Week 3 (protein Structure)

Question 1

How many different natural amino acids are there?

Answer 1

20

Question 2

Why are proteins known as polypeptides?

Answer 2

They are made up of long unbranded chains of amino acids,each linked to its neighbour through a covalent peptide bond

Question 3

What gives each amino acid it’s unique properties?

Answer 3

side chains

Question 4

What is the folding of a protein determined by?

Answer 4

Many sets of weak non-covalent bonds that form between one part of the chain and another

Question 5

What are the 3 main types of weak bonds in proteins?

Answer 5

• hydrogen bonds
• electrostatic attractions
• Van der Waals attractions

Question 6

How can the combined strength of a large number of weak non covalent bonds determine the stability of each folded protein shape?

Answer 6

Many weak bonds acting in parallel can hold two regions of a polypeptide chain tightly together

Question 7

What is the fourth weak force that has a central role in determining the shape of a protein and how do they do so?

Answer 7

Hydrophobic molecules tend to be forced together in a naqueous environment in order to minimise their disruptive effect on the hydrogen bonded network of water molecules

Question 8

What groupings are used for amino acids based on their side chains?

Answer 8

• acidic
• basic
• uncharged polar
• non polar

Question 9

How do hydrophobic and hydrophilic side groups behave in relation to the molecule?

Answer 9

• The hydrophobic side chains tend to cluster in the interior of the molecule to avoid contact with the water that surrounds them inside a cell
• The hydrophilic side groups arrange themselves near the outside of the molecule where they can from bonds with the water and polar molecules

Question 10

What does the final structure of a polypeptide chain aim to minimise?

Answer 10

Free energy

Question 11

What happens when the non covalent bonds between proteins are disrupted?

Answer 11

This unfolds/denatures a protein

Question 12

Can a protein ‘renature’ after it has been denatured from its original conformation?

Answer 12

Possibly but when the denature gets solvent is removed

Question 13

What is the name of proteins that often assist in protein folding?

Answer 13

Molecular chaperones

Question 14

What is another function of protein chaperones?

Answer 14

They prevent eh temporarily exposed hydrophobic regions in newly synthesises protein chains from associating with each other to form protein aggregates

Question 15

What are protein domains?

Answer 15

Structural units that fold independently of each other

Question 16

Name a structure present in different proteins that is involved in cell signalling

Answer 16

SH2

Question 17

What are the two main polypeptide folding patters?

Answer 17

Alpha helices and beta pleated sheets

Question 18

Why are alpha helices and beta pleated sheets common folding patterns?

Answer 18

They result from hydrogen bonding between the N-H and C=O groups in the polypetide backbone that did involve side chains

Question 19

Describe the structure of an alpha helix

Answer 19

Formed when a single polypeptide chain twists around on itself to form a rigid cylinder.The N-H of every peptide bind is hydrogen bonded to the C=O of a neighbouring bond. The N-H groups point up and the C=O point down and this gives polarity to the helix. The C terminus has has a partial negative and the N terminus a partial positive charge

Question 20

Describe the structure of a beta pleated sheet

Answer 20

Adjacent peptide chains are antiparallel. Hydrogen bonding between peptide bonds in different strands holds the individual polypeptide chains together in a beta sheet

Question 21

Give an example of a protein with alpha helices

Answer 21

Alpha keratin

Question 22

Give an example of a protein with beta pleated sheets

Answer 22

Fibroid

Question 23

How many different polypeptide chains that are n amino acids long?

Answer 23

n

20

Question 24

What is a binding site?

Answer 24

Any region of a proteins surface that can interact with another molecule through sets of non covalent bonds

Question 25

What is a protein subunit?

Answer 25

Created when a binding site of one protein recognises the surface of a second protein, the tight binding of the two folded polypeptide chains at this site creates a larger protein molecule with a precisely defined geometry

Question 26

What can identical proteins each with one binding site form?

Answer 26

A dimer

Question 27

What can identical proteins with two binding sites form?

Answer 27

A long helical filament or a closed ring

Question 28

What is the 2 main classes of protein?

Answer 28

Globular and fibrous

Question 29

What are some important functions of intrinsically disordered protein sequences

Answer 29

• form binding sites for other proteins
• they can be easily modified to change their binding site preferences
• they create tethers to hold interacting protein domains in close proximity

Question 30

What is the function of disulphide bonds in proteins?

Answer 30

Act as atomic staples to reinforce its most favoured conformation. This is important to help maintain their structures when exposed to extracellular conditions and are not needed in mild intracellular conditions

Question 31

what are the advantages of building a large subunit from smaller ones.

Answer 31

1. Requires only a small amount of genetic information
2. Assembly and disassembly can be readily controlled because subunits associate through multiple bonds of relatively low energy
3. Errors in the synthesis of the structure can be more easily avoided

Question 32

What are the function of assembly factors?

Answer 32

Special enzymes that guide construction but take no part in the final assembled structure

Question 33

What are amyloid fibrils?

Answer 33

A special class of protein structures utilised for some normal ell functions that can also contribute to human diseases when not controlled

Question 34

How is evolutionary tracing used to identify which sites of the protein domain is mist crucial to the domains function ?

Answer 34

Those sites are most likely to be maintained, unchanged as organisms evolve

Question 35

Name the 3 was in with two proteins can bind to each other?

Answer 35

1. A rigid surface on one protein can bind to the extended loop of polypeptide chain on a second one
2. Two alpha helices can bind together to form a coiled coil
3. Two complementary rigid surfaces often link two proteins together

Question 36

Which family of proteins is notable for their capacity for tight, highly selective binding

Answer 36

Antibodies (immunoglobulins)