Symbol and Picture Cards

Question 1

Recall the general structure of an amino acid at physiological pH

Answer 1

Question 2

What are the aromatic amino acids? Recall their structures.

Answer 2

Question 3

What are the 5 alophatic (hydrophobic) amino acids?

Answer 3

Question 4

Recall the 9 hydrophilic amino acids

Answer 4

Question 5

Recall the nonpolar amino acids

Answer 5

• Glycine
• Alanine
• Valine
• Leucine
• Isoleucine
• Methionine

(Almost all alophatic, except methionine)

Question 6

In glyceraldehyde (the reference for stereochemical classifications), is the hydroxyl group pointing left or right in L-glyceraldehyde?

Answer 6

Left

Question 7

Recall the stereochmemical geometry of a L-α-amino acid

Answer 7

Question 8

Recall the three dimensional projection of an amino acid using the CORN crib mnemonic

Answer 8

Question 9

Recall the mechanism for the formation of a peptide bond

Answer 9

Condensation reaction

(a water molecule leaves)

Question 10

Recall the configuration of a parallel coiled coil

Answer 10

• a and d might be hydrophobic side chains allowing tight packing and stabilization by van der Waals interactions OR paired acid/basic residues (charge-charge interaction to make a salt bridge)
• b,c,e,f and g must be able to interact favourable with surrounding environment.
• e/g positions can also interact with each other.

Question 11

In a parallel coiled-coil, which residues interact?

Answer 11

a-a’

d-d’

Question 12

In an anti-parallel coiled coil, which residues interact?

Answer 12

a-d’

d-a’

Question 13

Is it possible to form coiled coils with more than two helices?

Answer 13

YES! Such as 3-helix parallel coiled-coil of viral surface glycoproteins

Question 14

Give the basic structure of human tropoelastin

Answer 14

Alternating hydrophobic and cross linking domains

Question 15

Recall the following motifs

• βαβ
• β-hairpin
• αα

Answer 15

Question 16

What happens when a molecule absorbs a photon of light?

Answer 16

The Bohr Frequency condition states that the full energy of the photon is transfered to the molecule

ΔE = (E2-01) = hv = hc/λ

Question 17

Give the Beer-Lambert law

Answer 17

• ε: molar absorptivity*
• c: concentration of absorber*
• l: pathlength*

Question 18

Define HOMO and LUMO and recall an example of this with ethene

Answer 18

HOMO and LUMO are acronyms for highest occupied molecular orbital and lowest unoccupied molecular orbital, respectively. The energy difference between the HOMO and LUMO is termed the HOMO–LUMO gap. HOMO and LUMO are sometimes referred to as frontier orbitals

This is important for spectroscopy, where electrons are briefly moving from HOMO to LUMO

Question 19

How does a UV/vis spectra change with increasing collisions between molecules?

Answer 19

Question 20

Recall the relative intensities of aromatic side chain absorbance for the three aromatic amino acids

Answer 20

Question 21

Contrast the CD spectra for cytochrome C and a lysozyme

Answer 21

Question 22

Recall the absorbance spectra of tyrosine at pH 6 and 13

Answer 22

Solid line: pH 6

Question 23

Recall an absorbance spectra of poly-L-lysine in solution. What does the spectra look like for random coil? Alpha helix? Beta strand?

Answer 23

Solid line: random coil

Short dash: alpha helix

Long dash: beta strand

Question 24

Compare and contrast absorbance vs. CD

Answer 24

Question 25

When looking at a CD spectrum, you look at units of ellipticity (in degrees). This is then converted to either ____ or \_\_\_. Give the formula.

Answer 25

Molar ellipticity or mean residue ellipticity (denoted same way!) Where M is molecular weight (molar ellipticity) OR mean residue mass (mean residue ellipticity). c is concentration in g/mL.

Question 26

Why are CD results reported as ellipticity?

Answer 26

Although ΔA is usually measured, for historical reasons most measurements are reported in degrees of ellipticity. Molar ellipticity is circular dichroism corrected for concentration. Molar circular dichroism and molar ellipticity, [θ], are readily interconverted

Question 27

Recall the circular dichroism signal for: * α-helices * β-sheets * random coils

Answer 27

Random coils are the only ones with a positive dichroism signal (can be differentiated from alpha/beta structures)!

Question 28

How can alpha helices be differentiated from beta sheets on CD spectra?

Answer 28

Alpha helices have double band patter at 208 and 222 nm. Beta sheets have a single negative band at 215 nm

Question 29

Recall the hypothetical absorption/emission profile of singlets, fluorescence and phosphorescence

Answer 29

Question 30

Define FRET quenching

Answer 30

A special class of quenching. Förster resonance energy transfer (FRET or FET) is a dynamic quenching mechanism because energy transfer occurs while the donor is in the excited state. FRET is based on classical dipole–dipole interactions between the transition dipoles of the donor and acceptor and is extremely dependent on the donor–acceptor distance, R, falling off at a rate of 1/R6. FRET also depends on the donor–acceptor spectral overlap (see figure) and the relative orientation of the donor and acceptor transition dipole moments.

Question 31

FRET quenching requires that the donor and acceptor must be sufficiently close to transfer energy. Give the equation for determining the efficiency of this energy transfer.

Answer 31

Question 32

Recall which areas of an NMR spectra contain peaks for: * N-H, O-H and aromatics * H_α * Side chain aliphatics

Answer 32

Question 33

Why is the cis conformation less (though still) disfavoured in proline?

Answer 33

Because of the steric hindrance from its ringed amino substitution . the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly.

Question 34

Give the partial coefficients for hydrophilicity and hydrophobicity

Answer 34

Question 35

Define the backbone dihedral angles

Answer 35

* Φ: Between the alpha carbon and N * Ψ: Between the alpha carbon and carbonyl beta carbon * ω: Between the carbonyl beta carbon and the next N (peptide bond)

Question 36

Recall the conformation of antiparallel and parallel beta sheets and the H bonding configuration of each.

Answer 36

Question 37

Recall the three major beta sheet topologies

Answer 37

Question 38

* What are the two most common β-turns

Answer 38