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BCMB20002- Midterm Exam Guide - Comprehensive Notes for the exam ( 14 pages long!)


Department
Biochemistry and Molecular Biology
Course Code
BCMB20002
Professor
Terry Mulhern
Study Guide
Midterm

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UniMelb
BCMB20002
MIDTERM EXAM
STUDY GUIDE

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Afyeda BCMB20002 Notes Semester 1 2017
BCMB20002: Biochemistry and Molecular Biology
Lecture 10
All figures from Lecture 10 slides of T. Mulhern, Melbourne University, March 2017 (unless stated)
Learning Objectives (Enzymes):
1. Explain how enzymes speed up chemical reactions
2. Discuss why enzymes are important in biology, medicine & industry
3. Define the following terms: enzyme, active site, activation energy, transition state, initial rate,
steady-state kinetics, Km, and Vmax.
4. Explain how to experimentally determine Km and Vmax.
5. List the assumptions associated with the Michaelis-Menten steady-state description of enzyme
kinetics
6. Be able to derive the Michaelis-Menten equation using the Calculate the enzyme activity from
experimental data.
7. Generate and analyse plots describing enzyme kinetics
What are enzymes
- Biomolecules, and usually proteins (exceptions include ribosomes, which need RNA)
- Distinctive 3D structure and employ catalytic mechanisms such as weak interactions, acid-base,
covalent and metal ion catalysts
- Enzymes provide a specific environment, i.e. active site, for a given reaction to proceed rapidly
compared to the uncatalyzed or spontaneous reaction
o Cleft or shallow surface
- The active sites of enzymes are lined with functional groups (usually from amino acids) that bind
the substrate(s) and catalyse the chemical transformation to product(s)
- Enzymes affect reaction rates, but not equilibria: E+ S ES EP E + P
- Enzymes LOWER the activation energy required to convert a substrate(s) to product(s) and perform
this function with a high degree of specificity.
o Bind one molecule, or similar molecules
o They provide a different environment for the same reaction to occur in.
- Enzyme catalysed reactions are characterized by the formation of a COMPLEX between enzyme and
substrate (ES)
- Enzyme catalysis is formally described as the stabilization of the transition state through tight
binding to the enzyme. William P. Jencks (1975) Adv. Enzymol.
- deltaG lower is more product.
o We write the equation based on what we think is the product, however reactions always go
towards the side that has the lowest free energy (deltaG).
o Initial conditions is key
o deltaG and equilibrium
o ΔG°' = –RT In Keq
Why are enzymes important
- Some diseases are caused by excessive enzymatic activity, whilst others are caused by deficiency in
enzymatic activity; e.g. Phenylketonuria is caused by a deficiency in the enzyme Phenylalanine
Hydroxylase.
o Autosomal recessive disease
o 1 in 8,000-10,000 newborns
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Afyeda BCMB20002 Notes Semester 1 2017
o Defective phenylalanine hydroxylase
o Sever mental retardation
o Characterized greatly increased concentrations of phenylpyruvate (keto acid of Phe) in
blood and urine
o Decrease in phenylalanine in diet is the treatment
- Many drugs target enzymes either by inhibiting or activating the enzyme target: RELENZA inhibits
the enzyme Neuraminidase from flu virus.
o Inhibits the virus snipping a sugar from a protein.
- Taking pyruvate, take it through acetaldehyde and make ethanol.
Cofactors and Coenzymes
- Not all enzymes
act alone
- Not substrates but
take part in the
reaction
- Some enzymes
require one or
more additional chemical components for activity
- Such heial opoets a e:
o Small inorganic molecules called cofactors, eg Mg2+, K+
o More cople olecules called coezes that transiently carry
functional groups during catalysis of a reaction
Makig ufavourale reatio go
Enzymes provide environments for couple reactions: two reactions happen in the same place at the same
time temporal and special juxtaposition, and deltaG can be added. Big deltaG negative + positive deltaG =
negative delta G = favourable reaction.
How do enzymes work
For simple reversible uncatalyzed reaction:
- Wall between S and P, and that wall is a hill
- Rate of reaction
- the higher the barrier the
slower the reactions
- The rate from S P is faster
than P S
- Transition state: the reaction
can go either way
- The higher the ΔGSP, the slower the reaction
- Transition state is meta stable, cannot be purified
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