Biochemical spectroscopy and human vision

Question 1

Refraction

Answer 1

When the speed of light slows down in a crystal

Question 2

What does the lens do and contain?

Answer 2

Contains crystalins (proteins that focus the light) and performs the resonance effect

Question 3

What happens to rhodopsin when a photon is detected?

Answer 3

Light absorbing chromophore drops out of receptor (has to re-bind)

Question 4

Photoisomerisation

Answer 4

Structural change between isomers caused by photo excitation

Question 5

What happens to the bond order in the excited state

Answer 5

It is reduced

Question 6

What is the excited state bond lengthening in retinal

Answer 6

4% - because of reduced bond order

Question 7

What speed is photoisomerisation

Answer 7

200fs

Question 8

Natural frequency

Answer 8

The frequency at which a system oscillates when its not subjected to continuous or repeated external force

Question 9

Electronic (UV) spectroscopy

Answer 9

Light absorbed - electron excited to higher molecular orbital

Question 10

When can the Beer Lambert law be used

Answer 10

Particles regarded as acting independently (low conc), measurable intensity exponentially related to conc, high values generally unreliable, parasitic effects (scattering and fluorescence)

Question 11

Chromophore

Answer 11

Part of molecule responsible for absorption of light

Question 12

Auxochromes

Answer 12

Groups that modify absorption of neighbouring chromophore (often have lone pairs)

Question 13

Bathochromic shift

Answer 13

Towards longer wavelengths

Question 14

Hypsochromic shift

Answer 14

Towards shorter wavelengths

Question 15

Hyperchromic effect

Answer 15

Increase in peak absorbance

Question 16

Hypochromic effect

Answer 16

Decrease in peak absorbance

Question 17

UV range

Answer 17

200-400nm

Question 18

Effect of conjugation

Answer 18

Increased conjugation leads to longer absorption wavelengths

Question 19

What do auxochromes cause

Answer 19

With lone pairs - increase delocalisation and conjugation - bathochromic shift

Question 20

Peptide bond absorption at

Answer 20

190nm

Question 21

Trp absorbs at

Answer 21

280nm

Question 22

Tyr, Phe, Cys absorb at

Answer 22

> 250nm

Question 23

What are the 3 energy levels

Answer 23

Vibrational, rotational, electronic

Question 24

Possible fates of an optically excited state

Answer 24

Fluorescence, phosphorescence, FRET, internal conversion (heat), photoisomerisation, photochemistry (covalent bond rearrangement), electron transfer

Question 25

What does the Franck-Condon principle explain

Answer 25

Intensity of vibronic transitions - during electronic transition, changer from one vibrational level to another more likely if the 2 vibrational wave functions overlap more significantly

Question 26

Born-Oppenheimer approximation

Answer 26

Nuclei don’t move in time that electrons are excited

Question 27

What vibrational level do absorption and emission start?

Answer 27

The lowest

Question 28

What happens to the vibrations during electronic excitation?

Answer 28

They are static

Question 29

Stokes shift

Answer 29

The energy (wavelength) difference between the lowest energy peak of absorbance and highest energy of emission

Question 30

Why is there an energy difference?

Answer 30

Reorganisation of molecular structure and solvent around molecular structure (stabilisation)

Question 31

What is R0?

Answer 31

Distance at which FRET = 50%

Question 32

What is FRET?

Answer 32

The distance dependent interaction between electronic excited states of 2 dye molecules

Question 33

What is special about FRET Jablonski diagrams?

Answer 33

They are radiationless (not emitting photo which is absorbed by donor)

Question 34

What’s the maximum FRET distance

Answer 34

100 angstroms