Physical Chemistry Flashcards
1
Q
What are the two types of molecular bond?
A
Ionic and covalent
2
Q
Define an atom
A
The smallest part of an element which can take part in chemic reactions
3
Q
Define an element
A
A group of atoms all having the same atomic number
4
Q
Define a molecule
A
A combination of atoms which is the smallest unit of a chemical substance that can exist whilst still retaining the properties of the original substance
5
Q
Define atomic number and mass number
A
Atomic number: The number of protons in each atom of an element Mass number: The total number of protons and neutrons in the nucleus
6
Q
Describe the make up of an atom
A
A nucleus of neutrons and protons, surrounded by a cloud of negatively charged electrons
7
Q
Where does the mass of an atom lie?
A
Almost all of the mass of an atom lies in the nucleus
8
Q
How is the charge of an atom determined?
A
The total number of protons (positive charge) minus the total number of electrons (negative charge)
9
Q
Define an isotope
A
Same number of protons (and therefore same element) with a different number of neutrons
10
Q
Define a radio-isotope
A
An isotope which releases particles (i.e. is radioactive)
11
Q
Explain the difference between carbon 12 and carbon 14
A
Carbon 12 - 6 protons, 6 neutrons, not radioactive Carbon 14 - 6 protons, 8 neutrons, radioactive
12
Q
How are mass number and atomic number traditionally written?
A
Mass number: Superscript Atomic number: Subscript. e.g 12 6C
13
Q
What is the relative mass and charge of each of the three constituents of an atom?
A
Proton Mass: 1 Neutron Mass: 1 Electron Mass: 1/1836 Proton charge: +1 Neutron charge: 0 Electron charge: -1
14
Q
Electrons are arranged around the atom in a pattern called _______
A
Shells
15
Q
From innermost to outermost, what are the shells of an atom?
A
K, L, M, N, O, P, Q.
16
Q
How are shells filled?
A
In alphabetical order
17
Q
Give the number of electrons each shell from K to N can hold
A
K - 2 L - 8 M - 18 N - 32
18
Q
Explain the theory of sub-shells
A
Each shell has subshells; s, p, d and f shells. s shells can contain two electrons p shells can contain six electrons d shells can contain ten electrons f shells can contain fourteen electrons
19
Q
At what shells are each sub shell located?
A
s sub-shells - in every shell p sub-shells - every shell after the K shell d sub-shells - every shell above the K and L shells f sub-shells - every shell above the M sub shell
20
Q
Explain how an atom with 50 electrons would be arranged using the spdf sub-shell arrangment
A
1s2, 2s2, 2p6, 3s2, 3p6, 3d10, 4s2, 4p6,4d10, 4f4
21
Q
Define “valency”
A
The number of atoms of hydrogen that one atom of an element can combine with or replace
22
Q
True or false: an atom can have only one valency
A
False - can have multiple valency states
23
Q
What is the connection between periodic table groups and valency?
A
The same groups have the same valency; group 1 all have a valency of +1, group 2 = +2, group 3 = +3 and group 4 = +4 etc.
24
Q
Give the difference, in terms of electron transfer, between an ionic and a covalent bond
A
ionic - complete loss or gain of electron(s) from atom to another covalent - two atoms “share” electron(s) to give both a full shell.
25
What is special about the inert gases?
They have full electron shells and are at their most stable; therefore they do not gain or lose electrons and do no react with other elements
26
Why is carbon the most important element in terms of organic chemistry?
It can both lose or gain electrons to gain stability
27
What is the point of a bond?
To allow formation of a stable outer shell
28
In terms of sodium and chlorine, explain what is happening when an electrocovalent (ionic) bond is formed
sodium loses 1 electron, giving it a charge of +1. It now has a full shell (2, 8) in its outermost orbit, taking on the electron configuration of neon (stable gas) Chlorine picks up the electron that sodium has lost and becomes a chloride ion, with an outer shell which is also full (2, 8, 8) and takes on the configuration of argon (stable gas). the chlorine atom now contains a negative charge of -1. The positive charge of the sodium ion and the negative charge of the chloride results in a strong attraction and therefore a bond between the two ions, sufficient enough to maintain the crystalline structure. Ionic compounds are very stable and require a very large amount of heat energy to convert to liquid or gas - therefore they are usually solids at room temperature
29
True or false: Carbon can lose or gain electrons to become stable
True - can lose 4 electrons so that shell K is the outermost shell and full with 2 electrons, or can gain 4 so that shell L is the outermost shell and full with 8 electrons
30
How many types of covalent bond are there? Define the difference
single - one pair of electrons shared double - two pair of electrons shared triple - three pair of electrons shared
31
Methane is an example of which kind of covalent bond?
single bonds - carbon gains 1 electron from each hydrogen atom, taking on the configuration of neon while each hydrogen takes on the configuration of helium. Each bond shares one pair of electrons.
32
In terms of bonds/shape/state of matter/vaporisation/conductance/solubility, compare and contrast ionic and covalent bonds
Bonds - Ionic no sharing therefore non-directional/covalent sharing therefore direction Shape - ionic no particular shape/covalent definite shape therefore able to have isomers State of matter - ionic solid and usually crystalline/ covalent usually highly volatile liquids or gases Vaporisation - ionic not easily vaporised/covalent easily vaporised Conductance - ionic when melted good conductor/covalent poor conductor Solubility - ionic readily dissolves in water/covalent not readily soluble in water
33
Dative bonds: What are they?
A type of covalent bond in which both electrons of the shared pair come from the same atom.
34
Give an example of a dative bond
Ammonium chloride; also possesses covalent and ionic bonds. Bond between NH3 and hydrogen ion is dative as the hydrogen ion possesses no electrons to transfer
35
Van der Waals Forces - define them
Attraction and repulsion of weakly charged areas to similar areas in neighbouring molecules
36
Why do Van der Waals forces occur?
Particles which are neutral can have permanent dipoles or have dipoles induced by the interaction with particles which has a permanent dipole. These dipoles then attract each other and Van der Waals are the electromagnetic forces between these particles.
37
True or false: Van der Waals forces are weak forces and as thus the melting point of substances held by them is quite high
False - Van der Waals forces are weak but this means their melting point is relative low and they tend to be softer than those held by ionic or covalent bonding
38
Graphite is an example of Van der Waals interactions - how?
It is made of sheets formed from covalent bonds between carbon atoms and each sheet is held to the next one by Van der Waals forces
39
What is a highly electronegative atom?
An atom which has a high propensity to attract electrons and become a negative ion
40
Hydrogen bonds - explain them
Weak electrostatic bond between the positive nucleus of the hydrogen atom in a covalent bond and the unshared pair of electrons in a highly electronegative atom of a neighbouring molecule
41
Give examples of highly electronegative atoms
Oxygen, sulphur, nitrogen
42
True or false - the high boiling point of water and crystalline structure of ice is due to Van der Waals interactions
False - these are due to hydrogen bonds forming between molecules of water, with the free pair of electrons on the oxygen atom on one molecule of water being attracted to the positive nucleus (proton) of hydrogen on another molecule
43
Explain hydrophobic bonding
Individual water molecules are attracted to each other by hydrogen bonds. Any molecule added to water will disrupt the structure. If the substance has polarity or is ionised it will spread easily and form bonds with the water molecules. If however electron distribution is even (i.e. not ionised or polarised) then the energy released by making new bonds is less than that required for breaking of hydrogen bonding. Therefore the additive becomes most stable by collecting together and leaving as much of the water as possible, undisturbed.
44
An example of a hydrophobic bond can be demonstrated by something readily available in your home: what is it?
Oil - when added to water it will remain grouped together, only being broken up temporarily by very vigorous stirring.
45
Why are hydrophobic and hydrogen bonds physiologically important?
Areas of membranes and proteins which do not have polarity do not attract water, allowing water to maintain bonds with other water molecules. Therefore the hydrophobic areas remain vacant promoting the movement of non-polar hydrophobic molecules into these sites.
46
Hydrophobic areas and molecules do not attract each other - explain
There is no net polarity or force present to allow for movement. However these molecules and areas become grouped. This is not due to any attraction or force but is actually due to the displacement of hydrophobic molecules by water and other hydrophilic molecules.
47
Give the strength of bond energy (in kcal.mol-1) for each of the following: Covalent Ionic Hydrogen Van der Waals
Covalent: 50-150 Ionic: 5-10 Hydrogen: 2-5 Van der Waals: 0.5
48
What is the relationship between bond strength and energy for breaking bonds?
Stronger bond = higher energy to break it
49
Covalent bonds are the hardest to break. True or false
True
50
In physiological and pharmacological terms, which bond is effectively irreversible?
Covalent bonds
51
How are covalent bonds in pharmacological or physiological systems broken?
They are reversed by metabolising the receptor - (ant)agonist or enzyme - substrate complex and subsequent replacement of the enzyme or receptor
52
Give examples of pharmacological covalent bonding
* Phenoxybenzamine and a-adrenoceptors
* Organophosphates and acetylcholinesterase
* MAOIs and MAO
53
What is the relationship between distance and: 1) ionic bonding 2) Van der waal's forces
Ionic - inversely proportional to the distance to the power of 2 Van der Waal's - inversely proportional to the distance to the power of 7 Once closer than a critical distance, van der waal's forces become repulsive as neighbouring electrons repel each other
54
In terms of electron transfer, define oxidation and reduction
OIL RIG Oxidation Is Loss Reduction Is gain
55
Explain oxidation and reduction using:
ethanal + oxygen --\> ethanoic acid
Ethanal loses an electron and therefore becomes oxidised whilst the oxygen accepts an electron to become reduced.
2CH3COH - 2e- --\> 2CH3COH-
O2 + 2e-
--\> 2CH3COH+ + 2O-
--\> 2CH3COOH
56
Why is oxidation and reduction relevant in physiology?
In mitochondria, energy is released by serial oxidation and reduction reactions in cytochrome oxidase electron transport chain. Anaerobic dehydrogenase remove hydrogen
57
Local anaesthetic ionisation constitutes oxidation or reduction?
Oxidation - loss of electrons or acceptance of a proton
58
In the simplest terms, what is diffusion?
Movement of ions or molecules down a concentration or electrical gradient until all gradients have disappeared, resulting in an even distribution of all the ions or molecules in the container.
59
State Graham's law of gaseous diffusion
Rate of diffusion is inversely proportional to the square root of the density of the gas.
60
The majority of drugs are weak acids or bases. True or false
True - majority of drugs are categorised as weak acids or bases
61
Why are weak acids or bases preferable for pharmacology?
Higher degree of ionisation = increased solubility in water Unionised form of the drug is required to get through the lipid membrane and therefore to deliver to the target
62
The proportion of a drug present in ionised form is dependent on \_\_\_\_\_\_\_\_
pH
63
Explain how with a weak acid will dissociate
HA --\> H+ + A-
64
Give the equation which is required to give the relationship between pH and dissociation for acids and for bases
Henderson hasselbach acids: pH = pKa + Log10(A-/HA) bases: pH = pKa + Log10(BH+/B)
65
What is pKa
The negative log of the dissociation constant; the pH at which 50% of the drug is ionised
66
What is the connection between pKa and protonation of an acid or base?
Lower the pKa relative to the pH, more protonated. Higher the pKa relative to the pH, less protonated Protonated form of an acid is NEUTRAL Protonated form of a base is ALKALINE
67
What is the partition coefficient?
A numerical constant that is the ratio at equilibrium of the concentration of a substance in two adjacent compartments that are seperated by an interface through which the substance can readily pass.
68
Why does a partition coefficient exist in physiological systems?
The two adjacent compartments are likely to have different affinities for the substance and therefore the equilibrium will contain different amounts of the substances at the same partial pressure.
69
Partition coefficients are often used to distributions of an anaesthetic gas. What is the Ostwald coefficient?
A co-efficient which is used to specify the partition coefficient of a given agent at body temperature
70
How does diffusion of gases work between two solvents which are of different affinity for the solute?
Gases travel along their partial pressure gradient until the partial pressures are equal, not the concentrations. So at equilibrium the partial pressure is equal and if the partial pressure is equal then the net movement of substance will cease between the two compartments.
71
Explain the Ostwald Coefficient using sevoflurane (Blood:gas = 0.69)
If you have a partial pressure of 1.69kPa in the gas phase and 0kPa in the blood phase, the sevoflurane will begin to move along this gradient into the blood. The partial pressure in the gas phase will drop and will rise in the blood phase until both are equal (1.0). However as sevoflurane is more soluble in gas than in blood, the 1.69ml/100ml will end up with 1ml/100ml of sevoflurane remaining in the gas phase and 0.69ml/100ml entering the blood.
72
Define osmosis
Movement of a solvent, through a semipermeable membrane which seperates two compartments, having two different concentrations of a solute or solutes, to which the membrane is impermeable.
73
What is a pure semipermeable membrane?
One which is impermeable to a solute but freely permeable to a solvent.
74
Give an example of a pure semipermeable membrane
The glomerular membrane - freely permeable to water and small solute molecules but impermeable to larger solute molecules (\>69000 daltons)
75
How does solvent move in osmosis?
From low solute concentrate to high solute concentration (more dilute to less dilute)
76
What is the osmotic potential/pressure?
The pressure required to prevent passage of solvent across a semipermeable membrane
77
True or false: osmotic potential is always the result of a single solute
False - it may be the result of a single solute but it is often the result of many different molecules
78
What molecules are osmotically active?
Those which are impermeable to the membrane. However this becomes more complex in physiology due to existence of ion transport systems and channels for passage of molecules through the semipermeable membrane
79
Define osmolarity and osmolality
Osmolarity: concentration by volume of solution (mOsm/L) Osmolality - concentration by mass of solvent (mOsm/kg water)
80
In the following diagram, what does P respresent?
P represents the osmotic pressure, in cmH2O and is the pressure required to prevent movement of the solvent.
81
Why is osmosis important in pharmacology?
Drugs affecting the distribution of solutes between compartments will have an osmotic effect. Diuretics for example will interfere with membrane transport of ions and other solutes in renal cells/the renal lumen and the renal circulation, manipulating ionic concentrations which causes water to flow with the ionic concentrations in the tubules resulting in increased urine output
82
Explain the effects of mannitol
83
What is an isomer?
Chemical compounds with the same empirical chemical formula and the same molecule weight but with differing physical or chemic properties
84
Define chain isomerism and give an example
Same chemical formula
Carbon skeleton changes whilst still retaining the same functional group.
Example: butane and 2-methylpropane
85
Define Position Isomerism and give an example
Same chemical formula
Component atoms or functional group are in different positions on an identical carbon skeleton
Isoflurane and enflurane
86
Define functional isomerism and given an example
In this form of isomerism, the functional group changes. For example, the movement of the oxygen from an alchol into the middle of the chain makes it into an ether.
Example: Propanol and methyl ethyl ether (both C3H8O)
87
88
# Define dynamic isomerism.
Give an example
Variant of functional group isomerism where two isomers exist in dynamic equilbrium, obeying the law of mass action. Typically this involves movement of a hydrogen ion from one point in the chain to another
Methohexital
=S/-SH groups are in dynamic equilibrium
89
Define steroisomerism
Same carbon skeleton, same structure, same molecular formula but different spacial arrangement. Divided into two types; optical and cis-trans
90
Define optical isomerism and give an example
A tetravalent atom (usually carbon) with four different groups around it which when two of these groups are swapped, is non-superimposable mirror image of the former atom.
Glucose (levo and dextro forms)
91
What do different enantiomers do to light when passing through it?
They rotate polarised light in opposite directions
Dextro - right handed - rotates polarised light to the right
Levo - left handed - rotates polarised light to the left
92
Will molecules with multiple chiral centres (e.g. dextrose) form superimposable molecules?
93
What is the difference between L-glucose and D-glucose?
How many chiral carbons are there in a glucose molecule?
L-glucose is a mirror image of all of the chiral carbons in D-glucose (dextrose)
there are 4 chiral carbons in glucose
94
Why is optical isomerism important in pharmacology?
Different enantiomers may have different potencies and side effects
95
What is a racemic mixture?
A mixture of equimolar concentrations of both enantiomers, resulting in a net rotation of polarised light of 0.
96
What is the relationship between number of chiral centres and stereoisomers?
The more chiral centres, the higher the number of enantiomers.
97
What is stereospecificity?
Stereospecificity is the property of receptors where they will only/mainly interact with one of the two racemates. Therefore in a racemic mixture, half of the drug will be mostly/entirely inactive.
98
What effect does stereospecifity have on pharmacokinetics?
As the two racemates are chemical identical, there is no distinction between each enantiomer meaning measurement may be much higher than the effective dose. Similarly elimination halflife may be different for each racemate and their active metabolisms so each may have a different pharmacokinetic profile.
99
In a racemic mixture, is the "redundant" enantiomer entirely redundant?
No, in some cases it may be the cause of unwanted side effects and restrict the drug's use unless able to isolate the two racemates from each other and use only the useful one (e.g. r-bupivicaine is more cardio/neurotoxic than l-bupivicaine, whilst both are equipotent)
100
What is geometric isomerism?
Give two examples
The difference in possible atomic orientational variants around a double bond - have a non-superimposable variant but no chiral carbon.
1,2-dichloroethene
Fumaric Acid/maleic acid (HOOC-CH=CH-COOH)
101
Mivacurium holds multiple carbon-carbon double bonds which form non-superimposable diasteromeres. How many geometric isomers does it have? Name them.
2 bonds allowing geoisomerism - therefore there is trans-trans, cis-trans, trans-trans forms of Mivacurium. All of these have different pharmacokinetic profiles.
102
What are the four levels of protein structure?
Primary structure - the chemical formula usually expressed in terms of the amino acid sequence and the covalent bonds that are used to bind it (not including hydrogen or disulfide bonds)
Secondary structure - the relative spatial positioning of neighbouring covalently bonded molecules to each other. Free rotation occurs around single bonds to allow a molecule to settle into its most stable form. This usually results in a specific coiled lay out held together by disulphide bonds and often forms a coil called an alpha helix.
Tertiary structure - the shape in which the alpha-helix is arranged which may be long and straight but usually curled around itself
Quaternary structure - the interrelationship between individual amino acid chains when more than one subunit forms the protein. These are held together by hydrogen bonds and Van der Waals forces.
103
True/False
Proteins are highly complex compounds and can have multiple sites which are active/attract certain molecules/individual properties
True
Proteins are highly complex molecules and may have multiple areas/sites with individual properties/electrostatic charges/shapes/sites/relationships with other sites
104
True/False
Protein sites can work like a lock and key system in 2-dimensional space
False
Proteins work like a lock and key system, that part is true but they are three dimensional shapes
105
How do plasma proteins work for transportation?
Plasma proteins bind poorly soluble molecules in a lock and key way in three dimensional shapes and transport them to other locations. As they are in equilibrium with the plasma, if the free plasma concentration falls, the binding becomes undone and more of the substrate is released into the plasma as free molecules
106
What are enzymes?
Enzymes are specific proteins that bind molecules and facilitate the destruction or creation of covalent bonds within them to create new molecules or destroy old molecules.
107
Define a receptor
Proteins or glycoproteins which bind to certain molecules and cause a conformational change in the receptor that is responsible for an effect
108
Define a drug agonist
Drugs with a similar structure to the intended molecule which binds to the receptor site and mimics the endogenous agonist i.e. by activating the receptor/causing a conformational change
109
Define a drug antagonist
Drugs which have a similar structure to the intended molecule, bind to the receptor site without causing any change and prevent the endogenous agonist from binding the receptor
May also bind to another part of the protein and prevent the configuration change necessary for the physiological effect.
May also bind and cause a configuration change to prevent the agonist from binding
Antagonists may bind to the protein and prevent ions reaching the open channel
110
Why is plasma protein binding important?
the degree of binding to plasma proteins is relevant to the transport of poorly soluble drugs and also in determining the required doses
111
What are the two main plasma proteins involved in drug transport?
Albumin and glycoprotein
Others which are less important are alpha-1-acid glycoprotein (carries basic molecules) and specific carriers for cortisol and thyroxine.
112
True/false - albumin
Albumin is a small molecule with relatively few binding sites which are specific to certain drugs
False
Albumin is a large molecule - ~69,000 daltons.
It has multiple, relatively non-specific, binding sites
113
What is important about shape and charge of the binding sites on plasma proteins?
114
What bonds are involved in protein binding of drugs?
115
Why are weaker bonds important in protein binding?
They allow rapid dissociation of the drug at the site of action and for elimination (based on the concentration gradient)
116
Describe the chemical relationship between drugs and protein binding sites
Drug + protein binding site ⇌ drug-protein complex
117
How does the following equation effect drug binding and distribution?
Drug + protein binding site ⇌ drug-protein complex
as concentration of free drug falls due to diffusion at locations with a low drug concentration so the balance of the equation will shift to the left.
