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45 Cards in this Set

  • Front
  • Back
Information transfer in cells
info encoded in DNA is transcribed thru RNA synthesis
RNA is read and translated into a sequence of aa in protein
DNA gives 2 identical copies
DNA to complement mRNA
sequence aa into protein,tRNA

C,U,T (ring with 2 N)

A,G (hex & pent with 4 N)
=O and NH2
=O,=O, and N-H
=O,=O,CH3, and N-H

hex:NH2, pent:N-H

hex:NH2,=O pent:N-H
UV absorption spectra of ribonucleotides
determine the []
nucleotides and NA absorb UV light
compounds formed when a base is linked to a sugar (no P).
C2:DNA has H, RNA has OH
Nucleoside factorals
base is linked by glycosidic
C of glycosidic is anomeric
conformation of base:syn,anti
sugars make more H2O-soluable
Rotation around the glycosidic bond
is sterically hindered
steric hindrance:CH2OH projects above the ribose ring
syn vs anti: base pairing
Mnemonic:syn is bad, favor anti
Kaguni rule
a bad mnemonic is a good mnemonic
four common ribonucleotides
AMP:adenylic acid
GMP:guanylic acid
CMP:cytidylic acid
UMP:uridylic acid
Structure and chemistry of nucleoTIDES
most abundant are ribonucleos
are polyprotic acids: 3-4 protons that can dissociate from each P
functions of nucleotides
nucleoSIDE 5'-triP carry energy
serve as recognition units
cyclic nucleotides:signal, regulate cell metabolism
more functions
ATP is central energy to metabolism
GTP drives protein synthesis
CTP drives lipid synthesis
UTP drives carb metabolism
structures of cyclic nucleotides
cAMP and cGMP
addition of P to the available ribose OH groups found in all cells
ATP synthesis
Formation of ADP and ATP successive addition of P groups by phosphoric anhydride linkages. Remove H2O in dehydration synthesis
Phosphoryl group transfer

Pyrophosphoryl group transfer
PO4(NTP) + ROH-->NDP + R-PO4

2PO4(NTP) + ROH-->NMP + R-2PO4
Nucleic acids
polymers linked 3-5' by phosphodiester
always reads 5-3'
N to C terminus (in proteins)
Different classes of NA
DNA:one type/purpose
rRNA:structure/f of ribos
mRNA:carries message
tRNA: carries aa
notation for NA structures
furanoses are vertical
phosphodiesters are diagonal
Several forms of RNA
m, r, t
small nuclear, sn
small non-coding RNA
DNA double helix
bp from H-bonds
Franklins x-ray diffractions
Crick:knew it was a helix
Watson: found H-bonds
DNA structure
l=1.6 million nm
eukaryotic DNA wrapped around histone (nucleosomes)
alternating DNA double helix and histone octamer
consist of 2 turns of DNA supercoiled about a histone "core" ocatmer
transcription pdt of DNA
prok:single contains info for many proteins
euk:single for one protein has introns and extrons
mRNA between pro and eu
pro:meets RNA polymerase near 5' end
eu:remove ex, keep in, get mRNA
Eukaryotic mRNA
DNA is transcribed to produce heterogeneous nuclear RNA
intron:intervening sequence
extron:coding sequence
ribos are 2/3 RNA and 1/3 protein
Unusual bases of rRNA
pseudouridine, ribothymidylic acid and methylated bases
small polypep chains 73-94 residues
several bases usually methylated
each aa has 1 unique tRNA to take it to the ribo
aminoacyl tRNA are the S's of protein synthesis
RNA (bases)
C deaminates to form U
repair enzymes recognize these mutation ans replace U's with C's
Nature uses T in place of U to determine natural vs mutation
deamination of C forms U
C + H2O-->NH3 + U
the 5-methyl group on T labels it as a special kind of U
OH and H diff b/w the NA's
DNA and RNA diffs
DNA lacking OH is more stable
RNA is designed to be used and then broken down
Hydrolysis of NA's
resistant to dilute acid
hydrolyzed by dilute base
Hydrolysis of NA's
depurinated by dilute acid
not susceptible to base
vicinal OH groups
of RNA are susceptible to nucleophilic attack leading to hydrolysis of the phosphodiester bond.
cleavage of polynucleotide chains
the 3'side of each phosphodiester is a and 5' is b.
Hydrolysis of a yields 5'-PO4 products and of b yields 3'-PO4 products
snake venom phosphodiesterase
removal of 5'NMP from 3' end resulting in 5'-AMP
("a" specific exonuclease)
spleen phophodiesterase
removal of 3'-NMP from 5' end
resulting in 3'-CMP
("b" specific exonuclease)
RNaseA (pancreas)
"b" specific exonuclease
cleaves b at 3'pyrimidine, yielding oligos with pyrimidine 3'-PO4 ends
restriction enzymes
bacteria restrict attack from foreign DNA by this enzyme
Type II & III cleave DNA
recognition of 6-base sequence is "six-cutter"
Type II restriction enzymes
No ATP required
recognition in DS-DNA have 2-fold axis of symmetry
cleave leaves sticky/blunt end
more Type II restriction
names are 3-letter code
1st:genus 2nd,3rd:species
following letter = strain
EcoRI is 1st is R strain of ecoli