Lecture 6

Question 1

What is a supersecondary structure?

Answer 1

Elements of a secondary structure (helices and strands) connected by turns or regions of less ordered structures (loops/coils)

Question 2

What are the examples of common supersecondary structures?

Answer 2

Helix - turn - Helix
Beta hairpin
Greek key
Strand - helix - strand

Question 3

What are examples of helix - turn - helix

Answer 3

DNA binding proteins and Calcium binding proteins

Question 4

Describe a beta hairpin

Answer 4

Common, antiparallel beta strands, variable length

Question 5

What is a greek key?

Answer 5

Four antiparallel beta strands

Question 6

What are protein domains?

Answer 6

Elements of supersecondary structures combined where independently folded regions often possess specific functions within the protein

Question 7

What is the arrangement of elements within protein domains?

Answer 7

Arranged into a hydrophobic core and hydrophilic exterior for stability

Question 8

What are the three tertiary protein domains?

Answer 8

Alpha domain family
Alpha/beta family
antiparallel beta family

Question 9

What are examples of the alpha domain family?

Answer 9

Four helix bundle and Globin fold

Question 10

Describe a four helix bundle

Answer 10

Four helices with three turns arranged to to form a hydrophobic core

Question 11

Describe the globin fold

Answer 11

Amphipathic helices with side-chains packed closely together within a hydrophobic core, packing can occur between nonadjacent helices

Question 12

What are examples of the alpha/beta family? (3)

Answer 12

alpha/beta barrel, alpha/beta open twisted sheet, alpha/beta horseshoe fold

Question 13

Describe the alpha/beta barrel

Answer 13

alternating alpha helices and beta strands connected with loops and arranged so the hydrophobic core is deep within the barrel

Question 14

Describe the alpha/beta horseshoe fold

Answer 14

16 strand, helix motif repeats

Question 15

What is an example of the antiparallel beta family?

Answer 15

The anti-parallel beta barrel

Question 16

What is the arrangement of the anti-parallel beta barrel?

Answer 16

A hydrophobic core and hydrophilic exterior

Question 17

What is the function of the anti-parallel beta barrel?

Answer 17

Retinal binding

Question 18

How are proteins synthesised?

Answer 18

As linear polymers that fold into a 3D functional structures

Question 19

Where are proteins made?

Answer 19

At the ribosomes

Question 20

How do proteins fold?

Answer 20

Spontaneously through their amino acid structure acting as the instructions

Question 21

What is the Anfinsen experiment

Answer 21

Where the protein was unfolded and denatured to remove any ribosomes or extra cells to determine that they fold spontaneously

Question 22

What is the protein folding pathway?

Answer 22

1. Formation of short secondary structure segments
2. Subdomains form
3. Subdomains come together to form a partly folded domain - ‘molten globule’
4. Final domain structure emerges, small conformational adjustments to give final compact native structure

Question 23

What stabilises protein folding?

Answer 23

Non-covalent interactions e.g. H-bonds, metal bonding, disulfide bonds, salt links, hydrophobic core

Question 24

What are chaperones?

Answer 24

Structures that assist in protein folding

Question 25

What are the three chaperone pathways?

Answer 25

Chaperone-independant, Chaperone-dependant, Chaperonin-dependant

Question 26

What is chaperone dependant?

Answer 26

Protein folding with the assistance of only a chaperone e.g. Hsp70

Question 27

What is chaperonin-dependant?

Answer 27

Protein folding with the aid of a chaperone and a chamber e.g. GroEL-GroES

Question 28

What factors can cause unfolding of proteins?

Answer 28

pH, temperature, detergents, organic solvents, urea, guanidium HCL

Question 29

How does unfolding of proteins occur?

Answer 29

From the weakening of the non-covalent interactions

Question 30

What is prion disease?

Answer 30

When the PrP protein changes its shape and triggers other PrP proteins to misfold. It is an alpha to beta transformation

Question 31

What are examples of prion diseases?

Answer 31

BSE, CJD, Kuru

Question 32

What are other examples of diseases from misfolded prions?

Answer 32

Alzheimers disease and Type 2 diabetes