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Doc
Brown's Chemistry Clinic
My unofficial
support for Salters
A2
Advanced Chemistry
Salters A2 Chemistry - 'exam
bashing' thoughts for
Unit EP "Engineering Proteins"
- part of module 2849
My revision
index * EP unit
map-learning objectives * other EP backup
stuff *
My Salters AS homepage *
My Salters A2 homepage *
Email
PLEASE REMEMBER, THESE ARE NOT 'STAND
ALONE' NOTES, and were designed for my classes for use alongside the Salters
resources - Chemical Ideas, Chemical Storylines, Practical
Activities-Investigations and the AS-A2 Revision guides all published by
Heinemann Secondary Series, to reduce the reading workload and offer a study
strategy. From your teacher (not
me!), its handy to have the answers to the Chemical Ideas, Storylines
Assignments and Activities Questions side by side with the texts and these
strategy pages. You haven't time to redo the Q's but a quick read of the Q's and
connecting with the official answers is valuable revision - there is too much
hit and miss revision from doing past papers in my opinion.
CHEMICAL
STORYLINES EP1 "Christopher's Story"
Chemical
Storylines EP2 "Protein building"
-
Amino acid structure - the
primary amine and carboxylic acid functional groups
-
A protein is a sequence of amino acids joined together.
The amino acids join together by
losing a water molecule between two amino acids in a condensation reaction
making a
peptide link (-NH-CO-) which is an amide (secondary).
-
The amino acid sequence of a protein its primary structure.
-
Chiral carbon of amino
acid:
-
4 different groups on a
carbon, -R, -H, -NH2 and -COOH.
-
Its the R group that
varies.
-
3D shape and D and L
optical isomers except for aminoethanoic acid (glycine).
-
Using shorthand to represent amino acid sequences
...
-
Cells build
proteins from L amino acids.
-
Use of bacteria/yeast cells to make proteins
(see also in CS EP3)
-
need to know three things to make protein
-
a set of instructions
for the protein sequence of amino acids (primary structure)
-
a ready supply of the
amino acids
-
a way of efficiently
combining the amino and carboxylic acid together to make the peptide
linkage
-
Messenger ribonucleic
acid (mRNA) carries the sequence code for the primary polypeptide
structure. Each protein has its own mRNA
-
Each amino acid has its own
transfer ribonucleic acid (tRNA) and with the aid of enzymes that
also recognise a particular amino acid, the acid is esterified to an OH
group on the tRNA (Fig 15 p146).
-
The cell's catalyst for
protein production is ribosomal nucleic acid (rRNA), which
interacts with the mRNA reading the code (Figs 16 and 17 p146-147).
-
The structure of RNA
consists of
-
a backbone of ribose
and phosphate groupings with 'side-chains' of bases (fig
14 p145)
-
four bases are used as a
triplet code for amino acids (codons on the
mRNA, table 2 p146)
-
and the matching
anticodons base codes are on the tRNA
-
To consistently redo the molecular process
of building a protein a permanent record of instructions is 'stored' on
deoxyribonucleic acid (DNA)
-
Figs 19-20 p148 show
that DNA consists of a double
helix molecular structure of two strands are held together by hydrogen bonding
between base pairs, A...T and G...C (note in DNA, compared to
RNA, thymine has replaced uracil)
-
Overall the 'process
sequence' is DNA codes for RNA and then RNA codes for
proteins (summarised in Fig 23 p149)
-
Many DNA segments
are stored together in genes, the permanent 'filing cabinet records' of
all the instructions to reproduce any part of the organism.
-
Assignments 1 to 6 are exam
like questions well worth revising.
-
Scribbled
'detailed'? summary of pages 144-150 written in typical surgery
handwriting, hmmmm!!!! I may find time to type it up neatly, but not just at
the moment.
CI 13.3 Carboxylic acids and their derivatives
(revision
link)
CI 13.4 The -OH group in alcohols, phenols and acids
(revision
link)
Chemical
Ideas13.8 Amines and amides (revision)
-
The structure and naming of
primary, secondary and tertiary amines.
-
The properties of ammonia and amines eg
-
Amide structure and
hydrolysis (eg reflux with HCl(aq) or NaOH(aq))
and structure of the hydrolysis products.
Chemical
Ideas 13.9 Amino acids H2N-CHR-COOH
-
The naming and structure of amino
acids and their bi-functional group nature.
-
The formation of zwitterions.
+H3N-CHR-COO-
-
Their condensation to form polyamides (peptide
linkage in polypeptides and protein)
-
Describe the use of paper
chromatography to analyse the amino acids ('residues') from hydrolysed
(degraded) protein.
-
Need practice in naming, drawing
structures, hydrolysis equations of amides, equations for amino acid
reactions.
-
Carboxylic/amino
acid structures and organic
nitrogen compound structures.
CI 6.6 Nuclear magnetic resonance spectroscopy
(NMR)
-
A very powerful tool for
molecular structure analysis.
-
Hydrogen nuclei (protons)
behave like tiny spinning magnets* and can align
with, or against (if energy supplied) an external magnetic
field. * A spinning/moving charge always
produces a magnetic field, cross-reference, the magnetic field created
around any wire carrying an electric current and its direction depends on
the direction of current flow.
-
Fig 36: If the
'environment'-proton
poles are aligned against each other, the proton is in a slightly higher energy level,
and when the poles are aligned with the field, the proton is in a lower
energy level. (Yes, everything is quantised again!)
-
If the appropriate quantum
of energy,  E, is
supplied, the proton can be made to flip from the lower to the higher
energy level, and of course, relax down again, emitting quanta of
energy.
-
These spinning protons
behave slightly differently in different electronic (and therefore
magnetic) environments. In other words, the atoms of different
near-neighbour
molecular structure affect the proton's behaviour. This means E
will vary depending on the local electronic environment and it also
depends on the strength of magnetic field applied (though the latter need
not concern us).
-
The E
change can be produced by radio frequencies (RF), see Fig 37,
and the sample is irradiated with the RF signal (raise quantum level) and a
detector picks up the RF signal of the relaxing E
change as the proton returns back to the lower energy level.
-
The proton E
signal ie the emission frequency is slightly different for protons in a
different electronic situation.
-
All these emitted 'proton
frequencies' are measured against a standard called tetramethylsilane, Si(CH3)4,
TMS.
-
The TMS frequency is given
an arbitrary value of 0.0 and the difference in
frequency for other protons compared to the 12 identical protons
in TMS is called the chemical shift and measured in ppm.
-
Two important pieces of
information are now available:
-
Tables of proton
chemical shift data are now available, and from them you can assign the
molecular structure of the atoms neighbouring the particular proton.
-
The ratios of the
different signal strengths bear a direct relationship to the number of
protons in that particular 'environment' in a particular molecule.
Technically this is the ratios of the areas underneath each signal peak
curve.
Chemical
Ideas 3.3 Shapes of molecules (revision)
-
Electron pair repulsion theory
– both bond pairs and lone pairs affect shape.
-
Shapes to know - linear, bent, pyramidal,
tetrahedral, trigonal planar, larger planar (also square planar ions in SS)
and octahedral. The name is based on the other atoms connected to the
central atom and NOT on the number of bond + lone pairs of electrons.
-
Constructing dot/cross
diagrams, predicting shape and subsequent bond angles.
Chemical
Ideas 3.5 Geometric isomerism (revision)
Chemical
Ideas 3.6 Optical Isomerism
-
Optical isomers or enantiomers
are isomeric 'non-superimposable' mirror image forms
- Old notation in biochemistry was D/L enantiomers.
- One example of their occurrence is when four
different 'groups' are joined to a saturated carbon atom eg Cabde,
where a, b, d and e are atoms or groups of atoms.
- The atom is known as a 'chiral' or
'asymmetric' carbon atom.
- A good example is an alpha amino acid (other
than aminoethanoic acid, glycine), a, b, d and e are
-COOH, -NH2,
-H and -R.
- If two 'groups' are the same, there is a
'plane of symmetry' through the molecule and the mirror images are super-imposable, meaning
they are the same, and can't be isomers.
-
The isomers have very similarity of
most physical properties eg identical melting points, solubility,
density etc. but their crystal structures are mirror images in shape. (CI p54)
-
Important chemical differences - all down to
the 'steriochemical situation' - at least 3 examples listed and described on CI p55
and they are all essentially 'will the
key fit in the lock' situation?
-
If an asymmetric molecule (eg enzyme)
collides with another asymmetric molecule (eg substrate) then the
interaction is 'steriochemically' or '3D spatially' controlled. A reaction
may readily or slowly happen or not at all, depending on the 'docking'
interactions prior to the molecular changes.
- recognising possibility of optical isomers
– spotting the chiral centre – drawing '3D' diagrams of optical isomers properly
(top of CI p54).
Activity
EP2.1 Investigating amines and amino acids
Activity
EP2.2 What's in aspartame?
Activity
EP2.3 Using NMR spectroscopy for structure
determination
Activity
EP2.4 The shapes of alpha-amino acids
Activity
EP2.5 A testing smell
Activity
EP2.6 Taking note of proteins
Activity
EP2.7
Modeling DNA
Activity
EP2.8 Life reveals its twisted secret
Chemical
Storylines EP3 "Genetic engineering"
-
Fig 29 CS EP3 sums it all up
the technique for changing genes with an outline of how insulin is produced by genetic engineering (recombinant DNA
technology).
-
Plasmids (circles of DNA)
can be extracted from bacterial cells cut by restriction enzymes which
cut particular sugar-phosphate bonds.
-
A gene can be inserted into
the plasmid by recombinant enzymes which reform the sugar-phosphate
bonds and complete the circle of DNA - now modified.
-
The modified plasmid is put
back into bacterial cells which multiply in a fermenter.
-
The modified bacteria
produce the insulin and separated from the bacterial cell waste.
-
There is an increasing use of genetically engineered molecules:
eg
-
Human
growth hormone.
-
Factor 8 for haemophiliacs.
(Those used in
medicine products have the advantage of being purer than traditional
sources)
-
Vaccines.
-
Modified bacteria
and fungi for treating harmful => harmless waste in pollution control.
-
Genetically modified
plants for greater yields, increased pest resistance etc.
-
Gene therapy to tackle
diseases like cystic fibroses.
Chemical
Storylines EP4 "Proteins in 3-D"
-
Primary structure of protein is
the sequence of amino acids, but the protein has a precise shape arising
from folding of the chains and the shape is critically linked to proteins
function (eg key and lock' mechanism for enzymes - particularly the positioning of chemical groups to interact most effectively.
-
The 3-D shape ie by chain
or sheet folding, is by four types of interaction
-
Instantaneous dipole-induced dipole attractive forces
from non-polar side chains (Van der Waals in my
days in the 60's and shorter!, but more correct and give unto Salters what
is Salters!
-
Hydrogen bonding via -OH
and -NH2 groups in the sidechain
-
Ionic attractions via -NH3+
and -COO- groups from
ionisable -NH2 and -COOH
groups in the side chains.
-
Covalent bonding between
-SH side chain groups via -S-S- bonds (oxidation reaction to
remove H).
-
The two common
arrangements of the secondary structure (often via H-bonding) are (a) coiled into helix,
(b) parallel
extended chains forming a sheet.
-
The helix chains or sheets are further folded via
the four bonding forces listed above to give
the overall 3-D shape or tertiary structure.
-
The quaternary structure is
when multiples of the tertiary structure can 'club together' eg the insulin dimer
-
So overall you should now appreciate insulin in terms of prim/sec/tert/quat structure!
CI 5.3 Forces between molecules: temporary & permanent dipoles
(revise)
-
Relating boiling points to
intermolecular forces.
-
Bond polarisation: polar
and non-polar bonds.
-
To understand origins and
describe examples of
permanent, temporary/instantaneous and induced dipoles
d+
and d-.
-
Giving rise to three kinds of dipole interaction
(weak intermolecular force):
-
permanent dipole-permanent
dipole (between two molecules both with a polar bond)
-
permanent dipole-induced
dipole (molecule with polar bond inducing a dipole in a non-polar
molecule)
-
instantaneous dipole-induced dipole
(occurs between any two molecules irrespective of polarity factors)
-
Note that shape can influence the strength of intermolecular attraction.
-
As well as hydrogen-bonding
(below) they all contribute to hold together the 2D/3D structures in
proteins and DNA etc.
CI 5.4 Forces between molecules: hydrogen bonding (revision)
-
Looking in more detail at
permanent dipoles via bond polarity and dipole d+/d- diagrams,
remember the dipole
originates from electronegativity differences and permanent dipoles also
produce induced dipole interactions.
-
Origin of large dipole effects:
the effect is at its greatest when ...
-
one or more very electronegative atoms in
molecule,
-
where dipoles can
approach closely, (special case of H-bonding,
small H atom)
-
very electronegative O and
small H atom
-
O, N and F are very electronegative and lone pair of electrons to
line up with d+H
-
see hydrogen-bonding diagrams (remember it isn’t an actual covalent bond )
-
examples and effects of H-bonding in eg HF (wrt to other HX),
H2O, nylon
polymers, protein
-
The CI 5.4 problems on
intermolecular forces - concentrate on the recognising the possibility of significantly polar bonds, recognising possible types of
dipole interaction between molecules, H-bonding diagrams (polymer Q’s 6-9
only relevant to PR)
Chemical
Storylines EP5 "Giving Evolution a Push"
-
Meaning of dynamic equilibrium
and using Kc and equilibrium expressions by looking at insulin monomer/dimer/hexamer
equilibria.
-
The idea of modifying insulin
structure to change the equilibrium concentration of the monomer.
-
Using designer
genes to modify DNA structure in bacteria to produce monomeric insulin,
rather than the less effective dimer and hexamer.
-
This is achieved by
modifying parts of the insulin molecule that are responsible for the
intermolecular attraction producing the dimer and hexamer.
-
This may involve, in
principle, (i) changing a positive and negative polar groups into
non-polar groups in the side chain, or (ii) two negative side chain
groups that repel each other, or (iii) even the presence of an
intervening molecule (see about phenol in Fig 49).
-
The result is impressive as
shown in Fig 48 p158.
Chemical
Ideas 7.1 Chemical equilibrium (revision)
-
Meaning of dynamic equilibrium
and 
sign.
-
Conditions for dynamic equilibrium eg rate forward = rate
backward
-
No
net change in concentrations at equilibrium.
-
Reversible reactions and the position of
the equilibrium ie revising factors affecting it eg temperature and
concentration (and pressure).
Chemical
Ideas 7.2 Equilibria and concentrations
-
Introduction to
equilibrium expressions and quantitative interpretation .
-
Writing out equilibrium
expressions with/without powers.
-
Constancy of Kc at constant temperature.
-
Numerical analysis of data to show
constancy of Kc, units of Kc.
-
How position of equilibrium changes if
particular concentrations of components are changed by Le Chatelier’s
principle
-
Writing out equilibrium expressions and solving problems via
Kc
expressions (may be given Kc and some
[concentrations] to solve for a [], or given all [] to calculate Kc
and watch units).
Chemical
Storylines EP6 "Enzymes"
-
Testing for glucose levels
illustrates four important points about enzymes
-
catalysts
-
highly specific
-
sensitive to pH
-
sensitive to temperature
-
Active site matching bound
substrate - ‘key and lock mechanism’
-
Activation energies
catalysed/uncatalysed - reaction profile diagrams [single, double (see also
CI
10.3/10.5) and triple 'bump' diagrams depending on the step sequence.
-
Enzymes as catalysts,
acting by lowering of activation energy by helping breaking bonds and
rearranging atoms, often facilitating reaction that would normally not
happen at all!
-
Enzymes can act effectively in very low concentrations,
they are that good!!!!
-
Reaction kinetics: usually
1st order wrt substrate and enzyme, but enzyme active
sites can be saturated at high substrate
concentration giving zero order kinetics wrt substrate, the rate
becomes dependent on the rate of diffusion of reactants in and products out.
-
The denaturing
effects on enzymes of eg acid or heat is explained by these factors
changing the structure of the enzyme so the 'key no longer fits in the
lock'! eg (and x-ref p153)
-
decreasing pH protonates
-NH2 (to -NH3+) groups inhibiting
hydrogen bonding or increasing unwanted attraction?
-
decreasing pH protonates
-COO- groups (to -COOH) inhibiting ionic attraction
-
increasing pH de-protonates
-NH3+ (to -NH2) groups inhibiting ionic
attraction
-
increasing pH de-protonates
-COOH (to -COO-) groups inhibiting hydrogen bonding or
increasing unwanted attraction?
-
increasing temperature
weakens all intermolecular forces, so important in determining the 3D
shape
-
Examples of enzymes at work and possible future
applications:
-
diabetes strip to detect
glucose
-
producing glucose syrup
with alpha-amylase
-
cheese making with rennet
enzymes
-
stain removing enzymes in
washing up powders (proteins or fats)
-
water treatment enzymes to
remove toxins
CI
10.1/10.2 Factors and effect of temperature on rate (revision)
-
Revise the factors affecting
rates, collision theory and activation energy.
-
Revise the ideas of activation
energy and reaction profiles.
Chemical
Ideas 10.4/10.5 catalysts (revision)
Chemical
Ideas 10.3 The effect of concentration on rate
-
The meaning of rate -
speed of reaction.
-
The methods of
measuring rate eg gas/burette for collecting gas, iodine clock,
-
How concentration affects rate
-
Graphical methods of
processing rate data eg to get initial rate or half-life.
-
Further analysis to get to
the orders (0,1,2,3) of
reaction with respect to an individual reactant or the overall reaction
order.
-
Writing out the rate equation,
calculating the rate constant and its units
-
The meaning of
half-life of a reaction - constancy of half-life for 1st order
reaction - graphical/computational methods of determining order of reaction
- interpreting rate equations wrt mechanisms - rate determining step -
mechanism of enzyme catalysed reactions and reaction profiles
-
Scribbled
summary of CI 10.3 pages 227-235, Scribble
on units of rate constant k.
-
Problems
- practice being able to interpret rate equations, deriving orders
and rate equations from given data, half-life calculations etc.
Activity
EP6.1 Testing for glucose
Activity
EP6.2 Succinate dehydrogenase (option)
Act.
EP6.3 The effect of enzyme and substrate concentration on rate of reaction
Activity
EP6.4 Using the iodine clock method to find the order of a reaction
Activity
EP6.5 Enzyme kinetics
Chemical
Storylines EP7 "Summary", Activity EP7 Check your notes on Engineering
Proteins, EP learning objective list and EP Unit Test
should all help prepare for the module exam.
GENERAL
REVISION
NOTES
* Salters
Advanced Level Chemistry * Salters Advanced Level Chemistry * Salters
Advanced Level Chemistry * Salters Advanced Level Chemistry * Salters
Advanced Level Chemistry *
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