amino acids, proteins and DNA Flashcards
what is the general structure of an amino acid
NH2-CH-COOH with a R group attached to it
the R group can be a variety of different things depending on what amino acid it is
the NH2 and the COOH group are attached to the same C group
what is the simplest amino acid
the simplest amino acid group is glycine where the R group is H
NH2- CH2-COOH
describe the optical activity of amino acid
all amino acids exept glycine are chiral because there are four different groups around the C
they rotate plane polarised light
how do you name amino acids
amino is often the lower priority group and therefore you use the prefix amino
you then use the suffix of the higher priority group
e.g.
NH2 - CH2 - COOH
2-aminoethanoic acid
what are acid or basic amino acids
some amino acids have an extra carboxylic acid or an amine group on the R group.
These amino acids are classed as acidic or basic amino acids
e.g. 2,6-diaminohexanoic acid
what are Zwitterions
The no charge form of an amino acid never occurs
The amino acid exits as a dipolar Zwitterion
what is the state of an amino acid
amino acids are often acids
why do amino acids have high melting points
The ionic interaction between zwitterions explains the relatively high melting points of amino acids opposed to the weaker hydrogen bonding that would occur in the in the no charge form
describe the ph of amino acids in certain solutions
the amino group is basic and the carboxylic acid group is acidic
species in alkaline solution high ph:
- the amino acid loses a H+ from COOH
species in neutral solutions:
-forms the Zwitterion of amino acids
species in acidic solution low ph
-the amino group in the amino acid gains a H+ forming NH3
Therefore amino acids can act as weak buffers and will gradually change pH if small amounts of acid or alkalis are added to the amino acids
The extra carboxylix acid or amino amine group on the R group will also react and change form in alkaline and acid conditions
what is an equation for an amino acid in a strong acid (low ph)
+NH2CH2COO- + HCL =CL-NH3+CH2COOH
give an equation for an amino acid in a strong alkali (high ph)
+NH2CH2COO- + NaOH = NH2CH2CO2-Na+ + H2O
what are dipeptides
dipeptides are simple combination molecules of two amino acids with one amide (peptide) link
for any two different amino acids, there are two possible combinations of the amino acids in the dipeptide
what are the other reactions of amino acids
the carboxylic acid group and amine group in amino acids can undergo the usual reactions of these functional groups
e.g. esterfication reactions
how do you hydrolyse dipeptides/ proteins
add aqueous concentrated hydrochloric acid and then heat the mixture under reflux for 24 hours
The composition of the protein molecule may then be deduced by using TLC chromatography
describe thin-layer chromatography
1) wearing gloves, draw a pencil 1 cm above the bottom of a TLC plate and mark spots for each sample equally spaced along a line
2) use a capillary tube ti add a tiny drop of each solution to different spot and allow the plate to air dry
3) add a solvent to a chamber or large beaker with a lid so that it is no more than 1cm in depth
4) place the TLC plate into the chamber, making sure that the level of the solvent is below the pencil line. Replace the lid to get a tight seal
5. when the level of the solvent reaches about 1 cm from the top of the plate, remove the plate and mark the solvent level with a pencil. Allow the plate to dry in the fume cupboard
6. spray paper with ningydrin and put in oven - draw around them lightly in pencil
7. calculate the Rf values of the observed spots
what is the Rf value
distance moved by the amino acid/ distance moved by the solvent
measure how far each spot travels relative to the solvent front and calculate the Rf value
Each amino acid has its own Rf value
compare Rd values to those known substances
why do some substances don’t separate
some substances won’t separate because similar compounds have similar Rf values
So some spots may contain more than one compound
why must plastic gloves be worn
to prevent contamination from the hand to the plate
why must a pencil line be drawn
so that it will not dissolve in the solvent
why must tiny drops be used
too big a drop will cause different drops to merge
why must the depth of the solvent be monitored
if the solvent is too deep it will dissolve the sample spots the sample spots form the plate
why must a lid be used
ti prevent evaporation of the toxic solvent
why must we wait for the solvent to rise to the top
so it will get more accurate results if the solvent is allowed to rise to near the top of the plate but the Rd value can ve calculated if the solvent does not reach the top of the plate
why must we allow the solvent to dry in a fume cupbaord
the solvent is toxic
why must ninhydrin be sprayed
if ninhydrin is sprayed on amino acid and then heated for 10 minutes then red to blue spots appear
This is done because amino acids are transparent and cannot be seen
We can also shine UV light to see the position of spots
what is the primary structure of amino acids
the primary structure of proteins is the sequence of the 20 different naturally occurring amino acids joined together via a series of condensation reactions with peptide links (also known as the amide functional group)
what is the secondary structure of a protein
the 3D arrangement of amino acids with the polypeptide chain in a - helix shape is held in place by hydrogen bonds between the H of N-H group and the O of the C=O of the FOURTH amino acid along the chain
The R groups on the amino acids are all points to the OUTSIDE of the helix
what is the other form in which the secondary structure be
the secondary structure can also take the form of a B- pleated sheets
The protein chain folds into parallel strands side by side
The protein chain is held into the pleated shape by hydrogen bonds between the H of N-H group and the O of C=O of the amino acid much further along the chain in the parallel region (like cellulose)
what is the tertiary structure of proteins
the tertiary structure is the folding of the secondary structure into more complex shapes
It is held in place by interactions between the R- side in more distant amino acids
These can be a variety of interactions including hydrogen bonding sulfur-sulfur bonds and ionic interactions
how can hydrogen bonds be held in place in a tertiary structure
hydrogen bonding is one type of force that holds proteins in shape.
Hydrogen bonds only exist between polar groups such as -OH and -NH2
These groups contain electronegative atoms which induce a partial positive charge on the hydrogen atom
The hydrogen is attracted to lone pairs of electrons on adjacent polar bonds and a hydrogen bond is formed
how can ionic bonds form in a tertiary structure
ionic interactions could form between acidic amino acids and basic amino acids
There is a transfer of a hydrogen ion from the -COOH to the NH2 forming a zwitterion
how can disulfide bonds be formed
if two cysteine side chains end up near each other due to folding on the protein chain, they react to form a sulfur bridge which is a covalent bond
cysteine contains a thiol group and this thiol group lose its H atoms and join together to form a disulfide -S-S bond with another thiol group
These disulfide bonds link together different parts of the protein and help to stabilise the tertiary structure
the reaction would lead to have the amino acid residues (which is the amidno acids that make up a protein) + 2H+ + 2e-
what are enzymes
enzymes are proteins
what is the structure of the amino acid active site
The active site of an enzyme is usually a hollow in the globular protein structure into which a substrate molecule can bond to the amino acid side chains through a variety of interactions:
- hydrogen bonding
- Van der Waals forces
- Permanent dipole forces
- ionic interactions
how strong must be the interactions in the active site
the interactions need be strong enough to hold the substrate for long enough for the enzyme catalysed reaction to occur, but weak enough for the product to be released
what are the only molecules that can fit in the active site of an enzyme
only substrate molecules with the right shape and corrected positions of functional groups will fit and bind to the active-site
This is called the lock and key hypothesis
what happens when the substrate is chiral
if the substrate is chiral then it is likely that only one enantiomer will fit in the enzyme and so only one isomer will be catalysed
The active site is therefore stereospecific
how can we drugs as enzyme inhibitors
many drugs act as enzyme inhibitors by blocking the active site
The inhibitor will often bind to the active site so stopping the substrate from attaching to the enzyme
some inhibitors can also attach elsewhere on the enzyme but in doing so can change the shape of the active site which stops its effectiveness
Computers can be used to help change design such as drugs
what are the key molecules in DNA
A phosphate ion
2- deosxyribose (a pentose sugar)
the 4 bases:
- adenine
- guanine
- thymine
- cytosine
what are nucleotides
a nucleotide is made up from a phosphate ion bonded to 2 - deoxyribose which is in turn bonded to one of the four bases:
- adenine
- cytosine
- guanine
- thymine
what is a sugar phosphate chain
a single strand of DNA (deoxyiribonucleic acid) is a polymer of nucleotides linked by covalent bonds between the phosphate group of one nucleotide and the 2- deoxyiribose of another nucleotide
This results in a sigar phosphate polymer chain with bases attatched to the sugars in the chain
how does DNA exist
DNA exists as two complementary strands of the sugar-phosphate polymer chain arranged in the form of a double helix
What does the term complementary base strands mean
complementary means the two strands must have sequences that match all A to T and C to G
there are hydrogen bonds between base pairs which lead to the two complementary strands of DNA
Guanine pairs wi
what is cisplatin
cisplatin is used as an anticancer drug
The cisplatin version only woks as two chloride ions are displaced and the molecule ins on the DNA
In doing this, it stops the replication of cancerous cells
Cisplatin prevents DNA replication in cancer in cancer cells by a ligand replacement reaction with DNA in which a dative covalent bond to formed between platinum and a nitrogen atom on guanine
what else can cisplatin do
cisplatin can also prevent the replication of healthy cells by bonding on to the healthy DNA which may lead to unwanted side effects like hair loss
Unwanted side effects can be minimised by giving cis-platin in small doses
Society needs to assess the balance between the benefits and the adverse effects of drugs such as the anticancer drug cisplatin
