Cellular Metabolism And Enzymes

Question 1

What types of bonds link amino acids in polypetides

Answer 1

Covalent peptide bonds

Question 2

Describe the two most common arrangements of polypeptide chains when shaped to form structured proteins

Answer 2

Alpha helix
- spiral shape

Beta pleated sheets
- like a sheet folded back on itself (think of a curtain)

Question 3

How do bonds between peptides differ from bonds between polypeptides in formed proteins

Answer 3

Covalent (STRONG) bonds between peptides

Hydrogen (Weaker) bonds between secondary structures

Question 4

Describe the structure of a haemoglobin molecule

Answer 4

2 x alpha globin chains
2 x beta globin chains
4 x haem proteins
- haem = Protoporphyrin ring containing iron molecule

Question 5

Describe the function of an enzyme

Answer 5

Protein catalysts that increase the rate of chemical reactions by lowering the activation energy associated with the uncatalysed reaction. The enzyme is UNCHANGED in this process.

Question 6

Describe the function of enzymes in terms of ‘delta G’ (free energy) and the catalyzed and uncatalyzed reaction

Answer 6

The activation energy required during uncatalyzed chemical reactions is supplied by the existing kinetic energy of molecules at a specific temperature. Enzymes work by lowering this energy requirement. The delta G required to activate the reaction is reduced by an enzyme. The ‘delta G’ for the actual reaction is unchanged.

Question 7

Describe the lock and key model for enzymes

Answer 7

Enzymes are highle specific with specific ‘ active sites’ complemented by its substrate. Essentially the enzyme’s active site ‘fits’ only the substrate, like a lock and key

Question 8

What is the induced fit model for how enzymes work? give an example of an enzyme that works like this

Answer 8

Substrate binds and causes a conformational change in the enzyme leading to lower energy transition states.

           Hexokinase  GLUC + ATP  G6P + ADP

Question 9

Give two examples of enzymes which demonstrate the efficiency of enzymes in catalysing chemic reactions

Answer 9

1. Carbonic Anyhdrase: speeds its rxn by 10^5

2. Urease (Urea CO2 + NH3) speeds its reaction by 10^14

Question 10

Classify the co-enzymes and co-factors

Answer 10

1. Co-factors = Metal ions
   Mg2+ : Hexokinase
   Zn+ : Carbonic Anhydrase
   Fe2+ : Cytochrome Oxidase
2. Co-enzymes = Organic molecules
   Co-enzyme A involved in acyl group rxns
   Co-enzyme B12 involved in alkyl grp. rxns.

Question 11

List the factors that determine the rate of a reaction in order of impact

Answer 11

1. Substrate concentration
2. Enzyme intrinsic ability to catalyse rxn
3. Temperature (affect enzyme kinetics)
   - denaturation
4. pH (affect enzyme kinetics)
   - H+ affect charge of amino acids at active site
   - Alter general structure of the protein

Question 12

Draw the graph to demonstrate the meaning of Km as it relates to the Michaelis Menton equation. Define Km

Answer 12

Km is the substrate concentration at which the reaction velocity is half the maximal value (Vmax/2)

Graph
Y - axis Rection Velocity (Vo)
X - Substrate concentration
Curve - hyperbolic: increasing initially to and then slowing to a plateau = Vmax.
Then Vmax/2 –> draw a line vertically down from here and get Km which is the substrate concentration at which the reaction velocity is half its maximal value.

Question 13

Define the Michaelis and Menton equation

Answer 13

This equation relates the initial reaction velocity (Vo) to the maximum reaction velocity (Vmax), The Michaelis constant (Km) and a specific substrate concentration ( [s] ).

Vo = Vmax [s]
_______
Km + [s]

      k1         k2 E + S ES  E + P
      (k-1)

Km = (k-1) + k2
______
k1

Question 14

What is the Lineweaver-Burke plot and what is this used for?

Answer 14

Michaelis and Menton equation re-arranged into the y = mx + c format which allows for a plot of a straight line graph which can be useful for interpreting effect of enzyme inhibitors on enzyme kinetics

1 = Km + 1
__ ______ ______
Vo Vmax.[s] Vmax

Question 15

Draw a graph to illustrate enzymes with a higher and lower Km value as well as Higher and lower Vmax

Answer 15

X-axis: Substrate concentration
Y-axis: Reaction velocity (Vo)

Graph 1: hyperbola increasing then decreasing to plateau

Graph 2: hyperbola slower rise (steeper gradient) and more gradual approach to same Vmax

Graph 3: hyperbola showing same rate of rise to lower Vmax

Interpretation:
Km in graph 1 is > Km in graph 2
- this means that enzyme in reaction 1 has a higher affinity for the substrate versus 2.

Km in graph 1 = Km in graph 3 but different Vmax
- Same enzyme affinity but lower Vmax

Question 16

Compare first order and zero order kinetics

with reference to the Michaelis and Menton graph

Answer 16

First order kinetics
- The rate of reaction is proportional to the amount of substrate present –> the initial part of the curve

Zero order kinetics
- the rate of the reaction is independent of the concentration of the substrate present –> the end of the Michaelis and Menton curve once the rate of the reaction has reached Vmax = plateau

Question 17

Distinguish competitive enzyme inhibitors from non-competitive enzyme inhibitors

Answer 17

Competitive enzyme inhibitors bind to the active site of the enzyme and prevent substrate binding/the reaction

Non-competitive enzyme inhibitors bind to a distal site on the enzyme and cause a conformational change on the active site so that the substrate can no longer bind and the reaction can no longer be catalysed.

Question 18

How does the presence of a competitive enzyme inhibitor affect the rate of the reaction as illustrated by the Vo - [S] curve

Answer 18

The Km will increase as the Vmax/2 value will now be shifted to the right as the reaction has been slowed by the inhibitor.. The same Vmax may be reached with sufficiently high [S].

Km increased
Vmax unaffected

Question 19

How is the lineweaver-Burke plot affected by the presence of a competitive enzyme inhibitor

Answer 19

Straight line graph with steeper gradient as ‘m’ in y = mx + c is essentially Km. Km increases in the presence of a competitive enzyme inhibitor

Question 20

How is the Km and Vmax affected by the presence of a non-competitive enzyme inhibitor and why

Answer 20

Km unchanged - binding of substrate to enzyme is unaffected

Vmax is reduced - Non-competitive enzyme inhibitor often bind covalently to the enzyme causing permanent conformational change of the enzyme–> reduced catalytic enzyme activity is the result –> Reduced Vmax.

Question 21

What is an allosteric enzyme and how do the kinetics of these enzymes differ from from the classical Michaelis Menton velocity/[Substrate] profile? Draw both curves and give an example of a cell which demonstrates a similar velocity/substrate profile.

Answer 21

Allosteric enzyme = have multiple subunits - binding of molecules at sites distant to the active site can cause conformational change to the active site (either increaseing or decreasing the activity of that enzyme)

X - axis: [S] and Y - axis: Reaction velocity (Vo)

Michaelis Menton = hyperbolic
Allosteric = Sigmoid (e.g. like Haemoglobin and co-operative O2 binding)

Question 22

Do allosteric effectors affect the Km or the V max of the velocity/[S] kinetics

Answer 22

Can affect either or both - remember the difference is sigmoid shape

Question 23

How do competitive inhibition and non-competitive inhibition of enzymes alter the Velocity/[Substrate] curve

Answer 23

Competitive inhibition: Km changes

Non-competitive inhibition: Vmax changes

Question 24

Why are allosteric enzymes and their effectors important

Answer 24

End products can inhibit the initial enzymatic process, providing for a negative feedback system

Question 25

Differentiate a kinase from a phosphorylase

Answer 25

Kinase: adds Phosphate (PO4^-3)
Phosphorylase: adds Phosphoryl (PO3^-2)

Question 26

What are the functions of the following enzymes

1. Glycogen phosphorylase
2. Glycogen synthase
3. Protein Kinase

Answer 26

Glycogen phosphorylase
- Increased breakdown of glycogen

Glycogen synthetase
- Increased production of glycogen

Protein kinase

• Activates glycogen phosphorylase
• Inactivates glycogen synthetase
• -> favouring glucose production

Question 27

What are zymogens

Answer 27

Zymogens are pro-enzymes which are modified outside of the cell (cleavage of part of the protein) to become activated.

Question 28

True or false for the following

1. Catalysed enzyme reactions consume energy
2. Enzymes are always proteins

Answer 28

1. False - Lower activation energy –> catalysis

2. False - Occasionally are RNA

Question 29

Draw the graph which represents the concept of lowering activation energy

Answer 29

Slide 33/37 from eintegrity Cellular Metabolism, Enzymes

Label the following

1. Free energy (Y axis)
2. Reaction progress (X-axis)
3. Substrate energy (start) higher
4. Product energy (end) lower
5. Activation energy for uncatalyzed reaction (higher initial spike)
6. Activation energy fo catalyzed reaction (lower initial spike)
7. Delta G (change in energy substrate to product)