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Chemistry of Biological Interactions (CBI) > CBI 4: Bimolecular Reactions > Flashcards

CBI 4: Bimolecular Reactions Flashcards

1
Q

What can thermodynamics tell us about a reaction and what can it not?

A
  • it tells us whether a reaction proceeds spontaneously
  • but it cannot tell us about the rate of reaction
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2
Q

What is thermodynamics?

A
  • thermodynamics focuses on the relative energies of reactants and products in a chemical system and the exchange of energy between that system and the surroundings
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3
Q

What three topics are considered when talking about thermodynamics?

A
  • enthalpy
  • entropy
  • Gibbs Energy
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4
Q

Define system

A
  • The system is simply the set of (biochemical) reactions and interactions we are interested in studying within a particular boundary
  • For example, this might be the reactants and products in a reaction
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5
Q

Define surroundings

A
  • everything else that is outside the system of interest that is in contact with the boundary of the system, usually the rest of the universe
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6
Q

Define boundary

A
  • This is conceptually where the system and the surroundings meet
  • the boundary has no effect in the interaction between system and surroundings
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7
Q

Describe an open thermodynamic system

A
  • Both mass and energy can be transferred between the system and surroundings
  • e.g. pan of water with no lid on the stove
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8
Q

Describe a closed system

A
  • Only energy (no mass) can be transferred between the system and surroundings
  • E.g. pot of water with a lid on the stove
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9
Q

Describe an isolated system

A
  • No mass or energy can be transferred between the system and surroundings
  • e.g boiling water placed in a well-insulated sealed vessel
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10
Q

What is the First Law of Thermodynamics?

A
  • energy can neither be created nor destroyed; it can only be transferred or changed from one form to another
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11
Q

Define chemical energy

A
  • a type of potential energy related to chemical bonds
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12
Q

What is thermodynamic temperature?

A
  • an absolute measure of the average total internal energy of an object or objects - namely its kinetic energy plus other contributions from other factors
  • units: Kelvin (K)
  • it is proportional to the average of all the energies in all the ways in which it is possible for an object to move, known as degrees of freedom
  • the more components there are in a complex object, the greater the number of possible motions and degrees of freedom
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13
Q

Define enthalpy

A
  • the internal energy of a system plus the product of pressure and volume
  • simply put, it is the total amount of energy (sum of kinetic and chemical potential energy) that a chemical system possesses
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14
Q

What forms can kinetic (heat) energy be in the form of?

A
  • The moving of electrons within an atom
  • The vibration of atoms connected by chemical bonds
  • The rotation and translation of molecules made up of these atoms
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15
Q

What forms can chemical potential energy be in?

A
  • The covalent and/or ionic bonds between atoms/ions
  • The intermolecular forces between molecules
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16
Q

What is bond energy?

A
  • the average amount of energy required (under the gas phase and standard conditions) to break 1 mol of all bonds of the same type within the same chemical species
  • units: kJ mol-1
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17
Q

What is enthalpy change?

A
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18
Q

What happens when deltaH (enthalpy change) is greater than 0?

A
  • an endothermic reaction
  • products have a greater chemical potential energy than the reactants
  • endothermic reactions require input of heat energy in order to proceed
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19
Q

What happens when deltaH (enthalpy change) is less than 0?

A
  • an exothermic reaction
  • reactants have greater chemical potential energy than the products
  • they give out heat energy when they proceed
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20
Q

If enthalpy change is negative, will the reactants or products be more stable?

A
  • the products will be more stable
  • their total bond enthalpy is greater
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21
Q

What is Hess’ Law?

A
  • the total enthalpy change that occurs for a given reaction is independent of the reaction pathwayb
22
Q

Define entropy

A
  • S, the measure of thermodynamic randomness of a system
  • units: J mol-1 K-1
23
Q

What is the Second Law of Thermodynamics?

A
  • the entropy of the entire universe, will always increase over time
24
Q

How do you find the total change in entropy?

A
25
Q

How do you find entropy change of a reaction?

A
26
Q

What does an entropy change greater than 0 mean?

A
  • the reaction increases the dispersal of energy in the system
27
Q

What does an entropy change of less than 0 mean?

A
  • the reaction decreases the dispersal of energy in the system
28
Q

What is Gibbs Free Energy and how would you calculate it?

A
  • it calculates whether a particular reaction will be spontaneous, by relating entropy and enthalpy change
  • G, kJ mol-1
29
Q

Describe what type of reaction when Gibbs energy is less than zero, more than zero and equal to zero

A
30
Q

How does Gibbs energy show that the spontaneity of a reaction?

A
  • once we have accounted for changes in both enthalpy and entropy of a reaction, only those with some free energy (Gibbs energy) are able to proceed without further input of energy
31
Q

What entropy, enthalpy change and hence Gibbs energy do you need for a favourable reaction?

A
32
Q

How does equilibrium affect Gibbs energy? How is that calculated?

A
33
Q

Define transition state

A
34
Q

Define activated complex

A
35
Q

Define activation energy

A
36
Q

Familiarise yourself with where transition state, activation complex and activation energy on a reaction profile

A
37
Q

Familiarise yourself with where transition states, activated complex, activation energy, and intermediates are in a multi-step reaction

A
  • intermediate exists at a local energy minimum between two transition states
38
Q

What is a catalyst?

A
  • a substance that increases the reaction rate without being consumed
  • provide an alternative reaction mechanism that lowers Ea by providing an alternative, or modified reaction pathway, or one in which the transition state is more stabilised
39
Q

What are biological catalysts and how do they work?

A
  • enzymes
  • the active sites of these enzymes are designed to stabilise the transition state, decrease Ea
40
Q

Familiarise yourself with how biological catalysts affect the reaction profile

A
41
Q

Define an addition reaction

A
  • a chemical reaction between two or more molecules species resulting in a single reaction product containing all the reactant products
  • the reactions occur at multiple bonds in molecules
42
Q

Define an elimination reaction

A
  • the reverse of an addition reaction
  • two components (atoms or functional groups) are lost
  • they result in the formation of multiple bonds in molecules
43
Q

Define a substitution reaction

A
  • a chemical reaction in which one atom or functional group in a molecule is replaced by another
44
Q

Define rearrangement reactions

A
  • the internal connectivity of the atoms within a molecule is changed
45
Q

Define redox reactions

A
  • a type of chemical reaction where electrons are transferred from one reactant to another
46
Q

Describe SN1 reactions

A
  • the rate-determining step only depends on one chemical species
  • in the reaction profile, the first (larger) activation energy must be overcome for the reaction to proceed (RDS)
47
Q

Describe SN2 reactions

A
  • the rate-determining step depends on two chemical species
  • one group is attached to a central atom, and at the same time, another is becoming detached (the leaving group)
  • hence a single step determines the reaction rate
48
Q

Compare SN1 and SN2 reactions

A
  • in the SN1, it is possible for the nucleophile to attack the carbocation from either side of the molecule, which is relevant when the substitution is occurring at a stereocentre
49
Q

Which type of substitution reaction is more common in biological systems?

A
  • SN2
  • SN1 are less common
50
Q

What is NAD and what is its role in biological systems?

A
  • nicotinamide adenine dinucleotide (NAD) is a redox agent
  • the nicotinamide ring of NAD+ acts as the hydride/electron acceptor
51
Q

What is FAD and what is its role in biological systems?

A
  • flavin adenine dinucleotide (FAD) is a common redox reagent
  • the ring system of FAD acts as a hydrogen/electron acceptor
  • FAD is the electron acceptor/carrier
  • FADH2 is the electron donor

Chemistry of Biological Interactions (CBI) (8 decks)

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