Lecture 6 - Protein Structure & Protein Folding

Question 1

Building up Protein Tertiary Structure

Answer 1

• Secondary structure
• Supersecondary structure
• Protein domains
• Complete protein structures

Question 2

Supersecondary structure

Answer 2

helices
strands

connected by turns or by loops or coil

Question 3

Common motifs of supersecondary structure

Answer 3

• Helix - turn – helix
• b hairpin
• Greek key
• Strand-helix-strand

Question 4

Helix-turn-helix

Answer 4

2 helices together joined by a loop or turn

Common supersecondary structure

Question 5

Helix - turn - Helix examples

Answer 5

DNA binding proteins

Calcium binding protein (longer turn) - hand

Question 6

β hairpin

Answer 6

Strands antiparallel
Length varies

β strand goes up has a turn and back down

Question 7

β hairpin examples

Answer 7

Bovine pancreatic trypsin inhibitor

Snake venom toxin

Question 8

Greek key

Answer 8

4 antiparallel strands

Connected starting in centre

Question 9

Strand, Helix, Strand

Answer 9

Strands Interact with H bonds

Helices above or below

Question 10

Supersecondary structure elements combine to form

Answer 10

Domains or motifs

Question 11

Domains or motifs

Answer 11

Independently folded region in a protein that sets apart from other regions

Question 12

Small protein

Answer 12

1 domain

Question 13

Long big protein

Answer 13

Multiple domains packed together

Question 14

Domain size

Answer 14

150 - 200 amino acids stretch

Question 15

Protein domain has

Answer 15

Hydrophobic core

Hydrophilic parts on surface

Question 16

Glyceraldehyde 3 phosphate dehydrogenase

Answer 16

2 domains (1 binds NAD cofactor helps coenzyme work)
1 protein chain

Question 17

Proteins can be grouped into families based on tertiary structure 3 examples

Answer 17

α domain family (helices)

α / β family (Strand helix strand)

Antiparallel β family

Question 18

α domain family

Answer 18

4 helix bundle

Eg myoglobin

Question 19

4 helix bundle

Answer 19

Hydrophobic sidechains in middle (up to vanderwaal radius - max energy)

Hydrophilic sidechains outside
Good for stabilisation

Tilted helices (20 degrees) stabilize sidechains & can nestle next to each other

Question 20

Myoglobin

Answer 20

Globin fold

Wraps around heme group

Question 21

α / β family

Answer 21

Mix of α and β structure
Strand helix strand

α / β barrel
α / β open twisted sheet

Question 22

α / β barrel

Answer 22

8 strands 8 helices
Barrel of strands in middle helices on outside
H bond to each other

Hydrophobic interior
Hydrophilic outside (asp, lys, glu)

Question 23

α / β open twisted sheet

Answer 23

a helices and b strands alternating

Sequence determines pathway

Question 24

Antiparallel β family

Answer 24

Antiparallel β barrel
Hydrophobic interior of barallel
Eg retinal binding protein

Question 25

Retinal binding protein

Answer 25

Hydrophobic Retinal inside barrel b strands nestles retinal Retinal nose hydroxide sticking out Carries retinal around body Surround retinal with hydrophobic sidechains, OH sticks out

Question 26

In nature common structural motifs and domains are repeated and combined to make

Answer 26

different types of proteins

Question 27

Domains are often reused by nature and combined with other domains to make

Answer 27

proteins with different functions.

Question 28

Common Protein Domains

Answer 28

EGF (Hexagon) Chymotrypsin (Oval) Kringle Protein (K) - held by disulfide bridges Ca bind protein (Triangle)

Question 29

Urokinase

Answer 29

3 domains together EGF, K, Chymotrypsin

Question 30

Factor IX

Answer 30

4 domains 1 Ca bind protein, Chymotrypsin, 2 EGF

Question 31

Plasminogen

Answer 31

6 domains 5 K, 1 Chymotrypsin

Question 32

Proteins are synthesized as

Answer 32

linear polymers that have | to fold into a 3D functional structure

Question 33

Protein are made at the

Answer 33

ribosome, | fold into active shape spontaneously

Question 34

Where are the instructions that proteins need?

Answer 34

embedded in amino acid sequence sequence contains the instructions

Question 35

Afinsen experiment | in nutshell

Answer 35

Unfold ribonuclease A structure by Urea and b mercaptoethanol Remove urea and b merca Amino acids fold themselves up Made correct disulfide bonds, and tertiary structure, became active

Question 36

Proteins contain

Answer 36

information that leads to own structure in their sequence

Question 37

Collectively what makes a significant contribution to protein conformational stability?

Answer 37

Non-covalent interactions, while individually weak in proteins, collectively covalent bonds (eg. disulfide bonds)

Question 38

what's the most important noncovalent contributor | to protein stability in aqueous solution?

Answer 38

hydrophobic core

Question 39

Protein folding is directed by

Answer 39

internal hydrophobic residues, hydrophilic residues are solvent exposed.

Question 40

is protein folding a random process?

Answer 40

Yes

Question 41

Folding pathways events

Answer 41

(i) Formation of short secondary structure segments (ii) Nuclei come together, growing cooperatively to form a domain (iii) Domains come together (but tertiary structure still partly disordered) (iv) Small conformational adjustments to give compact native structure

Question 42

Some protein folding is | assisted by

Answer 42

chaperones

Question 43

Chaperones

Answer 43

(a) ‘chaperone’-independent (b) Chaperone-dependent eg Hsp70 (c) Chaperonin-dependent eg GroEL-GroES

Question 44

What can lead to unfolding | and loss of biological function (denaturation)?

Answer 44

Weakening of non-covalent interactions

Question 45

Unfolding of proteins may result from...

Answer 45

``` Change pH Heating Detergents Organic solvents Urea Guandium HCL ```

Question 46

Proteins in living organisms that are folded normally can | sometimes

Answer 46

change their shape and become misfolded

Question 47

Some misfolded proteins can cause

Answer 47

other proteins to change their shape sometimes with disastrous consequences

Question 48

In the brain three conditions have been identified as being due to a protein,

Answer 48

PrP changes shape and forms aggregates that cause brain damage BSE bovine spongiform encephalopathy CSD Creutzfeld-Jacob Disease

Question 49

PrP

Answer 49

abnormal form of prion protein induces the normal form of this protein to become misfolded a → b transformation No treatment, fatal

Question 50

Kuru The proteins that cause the problem are called

Answer 50

prions for | “proteins infectious agent”

Question 51

Other diseases in which protein misfolding or | aggregation is thought to contribute:

Answer 51

* Alzheimer’s Disease * Type 2 Diabetes amyloid (abnormally folded protein) Prions not involved