Nucleic acids structure & function

NUCLEIC ACIDS - STRUCTURE &
FUNCTION
DR. ANU P. ABHIMANNUE,
ASSISTANT PROFESSOR,
DEPARTMENT OF BIOTECHNOLOGY,
ST. MARY’S COLLEGE, THRISSUR

DISCOVERY – NUCLEIC ACID
• First observed by Frederich Miescher in 1869.
• The isolated crude extract of DNA & RNA was called nuclein.
• He observed the presence of phosphorus and nitrogen, but not sulfur.
DR ANU P. A., ST. MARY'S COLLEGE, THRISSUR.
2
13 August 1844 – 26 August 1895; Swiss
physician and biologist.

Researchers – Structure of DNA
• In 1953, James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin
figured out the structure of DNA.
• Watson, Crick and Wilkins were awarded the Nobel Prize in Medicine in 1962.
3
James Watson: (born April 6, 1928)
American molecular biologist,
geneticist and zoologist
Francis Crick: (8 June 1916 – 28 July 2004), British
molecular biologist, biophysicist, and
neuroscientist.
Maurice Wilkins: (15 Dec 1916
– 5 Oct 2004), New Zealand-
born British physicist &
molecular biologist
Rosalind Elsie Franklin:
25 July 1920 – 16 April
1958, English chemist &
X-ray crystallographer

The most important photo ever taken?
• Photo 51 – Taken by Rosalind
Franklin and Ray Gosling in the
Biophysics Department in 1952.
• This image gave final clue that
enabled others to put together
research from previous two
decades and understand that DNA
was a double helix.
DR ANU P. A., ST. MARY'S COLLEGE, THRISSUR. 4

STRUCTURE
5

STRUCTURE
• Double helix
• 1 complete turn = 34 A°
• Distance between 2 nucleotides = 3.4 A°
• DNA makes a complete turn every 10 residues
• Width of double helix = 20 A°
• Has a minor and major groove (spaces between adjacent turns)
• Runs anti parallel, 5´ 3´ & 3´ 5´
6

DNA - COMPONETS
• Nucleotide is the building block of DNA.
Nucleoside vs. Nucleotide. A nucleoside consists of a nitrogenous base and sugar
but without the phosphate group. A nucleotide consists of a nitrogenous base, a
sugar (ribose or deoxyribose) and one to three phosphate groups.
7

NUCLEOTIDE
1. 5 carbon sugar – deoxy ribose
2. Phosphate esterified at 5´ position
of sugar ring
3. Nitrogen base at 1´ site.

Pentose sugar
9

PHOSPHATE GROUP
• Sugar and phosphate group link by
phosphodiester bond.
• sugar – phosphate - sugar – phosphate
backbone is located outside the molecule
with 2 sets of bases projecting towards the
center.
• Phosphate gives a net negative charge to
DNA molecule

CHEMICAL BONDS
• Ester bond between phosphate and 5′OH of deoxyribose sugar.
• Diester bond between 5′phosphate of one nucleotide to
3′carbon of deoxyribose sugar of next nucleotide.
• Glycosidic bond between deoxyribose sugar at its 1st carbon
and nitrogenous Base.
• Double or triple hydrogen bond between nitrogenous bases.
• The A-T pair forms two hydrogen bonds and C-G pair forms
three.
• Hydrogen bonds can be easily disrupted and permits
the strands to separate for transcription and replication.

NITROGEN BASES : 2 TYPES
PURINES PYRIMIDINES
• Double ring structure
• Heterocyclic aromatic organic compound
• Consists of a pyrimidine ring fused to an
imidazole ring.
• IUPAC Name = 9H-purine.
• Chemical formula = C5H4N4
• Aromatic heterocyclic organic compound.
• Six-membered single ring with two nitrogen
atoms at 1 and 3 (positions).
• IUPAC Name = Pyrimidine.
• Chemical formula = C4H4N2.

COMPLEMENTARY BASE PAIRING
13
• Purine always pairs with pyrimidine and vice versa
• Adenine pairs with Thymine & Guanine pairs with Cytosine
Information about base composition was provided by Erwin
Chargaff.
First parity rule : %A = %T and %G = %C.
Second parity rule: Ratio [C + G] / [A + T] was typically less than
the unity with [C + G] is less abundant.
Chargaff: 11 August 1905 – 20 June
2002; Austro-Hungarian biochemist

FUNCTIONS
• Storage of genetic information
• Replication and inheritance
• Expression of genetic message
14

RNA

COMPONENTS
• Ribonucleic acid (RNA) is comparatively shorter and are single
stranded.
• A ribonucleotide in the RNA chain contains
• Ribose (Pentose Sugar)
• Nitrogenous Bases (A, U, G, And C)
• Phosphate Group.
16

Thymidine is replaced by URACIL in RNA
• Aromatic heterocyclic organic
compound.
• Six-membered single ring with
two nitrogen atoms at 1 and 3
(positions).
• IUPAC Name = Pyrimidine.
• Chemical formula = C4H4N2.

3D STRUCTURE
• Even though RNA is single
stranded, most types of RNA
molecules show extensive intra-
molecular base pairing creating a
three-dimensional structure.

MODIFIED BASES
• The bases and attached sugars in RNA can be modified in numerous
ways as the RNAs mature.
• Pseudouridine (Ψ) - the linkage between uracil and ribose is changed from a
C–N bond to a C–C bond
• Ribothymidine (T) - 5-methyluridine abbreviated as m5U
• Hypoxanthine – has a deaminated adenine base whose nucleoside is
called inosine (I).
19

RNA – CLASSIFICATION
Briefly classified into:
• Coding-RNA
• Non-coding RNA (ncRNA)
20

CODING RNA
• Coding RNA is messenger RNA (mRNA).
• The genetic code from DNA is transformed as the coding sequence of
the mRNA to carry out protein synthesis.
• Immature eukaryotic mRNA is “precursor mRNA (pre-mRNA)” which
later process into mature mRNA.
21

STRUCTURE - mRNA
22

NON CODING RNA
• Ribosomal RNA (rRNA)
• Transfer RNA (tRNA)
• Small nuclear RNAs (snRNA)
• Small nucleolar RNAs (snoRNA)
• MicroRNAs (miRNA)
• Long noncoding RNAs (lncRNA)
23

Ribosomal RNA (rRNA)
• rRNA is the catalytic component of the ribosomes that are basically
nucleoprotein complex.
• Constitutes 80% of total RNA
• DNA encoding rRNA is present as tandem repeats and is called rDNA.
• The part of chromatin containing rDNA is called nucleolar organizer.
24

STRUCTURE - rRNA
• Undergoes secondary folding and produce a sphere like structure
25

rRNA - FRAGMENTS
26

FUNCTION
• Contains ribozymes (28 S rRNA in eukaryotes and 23 S rRNA in
prokaryotes)
• Ribozymes catalyse synthesis of peptide bond between amino acids.
27

TRANSFER RNA
• 10-15% of total RNA
• Family of 60 small sized (75-93 nucleotides long) RNA
• It has 3ˊOH & 5ˊmonophosphate group
• Also known as soluble, supernatant or adaptor RNA
• Undergoes secondary and tertiary folding
28

STRUCTURE
• Holley described the structure of
alanine transfer RNA in 1964
• Inspired by Holley’s discovery,
other scientists proved the
structure to be of clover leaf model
Robert William Holley (January 28, 1922 – February 11,
1993), American biochemist. Nobel Prize in Physiology
or Medicine in 1968

The structure of tRNA resembles clover leaf and
hence known as Clover Leaf Model

Amino acid/acceptor arm
• Contains both 5ˊ and 3 ˊ end
• Unpaired end of the arm has CCA always with –
OH at the tip
• -COOH group of amino acid pairs with –OH group
of adenosine base of CCA, in presence of ATP
forming amino acyl tRNA
• Hence, 3 ˊ end is called carrier end

TΨC ARM
• Site for attachment of ribosome
• 5 base pairs in the stem
• 7 nitrogenous bases in the loop

VARIABLE ARM
• Most variable tRNA
• Classified into class I and class II
• Class I – comprise 75% and has 3-5 bp
• Class II – 13-20 bp long
• Generally, 4 -21 nucleotides
• Function not known

ANTI – CODON ARM
• Opposite to amino acid arm
• Loop contains 7 to 11 unpaired nitrogenous
bases
• 3 bases are complementary to codons on
mRNA molecule and known as wobble base
• Terminal end is known as recognition end.

D ARM
• Has enzyme recognition site that binds
specific amino acid activating enzyme which
catalyses the union of specific amino acid to
tRNA molecules.

FUNCTION
• Key role in protein synthesis. Pick up specific amino acid from
cytoplasm and deliver it to the site of protein synthesis. Attach to
ribosome in accordance with the sequence specified by mRNA.
36

Small nuclear RNAs (snRNA)
• Small nuclear RNAs are always associated with a group of specific proteins to
form the complexes referred to as “small nuclear ribonucleoproteins (snRNP)”
in the nucleus. Their primary function is to process the precursor mRNA (pre-
mRNA).
37

Small nucleolar RNAs (snoRNA)
• Small nucleolar RNAs are components of small nucleolar
ribonucleoproteins (snoRNPs), which are complexes that are
responsible for sequence-specific nucleotide modification.
38

MicroRNAs (miRNA)
• MicroRNAs are small ncRNAs of ~22 nucleotides.
• Mediate post-transcriptional gene silencing through RNA interference (RNAi), where
an effector complex of miRNA and enzymes can target complementary mRNA by
blocking the mRNA from being translated or accelerating its degradation.
• In human, miRNAs are estimated to regulate the translation of >60% of protein-
coding genes.
39

Long noncoding RNAs (lncRNA)
• Long noncoding RNAs are a heterogeneous group of non-coding
transcripts larger than 200 nt in size and make up the largest portion
of the mammalian non-coding transcriptome.
• lncRNAs are essential in many physiological processes.
40

REFERENCES
• Gerald Karp (2010). Cell and molecular biology: concepts and
experiments (6th ed.). John Wiley & sons. ISBN-13 978-0-470-48337-4.
• https://www.livescience.com/37247-dna.html
• https://www.bbc.com/news/health-18041884
• http://molecularwiki.blogspot.com/2016/08/nucleotides.html
• https://openstax.org/books/microbiology/pages/10-3-structure-and-
function-of-rna

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