Download IB Chemistry Definitions

Chemistry: Definitions
Topic 1 - Stoichiometry
Avogadro’s constant:
Chemical reaction:
Compound:
Element:
Excess:
Formula, empirical:
Formula, structural:
Ion:
Limiting reagent:
Molar mass:
Mole:
Yield, percentage:
Yield:
The number of particles in 12g of 12C. (NA)
A reaction in which bonds in the reactants are broken and bonds in the products are
formed resulting in an energy change between the reacting system and its
surroundings.
Two or more types of atoms chemically bonded together.
A substance that contains only one type of atom.
The reactant which there is more of than needed to react with all of the limiting
reagent.
The formula obtained by experiment, showing the simplest whole number ratio of
atoms of each element in a particle of the substance.
Shows the arrangement of atoms and bonds within a molecule.
Charged particles.
The reactant which will determine the theoretical maximum amount of product
formed.
The mass of a mole of a substance.
The amount of substance that contains a number of specified species equal to
Avogadro’s constant.
The experimental yield as a percentage of the maximum theoretical yield.
The amount of product.
Topic 2 and 12 – Atomic Theory
Atomic emission spectra: The characteristic line spectrum that occurs as a result of energy being supplied to
individual elements. When energy is supplied to an atom, e - are excited from their
ground state to a higher energy level. The e- dropping from higher energy levels to
lower emit energy, which can be observed in a spectrum. As e- can only exist in
fixed energy levels, the energy in the emissions are characteristic for each type of
atom. Lines converge toward high energy end of spectrum as the energy levels
themselves are convergent.
Atomic number:
Number of protons in the nucleus.
Aufbau principle:
The principle that states that lowest energy levels are filled first. The starting
order is 1s2s2p3s3p4s3d…
Hund’s rule:
Orbitals within the same sub-shell are filled singly first.
Ionization energy, first: Energy required to remove one e- from an atom in its gaseous state. Increases across
a period (due to increasing nuclear attraction), except for slight drops (due to the
commencement of pairing of e- into orbitals  greater electron repulsion).
Decreases down a group (due to increased number of energy levels  increased
electron shielding).
Isotope:
An atom that contains the same number of protons but a different number of
neutrons.
Mass number:
Total number of nucleons.
Mass spectrometer:
A device for determining relative atomic masses and their relative abundances.
Composed of:
1) vaporizer (where the sample is vaporized),
2) ionizer (where atoms are bombarded with high energy e-  e- knocked
off the atoms. Only ions with a +1 charge are formed, in practice),
3) accelerator (where an electric field accelerates them),
4) deflector (where a magnetic field deflects them; the smaller the mass
and the higher the charge, the greater the deflection) and
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5) detector (which measures both the mass and relative amounts of ions
present.
Orbital:
A region of space around the nucleus of an atom that is occupied by a maximum of
two e- at any given time. The types of orbitals are s (spherical), p (dumbbellshaped), d and f.
Pauli’s exclusion principle: e in single orbital must have opposite spin.
Relative abundances:
The percentage of natural occurrence of an isotope of an element.
Relative atomic mass:
The weighted mean of all the naturally occurring isotopes of the element relative to
12
C. No units.
Valence electrons:
The e- in the highest main energy level.
Topic 3 and 13 – Periodicity
Alkali metals:
Group 1 elements. Strength of metallic bond gets weaker as atoms get larger.
Anion:
A – charged ion. Decrease in size across a period as they are isoelectronic but have
an increased nuclear charge. Contain more e- than their parent atom, so they are
larger in size.
Atomic radius:
Half the distance between the nuclei of two bonded atoms of the same element.
Decreases across period as nuclear charge increases. Increases down a group
because of greater number of energy levels.
Catalyst:
A substance that increases the rate of reaction while being recoverable in the end
stage of the reaction, unchanged. Examples of catalytic transition metals: Fe is
used in Haber process; V2O5 in Contact process; Ni in hydrogenation reactions;
MnO2 with hydrogen peroxide.
Cation:
A + charged ion. Decrease in size across a period. Contain less e - than their parent
atom, so they are smaller in size.
Chloride:
Chlorides of Na and Mg have an ionic structure, while all the remaining chlorides of
period 3 elements have simple covalent structures. Still, Al2Cl6 can act as a poor
conductor. NaCl dissolves in water to give a neutral solution, MgCl 2 gives slightly
acidic solution, while all other chlorides react vigorously with water to produce
acidic solutions of HCl together with fumes of hydrogen chloride.
Colored complex:
A complex is a compound in which molecules or ions form dative bonds to a metal
atom or ion. Colors are due to e- transitions between different d orbitals.
Co-ordination number:
Number of lone pairs bonded to the metal ion. Cl - often gives 4 coordinate bonds, CNgives 6, H2O gives 6 and NH3 gives 4 or 6.
D-d transition:
The excitation of an e- from the lower of two energy level groups to the upper. As
the ligand approaches the metal, the five d orbitals split. The difference in energy
between the two levels corresponds to the wavelength of visible light, as incoming
light causes energy of a particular wavelength to be absorbed by e- that are
excited from the lower level to the higher. The amount that the d orbitals are split
will determine the exact color.
Degenerate:
Of equal energy. In a free ion, the five d orbitals are degenerate.
Electronegativity:
Relative measure of the attraction that an atom has for a shared pair of e- when it is
covalently bonded to another atom. Inversely proportional to size of atom  F is
most electronegative.
Group:
Elements with the same number of valence e-.
Halide ions:
Ions of the halogens. Their presence can be detected by the addition of silver
nitrate. AgCl is white, AgBr is cream-colored, and AgI is yellow. Silver halides react
with light to form silver metal.
Isoelectronic:
Containing the same number of e-.
Ligand:
A molecule or ion that can donate e-.
Melting point:
Depends on both the structure of element and type of attractive forces holding the
atoms together. Increases across the period while following elements which exhibit
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metallic bonding (due to increased strength following increased number of valence
e-.) Highest m.p. of period lies with macromolecular covalent structure (with very
strong bonds). Sharp decrease in m.p. with elements that exhibit simple molecular
structures with only van der Waals’ forces between them. Lowest m.p. with noble
gases, which are monatomic. Down Group 1, m.p. decreases as atoms get larger and
strength of metallic bond get weaker. Down Group 7, van der Waals’ forces
increase as molar mass increases  m.p. increases.
Metalloid:
An element that possesses some of the properties of a metal and some of a nonmetal. While metal oxides tend to be basic and non-metal oxides tend to be acidic,
metalloid oxides such as aluminium oxide can be amphoteric.
Oxide:
Metal oxides are ionic (explains conductivity, m.p. and b.p.) and react with water to
form alkaline solutions. SiO2 is covalent macromolecular, and the remaining oxides
are simple covalent. Oxides of period 3 elements are solid from Na2O to P4O10 and
P4O6, while SO3 and Cl2O7 are liquid and SO2 and Cl2O are gases at 25C. Al2O3 and
SiO2 do not react with water, but Al2O3 can act amphoterically depending on
whether it is reacted with a base or an acid. Remaining oxides are acidic.
Period:
Elements with the same outer shell of valence e-.
Periodicity:
The repeating pattern of physical and chemical properties as shown by the different
periods.
Structure, giant covalent: Very hard but brittle. Very high m.p. and b.p. Do not conduct in any state. Insoluble.
Structure, giant ionic:
Hard but brittle. High m.p. and b.p. Conduct when molten or aqueous, but not as
solids.
Structure, giant metallic: Malleable, not brittle. M.p. and b.p. dependent on no. of valence e -. Good conductivity.
Structure, molecular covalent:
Usually soft and malleable unless hydrogen bonded. Low m.p. and b.p. Do not
conduct in any state. Often soluble in non-aqueous solvents, unless they can
hydrogen bond to water.
Transition element:
An element that possesses an incomplete d sub-level in one or more of its oxidation
states. Often very efficient catalysts as they can exist in a variety of oxidation
states (all except Ti have oxidation state of +2). Form colored complexes.
Topic 4 and 14 – Bonding
Allotrope:
Occur when an element can exist in different crystalline forms, such as in carbon,
which can exist as graphite, buckminsterfullerene and diamond (ooh, pwetty).
Diamond is exceptionally hard because there is no plane of weakness in the molecule
made up of sp3 hybridized carbon atoms. In graphite, the carbon atoms are sp 2
hybridized. Remaining e- after the three  bonds, are delocalized, resulting in the
fact that graphite is an excellent lubricant and a good conductor of electricity.
Bond length and strength: Depends on strength of attraction that two nuclei have for the shared e -. Generally,
the stronger the bond, the shorter its length.
Bond polarity:
A polarity caused by a difference in electronegativity between the elements. The
greater the difference, the greater the polarity.
Bond, :
Pi bond. A radial bond caused by the sideways overlapping of p-orbitals. Has two
regions of e- density. Double bonds have one  bond, while triple bonds have two
which are perpendicular to each other.
Bond, :
Sigma bond. An axial bond caused by orbitals overlapping along a line drawn through
the two nuclei. Single, double and triple bonds have one  bond.
Bond, covalent:
Bonding by the sharing of e-. The e- are shared and attracted by both nuclei resulting
in a directional bond between the two atoms.
Bond, dative:
A bond in which both e- come from one of the atoms. Also known as coordinate bond.
Bond, ionic:
A bond by which e- are transferred from one atom to another to form ions with
complete outer shells. In an ionic compound the + and – ions are attracted to each
other by the electrostatic force between them, and build up into a strong lattice.
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Have relatively high m.p. Ionic bonds occur between elements with a great
difference (>1.8) in electronegativity.
Conductivity:
The extent to which a substance can conduct electricity. Must possess e - or ions that
are free to move.
Delocalization:
The sharing of a single e- pair by more than two atoms.
Forces, dipole:dipole:
Permanent electrostatic forces of attraction between polar molecules. Stronger than
van der Waals’.
Forces, Hydrogen bonding: Occurs when hydrogen is bonded directly to a highly electronegative element (N, F,
or O). Stronger than dipole:dipole forces.
Forces, van der Waal’s:
Temporary dipole forces due to momentary unevenness in spread of e -. Weakest of
intermolecular forces. Increase with increasing molar mass.
Formal charge theory:
1) If compound is covalent, treat the entire molecule; if ionic, treat each
ion separately.
2) Determine total no. of valence e- available.
3) Organize atoms such that there is a central atom (usually the most
electronegative) surrounded by ligands.
4) i) One pair of e- between central atom and each ligand atom, ii)three
more pairs on each ligand (except hydrogen), iii)remaining e- pairs around central
atom.
5) Calculate formal charge on central atom. Should be equal to charge on
species, otherwise form a multiple bond with ligand atom that has most – formal
charge. Repeat 5.
Formal charge:
A hypothetical measure of the number of e- originating from an atom. F = V – (n +
b/2), where V is valence e-, n is e- in lone pairs and b is e- shared as bonds.
Hybridization:
The combination of orbitals to create new orbitals that are more energetically
feasible for bonding. Bonds that are sp3 hybridized have a regular bond angle of
109.5, sp2 have 120, and sp have 180.
Lewis structure:
Diagram showing arrangement of e- in a molecule. Usually only shows valence shells.
Metallic bonding:
The valence e- in metals become detached from the individual atoms so that the
metals consist of a closely packed lattice of + ions in a ‘sea’ of delocalized e -. Forces
of attraction are between ions and e- and not between the ions themselves, which
means that metals are malleable and ductile.
Molecular polarity:
Depends on both the bond polarity and the symmetry.
Resonance hybrid:
Structures that arise from the possibility to draw a multiple bond in different
positions equivalently. Can be better explained by delocalization.
Solubility:
The extent to which one substance dissolves in another. ‘Like tends to dissolve like.’
VSEPR theory:
Valence Shell Electron Pair Repulsion theory. States that pairs of e- arrange
themselves around the central atom so that they are as far apart from each other
as possible. Greater repulsion between lone pair of e- than bonded pairs.
Topic 5 – States of Matter
Gas:
Widely spaced particles that completely fill the container.
Ideal gas:
A gas for which the relationship pV = nRT holds true.
Liquid:
Has fixed volume and takes up shape of container.
Maxwell-Boltzmann distribution:
Graph showing the distribution of kinetic energies among molecules.
Molar volume:
At 273 K and 1 atm, one mole of any gas will occupy 22.4 dm 3.
Solid:
Has fixed shape and fixed volume. Particles held together by intermolecular forces in
a fixed position.
Topic 6 and 15 – Energetics
Bond enthalpy:
The average enthalpy change of breaking a bond between gaseous atoms into its
constituent gaseous atoms.
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Born-Haber cycle:
Energy cycles for the formation of ionic compounds. If there is little agreement
between the theoretical and experimental values, this could indicate a degree of
covalent character.
Hf = Hat(1) + Hat(2) + HIE(1) + HEA(2) – HLatt
Calorimetry:
A device for measuring enthalpy changes for reactions. In a simple calorimeter all
the heat evolved in an exothermic reaction is used to raise the temperature of a
known mass of water.
Electron affinity:
Enthalpy change when an e- is added to an isolated atom in the gaseous state.
Endothermic:
A reaction in which energy is absorbed. H is +. Reactants more stable than products.
Enthalpy of atomization, standard: Standard enthalpy change when one mole of gaseous atoms is formed from
the element in its standard state under standard conditions.
Enthalpy of combustion, standard: Standard enthalpy change for complete combustion of a substance in
oxygen.
Enthalpy of formation, standard:
Enthalpy change when one mole of the compound is formed from its
elements in their standard states under standard conditions.
Enthalpy:
The internal energy stored in the reactants. Only changes in enthalpy can be
measured.
Entropy:
A measure of the disorder of a system. The absolute entropy can be found in terms
of the probability of a state existing. Things causing entropy to increase: 1)
increase of number of moles of gaseous molecules; 2) change of state from solid to
liquid or liquid to gas
Exothermic:
A reaction in which energy is evolved. H is –. Products more stable than reactants.
Gibb’s free energy:
Must be – for reaction to be spontaneous.
G = H – TS
Heat:
A measure of the total energy in a given amount of substance.
Hess’ law:
Enthalpy change for a reaction depends only on difference between enthalpy of
products and enthalpy of reactants  independent of pathway.
Lattice enthalpy:
The endothermic process of converting a crystalline solid into its gaseous ions, or the
reverse exothermic process. The lattice enthalpy increases with decreasing size of
the ions and increasing charge.
Spontaneity:
A reaction that has a natural tendency to occur.
Standard conditions:
298 K and 1 atm.
Temperature:
A measure of the average kinetic energy.
Topic 7 and 16 – Kinetics
Activated complex:
Created during a bimolecular process. Not a chemical substance which can be
isolated, but consists of reacting particles in which bonds are in the process of
being broken and formed. Can break down to form either the products or back to
the original reactants.
Activation energy:
The minimum amount of energy required for a reaction to occur between two
particles. The other requirement is that the particles have to have an appropriate
geometry of collision.
Arrhenius equation:
An equation showing the relationship between the temperature and the rate
constant.
K=Ae(-Ea/RT)
Bimolecular process:
A reaction which occurs when two species collide and interact.
Catalyst:
Provide an alternative pathway for a reaction such that the activation energy
required to reach the activation complex is lowered. Can be divided into two types:
homogenous catalysts are in the same phase as the reactants, while heterogeneous
ones are in a different phase. Heterogeneous catalysts tend to work by bring the
reactant particles into close alignment by adsorbing them onto the catalytic
surface.
Concentration, effect of: Increasing concentration results in an increased frequency of collisions. Where the
curve evens out depends on the total amount of the limiting reagent involved. If
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Half-life:
Molecularity:
Order of reaction:
Rate constant:
Rate expression:
Rate of reaction:
Rate-determining step:
Surface area, effect of:
Temperature, effect of:
Unimolecular process:
the concentration of the limiting reagent is doubled without compensation in volume
for the increase in amount, then curve will stabilize at a different level.
The time taken for the concentration of the reactant to fall to half of its initial
value.
Number of species taking part in any specified step in the reaction.
The rate is always proportional to the concentration of a reactant raised to a power,
where the power is the order of the reaction with respect to that reactant.
The constant of proportionality in the rate expression. Unit is: (mol dm -3)1 – overall order
s-1.
An equation that shows the relationship between the concentrations of the reactants
and the rate of the reaction. Every species in the rate expression must occur in the
rate determining step or in an equilibrium occurring before it.
The rate of increase of concentration/mass of one of the products or the rate of
decrease of concentration/mass of one of the reactants.
The slowest step of a reaction. This determines the rate of the entire reaction.
Increasing surface area results in an increased frequency of collisions.
Increasing the temperature increases the frequency of collisions of the molecules,
but more importantly, increases the proportion of molecules with kinetic energy
greater than or equal to the activation energy.
A process in which a single species breaks down into two or more products.
Topic 8 and 17 – Equilibrium
Closed system:
A system in which neither matter nor energy can be lost or gained. An equilibrium can
never occur in a system that is not closed.
Contact process:
The synthesis of sulphuric acid, where V2O5 is used as a catalyst.
Equilibrium constant:
For a reaction aA + bB  cC + dD, where the small letters are coefficients and
capital letters are the reactants, the equilibrium constant is [C]c[D]d/[A]a[B]b.
Variable units.
Equilibrium, dynamic:
An equilibrium in which the rates of the forward and reverse reactions are the same.
Haber process:
The synthesis of ammonia, where Fe is used as a catalyst.
Optimum temperature:
For exothermic reactions such as the Haber process, the optimum temperature is the
best compromise between yield and rate.
Homogeneous reaction:
A reaction in which all the species involved are in the same phase.
le Chatelier’s principle:
If an equilibrium is subjected to a stress, the equilibrium will shift to minimize the
effect of the stress.
Phase equilibrium:
When the rate of vaporization is equal to the rate of condensation.
Vapor pressure:
The partial pressure of a vapor. Boiling occurs when a liquid’s vapor pressure equals
the external pressure. The stronger the intermolecular forces the lower the vapor
pressure at a particular temperature.
Topic 9 and 18 – Acids and Bases
Acid properties:
React with:
1) Indicators;
2)Bases, in neutralization reactions (form a salt and water with hydroxides
and metal oxides; form a salt with ammonia);
3) Reactive metals (those above copper in reactivity series) (form salt and
hydrogen);
4) carbonates and hydrogencarbonates (form a salt, CO2 and water).
Amphoteric:
Can have the properties of both a base and an acid, depending on whether it is
reacting with a base or an acid.
Brønsted-Lowry:
An acid is defined as a proton donator, while a base is a proton acceptor.
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Buffer:
Charge density:
Concentrated:
Conductivity:
Conjugate:
Diprotic:
End point:
Equimolar:
Equivalence point:
Indicator:
Lewis theory:
Monoprotic:
pH:
Salt hydrolysis:
Strong:
Titration:
Water, ionic product of:
Weak:
A solution that resists changes in pH when small amounts of acid or alkali are added
to it. When a small amount of acid is added, the excess of H + ions causes the
equilibrium to shift to the left  balances the difference. When a small amount of
alkali is added, the OH- ions react with the H+ ions to form water. The decrease in
[H+] is compensated for by an equilibrium shift to the right. Vice versa for alkali
buffers. Buffer solutions are made by several means:
1)strong base + excess weak acid;
2) strong acid + excess weak base;
3) weak acid + same acid’s salt;
4)weak base + same base’s salt.
Charge over size.
High number of moles of solute per dm3 of solution.
The more a solution is dissociated into its ions, the greater its conductivity.
The species remaining after an acid has lost a proton (conjugate base) or a base has
gained one (conjugate acid).
pKa + pKb = pKw
Where one mole of sulphuric acid produces two moles of hydrogen ions, e.g. H 2SO4.
The point at which the indicator changes color most rapidly.
Containing equal concentrations.
Where the acid and base are in equimolar quantities. Exactly enough to react with
each other.
A weak acid or base in which the dissociated form is a different color to the
undissociated form. The end point occurs when the pH is approximately equal to the
pKin value, assuming that the color changes when [In-]  [HIn]. Ideally, the end
point corresponds to the equivalence point in a titration.
An acid is defined as an e- acceptor (e.g. BF3) and a base is an e- donator (e.g. NH3) by
dative bond.
Where one mole of the acid produces one mole of hydrogen ions, e.g. HCl.
Power of hydrogen.
– log [H+]
The process by which a salt is broken down by water. The acidity of the salt depends
on:
1) its derivations (salts derived from a strong acid and weak base will be
acidic in solution, considering that the ions of the weak base will combine, leaving an
excess of H+. The strong acid will not combine as it is completely dissociated, as
per definition. Vice versa with strong acid and weak base);
2) charge density of cation (high charge density results in strong
attraction to the lone pair of one of six water molecules surrounding the ion, a
process by which the water molecule loses a hydrogen ion, i.e. leaving the solution
acidic).
An acid or a base that dissociates completely into its ions. K a >> 1. Some strong acids:
hydrochloric, sulphuric, nitric (weaker than other two). Strong bases: hydroxides
of alkali metals.
Technique for quantitative measure of concentration of a solution. Consider when
90% of the required base has been added to a 1M strong acid that is to be
neutralized. Only 10% of the acid remains, meaning 0.01M, giving a pH of 2. When
99% has been added, the pH is 3, etc.
The equilibrium constant for the dissociation of water into its ions, where [H 2O] is
taken to be constant. Value of Kw increases as temperature is increased, as the
dissociation is an endothermic process.
pKw
An acid or base that only slightly dissociates into its ions. K a << 1. Some weak acids:
ethanoic, carbonic. Weak bases: ammonia, aminoethane.
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Topic 10 and 19 – Oxidation and Reduction
Anode:
Where oxidation takes place. In electrolysis, it is the + electrode and anions are
attracted here.
Cathode:
Where reduction takes place. In electrolysis, it is the – electrode and cations are
attracted here.
Electrolysis:
Passage of electric current through an electrolyte. Amount of discharge is affected
by: 1) current; 2) charge on ion,
3) duration of electrolysis.
Electrolyte:
A substance which does not conduct electricity when solid, but does when molten or
in aqueous solution and is chemically decomposed in the process.
Electrolytic cell:
Used to make non-spontaneous redox reactions occur by providing energy in the form
of electricity from an eternal source.
Electroplating:
A process of coating one metal with a thin layer of another metal, by electrolysis.
Half cell:
A metal in contact with an aqueous solution of its own ions.
Oxidation number:
Ox. no. of:
a) elements: 0;
b) ion: its charge;
c) oxygen: -2 (except in peroxides, -1);
d) hydrogen: +1 (except metal hydrides, -1);
e) fluorine: -1.
Oxidation:
The loss of e-, the gain of oxygen, the loss of hydrogen or the increase in oxidation
number.
Oxidizing agent:
A substance that readily oxidizes other substances. Oxidizing agents are thus
reduced. The higher the oxidation number, the better an oxidizing agent it is,
generally.
Reactivity:
A measure of the readiness of a substance to gain or lose e .. The stronger the
reducing agent or oxidizing agent, the more reactive it is.
Redox reaction:
A reaction in which there is a transfer of e-, i.e. reduction and oxidation occurring
simultaneously.
Reducing agent:
A substance that readily reduces other substances. Reducing agents are thus
oxidized.
Reduction:
The gain of e-, the loss of oxygen, the gain of hydrogen or the decrease in oxidation
number.
Salt bridge:
Allows the free movement of ions in a voltaic cell. Paper dipped in a saturated
solution of KNO3 is an example of a salt bridge.
Shorthand notation:
For a voltaic cell. Example: Cu(s)/Cu2+(aq) || H+(aq) / H2(g)
Standard conditions:
298 K, 1 atm, 1.0 M.
Standard electrode potential:
Measuring a potential cannot be done as this interferes with the system
being investigated. However, the electrode potential of one half cell can be
compared against another half-cell, by convention, the hydrogen half-cell, which is
arbitrarily given a value of 0 V.
Standard electromotive force:
Difference between the two standard electrode potentials of the two half
cells. Ecell
Standard hydrogen electrode:
Arbitrarily assigned a potential of zero. Electrode consists of an inert
metal such as platinum dipped into a 1 M solution of HCl, where hydrogen gas at 1
atm flows in. Platinum black, a very finely divided platinum, catalyzes the electrode
equilibrium.
Voltaic cell:
Two different half-cells connected together to enable to e- transferred during the
redox reaction to produce energy in the form of electricity. The e - are produced at
the half-cell that is most easily oxidized.
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Topic 11 and 20 – Organic Chemistry
Acidity:
Carboxylic acids are weak acids as the – charge on acid anion can be delocalized over
three atoms and does not readily attract H+ ions. Amines are weak bases. Can be
considered as substituted compounds of NH3.
Alcohol, primary:
With two hydrogen atoms on the neighboring carbon atom (next to the hydroxyl
group). Can be oxidized to aldehydes (by loss of hydrogens) and then to carboxylic
acids (by gain of oxygen). Ethanol can be oxidized to ethanal by the orange Cr 2O72ion, which itself becomes reduced to the green Cr 3+ ion.
Alcohol, secondary:
With one hydrogen atoms on the neighboring carbon atom. Can be oxidized to ketones
(by loss of hydrogens).
Alcohol, tertiary:
With no hydrogen atoms attached to the neighboring carbon atom. Cannot be
oxidized further.
Benzene:
Hexagonal shape with delocalized  bonds. Undergo substitution rather than addition
reactions.
Boiling and melting point: Depend on intermolecular forces. The greater the intermol. forces, the higher the
m.p. and b.p.
Bromination:
Yellow/orange bromine is decolorized when added to an alkene due to addition
reaction. Used to test for alkenes.
Carbocation:
A cation in which the carbon carries most of the + charge. Can be formed during S N1
substitution.
Carbon:
Group 4 element which always forms 4 covalent bonds, as it has 4 e- in its valence
shell.
Chiral center:
An asymmetric carbon atom, i.e. has four different functional groups attached to it.
Cis-isomer:
The geometric isomer in which the similar groups are on the same side of the double
bond. Commonly polar.
Condensation reaction:
Reaction in which two molecules join together with the loss of a small molecule,
typically water.
Dehydration:
Loss of water. Alcohols can be dehydrated when they are refluxed with condensed
sulphuric acid. As sulphuric acid is an oxidizing agent  able to react with the
product, phosphoric acid is frequently used instead.
Enantiomer:
See ISOMERS, OPTICAL.
Environment, hydrogen:
The immediate neighborhood (neighboring and next carbon) of a hydrogen atom.
Esterification:
Process by which an alcohol and a carboxylic acid are converted into an ester and
water, often with acid catalysis.
Fission, heterolytic:
Bond breaking in which the more electronegative of the two atoms joined by the bond
takes both of the e-.
Fission, homolytic:
Bond breaking in which each atom takes one of the e- in the bond, creating free
radicals.
Fragmentation pattern:
Excess energy from impact of e- forming ion in mass spectrometer will often cause
molecule to fragment. The mass of the fragments can indicate details about
structure of original molecule.
Free radical:
A species containing at least one unpaired e-, as a result of homolytic fission. Very
reactive.
Func. gr., alcohol:
-OH. IUPAC: -anol.
Func. gr., aldehyde:
-CHO. IUPAC: -anal.
Func. gr., alkane:
No functional group. IUPAC: -ane.
Func. gr., alkene:
C=C. IUPAC: -ene.
Func. gr., amide:
-CONH2. IUPAC: -anamide.
Func. gr., amine:
-NH2. IUPAC: amino- or –ylamine.
Func. gr., carboxylic acid: -COOH. IUPAC: -anoic acid.
Func. gr., ester:
-COO-. IUPAC: alkyl acid-oate, e.g. methyl propanoate. Derived from carboxylic acid
and alcohol. Often used as flavoring as they have characteristic smell.
9
Func. gr., ether:
Func. gr., halogenoalkane:
Func. gr., ketone:
Halogenoalkane, primary:
-O-.
-X (i.e. –Cl, -Br, -I). IUPAC: halogeno-.
-CO-. IUPAC: -anone.
Halogenoalkanes that have one alkyl group attached to the carbon atom bonded to
the halogen. Undergo SN2 mechanism in nucleophilic substitution.
Halogenoalkane, tertiary: Halogenoalkanes that have three alkyl groups attached to the carbon atom bonded to
the halogen. Undergo SN1 mechanism in nucleophilic substitution.
Homologous series:
A group of compounds that can be described by a general formula. Have similar
chemical properties, but gradually changing physical properties. When all other
factors remain constant, increased molar mass means increased intermolecular
forces. Often, long carbon chains can negate the effect of a polar end  molecule
is non-polar.
Hydration:
Addition of water. Ethanol can be formed from addition of water to ethene.
Hydrocarbon:
Compounds containing only carbon and hydrogen.
Hydrogenation:
Addition of hydrogen. Can be used to reduce number of double bonds in
polyunsaturated vegetable oils present in margarine, causing it to become a solid at
room temperature.
Hydrolysis:
Process by which a molecule is broken down by water.
Isomer:
Different compounds that have the same molecular formula.
Isomers, functional group: Where the isomers contain different functional groups.
Isomers, hydrocarbon chain: Where there is a difference in the structure of the hydrocarbon chain.
Isomers, optical:
Where a molecule shows optical activity in its mirror images. Occurs when there is
one or more chiral centers.
Isomers, positional:
Where the position of the functional group is different.
Isomers, stereo-:
Where the molecules have a different spatial arrangement of atoms and hence
different 3D shapes. Subdivided into geometric and optical isomers (enantiomers).
Isomers, structural:
Where the atoms have a different structural formula altogether. Subdivided into
positional, hydrocarbon chain and functional group isomers.
Knocking:
Pre-ignition, a result of a great number of free radicals. The greater the octane
rating, the less likely it is that knocking occurs. Knocking can also be reduced by
antiknock agents, such as lead. Unfortunately, lead is poisonous when released into
atmosphere.
Mechanism, SN1:
A unimolecular process by which a halogenoalkane undergoes nucleophilic substitution.
A two-step mechanism: a rate-determining step in which the bond between the
carbocation and the halogen are broken, followed by a step in which the nucleophile
is attracted to the carbocation. Faster than SN2, as the formation of the
intermediate carbocation is faster than the S N2 route which involves a transition
state with relatively high activation energy.
Mechanism, SN2:
A bimolecular process by which a halogenoalkane undergoes nucleophilic substitution.
Mechanism involves formation of a transition state which involves both of the
reactants.
Monomer:
Components of a polymer.
Nucleophile:
According to Siw, “nuclear loving.” The species that donates the e - pair in an organic
chemical reaction. A nucleophile is also a Lewis base. Typical nucleophiles are CN -,
OH- and NH3.
Nucleophilic substitution: Substitution that occurs with a halogenoalkane reacting with a nucleophile. Rate
depends on:
1) nature of halogen atom (the less reactive the atom  the weaker the
bond with the C  it reacts more readily);
2) nature of halogenoalkane (tertiary > secondary > primary).
Octane number:
Measure of the combustion efficiency of petrol engine fuel Heptane is assigned an
arbitrary value of 0, while isooctane is assigned an octane number of 100.
10
Optically active:
Can rotate the plane of polarization in opposite directions. Enantiomers are optically
active.
Organic chemistry:
The chemistry of carbon compounds.
Peptide bond:
-C=ONH-. Bond formed as the result of condensation reaction between carboxyl
group from one aa and the amino group from the other.
Peptide, di-:
Two aa’s joined together.
Peptide, oligo-:
Several aa’s joined together.
Peptide, poly-:
More than 20 aa’s joined together.
Peptide, tri-:
Three aa’s joined together.
Peptide:
Molecule formed by aa’s joined together by peptide bonds (by condensation reaction
in which water is lost).
Polarimeter:
An instrument for measuring the degree of rotation of the plane of polarization.
Polymer:
Gigantic molecule made up of monomers.
Polymerization, addition: Forming a polymer by addition of monomers.
Polymerization, condensation:
Forming a polymer by substitution reaction between monomers, each having
two functional groups.
Potassium dichromate:
K2Cr2O7. A strong oxidizing agent.
Reaction, addition:
A reaction in which the reactant is added across a C=C bond, converting it to a C-C
bond. Addition reactions with water requires an H2SO4 catalyst. Addition reactions
with hydrogen use Ni as catalyst.
Reaction, substitution:
A reaction in which one group is substituted for another. Substitution reactions with
halogenoalkanes are nucleophilic substitutions. Benzene does not undergo
substitution reactions readily as its  bonds are delocalized.
Reflux:
A condenser which causes any vapor produced to condense and returns to the flask
and continues to react. If the carboxylic acid is desired from the oxidation of a
primary alcohol, this must be done under reflux. On the other hand, if the aldehyde
is desired, this can be distilled from the reaction mixture as soon as it is formed.
Saturated:
Containing only single bonds. Alkanes are saturated.
Spectrometry, mass:
Separating ions according to mass.
Spectroscopy, IR:
Analyzing the bonds present within a molecule by sending infrared light through it,
causing the bonds to absorb radiation of characteristic frequencies.
Spectroscopy, NMR:
Analysis of hydrogen environments to deduce the structure of a molecule. Measured
in ppm relative to TMS.
Trans-isomer:
The geometric isomer in which the similar groups are on different sides of the
double bond. Commonly non-polar.
Unsaturated:
Containing double bonds. Alkenes are unsaturated. Can be tested for by bromination.
Option B – Medicine and Drugs - SL
Addiction:
Problem with opiates, in which a dependency on a drug is created.
Adrenaline:
A naturally occurring hormone and stimulant. Released during stress. Responses:
1) Increased pulse;
2) dilation of pupils;
3) sweating;
4) diversion of blood to muscles;
5) decreased blood clotting time. Fat insoluble. Both amphetamine and
adrenaline are based on the framework of a benzene ring with a two carbon chain
and an amine (NH2 or NH) group at the end.
AIDS:
Acquired Immune Deficiency Syndrome. Develops from HIV.
Alginates:
Often combined with antacids. Prevent acid in stomach from rising into esophagus
and causing ‘heartburn.’
Amine:
Primary amines have one R group attached to N atom. Secondary have two on at least
one N atom. Tertiary have three on at least one N atom.
11
Amphetamine:
Fat soluble molecule which mimics noradrenaline. Similarity is so strong that it can
replace noradrenaline in its storage sites, resulting in a flood of displaced
noradrenaline molecules that bind to other neural proteins and set of a number of
signals  euphoria.
Analgesic, mild:
Have triad of properties:
1) analgesic (pain relief);
2)antipyretic (fever reduction);
3) anti-inflammatory (reduces swelling). Believed that they work by
blocking synthesis of prostaglandins.
Analgesic, strong:
Analgesics that bind with specific chemical receptors in brain that receive pain
messages  stopping the transmission of pain. They are almost all related to
morphine. Family is called the opium alkaloids.
Analgesic:
A drug which relieves pain without the aid of sleep. Two types:
1) mild;
2)strong.
Antacids:
Bases that neutralize excess acid. They are just barely soluble  neutralize
gradually.
Antibiotics, broad spectrum: Antibiotics that are effective against a wide range of bacteria. This is initially
prescribed until the specific diagnosis is found.
Antibiotics, narrow spectrum:
Antibiotics only effective against certain types of bacteria. Prescribed
once the specific diagnosis is found.
Anti-coagulant:
Has blood-thinning properties.
Antivirals:
Three possible approaches:
1) Trojan Horse (joins the replication process, inhibiting replication of the
virus. Selectively toxic as it is activated by viral enzyme);
2) Retrovirus inhibitor (inhibits RNA from acting as a template for DNA
replication);
3) blunting (preventing escape of new viruses by inhibiting neuraminidase
enzyme which cuts open cell membrane).
Aspirin:
Derived from salicylic acid, which was unpleasant to use due to its acidity. The phenol
group is substituted with an acetyl group in aspirin, but it is still acidic due to its
alkanoic acid group. Has anti-coagulant properties, but there can be allergic
reactions to it and it can induce Reye’s Syndrome in children, a potentially fatal
liver and brain disorder.
Bacteria:
Have slightly different structure to mammalian cells: have a cell wall. Penicillin
prevents this wall from being made, and the internal pressures within the cell
builds up and causes it to burst.
Benzodiazepenes:
Class of depressants, including valium, prozac and mogadon. Benzodiazepenes work on
chemical receptors in brain by binding to a special protein at the synapse of nerve
junctions, causing gap between nerves to widen  prevents nerve cell from
producing signal. The ethanol works on a different part of the same protein. The
synergistic effect of these two working together can result in neural shutdown.
Blood-brain barrier:
Can only by passed by fat soluble molecules.
Caffeine:
A tertiary amine. Can
1) promote mild dependence;
2) act as a mild diuretic;
3) increase anxiety (when taken in excess);
4) cause insomnia. Known as respiratory stimulant, as it increases rate of
respiration, by blocking inhibition of ATP. It does so by mimicking the shape of the
ATP and causes the inhibiting enzyme to bind to it instead.
Cephalosporins:
Variants of penicillin created to overcome the action of penicillinases. Broad
spectrum antibiotics.
12
CNS:
Codeine:
Depressant:
Designer drugs:
Dimethicone:
Drug administration:
Drug development:
Drug:
Endorphins:
Ethanol:
Gas chromatography:
Heroin:
HIV:
In vitro:
Central Nervous System.
Derived from morphine by replacing H in one of alcohol groups with methyl group.
Drugs which depress CNS by interfering with transmission of nerve impulses in the
neurons. Effects depend on dosage: no effect  tranquilizing effect  sedative 
sleep-inducing  lethal.
Modifications to structure of natural drugs.
An anti-foaming agent often used with antacids. Allow gas bubbles to coalesce and be
expelled.
Five methods:
1) Oral (subjected to digestive process; easiest);
2)Rectal (efficient, cultural biases);
3) inhalation (drug can only be absorbed through lungs);
4) Parenteral (see PARENTERAL);
5) Patches (absorbed directly through skin barrier, allow absorption to take
place gradually).
A disease is selected, and targets along the disease process are identified, which
may be vulnerable to interference by a drug. Lead molecules are considered, and
selected according to the drugs which seem most effective, easiest to
manufacture, have an advantage over existing drugs and are profitable. Phase I
trials assess toxicology of drug. Phase II trials are clinical; the efficacy and
dosage are determined. Phase III trials give the drug to thousands of closely
monitored patients. If approved at this stage, drug is launched, after which comes
the Phase IV trials, which is the post-launch monitoring of drug, which may lead to
product extension.
A chemical which does one or more of the following:
1) alter mood or emotions;
2) alter incoming sensory sensations;
3) alter physiological state.
Pain killers produced in the brain. Explain how people under great trauma feel little
pain despite terrible injuries. Withdrawal symptoms of a heroin addict might be
behavior of body without any endorphins at all.
Mild depressant in which side effect mask the main effect in moderate doses.
Physiological effects:
1) decreasing inhibitions;
2) short term reduction in reaction speed;
3) short term hangover;
4) long term liver damage.
Social and economic effects:
1) violent behavior;
2) increase in car accidents;
3) absenteeism;
4) cost of intensive medical care.
The amount of alcohol that can be safely drunk depends on
1) body mass;
2) tolerance.
Test for ethanol. Under pressure, sample can be passed through thin tube containing
inert material. Components of sample separate and can be identified.
Derived from morphine by replacing H’s from both alcohol groups with acetyl (COCH3) groups. More soluble in fatty tissue due to removal of both -OH groups.
Human Immunodeficiency Virus. Specific proteins on HIV bind to receptor protein on
certain WBC’s called T cells. Quick mutation.
Testing potency of molecule and selectivity; done in a laboratory environment.
13
In vivo:
Meaning “in life.” Tests conducted in living species, to test for side effects and the
effect of the body on the drug.
Intoximeter:
Test for ethanol. Work by infrared spectroscopy, where the vibration of OH bond in
ethanol can be detected.
LD50 value:
The Lethal Dose of a substance that kills of 50% of a population. The lower the
number the more toxic the substance.
Maximum daily tolerance: How much of a chemical can be taken into the body before undesirable symptoms
occur. Related to rate at which body’s biochemistry is able to get rid of the same
agent. Minimum doses should be used due to body’s increasing tolerance to drug.
Medicine:
A drug used to cure a disease.
Nicotine:
Sympathomimetic. Quickly reaches CNS.
Short term effects:
1) Increased pulse and BP;
2) reduction in urine output;
3) decrease in reflex times,
4) increases concentration;
5) relieves tension.
Long term effects:
1) Risk of heart disease;
2) coronary thrombosis;
3) peptic ulcers;
4) number of diseases, incl. lung cancer.
Nicotine is a tertiary amine.
Noradrenaline:
Variation of adrenaline which is produced in the brain. A neurotransmitter which
sends signals to brain by binding with neural proteins.
Opiate:
Cause addiction and lead to tolerance.
Short-term effects:
1) euphoria;
2) depression of CNS;
3) high doses  coma/death.
Long-term effects:
1) constipation;
2) loss of sex drive;
3) social problems (e.g. theft, prostitution, etc).
Paracetamol:
Has none of the side effects of aspirin given that the correct does is used. If doses
are exceeded, it can induce massive liver damage.
Parenteral:
Administering drugs by injection. Can be administered locally  reducing dose
necessary and also possibility that body will alter molecular structure. Often
required medically trained staff to administer. Three types:
1)intravenous (bypasses digestive system, quick arrival; still spreads out
dose);
2) subcutaneous (directly into body fat – only for fat soluble molecules);
3)intramuscular (into muscle tissue).
Pathogen:
Organism or virus that causes disease.
Penicillin:
Discovered by Alexander Fleming, who noticed that some of the bacteria in his petri
dish had died off after some foreign appearance. Prevent cell walls from being
made in bacteria; does not affect mammalian cells or viruses as they do not have a
cell wall  selectively toxic. [Relatively] narrow spectrum antibiotic.
Penicillinases:
New enzymes produced by bacteria to counter the action of penicillin. Degrade
penicillin molecule.
Physiological state:
Includes consciousness, activity level and co-ordination.
14
Placebo effect:
Prostaglandins:
Retrovirus:
Selective toxicity:
Side effects:
Stimulant:
Sympathomimetic amine:
Synergistic effect:
Thalidomide:
Tolerance:
Toxicology:
Trial, blind:
Trial, double blind:
Virus:
A drug with no chemical effects. Used to test brain’s ability to influence physiology
and to test the efficacy of new drugs.
Local action hormones which have a range of functions in body. One of these may be
pyrogenic (raise body temperature). Also responsible for altering of signals across
synapse junctions of nerves. Mild analgesics are believed to work by blocking the
synthesis of these prostaglandins.
Virus that contains RNA instead of DNA.
The process of inhibiting processes vital to the pathogen, but absent in the host (see
PENICILLIN).
Unwanted effects of a drug. Risk-to-benefit ratio has to be considered. Thalidomide
had an unacceptable ratio, while chemotherapy – causing hair loss and nausea – still
has life-saving potential.
Drugs that increase a person’s state of mental alertness.
Amines which mimic chemical behavior of hormones of the CNS.
Creating a cumulative effect greater than the sum of each individual effect.
Benzodiazepenes have synergistic effect with ethanol. Ethanol also has synergistic
effect with aspirin (may cause stomach bleeding).
Morning sickness drug sold world-wide despite severe side-effects. Early clinical
trials had shown problems, but due to profitability, drug was not withdrawn. Later
withdrawn, but many children had been born with absent or malformed limbs.
The body’s adaptation to the action of a drug, resulting in a requirement for larger
doses to achieve original effect.
Poisonous effect of drug.
A trial of drugs where half of the patients are given the real drug and the other half
a placebo. The administering doctors know which patient receives which drug.
Similar to blind trial except that neither the administering doctor nor the patient
knows which patient receives which drug.
Contains DNA but cannot replicate by itself. Works by sticking to the outside of a
cell, and inject its own DNA, effectively causing cell to replicate the virus for it.
New viruses break through cell and infect other cells. All viruses have a central
core of DNA or RNA surrounded by a capsid of regularly packed protein units
(capsomeres). Have no nucleus or cytoplasm.
Option B – Medicine and Drugs - HL
Anesthetic, general:
An anesthetic that renders the patient unconscious so that they can feel no pain.
First anesthetic to be used was ether. This was highly inflammable, so later
chloroform and nitrous oxide (laughing gas) was used. Chloroform was found to
possibly lead to liver damage, while nitrous oxide was not very efficient. Objectives
for anesthetic:
1) able to put patient to sleep;
2) non-toxic;
3) non-inflammable;
4) volatile;
5) stable.
Halothane was found to satisfy these requirements, but it is a CFC, which can cause
damage to ozone layer.
Anesthetic, local:
An anesthetic that blocks pain in a specific area without affecting overall level of
consciousness.
Cannabis, arguments for/against:
1)
Cannabis addictive: contested.
2) May lead to harder drugs.
3) Toxic.
15
Chiral auxiliary:
Cisplatin:
Cocaine:
Combinatorial library:
Form, cis-:
Form, trans-:
Hallucination:
Hallucinogen:
Indole ring structure:
Isomers, geometric:
LSD:
Marijuana:
Mescaline:
Mix and split:
Partial pressure:
Procaine and lidocaine:
Psilocybin:
Racemic mixture:
Thalidomide:
Virtual library:
4) If cannabis legalized  demands to legalize other drugs.
5) Should be legalized to remove profits from criminals.
6) Ensure correct dosage.
The main component of a technique used to obtain only a desired enantiomer.
Attaching an auxiliary which is itself optically active creates the stereochemical
conditions for the reaction to form only one enantiomer.
Cis form of a chemical which is highly effective in the treatment of testicular and
ovarian cancers. Transplatin is not as effective an anti-cancer drug. Causes
alteration in the cancer cell’s DNA  cannot replicate properly.
First anesthetic to be used. Work by suppressing nerve transmissions. Side effects:
1) anxiety;
2) nausea;
3) headaches;
4) possible coma/death.
A technique to form a library of combinations of aa or other types of active
molecules, by use of mix and split process.
Geometric isomer where the similar groups are on the same side.
Geometric isomer where the similar groups are on different sides.
Distortions in sound and visual perceptions.
Causing hallucinations.
A common structure in many hallucinogenic drugs such as LSD and psylocybin.
Stereoisomerism where the isomers differ in positions of a group relative to the
double bond.
Does not occur naturally. Believed to work by blocking serotonin, one of the
compounds responsible for transmitting impulses across synapses in brain.
Short term effects:
1) restlessness;
2) dizziness;
3) hallucinations.
Long term effects:
1) severe depression;
2) recurrences of LSD effects (flashbacks).
Cannabis when dried. Not based on indole ring. Causes feeling of relaxation and
enhanced auditory and visual perception. Synergistic effect with depressants.
Long term effects:
1) apathy;
2) lethargy (state of sluggishness);
3) reduced fertility.
One of oldest known hallucinogens. Causes hallucinations, and decrease in appetite.
Synergistic effect with alcohol.
Coupling resulting in a combination of active molecules. Gives all permutations
possible.
The pressure a gas would exert if it occupied the total volume on its own. Found by
mole fraction of gas multiplied by total pressure.
Derivatives of cocaine.
Mildly hallucinogenic. Tolerance may develop but it is not addictive. Biggest danger
lies in inability to recognize “magic mushrooms” correctly; similar looking fungi are
poisonous.
A mixture containing equal amounts of both enantiomers.
One enantiomer helped against morning sickness, while the other was responsible for
causing fetal deformities.
Modeling permutations virtually.
16
Option D – Human Biochemistry - SL
Amino acid:
A compound in which an amino group and a carboxylic acid group are present. There
are 20 aa that occur naturally. Can be polymerized to form proteins. Exists as a
zwitterion at their isoelectric point. All except glycine can show optical activity.
aa
Amino acids, essential:
Aa’s that our body is not able to produce and we need to have them as nutrients.
There are 10 of these.
Amino-acids, non-essential: Aa’s that we are able to produce in our body.
Anabolic steroids:
All steroids contain characteristic four-ring structure. Have similar structure to
testosterone. Build up muscle.
Anabolic:
Processes in which complex molecules are made from simpler ones, such as in
photosynthesis.
Calorie:
The energy required to raise the temperature of 1g of water by 1C.
Calorific value:
The energy content of food.
Carbohydrates:
Produced by photosynthesis in plants. Used to
1) provide energy;
2) store energy (starch is stored in liver in form of glycogen);
3) precursors for important biological molecules (e.g. they are components
of nucleic acids).
Catabolic:
Processes in which molecules are broken down into simpler ones, such as aerobic
respiration.
Denaturation:
When the three-dimensional conformation of the structure is destroyed, and the
protein becomes biologically inactive. Denaturing agents are:
1) heat;
2) UV-radiation;
3) strong acids and bases;
4) concentrated salt solutions;
5) heavy metals (no, not that kind… examples are Pb, Hg, etc).
Diet:
Well-balanced diet consists of about 60% carbohydrate, 20-30% protein and 10-20%
fat. Should include essential vitamins and fifteen essential minerals. Amount of
food required depends on age, weight, gender, and daily activity.
Eluent:
The solvent in which the chromatographic paper is placed in paper chromatography.
Fats:
Solid triglycerides at room temperature. Contain only saturated carboxylic acid
groups. Uses of fats:
1) efficient way to store energy (in adipose tissue);
2) thermal insulation;
3) protection;
4) form part of cell membranes,
5) source of energy (can be oxidized more than carbohydrates).
Fatty acid:
Long chain carboxylic acids.
Feedback mechanism:
When a product of a process or a hormone reaches a certain level, it inhibits
(negative feedback) or promotes (+ feedback) a further response.
Food calorimetry:
Measuring the energy content of food.
Furanose:
Five membered ring containing an oxygen atom, such as in fructose.
Glucose:
A hexose monosaccharide. Form of glucose found in nature is D-glucose, which can
exist in two separate crystalline forms:
1) -D-glucose (OH groups are down, down, up, down; following carbon
chain);
2) -D-glucose (up, down, up down).
C6H12O6
Glycosidic link:
Link between two sugar in a polysaccharide, formed by condensation reaction.
17
GM food:
Hard water:
Hormone, adrenalin:
Hormone, insulin:
Hormone, thyroxine:
Hormones, sex:
Hormones:
Hydrophilic:
Hydrophobic:
Iodine number:
Isoelectric point:
Lactose:
Lipids:
Menstrual cycle:
Metabolism:
Micelle:
Ninhydrin:
Nutrient:
Oils:
Oral contraceptives:
PAGE:
Phospholipid:
Polyunsaturated oils:
Genetically modified food. Benefits: Improve flavor, nutritional value, and shelf life.
Could incorporate anti-cancer substances. Could make plant more resistant to
disease. Concerns: unpredictable outcome. May cause antibiotic-resistance. May
alter balance of ecosystems.
Contains Mg2+ or Ca2+. Prevents soap from working efficiently as it reacts with the
anion of the soap, producing a precipitated salt.
Responsible for ‘fight or flight’ response (goose bumps, increased pulse/BP). Produced
in adrenal medulla.
Made up of 51 aa residues. Decreases glucose levels in blood by making liver absorb
glucose in the form of glycogen. Insulin produced in -cells of Islets of Langerhans.
Regulates metabolism. Produced in thyroid gland. Hypothalamus releases local
hormone which tells anterior pituitary to release thyroid SH (+ feedback). TSH
tells thyroid glands to release thyroxine (+ feedback). When the concentration of
thyroxin reaches a certain level, a – feedback is sent to hypothalamus, ceasing
production of the local hormone.
Responsible for development of secondary sexual characteristics. Both estrogen and
testosterone produced in testes (males) and ovaries (females). They are all
steroids  contain characteristic four-ring structure.
Chemicals produced in glands and transported to specific target cell by blood stream,
and binds to a receptor site on or within the target cell  produces a specific
physiological response. Glands are controlled by pituitary gland, which in turn is
controlled by the hypothalamus. Hormones act as chemical messengers.
Describing part of molecule that is attracted to water.
Describing part of molecule that repels water.
Number of grams that reacts completely with 100g of a triglyceride. The higher the
iodine number, the more unsaturated the triglyceride.
The pH value at which an aa exists as a zwitterion.
Disaccharide in which -D-galactose and -D-glucose are joined by glycosidic link.
Biological substances that are soluble in non-polar solvents (generally). Lipases in
digestive system degrade lipids.
Pituitary gland releases follicle SH, which travels to ovaries causing release of
estradiol. Two weeks later, – feedback stops release of FSH and triggers release
of luteinizing hormone, which travels to ovaries and releases progesterone.
Progesterone causes egg to be transported to uterus. If egg is fertilized, it
embeds itself on uterine wall and hormone levels rise dramatically, otherwise
hormone levels fall and menstruation occurs.
The network of biochemical reactions that supports life.
The particle formed when the hydrophilic tail dissolves in oil or grease.
An organic dye. Causes coloration of aa’s. Used to see how far aa’s have moved in both
paper chromatography and electrophoresis.
Substances that are required by an organism as food.
Liquid triglycerides at room temperature. Contain at least one double bond, i.e. they
are unsaturated. The more unsaturated, the lower the m.p. due to its inability to
pack so closely together  the surface area decreases  decrease in the van der
Waals’ forces between the molecules. Number of C=C bonds can be determined by
addition reactions with I2. See IODINE NUMBER.
Most common ‘pill’ contains a mixture of estradiol and progesterone  mimics the
high hormonal levels of pregnancy, in turn preventing the release of more eggs.
Polyacrylamide gel electrophoresis.
Form major part of plasma membranes. Phosphate group is hydrophilic while lipid part
is hydrophobic.
An oil containing several double bonds.
18
Protein structure, electrophoresis: Electrophoresis is carried out on a medium called PAGE. Sample is placed in
center of gel, and a potential difference is applied across it. The movement of the
aa depends on the pH of the buffer: at low pH, the amine group will be protonated,
while at high pH, the carboxylic acid is deprotonated. At the isoelectric point –
characteristic for each aa – the aa exists as a zwitterion, and will not move
(charges balanced). When satisfactory separation is complete, the aa can be
sprayed with ninhydrin, and their isoelectric points can be compared.
Protein structure, paper chromatography:When a piece of chromatographic paper containing a small sport of the
unknown aa is placed in an eluent, the eluent rises up the paper (capillary action).
The different aa’s spread out to different extents, and move up the paper at
different rate.
Proteins:
Large macromolecules of chains of 2-amino acids. Formed by aa’s bonding to each
other by peptide bonds.
1) The primary structure of the proteins is their strict sequence of aa
residues.
2) The secondary structure describes how the chain folds itself due to
intramolecular hydrogen bonding (can be -helix – hydrogen bonds within single
chain, causing spiraling – or -pleated – hydrogen bonds between chains).
3) The tertiary structure describes overall folding of the chain, giving the
protein its three-dimensional shape (may be due to hydrogen bonds, van der Waals’,
and ionic attraction. Two Cys residues can form disulphide bridges).
4) The quaternary structure results from the interactions between
separate polypeptide chains.
Uses of proteins:
1) Many are enzymes;
2) can give structure;
3) source of energy;
4) regulation hormones.
Pyranose:
Six-membered monosaccharides such as glucose.
Retention factor:
The ratio of the distance traveled by the sample to the distance traveled by the
solvent in paper chromatography. Each aa has a specific R f value.
Saccharide, mono-:
Simple sugars. Empirical formula CH2O. Water soluble. Two families:
1) hydroxyaldehydes (contain aldehyde group and at least 2 OH groups.
Reducing sugars);
2) hydroxyketones (contain ketone group and at least 2 OH groups. Nonreducing sugars). Monosaccharides containing more than 5 C-atoms can make cyclic
molecules.
Saccharide, oligo-:
Containing 2-9 monosaccharides.
Saccharide, poly-:
Polymers of monosaccharides. Formed by condensation reactions, forming glycosidic
links.
Saponification:
The process in which a triglyceride is hydrolyzed, forming soap. Reverse of
esterification.
SH:
Stimulating Hormone.
Soap:
The sodium or potassium salt of the fatty acids produced from the saponification
process. Functions because of hydrophilic head and hydrophobic tail. The tail
dissolves in oil or grease to form a micelle. Surrounded by hydrophilic heads, which
makes it soluble in water.
Starch:
Polymer of -D-glucose. Exists in two forms:
1) amylose (water soluble);
2) amylopectin (water insoluble). Most plants use starch as a store of
carbohydrates.
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Structure-function relationship:
The structure of a chemical compound is adapted to its function by
evolution.
Sucrose:
Disaccharide in which -D-glucose and -D-fructose are joined by glycosidic link
between the C1 from the glucose and the C2 from the fructose.
Synthetic detergents:
Soap molecules of which the calcium or magnesium salts are soluble  that they can
work well in hard water as well. Cause more pollution than soaps.
Triglyceride:
Formed from condensation reaction between glycerol and fatty acids.
Vitamin A:
Retinol. Found in cod liver oil, green vegetables and fruit. Fat soluble despite OH
group, due to long hydrocarbon chain. Not broken down readily by cooking. Aids
night vision. Retinol is oxidized to retinal in body. Retinal combines with protein
opsin to form rhodopsin, the active agent for converting light signals into electrical
signals that travel along optical nerve to brain. Deficiency  xerophtalmia or nightblindness.
Vitamin C:
Ascorbic acid. Found in fresh fruit and vegetables. Water soluble. Involved in
biosynthesis of the protein collagen (found in connective tissue). Deficiency 
scurvy.
Vitamin D:
Calciferol. Found in fish liver oils and egg yolk. Can be formed on surface of skin by
UV light reacting with 7-dehydrocholesterol. Involved in uptake of Ca2+ and PO43+
ions from food, and in formation of bone structure. Deficiency  rickets.
Vitamins, fat soluble:
A, D, E, F and K. Characterized by long non-polar hydrocarbon chains or rings.
Vitamins, water soluble:
C and the 8 B’s. Contain NH or OH groups  has ability to hydrogen bond to water.
Do not accumulate in body.
Vitamins:
Vitamin D is the only vitamin that the body is capable of synthesizing. Can be defined
as: 1) fat soluble or 2) water soluble. Vitamins containing C=C bonds and OH groups
are readily oxidized. Refrigeration slows this process.
Water equivalent:
The equivalent addition of energy to water as released when burning 1.00g of a food,
causing a temperature increase.
Zwitterion:
Ion with + and – charge. Aa’s exist as zwitterion at their isoelectric point.
Option D – Human Biochemistry - HL
Active site:
The part of the protein that is involved in the catalysis.
ADP:
Adenosine diphosphate. Made of base A, ribose, and two phosphate groups. Addition
of another phosphate group makes ATP.
ATP:
Adenosine triphosphate. Made up of base A, ribose, and three phosphate groups
bonded together by high-energy phosphate bonds. Breaking the last of these bonds
releases energy for use in cells, leaving ADP.
Chromosome:
A structure composed of DNA and associated proteins.
Codon:
Each of 64 permutations of the triplet code.
Coenzyme:
Organic cofactors. Example: B-vitamins. Two types:
1) permanent coenzymes (always bonded to enzymes);
2) non-permanent coenzymes (only bonded to enzymes during catalysis).
Cofactor:
A substance that is a part of the active site, and that is involved in the catalysis. Can
be:
1) inorganic (metal ions);
2) organic (coenzymes).
Concentration, effect of: 1) Increasing concentration of the substrate: proportional increase in rate, but
eventually evens out as all active sites of enzyme become saturated. 2) Increasing
concentration of enzyme: proportional increase in rate.
Cyanide:
A poison which works in the same way as CO: by forming irreversible complexes with
the iron in Hb. Taken up by the hemoglobin easier than oxygen is.
Cytochrome:
Oxidizing enzymes in mitochondria. Contain Cu2+/Cu+.
Deoxyribose:
The pentose sugar found in DNA.
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DNA profiling:
Using a small amount of cellular material, DNA is extracted and broken down into
minisatellites using restriction enzymes. Splits where there are no coded messages
in the base sequence are unique to the person giving the sample, and so this can be
used to identify them.
DNA replication:
DNA in cell begin to partly unzip as hydrogen bonds between the bases break. New
sugar base units are taken up from the aqueous solution. Due to set pairs (AT and
CG), the new strands will be identical to the original one.
DNA:
Deoxyribonucleic acid. Double-stranded. Made up of nucleotides. Have – charge due
to phosphate group. Cannot penetrate nucleus.
Electron transport:
Occurs in inner membrane of mitochondria, which contains different proteins and
enzymes, incl. cytochromes. The H+ ions from the NADH2 (product from the citric
acid cycle) move along cytochromes by repeated redox reactions, due to presence
of stronger oxidizing agents. Enzyme cytochrome oxidase causes H+ ions, e- and O2
to react to form water, releasing energy in the process.
Enzyme saturation:
When all the active sites of the enzymes are occupied by a substrate. At this
saturation, increasing substrate concentration has no effect.
Enzyme, factors affecting:
1) Enzyme concentration;
2) substrate concentration;
3) temperature;
4) pH;
5) inhibitors (reversible/irreversible).
Enzyme:
Proteins that act as biological catalysts, for specific substrates.
Gene:
A specific sequence of DNA which codes for the synthesis of a protein.
Glycolysis:
First phase of breakdown of glucose in respiration. Occurs in cytoplasm.
Haemoglobin:
Found in RBC’s. Contains four large polypeptide groups and four Fe 2+ ions surrounded
by hem groups. At high oxygen concentrations, oxygen bonds onto the iron in hem
group as an extra ligand. At low concentrations, the reverse occurs.
Hb
Heavy metal ions, effect of: Can poison enzymes by reacting with –SH groups replacing the hydrogen atom with
a heavy metal atom or ion. Enzyme is denatured.
Induced fit theory:
The active site can alter its shape to allow for a better fit with the substrate. An
enzyme-substrate complex is created, and the catalyzed reaction takes place,
leaving an enzyme-product complex. The products are released, and the enzyme
reverts to its original shape.
Inhibition, competitive:
Reversible inhibition. Resemble the substrate in shape, but cannot react. Slow down
reaction by occupying active site. Does not affect V max but does affect Km.
Inhibition, irreversible:
The inhibitor reacts with a part of the enzyme, and a covalent bond is formed
between the inhibitor and enzyme. Enzyme activity is permanently destroyed.
Example: nerve gases work by alkylation of an OH-group in the active site of an
enzyme.
Inhibition, non-competitive: Reversible inhibition. Prevents enzyme reactions by binding to another part of the
enzyme than the active site. This causes the enzyme to alter its shape and be
unable to receive its substrate. Does not affect Km but does affect Vmax.
Inhibition, reversible:
The inhibitor makes weak (intermolecular) bonds with the enzyme. The enzyme can
become biologically active again. Two types:
1)competitive;
2) non-competitive.
Metal ions:
Examples of important ions: Na+ and K+ (nerve impulses and water balance); Ca2+
(bones and teeth); Cu2+ (enzymes); Co2+ (vitamin B12); Fe2+ (Hb). All depend on one
of the following:
1) difference in charge density between two ions;
2) variable oxidation states;
3) forming complexes with ligands.
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Michaelis-Menten constant: The substrate concentration when the rate of the reaction is at ½ Vmax. The
constant will always be the same for a particular enzyme and particular substrate.
Km
mRNA:
Messenger of genetic information (transcription).
Nucleotide:
Repeating base-sugar-phosphate units that make up the nucleic acids. The base can
be one of four nitrogen-containing bases, adenine (A), guanine (G), cytosine (C) or
thymine (T). In RNA, uracil (U) replaces T. The phosphate bonds to the C4, while
the base bonds to the C1.
pH, effect of:
The pH value affects the tertiary structure. Enzymes have an optimum pH; outside
of this, they can be denatured.
Phosphodiester bond:
Bonding between nucleotides in a polynucleotide. Each nucleotide is joined between
the C3 of the sugar and the neighboring phosphate group.
Phosphorylation:
Addition of phosphate group. Phosphorylation in the sodium-potassium pump causes
shape of pump to change.
Protein synthesis:
Happens in ribosomes.
1) Transcription in nucleus; followed by
2) processing by mRNA;
3) translation by ribosome.
Ribose:
The pentose sugar found in RNA. Same as deoxyribose, except with an extra O
bonded to the C2.
Ribosome:
Particle that causes protein synthesis. Sequence of aa’s determined by nucleotide
sequence in mRNA.
RNA:
Ribonucleic acid. Single stranded. Contains base U instead of DNA’s base T. Two
functions:
1) transcription (messenger of genetic information);
2) translation (translating gene information into protein synthesis).
Sodium-potassium pump: Protein structure in cell membrane act as valves pumping Na + ions out of cell and K+
ions into the cell. Works due to difference in charge density between Na + and K+.
The Na+ binds to three sites on the protein molecule. Energy is extracted from
ATP by hydrolyzing to ADP, and the phosphorylation causes the pump to change its
shape. Na + ions are expelled, and K+ ions bind to two sites on the protein molecule.
The loss of the phosphate causes the pump to change its shape again, expelling the
K+ ions into the cell.
Substrate:
The substance on which an enzyme acts.
Temperature, effect of: Increasing temperature will initially increase rate of enzyme-catalyzed reactions
(greater proportion of reactants will have the minimum activation energy). Optimum
temperature for most enzymes is ca. 40C. Above this temperature enzymes rapidly
denature.
Transcription:
Copying of DNA onto a strand of RNA by unwinding temporarily due to the action of
RNA polymerase. Takes place in nucleus.
Translation:
The reading of the base sequence of the mRNA by ribosomes to make a sequence of
aa’s to form a polypeptide.
Triplet code:
A sequence of three bases that represents one aa.
tRNA:
RNA that brings the right aa’s to the ribosomes.
Vmax:
The maximum rate at which enzyme activity can occur, given a constant enzyme
concentration. This is when the active sites of the enzyme are saturated.
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