Protein structure (4)

Question 1

What is the primary structure of a protein?

Answer 1

The linear sequence of amino acids in the polypeptide chain

Question 2

What does the sequence of a polypeptide have?

Answer 2

Directionality

Question 3

What is the secondary structure of a protein?

Answer 3

-folding of the polypeptide backbone into regular structures
-structures such as: alpha helix, the beta sheet, turns + loops
-generally stabilised by H bonding between amino acid residues

Question 4

Describe the alpha helix

Answer 4

-coiled structure held together by H bonds
-right handed (can have left handed, but rare)
-often amphiphilic (amphipathic) - have both hydrophobic + hydrophilic character

Question 5

Where do the hydrogen bonds form in an alpha helix?

Answer 5

Between the main chain C=O of residue i and the main chain N-H of residue i+4 (every 4th residue)

Question 6

How many residues are there per turn in an alpha helix, how much rise is there and rotation per residue?

Answer 6

-3.6 residues per turn
-1.5A rise per residue
-100 degrees per rotation

Question 7

What is the alpha helix terminator?

Answer 7

Proline:
-contains a secondary amine
-doesn’t support the helix geometry

Question 8

Describe beta sheets

Answer 8

-constructed from 2 or more polypeptides H bonded to each other
-each strand is in a nearly extended conformation
-sheets can be constructed from mixed parallel + antiparallel strands
-contains beta turns

Question 9

What characteristic can beta sheets have due to certain sequences?

Answer 9

Amphipathic character

Question 10

Describe beta turns

Answer 10

-compact globular nature of many proteins requires reversal in the direction of polypeptide chains
-H bonds between C=O of i residue + N-H of i+3 residue

Question 11

Describe the supersecondary structure

Answer 11

-molecules of secondary structural elements can be combined with other secondary structure elements or supersecondary structures
-combined using connecting loops
-forms tertiary structure of proteins

Question 12

Describe the tertiary structure

Answer 12

-assembly of secondary structure elements into native protein structure
-elements of secondary structure are connected by remaining segments in amino acid sequence
-forms connecting loops
-loops can move, so are useful for function

Question 13

What is the quaternary structure?

Answer 13

-assembly of polypeptide chain into multi-subunit structures
-subunits usually associate non-covalently

Question 14

What is the subunit interface constructed from?

Answer 14

-H bonds
-buried hydrophobic residues
-sometimes disulfides

Question 15

What is haemoglobin?

Answer 15

A tetramer of 2 identical alpha subunits + 2 identical beta subunits - hetero-oligomer

Question 16

What are allosteric interactions?

Answer 16

In many multimeric proteins, the binding of a ligand to 1 subunit can alter the affinity of the other subunit

Question 17

What are domains?

Answer 17

-polypeptides of more than roughly 200 residues fold into 2 or more globular clusters
-each domain of a protein has a specific function

Question 18

Where are binding sites on proteins often found?

Answer 18

Occupy the clefts between domains

Question 19

Describe the structure of immunoglobulins

Answer 19

-made of a light + heavy chain that have disulfide bonds between them
-have hypervariable loops, which are often functionally important