BIOCHEM lecture 1-10 Flashcards
strength between non-covalent interactions
permanent dipoles> dipole-induced dipole> London dispersion forces
The water
molecule is non-
linear and
carries a
permanent
dipole moment.
The “van der Waals envelope” is the
effective “surface of the molecule”.
Two atoms from different molecules rarely come closer together than the sum of
their van der Waals
radii
exception to van der waals radii being the closest two atoms can get
Hydrogen
unit conversion for vdW radius
10 Å = 1 nm = 10 -9 m
when water is ice it
interacts tetrahedrally with four other molecules
D-H =
weakly acidic “donor” group, such as O-H, N-H
A =
weakly basic “acceptor” atom such as O, N
D-H…A
hydrogen bond
The permanent dipoles of water molecules interact very favorably with charged ions in
solution,
forming a “hydration shell”.
no difference in enthalpy (entropy drive) in a
transfer of hydrocarbaons from water to nonpolar solvents
amphiphillic/amphipathic
have both polar and non-polar segments
clustering lipids
increase the entropy of a system (less rotational restriction)
H-bonding within water facilitates its
ionization
H+ should be written as
H3O+ technically
1 liter of water there is
55.5 moles
Kw[10E-14]=
[H+ 10E-07][[OH- 10E-07]
HH equation
pH = pKa +log ([base]/[acid])
protons can be used to:
- Induce a large conformational change of a protein.
- Store energy – as a proton concentration difference
across a membrane
The pH of fluids surrounding
cells, and of the cytosol inside
the cell, is around 7.
However, in the organelles
called endosomes, the pH is
lower. -> used by influenza virus to infect a host cell bc pH differences inducesconformational change in surface protein
protons cannot cross a
lipid membrane
periplasm
the space between two membrane of bacterial cells
low proton concentration in
cytoplasm
high proton concentration in
periplasm
serine=ser=s
polar
hydrophobicity of side chains
phe>ile>ala
proline
makes ring with N in backbone
isoleucine
1 of 2 CHIRAL side chaines
uncharged + polar
serine
uncharged + polar
cycsteine
uncharged + polar
threonine
uncharged + polar
glutamine
uncharged + polar
asparagine
aliphatic + nonpolar
glycine
aliphatic + nonpolar
alanine
aliphatic + nonpolar
proline
aliphatic + nonpolar
valine
aliphatic + nonpolar
leucine
aliphatic + nonpolar
isoleucine
aliphatic + nonpolar
methionine
Threonine
1 of 2 CHIRAL side chains
His
pK of ~ 6 means that at neutral pH the imidazole ring is both in its protonated and unprotonated state; at a pH below the pK a larger fraction is protonated than unprotonated; at pH
values above the pK a larger fraction of the side chain is unprotonated than protonated.
negatively charged
aspartate (COO-)
negatively charged
glutamate (COO-)
aspartate and glutamate
- These side chains are very hydrophilic.
- The side chain carboxylates are often found in active sites
- The carboxylates can coordinate metals – in particular Mg2+ and Ca 2+.
aromatic
phenylalanine
aromatic
tyrosine
aromatic
trytophan
alanine
a
arginine
R
pKa 12.5
asparagine
N
aspartic acid
D
pKa 3.9
cycsteine
C
pKa 8.3
glutamine
A
glutamic acid
E
pKa 4.2
glycine
G
Histidine
H
pKa 6
isoleucine
I
leucine
L
lysine
K
pKa 10
methionine
M
phenylalanine
F
proline
P
serine
S
threonine
T
tryptophan
W
tyrosine
Y
pKa 10.1
Valine
V
amino group
-below pka nh3+
-above pka nh2
hydroxyl group
-below pka oh
-above pka o-
SH-group
-below pka sh
-above pka s-
imidazole
-below pka one positive charge
-above pka uncharged
the pka of the SAME functional group can be different in
different molecules
oxidation of cysteine to cystine
forms disulfide bonds
non-standard enzymes come from
post-translational modifications
protein kinases
attach phosphates
O-glycosylation
The oligosaccharide is attached to side chain O of a Ser or Thr
N-glycosylation
The oligosaccharide is attached to side chain N of an Asn
core protein
pentasaccharide “core in protein glycosylation
antenna protein
Such complex
antennas are very
specific markers
of proteins on a
cell surface.
protein glycosylation
addition of suagrs onto aa side chains
pka of N-terminal NH3+
8
pka of C-terminal COO-
4
if one peptide unit is fixed phi and psi define
orientation of second peptide unit
course of a polypeptide chain is defined by a
pair of dihedral angles (phi and psi) per aa residue
