Biochemistry
of
heredity:
the
structure of Deoxyribonucleic Acid (DNA)
In
principle:
Genes are
made of nucleic
acids
The
identity of the
hereditary substance was unknown until 1940;
its
structure
was
unknown until 1953
"Genetics"
was
taught
for 50 years without this information (see Orientation)
The history of the
discovery of DNA is a fascinating detective story
The Watson-Crick
structure
for Deoxyribonucleic
acid (DNA) (1953) (MGA2
Box
2-2, p.31)
a
double-stranded
helix
sugar-phosphate
backbone outside
nitrogenous
bases (A,C,G, T)
inside
bases
held
together
by hydrogen
bonds (AKA H-
or hydrostatic bonds)
Fundamental
insight:
bases
on
alternative
strands pair according to specific rules:
A with T
G with C
each
pair
has
similar structure
A second form of nucleic acid
is ribonucleic
acid (RNA)
Building
blocks
of
nucleic acids (DNA & RNA)
bases
pyrimidines (single
ring)
cytosine(C)
thymine (T)
[
uracil
in RNA (U) ] [iGen3_02-08]
"PYRamids
were CUT
from
stone"
purines (double
ring)
adenine (A)
guanine (G)
"AGs are PURe"
nucleoside
= base
+ sugar
deoxyribose sugar
in DNA (-
H on 2'-C)
[iGen3_02-07]
ribose
sugar in RNA
(- OH on 2'-C)
deoxyadenosine
(dA) deoxyguanosine
(dG)
deoxycytosine (dC)
deoxythymidine (dT)
nucleoide = nucleoide +
phosphate(s) [PO4]
[iGen3_02-09a]
in DNA,
one
phosphate
=> deoxyucleoide monophosphate
(dNMP)
three
phosphates => deoxynucleoide triphosphate
(dNTP)
deoxyadenosine-5'-phosphate or deoxyadenylic
acid
deoxyadenylic acid (dAMP)
/ deoxyguanylic
acid (dGMP)
deoxycytidylic acid (dCMP)
/
deoxythymidylic
acid (dTMP)
polynucleotide =
nucleotide + nucleotide + nucleotide + etc [iGen3_02-09b]
nucleotides
are
linked by 3' 
5' phosphodiester
bonds
polynucleotides have directionality
hydroxyl
(3') &
phosphoryl (5') ends
Structure
of
B-DNA
(3-D model: requires MDL
chime plugin) [iGen3_02-12]
1)
Two plectonemic (twisted) right-handed polynucleotide helices ()
2)
Helices antiparallel strands wrt
5' 3'
orientation [MGA2-02-05]
3)
Strands held together by hydrogen
(H-) bonds
between bases
4) H-bonds
form
according
to specific base-pairing
rules
A pairs with T:
two H-bonds 
G pairs with C:
three H-bonds 
A+T & G+C pairs have very
similar
shapes
&
sizes [iGen3_02-13]
5)
Base pairs co-planar:
interval = 0.34 nM [= 3.4 Ǻngstroms]
6)
Period of
helix is 10 bp (base
pairs) =
3.4 nM
7) 3-D
structure has major & minor grooves [MGA2_02-07]
8)
Order of
bases in each strand aperiodic
Homework
Assignment #2
Homework Assignment #3
Other
structures for nucleic acids
[iGen3_02-14]
A-DNA
: not groovy, base pairs not
co-planar
Z-DNA: left-handed
helix ()
Ribonucleic
Acid (RNA):
substitute
uracil for thymine [ thymine =
5-methyl-uracil
]
ribose sugar for deoxy-ribose
typically
single-stranded or
with complex double-stranded
folding:
mRNA (messenger RNA): long, single-stranded
rRNA (ribosomal RNA): medium-sized, complex 'stem
& loop'
folding
tRNA (transfer RNA): small, 'cloverleaf' structure
[more
on
RNA structures later]
Implications
of
DNA
structure for its genetic function
"The sequence of bases
on a
single chain does not appear to be restricted in any
way....
It has not
escaped
our notice that the specific pairing we have postulated
immediately
suggests a
possible copying mechanism for the genetic material."
(Watson
& Crick
1953. Nature
112:753)
DNA is an aperiodic
crystal:
order of bases conveys
information
Antiparallel
strands are self-complementary:
DNA is potentially autocatalytic
All text
material © 2011 by Steven
M. Carr
