Nucleotides and Nucleic Acids: CH HO Base P O O O O CH Base P O O O O CH Base
Nucleotides and Nucleic Acids: CH HO Base P O O O O CH Base P O O O O CH Base
Nucleotides and Nucleic Acids: CH HO Base P O O O O CH Base P O O O O CH Base
Nucleotides have a wide variety of functions. One major function is to provide the
thermodynamic driving force for a number of chemical reactions. This is especially
well-known for ATP, but GTP is also used for a variety of reactions, UTP is used in
glycogen and complex carbohydrate biosynthesis, and CTP is used in complex lipid
synthesis.
Nucleotides are used to form intracellular signaling molecules such as cAMP and
cGMP. In addition, ATP, ADP, and AMP act as signals to modulate energy
metabolism. Nucleotides form parts of some cofactors, including NAD, FAD, and
coenzyme A. Finally, nucleotides are the monomer units that comprise the nucleic
acids RNA and DNA.
The base and ribose ring together are termed a nucleoside (the suffix “-oside” means
a compound covalently bonded to carbohydrate). The base and the ribose with one
or more phosphate attached are termed a nucleotide. The ribose ring numbering is
22 DNA and RNA exhibit a maximum absorption at about 260 nm, due to the absorbance of the
nucleotide bases. Most proteins have a maximum absorption at 280 nm, due to the absorbance of
tryptophan and tyrosine. One method for assessing the relative amount of protein and nucleic acid in
a sample is to measure the A260/A280 ratio; a ratio of above 1.8 indicates that the solution contains
nucleic acid with little protein.
The base in the nucleoside can have one of two possible conformations: syn and anti.
Both are present, although the anti conformation is more common physiologically,
due both to the lower steric strain and to that fact that this conformation is
required for nucleic acid structure. The rotation about the base-ribose bond is
restricted by steric hindrance, so the nucleotide must be synthesized in one form or
the other. (For purines, the syn structure is drawn most frequently; this is not a
reflection of the common conformation, but instead merely allows the drawing to
occupy less space on the page!)
NH2 NH2
syn anti
N N
N N
O N O N
N N
O P O CH2 O P O CH2
O O
O O
HO OH HO OH
The most common bases are the two purine and three pyrimidine derivatives
shown below.
Purines Pyrimidines
NH2 NH2
Base Nucleotide Base Nucleotide
N
N N
Adenine Adenosine Cytosine Cytidine
N N N O
H H
O
O
N NH
HN Uracil Uridine
Guanine Guanosine
N O
H2N N N H
H
O
H3C
NH
Thymine Thymidine
N O
H
O O O O O CH3
H
N N N H3C N
N HN HN HN NH N
O
N N O N N O N N O O N N
H H H H H
CH3
Hypoxanthine Xanthine Uric acid Pseudouracil 1,3,7-Trimethyl
xanthine
NH2 NH2
AMP 3´-AMP
N N
N N
O N N
N N
O P O CH2 HO CH2
O O
O
O
HO OH O P O OH
O
Additional
DNA
O
Additional
DNA
5´
carbon O
O H2C O
G
O P O O P O
C
5´ O CH2 O
O
O
O H2C O
Direction A
of O P O O P O
DNA T
O CH2 O
synthesis O
O
O H2C O
C
O P O O P O
3´ G
O CH2 O
O
3´
carbon O
O O HO H2C O
O A T
O P O P O P O CH2 O P O
O 3´
O O O O
hydroxyl
Additional
HO DNA
As with proteins, nucleic acids can have a wide variation in number of monomer
units present. However, most DNA molecules have much higher numbers of
monomer units than are present in any known protein.
In a classic one-page 1953 paper, James Watson and Francis Crick25 proposed a
structure for DNA. Their proposed structure was based on molecular models
constructed on the basis of relatively limited data. Some of the data that Watson
and Crick used were obtained (in a somewhat controversial manner) from the fiber
X-ray diffraction work of Rosalind Franklin and Maurice Wilkins (who were
acknowledged in the Nature paper, but published their own results separately).
Watson and Crick also took into account experiments by Edwin Chargaff that
showed that in all organisms tested, the nucleic acid A content was comparable to
T, and the G content was comparable to C.
Watson and Crick proposed that DNA exists as an anti-parallel double helix, in
which the phosphate backbone was on the outside, and in which the strands were
held together by the hydrogen bonding interactions between pairs of A and T and
pairs of G and C. Examination of the structure below reveals that the ribose-
phosphate backbone has the same shape for both A:T pairs and G:C pairs.
CH3 H
Thymidine Cytidine
O H H N
N H O
Adenosine Guanosine
N N N N N H N
Ribose H N Ribose N
O O H
N N N N N
Ribose H Ribose
Studies performed since the original Watson and Crick proposal have revealed that
at least six different structures are possible for DNA. The Watson-Crick double
helix is known as B form DNA. The B form (a short segment of which is shown
below) is the major form under physiological conditions. B form DNA has a rise of
3.4 Å per base pair, with each full turn requiring a total of 10.5 base pairs, and the
helix is ~20 Å in diameter. The major groove and minor groove indicated allow
23 Avery, et al., “Studies on the Chemical Nature of the Substance Inducing Transformation of
Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated
From Pneumococcus Type III.” J. Exp. Med. 79, 137-158 (1944)
24 The apparent simplicity of DNA was in part because no hypotheses had been proposed for how
DNA might store information. In addition, the true size of DNA molecules had yet to be established;
in fact, DNA molecules are the largest molecules known. The largest molecule in the human body,
chromosome 1, has a molecular weight of ~1.5 x 1011 g/mol (0.15 million metric tonnes/mol).
25 Watson, J.D. and Crick, F.H.C., “A Structure for Deoxyribose Nucleic Acid.” Nature 171, 737
(1953)
Some DNA bases are modified after synthesis of the nucleic acid molecule. Some of
these modifications, such as the methyl and hydroxymethyl derivatives shown
below, are thought to play a role in proof-reading the DNA for errors during
synthesis, and to have regulatory functions for assisting in controlling gene
expression. Examination of the structures of these modified bases suggests that
they are still capable of base-pairing normally, and that the role of the modification
is to change the shape of the base to alter interactions with other molecules.
H CH3 HO
N CH3 CH2
NH2 NH2
N
N
N N N N
N N Ribose Ribose
Ribose O O
N6-methyladenosine 5-methylcytidine 5-hydroxymethylcytidine
RNA
RNA differs from DNA in both structural and functional respects. RNA has two
major structural differences: each of the ribose rings contains a 2´-hydroxyl, and
RNA uses uracil in place of thymine. RNA molecules are capable of base pairing,
but generally will not form large regions of stable RNA-RNA double helix. RNA can
act as a genetic material (although this role, at least for current organisms, seems
to be restricted to viruses).
RNA bases
The bases used for RNA are attached to ribose. However, many are significantly
modified from the typical four bases normally considered to be part of RNA. This is
particularly true for tRNA. The modified bases include pseudouracil and
methylated versions of cytosine and adenine, as well as a number of others.
In general, RNA is less suited to acting as genetic material than DNA, and is less
suited to forming efficient catalysts than proteins. Assuming that the RNA world
once existed, nearly all of its functions have been taken over by other biological
molecules. However, some vestiges of the RNA world may still exist.26
The vast majority of RNA functions are concerned with protein synthesis.
The eukaryotic 40S Ribosome contains 1 rRNA (18 S rRNA = 1900 bases) and about
35 different proteins. The 60S ribosome contains 3 rRNA (5 S = 120 bases, 5.8 S =
160 bases, and 28 S = 4700 bases), and about 50 proteins. The 5 S rRNA has its own
gene; the others are synthesized as a single transcript that is then cleaved to
release the mature RNA molecules that become part of the ribosome.
26 Side Note: Many of the assumptions and data concerning the RNA-world hypothesis are
discussed in Penny, D., “An Interpretive Review of the Origin of Life Research.” Biol Phil. 20, 633-
671 (2005). Assuming that the “RNA world” hypothesis is correct, it would seem that the phosphate-
based RNA structure had a major role in the origin of life. Phosphate has useful properties that
make it a good candidate for participating in a variety of biologically important chemical reactions.
The advantages of phosphate are summarized in: Westheimer, F.H., “Why Nature Chose
Phosphates.” Science 235, 1173-1178 (1987).
Recently, a controversial paper reporting the discovery of an organism (GFAJ-1) was published:
Wolf-Simon, F., et al., “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.”
Science 332, 1163-1166 (2011). The results reported in this paper have been questioned at length, in
part because arsenate esters are much more rapidly hydrolyzed than phosphate esters, suggesting
that nucleic acids using arsenate instead of phosphate would be too unstable to support life, and
criticizing the authors for making extraordinary claims without extraordinary evidence However, if
the GFAJ-1 organism is actually capable of using arsenic in place of phosphorus, GFAJ-1 may
become a useful model system for exploring issues related to phosphate chemistry and the origin of
life.
Object sizes can be measured in Svedberg units (S). Prokaryotic ribosomes are 70 S particles, with
each comprised of a large (50 S) and a small (30 S) subunit. Eukaryotic ribosomes are 80 S particles,
comprised of a large (60 S) and a small (40 S) subunit. You will notice that the Svedberg units are
not additive for the particles sizes; this is due to the effects of shape on sedimentation.
Until relatively recently, it was assumed that the ribosomal RNA performed a
largely structural function. However, more recent data strongly suggests that the
rRNA acts as the enzyme, with the protein acting as the structural scaffolding.
These data include results from high-resolution X-ray diffraction structures of the
individual subunits27 and complete ribosome28 from both bacterial and eukaryotic
organisms.
27 Ban, N., et al., “The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution.
Science 289, 905–920 (2000). The large subunit structure figure was created in VMD from PDB ID
1FFK.
28 Voorhees, R.M. et al., “Insights in substrate stabilization from snapshots of the peptidyl
transferase center of the intact 70S ribosome.” Nat. Struct. Mol. Biol. 16, 528-533 (2009); Ben-Shem,
A., et al., “Crystal structure of the eukaryotic ribosome.” Science 330, 1203-1209 (2010); Khatter, H.
et al., “Structure of the human 80S ribosome.” Nature 520, 640-645 (2015), and others.
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A site
mRNA
P site
E site
29 Protein synthesis is a topic for CHEM 331 (Biochemistry II), and will not be covered here. The
textbook has more information. A recent review article by one of the Nobel Laureates involved in
ribosome structural analysis is another good source of information about ribosome function and
protein synthesis: Schmeing T.M.& Ramakrishnan V. “What recent ribosome structures have
revealed about the mechanism of translation.” Nature 461, 1234-124 (2009).
23S rRNA
E site
P site
mRNA
A site 5S rRNA
mRNA metabolism is very complex, and is a topic for CHEM 331 Biochemistry II
and other courses.
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micro RNA
Relatively recently, it has become apparent that RNA has a much larger role in
protein synthesis than was previously thought. In addition to the roles of rRNA,
mRNA, and tRNA, smaller RNA molecules appear to have regulatory functions.
Small RNA molecules called microRNA (miRNA) can inhibit translation of mRNA
both with and without causing degradation of the mRNA. Different miRNA
sequences are transcribed at different times, and probably have functions in
development and differentiation of cell lineages, and may have a protective role
against viruses, especially viruses with RNA genomes.
Other RNA
Some RNA molecule do not fall into the classes listed above. One example is the
RNA portion of some enzymes, including RNaseP and telomerase, which require the
RNA for function. In the case of RNaseP, the RNA has the catalytic activity,
although the protein portion is required for full activity. The types of functions
exhibited by RNA are thus far more diverse than they were thought to be a few
years ago, and are far more diverse than those of DNA.
In humans and most other higher eukaryotes, the actual protein coding sequences
in the DNA comprise a small fraction of the genome (in humans, protein coding
sequences probably comprise less than 2% of the genome). However, a large fraction
of the rest of the genome is probably transcribed into RNA, in at least some cell
types. The function of much of this RNA is not yet understood, and, in fact, there is
some controversy as to whether considerable amounts of RNA are synthesized with
no actual function, or whether the RNA has functions that have not been
determined.
Nucleotides are comprised of the aldopentose ribose and a nitrogenous base, The
most commonly used base are the purines adenine and guanine, the pyrimidines
cytosine, thymine, and uracil, and slightly modified forms of these compounds.
DNA is a storage medium for information. RNA is largely used as part of the
mechanism for elaboration of the information into more directly usable form.