Exam 1 review Flashcards
molecules recognize each other by
interactions
van der waals interactions
give strong repulsions, weak “flickering” attractions
dipole interactions
between molecules with hetero atoms
hydrogen bonds
a type of dipole interaction with hydrogen that is important in biology
strong interactions
covalent bonds and ionic interactions are responsible for stable, long-lived, structures
water is the
ultimate hydrogen bonding liquid
as ice, water forms how many bonds
4 h bonds
2 accept
2 donate
tetrahedral in shape
as a liquid water forms how many bonds
4.5 h bonds
makes liquid more dense than ice
life requires
water`
water properties
liquid solvent
concentration gradients
biopolymers adopt unique shapes
hydrogen bonding networks
tetrahedral bonding
large void volume, dissolution of gasses
liquid from 273K to 373K
density maxima
liquids and polymers are dominated by weak forces from potential interactions around RT in size. All of biology depends on using weak forces to allow
biological changes
the purine groups are synthesized on the
ribophosphate
PRPP
that displaces the phosphate at C1 on PRPP
the amide group of glutamine
where is RNA hydrolyzed by water or base
2’OH
RNA hydrolyzation creates
a 2’,3’ cyclic monophosphate nucleotide and a truncated RNA
each base has a unique UV absorption spectrum due to the
electronic differences in the rings and substitutions
for sequencing via UV, what wavelength is used
260nm
blue!
tautomers for pyrimidine bases
lactam
lactim
double lactim
tautomers are stabulized by different environments including
solvent polarity and pH
pH causes different H-bonds to be stable and can
change the UV spectrum
different electronic states are allowed due to the
number of hetero atoms in conjugation in the rings coupled to tautomers
pH differences for UV are more prevelant in
pyrimidines
in terms of the particle in a lox, pyrimidines have a
smaller box
greater % change
attractive forces in DNA stability
base pair hydrogen bonds
base pi stacking
repulsive forces in DNA stability
excluded volume
phosphate-phosphate repulsions
2 molecules q1 and q2 interact with each other by
coulombs law for the potential energy U
water diminishes (screens) the interactions between two charges via
the dielectric constant of 80
water divides the interactions between to charges by
80
excess salt further diminishes (screens) interactions between charges as found by debye and huckel meaning that
it goes exponentially to zero with ionic strength
right handed form of DNA
A and B
left handed form of DNA
z
diameter of A form
26 A
diameter of B form
20A
diameter of z form
18A
base pairs per helical turn for A form
11
base pairs per helical turn for B form
10.5
base pairs per helical turn for Z form
12
base tilt normal to the helix axis for A form
20 degrees
base tilt normal to the helical axis for B and Z form
6-7 degrees
sugar pucker conformation for A form
C-3’ endo
north
sugar pucker conformation for B form
c-2’ endo
south
sugar pucker conformation for Z form
C-2’ endo for pyrimidines
C-3’ endo for purines
DNA changes shape with respect to
salt concentration
at zero salt DNA
does not form a dimer
DNA shape with increasing salt concentration
single
B
A
Z
there are many base pairing possibilities due to
the number of hydrogen bonding groups
triple helices
major groove binding
base triple specific
high salt requirement
quadruplex
g-quartets
loops of 3-4 bases
binds ions specifically in the core
if you add poly- a and poly - t to a solution,
TAT will form a triple helix
A will go in solution (more soluble)
triplets of bases are reasonably
stable
common base triplets
TAT
CGC
in a quadruplex, how many hydrogen bonds does each base have
4 h bonds per base
the center of a quadruplex is full of
oxygens and lone pairs
what ion goes in the middle of a quadruplex
K+
more stable than Na+
g tetrads can form in
any G-rich sequence
how to break a g tetrad
12M LiCl and boiling
many RNAs are inherently
single stranded
most RNAs fold up forming
secondary and tertiary structures
how do RNAs fold
each strands find complementary sections, often times short sections where complementary holds
structures in RNA
stems
loops
bulges
try on MFOLD
mRNA carries the code from DNA to the
synthesis machinery
before mRNA can be read
it must be processed into a mature form by removing the introns
the genetic code has some redundancies in
the third slot of the codon
some species are specific in their codons requiring
codon optimization
domains in rRNA are more structurally varied than in
proteins
robosomal subunits
30S (lower)
50S (upper)
what ribosomal subunit holds the mRNA
30S
what subunit catalyses the peptide bond formation
50S
translocation and successive binding of tRNA are
GTP dependent
three sites of tRNA binding
APE
as the peptide is made it can either coil into an alpha helix or
await pickup by a chaperonin (beta sheets)
what signals the end of protein synthesis
release factor
release of the ribosome subunits allows for
ribosome recycling and energy conservation
what do helicases do
twist and untwist DNA
twisting a duplex can change
local and large scale structure
twist equation
L=T+W
linking number = twist + writhe
what is twisting equilibrium
how an open transcription bubble is in equilibrium with the various shapes
twisting can lead to
strand separation
what can mechanically separate strands of DNA
gyrase
topoisomerase
helicase
what transcribed mRNA
RNA polymerase
the RNA DNA hybrid is known as
RNA-DNA double helix D-loop
DNA synthesis goes in a
5’ to 3’ direction
enzymes involved in the replication process
helicase
DNA binding protein
dnaB
primase
DNA polymerase
DNA ligase
