Nucleotides: Structure, Function, and Applications

The Central Dogma

• Genetic information transfers from DNA to RNA via transcription, then from RNA to protein via translation.
• This flow is vital for protein synthesis, which is essential for the structure and function of organisms.

Summary Of The Process

• DNA carries hereditary information in cells.
• Transcription is the process in which information from DNA is transcribed into RNA, occurring in the cell nucleus.
• RNA is a messenger carrying genetic information from DNA to the site of protein synthesis.
• Translation process: RNA information is used to build a protein at the ribosomes of the cell.
• Proteins are synthesized through translation and are essential for the structure and function of cells, tissues, and organisms.

Nucleic Acids

• Nucleosides consist of a nitrogenous base and a pentose sugar connected by an N-glycosidic bond.
• Nucleotides are nucleosides with one or more phosphate groups attached via an ester bond.
• Nitrogenous bases include purines (guanine and adenine) and pyrimidines (cytosine, uracil, and thymine).
• In RNA, the sugar is D-ribose, while in DNA, it's 2'-deoxy-D-ribose.
• RNA has a hydroxyl group (OH), while DNA does not have a hydroxyl group (H only).
• Nucleotides function as building blocks of nucleic acids and carriers of activated intermediates.
• They are also structural components of coenzymes and act as second messengers in signal transduction pathways.

History

• Erwin Chargaff discovered that the amount of purines equals the amount of pyrimidines.
• Adenine pairs with thymine via two hydrogen bonds, while guanine pairs with cytosine via three hydrogen bonds.
• Rosalind Franklin produced X-ray crystallography images of DNA.
• James Watson and Francis Crick developed the double-helix model of DNA.

Structure And Properties Of DNA

• DNA consists of nucleotides held together by 3' to 5' phosphodiester bonds, forming a double helix.
• The two chains are complementary, antiparallel, and hydrogen-bonded through the bases.
• The double helix is usually right-handed with 10.5 base pairs per turn.
• Bases project inward within the structure to be safely bonded together.

DNA Forms

• A-DNA occurs in low humidity and high salt conditions, is right-handed, and has 11 base pairs per turn.
• B-DNA is the most common form, is right-handed, and has 10 base pairs per turn.
• Z-DNA is found in areas with consecutive GCGCGC sequences, is left-handed, and has 12 base pairs per turn.

Levels Of DNA Organization

• Begins with the 2 nm DNA double helix.
• This coils around a histone octamer to form a 10 nm chromatin fibril.
• The nucleosomes are separated by linker DNA, with the DNA wrapping 1.75 times around each histone octamer
• Nucleosomes group together to form a 30 nm chromatin fibril (Solenoid).
• DNA is further organized into a supercoiled structure to save space.
• Condensation of DNA during prophase of mitosis leads to the formation of chromosomes, with 23 pairs (46 total) in humans.

Base Stacking

• Bases resemble a staircase due to hydrophobic interactions and van der Waals forces.
• Hydrophobic interactions cause bases to cluster inside.
• The forces maintain structural integrity by stabilizing the close packing of bases along the helical axis.

Grooves

• Minor grooves have backbones closer together, while major grooves have backbones wider apart.
• Grooves are important sites for DNA and protein interactions.

Heterochromatin vs. Euchromatin

• Heterochromatin: condensed, sterically inaccessible, transcriptionally inactive, and increased methylation, decreased acetylation.
• Euchromatin: less condensed, sterically accessible, transcriptionally active, decreased methylation, increased acetylation.

Nucleic Acids

• Similar to DNA with purine and pyrimidine bases (although they have a Uracil instead of a Thymine).
• Functions depend on the type and can be coding or non-coding.

Messenger RNA (mRNA)

• Most heterogeneous RNA, comprising 5% of total RNA.
• Carries information from DNA to ribosomes for protein synthesis.
• Contains a methylguanosine cap at the 5' end and a poly(A) tail at the 3' end in eukaryotes.
• The cap guides the ribosome, and the tail provides protection.
• Primary transcript undergoes splicing prior to protein synthesis, where exons are retained.

Ribosomal RNA (rRNA)

• Most abundant RNA, making up 80% of total RNA and contains many loops and base pairing.
• Molecules differ in sedimentation coefficients:
  • Prokaryotes: 50S and 30S subunits, with 16S, 23S, and 5S RNA types.
  • Eukaryotes: 60S and 40S subunits, with 18S, 28S, 5S, and 5.8S cytosolic rRNA types.

Transfer RNA (tRNA)

• Smallest RNA (15% of total RNA) consisting of 74 to 95 nucleotides with high % of unusual bases
• Adapter molecules translate nucleotide sequences of mRNA into specific amino acids.
• Contains at least 20 different species, with one tRNA for each amino acid.
• Anticodon connects a codon to a corresponding amino acid or a stop codon.
• Cloverleaf appearance in 2D, with an acceptor arm terminating in -CCA for amino acid binding.

Small Nuclear RNA (snRNA)

• Functions in mRNA and rRNA processing to splice together exons to form the mature mRNA.

Micro-RNA (miRNA)

• Can interfere with the 3' untranslated region of mRNA inducing mRNA degradation and translational repression.

Long Non-Coding RNA (lncRNA)

• Non-coding transcripts of >200 nt and is involved in regulation of cell differentiation & development, and maintenance of telomere length (TERC and TERRA)
• TERC acts as a template for the synthesis of telomeres.
• TERRA is the RNA component of telomeres.

Silencing RNA (siRNA)

• Double-stranded RNA (20-24 bp) that interferes with gene expression by inducing mRNA degradation.

Sugar

• DNA contains deoxyribose; RNA contains ribose.
• DNA has adenine and guanine as purines; RNA also shares these.
• DNA uses cytosine and thymine as pyrimidines; RNA uses cytosine and uracil.
• DNA is double-stranded and follows Chargaff's rule; RNA is single-stranded and does not follow the rule.
• DNA is stable and is not hydrolyzed by alkali due to the absence of a 2' hydroxyl group.
• RNA unstable as it can be hydrolyzed by alkali to 2',3'-cyclic diesters of mononucleotides.

Proteins

• Linear polymers of amino acids linked together by polypeptide bonds including N-CX-COOH
• Most diverse molecules in living systems.

Amino Acid Side Chains

• Classified into groups based on their structures:
  • Nonpolar: alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, tryptophan, glycine, cysteine.
  • Acidic: aspartic acid, glutamic acid.
  • Basic: lysine, arginine, histidine.
  • Uncharged Polar: asparagine, glutamine, serine, threonine, tyrosine.
• Disulfide bonds can form between two cysteine side chains.
• Glycine & Proline can affect the protein structure
• Cysteine can form disulfide bonds because they contain sulfur.
• Oxytocin is the smallest AA
• Protein sequence is determined by removing one AA at a time

Protein Functions

• Regulate metabolism, facilitate muscle contraction, provide structural framework, and shuttle molecules.
• Are components of the immune system

Primary Structure

• Determined by the AA sequence
• Peptide bonds attach to form a carbonyl group
• Partial double-bond character, TRANS - configuration
• Can be disrupted by hydrolysis

Secondary Structure

• Involves folding short segments of polypeptide into ordered units, stabilized by hydrogen bonds.
• Motifs: supersecondary structures produced by the packing of side chains from adjacent secondary structural elements.
• Alpha Helix: spiral with polypeptide backbone core and side chains extending outward to form Keratin & Hemoglobin
• Beta Sheet: AA residues form zigzags or a pleated pattern with R groups projecting towards the residues
• Stabilized by hydrogen bonds.
• Alpha Helix has ~3.6 AAs per turn
• BETA SHEETS have R groups of adjacent residues that project in opposite directions and parallel or antiparallel

Tertiary Structure

• Involves overall 3D shape by chain interactions
• Folded Polypeptide stabilized by hydrophobic clustering force,
• Unfolded polypeptide: Disulfide bridges (Cysteine)
• Unfolded polypeptide: Hydrogen bonds (between polar side chains)
• Unfolded polypeptide: lonic interactions (charged side chains)
• Unfolded polypeptide: van der Waals forces (to avoid overlapping)

Quaternary Structure

• Exists when 2 or more polypeptide chains form one macromolecule.
• Not all proteins have a corresponding quaternary structure.
• Molecular chaperones assist in protein folding.

Protein Folding

• Requires the correct AA sequence and the Proteins fold into a conformation of LOWEST ENERGY
• Most proteins fold to a single stable conformation
• Molecular chaperones hasten the process but are not the determinants of the final structure
• A molecular chaperone speeds up the folding of the molecule

Clinical Correlate: Sickle Cell Disease:

• Is the result of the Homozygous recessive disorder
• Causes polymerization and reduced solubility of the deoxy form of Hb in conditions of low oxygen tension
• Point Mutation (missense) in both the genes in which it occurs
• Abundant HbS than normal in the body
• Occurs in the blood stream after HbS lowers the 02 afffinity
• Changes from a Glu Val at carbon position 6

Explore the multifaceted roles of nucleotides beyond DNA and RNA. Learn how nucleotides function as energy carriers, signaling molecules, metabolic regulators, and therapeutic agents, highlighting their importance in various biological processes and medical treatments.