NUCLEIC ACIDS CHAPTER V : ARTS AND SCIENCES DEPARTMENT

Nucleic Acids: Brief History

●​ Swiss physiologist Friedrich Miescher discovered nucleic acids in 1869 while
studying the nuclei of white blood cells
●​ the fact that they were found in cell nuclei and are acidic accounts for the
term nucleic acids
●​ Cells have ability to produce exact replicas of themselves
●​ Cells contain all instructions needed for making a complete organism
●​ Nucleic acids are biopolymers essential to all forms of life
Nucleotides: Structural Building Blocks for Nucleic Acids
●​ Nucleic acid: unbranched polymer; monomer unit is nucleotide
●​ Nucleotide - three subunit molecule: pentose sugar bonded to both
phosphate group and a nitrogen-containing heterocyclic base
●​ ● Nucleoside - molecule without phosphate group Nucleotides: Structural
Building Blocks for Nucleic Acids Pentose Sugar - Structural difference occurs
at carbon 2’ (deoxy - without oxygen) - Deoxyribose in DNA & Ribose in RNA
Nucleotides: Structural Building Blocks for Nucleic Acids Phosphate Group -
Under cellular pH conditions, the phosphoric acid loses two of its hydrogen
atoms to give a hydrogen phosphate ion HPO4 2- Nitrogen-Containing
Heterocyclic Bases - contain basic amino functional groups (proton acceptors)
Nucleotides: Structural Building Blocks for Nucleic Acids Pyrimidine =
monocyclic base, 6 membered ring Thymine (T), Cytosine (C), Uracil (U)
Purine = bicyclic base w/ fused 5 & 6 membered rings Adenine (A), Guanine
(G) The Nucleoside ● Nitrogenous base ○ Purine bases ○ Pyrimidine bases ●
Sugar ○ Ribose ○ Deoxyribose NUCLEOSIDE FORMATION Nucleoside
Formation ➔ Base attached to C-1 of sugar in β-configuration, N-9 in purine
while N1 for pyrimidine connected through β-N-glycosidic linkage ➔
Condensation reaction occurs as water molecule is formed upon bonding of
base and sugar Nomenclature: ❏ For pyrimidine bases – suffix -idine is used
(cytidine, thymidine, uridine) ❏ For purine bases – suffix -osine is used
(adenosine, guanosine) ❏ Prefix “-deoxy” is used to indicate deoxyribose
present (e.g: deoxythymidine) Nucleoside Formation Nucleosides OF RNA &
DNA RNA DNA * Ribonucleoside *deoxyribonucleoside adenosine
deoxyadenosine guanosine deoxyguanosine cytidine deoxycytidine uridine
deoxythymidine The Nucleotide ● Nitrogenous base ○ Purine bases ○
Pyrimidine bases ● Sugar ○ Ribose ○ Deoxyribose ● Phosphate NUCLEOTIDE
FORMATION Nucleotide Formation ➔ phosphate group is attached to the
sugar at the C-5’ position through a phosphate-ester linkage ➔ Condensation
reaction occurs, overall two water molecules are produced in combing
bonding base, sugar and phosphate Nomenclature: ❏ Nucleotides are named
by appending the term 5' -monophosphate to the name of the nucleoside
from which they are derived. Nucleotide Formation Nucleotide Formation
Some nucleotide that is not part of a chain The Nucleic Acid ● The long chain
of nucleotides ● Long unbranched chain ● Two types ○ RNA ○ DNA A fragment
of DNA/RNA chain Types of Nucleic Acids DEOXYRIBONUCLEIC ACID (DNA):
Primary function is the storage and transfer of genetic information -
Information used to control many cell functions - DNA passed from existing
to new cells during cell division RIBONUCLEIC ACID (RNA): Primary function
is the synthesis of proteins - RNA Occurs in all parts of the cell - Proteins
carry out essential cellular functions Differences DNA and RNA DNA RNA
Location Nucleus, mitochondria, choloroplasts Nucleolus, chromosomes,
cytoplasm Composition pyrimidine bases purine bases sugar acid
Cytosine,thymine Adenine, guanine 2-deoxyribose H3PO4 Cytosine, uracil
Adenine, guanine Ribose H3PO4 Structure Double helix Single stranded
Function for DNA only Molecular repository for all genetic information Primary
➔ The order of the base pairs in a polynucleotide sequence Secondary ➔ Is
the three-dimensional conformation of the backbone Tertiary ➔ The
supercoiling of the molecule Quaternary ➔ the interaction of nucleic acids to
other molecules Levels of Nucleic acid Structure ❖ Primary Nucleic Acid
Structure - sequence in which nucleotides are linked together in nucleic acid
❖ Nucleic acid backbone - alternating sugar-phosphate chain Primary Nucleic
Acid Structure - nonterminal phosphate group of the sugar–phosphate
backbone is bonded to two sugar molecules through a 3’,5’-phosphodiester
linkage - Directionality; 5’ end: free phosphate group, 3’ end free hydroxyl
group - Nonterminal phosphate group has -1 charge; hence give acidic
properties Reading Primary Structure CHARGAFF'S RULE - The concentration
of ADENINE and THYMINE are identical as are the amounts of CYTOSINE and
GUANINE. - A = T and C = G ● The DNA of different species differs in its
proportions ADENINE and GUANINE. ● The base-pairing pattern ( A to T, G to
C ) is the same in all molecules of DNA ● The information encoded by that
sequence is the basis of traits that define species and distinguish individuals.
● VARIATIONS IN ITS NUCLEOTIDE SEQUENCE ARE THE FOUNDATIONS OF
LIFE'S DIVERSITY Secondary Structure - The DNA Double Helix Secondary
Structure ➔ is the base pairing of complementary nucleotides of nucleic acid
Base Pairing ➢ No room for two large purine (overlap), and two pyrimidine
too far apart to hydrogen bond ➢ Complementary Base Pairing - A with T, C
with G, complementary bases that can hydrogen bond, hence amount of A
=T, and amount of C=G ➢ Complementary DNA strand - strands with each
base located opposite to complementary base ➢ Base sequence of DNA
segment written 5’ to 3’ The DNA Double Helix Base Pairing ➢ No room for
two large purine (overlap), and two pyrimidine too far apart to hydrogen
bond ➢ Complementary Base Pairing - A with T, C with G, complementary
bases that can hydrogen bond, hence amount of A =T, and amount of C=G ➢
Complementary DNA strand - strands with each base located opposite to
complementary base ➢ Base sequence of DNA segment written 5’ to 3’ The
DNA Double Helix ● Predict the sequence of bases in DNA strand that is
complementary to the single DNA strand shown. 5’ C-G-T-T-A-T-G-G-C-G-T-A
3’ PRACTICE Hydrogen Bonding Interaction ➢ Stabilizes helix structure,
although weak force number of base pairs result to significant strength Base
Stacking Interactions ➢ Bases positioned parallel with planes of their rings ➢
Stacking interactions as purines and pyrimidines are hydrophobic ➢ DNA
Molecule not neutral, with cellular pH phosphate groups are charged ➢
Strands held by noncovalent interaction Hydrogen bond not by covalent bond
Pi-pi interactions ➢ Happens between the aromatic rings of the bases Factors
that stabilizes the helix Tertiary Structure ➔ is arrangement of atoms in
space which results to a folding that accommodates the steric and geometric
constrains Quaternary Structure ➔ relationship to other molecules Transfer
RNA (tRNA) or soluble RNA ➢ Holds a specific amino acid for incorporation
into a protein molecule ➢ smallest RNA, size range between 73 & 93
nucleotides, average is 75 ➢ structure resembles a warped cloverleaf
Ribosomal RNA (rRNA) ➢ the most abundant RNA, constitutes 80% of the
total RNA(guanylic acid is most abundant) ➢ Combines with protein to form
the ribosome ➢ Nucleoprotein (eukaryotic ribosomes contain 60S & 40S
subunits) ➢ initiates the synthesis of polypeptides in ribosome KINDS OF
RNA (product of DNA transcription) Messenger RNA (mRNA) ➢ Concerned
with the transmission of genetic information from DNA to the site of protein
synthesis ➢ Unstable, short-lived product in the cell (constitutes 5% of
cellular RNA) ➢ * the sequence of nucleotides in mRNA is complimentary to
the sequence of bases in the template DNA. Heterogeneous nuclear RNA
(hRNA) ➢ A precursor of mRNA, found in the nucleus of cell KINDS OF RNA
(product of DNA transcription)