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Grammar
isn’t easy. Small changes can lead to large
differences
in meaning. It is like this with the terminology
in
molecular biology as well. TK is a tyrosine kinase, while
TK1
is a thymidine kinase. Thymine is a nitrogenous base
of
DNA while thiamine is a vitamin. Not knowing the
difference
can keep you from that PhD you’ve been wanting.
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Today we are going to talk about the building blocks of DNA
and RNA – they can be as confusing as grammar. Terms and structures will look and
sound similar, but their functions are very different. We’ll try to minimize
the confusing details and maximize the amazing differences.
The basic building block of a nucleic acid is the nucleotide. This is a complex molecule
made up of one or more phosphate groups, a ribose or dexoyribose sugar, and one
of five nitrogenous bases (A, C, G, T, or U – those are the 5 – for now).
Already it's a little confusing, but we can add more complexity; if you have
just the base and sugar, it is called a nucleoside,
not a nucleotide. Let’s use one base as an example.
Adenine (A) is
the name of one nitrogenous base. If it is bound to a ribose, it is called adenosine (A), if it is bound to
dexoyribose, it is called deoxyadenosine
(dA). If you add a phosphate, you get the nucleotide, but the name depends on
how many phosphates; one phosphate = adenosine monophosphate (AMP) or
deoxyadenosine monophosphate (dAMP), 2 phosphates = adenosine or deoxyadenosine
diphosphate (ADP or dADP), 3 phosphates = the triphosphate (ATP or dATP).
The other nitrogenous bases use the same system – mostly.
Cytosine (C) and guanine (G) form cytidine
or guanosine nucleosides or
nucleotides. The exceptions are thymine
(T) and uracil (U). T is formed
from dUMP by adding a methyl (-CH3) group, but not from UMP. Therefore,
you don’t really find thymidine, only deoxythymidine. Since they know it only
comes in one form, scientists go ahead and call it thymidine - thanks a lot.
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As
alluded to in the text, base plus sugar equals nucleoside. Add
a
phosphate, or two, or three and you have nucleotides. The sugar
can
be ribose or dexoyribose, the difference being the OH at the
second
carbon position. On the right are the possible bases, the purines
have
two rings, the pyrimidines have one. Notice how adding a
methyl
group to uracil makes thymidine or how taking away an
amine
group from cytosine makes uracil. These will be important later.
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We said above that nucleotides are the building blocks of
DNA and RNA. Specifically, it's the triphosphate nucleotides (NTP or dNTP,
where N means any of the bases) that are used for incorporation into the
growing chains of RNA and DNA. The energy for the bond comes from releasing two
of the phosphates, so the nucleotides in
DNA and RNA are bonded through one phosphate linkage.
The building of nucleic acids comes from pools of NTPs and
dNTs in the cell. Evidence shows that the pool of dNTPs is about 1/10 that of
NTPs. This means that there are only enough dNTPs in the cell to support DNA
replication for about 30 seconds. This implies that it's the rate of turning
NMPs into dNMPs (then to dNTPs) that controls things like cell cycle and cell
division; no replication of DNA, no division.
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Ribonuclease
reductase turns NDPs into dNTPs. It is well
controlled,
the catalytic site is where the reaction takes
place,
so the NTP goes there. The activity site requires an
ATP
to activate or a dATP to inactivate the enzyme (this
keeps
the dNTP levels in check). The specificity site says
which
NDP can be acted on. When dATP or ATP is bound
at
the specificity site, the enzyme accepts UDP and CDP
into
the catalytic site; if dGTP is bound, ADP can be acted
on;
if dTTP is bound in the specificity site, GDP enters the
catalytic
site.
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Uses for nucleotides A, G, and C beside inclusion in DNA or
RNA are more apparent (nature hates unitaskers). ATP should be near and dear to
all our hearts - all our organs for that matter. ATP is the energy currency of
the cell. The energy released when two phosphates are lost to incorporate a
nucleotide into a growing nucleic acid is the same energy when ATP is
hydrolyzed to ADP during an enzyme reaction or relaxation of a muscle.
An adenosine variant, called cyclic AMP (cAMP) is just as
crucial as any other biomolecule you can name. An uncountable number (O.K., I’m
sure someone knows) of cellular reactions are regulated by the levels of cAMP
in the cell.
Cyclic GMP is a signaling compound similar to cAMP. Each
controls a varied number of regulatory pathways and second messengers to convey
information in the cell. There are also cyclic
dinucleotides. Bacteria use c-di-AMP and c-di-GMP as second messengers. This
has been know for some time, but a new study shows that these cyclic dinucleotides
stimulate specific inflammation in a mammalian host by triggering production of
the proinflammatory molecule IL-1beta. This stimulation pathway is via a
completely new pathway. These are most definitely important molecules outside the
nucleic acids.
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cAMP
and cGMP are single nucleotides in which the phosphate group
binds
to the sugar at two points – it circularizes. Just because they
aren’t
shown here, don’t think that cUMP or cCMP don’t exist – they
do,
and they are second messengers too. In the case of the cyclic
dinucleotides,
the phosphate of each nucleotide is joined to two
different
sugar molecules. It is still circular, but in a way that
involves
both nucleotides. The cGMP and cAMP are used in higher
organisms,
the c-di-GMP and c-di-AMP are used by bacteria for
various
operations, everything from gene regulation to virulence.
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CTP can act as an enzyme cofactor, especially in the
production of one of the phospholipids that is most important in biological
membranes (phosphatidylcholine). A similar reaction using CTP as a cofactor is
the focus of a new study because the product of the reaction is important in
the life cycle of the parasite that causes malaria (P. falcipaurm). The new study shows that the levels of CTP and CDP
will regulate the efficiency of the enzyme using CTP, so manipulating these
levels might be a target for anti-malarial drugs.
Lastly, uridine (U) is important outside of nucleic acids as
well. When combined with an adenosine and four (yes, 4) phosphates, it is
called uridine adenosine tetraphosphate
(Up4A). This dinucleotide has recently been identified as an
important controlling molecule in vascular endothelium physiology. It causes a
contraction in several types of muscle cells in vessel walls, thereby
regulating the tension of the walls, called vascular tone. In this way, Up4A
helps manage pressure and its dysfunction is important in many vascular
diseases.
As we discussed a couple of weeks ago, DNA is double
stranded and the bases are paired - A with T and G with C. Chargaff first
showed that the levels of dG and dC and of dA and dT were always the same in a
cell. Donahue then showed that they
could base pair by hydrogen bonds.
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Different
amounts of G+C vs. A+T in regions of DNA lead
to
different staining of the chromosome regions. GC regions
are
more dense, so some stains are excluded and they show
up
unstained. This difference in GC content has functional
consequences
as well. High GC areas are more gene dense,
and
have regulatory regions as well. A new study shows that
in
chickens, high GC regions are associated with regulatory
regions
of genes – the higher the GC content, the more
expression
from that gene.
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So DNA has dA, dC, dG, and dT, while RNA uses U instead of
T. Why? Such a simple question, but not many people bother to ask. There is more
than one reason, but they’re all related to long-term protection of genetic
information.
The cytosine base can be deaminated (removal of an amine
group) to form uracil. In RNA, this mistaken identity would lead to an
incorrect translation or perhaps a loss of function of a structural RNA.
Fortunately, these are short-term problems because each RNA is short lived. But
if U was used in DNA, then how would the repair enzymes know which U’s were
correct and which were actually deaminated C’s?
Since dT is used in DNA instead of dU, any dU must be a deaminated C and should be
replaced. If it were allowed to remain, then an incorrect U would be copied as
an incorrect A (U is like T because it pairs with A) and this would be forever kept
in the DNA - a permanent mistake. Not good.
Second, uracil forms a stable product when damaged by
radiation, while radiation damage to T’s can be detected and replaced by repair
enzymes. So again, using dT in DNA leads to a more stable, more protected,
long-term storage molecule.
A third reason for dT in DNA is related to base pairing. U
pairs best with A, but it can base
pair with G, T, or C. This increases the chances of mismatched pairs in the DNA
double strand - not good for keeping information pristine in the long run.
Protection against damage is also illustrated by the fact that dT is basically
methylated U.
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This
is a cartoon representation of a tRNA that is charged
with
a phenylalanine amino acid. The
different loops are
associated
with efficiency of action with the template,
binding
to the ribosome, and binding of the amino acids.
The
T loop actually contains a T base (at grey arrow), it’s
an
RNA, but it includes a T – that’s the very definition
of
an exception.
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Whew, good thing we use U for RNA and T for DNA, right.
Well….. not always. tRNAs are a huge exception, which we will talk about much
more in future posts. Thymidine is found in the T arm or T loop of tRNA; here
it is important for binding the tRNA to the ribosome during translation. A DNA
nucleotide in an RNA??? What gives?
Remember, T only occurs naturally as dT. T ends up in tRNA
by virtue of a modification that methylates a U. Once modified, you can’t tell
it from any other T – except that now it is bound to a ribose, not deoxyribose.
English grammar seems a lot easier by comparison, doesn’t it.
For
more information and classroom activities, see:
Nucleotide/nucleoside
–
Cyclic
nucleotides/dinucleotides –
Why
thymidine is used in DNA –
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