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

Question 24

What are unique characteristics of allosteric regulation

Answer 24

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

Question 25

What are teh two conformations that the binding of allosteric site can cause

Answer 25

Taut (T) which means the enzyme won’t bind
Relaxed (R) which means the enzyme will bind

Question 26

What does the S shaped, sigmoidal, kinetics indicates

Answer 26

this display is by teh allosteric enzymes which means there is cooperativity of binding of subtrates to adjacent active site

Question 27

What is an example of allosteric regulator of hemoglobin

Answer 27

2,3-BPG which binds to deoxyhemoglobin and stabilize the T state and facilitate release of O2 and prevent rebidninh