L6- tertiary and quaternary structures

Question 1

What do loops and turns do?

Answer 1

Connect alpha helices and Beta strands and allow a peptide chain to fold back on itself to make a compact structure

Question 2

What are loops?

Answer 2

Connections which often contain hydrophilic residues and are found on protein surfaces

Question 3

What are turns?

Answer 3

Loops containing 5 residues or less

Question 4

What are tertiary structures primarily stabilised by?

Answer 4

Non-covalent interactions between side chains

Question 5

What, apart from non covalent interactions between side chains, stabilises tertiary structures?

Answer 5

disulfide bridges

Question 6

How many amino acids in each alpha helix turn?

Answer 6

3.6

Question 7

What are supersecondary structures/ motifs?

Answer 7

Recurring folding patterns comprising at least 2 connected secondary structure elements

Question 8

What are the 8 motifs?

Answer 8

1. Helix-loop-helix (2 helices connected by turn)
2. Coiled-coil (2 helices that interact in parallel through their hydrophobic edges)
3. Helix bindle (several alpha helices that associate antiparallel manner to form bundles)
4. B-alpha-B unit (2 parallel B strands linked to alpha helix by 2 loops)
5. Hairpin (2 anitparralel B strands connected be a B turn)
6. B meander (antiparallel sheet made of B strands connected by loops or turns)
7. Greek key (4 antiparallel strands - 1,2 in middle, 3,4 on outside)
8. B sandwich (stacked B strands or sheets)

Question 9

What are domains?

Answer 9

• Independently folded compact units in proteins
• 25 to 300 amino acid residues
• Domains can be connected by loops and associated together by non-covalent interactions between side chains

Question 10

What do domains do?

Answer 10

Domains usually have a stand alone function. Can combine domains for multi-function protein.

Question 11

What can domains show us?

Answer 11

Can show evolutionary conservation of protein structure. A domain fold can be conserved in many proteins shen the primary structur is undetectable different.

Question 12

What are the 4 common domain folds?

Answer 12

1. Parallel twisted sheet
2. B-barrel
3. alpha/beta barrel
4. B helix

Question 13

What do folding patterns allow us to do?

Answer 13

Classify protein structure into 4 categoriees with common domains and motifs

Question 14

What are the 4 categories of protein structure?

Answer 14

1. All alpha
2. All beta
3. Mixed alpha/beta (alternating alpha and beta bits)
4. Alpha and beta (cluster of alpha then beta seperate)

Question 15

What are quaternary structures?

Answer 15

Organization of subunits. Subunits have defined stoichiometry and arrangement.