Proteins 1

Question 1

Why we need to study proteins

Answer 1

HGP has allowed us to map the entire genome and the proteins that genes code for. This allows pharma companies to create targeted therapies based on the proteins associated with genes and diseases. Determining the structure of a proteins also allows us to see how the protein works- aiding drug discovery.

Question 2

What constitutes a protein?

Answer 2

A protein is a organic compound consisting of one or more chains of amino acids. The human body is around 20% protein.

Question 3

How do we know the structure of proteins?

Answer 3

NMR and crystallography

Question 4

How many amino acids exist in nature?

Answer 4

20

Question 5

Which amino acids have hydrophobic R groups/

Answer 5

glycine and proline.

Question 6

Which amino acids have hydrophilic sidechains

Answer 6

serine, threonine, thyosine, aspargine, cysteine, lysine and arginine.

Question 7

Characteristics of arginine and lysine

Answer 7

At physiological pH they are protonated and hence they are basic.

Question 8

When is histidine protonated

Answer 8

Below pH 6

Question 9

Characteristics of glutamic acid and aspartic acid

Answer 9

Donates protons at physiological pH and so are negatively charged.

Question 10

Why is the state of ionisation of the amino acid important

Answer 10

The state of ionisation provides vital biological properties to proteins and enzymes- which is why cells cannot tolerate wide changes in pH.

Question 11

How can we determine between normal and mutant forms of charged amino acids

Answer 11

Gel electrophoresis- will travel different distances along the gel to the opposite charge on the other side.

Question 12

Describe chirality

Answer 12

The central carbon atom of all amino acids ( except glycine) are chiral carbons, meaning that they have 4 different atoms or groups bonded to it. This gives rise to optical isomers (enantiomers)

Question 13

Which form are amino acids represented in.

Answer 13

L-isomer is drawn- more stable- the most stable isomer.

Question 14

Why do proteins have structure?

Answer 14

Proteins have functions and these functions rely on specificity- hence a definite 3D structure (conformation) of the polypeptide chain is required. Proteins often posses flexibility to function - muscle fibres.

Question 15

What are the characteristics of a peptide bond

Answer 15

No free rotation about the peptide bond. C=O and N-H are in the same plane. C-R and C-H bonds can rotate. Only conformations where R groups do not clash with the main chain (steric hindrance) are allowed- hence different sized R groups must be adjacent.

Question 16

What are the bonds that hold a protein together.

Answer 16

Covalent bonds- shared pair of electrons between atoms- strongest bonds within a protein, exist within primary structure. May also exist as disulphide bridges- cysteine side chains are oxidises resulting in a covalent link between the two amino acids.
Hydrogen bonds- occur when two atoms bearing partial negative charges share a partially positively charged hydrogen- this can occur between atoms on different sidechains and the backbone of the protein,
Ionic interactions- electrostatic attraction between charged side chains- strongest when within protein interior and excluded from water- the majority of charged groups are at the surface- where they can be neutralised by counterions such as salts.

Van der waals- transient, weak electrostatic interactions between two atoms due to the fluctuating electron cloud surrounding each atom which has a temporary dipole- when close- temporary dipole induces a complementary dipole in another atom, giving rise to attractive properties. However if the electron clouds are too close- repulsive forces come into play.

The distance required for van der waals attractions varies from atom to atom due to the size of each electron cloud- van der waals radius- although weak and temporary- due to the sheer number of them- they have a large role in the conformation of the protein.

Hydrophobic and hydrophilic interactions: Protein with hydrophobic R groups- interior.

Question 17

How are alpha helices established

Answer 17

H-bonds between carboxyl group of one residue and amino group of another along the helix- stabilising it. Side chains of individual amino acids project out from the alpha helix.

Question 18

How are beta pleated sheets stabilised

Answer 18

Hydrogen bonds between N-H and C=O groups of two or more beta strands hold the structure together.

Question 19

Which sided helices are favoured

Answer 19

Right handed helices- as it conforms with use of L-amino acids.

Question 20

What happens when proline is joined to a polypeptide chain

Answer 20

NH group of the amino acid is lost- hence preventing the h-bonding with other residues- distorting the helical conformation- putting a kink into it.

Question 21

Where do the NH and C=O groups point in the beta pleated sheet

Answer 21

At right angles to the backbone.

Question 22

What are the two types of beta pleated sheet

Answer 22

Parallel- beta strands run in same direction
Anti-parallel- beta strands run in opposite directions
The pleating allows for the best alignment of the hydrogen bonded groups.

Question 23

What do proteins generally fold into

Answer 23

A single conformation with the lowest energy- this can occur spontaneously or it may involve other molecules called chaperones which bind to the partly folded polypeptide chain to ensure that the folding continues along the most energetically favourable pathway.

Question 24

What happens when the protein is denatured?

Answer 24

It returns to the original flexible polypeptide. Common denaturants are urea (breaks H-bonds) and 2-mercaptoethanol (breaks disulphide bonds)

Question 25

Describe the primary structure

Answer 25

Linear sequence of amino acids that make up the protein- standard nomenclature dictates that we write the sequence form amino terminus to carboxyl terminus.

Question 26

Describe the secondary structure

Answer 26

Local structural motifs within a protein- alpha helices and beta pleated sheets. Existence depends on the primary structure.

Question 27

Describe the Tertiary structure

Answer 27

Arrangement of the secondary structure motifs into compact globular structures called domains.

Question 28

Describe the quaternary structure

Answer 28

Defined as the 3D structure of a multimeric protein composed of several subunits.

Question 29

Why are post translational modifications important.

Answer 29

It can create new amino acids- enhancing the capabilities of the protein. For example N-linked glycosylation- addition of sugar residue to aparagine ensures that it adopts the correct conformation in the cell membrane. Mutation of the two asparagines can be picked up by electrophoresis- change in molecular weight.