Symbol and Picture Cards Flashcards
Recall the general structure of an amino acid at physiological pH
What are the aromatic amino acids? Recall their structures.
What are the 5 alophatic (hydrophobic) amino acids?
Recall the 9 hydrophilic amino acids
Recall the nonpolar amino acids
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Methionine
(Almost all alophatic, except methionine)
In glyceraldehyde (the reference for stereochemical classifications), is the hydroxyl group pointing left or right in L-glyceraldehyde?
Left
Recall the stereochmemical geometry of a L-α-amino acid
Recall the three dimensional projection of an amino acid using the CORN crib mnemonic
Recall the mechanism for the formation of a peptide bond
Condensation reaction
(a water molecule leaves)
Recall the configuration of a parallel coiled coil
- 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.
In a parallel coiled-coil, which residues interact?
a-a’
d-d’
In an anti-parallel coiled coil, which residues interact?
a-d’
d-a’
Is it possible to form coiled coils with more than two helices?
YES! Such as 3-helix parallel coiled-coil of viral surface glycoproteins
Give the basic structure of human tropoelastin
Alternating hydrophobic and cross linking domains
Recall the following motifs
- βαβ
- β-hairpin
- αα
Give the Beer-Lambert law
- ε: molar absorptivity*
- c: concentration of absorber*
- l: pathlength*
Define HOMO and LUMO and recall an example of this with ethene
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
How does a UV/vis spectra change with increasing collisions between molecules?
Recall the relative intensities of aromatic side chain absorbance for the three aromatic amino acids
Contrast the CD spectra for cytochrome C and a lysozyme
Recall the absorbance spectra of tyrosine at pH 6 and 13
Solid line: pH 6
Recall an absorbance spectra of poly-L-lysine in solution. What does the spectra look like for random coil? Alpha helix? Beta strand?
Solid line: random coil
Short dash: alpha helix
Long dash: beta strand
Compare and contrast absorbance vs. CD
When looking at a CD spectrum, you look at units of ellipticity (in degrees). This is then converted to either ____ or ___. Give the formula.
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.
Why are CD results reported as ellipticity?
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
Recall the circular dichroism signal for:
- α-helices
- β-sheets
- random coils
Random coils are the only ones with a positive dichroism signal (can be differentiated from alpha/beta structures)!
How can alpha helices be differentiated from beta sheets on CD spectra?
Alpha helices have double band patter at 208 and 222 nm. Beta sheets have a single negative band at 215 nm
Recall the hypothetical absorption/emission profile of singlets, fluorescence and phosphorescence
Define FRET quenching
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.
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.
Recall which areas of an NMR spectra contain peaks for:
- N-H, O-H and aromatics
- Hα
- Side chain aliphatics
Why is the cis conformation less (though still) disfavoured in proline?
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.
Give the partial coefficients for hydrophilicity and hydrophobicity
Define the backbone dihedral angles
- 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)
Recall the conformation of antiparallel and parallel beta sheets and the H bonding configuration of each.
Recall the three major beta sheet topologies
- What are the two most common β-turns
