Protein Diversity & Amino Acids

Question 1

What is the proteome?

Answer 1

The full set of proteins encoded by the human genome

This is NOT the same as the number of genes

Question 2

What mechanisms mean that one gene does not result in one protein?

Answer 2

1. single nucleotide polymorphisms give rise to proteins that differ by 1 AA
2. alternative splicing of RNA
3. post-translational modifications

Question 3

What are the functions of proteins within the cell?

Answer 3

1. 2/3 are either binding molecules or enzymes
2. receptors
3. signalling molecules
4. structural molecules
5. translation factors
6. transporters

Question 4

What causes phenylketonuria?

Answer 4

The absence of the enzyme phenylalanine hydroxylase

This means phenylalanine cannot be broken down

Question 5

What are the two main proteins involved in transport?

Answer 5

Haemoglobin and ferritin

Ferritin is needed to transport iron

Question 6

What causes Duchenne muscular dystrophy?

What does this result in?

Answer 6

Dystrophin is absent/ineffective

Patients lose the ability to use their muscles

Question 7

What is osteogenesis imperfecta?

What causes it?

Answer 7

Brittle bone disease

A mutation in the collagen gene means that collagen is not correctly formed

Question 8

What causes scurvy?

Answer 8

A lack of vitamin C

Vitamin C is crucial in collagen formation

Question 9

How are proteins involved in regulation?

Answer 9

They are involved in the regulation of cell division, protein synthesis and hormones

Question 10

What is self-recognition?

Answer 10

The immune system checks that all the cells belong to us and identifies those that don’t

Question 11

What causes myasthenia gravis?

Answer 11

Antibodies bind to a neurotransmitter receptor at the neuromuscular junction

This means the body cannot respond to neurological signals

Question 12

What is the general structure of an amino acid?

Answer 12

It has a central alpha carbon atom

This is attached to an amino group and a carboxyl group

It is also attached to a H atom and an R-group

Question 13

How are amino acids named?

What are the abbreviations of their names?

Answer 13

Alpha-amino acids are named according to the R group they contain

They have a full name, a 3-letter code and a 1-letter code

Question 14

How does the R-group determine the behaviour of an amino acid?

Answer 14

The R-groups of amino acids have different chemical properties

The R-group determines the behaviour of an amino acid when it is incorporated into a polypeptide chain

Question 15

How many amino acids are there?

Answer 15

There are many, but only 20 are found in proteins

The others may have metabolic roles

Question 16

What are the 5 different ways of categorising R-groups?

Answer 16

1. size (large/small)
2. shape (aliphatic/aromatic)
3. hydrophobicity (polar/non-polar)
4. charge (acidic/basic)
5. sulphur-containing

Question 17

What are the 2 sulfur containing amino acids?

Answer 17

Cysteine and methionine

Question 18

What is significant about the structure of proline?

Answer 18

It is NOT an amino acid

It is an imino acid

Question 19

What are the 9 amino acids that have non-polar side chains?

Answer 19

1. glycine
2. alanine
3. valine
4. leucine
5. isoleucine
6. methionine
7. phenylalanine
8. tryptophan
9. proline

Question 20

What are the 6 amino acids that have polar side chains?

Answer 20

1. serine
2. threonine
3. cysteine
4. tyrosine
5. asparagine
6. glutamine

Question 21

What are the 2 acidic amino acids that have negatively charged side chains?

Answer 21

1. aspartate

2. glutamate

Question 22

What are the 3 basic amino acids that have positively charged side chains?

Answer 22

1. lysine
2. arginine
3. histidine

Question 23

How does the structure of proline differ from the other amino acids?

Answer 23

The alpha amino group is covalently linked to the side chain

This makes it a secondary amine, rather than a primary amine

Question 24

How does the structure of proline affect its properties?

Answer 24

The C-N bond is very inflexible

This limits the conformations that it can take up in the 3D structure of a protein

Question 25

Which amino acid does not have optical isomers? Why?

Answer 25

All a-amino acids are chiral molecules, except glycine Glycine does not have an optical isomer because it has a H atom as an R group

Question 26

What is a chiral molecule? What types of isomers does it produce?

Answer 26

It has 4 different groups attached to the central carbon atom This produces D- and L-isomers

Question 27

What type of optical isomers are found in proteins? Why?

Answer 27

L-isomers This is due to the specificity of enzymes - an enzyme could not catalyse a reaction with a D-isomer

Question 28

What determines the charge on amino acids with ionisable R groups?

Answer 28

The charge on amino acids with ionisable R-groups is pH dependent

Question 29

What groups are present in amino acids that are charged?

Answer 29

Charged amino acids contain either a weak acid or a weak basic group This can exist in the ionised or unionised form, depending on the pH of the surroundings

Question 30

What value will tell you the pH at which an ionisable group ionises?

Answer 30

The pKa value for an ionisable group tells you at which pH the group ionises The pKa value is the pH at which a group is 50% ionised

Question 31

What is the pKa value of carboxylic acid groups?

Answer 31

pH 1.8 - 2.5 This means at pH 7, in the body, these groups are almost always negatively charged

Question 32

What is the pKa value for amino groups?

Answer 32

pH 9 - 10 This means at pH 7, in the body, these groups are almost always positively charged

Question 33

What is the pKa value of histidine? How does this affect its charge in the body?

Answer 33

pH 6 is close to the body pH (7) Histidine residues are either positively charged or neutral depending on the immediate surrounding environment

Question 34

What function is significant about the pKa value of histidine?

Answer 34

Histidine residues are found in the active sites of enzymes They act as donors or receptors of protons during enzymatic action