Thermodynamics Lectures 1-11 Flashcards
1
Q
What is the sign for delta, sigma and proportional to?
A
∆
∑
∝
2
Q
What is Boyles Law?
A
Pressure and Volume are inversely proportional to eachother.
pV = nRT
Pressure: Pa or J/m^3
Volume: m^3
Number: mol
Temperature: K
R = 8.314 J/Kmol
3
Q
Forms of energy in biochemistry:
A
Potential:
Bond Energy.
Chemical Energy (conc difference across gradient).
Electrical Energy (of charge seperation).
Kinetic:
Thermal Energy (of molecular motion).
Radiant Energy (of photons).
Electrical Energy (of moving charged particles).
4
Q
What is the first law of thermodynamics?
A
Energy cannot be created or destroyed, it just exists in different forms.
5
Q
Relationship between System and Surroundings?
A
Universe - System = Surroundings.
6
Q
What is an open system?
A
A system in which energy and matter are exchanged.
7
Q
What is a closed system?
A
A system where only energy is exchanged.
8
Q
What is an isolated system?
A
A system where no exchange is taking place.
9
Q
What is internal energy?
A
The energy within a system.
A substance which has:
-energy of bonds,
-energy of molecular movements,
-a state function.
10
Q
What is the equation for change in energy?
A
∆E = q + w
Change in energy = heat + work.
11
Q
What is work and heat?
A
Work is the displacement of an object.
Heat is a change in the temperature of an object.
12
Q
What is the equation for work?
A
Work = force x distance.
Can be calculated if you run a reaction through a closed vessel fitted with a piston.
The volume of gas increases, pushing out the piston. Work done is the change in volume of gas.
w = -P∆V
Negative because energy is being transferred into the surroundings.
13
Q
What is the equation for enthalpy?
A
H = E + PV
When a system is at constant pressure, enthalpy change depends on change in internal energy and volume.
∆H = ∆E + P∆V
14
Q
Combining the equations for ∆E, w and ∆H.
A
∆H = q
15
Q
What is positive enthalpy?
A
Heat is absorbed into the system.
System gains enthalpy from surroundings.
∆H(sys) > 0
16
Q
What is negative enthalpy?
A
Heat is released by the system.
The system loses enthalpy.
∆H(sys) < 0
17
Q
What is the change in enthalpy?
A
∆H = H(products) - H(reactants)
18
Q
How can we measure ∆H?
A
Bomb Calorimeter.
∆H = q = ms∆T
specific heat capacity = energy needed to raise 1 kg of water by 1 degree.
For water, its 4.184 J g^-1 K^-1
19
Q
What are standard conditions?
A
1 mol
298.15 K
1 atm
∆H0 = q = ms∆T
20
Q
What is Hess’s Law?
A
∆H0 = ∑n∆Hf0(products) - ∑m∆Hf0(reactants)
∆Hf0 is enthalpy of formation.
Is negative if reaction is exothermic.
21
Q
What is the enthalpy of formation?
A
The amount of enthalpy involved in generating 1 molecule of it from its elements.
Forward and reverse reactions are equal in magnitude but opposite in sign.
22
Q
Entropy on a molecular scale:
A
S = k lnW
where k = Boltzman constant, 1.38 x 10^-23
S ∝ W
23
Q
What is the standard entropy, S0?
A
∆S0 = ∑products - ∑reactants
24
Q
Relaxed state vs Stretched state:
A
Relaxed:
molecules move freely,
high entropy,
low enthalpy.
Stretched:
molecules are aligned orderly,
low entropy,
high enthalpy.
25
Entropy and protein structure:
Denatured state:
very flexible, free rotation,
high entropy,
low enthalpy.
Native state:
rigid structure,
low entropy,
high enthalpy.
26
∆universe = ?
∆system + ∆surroundings
27
Summary:
Some processes are spontaneous and irreversible.
Spontaneity is determined by change in entropy.
28
What is the equation for Gibbs Free Energy?
G = H - TS
∆G = ∆H - T∆S
All the available energy in a system.
The maximum amount of work which may be performed.
29
∆G is less than, greater than or equal to 0:
If ∆G<0, the reaction is spontaneous.
If ∆G = 0, the reaction is at equilibrium.
If ∆G>0, the reverse reaction is sponteanous.
30
How do you calculate standard free energy, ∆G0?
∆G0 = products - reactants.
31
What is the equation for standard free energy?
∆G0 = -RT LnK(eq)
32
What are the standard conditions for biochemists?
pH 7
55.5 M for water
1mM
33
What does the equilibrium constant K'eq describe?
The product:reaction ratio at equilibrium.
34
What types of bonds can you name?
Ionic Bonds
Covalent Bonds
Non-covalent Bonds
Hydrogen Bonds
Dipole-Dipole interactions
Induced Dipoles
Van der Waals
35
What is electronegativity?
The ability of an atom to pull bonding electrons in a covalent bond towards itself.
36
What is a dipole?
A dipolar molecule has a gradient of electronegativity.
37
What is and induced dipole?
When a dipole encounters a non-polar molecule, it attracts the bonding electrons towards itself, inducing a dipole.
38
What are Van der Waals forces?
London forces, dipole-dipole interactions and hydrogen bonding.
39
What is the cause of steric hindrance?
Van der Waals forces cause other particles to repel.
Repulsive force dominates at very short distances.
Steric hindrance refers to the physical obstruction of a chemical reaction by the presence of bulky or large groups on a molecule. These groups can hinder the approach of other molecules or reagents, making it more difficult for a chemical reaction to occur.
40
What is a hydrophobic interaction?
Water molecules straddle hydrophobic surfaces.
Low entropy.
To increase entropy, polar and non-polar molecules segregate.
41
What is a buffer?
A solution of an acid and its conjugate base.
Resistant to changes in pH.
42
What is proton hopping?
pH is a measure of free protons, but they cannot exist freely in solution.
They are immediately hydrated to form hydronium, H₃O+.
When one H joins H₂O, another quickly leaves.
It immediately joins a neighbouring water molecule.
This is proton hopping.
43
Ionisation of Acids and Bases:
Acids are proton donors
Bases are proton acceptors
A proton donor and corresponding acceptor form an acid-conjugate base pair.
44
What is Ka?
The acid dissociation constant.
45
Does a strong acid/base have a high or low pKa?
Strong acids have low pKa
Strong bases have high pKa
High pKa means not willing to give up a proton.
46
What is the Henderson-Hasselbach equation?
pH = pKa + log A-/HA
47
What is an amphipathic compound?
A compound with both philic and phobic molecules.
48
What is the difference between the gel phase and fluid phase?
Gel:
individual molecules do not diffuse.
Polar heads in uniform.
Fatty acid chains are motionless, tightly packed.
Fluid:
individual molecules diffuse into the plane.
Fatty acid chains are irregularly organised.
49
What is lateral diffusion?
Movement of molecules within inner/outer layer of the bilayer.
Very rapid, no catalysis needed.
Confined to one region of the membrane.
50
What is transverse diffusion?
Movement of molecules between the leaflets of the bilayer.
Rarely occurs spontaneously.
Catalysed by specialised enzymes.
51
What are the three types of lipid transporter enzymes?
Flippase:
Inner -> Outer
Floppase:
Outer -> Inner
Scramblase:
Moves lipids to reach equilibrium.
52
What equation tells us how much energy a particular substance will introduce into a system?
For n moles of substance A, potential µ:
µA = µA⁰ + ∆Ga/na
µA⁰ is the chemical potential under standard conditions.
53
∆G = ∆G0 + RT Ln(A)
(A) is the concentration.
54
what are the units and symbol for activity?
weird looking y
units are mol^-1
Use activity when (A) > 20mM
55
what are the units and symbol for activity?
weird looking y
units are mol^-1
Use activity when (A) > 20mM
56
How do you estimate the mean velocity of a molecule moving randomly?
V = √3kBT/m
kb = Boltzmann constant.
m = mass.
57
What is the equation for osmotic pressure?
Π = iCRT
c = concentration
R = 8.314
T = temperature
i = van't hoff index
58
What do the terms isotonic, hypotonic and hypertonic mean?
isotonic means pressure inside and out is equal.
hypotonic means water enters the cell, causing it to burst because there is more water inside the cell.
hypertonic causes the cell to shrink because there is more water on the outside of the cell.
59
What is the Nernst Equation?
How do you calculate electrical energy?
∆V = -RT/zF x LnCb/Ca
∆U = zF∆V
z = electrons
F = faraday constant = 98,485 C mol^-1.
60
What equation enables you to calculate the electrochemical potential?
Vm = RT/nF x LnQ
61
How do polar solutes diffuse?
they must shed their hydration shell to diffuse through a non-polar space.
Very endergonic, ∆G very high.
A transporter forms a non-covalent interaction with the dehydrated solute.
This is a substitution for hydrogen bonding. Reduces ∆G of diffusion.
62
what is oxidation?
loss of electrons by one molecule
63
what is reduction?
gaining electrons of one molecule
64
what is the oxidation state?
the theoretical charge of an atom of all of it bonds were ionic.
65
what is electron affinity?
The relative tendency of a molecule to accept or donate am electron.
66
what is an electrochemical battery?
Two half cells containing chemical species with different electrochemical potentials.
Electrons flow spontaneously from donor to acceptor.
Driven by electromotive force (emf)
67
What is the standard potential? E'⁰
tendency of a chemical species to acquire electrons from an electrode.
(its tendency to become reduced).
If total potential for redox pair is positive, redox will proceed spontaneously.
Defined with reference to Hydrogen.
68
potential vs free energy and the link between them.
w = nFE'⁰
w = -∆G
∆G = -nFE'⁰
69
∆G = -nFE'⁰
taken one step further,
∆G = -RT x LnK(eq)
nFE'⁰ = RT x LnK(eq)
E'⁰ ∝ LnK(eq)
70
when T = 25 degrees,
E = ?
E = E'⁰
the actual electrical energy, transferred via electrons during a reaction as it proceeds towards equilibrium.
the amount of energy transferred can be tuned by altering Q ( E ∝ Ln)
71
ATP is the common intermediate linking processes in living organims. Favourable under standard conditions;
relieves electrostatic repulsion bettwen O- in resulting ADP
relieves electrostatic repulsion between O- in released phosphate groups.
ADP and Pi are each more soluble than ATP.
72
Energy from ATP doesn't come from hydrolysis, where does it come from?
Chemical group transfer.
2 step reaction:
Transfer of Pi to another molecule, more reactive now.
Exchange of Pi for some other desired group.
73
What is a co-enzyme?
They require components of a system to do their job.
NAD+ and phosphorylated analogue NADP+ undergo reduction to NADH and NADPH.
They accept a Hydride. Added to front or back of the nicotinamide ring.
74
NAD+ usually functions in what sort of reaction?
catabolic oxidation.
75
NADPH usually functions in what sort of reaction?
anabolic reduction.
76
what do you know about FAD?
contains 2 redox sites, can adopt 3 states.
FAD - electron acceptor.
FADH - acceptor or donor
FADH₂ - electron donor
77
FAD deficiency:
synthesised by riboflavin
deficiency causes ariboflavinosis
inflammation, itchy eyes and anaemia.
78
Ubiquinone: Lipid-soluble e- carrier.
readily accepts electrons.
upon accepting two electrons, picks up two protons forming ubiquinol.
Ubiquinol can diffuse freely through membranes, carrying e- and protons with it.
79
what is the equation for photosynthesis?
6H₂O + 6CO₂ -> C₆H₁₂O₂ + 6O₂
80
Chloroplast Structure:
Organelle filled with thylakoids which stack to form grana.
Thylakoids contain photosystems.
Grana increases SA:V.
PS 680 and 700
81
What is chlorophyll?
A pigment found in the light-harvesting complex of a photosystem.
Chlorophyll a is very efficient, b not so much.
Absorbs energy from sunlight.
82
Photosystem II:
Chlorophyll at reaction centre P680 gives up an electron.
Electron goes to electron transport chain.
Electron replaced by one taken from water.
2H₂O -> O₂ + 4H+ + 4e-
83
Proton Translocation:
Electrons from PSII transferred to cytochrome b₆f complex.
Passage is energetically unfavourable, coupled to unfavourable translocation of protons through the thylakoid membrane.
Protons accumulate in the lumen.
84
ATP synthesis:
protons flow down the concentration gradient, into the stroma, via ATP synthase.
Energetically favourable, coupled to unfavourable ADP phosphorylation.
85
Photosystem I:
chlorophyll at reaction centre P700 accepts PSII electron.
P700 absorbs more light energy, releases electron.
Electron enters another electron transport chain
Electron replaced by another one from PSII.
86
NADPH synthesis:
Electron from PSI enters a second transport chain.
Rerredoxin is key component
2 ferredoxins transfer two electrons to reduce NADH+ to NADPH.
catalysed by ferredoxin-NADP reductase.
Whole process costs 4 photons, 8 ATP is generated.
87
Cyclic Phosphorylation:
ferredoxin transfers electron to cytochrome b6.
electron transferred to pump-driving electron transport chan.
Proton gradient drives ATP synthase.
88
LDR:
water split into molecular oxygen, protons, electrons.
Electron transport to drive H+ pumps, driving ATP synthase.
Reduction of ferredoxin, driving NADPH formation.
89
What are the three main steps in the Calvin Cycle?
Carbon fixation.
Reduction.
Regeneration.
90
What is involved in Carbon Fixation in the Calvin Cycle?
Ribulose bisphosphate reacts with carbon dioxide, to form an unstable 6 carbon compound. (catalysed by rubisco).
6 carbon compound splits into two 3-phosphoglycerates.
91
What is involved in reduction in the Calvin Cycle?
3-phosphoglycerate is phosphorylate to make 1,3-bisphosphoglycerate.
dephosphorylated to give glyceraldhye-3-phosphate.
Uses NADPH and ATP made during the LDR.
92
What is involved in Regeneration during the Calvin Cycle?
every 6 glyceraldehyde-3-phosphate, five are regenerated into three 5-carbon Ribulose Bisphosphate.
One G3P goes towards the synthesis of glucose.
93
What is glycolysis?
Splits 1 glucose into 2 pyruvate, get 2 NADH and 2 ATP.
Costs 2 ATP, produces 4 ATP.
94
What is involved in pyruvate decarboxylation?
pyruvate to acetyl-CoA, yields 2 NADH per glucose.
95
Describe the citric acid cycle:
acetyl-CoA and oxaloacetate
Energy released from acetyl-CoA, which is split into C2, which joins oxaloacetate to form citrate.
CoA is recycled back to pyruvate decarboxylation.
This process is catalysed by citrate synthase.
96
Describe the Citric Acid cycle:
a-ketoglutarate
Citrate is oxidised to ἁ-ketoglutarate (C5).
CO₂ is released as a byproduct.
NAD+ reduced to NADH.
This is oxygen dependent, so NAD+ must be recycled.
Ketoglutarate used to synthesise glutamate, cells can now synthesise other amino acids, which slows the cycle down.
97
Describe the citric acid cycle:
Succinyl-CoA
a-ketoglutarate (C5) is oxidised to succinyl-CoA (C4).
carbon dioxide released as byproduct.
NAD+ reduced to NADPH.
98
Describe the citric acid cycle:
Succinate
Succinyl-CoA is hydrolysed
CoA is removed, energy released.
Energy drives GDP phosphorylation.
GTP readily converted to ATP, so cycle yields 2 ATP per glucose.
99
Describe the citric acid cycle:
Fumarate.
Succinate (C4) is oxidised to fumarate (C4)
FAD is reduced to FADH₂, which later reduces ubiquinone in oxidative phosphorylation.
100
Describe the citric acid cycle:
Malate.
Fumarate is hydrated to malate (C4).
101
Describe the citric acid cycle:
oxaloacetate after malate.
Malate is oxidised to oxaloacetate.
NAD+ is reduced.
Oxaloacetate is a precursor in aspartate biosynthesis.
102
What are the products, per glucose, of the citric acid cycle?
6 NADH
2 FADH
2 GTP
4 CO2
103
What is oxidative phosphorylation and how does it work?
NADH donates electron to complex 1 of the electron transport chain (etc).
Complex 1 pumps protons into the intermembrane space.
Complex 1 donates electron to ubiquinone, the nonpolar carrier.
FADH₂ from succinate oxidation donates to complex II which in turn reduces ubiquinone, to ubiquinol.
104
THE ETC continued:
starting with ubiquinol
ubiquinol travels through the membrane, finds and reduces complex III.
Complex III pumps protons into the intermembrane space.
Complex III eventually reduces cytochrome C.
Cytochrome C travels through the IMS, finds and reduces complex IV.
Complex IV pumps protons into IMS.
Complex IV reduces oxygen, forming water.
105
What is the role of ATP synthase in the ETC?
F0 and F1
ETC mkes gradient between IMS and mitochondrial matrix.
Protons diffuse in matrix, a channel facilitates this.
F0 region of ATP synthase is integrated into the membrane.
F1 region occupies the matrix.
106
What does F0 do?
proton channels utilise proton hopping to facilitate net movement of protons.
Protons bind to IMS side of the channel.
Another proton is dislodged within the channel.
Proton released from matrix side of the channel.
In F0, proton hopping drives rotational movement of the channel.
107
F1 in ATP synthase, what is important about it?
has alternating subunits around a central, asymmetrical spindle. (alpha and beta, bind ADP and Pi).
Rotation of F0 causes spindle to turn.
Chemical environment of subunit active sites is altered, driving ATP synthesis.
108
Anaerobic respiration:
only glycolysis can occur when oxygen isn't present.
You get 2 NADH and 2 ATP.
Glucose -> 2 pyruvate + 2H+ + 4e-
2 NAD+ + 4e- + 2H+ -> 2 NADH
2 Pi + 2 ADP -> 2 ATP + 2 H2O
109
Methanogens use carbon dioxide as a terminal electron acceptor, this allows what to proceed?
oxidative phosphorylation.
CO2 + 4H2 + 8e- -> CH4 + 2H2O
110
Fermentation:
extracts additional chemical energy from pyruvate.
Makes NAD+ from NADH
111
Lactic acid fermentation:
Pyruvate + NADH -> lactic acid + NAD+
