Amino acids, proteins and DNA

Question 1

What two functional groups does an amino acid have?

Answer 1

Amine group
Carboxyl group

Question 2

Amino acids can be described as …. meaning they have both … and …. properties

Answer 2

Amphoteric, basic and acidic

Question 3

Why can amino acids act as acids?

Answer 3

Becuase of the carobxyl group being acidic - it can donate a proton COOH –> COO-

Question 4

Why can amino acids act as bases?

Answer 4

Because of the basic amine group - accepts a proton NH2 –> NH3+

Question 5

Amino acids are also said to be ….. molecules meaning that they can rotate plane polarised light.

Answer 5

Chiral, a solution of a single amino acid enantiomer can rotate plane polarised light

Question 6

How do you name an amino acid?

Answer 6

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

Question 7

What is a zwitterion and what is their relevance to amino acids?

Answer 7

They are dipolar ions (they have two charges both a positive and a negative charge)
Amino acids can exist as zwitterions

Question 8

Where can zwitterions only exist?

Answer 8

Near an amino acid’s isoelectric point

Question 9

What is an amino acid’s isoelectric point? And why is it different for different amino acids?

Answer 9

This is the pH where the overall charge on the amino acid is 0. And it depends on their ‘R’ group

Question 10

When does an amino acid become a zwitterion?

Answer 10

When it’s amino group is protonated to NH3+ and its carboxyl group is deprotonated to COO-

Question 11

In acidic conditions/conditions more acidic than the isoelectric point, what happens to the amino acid?

Answer 11

NH2 is protonated to NH3+
COOH group is likely to remain unchanged
It will carry a positive charge and not a negative charge

Question 12

In conditions more basic than the isoelectric point, what happens to the amino acid?

Answer 12

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.

Question 13

What happens only at or near the isoelectric point of an amino acid?

Answer 13

The carboxyl group and amino group are likely to be ionised - forming a zwitterion

Question 14

Why do amino acids have different solutbilities in the same solvent?

Answer 14

Because they have different ‘R’ groups

Question 15

What can you use to easily separate and identify amino acids in a mixture?

Answer 15

Thin layer chromatography

Question 16

What is the solvent front?

Answer 16

The distance moved by the solvent?

Question 17

What would you do to colour the amino acids - seeing as they aren’t visible

Answer 17

Spray ninhydrin solution on the plate

Question 18

What does ninhydrin solution do to the amino acids?

Answer 18

Turns them purple

Question 19

What else could you do to make the amino acids visible?

Answer 19

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.

Question 20

How can you idemtify amino acids?

Answer 20

Using the chromatogram, calculate and compare their Rf values

Question 21

How do you work out the Rf value?

Answer 21

Rf = distance travelled by spot/distance travelled by solvent

Question 22

What are proteins?

Answer 22

Condensation polymers of amino acids

Question 23

How is a dipeptide formed?

Answer 23

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

Question 24

What is a peptide link?

Answer 24

Where two amino acids join
O H
II I
C—N

Question 25

Why can the dipeptides undergo further condensation reactions?

Answer 25

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.

Question 26

Describe one way of hydrolysing proteins to form individual amino acids?

Answer 26

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

Question 27

What is the primary structure of a protein?

Answer 27

The sequnce of amino acids in the polypeptide chain

Question 28

What is the secondary structure of a protein?

Answer 28

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.

Question 29

What is the tertiary structure of a protein?

Answer 29

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.

Question 30

What two structures of a protein are formed by intermolecular forces?

Answer 30

Secondary and tertiary structure
They cause the amino acid chains to fold or twist

Question 31

What 2 main types of bond hold the protein in shape?

Answer 31

Hydrogen and disulphide bonds

Question 32

How does hydrogen bonding work?

Answer 32

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.

Question 33

What is a residue?

Answer 33

An amino acid that is part of a protein

Question 34

How does disulphide bonding work?

Answer 34

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

Question 35

What two factors can change the shape of proteins and why?

Answer 35

Temperature and pH because they affect hydrogen bonding and the formation of disulphide bonds

Question 36

What are active sites of an enzyme that means they can only work on one enantiomer of a substrate?

Answer 36

Stereospecific

Question 37

What affects the amount of enzyme inhibition?

Answer 37

The strength of the bond between the enzyme and the inhibitor and the concentration of inhibitor to substrate