tertiary structure

Question 1

What other bonds are important in protein folding?

Answer 1

Disulphide bond, ionic bonds, hydrogen bond, hydrophobic interactions and van der Waals interactions.

Question 2

What is disulphide bond

Answer 2

It stabilises the folding of the protein and makes them less susceptible to degradation.
Disulphide bonds can hold different polypeptide chain together, eg. insulin have A and B chain held together by 2 disulphides.

Question 3

What is REDOX reaction?

Answer 3

Oxidation (lose electron), the lost of hydrogen on sulphur can lead to the formation of disulphide bond.
Reduction (gain electron), the disulphide bond is broken as hydrogen is added to sulphur.

Question 4

What is the purpose of Glutathione (GSH)?

Answer 4

it is a redox buffer, it put energy to keep cysteine reduce (has H on S) and not letting them form accidental disulphide bond. All cysteine in cell is in free S-H form.

Question 5

How Glutathione acts as a reducing agent (lose electron oxidation)?

Answer 5

• It keeps cysteines in proteins reduced

- It detoxifies reactive oxygen species like peroxide.

Question 6

What are ionic bonds (salt bridges)?

Answer 6

• Strong ionic interactions can form between +ve charged side chain and -ve charged side residue.
• Charged side chains are usually at the surface of proteins.
• The charged side chains are buried in the hydrophobic core of the protein ( single unpaired charge can be very energetically unfavourable in a hydrophobic environment.

Question 7

What are hydrogen bonds?

Answer 7

Hydrogen atom shared between two relatively electronegative atoms make hydrogen bond.

• H bonds are strong dipole bonds between sigma + hydrogen atoms and the lone-pair electrons of strongly electronegative atoms.
• H bonds are relatively strong non-covalent bonds.

Question 8

What are hydrophobic interactions?

Answer 8

Hydrophobic side chains are usually buried in the protein core, wich the driving force behind protein folding.
- The main component of this interaction is solvent shielding (hydrophobic effect) rather than van der Waals interaction (dispersion force).

Question 9

What are Van der Waals interactions?

Answer 9

It is the weakly attractive interactions between two close atoms. It is a very short-range force.

Question 10

What is the hydrophobic effect?

Answer 10

close-packed hydrophobic interior.
Hydrophobic to hydrophilic mutations in the interior of a folded protein are essentially forbidden because they are so destabilizing.

Question 11

How the classification of structures work?

Answer 11

• Protein structure is more conserved than amino acid sequence, as proteins that have diverged beyond detactable sequence similarity may still retain the architecture and topology of their ancestral fold.
• Two proteins show structural similarity but seem otherwise unrelated. It may be that evolution has converged onto a physically stable fold or independently evolved the same structure to answer common functional requirement.

Question 12

what are architecture and topology?

Answer 12

Architecture- an arrangement in the shape of those secondary structure element.
Topology- an arrangement in three dimensions.

Question 13

What are the types of non-globular proteins?

Answer 13

• Fibrous protein
• membrane proteins
• Intrinsically disordered proteins

Question 14

What is a fibrous protein?

Answer 14

• Repetitive sequences, which is not water-soluble.
• it gives structural roles, which provide architectural support for the cells and tissues.
• Many fibrous proteins are formed by coiled-coil interactions:
  Myosin (muscle)
  Fibrinogen (blood clotting)
  Intermediate filaments

Question 15

What are the fibrous proteins that formed by coiled-coil interaction (alpha interaction)?

Answer 15

• Myosin (muscle)
• Fibrinogen (blood clotting)
• Intermediate filaments (keratins)

Question 16

What is membrane protein?

Answer 16

It has a limited number of possible topologies compared to globular proteins.

Question 17

What is the characteristic of collagen?

Answer 17

• the most abundant protein in mammals, essential component of skin, bone, tendon, blood vessels, teeth.
• Very simple sequence: Gly-Pro-HydroxyPro. (HydroxyPro formed by post-translational modification by proline hydroxylase, which is dependent on Vitamin C).
• Gly-Pro-HydroPro repeat gives rise to extended, left-handed helix. Three helices wind together in a right-handed super-helix, called tropocollagen.

Question 18

What are the type of membrane protein topologies?

Answer 18

Single pass
TM beta-barrel
TM helical bundle
Monotopic

Question 19

What are the example of TM helical bundles?

Answer 19

• Potassium channels (hydrophobic outside and hydrophilic
  inside)
• Beta-adrenergic receptor: G protein-coupled receptor protein.
• OmpF ( a porin in the outer membrane of Gram-ve bacteria. Big hole with hydrophobic outside and hydrophilic inside).

Question 20

What are the three major methods for protein structure determination?

Answer 20

• X-ray crystallography
• Nuclear magnetic resonance (NMR)
• Electron microscopy

Question 21

Why can’t we build an X-ray microscope?

Answer 21

• Refractive X-ray lenses don’t exist, because the refractive index of all material is very similar (and close to vacuum) for x-ray.
• X-rays are very energetic and would be very chemically damaging on the sample

Question 22

What is X-ray diffraction?

Answer 22

Diffraction is the scattering of a wave as it encounters an object or a slit of comparable size to its wavelength.
- Make a protein solution into a crystal through crystallisation by vapour diffusion.

Question 23

what is refraction?

Answer 23

refraction is the change in direction of a wave passing from one medium to another, this can be achieved using magnetic lenses for electrons, as they are charged particles, so we can build an electron microscope.

Question 24

What is being measured in the X-ray diffraction experiment?

Answer 24

• the intensity (I) of the scattered X-ray at each point. From these measurements, one can calculate the amplitudes of the diffracted waves: the structure factor amplitudes, F. The final product of the experiment is an electron density map (shows the distribution of electrons in the molecules in the crystal).

Question 25

What is a electron microscopy?

Answer 25

Based on the scattering of electrons by the atoms in a molecule. The electrons can be focused on using electromagnetic lenses.
It is a direct imaging device.

Question 26

What are the things to note in electron microscopy?

Answer 26

1) the image is just an approximately a projection of the structure, so computational procedures are required to recover the actual structure from projection data,
2) For unstained the single particles in cryo-EM, the raw image data will have a very low contrast.
3) transmission electron microscopy (TEM), the resolution possible from cryo-EM single-particle reconstructions has recently increased with the advent of new electron detectors. in favourable cases, the results are now matching from structure determination by X-ray diffraction.

Question 27

What is NMR spectroscopy?

Answer 27

Based on the absorption of radio-frequency radiation by atomic nuclei.
- the spin changes energy state (resonates) when perturbed with radio waves.