Notesale: Turn your study into money

Document Preview

Extracts from the notes are below, to see the PDF you'll receive please use the links above

---

Thread of Life
Recognise and describe the structure of amino acids and recall that proteins are condensation polymers
formed from amino acid monomers

The systematic name of an amino acid is usually 2-aminocarboxylic acid
...

Amino acids are bifunctional compounds with at least one secondary amine and
one carboxylic acid
...
This amide link is also known as a peptide link and produces a dipeptide
...
Explain the role of hydrogen bonds and
other intermolecular bonds in maintaining the secondary and tertiary structure of proteins, and hence their
properties
...

The secondary structure of a protein is the structure formed from
hydrogen bonding between polar side chains on a polypeptide
...

The tertiary structure of a protein is the overall specific 3D
structure of a polypeptide chain formed from ID-ID, covalent,
hydrogen bonding and ionic attractions
...
This is a zwitterion
...

The pH of the solution can influence whether an amino acid forms a zwitterion or not
...

Placing a zwitterion ion in alkali results in the OH- taking an H+ from the NH3+ to form water
and a secondary amine
...

Describe the formation and hydrolysis of the peptide link between amino acid residues in proteins

The carboxylic acid on one amino acid reacts with the amine on another to form an amide (a
dipeptide)
...
In acidic conditions a
carboxylic acid and ammonium are formed, whilst in alkaline conditions a carboxylate ion
and amine are formed
...

A chiral centre is one with four different species
bonded to a carbon atom
...

An enantiomer is a molecule with a chiral centre, which is a nonsuperimposable mirror image
...

The general rate equation is represented as:
𝑅𝑎𝑡𝑒 = 𝑘 [𝐴] 𝑚 [𝐵] 𝑛
Where A and B are reactants and k is the rate constant
...
Order is usually 0, 1 or 2 and the
overall order of the reaction is the combined order of each reactants
...

Working out order with respect to each reactant

H2

NO

Rate

2
...
0
2
...
0

2
...
00
1
...
25

4
...
2
1
...
6

First we can work out the order of H2, by comparing the two values in blue
...
This
means that the order with respect to H2 is 1st
...
This suggests
the order with respect to NO is 2nd
...

We take one of the experimental conditions in the table, and inset our known values in the
rate equation:
4
...
0][2
...
8
= 𝑘 = 0
...
0][2
...

Understand the laboratory methods which can be used to follow the course of a reaction







Measure the volume of gas evolved from a reaction using a gas syringe
Measure the change in mass of a reaction mixture (e
...
mass loss due to evolution of
gas)
Monitor Ph
Colorimetry
Titration (quenching
o Neutralise samples of the reaction
mixture at regular intervals then
analyse the progress of the mixture
using titration

Once a reaction mixture of a particular concentration
over time has been recorded in a graph, the shape of
the graph is likely to appear a steep curve which
gradually flattens out
...
The gradient of this tangent is measured using:
𝑔𝑟𝑎𝑑𝑖𝑒𝑛𝑡 =

𝑐ℎ𝑎𝑛𝑔𝑒 𝑖𝑛 𝑦
𝑐ℎ𝑎𝑛𝑔𝑒 𝑖𝑛 𝑥

This process is repeated using different concentrations of one reactant (keeping all other
reactants in excess and temperature consistent) to give several tangents and gradients
...


This graph gives the different lines which could be produced by
different orders
...
This involves measuring how the
concentration of a reactant decreases as the reaction progresses, then measuring the half
lives
...

Use and explain the term rate determining step
...


The rate determining step is usually the slowest step in the mechanism and will contain all
the reactants in the rate equation
...
This reaction is slow because it often has a large activation
enthalpy
...
e
...
This active site
contains amino acid side groups which can react and
bind to one substrate
...
The bonds formed with the active site are
weak so they can easily be reversed when the
products need to leave
...

When substrate concentration is low, the rate equation is rate = k [E] [S]
From this we know the rate determining step must contain one molecule of both enzyme
and substrate – E + S = ES (enzyme substrate complex)
The steps following this are ES = EP = E + P
The first step is the rate determining step because
there will be empty enzyme active sites due to the
lack of substrate
...

However as the substrate concentration increases,
the rate equation becomes: rate = k [E]
This is because there all active sites are occupied by substrate molecules, meaning the
quantity of enzyme is the limiting factor in the rate of the reaction so substrate has 0 order
...

Additionally, they reduce the number of steps in a reaction, improving the atom economy
...


Deoxyribonucleic acid (DNA) is a double helix made up of two
anti-parallel strands of nucleotides
...

Each bonded sugar/phosphate reacts in another condensation
reaction with one of four bases (adenine,
thymine, guanine and cytosine) to form a
nucleotide
...

Various models were devised for the structure of DNA before the current accepted version

The first model was created by Crick and Watson, who hypothesised that DNA was made up
of three chains twisted together and held in place by double charged cations
...

Pauling then devised the three helix model, where phosphate groups were in the middle
and sugars/bases on the outside
...


Explain the significance of hydrogen bonding in DNA structure and how DNA encodes for amino acids in a
protein

Hydrogen bonds between nucleotiedes can easily be broken to open up the double helix,
exposing the bases for:



Replication of each strand to form an identical copy of DNA
Production if mRNA in protein synthesis

Transcription is where mRNA is formed from a section of single stranded DNA:




An enzyme unzips the double helix of DNA section to reveal a strand of DNA to act
as a template
mRNA nucleotides in the cell (C,U,A,G) align with complementary DNA nucleotides
and an enzyme catalyses the formation of a single mRNA strand
mRNA moves out of the nucleus and the double helix reforms its helix structure
using hydrogen bonding

Translation allows the production of a specific amino acid sequence of a protein, as coded
for by a section of DNA:






the mRNA passes to the ribosomes to act as a template for protein synthesis
tRNA molecules are each bound to an amino acid
The complementary anti-codon aligns with the codon on each mRNA molecule in a
specific sequence
This results in amino acids being aligned in the correct sequence, so an enzyme can
catalyse the formation of an amino acid chain
tRNA molecules move away from the mRNA to reform with lone amino acids

Ways mRNA differs from DNA:




The sugar in mRNA is a ribose rather than a deoxyribose
mRNA has the bases Adenine, Cytosine, Guanine and Uracil rather than Thymine
mRNA is single stranded

The DNA code is degenerate, as there is more than one codon for each amino acid
...

Understand DNA analysis can be used in genetic fingerprinting and the ethical issues of storing human DNA




A trace of blood/skin is mixed with an enzyme which cuts up the double strand at
specific sites in the DNA
The DNA fragments undergo gel electrophoresis (voltage applied and distance
travelled compared)



Radioactive tracers than bind to the fragments in their positions and a photographic
film with x-rays passed through reveals the pattern

This genetic fingerprinting can be used in paternity tests, body identification in forensics and
medical analysis of genetic populations

---