OCHEM important molecules Flashcards
what is the difference between L and D amino acids?
they are enantiomers
how can you identify an L or D amino acid?
with all amino acids, we view them as a Fischer projection with the carboxylic acid on the top. If the amino group points to the LEFT it is then an L amino acid.
Fischer projection. horizontal lines are?
pointing out of page (bow tie)
what amino acid do animals have naturally?
L-amino acids
how do we orient carbohydrates in Fischer projections?
the most oxidized group goes on top –> typically CHO.
how do we assign L and D to carbohydrates?
we look at the Fischer projection. with the CHO group on top.
if the bottom most OH is pointing to the right: this is a D sugar
If the bottom most OH is pointing LEFT: this is an L sugar
what natural carbohydrate exists in animals?
D- sugars (think sugars are Delicious!!)
this opposes L-AA’s
t of f, +/1 system. R/S system, and D/L system are all different
true - ish
\+/- = optical activity R/S = absolute configuration D/L = similar concept as R/S with emphasis on the location of the stereocenter
list the ionizable amino acids
D E R K H Y (pka = 10) C (pka = 8)
what does the strecker synthesis produce?
a racemic mixture of L and D amino acids
what is the general mechanism for the strecker synthesis?
- react an aldehyde with an amine to form an imine
- HCN protonates the nitrogen of the imine making it positive
- CN- then nucleophilic attacks the carbonyl centre
- acid-catalyzed hydrolysis converts the nitrile to carboxylic acid
pg. 211
what is malonic ester synthesis?
another way to form amino acids. the use of phthalimide and malonic ester
still forms a racemic mixture
what is gel electrophoresis?
this separates molecules based on size or charge (and moves molecules based on charge)
i.e. a molecule is given a charge so that it will move in the gel with an electric field.
Often used for amino acids and nucleic acids
in peptide bond formation what is lost?
H2O!
t or f, a dipeptide is at higher energy than 2 lone AA’s
true! this explains the driving force of protein folding.
usually bonds are made since whats being made is favourable. that is not that case here.
what is DCC coupling?
we react incoming amino acids with DCC
(cyclohexane-n=c=n-cyclochexane).
the carboxylic acid attacks the delta positive C. then another AA attacks that AA’s carbonyl centre.
the normal backbone of a peptide goes
{N-C-C-N}-C-C-N etc.
explain the core bonds
draw it.
{N-C-C-N}
the C-C bond can rotate normally
the C-N bond cannot –> this is because the lone pair of e on the nitrogen delocalizes to form a resonance with the C=O bond. this makes it planar and rigid
hydrolysis of peptides are kinetically fast and thermodynamically favourable.
false
favourable yes –> since peptide energy is high
but they are slow!!
how do we number carbons in a simple sugar?
we give number 1 to the most oxidized carbon in the chain. typically the CHO carbon.
what is a pyranose and furanose?
these are cyclic sugars .
pyranose - 6 sugar ring
furanose - five sugar ring
how does a sugar cyclize?
when its penultimate carbon attacks the carbonyl group of the sugar creating a HEMI-ACETAL.
Can a cyclized sugar become linear again?
only when its anomeric carbon is in the hemi-acetal form. if it becomes an acetal, then it cannot be in equilibrium.
