CBI Definitions Flashcards
System
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.
Surroundings
This is simply 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.
Boundary
This is conceptually where the system and the surroundings meet
Thermodynamic temperature
Absolute measure of energy (Kelvin(K)) inside an object
Heat
The process of reaching equilibrium when two objects of different temperatures meet
Enthalpy
Internal energy of a system + pressure x volume
(kinetic + chemical energy)
Entropy
Measure of the number of ways in which energy is distributed across and within components of a
system - thermodynamic measure of system randomness
(thermal energy not able to do work)
Gibb’s Energy
A rationalisation of the relationship between energy available to do work and unavailable which defines spontaneity
Exergonic
Gibb’s energy decreases over the course of the reaction
Endergonic
Gibb’s energy increases over the course of the reaction
Transition state
This is the species of highest energy along a reaction pathway. Transition states occur at
energy maxima and cannot be isolated. In diagrams, the transition state is
commonly designated with a double-dagger symbol ‡.
Activated complex
The range of configurations that occur as a reaction proceeds that are near the transition
state are collectively known as the activated complex.
Activation energy
This is the energy in excess of that possessed by the reactant(s) that is required for the
reaction to proceed. It is denoted with the symbol Ea.
Addition reactions
A chemical reaction between two (or more) molecular species that results in a single
reaction product that contains all the reactants. Addition reactions occur at multiple
bonds in molecules.
Elimination reactions
The reverse of an addition reaction, whereby two components (atoms or functional
groups) are lost. Elimination reactions result in the formation of multiple bonds in
molecules.
Substitution reactions
A chemical reaction in which one atom or functional group in a molecule is replaced by
another.
Rearrangement reactions
The internal connectivity of the atoms within a molecule is changed.
Redox reactions
A specific type of chemical reaction where electrons are transferred from one reactant to
another.
Oxidation
The loss of electrons or increase in oxidation state
An oxidising agent gains electrons during a redox reaction and is therefore reduced during
Reduction
The gain of electrons or decrease in oxidation state
A reducing agent loses electrons during a redox reaction and is therefore oxidised
Aldose
Carbohydrate chain with C=O on the end
Ketose
Carbohydrate chain with C=O in the middle
Hemiacetal
Cyclisation of aldose
Proteinogenic
This refers to substances or molecules that contribute to the creation or synthesis of proteins. (Typically amino acids)
Isoelectric point
The pl or isoelectric point is the pH at which a protein has no net charge
Carbohydrates
Carbohydrates have the chemical formula (CH2O)n and are sugar molecules that are
involved in structure and energy storage in the cell.
Fatty acids
Fatty acids are long carbohydrate chains with a carboxylic acid group at the end. Those
that do not contain C=C double bonds are called saturated fatty acids; those that do
contain C=C double bonds are called unsaturated fatty acids.
Lipids
Lipids are amphiphilic molecules with a hydrophilic head group and a hydrophobic tail. We distinguish between phospholipids, triacylglycerides and sphingolipids.
Membranes
Membranes are lipid bilayers with a hydrophobic core and a hydrophilic border. They
form the diffusion barrier of cell membranes and cell compartments.
Nucleotides
Nucleotides are the basic elements that form DNA and RNA. They consist of a ribose
sugar, a phosphate group and a nitrogenous base.
Proteins
Proteins are comprised of amino acid subunits that are connected by peptide bonds.
Their structure is determined by secondary elements (i.e. alpha-helix and beta-sheets)
that are arranged in 3D. This structure is stabilised by several different covalent and noncovalent bonds.
The Michaelis-Menten equation
Describes the variation of enzyme activity as a function of substrate concentration
Competitive inhibitor
The inhibitor typically resembles the substrate and in the vast majority of cases binds to the active site of the enzyme. Inhibitor and substrate molecules compete to bind the enzyme - both cannot be bound at the same time. In this case, the degree of inhibition depends on the concentration of the substrate. This is the hallmark of competitive inhibitors, their effects can be overcome by the addition of sufficient substrate.
Uncompetitive inhibitor
Does not bind to the unbound enzyme, but to the ES complex once that forms. On binding to the ES complex, the inhibitor prevents the release of the products. Unlike competitive inhibition, uncompetitive inhibition cannot be overcome by the addition of more substrate.
Non-competitive inhibitor
Binds at a site other than the active site and does not prevent the substrate molecules from binding. The inhibitor prevents the enzyme from performing its catalytic function.
Cofactors
Small inorganic metal ions or coenzymes sometimes required for catalytic activity of enzymes
Coenzymes
Small, vitamin-derived organic molecules
Such as NAD+ and FAD
Kinase
A type of enzyme that catalyses the transfer of a phosphate group from a high-energy molecule (such as ATP) to a specific substrate molecule.
Catabolic reactions
Break down molecules into smaller subunits and release energy
Anabolic reactions
Require energy to synthesise complex molecules from simpler/smaller subunits)
Glycolysis
The metabolism of glucose to produce pyruvate with one molecule of glucose being
consumed, and two molecules of pyruvate being produced, alongside the reduction of
two molecules of NAD+ to form two molecules of NADH, and overall net production of two
molecules of ATP from ADP
Gluconeogenesis (GNG)
The de novo synthesis of sugars (typically glucose) from metabolic precursors
Investment phase (of glycolysis)
Steps in glycolysis that require the input of energy, provided by the hydrolysis of ATP
Payoff phase (of glycolysis)
Steps in glycolysis that produce energy in the form of ATP and NADH
Substrate level phosphorylation
A phosphate group is transferred from a high energy substrate to ADP to form ATP
Normoglycaemia
The condition in which there is a normal concentration of glucose in the blood.
Hypoglycaemia
The condition in which there is a concentration of glucose in the blood lower than the
range considered normal
Hyperglycaemia
The condition in which there is a concentration of glucose in the blood higher than the
range considered normal
Proton motive force
Describes the energy that is created by a chemical gradient due to the difference in the
concentration of protons on each side and a charge gradient due to the positive charge of these protons
Oxidative decarboxylation
Reaction that simultaneously reduces a compound and removes carbon dioxide. An
example is the conversion of pyruvate to acetyl-CoA that reduces NAD+ to NADH while releasing one molecule of CO2.
Krebs/TCA cycle
A series of reactions that take place in the mitochondrial matrix that convert acetyl-CoA to
two molecules of CO2, one molecule of ATP, and releases eight electrons that are used to
generate three molecules of NADH and one molecule of FADH2.
Electron transport chain (ETC)
A series of enzyme complexes that perform redox reactions, coupling the transfer of
electrons - from electron donors (NADH and FADH2) to the terminal electron acceptor
(oxygen) - to the movement of hydrogen ions across the mitochondrial inner membrane
into the mitochondrial intermembrane space.
Oxidative phosphorylation
Reaction of the ETC and ATP synthase. Electrons are used to reduce oxygen to water while
a proton gradient is established across the inner mitochondrial membrane. This proton
gradient is the driving force of the ATP synthase to catalyse the reaction of ADP and Pi to ATP.
Hybridisation
Produces degenerate orbitals such that bonding pairs can interact
Molar concentration
Amount of solute / overall volume of solution
Mass concentration
Mass of solute / overall volume of solution
Volume concentration
Volume of solute / overall volume of solution
Dilution factor
Volume of the sample aliquot in the volume of aliquot + solvent
(1:10 -> 1 aliquot and 9 solvent)
Dilution ratio
Volume of sample aliquot relative to the volume of solvent
(1:9 -> 1 aliquot and 9 solvent)
Bronsted Lowry acid
Proton donor
Bronsted Lowry base
Proton reciever
Stereocentre
Geometric point about which 4 different groups are attached
Diastereomer
Stereoisomer that differ in configuration in one or more but not all stereocentres
Epimers
Diastereomers that differ in only one stereocentre
Anomers
Form when saccharides cyclize
Structural isomer
Same composition/ molecular formula but different order
Stereoisomer
Same composition but different 3D arrangement
Optical isomers
Non-superimposable enantiomers
Racemate
Equal proportion of both enantiomers
Enantipure
A single enantiomer
Dipole
Permanent of transient induction of a charge due to slight charges
London dispersion forces
Non-permanent dipoles caused by the variations in electron density within an atom/molecule at any given moment
Permanent induced dipole
Dipoles created by permanent dipoles in neighbouring molecules with an intermediate strength
Ionic interactions
Electrostatic attraction between positively and negatively charged groups
Salt bridges
Electrostatic attraction of both +/ve and -/ve side chains of amino acids within protein molecules
Thermodynamics
the relative energies of reactants and end products in a chemical system and the exchange of energy between the system and it’s surroundings
Bond energy
Energy required to break 1mol of all bonds of the same type within a chemical species
Nucleophile
E- rich and tend to carry a partial of formal -/ve charge
Electrophile
e- poor and tend to carry a partial or formal +/ve charge
Triacylglycerols
Glycerol + 3 fatty acid chains bound by a condensation reaction which produces 3H20 molecules
Glycerophospholipids
Glycerol bound to 2 fatty acids leaving a free OH to bind to a phosphate
Sphingolipids
Have sphingosine synthesised from the amino acid serine and acetyl CoA
Sterol lipids
Derivatives of cyclopentanoperhydrophenanthrene cholesterol are most common in animal plasma membranes
Hydrophobic effect
Energetically unfavourable distribution of H bond network of water molecules
Lipid aggregation
Spontaneous aggregation of amphiphilic lipids into leaflets due to the hydrophobic effect
Nucleosides
Nitrogenous base + sugar
Nucleotides
Nitrogenous base + sugar + phosphate
Nucleic acid
Polynucleotide
Bioanalysis
The investigation of numerous biomolecules using a variety of techniques
