Enzyme Kinetics 2

Question 1 of 27

1

Which are true about bisubstrate reactions?

Select one or more of the following:

They use one substrate to yield two products
They use two substrates to yield two products
The two types of bisubstrate reactions are transferase and redox reactions
The two types of reactions are transferase and substitution reactions
10% of reactions are bisubstrate
60% of reactions are bisubstrate
80% of reactions are bisubstrate

Explanation

Question 2 of 27

1

A transferase reaction is one where the functional group on one substrate is transferred to another substrate

Select one of the following:

True
False

Explanation

Question 3 of 27

1

In redox reactions, oxidising equivalents are transferred between substrates

Select one of the following:

True
False

Explanation

Question 4 of 27

1

In bisubstrate reactions with a sequential mechanism, all substrates must combine with the enzyme before the reaction can occur and products are released. Which of the following are also true of sequential bisubstrate reactions?

Select one or more of the following:

Ordered sequential means that the substrates must bind in a particular order
Ordered sequential means that the substrates must bind and be released in a particular order
Random sequential means that the products may be released in any order
Random sequential means the substrates and products may be released in any order
A Bi Bi reaction is bisubstrate
A Bi Bi reaction has 2 substrates and 2 products
The Lineweaver-Burk plot will be like that of uncompetitive inhibition
The Lineweaver-Burk plot will be like that of competitive inhibition

Explanation

Question 5 of 27

1

In Ping-Pong reactions, one or more products are released before all substrates have combined with the enzyme. Which of the following are also true of Ping-Pong reactions?

Select one or more of the following:

They are also referred to as "double displacement" reactions
They are also referred to as "transient displacement" reactions
Functional groups are transferred to the substrate directly
Functional groups are sometimes transferred to the enzyme
Enzyme intermediates in Ping-Pong are stable and can be purified and characterised
Enzyme intermediates in Ping-Pong are transient and can't be purified or characterised
The Lineweaver-Burk plots are like those for competitive inhibition
The Lineweaver-Burk plots are like those for uncompetitive inhibition
Binding of one substrate will encourage binding of a second substrate
Binding of one substrate will inhibit binding of another one

Explanation

Question 6 of 27

1

Pancreatic triacylglycerol lipase catalyses the hydrolysis of the esters of fatty acids into free esters and is involved in protein digestion.

Select one of the following:

True
False

Explanation

Question 7 of 27

1

Pancreatic triacylglycerol lipase is secreted by the pancreas and also found in saliva and the stomach

Select one of the following:

True
False

Explanation

Question 8 of 27

1

Free esters released from lipid digestion of fatty acids, are more soluble than fatty acids.

Select one of the following:

True
False

Explanation

Question 9 of 27

1

Pancreatic triacylglycerol lipase catalyses the hydrolysis of triacylglycerols at position 1 and 2 on the glycerol molecule, and formation of 1,2-diacylglycerols and 2-acylglycerols

Select one of the following:

True
False

Explanation

Question 10 of 27

1

Which are true about lipase?

Select one or more of the following:

It is only present in an aqueous form
It is present in aqueous solution and as a micelle
It requires an Mg co-factor for activity
It requires a procolipase co-factor for activity
Lipase is a zymogen
Procolipase is a zymogen
The active site is permanently open
There is a flap that masks and closes the active site

Explanation

Question 11 of 27

1

What residues compose the catalytic triad of pancreatic triacylglycerol lipase?

Select one or more of the following:

His
Asp
Glu
Pro
Ser
Thr
Phe
Leu

Explanation

Question 12 of 27

1

The mechanism of triacylglycerol lipase:

Asp ❌. His can then ❌ to increase its nucleophilicity. Then Ser is able to launch a nucleophilic attack on the ❌ (the glycerol backbone). This forms a ❌, which is stabilised by ❌ (with residues ❌). The negative charge collapses as ❌ and the carbonyl reforms, releasing the first product, ❌.

His then abstracts a proton from a molecule of water, forming a reactive ❌. ❌ can than attack the ❌, forming another intermediate, which is stabilised in an oxyanion hole. The negative charge collapses when ❌, reforming the catalytic Ser and allowing release of a 2nd product, ❌.

Drag and drop to complete the text.

H-bonds to His, to increase its basicity

launches attack on glycerol

coordinates an Mg ion

abstract a proton from Ser

abtract a proton from Asp

abstract a proton from water

ester carbonyl of the fatty acids

glycerol backbone

carboxylic acids

tetrahedral intermediate

planar intermediate

octahedral intermediate

an oxyanion hole

a Mg ion

the active site

Phe and Leu

Asp, Ser and His

Glu and Asp

His protonates the glycerol backbone

water donates a proton to the glycerol

1,2-diacylglycerol

2-acylglycerol

a free fatty acid

1-acylglycerol

hydroxyl anion

proton

hydroxyl radical

This OH

This H

This OH radical

carbonyl carbon of the lipid

free fatty acid chain

carboxylic acid

His protonates Ser

His protonates Asp

Ser abstracts a proton from water

Ser abstracts a proton from Asp

a 1-acylglycerol

free fatty acid or monoglyceride

free fatty acid

Explanation

Question 13 of 27

1

PLCA2 (phospholipase A2) requires a conformational change to function.

Select one of the following:

True
False

Explanation

Question 14 of 27

1

In PLCA2, the hydrophobic binding pocket is blocked by an inhibitor

Select one of the following:

True
False

Explanation

Question 15 of 27

1

The active site of PLCA2, consists of which of the following catalytic residues?

Select one or more of the following:

His
Asp
Ser
Water
Glu

Explanation

Question 16 of 27

1

The active site contains a bound Mg.

Select one of the following:

True
False

Explanation

Question 17 of 27

1

PLCA2 mechanism: His is ❌ to activate for nucleophilic attack, so there is a ❌ which will later attack the scissile carbonyl carbon. Asp makes His more basic, His abstracts a proton from water. The activated water can nucleophilically attack the ❌, forming a tetrahedral intermediate. The role of Ca2+ is to coordinate the activated water molecule and eletrostatically stabilise negative charge on the oxygen of the tetrahedral intermediate (❌). Then there is the collapse of the tetrahedral intermediate. The ❌ to the hydroxyl group, causing it to abstract a proton from the lipid and reform water

Drag and drop to complete the text.

too far

too weak

too basic

second water

Ser residue

carbonyl carbon

phosphate group

His residue

metal catalysis

electrostatic catalysis

acid-base catalysis

His H-bonds

Ser abstracts a proton

His donates a proton

Explanation

Question 18 of 27

1

Which are true of monotopic enzymes?

Select one or more of the following:

They tend to bind hydrophobic substrates
Subtrates tend to be lipid-soluble and can diffuse through the lipid bilayer
Some oxidoreductases are monotopic and so are some peptidases
All transferases reactions are catalysed by monotopic enzymes
They bind hydrophilic, aqueous substrates

Explanation

Question 19 of 27

1

Which are true of multi-span enzymes?

Select one or more of the following:

Many peptidase are multispan and cleave peptides for transloaction
Transferases are a type of multispan enzyme
Multispan enzyme have multiple TMs

Explanation

Question 20 of 27

1

The gram negative cell wall is less robust and lacks mechanical strength as there is less peptidoglycan.

Select one of the following:

True
False

Explanation

Question 21 of 27

1

LpxC is an essential zinc-dependent deacetylase of bacterial lipid A synthesis producing UDP-3-O-N-glucosamine. Which of the following are true about it?

Select one or more of the following:

It is only present in gram-negative bacteria
It catalyses the reaction from UDP-3-O-N-acetylglucosamine (UDP-GlcNac) --> UDP-3-O-N-glucosamine + acetate
It catalyses the reaction from UDP-3-O-N-acetylglucosamine (UDP-GlcNac) --> 3-O-N-acetylglucosamine + UDP
The key residues involved are Asp and His
The key residues involved are Glu and His
A bound Mg ion is required
A bound Zn ion is required

Explanation

Question 22 of 27

1

1 proposed mechanism for LpxC action:

❌ binds the active site. Glu acts as a base and ❌, making a good nucleophile to attack the ❌. His stabilises the ❌ that develops. The negative charge collapses and ❌ and ❌ the lipid. ❌ is also formed which loses a ❌ to form ❌. The product leaves and the Zn-lipid complex is displaced by water molecule and a new substrate.

Drag and drop to complete the text.

Zn

Mg

deprotonates water

deprotonates Glu

protonates water

carbonyl carbon

hydroxyl group

alpha carbon

negative charge

positive charge

Glu acts as an acid

Glu acts as a base

donates a proton back to

abstracts a proton from

Acetic acid

UDP

proton

phosphate

acetate

UTP

Explanation

Question 23 of 27

1

Why is mechanism 1 for LpxC thought to be incorrect? What is the correct mechanism?

Select one or more of the following:

The mechanism suggests His is just stabilising, when it is actually acting as an acid by donating a proton to the tetrahedral intermediate as shown by mutagenesis
The correct mechanism is that the His is initially protonated, and then later protonates the lipid, and another water will bind Zn and be used
Mutating Glu to Ala, reduced activity, supporting the alternative mechanism
Mutating Glu to Ala, reduced activity, supporting both mechanisms
Mutating His to Ala, reduced activity, supporting both mechanisms
Mutating His to Ala, reduced activity, supporting the alternative mechanism
The mechanism suggests Asp is just stabilising, when mutagenesis shows that it is involved in the reaction as its mutation gives reduced activity

Explanation

Question 24 of 27

1

In terms of bacterial cell wall biosynthesis, which are true of transglycosylation?

Select one or more of the following:

The cell wall is purely an immune system physical barrier
The cell wall is an essential structure in scaffolding the cytoplasmic membrane and maintaining structural integrity of the bacteria
Glycosyltransferase (GT) and transpeptidase (TP) enzymes are involved in cell wall biosynthesis
There are antibiotics that inhibit the activity of GTs, such as beta-lactams (e.g. penicillin), glycopeptides (e.g., vancomycin) and glycolipopeptides
There are antibiotics that inhibit the activity of TPs, such as beta-lactams (e.g. penicillin), glycopeptides (e.g., vancomycin) and glycolipopeptides
Bacteria gain resistance to these antibiotics by accumulating mutations in the TP enzymes
Bacteria gain resistance to these antibiotics by mutating their cell wall
GT enzymes catalyse transfer of a sugar glycosyl nucleotide donor substrate to a specific hydroxyl group of another sugar, or to other acceptors (e.g. lipids)
GT enzymes transfer a glycosyl substrate to a tertiary hydroxyl on nucleotide sugar acceptors (e.g. lipids)
Peptidoglycan transglycosylation by the enzyme GT takes place through polymerization of lipid II substrates

Explanation

Question 25 of 27

1

To form peptidoglycans, enzymes exist to make trans additions of sugars. Which are true?

Select one or more of the following:

Glycosyltransferase catalyses the transfer of a sugar glycosyl to a nucleotide
Glycosyltransferase catalyses the linking of sugar molecules to other sugars or lipids
Transpeptidase links L-ala residues to other L-ala residues, cross linking them
Transpeptidase links D-ala residues to other D-ala residues, cross linking them
Transpeptidase is linked to glycosyltransferase by a linker and glycosyltransferase is partially embedded in the membrane
Lipids for cell wall composition are fed through the plasma membrane and deposited in the periplasmic space
Lipids for cell wall composition are derived from the cytoplasm and transported to the periplasm by active transport

Explanation

Question 26 of 27

1

Transglycosylation mechanism of glycosyltransferases (GTs):

Lipid binds to the membrane protein in a pocket and another lipid is fed through the membrane.
The E114 residue acts as a ❌, abstracting a proton from the ❌ group of the ❌.
Oxygen activates to act as a good nucleophile and can make attack on ❌ of sugar moiety.
Glu E171 stabilises the negative charge forming (phosphate groups), coordinating ❌ that form on the donor.
Stabilisation is either directly or indirectly, mediated by a ❌ to stabilise negative charge.
Upon attack on sugar, ❌ leaving group can diffuse out of active site to give higher oligomeric state of lipid (through addition of more sugar to the incoming lipid).
Must go from ❌ conformation (because SN2 attack)

Drag and drop to complete the text.

bronsted base

bronsted acid

4-OH

3-OH

2-OH

lipid II acceptor

lipid I acceptor

C1 position

C2 position

pyrophosphate groups

phosphate groups

divalent metal cation (e.g. Mg)

Lys residue

monovalent metal cation (e.g. Li+)

lipid-pyrophosphate

lipid-phosphate

boat to chair

chair to boat

Explanation

Question 27 of 27

1

Mechanism for lipid II polymerisation by TG (transglycosylase):

Glu acts as bronsted base and ❌ on ❌ of a lipid II molecule at the ❌.
This is followed by a simultaneous reaction with the C1 of another lipid II at S2 site with Glu.
❌ stabilise the negative charge of phosphate and facilitate its diffusion as a leaving group.
Then there is the ❌ to growing chain.
Essentially, the lipid II’s glycosyl ❌ reacts with the acceptor site (S1) of lipid II to form a ❌ linked glycan chain.
Lipid keeps growing until certain length before leaving.

Drag and drop to complete the text.

deprotonates 4-OH

deprotonates 3-OH

protonates H2O

GlcNAc

Acetate

UDP

acceptor site (S1)

donor site (S2)

Lys and Arg

Glu and Asp

His and Lys

transfer of the sugar and phosphate

elimination of the sugar and phosphate

S2 site

S1 site

β1–4-

α1-4-

β2-4

	Created by Davina Jugnarain over 8 years ago

Degree Biochemistry (Enzyme Kinetics) Quiz on Enzyme Kinetics 2, created by Davina Jugnarain on 26/05/2016.

Enzyme Kinetics 2

Question 1 of 27

Which are true about bisubstrate reactions?

Select one or more of the following:

Explanation

Question 2 of 27

A transferase reaction is one where the functional group on one substrate is transferred to another substrate

Select one of the following:

Explanation

Question 3 of 27

In redox reactions, oxidising equivalents are transferred between substrates

Select one of the following:

Explanation

Question 4 of 27

In bisubstrate reactions with a sequential mechanism, all substrates must combine with the enzyme before the reaction can occur and products are released. Which of the following are also true of sequential bisubstrate reactions?

Select one or more of the following:

Explanation

Question 5 of 27

In Ping-Pong reactions, one or more products are released before all substrates have combined with the enzyme. Which of the following are also true of Ping-Pong reactions?

Select one or more of the following:

Explanation

Question 6 of 27

Pancreatic triacylglycerol lipase catalyses the hydrolysis of the esters of fatty acids into free esters and is involved in protein digestion.

Select one of the following:

Explanation

Question 7 of 27

Pancreatic triacylglycerol lipase is secreted by the pancreas and also found in saliva and the stomach

Select one of the following:

Explanation

Question 8 of 27

Free esters released from lipid digestion of fatty acids, are more soluble than fatty acids.

Select one of the following:

Explanation

Question 9 of 27

Pancreatic triacylglycerol lipase catalyses the hydrolysis of triacylglycerols at position 1 and 2 on the glycerol molecule, and formation of 1,2-diacylglycerols and 2-acylglycerols

Select one of the following:

Explanation

Question 10 of 27

Which are true about lipase?

Select one or more of the following:

Explanation

Question 11 of 27

What residues compose the catalytic triad of pancreatic triacylglycerol lipase?

Select one or more of the following:

Explanation

Question 12 of 27

Drag and drop to complete the text.

Explanation

Question 13 of 27

PLCA2 (phospholipase A2) requires a conformational change to function.

Select one of the following:

Explanation

Question 14 of 27

In PLCA2, the hydrophobic binding pocket is blocked by an inhibitor

Select one of the following:

Explanation

Question 15 of 27

The active site of PLCA2, consists of which of the following catalytic residues?

Select one or more of the following:

Explanation

Question 16 of 27

The active site contains a bound Mg.

Select one of the following:

Explanation

Question 17 of 27

Drag and drop to complete the text.

Explanation

Question 18 of 27

Which are true of monotopic enzymes?

Select one or more of the following:

Explanation

Question 19 of 27

Which are true of multi-span enzymes?

Select one or more of the following:

Explanation

Question 20 of 27

The gram negative cell wall is less robust and lacks mechanical strength as there is less peptidoglycan.

Select one of the following:

Explanation