Amino acids, proteins and DNA Flashcards
What two functional groups does an amino acid have?
Amine group
Carboxyl group
Amino acids can be described as …. meaning they have both … and …. properties
Amphoteric, basic and acidic
Why can amino acids act as acids?
Becuase of the carobxyl group being acidic - it can donate a proton COOH –> COO-
Why can amino acids act as bases?
Because of the basic amine group - accepts a proton NH2 –> NH3+
Amino acids are also said to be ….. molecules meaning that they can rotate plane polarised light.
Chiral, a solution of a single amino acid enantiomer can rotate plane polarised light
How do you name an amino acid?
Find the longest carbon chain
Ensure the no.1 carbon is the carbon in the carboxyl group
Write down position of any NH2 groups - express this by writing ‘amino’
Write down the names of any other functional group and what carbon they are on.
e.g. 2-aminoethanoic acid, 2-amino-3-methylbutanoic acid
What is a zwitterion and what is their relevance to amino acids?
They are dipolar ions (they have two charges both a positive and a negative charge)
Amino acids can exist as zwitterions
Where can zwitterions only exist?
Near an amino acid’s isoelectric point
What is an amino acid’s isoelectric point? And why is it different for different amino acids?
This is the pH where the overall charge on the amino acid is 0. And it depends on their ‘R’ group
When does an amino acid become a zwitterion?
When it’s amino group is protonated to NH3+ and its carboxyl group is deprotonated to COO-
In acidic conditions/conditions more acidic than the isoelectric point, what happens to the amino acid?
NH2 is protonated to NH3+
COOH group is likely to remain unchanged
It will carry a positive charge and not a negative charge
In conditions more basic than the isoelectric point, what happens to the amino acid?
COOH is deprotonated to COO-
The NH2 group is likely to remain unchanged
The amino acid will carry a negative charge and will not carry a positive charge.
What happens only at or near the isoelectric point of an amino acid?
The carboxyl group and amino group are likely to be ionised - forming a zwitterion
Why do amino acids have different solutbilities in the same solvent?
Because they have different ‘R’ groups
What can you use to easily separate and identify amino acids in a mixture?
Thin layer chromatography
What is the solvent front?
The distance moved by the solvent?
What would you do to colour the amino acids - seeing as they aren’t visible
Spray ninhydrin solution on the plate
What does ninhydrin solution do to the amino acids?
Turns them purple
What else could you do to make the amino acids visible?
Use a special plate that has a fluorescent dye added to it. The dye glows when UV ight is shone on it. The amino acid spots cover the dye so they appear as dark spots. You can out the plate under a UV lamp and circle where the dark spots are.
How can you idemtify amino acids?
Using the chromatogram, calculate and compare their Rf values
How do you work out the Rf value?
Rf = distance travelled by spot/distance travelled by solvent
What are proteins?
Condensation polymers of amino acids
How is a dipeptide formed?
Via a condensation reaction
Loss of the OH from the carboxyl group and loss of H from amine group, the carbon and nitrogen from these groups then join together - losing a water molecule
What is a peptide link?
Where two amino acids join
O H
II I
C—N
Why can the dipeptides undergo further condensation reactions?
Because they still have an amine group at one end and a carboxyl group at the other end. They go on to form longer carbon chains.
Describe one way of hydrolysing proteins to form individual amino acids?
Add aq 6 moldm-3 HCl
Heat mixture under reflux for 24 hours
Once the peptide bonds break - either add a H or an OH group to each of the broken ends to get the amino acid back
What is the primary structure of a protein?
The sequnce of amino acids in the polypeptide chain
What is the secondary structure of a protein?
The peptide links can form hydrogen bonds with each other meaning that the chain isn’t a straight line
The shape of that chain is it’s secondary structure.
One of these structures is a spiral (alpha helix)
and the other is a beta-pleated sheet.
What is the tertiary structure of a protein?
The amino acid chain itself is coiled and folded
Extra bonds can form between other parts of the polypeptide chain - giving the protein a 3D shape.
What two structures of a protein are formed by intermolecular forces?
Secondary and tertiary structure
They cause the amino acid chains to fold or twist
What 2 main types of bond hold the protein in shape?
Hydrogen and disulphide bonds
How does hydrogen bonding work?
Exists between polar groups e.g. OH NH2
These groups contain electronegative atoms whihc induce a partially positive charge on the hydrogen.
The hydrogen is then attracted to lone pairs of electrons on adjacent polar groups and a hydrogen bond forms.
What is a residue?
An amino acid that is part of a protein
How does disulphide bonding work?
It occurs between residues of the amino acid cysteine
Cysteine contains a thiol group (-SH)
This thiol group can lose its hydrogen atom and join together to form a disulphide (-S-S-) bond with another thiol group.
These disulphide bonds link together different parts of the protein chain - helps to stabilise the tertiary structure
What two factors can change the shape of proteins and why?
Temperature and pH because they affect hydrogen bonding and the formation of disulphide bonds
What are active sites of an enzyme that means they can only work on one enantiomer of a substrate?
Stereospecific
What affects the amount of enzyme inhibition?
The strength of the bond between the enzyme and the inhibitor and the concentration of inhibitor to substrate
