Tutorial - Week 8 (thermodynamics) Flashcards
1
Q
Energy is transformed using…? List 5 points
A
biochemical reactions (chemical transformation)
- Energy is spent to do work
- Some energy is returned to the surroundings as heat
- Some molecules are end-products, which are simpler, less organised, than the original
source of energy (increased randomness of the universe) - Some energy is used to produce complex macromolecules (decreased randomness).
2
Q
Energy is spent to do…?
A
Work
3
Q
Some energy is returned to the surroundings as…?
A
Heat
4
Q
T/F: Some molecules are end-products, which are simpler, less organised, than the original
source of energy (increased randomness of the universe)
A
True
5
Q
Some energy is used to produce…? Increased or decreased randomness?
A
complex macromolecules (decreased randomness)
6
Q
What is energy and work? The three types of work?
A
Energy is the ability to do work (do something, change something in a system)
Work in living organisms:
1. Mechanical work: moves cells, organisms against gravitational force or frictional force
2. Gradient work: creates concentration gradients or electrical gradients across membranes
3. Synthetic work: making or breaking of bonds and production of molecules
7
Q
Mechanical work: Define
A
moves cells, organisms against gravitational force or frictional force
8
Q
Define Gradient work:
A
creates concentration gradients or electrical gradients across membranes
9
Q
Define Synthetic work:
A
making or breaking of bonds and production of molecules
10
Q
What is the main type of energy used?
A
Potential energy: is stored energy, and the energy attributed to the position or “condition” of an object
* Chemical bond energy: energy stored in chemical bonds, condition or position of the atoms &
electrons within molecule.
* Concentration gradient energy, nuclear energy
In biological systems, biomolecules can be converted into energy via biochemical reactions
11
Q
Chemicals store energy in their ____________
In biological systems, biomolecules can be converted into energy via _________
A
chemical bonds
biochemical reactions
12
Q
Chemical compounds can store energy in their…?
A
Chemical bonds
13
Q
What is an example of a compound that stores energy in its chemical bonds?
A
Petrol
14
Q
How is energy stored in chemicals?
A
- Food obtained from diet is converted into energy
- Covalent bonds store energy
Sugars
Fats - To obtain energy from biomolecules, they are rearranged into other
molecules following several biochemical reactions
Covalent bonds like in proteins, carbohydrates, and sugars
ATP!
15
Q
Describe ATP in terms of energy currency
A
ATP: Is the principal molecule for storing and transferring energy in cells
AKA energy currency
15
Q
Describe ATP in terms of energy currency
A
ATP: Is the principal molecule for storing and transferring energy in cells
AKA energy currency
16
Q
How are biochemical reactions controlled?
A
17
Q
What is the first law of thermal dynamics?
A
the total amount of energy in the universe remains constant, although the form of energy may change
- Energy is converted from one type to another, but it cannot be destroyed
- E.g. Potential energy from chemical bonds is converted into kinetic energy (heat & mobility)
18
Q
What is this an example of?
A
Chemical energy being utilised as the atoms and bonds are changed and energy is released
19
Q
How are biochemical reactions controlled?
A
- Living organisms together with their surroundings constitute the universe
- Living organisms are open systems constantly exchanging material and energy
20
Q
What is the second law of thermal dynamics? Explain
A
21
Q
Cells require sources of ‘free energy’ known as ________?
A
Gibbs free energy
22
Q
Cells can obtain energy from ________?
A
Nutrients (or sunlight)
23
Q
Cells transform free energy into…? Following which law of thermodynamics?
A
ATP, or other energy-rich compounds (1st Law of thermodynamics)
24
Cells are ___________ systems (i.e. temperature is constant)
isothermal
25
The Gibbs free energy function predicts...?
the direction of chemical reactions
26
What does the Gibbs free energy function also predict?
27
Cells produce _______ when they grow, by using free energy from the environment (e.g. sunlight, food)
but create _________ in their surroundings
order
disorder
28
T/F: the entropy of individual reactions might not increase, but the overall entropy of the universe increases
True
29
When considering the overall system (the universe), cells release to their environment...?
Equal amount of energy as heat and entropy
30
In terms of Gibbs free energy:
Reactions are thermodynamically favourable (∆G ___ 0 ) if:
* they release energy in the form __________ and/or,
* they increase the ___________
<
of heat (∆H < 0)
disorder of the system (∆S >0)
31
In terms of Gibbs free energy:
Reactions are thermodynamically favourable (∆G ___ 0 ) if:
* they release energy in the form __________ and/or,
* they increase the ___________
<
of heat (∆H < 0)
disorder of the system (∆S >0)
32
∆G is the...?
driving force in a biochemical reaction, which represents the effect of ∆H and ∆S and at a fixed temperature
33
∆S, Entropy change:...?
describes the variation
of entropy in the system
34
T = ?
Absolute temperature (in Kelvin, K)
35
∆H, Enthalpy change:
variation of the Heat content of the reacting system
It depends on the number and kind of molecular bonds formed/broken (bonds with lower energy are more stable)
36
Explain each part
37
Complete
38
Complete
39
The direction of the reaction depends on the variation of free energy content between reactant and products, ∆G:
* Concentration of each of the molecules in the reaction
* Experimental conditions (e.g. temperature)
* ∆G’0 of the reaction (this is constant to each reaction)
40
∆G < 0 = ?
the reaction proceeds to the right
41
∆G = 0 = ?
the reaction is in equilibrium
42
∆G > 0 = ?
the reverse reaction is favoured
43
What happens in each reaction? Give example
Reaction on the right is called spontaneous because it can occur without the addition of energy
44
T/F: Most reactions are irreversible
False - most are reversible
45
The direction of the reaction depends on...? Give 3 points
∆G
1. Concentration of each of the molecules in the reaction
2. Experimental conditions (e.g. temperature)
3. ∆G’0 of the reaction
46
The reaction tends to occur until the _________ is reached. At equilibrium, the rates of the forward and reverse reactions are ______
equilibrium
equal
47
∆G = 0, the reaction is in _________
equilibrium
48
Nomenclature:
1. ∆G is the measured ...? It depends on __________ conditions
2. ∆G’0 = ?
3. standard conditions (T = 298K, P = 1 atm or 101.3kPa, pH 7.0
(Add three points)
free energy in the reaction
experimental
standard free energy change:
* Initial concentration is 1 mol/L for reactants and products
* unit in Joules/mol (J/mol)
* It is a fixed value for a given reaction
49
The direction of the reaction depends on ∆G:
50
The reaction tends to occur until _______ is reached?
Equilibrium
51
The concentrations of A, B, C & D at equilibrium depend on the...?
equilibrium constant of the reaction, Keq
52
Keq is a constant, characteristic for each reaction?
53
Is this reaction thermodynamically favourable?
Yes - ∆G’0 is negative, the forward reaction proceeds with release of free energy
54
Is the reaction thermodynamically favourable?
Yes it is thermodynamically favourable
55
Is this reaction in equilibrium?
Delta G is less than 0 at -4.4kJ/mol therefore it is thermodynamically favourable and delta G is not equal to 0 therefore it is NOT in equilibrium
56
What does the direction of the reaction depends on? And what other aspects does it depend on?
57
What is this? Define
58
T/F: But in cells, reactions are dynamic, and therefore the concentration of each of the molecules in the
reaction might not be in equilibrium, the temperature is not 25 ̊C (298 K). The actual ∆G depends on the conditions of the reaction and on the concentration of products and reactants. For instance, in cells reactions occur at 37 0 C, the concentration of products and reactants vary
True
59
Label reactants and products
60
If the reactants and the products are in equilibrium then we can replace part of the equation with what?
Both equations on the right cancel out their equivalents in the main equation leaving only Delta G being equal to zero, therefore Delta G = 0 and reaction is in equilibrium
61
Explain this equation
62
What happens in biological systems? Describe bioenergetics and oxidation of glucose
63
A thermodynamically ___________ reaction can be driven by coupling with ____________ reactions
unfavourable
favourable
64
Label the reactions as thermodynamically favourable and unfavourable
65
In coupled reactions, the ∆G ’0 values are ________
additive
In these reactions we sum them together (the two reactions) and the sum becomes thermodynamically favourable - thermodynamically unfavourable can be coupled with favourable to become favourable overall
66
What is the strategy to overcome unfavourable reactions? Draw graph example of thermodynamically favourable and thermodynamically unfavourable reactions
67
High energy compound is a compound containing...?
one or more bonds that when hydrolysed release a large amount of energy (large negative ΔG°)
68
Living organisms use high-energy compounds to...?
drive endergonic reactions (i.e. ΔG >0)
69
List the high energy compounds we learned about
70
High energy phosphates are not a __________ energy. They are ________ and carry energy
long-term storage
transient
71
The usual source of free energy in coupled biological reactions is the energy released by breakage of
___________, such as those in...?
phosphoanhydride bonds
ATP and guanosine triphosphate (GTP)
72
Calculate the ∆G ’0 of these ATP-coupled reactions
Answer in image and Phosphocreatine is a molecule that serves as a rapidly mobilisable reserve of high energy
The sum of the reactions is thermodynamically favourable
73
Calculate the ∆G ’0 of these ATP-coupled reactions
The phosphorilation of the fructose is not thermodynamically favourable so we can pair it with a thermodynamically favourable reaction to make the sum thermodynamically favourable
74
Calculate the ∆G using physiological conditions and concentrations:
When temp is 37 celcius its the same as adding 273 to reach 310 K (kelvin)
Reaction is thermodynamically favourable in these conditions
75
List is releases or uses energy and if thermodynamically favourable or unfavourable
76
Thermodynamics depends on...?
the change of energy in the reaction (∆G) (i.e. it depends in the initial state vs final state)
77
T/F: ∆G does not provide information about
the kinetics (rate) of the reaction
True
78
Thermodynamics does not predict...?
how long the reaction is going to take
79
How fast is the reaction? What is used to calculate it?
Kinetics deals with the time of the reaction and it depends on the activation energy (EA)
80
Define activation energy (EA) (<---- a is little and below)
energy input to start a reaction
81
What is this showing with the purple line?
82
For chemical bonds (in A & B) to break and allow new ones to form (in C & D) the molecule goes into a...?
transition state (higher energy), which is unstable
83
The higher the EA, the _______- the chemical reaction
* The lower the EA, the ________ the chemical reaction
slower
faster
84
The EA of a reaction determines the...?
rate at which the
reaction proceeds
85
How can we speed up biochemical reactions in cells?
86
In a biological context, ________ are special molecules that catalyse biochemical reactions. Enzymes _______ the EA of biochemical reactions
enzymes
lower
87
Biological Oxidation-Reduction reactions (5 MAIN POINTS)
88
Universal electron carriers: A few types of coenzymes and proteins serve as universal electron carriers: What are they?
89
What are two of the Universal electron carriers:
NAD and NADP
90
Define NAD and NADP, describe the structures, and draw. Where is the energy contained?
91
What is a hydride ion?
A hydrogen with two electrons
92
Label the results after oxidised
93
NADH and HADPH act with __________ as soluble electron carriers
dehydrogenases
94
What are two more universal electron carriers? List 4 main points
95
Oxidation & reduction reactions (REDOX reactions), involve?
Are these reactions always coupled?
1. The loss of electrons by one chemical species (it becomes Oxidised)
2. The gain of electrons by another molecule (it becomes Reduced)
Yes
96
OIL RIG is a common mnemonic to remember which is the oxidation and which is the reduction:
Meaning?
Oxidation Is Loss (of electrons) and Reduction Is Gain (of electrons).
97
Electrons are transferred from one molecule (_______) to another (_______) in one of
four ways which are?
donor
acceptor
1) Directly as electrons: Fe 2+ + Cu 2+ ⇆ Fe 3+ + Cu +
2) As Hydrogen atoms: AH 2 ⇆ A + 2e - + 2H +
3) As a hydride ion (:H -) (e.g. NADH is oxidised to NAD + )
4) Through direct combination with oxygen: R-CH 3 + ½ O2 ⟶ R-CH 2 -OH
98
Give the headings for these two columns
99
Describe what happens to the lactate and the NAD+
1. Lactacte and NADH are reducing agents (they are oxidized in the process; they donate electrons)
2. Pyruvate and NAD+ are oxidising agents (they are reduced in the process; they accept electrons)
100
Remember: REDOX reactions, always involve...?
transfer of electrons, an electron donor and an electron acceptor
101
Complete
102
Standard reduction potential, E’ °:
It measures...?
the tendency of a chemical species to acquire electrons in standard conditions (i.e. when the
redox pair is at 1 M concentration, 25 0 C, and pH 7). This is a value in Volts.
103
The standard reduction potential, E’0 , of any redox pair is defined by the reduction reaction:
Oxidising agent + n electrons ---> reducing agent
104
Define Change in reduction potential, ∆E’ 0 , in a redox reaction:
The change in reduction potential of a redox reaction is dependent on the E’0 of the two reactions (i.e. oxidation and
reduction).
105
Label which part is oxidation and which is reduction
106
Each reduction reaction has a _____________, E’ 0 (defined at pH 7, and 250 C),
which is always defined from the _________
Give example?
standard reduction potential
reduction
Example see image
107
Change in reduction potential of a redox reaction, (∆E’0 ), is calculated as?
Give example
E’ 0 from the electron acceptor minus the E’0 of the electron donor
Example in image
108
What is the ∆G’ 0 for the conversion of lactate in pyruvate?
Is the reaction thermodynamically favourable in standard conditions?
No the reaction is NOT thermodynamically favourable in this direction because Delta G is above 0
However, in the opposite direction the reaction is thermodynamically favourable because it would be the opposite and below zero
109
Is the reaction thermodynamically favourable in standard conditions?
Yes because Delta G is below zero and therefore is thermodynamically favourable
110
Role of Enzymes?
catalyse and promote sequences of chemical reactions
111
What are Pathways?
Consecutive reactions catalysed by enzymes. The products of one reaction become the reactants of the next one
112
Define Catabolic pathways:
pathways that degrade organic nutrients into
simple end products to extract chemical energy and convert it into a
form useful to the cell (e.g. ATP, NADH, NADPH, FADH2),
113
Define Anabolic pathways:
pathways that start with small precursor
molecules and convert them into more complex molecules (e.g.
proteins, nucleic acids). These require the use of energy
114
Define Metabolism:
the overall network of enzyme catalysed pathways
(anabolic & catabolic)
115
What is this diagram representing?
116
Key concept: ________ is stored in food (or sunlight) and used in living organisms to do _______ (e.g. create _______, _______-)
Energy
work
order, mobility
117
Key concept: (1st law of thermodynamics)?
Energy is conserved but the form can change
118
Key concept: (2nd Law of thermodynamic)?
Energy is transformed using biochemical reactions but there is always an increase in entropy in the universe
119
Key concept: Changes in enthalpy or entropy create _____________
free energy change
120
A decrease in free energy in the reaction indicates that...?
the reaction is spontaneous and releases energy
(exergonic reaction)
121
In cells, _________ processes are coupled with __________ reactions of high energy compounds to be
_____________ (i.e. to create free energy)
endergonic
exergonic
thermodynamically favourable
122
Electron transfer drives...?
reduction potentials and supply's free energy
