BIOL 201 Study Guide - Winter 2018, Comprehensive Midterm Notes - Adenosine Triphosphate, Protein, Amplitude Modulation
BIOL 201
MIDTERM EXAM
STUDY GUIDE
Fall 2018
Living things convert energy from one form to another, but never created or destroyed!
○
Ex. Plants take energy from photon, convert to chemical energy through PS
○
Animals do NOT consume energy! (First law of thermodynamics!)
•
Ex. You can store chemical energy in the form of more biomass
○
Caveat: organisms store energy during growth
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ATP= energy currency of cells
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Conversions of chemical bonds into heat and work
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~20% of genome devoted to metabolism
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Number 2: organisms store energy temporarily during activity
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Metabolism: the science of energy conversions
We’re converting a simple molecule into a complex organism
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Seems to go against 2nd law of thermodynamics that disorder and entropy are always increasing in the universe!
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Not all energy is equal! It can differ in its quality
•
Doesn’t work both ways
○
Potential E of mass on pulley is very high quality energy, has high amount of order
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Energy in water tank low quality, due to random motion of molecules
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Joule showed that increase in water temperature (thermal E) was directly related to height of mass spinning paddles from pulley
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Are we getting something from nothing?
Consume high quality energy (food, chemical bonds) and convert it into low quality energy (heat and work)
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Quality can never be spontaneously recovered!
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Living organisms convert high quality energy into low quality energy!
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Gibbs: defined total energy as ENTHALPY (H)
○
G= free energy or available energy, or H - “unavailable energy”
○
G =H - TS (total energy minus that which is no longer available
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Entropy: disorder, number of states in which system exists (Microsystems)
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The quality of energy depends on how much is “free”
•
Cells capture the free energy released by atp hydrolysis to create order
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G = GFINAL - GINITIAL
G = H - T S **for an isolated system, H = 0
Entropy increases; S > 0
The change in Free Energy determines whether a process occurs spontaneously
•
G < 0 for spontaneous processes!
•
Standard free energies are ADDITIVE!
○
If not standardized, must convert to conditions of reaction under study
○
A
→
B
→
C
G° A
→ C
= G° A
→ B
+ G° B
→ C
Free Energy values are “standardized” ( G°’) where T=298K, P= 1 atm, pH = 7.0, [ ]’s = 1M
•
Animals consume ENERGY QUALITY
So how do you ever make it over a transition state?
•
Catalysts lower energy of transition state
•
Always have some reactants and products in equilibrium state
•
Delta G of transition state is positive?
•
Amount of free energy a molecule has fluctuates
○
Ex. Trk dimer can spontaneously undimerize, takes a few tries to form dimer
○
Interaction of surrounding molecules that collide with protein to alter
○
free energy state
If fluctuations exceed threshold, will drive formation of transition state
○
(can go in either direction!)
Probability of spontaneously acquiring this energy allows
○
calculation of rate constant
Signaling pathways are DYNAMIC and in EQUILIBRIUM
○
The energy of a molecule fluctuates!
•
Enzymes catalyze reactions by lowering the free energy
•
of transition states
Releasing Free Energy is not Always “Easy”
Capture energy in glucose to drive ATP formation!
○
Glucose (chemical E) →CO2+ H2O ( G < 0)
•
Can then use this energy via ATP hydrolysis
○
ADP + Pi→ATP ( G > 0)
•
Organisms burn ATP to drive unfavorable reactions
•
Cells capture free energy in ATP
Creates an overall negative delta G
○
Coupling: using energetically favorable reactions to drive energetically unfavourable
reactions
•
Lecture 1: Introduction to Energy
January 12, 2018
5:44 AM
Section 1 Page 1
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find more resources at oneclass.com
Creates an overall negative delta G
○
Coupling: using energetically favorable reactions to drive energetically unfavourable
reactions
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ATP can induce strain in protein structure
○
Every atom in structure moved away from energy minimum caused by protein folding,
raising overall energy of protein
○
If proteins is interacting with other reactant molecules, this strain can distort reactants
and catalyze reaction!
○
Ex glycogen phosphorylase: atp binding is distant from glycogen binding site, strain
○
rips apart glycogen and releases glucose
ATP binding, hydrolysis, phosphate release or ADP release can all trigger this step
○
ATP binding/hydrolysis can distort the 3D structure of protein
•
Reduction ; gaining an electron
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Oxidation: losing an electron
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Fuels are oxidized by metabolic enzymes
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Electrons are carriers of energy: hot potato of metabolism
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Redox reactions provide a basis for energy transduction
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Harvester molecule of energy for all of metabolism
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NAD+ may be useful in a wide range of therapies
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Tuberculosis: Active form binds NADH and inhibits cell wall synthesis enzyme
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Wlds mice have delayed degeneration, overproduction of NAD+
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NAD+ is the principle electron acceptor in metabolic redox reaction
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G°’NAD+= 52.6 kcal/mol, G°’FAD = 43.4 kcal/mol
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FAD is used when the available free energy could not reduce NAD
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Enzyme that capture electrons have evolved to bind and orient molecules in
○
redox to perfectly catalyze reaction
Large machines to catalyze reactions of small molecules, precise positioning
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of molecules required for proper reaction to occur
GAPDH brings NAD+into position to be reduced
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Ultimately passed to oxygen
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Electrons are passed to O2to generate the proton motive force in mitochondria
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GFINAL = GINITIAL, GPRODUCTS = GREACTANTS, G = 0
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But... Equilibrium is a dynamic state!
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“Equilibrium” is the state at which Free Energy has been minimized
•
What about the other definition of equilibrium?
•
A + B
↔
C + D
Rate forward= kf[A][B]
Rate reverse= kr[C][D]
At equilibrium: kf[A][B] = kr[C][D]
[C][D]/[A][B]= kf/kr= equilibrium constant, Keq.
All chemical reactions have a forward and reverse rate
○
Keq> 1 favors the forward reaction.
○
Energy can be released to drive a chemical reaction
•
G = GFINAL - GINITIAL
G = H - T S
Reactants
↔
Products
H < 0 and S > 0
a.
H < 0 and | H| > |T S|
b.
H > 0 and |T S| > | H|
c.
When is G < 0?
•
G°’ can be calculated from initial conditions and Keq
•
G°’ = -RT ln Keq
G = G°’ + RT ln [products]/[reactants] (initial concentrations!)
G°’ = -1362 log Keq (in kcal/mol)
G = G°’ + 1362 log [products]/[reactants] (in cal/mol)
Equilibrium
The reaction will proceed in the left to right direction, producing a net increase in the
concentration of B
a.
the reaction will proceed in the right to left direction, producing a net increase in the
concentration of A
b.
the reaction is at equilibrium
c.
If the equilibrium constant for the reaction A↔B is 0.5 and the initial concentration of A is 25
mM and of B is 0 mM, then:
1.
f the equilibrium constant for the reaction A↔B is 0.5 and the initial concentration of A is 25
Here are some practice problems..
Section 1 Page 2
find more resources at oneclass.com
find more resources at oneclass.com