Lecture 3: Amino Acids and Proteins

Question 1

What are the groups that constitute an amino acid?

Answer 1

A single hydrogen atom
Carboxylic acid group
Amino group
R ground

Question 2

What groups are ionised when protein is free in solution?

Answer 2

The amino group and carboxyl group.

H3N+ and COO-

Question 3

What optical isomers are most prevalent in nature?

Answer 3

L (levo) isomers, not D (dextro)

Question 4

Give three examples of properties of amino acids that result from their side chain.

Answer 4

Charged, acidic - Carboxylic acid side chain.
Non-polar, hydrophobic - Any hydrocarbon side chain
Uncharged, polar - Side chains with a polar group, e.g. OH, SH

Question 5

What are the two naturally occurring acidic amino acids?

Answer 5

Aspartate (Asp)
Glutamate (Glu)
(Negatively charged side chains)

Question 6

What is the difference between aliphatic and aromatic compounds?

Answer 6

Aromatic compounds must have at least one planar ring of atoms with pi electrons delocalised all the way around. Aliphatic molecules are any molecule that does not contain any aromatic qualities.

Question 7

What properties would a protein need to be embedded in a bilipid membrane.

Answer 7

It would require all the amino acids that will be embedded in the membrane to be non-polar.

Question 8

What bond links amino acids?

Answer 8

Peptide bonds, these involve 2H atoms from the NH3+ and an O atom from the COO- to be expelled as a H20 molecule.

Question 9

What are the four levels of structure that defines proteins?

Answer 9

Primary, Secondary, Tertiary, Quaternary

Question 10

What is the primary structure of protein?

Answer 10

The sequence of amino acids, this will define every other level of structure.

Question 11

What is the secondary structure of protein?

Answer 11

The three-dimensional structure of small sections of the side chain, caused by the interactions of the amino and carboxylic groups with each other on the amino acid backbone. (not the side chains).

Question 12

What kind of attractions can shape proteins?

Answer 12

Electrostatic attractions (Ionic bonds)
van der Waals forces
Hydrogen bonds
Disulphide bridges

Question 13

What determines amino acid sequence?

Answer 13

Genetic sequence.

Question 14

What is the tertiary structure of a protein?

Answer 14

Determined by the side chains and their effect on the 3D structure.

Question 15

What is the quaternary structure of a protein?

Answer 15

This is the aggregation of multiple polypeptide chains for subunits to form a single protein, can have dimers trimers, tetramers, etc.

Question 16

Give two examples of secondary structure in proteins.

Answer 16

Beta-pleated sheets and alpha helices.

Question 17

What are beta-pleated sheets linked by?

Answer 17

Beta-pleated sheets form hydrogen bonds between the COO- and NH3+ residues on the polypeptide chain backbone. These bonds mean two adjacent polypeptide chains can form this antiparallel sheet structure. Can also be parallel.

Question 17

Describe the structure of an alpha helix.

Answer 17

It is a right-handed helix in which the amino groups and carboxyl groups of amino acids four positions away will form hydrogen bonds and cause the structure to coil.

Question 18

What are chaperone proteins?

Answer 18

Chaperone proteins allow newly synthesised polypeptide chains to aggregate in a way that is correct and will mean it can perform it’s intended task. They achieve this by enclosing it in a chamber with a ‘barrel’ and chamber cap. ATP is needed to secure the chamber cap and isolate protein until protein has correctly folded.

Question 19

Finish revision cards by summarising the facts given at the end of the lecture.