PL - Amino acids and proteins

Question 1

What are amino acids made up of?

Answer 1

An amino group and a carboxyl group.

Question 2

What is the amino group of an amino acid?

Answer 2

NH2

Question 3

Are carboxyl groups acidic or alkaline/basic?

Answer 3

Acidic.

Question 4

What is the carboxyl group found in amino acids?

Answer 4

COOH

Question 5

Are amino groups acidic or alkaline/basic?

Answer 5

Alkaline.

Question 6

Because amino acids have both acidic and basic properties, what does this make them?

Answer 6

Amphoteric.

Question 7

Why are amino acids amphoteric?

Answer 7

Because they’ve got both acidic and basic properties.

Question 8

What part of amino acids is different?

Answer 8

The variable (R) group.

Question 9

What can amino acids exist as?

Answer 9

Zwitterions.

Question 10

What can exist as zwitterions?

Answer 10

Amino acids.

Question 11

What is a zwitterion?

Answer 11

An overall neutral molecule that has both a positive and negative charge in different parts of the molecule.

Question 12

When can an amino acid exist as a zwitterion?

Answer 12

Only when its near its isoelectric point.

Question 13

What is the isoelectric point of an amino acid?

Answer 13

This is the pH where the overall charge on the amino acid is zero.

Question 14

What does the isoelectric point of an amino acid depend on?

Answer 14

The R group of the amino acid - its different for different amino acids.

Question 15

What happens to an amino acid in conditions more acidic than the isoelectric point?

Answer 15

The NH2 group is likely to be protonated.

Question 16

What happens to an amino acid at the isoelectric point?

Answer 16

Both the carboxyl group and the amino group are likely to be ionised - forming a zwitterion.

Question 17

What happens for a zwitterion to be formed?

Answer 17

Both the carboxyl group and the amino group are likely to be ionised.

Question 18

What happens to an amino acid in conditions more basic than the isoelectric point?

Answer 18

The COOH group is likely to lose its proton.

Question 19

What method can be used to identify unknown amino acids?

Answer 19

Paper chromatography.

Question 20

What can paper chromatography be used to do?

Answer 20

To identify unknown amino acids.

Question 21

Describe an experiment/method using paper chromatography to identify unknown amino acids in a mixture

Answer 21

1) Draw a pencil line near the bottom of a piece of chromatography paper and put a concentrated spot of the mixture you want to investigate on it.
2) Place the paper into a beaker containing a small amount of solvent so that the solvent level is below the spot of mixture. Place a watch glass on top to stop any solvent evaporating out.
3) Different substances have different solubilities in the solvent. As the solvent spreads up the paper, the different chemicals in the mixture move with it, but at different rates, so they separate out.
4) When the solvent’s nearly reached the top, take the paper out and mark where the solvent has reached with a pencil. This is the solvent front.
5) Identify the positions of the spots of different chemicals on the paper. Some chemicals, such as amino acids, aren’t coloured so you first have to make them visible. You can do this by spraying ninhydrin solution (a developing agent) on the paper to turn them purple. You can also dip the paper into a jar containing a few crystals of iodine. Iodine sublimes from a solid straight to a gas, and the iodine gas in the jar causes the spots to turn brown. However, you visualise your spots, you should circle their positions with a pencil.
6) You can then work out the Rf values of the substances using this formula : Rf value = A/B = distance travelled by spot/distance travelled by solvent.
7) If you’ve done your experiment under standard conditions, you can use a table of known Rf values to identify the components of the mixture. Otherwise, you should repeat the experiment with a spot of a substance you think is in the mixture, alongside the mixture, to see if they have the same Rf value.

Question 22

What is the formula for working out Rf values?

Answer 22

Rf value = A/B = distance travelled by spot/distance travelled by solvent.

Question 23

What are proteins?

Answer 23

Condensation polymers of amino acids (made by joining together lots of amino acid monomers with peptide links).

Question 24

What forms the peptide links between amino acids in a protein?

Answer 24

The amine group of one amino acid can react with the carboxylic acid group of another in a condensation reaction.

Question 25

What reaction joins amino acids to form proteins?

Answer 25

Condensation reaction.

Question 26

What is the product of joining 2 amino acids together in a condensation reaction?

Answer 26

A dipeptide.

Question 27

What can lots of amino acids react together to make?

Answer 27

A polypeptide chain.

Question 28

What are the amino acid monomers in a protein chain known as?

Answer 28

Amino acid residues.

Question 29

What reaction breaks a protein down into its individual amino acids?

Answer 29

Hydrolysis reaction.

Question 30

What conditions are required to break a protein down into its individual amino acids?

Answer 30

Hot aqueous 6 mol dm-3 hydrochloric acid is added, and the mixture is heated under reflux for 24 hours. This produces the ammonium salts of the amino acids. The final mixture is then neutralised using a base.

Question 31

How do you break a protein down into its individual amino acids?

Answer 31

Hot aqueous 6 mol dm-3 hydrochloric acid is added, and the mixture is heated under reflux for 24 hours. This produces the ammonium salts of the amino acids. The final mixture is then neutralised using a base.

Question 32

What are the first three levels of a protein called?

Answer 32

The primary, secondary and tertiary structures.

Question 33

What are amino acids each given?

Answer 33

A three-letter code, which is usually the same as the first three letters of their name.

E.g. leucine is ‘Leu’.

Question 34

What is the primary level structure of a protein?

Answer 34

The sequence of amino acids in the long chain that makes up the protein (the polypeptide chain).

Question 35

What is the secondary level of structure of a protein?

Answer 35

The peptide links can form hydrogen bonds with each other, meaning the chain isn’t a straight line. The shape of the chain is called its secondary structure.

The most common secondary structure is a spiral called an alpha-helix chain.

Another common type of secondary structure is a beta-pleated sheet. This is a layer of protein folded like a concertina.

Question 36

What are the 2 common secondary structures?

Answer 36

Alpha-helix and beta-pleated sheets.

Question 37

What is an alpha-helix?

Answer 37

A spiral.

Question 38

What is a beta-pleated sheet?

Answer 38

A layer of protein folded like a concertina.

Question 39

What is the tertiary structure of an amino acid?

Answer 39

The chain of amino acids is itself often coiled and folded in a characteristic way that identifies the protein. Extra bonds can form between different parts on the polypeptide chain, which give the protein a kind of 3D shape. This is its tertiary structure.

Question 40

What is there at each end of a protein’s primary structure?

Answer 40

There is a free COOH group at one end and a free NH2 group at the other end.

Question 41

What is the tertiary structure held together and stabilised by?

Answer 41

1. Instantaneous dipole-induced dipole forces.
2. Ionic interactions.
3. Hydrogen bonds.
4. Disulfide bonds/bridges.

Question 42

Where are the different bonds/forces in the tertiary structure found?

Answer 42

1. Instantaneous dipole-induced dipole forces are weak attractions that can form between two non-polar side groups, e.g. CH3.
2. Ionic interactions are formed between charged side groups, like CO2 - and NH3 +.
3. Some R groups contain functional groups that are able to form hydrogen bonds, such as -OH, -COOH, -NH2 and -CONH2.
4. The amino acid cysteine contains a thiol group (-SH). Sulfide groups on different cysteine residues can join together by forming a disulfide bond (known as a disulfide bridge).

Question 43

What affects the properties of a protein?

Answer 43

Its 3D (tertiary) structure.

Question 44

What will the tertiary structure of an enzyme determine?

Answer 44

The shape of its active site.

Question 45

Where are ionic interactions found in a protein?

Answer 45

Ionic interactions are formed between charged side groups, like CO2 - and NH3 +.

Question 46

Where are instantaneous dipole-induced dipole forces found in a protein?

Answer 46

Instantaneous dipole-induced dipole forces are weak attractions that can form between two non-polar side groups, e.g. CH3.

Question 47

Where are hydrogen bonds found in a protein?

Answer 47

Some R groups contain functional groups that are able to form hydrogen bonds, such as -OH, -COOH, -NH2 and -CONH2.

Question 48

Where are disulfide bonds/bridges found in a protein?

Answer 48

The amino acid cysteine contains a thiol group (-SH). Sulfide groups on different cysteine residues can join together by forming a disulfide bond (known as a disulfide bridge).