Cellular Metabolism And Enzymes Flashcards
What types of bonds link amino acids in polypetides
Covalent peptide bonds
Describe the two most common arrangements of polypeptide chains when shaped to form structured proteins
Alpha helix
- spiral shape
Beta pleated sheets
- like a sheet folded back on itself (think of a curtain)
How do bonds between peptides differ from bonds between polypeptides in formed proteins
Covalent (STRONG) bonds between peptides
Hydrogen (Weaker) bonds between secondary structures
Describe the structure of a haemoglobin molecule
2 x alpha globin chains
2 x beta globin chains
4 x haem proteins
- haem = Protoporphyrin ring containing iron molecule
Describe the function of an enzyme
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.
Describe the function of enzymes in terms of ‘delta G’ (free energy) and the catalyzed and uncatalyzed reaction
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.
Describe the lock and key model for enzymes
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
What is the induced fit model for how enzymes work? give an example of an enzyme that works like this
Substrate binds and causes a conformational change in the enzyme leading to lower energy transition states.
Hexokinase GLUC + ATP G6P + ADP
Give two examples of enzymes which demonstrate the efficiency of enzymes in catalysing chemic reactions
- Carbonic Anyhdrase: speeds its rxn by 10^5
2. Urease (Urea CO2 + NH3) speeds its reaction by 10^14
Classify the co-enzymes and co-factors
- Co-factors = Metal ions
Mg2+ : Hexokinase
Zn+ : Carbonic Anhydrase
Fe2+ : Cytochrome Oxidase - Co-enzymes = Organic molecules
Co-enzyme A involved in acyl group rxns
Co-enzyme B12 involved in alkyl grp. rxns.
List the factors that determine the rate of a reaction in order of impact
- Substrate concentration
- Enzyme intrinsic ability to catalyse rxn
- Temperature (affect enzyme kinetics)
- denaturation - pH (affect enzyme kinetics)
- H+ affect charge of amino acids at active site
- Alter general structure of the protein
Draw the graph to demonstrate the meaning of Km as it relates to the Michaelis Menton equation. Define Km
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.
Define the Michaelis and Menton equation
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
What is the Lineweaver-Burke plot and what is this used for?
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
Draw a graph to illustrate enzymes with a higher and lower Km value as well as Higher and lower Vmax
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
Compare first order and zero order kinetics
with reference to the Michaelis and Menton graph
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
Distinguish competitive enzyme inhibitors from non-competitive enzyme inhibitors
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.
How does the presence of a competitive enzyme inhibitor affect the rate of the reaction as illustrated by the Vo - [S] curve
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
How is the lineweaver-Burke plot affected by the presence of a competitive enzyme inhibitor
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
How is the Km and Vmax affected by the presence of a non-competitive enzyme inhibitor and why
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.
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.
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)
Do allosteric effectors affect the Km or the V max of the velocity/[S] kinetics
Can affect either or both - remember the difference is sigmoid shape
How do competitive inhibition and non-competitive inhibition of enzymes alter the Velocity/[Substrate] curve
Competitive inhibition: Km changes
Non-competitive inhibition: Vmax changes
Why are allosteric enzymes and their effectors important
End products can inhibit the initial enzymatic process, providing for a negative feedback system
Differentiate a kinase from a phosphorylase
Kinase: adds Phosphate (PO4^-3)
Phosphorylase: adds Phosphoryl (PO3^-2)
What are the functions of the following enzymes
- Glycogen phosphorylase
- Glycogen synthase
- Protein Kinase
Glycogen phosphorylase
- Increased breakdown of glycogen
Glycogen synthetase
- Increased production of glycogen
Protein kinase
- Activates glycogen phosphorylase
- Inactivates glycogen synthetase
- -> favouring glucose production
What are zymogens
Zymogens are pro-enzymes which are modified outside of the cell (cleavage of part of the protein) to become activated.
True or false for the following
- Catalysed enzyme reactions consume energy
- Enzymes are always proteins
- False - Lower activation energy –> catalysis
2. False - Occasionally are RNA
Draw the graph which represents the concept of lowering activation energy
Slide 33/37 from eintegrity Cellular Metabolism, Enzymes
Label the following
- Free energy (Y axis)
- Reaction progress (X-axis)
- Substrate energy (start) higher
- Product energy (end) lower
- Activation energy for uncatalyzed reaction (higher initial spike)
- Activation energy fo catalyzed reaction (lower initial spike)
- Delta G (change in energy substrate to product)
