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1 Nucleic Acid
1 Nucleic Acid
ORGANISM
Store and preserve information STRUCTURAL CHEMISTRY OF NUCLEIC
Pass information to future generations ACIDS
Express information during life’s
processes Nucleotides, Nucleosides and
Nucleobases:
GENETIC INFORMATION
Coded along a polymeric molecule Building blocks of nucleic acids
(DNA) Nucleotides have three characteristics
- The chemical basis of heredity components
Organised into genes 1. A nitrogenous (nitrogen-
- Units of DNA that encodes a containing) base (nucleobase)
protein or DNA 2. A pentose
3. One or more phosphatase
Central Dogma of Molecular Biology Nucleosides: nitrogenous base
(nucleobase) + pentose only
Nucleobase: nitrogen-containing
aromatic compounds that make up the
coding portion of nucleic acids
Transcription is carried out by RNA
polymerase
Translation is performed on
ribosomes
Replication is carried out by DNA
polymerase
Reverse transcriptase copies RNA into
DNA
Nucleotide and Nucleic Acid Nomenclature
Base Nucleoside Nucleotide Nucleic
Gene Expression & DNA Replication acid
“the genetic information stored in the Purines
nucleotide sequence of DNA serves two Adenine Adenosine Adenylate RNA
Deoxyadenosine Deoxyadenylate DNA
purposes” Guanine Guanosine Guanylate RNA
Deoxyguanosine Deoxyguanylate DNA
Sources of information for synthesis of Pyrimidines
protein molecules of the cell Cytosine Cytidine Cytidylate RNA
Deoxycytidine Deoxycytidylate DNA
- GENE EXPRESSION Thymine Thymidine or Thymidylate or DNA
Provides information inherited by deoxythymidine deoxythymidylate
Uracil Uridine Uridylate RNA
daughter cells or offsprings
- DNA REPLICATION
NUCLEOBASES
Purines & Pyrimidines are heterocyclic
compounds
Heterocyclic compounds: cyclic
structures that contain, in addition to
carbon, other (hetero) atoms such as
nitrogen
Electron decolization among atoms in
the ring partial double-bond
character planar purines and
pyrimidines facilitates their close
association, or “stacking” that
stabilized double-stranded DNA
Are hydrophobic and relatively
insoluble in water at the near-neutral
PURINES pH of the cell
Hydrophobic staking interactions in
which the planes of their rings parallel
(like a stack of coins)
- The stacking also involves a
combination of van der Waals
and dipole-dipole interactions
between the bases
Base staking:
- Helps to minimize contact of the
bases with water
Is a heterocycylic aromatic organic
- Very important in stabilizing the
compound consisting of a pyrimidine
three-dimensional structure of
ring fused to an imidazole ring
nucleic acids
NUCLEOSIDES
Are derivatives of purines and
pyrimidines that have a sugar linked to
a ring nitrogen of a purine or pyrimidine
Numerals with prime (eg, 2’ or 3’)
Is a heterocyclic aromatic organic distinguishing atoms of the sugar from
compound similar to benzene and those of the heterocycle
pyridine consisting two nitrogen atoms The sugar in ribonucleosides is D-
as position 1&3 of the six-member ring. ribose
The sugar in deoxyribonucleosides is
2-deoxy-D-ribose
DURANGO, FAIRY JEN CHESKA E.
MOLECULAR BIOLOGY
NUCLEOTIDES
PHOSPHORYLATED NUCLEOSIDES
Pyrimidine Synthesis
Biosynthesis of pyrimidine nucleotides
can occur by a de novo pathway or by
the reutilization of preformed
pyrimidine bases or ribonucleosides
(salvage pathway).
The pyrimidine synthesis is a similar
process than that of purine
In the de novo synthesis of
pyrimidines, the ring is synthesized
Ribose-5-phophate (as provided by first and then it is attached to a ribose-
the penose-phosphate pathway) is phosphate to for a pyrimidine
converted into PRPP (Phosphoribosyl nucleotide
pyrophosphate) by PRPP synthetase, in
a step requiring one ATP De Novo Pyrimidine Synthesis
In the committed step in the process,
an alpha-amino group is then added to CO2 and glutamine are combined to
PRPP from glutamine to form 5- from carbamoyl phosphate. This
phosphoribosylamine. This reaction is reaction is catalysed by carbamoyl
Nucleic Acids
Levels of structure
3°Structure: supercoiling
Purine vs Pyrimidine Synthesis
DNA RNA
Molecule is a double Molecule is a single-
Watson and Crick Model of DNA
stranded helix stranded
DNA consists of two helical DNA chains
Sugar is Sugar is ribose
wound around the same axis to form a
deoxyribose
Contains thymine Contains uracil, and right-handed double helix
and no uracil no thymine The hydrophilic backbones of
A=T A =/≠U alternating deoxyribose and phosphate
G=C G =/≠C groups are on the outside of the double
helix, facing the surrounding water.
DNA - 2°Structure The furanose ring of each deoxyribose
Secondary structure: the ordered is in the C-2’ endo conformation.
arrangement of nucleic acid strands The purine and pyrimidine bases of
- The double helix model of DNA 2° both strands are stacked inside the
structure was proposed by James double helix, with their hydrophobic
Watson and Francis crick in 1953 and nearly planar ring structures very
Double helix: a type of 2° structure of close together and perpendicular to the
DNA molecules in which two long axis.
antiparallel polynucleotide strands are
The offset pairing of the two strands relationships it follows that the sum of
creates a major groove and minor the purine residues equals the sum of
groove on the surface of the duplex the pyrimidine residues; that is, A + G
= T + C.
Base Pairing
SAMPLE PROBLEM
B-DNA
Chargaff’s rule
- considered the physiological form
1. The base composition of DNA generally
- a right-handed helix, diameter
varies from one species to another.
11Å
2. DNA specimens isolated from different
- 10 base pairs per turn (34Å) of the
tissues of the same species have the
helix
same base composition.
A-DNA
3. The base composition of DNA in a given
- a right-handed helix, but thicker
species does not change with an
than B-DNA
organism’s age, nutritional state, or
- 11 base pairs per turn of the helix
changing environment.
- has not been found in vivo
4. In all cellular DNAs, regardless of the
Z-DNA
species, the number of adenosine
- a left-handed double helix
residues is equal to the number of
- may play a role in gene expression
thymidine residues (that is, A=T), and
the number of guanosine residues is
equal to the number of cytidine
residues (G=C). From these
DURANGO, FAIRY JEN CHESKA E.
MOLECULAR BIOLOGY
bp/helical
tern 10.5 11 12
Glycosyl Anti (for
bond pyrimidines
conformation Anti Anti ans syn (for
purines
)
Helical/Propeller Twists
Helix rise/bp 3.4 2.6 3.7 Bases that are exposed to minor
groove contact with water
Base tilt 6° 20° 7°
Structure
They twist in a “propeller twist”
fashion
Results in:
- less optimal base pair distance
- More optimal base pair stacking
(eliminates presence of water
molecules)
Comparison of A, B, and Z forms of DNA
both A and B-DNA are right-handed
helices DNA - 3°Structure
Z-DNA is left handed Tertiary structure: the three-
Z-DNA occurs in nature, usually dimensional arrangement of all atoms
consists of alternating purine- of a nucleic acid; commonly referred to
pyrimidine bases as supercoiling
Methylated cytosine found also in Z- Supercoiling: Further coiling and
DNA twisting of DNA helix.
Circular DNA: a type of double-
Other Features of DNA stranded DNA in which the 5’ and 3’
Base stacking ends of each stand are joined by
- bases are hydrophobic (Van der phosphodiester bonds
Waals Forces of their pi-cloud
electrons) and interact by
hydrophobic interactions DNA Topology
- in standard B-DNA, each base
rotated by 32° compared to the
next and, while this is perfect for
maximum base pairing, it is not
optimal for maximum overlap of
bases;
- bases exposed to the minor groove
come in contact with water
DNA Supercoiling
Removal of one turn induces structural Enzymes that affect the supercoiling of
strain DNA
Topoisomerases: enzymes that are
involved in changing the supercoiled
state of DNA
- Class I: cut the phosphodiester
backbone of one strand, pass the
end through, and reseal
- Class II: cut both strands, pass
some of the remaining DNA helix
between the cut strands, and
reseal
The strain is generally accommodated DNA gyrase: a bacterial topoisomerase
by formation of a supercoil
Histones
The carboxyl terminal two-thirds of the
histone molecules are hydrophobic
The amino terminal thirds are
particularly rich in basic amino acids
These four core histones are subject to
at least six types of covalent
modification or posttranslational
modifications (PTMs):
- Acetylation
- Methylation
- Phosphorylation
CHROMATIN - ADP-ribosylation
Chromosomal material in the nuclei of cells - Monoubiquitylation
of eukaryotic organisms - Sumoylation
Chromatin consists of:
Nucleosomes
Denaturation: disruption of 2°
structure
- most commonly by heat
denaturation (melting)
- as strands separate, absorbance at
260 nm increases
- increase is called hyperchromicity
- midpoint of transition (melting)
curve = Tm
- the higher the % G-C, the
higher the Tm
- renaturation is possible on slow
High Order Structure to Provide cooling
Compaction
Electron microscopy of chromatin
reveals two higher orders of structure—
the 10-nm fibril and the 30-nm
chromatin fiber
10-nm fibril: consists of nucleosomes
arranged with their edges separated by
a small distance (30 bp of linker DNA)
with their flat faces parallel to the fibril
axis
mRNA in Transcription
tRNA
miRNA
A microRNA (abbreviated miRNA) is a
small single-stranded non-coding RNA
molecule (containing about 22
nucleotides) found in plants, animals
and some viruses that functions in RNA
silencing and post-transcriptional
regulation of gene expression.
miRNAs function via base-pairing with
complementary sequences within
mRNA molecules.
As a result, these mRNA molecules are
rRNA silenced, by one or more of the
following processes: (1) cleavage of
Ribosomal RNA, rRNA: a ribonucleic the mRNA strand into two pieces, (2)
acid found in ribosomes, the site of destabilization of the mRNA through
protein synthesis shortening of its poly(A) tail, and (3)
- only a few types of rRNA exist in less efficient translation of the mRNA
cells into proteins by ribosomes.
- ribosomes consist of 60 to 65%
rRNA and 35 to 40% protein
- in both prokaryotes and
eukaryotes, ribosomes consist of
two subunits, one larger than the
other
- analyzed by analytical
ultracentrifugation
- particles characterized by
sedimentation coefficients,
expressed in Svedberg units (S)
mRNA
Messenger RNA, mRNA: a ribonucleic
acid that carries coded genetic
information from DNA to ribosomes for
the synthesis of proteins
- present in cells in relatively small
amounts and very short-lived
- single stranded
- biosynthesis is directed by
information encoded on DNA
- a complementary strand of mRNA
is synthesized along one strand of
an unwound DNA, starting from
the 3’ end
snRNA