lecture 6

Question 1

How can the EM spectrum be divided up?

Answer 1

Near IR , mid IR and far IR

Question 2

What can near IR detect?

Answer 2

quantitative determination of species such as proteins, fats, low low-molecular-weight hydrocarbons and water. Further use in the agricultural products, food, petroleum and chemical industries

Question 3

What can Mid IR detect?

Answer 3

Most popular of the IR fields, used in determining structure of organic and biochemical compounds

Question 4

What can far IR detect?

Answer 4

less popular though it has found uses in inorganic studies

Question 5

What causes vibrational motions?

Answer 5

due to the attraction and repulsion of charges in the atoms of a molecule

Question 6

What is a vibrational motion?

Answer 6

• where the bonds between atoms in a molecule move

Question 7

What is the vibrational motion for simple atomic molecules?

Answer 7

have one bond and one vibrational bond

Question 8

What are the 6 different types of vibrational motion?

Answer 8

• symmetric stretch
• asymmetric stretch
  bend
• vibration in the x
• vibration in the y
• vibration in the z

Question 9

What are the type of stretching vibrational modes?

Answer 9

• symmetrical

- asymmetrical

Question 10

What are the types of being vibrational modes?

Answer 10

• scissoring
• rocking
• wagging
• twisting

Question 11

What happens f the radiation matches the vibrational frequency of the molecule?

Answer 11

then the radiation will be absorbed

Question 12

How can a sample be “IR active”

Answer 12

it must be associated with changes in the dipole moment

Question 13

What is permanent dipole?

Answer 13

when 2 atoms have substantially different electronegativity, so one atom attracts more electrons than the other, for example in the image here, which shows electron density

Question 14

What is an instantaneous dipole?

Answer 14

occur due to chance when electrons happen to be more concentrated in one place than another in a molecule

Question 15

What is an induced dipole?

Answer 15

occurs when a molecule with a permanent dipole repels another molecule’s electrons, inducing a dipole in that moment – called polarised.

Question 16

What is the Four transform infrared spectroscopy?

Answer 16

A mathematical process, which decomposed a function of time into frequencies that make it up

Question 17

What does the Fourier transform actually do?

Answer 17

Converts the raw data into an actual spectrum

Question 18

What is the Fourier transformer based off?

Answer 18

The Michelson interferometer

Question 19

What does the Fourier transform need?

Answer 19

Beam splitter; 2. Fixed mirror; 3. Movable mirror

Question 20

How does the Fourier transform Infrared Spectroscopy (FTIR) work ?

Answer 20

• IR hits the beam splitter , transmits and reflects the other half
• 2 beams reflected by fixed and moving mirror recombine to form a resultant beam . Creates and interference pattern
• combined beam reaches detector by passing through the sample
• spectrum is called an interferogram

Question 21

What are the 3 main uses of IR spectroscopy?

Answer 21

• identification of functional groups
• Secondary structure information
• difference spectra

Question 22

How can you identify functional groups from the IR spectrum?

Answer 22

• graph with group frequency region and a fingerprint region

Question 23

How do breathalysers work?

Answer 23

collect evidence to determine levels of alcohol in breath with IR spectrometers

Question 24

How can secondary structure be determined by IR spec?

Answer 24

• proteins held together by H bonds

- these bonds absorb radiation n

Question 25

What is the main bond that absorbs IR radiation?

Answer 25

• The amide bond

Question 26

What happens when there is decomposition of the amide 1 bond?

Answer 26

β-sheet: 2 peaks at 1630 and 1690 cm−1

α-helix: peak at 1652 cm−1

Random coil: 1660 and 1700 cm−1

Question 27

What is difference spectra?

Answer 27

• looks at the difference between two spectra acquired in two different states of a protein
• i.e. the same protein but in different environments

Question 28

How is difference spectra measured?

Answer 28

• an initial spectrum is measured without light
• then light or chemicals is added
• the difference between these spectra is measured and compared

Question 29

What is advantage of the difference spectra method?

Answer 29

• Not only allows the meaurement of the difference between the final and initial states, but also the following of the the reaction time

Question 30

What is another advantage of the difference spectra method?

Answer 30

• comparison between resting and active state when light is added

Question 31

what differences might we observe In difference spectra between 2 samples of the protein in different conditions?

Answer 31

• Dark/light
• Different buffer pH
• Bound to different small molecules

Question 32

What differences might we observed in difference spectra in the same sample before/after activation?

Answer 32

• Intrinsic light reaction
• Electrochemical trigger
• After release of a photo-activated substrate

Question 33

What can the difference in bond peaks determine

Answer 33

the bond type - but not which exact bond in the protein it is

Question 34

How do e determine which exact bond in the protein it is?

Answer 34

• Site directed mutagenesis

- Isotopic labelling