Proteins - T&Q, Forces and Folding Flashcards Preview

1. BIOC 1301 S1 > Proteins - T&Q, Forces and Folding > Flashcards

Flashcards in Proteins - T&Q, Forces and Folding Deck (31)
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1
Q

What is the tertiary structure of proteins?

A

Describes the folding/organisation of secondary structure elements
Can be a/b or both and is very unique

2
Q

How can we determine the positions of atoms in proteins?

A

X-Ray crystallography - A crystal of the molecule is imaged resulting in a diffraction pattern (atomic resolution not achieved)

NMR spectroscopy - interactomic distance measurements and geometric constrainsts are used to build a 3D image

Cryo-electron microscopy - sample is cooled (-196 C) so fast it assumes a vitreous (glasslike) state = retains native state for viewing

3
Q

Where are amino acids normally found in globular proteins?

A

Non-polar residues - interior of the protein
Uncharged polar residues - on the surface but also occur in the interior
Charged polar residues - on the surface

Due to the hydrophobic effect

4
Q

What are groupings of secondary structure elements called?

A

Supersecondary structures or motifs (special folding)

5
Q

Name some supersecondary structures/motifs?

A
  1. Beta-alpha-Beta (the helix connects two parallel beta strands)
    e. g. triose phosphate isomerase
  2. Beta hairpin (antiparallel strands connected by tight turns
    e. g. erubotoxin
  3. Alpha-alpha (two successive antiparallel helices packed against each other with their axes inclines
    e. g. calmodulin
  4. Greek-key motif (a beta hairpin folded over to form a 4-stranded anti-parallel beta sheet)
6
Q

How are most proteins classified?

A

All alpha helices
All beta sheets

But most contain a mixture:
A/B mixed together
A/B with segregated regions

7
Q

How are the a, b and a/b classes further categorised?

A

Via topology - according to how their secondary structure elements are connected:

Beta barrels x3
2 are all B with beta hairpin motifs
1 is an a/b barrel with overlapping BaB motifs

8
Q

What do larger polypeptides form?

A

Domains
Each domain consists of 40-200 amino acids with an average diameter of 25 Å
e.g. Glyceraldehyde 3-phosphate dehydrogenase
Some domains are structurally independent - can be separated and be stable
Other multi-domain proteins have binding sites occupying clefts between domains

Rossmann folds often act as nucleotide binding sites (identification of this fold = clue to the function of the protein)

9
Q

Describe quaternary structure?

A

Many polypeptide chains non-colvalently assembled

Larger than 100 kDa

10
Q

Describe subunits within quaternary structures?

A

The subunits associate noncovalently
Proteins with more than one subunit = oligomers and their identical units = protomers

Homo oligomer - one type of protein subunit
Hetero oligomer - different types of protein subunit

11
Q

How are subunits within quaternary structures arranged?

A

Symmetrically
Each protomer occupies a geometrically equivalent position in the oligomer
Due to only L residues = rotational symmetry

12
Q

What are the types of rotational symmetry?

A

Cyclic symmetry - single axis of rotation

Dihedral symmetry - n-fold rotation axis intersects a twofold rotation axis at right angles

13
Q

What does protein stability depend on?

A
Hydrophobic effect 
Electrostatic interactions
Hydrogen bonding
Di-sulphide bridges
Metal ions

These stabilising forces work against destabilising (entropy)

14
Q

Why are proteins deemed relatively stable?

A

Energy needed to denature (100 residue protein) 40 kJ mol-1

Energy required to break H bonds = 20 kJ mol-1

15
Q

What is the hydrophobic effect?

A

Causes non-polar substances to minimise their contacts with water

= aggregation of non-polar side chain amino acids in the interior of the protein

16
Q

What electrostatic interactions contribute to protein stability?

A
Van der Waals 
Hydrogen bonds (not very effective) - they fine tune the tertiary structure

Ion pairs/salt bridge - electrostatic interactions between oppositely charged side chains e.g. Lys and Asp

17
Q

Describe the help of disulphide bridged?

A

They cross-link extracellular proteins i.e. within and between polypeptide chains

18
Q

What do metal ions do?

A

They stabilise some small domains - internally cross-link proteins
Example: Zinc fingers
1 or 2 Zn2+ ions are tetrahedrally coordinated by side chains of Cys, His
(usuful as it only has 1 stable oxidation state = no undergoing redox)

19
Q

What can denature proteins?

A

Temperature - alters optical rotation, viscosity + UV absorption
pH - alters ionisation states, changing protein charge distributions
Detergents - associate with nonpolar residues = interferes with hydrophobic interactions
Chaotropic agents

20
Q

What are chaotropic agents?

A

Ions or small organic molecules that increase the solubility of nonpolar substances in water

e.g. Guanidinium ion and urea

21
Q

Give an example of how a denatured protein can be renatured?

A
RNase A (4 disulphide bonds)
Denatured using urea and mercaptoethanol

Removing these and supplying O2 = spontaneous renaturisation

22
Q

What property of proteins allows us to monitor them?

A

They are dynamic = flexible and rapidly fluctuating
We can monitor:
bond vibrations, bond rotations, loop movements and side/main chain dynamics

23
Q

What pathway does protein folding follow?

A

An efficient folding pathway from high energy and high entropy to low energy and low entropy (AKA folding funnel)

They fold in a hierarchical manner

24
Q

What enzyme acts during protein folding?

A

Protein disulfide isomerase (PDI) catalyzes disulfide bond formation

25
Q

What molecules assist in protein folding?

A

Molecular Chaperones:
assist protein folding via an ATP-dependent bind-and-release mechanism

They reduce the effects of a mutation and therefoer facilitate protein evolution

26
Q

Name some types of molecular chaperones?

A

Hsp70 (Heat shock proteins) - facilitated folding of newly synthesised proteins

Tigger factor - prevents the aggregation of polypeptides as they emerge from the ribosome

Chaperonins - bind improperly folded proteins and induce them to refold

Hsp90 - facilitate the late stages of folding of proteins involved in cellular signaling

27
Q

What do most chaperones require?

A

Most are ATPases to catalyse ATP hydrolysis

28
Q

Give an example of an ATPase chaperonin?

A

In E coli - two subunits GroEL and GroES

Each GroEL subunit has a binding pocket for ATP that catalyzes the hydrolysis
All seven subunits of the GroEL ring act together, they are mechanically linked such that they change their conformations simultaneously

29
Q

What can mutations lead to?

A

Disease of protein misfolding

30
Q

What are some diseases caused by protein misfolding?

A

Amyloidoses
Alzheimer’s disease
Parkinson’s disease
Transmissible spongiform encephalopathies (TSEs)

All of which may be transmitted by prions

31
Q

What is a prion?

A

The infectious agent that lacks nucleic acid