Nucleic Acids, cAMP, RNA and DNA

• Nucleic acids are large and complex organic molecules.
• Friedrich Miescher discovered nucleic acids in 1871.
• Nucleic acids are present in all living organisms.
• Nucleic acids are present in the nucleus and are acidic i.e. has acidic properties.
• Most organisms store genetic information in DNA; some viruses use RNA.
• Nucleic acids store and transmit information from parent cells to daughter cells, which is used to synthesize proteins.
• Nucleic acids are polymers of nucleotides.
• Nucleic acids store information for cellular reproduction and growth.
• There are two types of nucleic acids which are Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).
• Nucleic acids are polymers consisting of long chains of monomers called nucleotides.
• A nucleotide consists of a nitrogenous base, pentose sugar, and a phosphate group.
• DNA and RNA are long, thread-like polymers made up of a linear array of monomers called nucleotides.
• All nucleotides contain a nitrogen heterocyclic base, a pentose sugar, and a phosphate residue.
• Nitrogenous bases are of two types: Purines and Pyrimidines.
• All nitrogenous bases of nucleic acids are derived from two heterocyclic bases: purine and pyrimidine.
• Purines are Adenine and Guanine.
• Pyrimidines include cytosine, uracil, and thymine.
• Purine bases are nine-membered ring structures which consists of a pyrimidine ring fused to an imidazole ring.
• The atoms of the purine rings are numbered in an anticlockwise manner.
• Major bases in nucleic acids are Adenine & Guanine
• Adenine, or 6-amino purine has an amino group at the 6th position.
• Guanine, or 2-amino 6-oxypurine, has an amino group at the 2nd position and oxygen at the 6th position.
• Cytosine is found in both RNA & DNA.
• Cytosine, or 2-oxy, 4-amino pyrimidine, has oxygen at position 2 & amino group at position 4.
• Uracil is found only in RNA.
• Uracil, or 2,6-dioxy-pyrimidine, has oxygens at positions 2 & 4
• Thymine is found in DNA.
• Thymine (methyluracil) has oxygen at positions 2 & 4 and a methyl group at position 5
• DNA & RNA are distinguished on the basis of the pentose sugar they contain.
• DNA contains β-D-2-deoxyribose.
• RNA contains β-D-ribose.
• Ribonucleotides have a 2'-OH group.
• Deoxyribonucleotides have a 2'-H group.
• Nucleosides are present in all types of cells.
• Nucleosides with a phosphoryl group esterified to a hydroxyl group of the sugar are mononucleotides.
• 3'- and 5'-nucleotides are nucleosides with a phosphoryl group on the 3'- or 5'-hydroxyl group of the sugar.
• Ribonucleotides consist of:
  • Adenine = Adenosine monophosphate (AMP)
  • Guanine = Guanosine monophosphate (GMP)
  • Cytosine = Cytidine monophosphate (CMP)
  • Uracil = Uridine monophosphate (UMP)
• Deoxyribonucleotides consist of:
  • Adenine = Deoxyadenosine monophosphate (dAMP)
  • Guanine = Deoxyguanosine monophosphate (dGMP)
  • Cytosine = Deoxycytidine monophosphate (dCMP)
  • Thymine = Deoxythymidine monophosphate (dTMP)
  • Uracil = Deoxyuridine monophosphate (dUMP)
• Phosphate esters of nucleosides are present within nucleotides.
• Nucleotides consist of a nitrogenous base, a pentose sugar, and a phosphate.
• Nucleotide = nucleoside + phosphate
• Esterification occurs at the 5th or 3rd hydroxyl group of the pentose sugar
• Most of the nucleoside phosphates involved in biological function are 5' phosphates.
• 5' AMP is abbreviated as AMP, but 3' variety is written as 3'-AMP.
• Minor bases are often found in DNA & RNA, including 5-methylcytosine, N4-acetylcytosine, N6 methyl adenine, N6 dimethyl adenine & N7 methylguanine.
• The unusual bases in nucleic acids provide specific enzymes recognition.
• Methylcytosine is found in DNA and dihydrouracil found in tRNA.
• Pyrimidine analogs have structural similarities to pyrimidines. They act as inhibitors of enzymes in the metabolism of pyrimidines or interact with nucleic acids.
• 5-fluorouracil: It inhibits the enzyme thymidylate synthase. Is used in the treatment of cancer.

Functions of Nucleotides

• Activated precursors of DNA & RNA.
• ATP - Universal currency of energy.
• Activates intermediates in many biosynthetic pathway.
• Carrier of methyl group as SAM.
• Proteins use GTP for biosynthesis as a source of energy.
• Component of coenzymes: NAD, FAD & CoA.
• Metabolic Regulators as cAMP and cGMP.
• DNA functions as a permanent storage of genetic information.
• DNA controls the synthesis of RNA.
• The sequence of nitrogenous bases in DNA determine the protein development in new cells.
• Some Important Nucleotides are Adenine, Guanine, Cytosine, Uracil and Hypoxanthine derivatives, and also Vitamin and Synthetic derivatives.
• Nucleotides of Adenine include Adenosine triphosphate (ATP), Adenosine diphosphate (ADP), Adenosine monophosphate (AMP), Cyclic adenosine monophosphate (cAMP), Phospho adenosine phospho sulfate (PAPS) and S-adenosyl methionine (SAM).
• ATP is energy currency of cells.
• In mammalian cells, ATP concentration is about 1 mM/L.
• Oxidative phosphorylation of the respiratory chain requires ADP, a high energy compound.
• ATP, ADP, and AMP are allosteric effectors of several enzymes.
• Several hormones affect the action cyclic AMP or CAMP
• Phosphoadenosine phosphosulfate (PAPS) is the donor of sulfate groups in many biosynthetic reactions.
• Adenine nucleotides are constituents of FAD and NAD+,NADP+coenzyme A and vitamin B12 co-enzyme.
• Diadenosine triphosphate and diadenosine polyphosphate are neurotransmitters affecting platelet aggregation and blood pressure.
• Oligoadenylate is a mediator for interferon action.
• ATP is required for protein biosynthesis.
• Cyclic AMP (cAMP) is a major metabolic regulator, which mediates the action of several hormones at the cellular level.
• Adenylate cyclase of cell membrane is activated by the hormone epinephrine, norepinephrine, and glucagon from cAMP from ATP.
• Thyroid hormones may increases the synthesis of adenylate cyclase.
• cAMP is destroyed in tissues by its conversions to AMP by the enzyme phosphodiesterase.
• Intracellular cAMP concentrations are near 1 micromole.
• In the lungs cAMP regulates many functions related to inflammatory cells, and also suppresses immune and inflammatory cell activity.
• GTP and GDP are high energy compounds. They participate in energy-dependent reactions.
• GTP is required for protein biosynthesis.
• Cyclic GMP or cGMP mediates the action of many hormones.
• cGMP is involved in vasodilation and smooth muscle relaxation.
• G-proteins, which requires GTP and GDP, are involved in signal transduction of several bio processes like vision, taste, metabolic regulation, olfaction, and cancer.
• In presence of GMP or Ribozyme RNA is catalytically active.
• Ribozyme action depends on GMP.
• GDP carrier molecule is activated by sugars in mucopolysaccharides biosynthesis.
• IDP and IMP are high energy compounds.
• IMP is an intermediate in purie ribonucleotide synthesis.
• UTP and UDP are high energy compounds.
• UDP is carrier of activated sugars and amino sugars needed for the synthesis of glycogen, glycoportein, gangliosides etc.
• UDP-glucuronate serves as a donor of glucuronide in conjugation reactions, such as the formation of bilirubin diglucuronide and detoxication reactions.
• CTP and CDP are high energy compounds.
• CDP-choline serves as a donor of choline in the biosynthesis of phospholipid.
• CMP-NANA is a donor of NANA in the biosynthesis of gangliosides.
• Cyclic CMP also exist in cells.
• S-adenosyl methionine, which donates methyl groups, is a adenine nucleoside in the biosynthesis reactions.
• Some synthetic analogs of purines and pyrimidines such as Mercaptopurine, Thioguanine, 2-Aminopurine , Allopurinol, Azathiopurine, and 5-Flurouracil, are used as anti-cancer agents.

Structure of DNA

• DNA is a polymer of deoxyribonucleotides and consists of Deoxyadenylate (dAMP), Deoxyguanylate (dGMP), Deoxycytidylate (dCMP), and Deoxythymidylate (dTMP).
• The monomeric 3'5'-phosphodiester bonds hold units together as a back bone..
• DNA exists as a Double-Helix.
• Determined by Rosalind Franklin, James Watson, Francis Crick, and Maurice Wilkins.
• Double helical structure was proposed by Watson & Crick in 1953.
• The DNA exists as a right handed double helix.
• DNA consists of two polydeoxyribonucleotide chains that are twisted around each other on a common axis of symmetry.
• Chains are paired in an antiparallel manner i.e. the 5'-end of one strand is paired with the 3'-end of the other strand.
• The two strands are antiparallel; one strand runs in the 5' to 3' direction the other runs in 3' to 5' direction.
• A double helix width or diameter is 20A° (2nm).
• Each turn of the helix is 34 A⁰ (3.4nm) with 10 pairs of nucleotides, and placed ca. 3.4 A°.
• A hydrophilic deoxyribose-phosphate backbone occurs on the outside of the molecule, while the hydrophobic bases are stacked inside.
• The polynucleotide chains are not identical but are complementary to each other via base pairing.
• The two strands are held together by hydrogen bonds: A = T, G = C
• The hydrogen bonds formed between a purine & pyrimidine.
• The helix spatial relationship between two strands, creates a major(wide) and minor(narrow) groove.
• Grooves provide access for regulatory proteins, to bind to specific recognition sequences along the DNA chain.
• DNA helix is proved by Chargaff's.
• Genetic info is found on the template/sense strand..
• The opposite stand is the anti sense strand.
• The two strands of DNA are not identical two strands rather they are are complementary to each other.
• Adenine pairs with thymine through two hydrogen bonds.
• Guanine pairs with cytosine through three hydrogen bonds.
• G-C base pairs are more stable than A-T base pairs.
• Complementary base sequence is the key to account for chargaff's rule.
• It accounts for each DNA strand acting as a template for the synthesis of its complementary strand during DNA replication.
• DNA contains equal numbers of adenine & thymine residues (A=T) and equal number of guanine & cytosine residues (G=C).
• RNAs which are usually single stranded, do not obey because Chargaff's rule.
• DNA doubles are found in 6 forms.
• Forms A, B, and Z are most important.
• The physiological condition for the form B is most predominant.
• A-from is also a right-handed helix with 11 base pairs.
• The base pairs have a tilt which occurs at 20 degrees.
• The Z form is a left helix and is equipped w/ 12 base pairs per helical turn.
• Polynucleotide strands that create DNA move in an zig-zag fashion, called as Z-DNA.
• DNA exists in unusual structures that are important for recognizing DNA, from proteins & enzmyes.
• B form - The most common conformation for DNA.
• A form - common for RNA/different sugar pucker/ deeper less major groove.
• A form is favored in low water conditions.
• Z form - narrow, deep minor groove with hardly existent major groove that is found in alternating DNA required sequences.
• Denaturation of DNA = The phenomenon of loss of helical structure.
• Phosphodiester bonds are not broken by denaturation.
• It is measured at with 260nm absorbance.
• Separation results in disrupting the hydrogen bonds by a pH imbalance or an elevated temperature.
• Defined as the specific temp in which half of the helical shape dies..
• Formamide can destabilizes Hydrogen Bonds
• Tm is greater for with high content of GC.
• This use is very helpful in rDNA Technology.

Renaturation (reannealing)

• Complement DNA separated creates a process where they double helix together.
• RNA is also a polymer of mononucelotides that connect from polynucleotides, and phoshodiester bonds. RNA differs from DNA.
• Much smaller in size & mostly single stranded.
• Has a ribose that differs within DNA.
• Contains pyrimidine uracil, instead of thymine.

Role of RNA:-

• Genetic info is a tool for viruses, and can carries its genetic information. Via RNA-M, tRNA.
• RNA is part of ribosomes/enzymatic activity.
• RNA Structure is a type of sugar phosphate based within ribose.
• 3 types of RNA are 5-10 % messenger, transfer RNA is 10-20, and 50-80 % which are synthesized from DNA, and mRNA.
• Cap is an inverted 7-methyl GTP attached to Messenger RNA.
• Inverted untranslates occur in the 5'utr/5'end, of Messenger RNA with 3 Codons.
• The initiator occurs in the codon, and are a always a part for methionine.
• Specific codons work for acids to connect at the terminators.
• At the 3' end the untranslators connect with (Poly tail A) using (200-300) .
• The transfer is about 71-80 nucleotides at a molecular rate of (25,000). Also at least of 20 tRNAs Species.
• Its unusual types Thymine/hypox/dimethyl.
• tRNA structure is that of a 5' amino acid chain to which molecule connect to at T psi C.
• Anticodon have bonds that connect and bind, as the tRNA connects to a specific acid with 3 ends. The structure is a clovular structure (5/Anticodun.)
• tRNA has short arms that range (3-5bases) and long arms that range (12-20)
• The tRNA is accounted for about 20-30 % of total cellular RNAds,.
• Ribsosomal RNA is often found in ribosomes, because they are factories for proteins.
• Eukaryotic ribosomes have a 60'ssubuinit, with RNA & 40's subunits .
• Ribozyme is a chemical reaction, using ribonucleic acid enzymes to perform molecular biochemical processes that are similar in enzymes, with the unique use of RNA.
• The specific features of the molecule are using RNA, using a substrate. The catalysts association between ribosomes, is used within a transcript, and will synthesize into replication.
• Investigators have learned to produce ribosomes in labs that can catalyze synthesis under high conditioned environments.
• Ribosomes are able to work as therapeutic agents to help with defined sequences,biosensors, genomic function, and find new gene structures.
• There are different structures such as the RNAse P(GroupIntron),and Hammerhead .

Explore the primary functions of nucleic acids, the structural differences between purines and pyrimidines, and cAMP's role in mediating hormone action. Learn about cAMP degradation, structural differences between RNA and DNA, and mRNA's role in gene expression.