What was thought to be the original biological catalyst in pre-cellular times?
RNA
What is RNase A?
Where is it secreted from and where does it function?
It is stable and purifies easily, as demonstrated by
endonuclease that indiscriminately cleaves RNA in the middle of the strand
secreted from pancreas
functions in digestive tract
Anfinsen, who demonstrated that primary sequence encodes protein structure
In water, RNA phosphodiester linkages are cleaves with a half life of
RNase accelerates this reaction by a factor of
4 years
10^15
Cells can protect themselves from the indiscriminate cleaving of RNase A by
ribonuclease inhibitors, a large protein that wraps around RNase A, and binds it tightly
Aufbau’s principle
Hund’s rule
s orbitals vs p orbitals
A: electrons fill lowest energy orbitals first
H: maximum number of unpaired electrons before paring
s: sphere
p: directional (px, py, pz)
geometry, example, number and type of orbital in sp hybridization
linear 180
carbon in CO2
two sp orbitals and 2 p orbitals
geometry, example, number and type of orbital in sp2 hybridization
trigonal planar (120)
oxygen in CO2
three sp2 and one p
geometry, example, number and type of orbital in sp3 hybridization
tetrahedral 109.5
carbon in CH4
4 sp3
What is electronegativity and what does it determine
measure of atoms attraction for electrons
relative, not absolute
determines bond polarity and ionic character
unequal sharing = partial charges
Orbitals on the same atom hybridize to
give directionality
Which atoms have stronger partial charges than side chains?
backbone atoms
n-term +1
c-term -1
All standard amino acids except for what are chiral
glycine
Projection in fischer and persepctive
fischer
horizontal bonds: toward viewer
vertical: away from viewer
perspective
solid bonds: toward viewer
dashed bonds: away from viewer
What is the CORN rule
with H pointing away, CO to R to N in clockwise direction = L amino acids
if H is facing toward you
Swap H with the group that is pointing away
What is the R/S Cahn Ingold Prelog system?
rank substituents by atomic number
view from lowest priority group
clockwise = R
counterclockwise = S
With the exception of what amino acid, all standard amino acids have a beta carbon
glycine
Which amino acids have branched beta carbons?
Valine, Isoleucine and Threonine
masses of amino acids and proteins are typically given in units of
daltons, 112 the mass of 12C
The average free AA mass is:
The average residue AA mass is:
Why are they different?
128 Da
110 Da
Lose water when incorporated
Which amino acids absorb strongly at 280 nm
tyrosine and tryptophan, but NOT phenylalanine
Two tautomer exist for which amino acid
histidine
(Nd or Ne protonated).
Formation of a disulfide bond by the oxidation of two molecules of cysteine involves the loss of
and occurs in
2 H and 2 e
extracellular space, ER lumen
Selenocysteine (Sec, U) and Pyrrolysine (Pyl, O) are non standard proteinogenic amino acids. describe both
Sec, U
derived from serine
incorporated during translation via variant codon, found in a few proteins
fxn: antioxidant and breaks down peroxides
Pyl, O
found in some methanogenic Achaea and bacteria, present in methyltransferase, side chain formed from two lysines, weakly basic nitrogen ring
Some uncommon AA are created by post translational modification, and can be:
Examples
irreversible (4-hydroxyproline)
reversible (O-phosphoserine)
Examples (both reversible)
O-phosphoserine: regulates protein protein interactions
Acetyl-lysine alters histone DNA binding (epigenetics)
