3.3.13 Amino acids , Proteins and DNA Flashcards
what’s the structure of an amino acid
have an amino group ( -NH2)
Carboxyl group (-COOH)
Have a hydrogen
Have an R group - but the exception of glycine where this would be a H
what does it mean if amino acids are amphoteric
They have acidic and basic properties
why are amino acids chiral molecules
They have 4 different groups around a central carbon atom
They rotate plane polarised light
how do we name an amino acid
1) find the longest carbon chain
2) number the carbons
3) note the number where the NH2 group sits
4) name any other groups
what is a zwitterion
A molecule with both positive and negative ions. Only exist at the amino acids isoelectric point
what is an isoelectric point
The pH at which the overall charge is zero. This is dependent on the R group
when is a zwitterion likely to be formed
when at pH at the isoelectric point
Both the carboxyl and amino groups are ionised
What will happen if the pH is lower than the isoelectric point ( in acidic conditions )
The COO- is likely to accept an H+
The NH3 group become positive
what will happen if the pH is higher than the isoelectric point
The NH3+ is likely to lose a H+
The COOH becomes COO-
what does Thin layer chromatography (TLC) allow us to do
Allows us to separate and identify amino acids as they have different solubility’s
what is the stationary phase of TLC
Uses a stationary phase of silica or alumina mounted on a glass metal plate .
A pencil base line is drawn and drops of amino acids mixture added
why must the base line be above solvent line
because if not the amino acid drops would just dissolve in the solvent
What happens after the stationary phase in a TLC
Place plate in a solvent
Leave until solvent has moved up to near the top of the plate .
Remove , mark the solvent front and allow to dry
What does it mean if the spots of an amino acid are higher up
the amino acid is more soluble
what does it mean if the amino acid spot are lower down the chromatogram
The amino acids are less soluble
How can we identify amino acids using a chromatogram
We can identify amino acids using the positions on the chromatogram
How can amino acids be seen even though they’re colourless
Using iodine / nihydrin solution
Or fluorescent dyes and UV light
how can fluorescent dyes and UV light be used to identify amino acids on a chromatogram
Adding a fluorescent dye to the silica / alumina can be seen using a UV light
The colourless spots on the chromatogram will block any glow from the fluorescent dye.
You can then draw around these spots to mark where they are
Why is a glass lid used in a TLC
prevents solvent evaporating
how can we use iodine / ninhyrdin to find amino acids in a chromatogram
Place the chromatogram in a sealed jar with a few iodine crystals
The iodine vapour sticks to the chemicals on the plate dying them purple
The iodine vapor is known as a locating agent
what mathematical value can amino acids be identified from
amino acids can be identified by calculating the Rf value from a chromatogram
what do the number of amino acids spots on the plate in a chromatogram tell you
tells you how many amino acids make up the mixture
what is the calculation to work out the Rf value of amino acid
Rf = distance travelled by spot / distance travelled by solvent
what do we do when we calculated the Rf value to find an amino acid
compare it to the data books to see which amino acid it is
What changes the Rf values for an amino acid
If the temperature , solvent or make up of TLC changes
EQ : state why each amino acid has a different Rf value (1)
each amino acid has different attraction / solubility in stationary and mobile phases
EQ : Suggest how the positions of the amino acids on the TLC plate were located (1)
Using ninhydrin or UV lamp
EQ Suggest why it was necessary to use two different solvents (1)
some of the amino acids did not dissolve with the first solvent
What are proteins
Polymers made from combinations of amino acids ( monomers ) .
The amino acids are linked by peptide links , which are the amide functional group
what happens when we join 2 amino acids together
we form a dipeptide molecule
why does a dipeptide have a -COOH and -NH2 at either end
So further reactions can occur to make a polymer chain
How can a protein be broken down into amino acids
Via hydrolysis
what conditions are needed for hydrolysis of dipeptides / proteins
severe conditions - 6moldm-3 hcl , 110 degrees and reflux for 24 hours
what’s the primary structure of proteins
sequence of the 20 different naturally occurring amino acids joined together by condensation reaction with peptide links
what is a secondary structure of a protein (alpha helix )
3D arrangement of amino acids with the polypeptide chain in a corkscrew shape is held in place by hydrogen bonds between the H of the delta N- and delta H+ group of the -O of delta C+=O delta minus of the fourth amino acid along the chain
The R groups on the amino acid are all pointed to the outside of the helix
what is a secondary structure of a protein ( beta pleated sheet)
The protein chain folds into parallel strands side by side .
The protein chain is held into a pleated shape by Hudrogen bonds between the H of the -NH group and the O of the -C=O of the amino acid much further along the chain in the parallel region
what is the tertiary structure of proteins
The folding of the secondary structure into more complex shapes. It’s held in place by interactions between R- side groups in more distant amino acids . These can be a variety of interactions including hydrogen bonding , disulphide bonds ( sulphur bridges ) and ionic interactions
what are enzymes
Proteins and are biological catalysts that speed up chemical reactions
Why do enzymes have chiral centres
They’re made up of amino acids
Explain the origin of the interaction represented by the dotted lines in an alpha helix secondary structure protein
- Nitorgen and oxygen are very electronegative
- therefore C=O and N-H are polar
- results in formation of a hydrogen bond between O and H
- In which a lone pair of electrons on an oxygen atom is strongly attracted to delta H+
what does the active site being stereospecific mean
If the substrate is chiral then it’s likely that only one enantiomer will fit in the enzyme and so only one isomer will be catalysed
what are the strengths of interactions in enzymes
need to 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 is the lock and key hypothesis in enzymes
Only substrate molecules with the right shape and correct positions of functional groups will fit and bind to the active site , forming an enzyme substrate complex
what is the active site of an enzyme
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 e.g
- hydrogen bonding
- VDW
- permanent dipole dipole
- ionic interactions
how do inhibitors lower the rate of reaction
Often bind to active site strongly so stopping the substrate attaching to the enzyme .
- higher the concentration of inhibitors , the more active sites will be blocked so rate of reaction decreases
- If inhibitor binds poorly to active site then rate of reaction will not be reduced much
how can drugs acts as enzyme inhibitors
By blocking the active site
- the inhibitor will often bind to the active site strong so stopping the substrate attaching to the enzyme
- computers can be used to help design those drugs
what is DNA
a polymer that is made up of monomers called nucleotides
what is a nucleotide
Made up from a phosphate ion bonded to 2-deoxryribose which is in turn bonded to one of the four bases : adenine , cytosine , guanine and thymine
Where are the nitrogen’s in the bases that bind with the deoxyribose molecule
At the bottom of the molecule , bonded to a H
how can we create a sugar phosphate polymer chain (sugar phosphate backbone )
By adding two nucleotides together via a condensation polymerisation reaction .
- They are linked by covalent bonds / phosphodiester bonds between phosphate group of one nucleotide and the 2-deoxyribose of another nucleotide .
how is DNA formed
from 2 polynucleotide strands that are twisted together to form a double helix
how are the polynucleotide strands are held together
By hydrogen bonds between the bases
which bases join bond together
adenine and thymine
cytosine and guanine
How does guanine pair with cytosine
By 3 hydrogen bonds
how does adenine pair with thymine
by 2 hydrogen bonds
what is cisplatin used as
an anti cancer drug
how does cisplatin prevent DNA replication in cancerous cells
By a ligand substitution reaction with DNA in which a dative covalent bond is formed between platinum and a nitrogen atom on guanine
- the two chloride ions are displaced
how can unwanted side effects like hair loss occur with cisplatin
cisplatin can also prevent the replication of healthy cells by bonding on to healthy DNA
what type of reaction would happen if they added methanol and a strong acid catalyst (h2so4) to an amino acid
esterification .
H2N would be H3N+
COOH group would turn into an ester and a CH3 attached
what type of reaction would it be if we added 2CH3COCl to an amino acid
esterification .
A C=O with a CH3 attached would be attached to the Nitrogen in NH2
what type of reaction would it be if we added 2CH3COCl to an amino acid
esterification .
A C=O with a CH3 attached would be attached to the Nitrogen in NH2
EQ: Explain why the strength of the interaction between two cysteine R groups differs from the strength of the interaction between a serine R group and an aspartic acid R group (4)
- R groups of serine and aspartic acid are an alcohol and a carboxylic acid which forms hydrogen bonds
- R group of cysteine is a sulphide , so will form disulphide bridges .
- disulfide bridges are stronger than hydrogen bonds due to being covalent bonds whereas hydrogen bonds are intermolecular forces
EQ : why are melting points of zwitterions or amino acids as solids higher than the melting point of it not in a zwitterion of a solid (2)
- electrostatic forces between ions ( or ionic bonding )
- is stronger than hydrogen bonding
EQ : give the IUPAC name of threonine (1)
2-amino-3-hydroxybutanoic acid
why is allowing the solvent to rise the the top in TLC not essential
because Rf value can still be calculated if solvent front does not reach the top of the plate
EQ :Describe the method on how you would find the Rf values of amino acids on TLC plate (4)
1) Use Uv light to locate spots of amino acids
2) measure distance from initial pencil line to each amino acid spot
3) measure distance from initial pencil line to solvent front
4) rf value = distance travelled by spot / distance travelled by solvent
what are some common fragmentations in amino acids
loss of COOH , NH2 or CH3 groups
