Protein Structure

Question 1

What are the main functions of proteins?

Answer 1

Structure, Motor, Enzymes, Antibodies, Haemoglobin, Transport

Question 2

Which two structural components is actin present in?

Answer 2

Monomer in microfilaments and thin filaments in muscles

Question 3

What is the role of kinases?

Answer 3

Move phosphate groups from ATP to AA

Question 4

What is HSA?

Answer 4

Human Serum Albumin, transport protein, most abundant in plasma

Question 5

What are the names of the two ways a peptide bond can rotate?

Answer 5

Phi and Psi

Question 6

Rotation around CH-NH bond is given what name?

Answer 6

Phi rotation, this rotation is also clockwise when viewed from amino terminus

Question 7

Rotation around CH-CO bond is given what name?

Answer 7

Psi rotation, this rotation is also anticlockwise when viewed from amino terminus

Question 8

What is a motif?

Answer 8

Cluster of conserved residues, carry out a specific and vital function/form (protein)

Question 9

What are the 3 elements in secondary structure?

Answer 9

Alpha Helix, Beta-pleated sheet, Beta-Turn

Question 10

Is an alpha helix right or left handed?

Answer 10

Right handed, stable

Question 11

Bonds form between which residues in an alpha helix?

Answer 11

Oxygen from a carboxyl group and nitrogen from amine group, i+4 residues along

Question 12

What bonds hold the tertiary structure together?

Answer 12

Hydrogen, Ionic/Electrostatic, Disulphide, Hydrophobic

Question 13

Which other motif is important for folding of beta pleated sheets?

Answer 13

Beta-hairpin, used to form adjacent sheets

Question 14

What is a greek key motif made up of?

Answer 14

4 antiparallel beta sheets connected by 2 beta-hairpins and a longer loop

Question 15

Is an EF hand motif made up from all alpha or all beta structure?

Answer 15

All alpha, 2 alpha helices joined together

Question 16

What is a useful feature of the EF hand motif?

Answer 16

Binds calcium ions, used in calmodulin

Question 17

What motif makes up Titin (big muscle fibre)?

Answer 17

Beta-sandwich, consists of 2 beta sheets held together, also present in antibodies

Question 18

What motif is often used as a pore?

Answer 18

Canonical beta barrel proteins, used as porins

Question 19

What motif uses alpha helices to connect beta sheets?

Answer 19

Beta-alpha-beta

Question 20

What is a motif containing alpha and beta secondary structure present in alcohol dehydrogenase?

Answer 20

Rossman Fold, NAD+ bind to rossman fold (or FAD in decarboxylase)

Question 21

What is a domain?

Answer 21

Occurs when different structural motifs pack together to form a stable independant unit

Question 22

Give an example of a single domain and multi domain protein

Answer 22

Single domain: GFP / Multi Domain: Firefly Luciferase

Question 23

What is a knot?

Answer 23

Rare, pulling polypeptide creates knot, rather thans string

Question 24

What percentage of proteins are intrinsically disordered?

Answer 24

30%

Question 25

What defines an intrinsically disordered protein?

Answer 25

No defined 2D/3D structure due to a lack of hydrophobic residues leading to a weak hydrophobic effect

Question 26

What is an example of an intrinsically disordered protein?

Answer 26

alpha-synuclein is intrinsically disordered, but becomes ordered when bound to calmodulin

Question 27

What is the change in structure of alpha-synuclein when it binds to calmodulin?

Answer 27

helix forms at N-terminus, same structural change induced when Alpha-synuclein binds to lipid membrane

Question 28

What disease is caused by aggregation of alpha-synuclein?

Answer 28

Parkinsons

Question 29

Parkinsons symptoms are caused by which fibrils/bodies?

Answer 29

Amyloid fibrils, leading to Lewy Bodies

Question 30

What is GroEL/ES?

Answer 30

A chaperonin, which assists in protein folding

Question 31

Which GroEL/ES subunit acts as the ‘cage’ and which acts as the ‘lid’

Answer 31

GroEL = cage, GroES = lid

Question 32

What changes does GroEL/ES undergo to help protein fold?

Answer 32

After GroES has bound, GroEL doubles in volume and becomes more hydrophilic

Question 33

How many rings make up the GroEL structure?

Answer 33

2

Question 34

How many subunits are present in each GroEL ring?

Answer 34

7

Question 35

How many domains are present in each GroEL subunit?

Answer 35

3: Apical (GroES binding), Intermediate (hinge), Equatorial (ATP binding)

Question 36

How many helices are present in the equatorial domain?

Answer 36

10

Question 37

What is the structure and function of DNA helicase?

Answer 37

Hexameric, separates strands of DNA to allow transcription (ATP hydrolysis)

Question 38

What is the structure and function of Recombinase?

Answer 38

Filamentous, manipulates structure of genomes

Question 39

What is the structure and function of SSB?

Answer 39

Tetramer, prevents premature annealing