Prof.MichelleAarts maarts@utsc.utoronto.ca OfficeHours:Tuesdays2 4pm inSW525 Contactmebyemail: forappointmentsoutsideofficehours for problems, conflicts or missed tests & assignments
Recommended Text
Fundamentals of Biochemistry: Life at the Molecular Level, 3rd Edition by Voet, Voet, and Pratt Wiley Publishing Online text and resources available
2
Publisher websites
Pearson-Prentice Hall Wiley whfreeman
Evaluations!
Quizzes (4) Jan26th,Feb16th,March16th,April6th together 20% of final grade 5 10 questions (MC and written) Midterm 30% of final grade MC, fillintheblanks, short answer Final Exam 50% of final grade (cumulative content) MC, fillintheblanks, short answer Please refer to Syllabus for dates and content
**If you are lacking a pre-requisite you must come see me in person**
Pre-requisites
BGYB10, BGYB11 CHMB41, CHMB42 (organic chemistry)
Bioenergetics
Anabolic Reactions
Catabolic Reactions
10
Metabolic Types
Autotrophs
(H2O, CO2, NH3, H2S)
Photoautotroph (plants) Chemoautotroph (bacteria) (NH3 , H2S, Fe2+)
Heterotrophs
Photoheterotroph (some bacteria) Chemoheterotroph (animals)
11
12
C. elegans
19,100 genes, 5300 metabolic enzymes (28%)
Drosophila
14,100 genes, 2400 metabolic enzymes (17%)
13
Why Study Metabolism? (a.k.a. what you should get out of this course) Whats involved?
Thermodynamics, free energy Reaction kinetics, pathway flux, regulatory mechanisms Enzymes (what do they do? How do they work?) Biosynthesis and breakdown of organic compounds Oxidation and reduction reactions Electron Transport and Photosynthesis
14
15
* Most pathways have branch points - isolated, linear pathways are rare
16
18
19
20
Most metabolic pathways occur in a single direction under physiologic conditions (irreversible) thus are far from thermodynamic equilibrium
21
Regulation of metabolic pathways occurs at the level of rate limiting enzymes 1. Allosteric Control 2. Covalent modification 3. Substrate cycles 4. Enzyme expression (genetic/degradation)
22
Metabolic Pathway Regulation by compartmental separation Concentrate enzymes & cofactors Movement of metabolites between compartments Co-ordinate enzyme regulation locally
23
Bioenergetics
Study of the changes in energy during metabolic reactions Organisms need an input of free energy for:
Mechanical work Active transport of molecules Biosynthesis
Bioenergetic Systems
Biochemical reactions Photosynthesis Oxidative Phosphorylation (Electron Transport Chain) ATP synthesis
Thermodynamics (free energy, G)
25
Entropy (S) of a system can decrease if the S of the surroundings increases Decreased S is accomplished by the release of heat (H, enthalpy)
H Ssystem
surroundings
26
27
28
29
The Standard Gibbs free energy difference (G) tells us if a reaction in one direction is favorable when the concentrations of both the substrates and products is 1.0M.
30
However
The difference between G and G depends on the cellular conditions most importantly concentrations
The actual Gibbs free energy difference (G) tells us if the reaction is favorable when the [substrates] and [products] are something other than 1.0M (Q = mass action ratio).
31
Concentrations at equilibrium (Keq) brings the free energy difference (G) between substrates and products to zero, so there is no net production in either direction.
32
Metabolic Flux and Equilibrium When flux through a pathway changes, the intracellular concentrations of metabolites vary.
Physiologic changes are relatively small Most enzymes catalyze near-equilibrium reactions Can restore balance quickly
G positive
G negative
G ~ 0
33
Near equilibrium reactions are influenced by changes in the [substrates] and [products] without changing flux through the pathway
Not a good control point
[substrates] and [products] have little effect on flux through irreversible reactions
34
35
Enzymes stabilize high energy transition states that would make a reaction unfavorable
36
3-D cleft that binds substrate Small portion of total protein Multiple intermolecular sites of attraction with substrate Unique microenvironment
Conformational change on binding Regulatory sites (specific inhibition) Use of cofactors or co-enzymes
37
38
Enzyme Classifications
Enzyme Class
Oxidoreductases Transferases Hydrolases Lyases Isomerases Ligases
Reaction Catalysed
Oxidation-reduction Move functional groups Hydrolysis Eliminate group & form double bond Isomerization Bond formation (ATP coupled)
39
67
68
Coenzyme A
carboxybiotin
69
40
Serial Coupling
41
Coupling 2 Reactions
2individualreactionsoccurinthesameenzyme activesite(2substrates,2products) Grouptransfer Oxidationreduction
42
43
Energy Currency?
Cells need to be able to store, transport and exchange energy
44
Carbohydrates
45
46
One phosphate ester linked to ribose 2 phosphoanhidrides ATP can donate a phosphoryl group (Pi + ADP) or a nucleotidyl group (AMP + PPi) Transfer is usually to acceptor molecules
47
48
Why ATP?
1. _ 2. _ 3. _
50
Overall G must be negative for a reaction to proceed in a given direction Positive G reactions need a driving energy source Accomplished by coupling hydrolysis of ATP (or other energy carrier) to reaction X+Y ATP XY ADP + Pi
51
Substrate Activation
Whatisactivation? Whydoweneedactivationofmetabolic intermediates?
52
53
Coupled Reactions/Role of ATP The substrate or a side chain of the enzyme may be used as an intermediate acceptor of the phosphoryl group thereby transferring energy to the reaction.
1. 2. X + ATP X-p + Y + H2O X-p + ADP XY + Pi + H+
54
55
56
58
electrons can be transferred or released In oxidation reactions released e- are transferred to cofactor or coenzyme such as NAD+, NADP+, FMN, FAD or ubiquinone (Q)
59
Reduction Potential
A measure of thermodynamic activity ability to accept eStandard reduction reaction is H+ to H2 gas (0.0V) Reduction potential is a measure of electromotive force as determined using an electrochemical cell for a half-reaction
Note: redox potential is often used but refers to the general ability of a molecule to accept or donate electrons (also called e- transfer potential)
60
Reduction potential
e- flow spontaneously from the more readily oxidized molecule to the more readily reduced molecule Std reduction potential for a given molecule is measured against H+ to H2
61
Redox reactions
Dehydrogenases
oxidation is accomplished by the removal of a hydrogen atom (H 1 proton, 1e-) or hydride ion (H+ 1 proton, 2e-)
62
64
Standard reduction potentials for biological half-reactions Erefers to the partial reaction as written: Oxidized + e- Reduced
65
71
NAD
FAD
72
73
66
Carbohydrate pathways
Carbon Fixation, Calvin cycle Glycolysis Gluconeogenesis Glycogen metabolism Pentose phosphate pathway Citric acid cycle
Fatty Acids and Lipid Metabolism (Ch. 16) Fatty acid synthesis Lipid formation
TAGs, phospholipids, eicosanoids, ether lipids, sphingolipids, cholesterol
75
Supplemental Reading
76
Next Class
77
70
78
79