Nucleic Acids & Proteins: Structure & Function - PDF

A Review ON Nucleic acids & Proteins Prelims: MLS 420 JOHN MARKE B. BERNARDO, RMT, MSMT  The Central Dogma of Mol Bio Learning Nucleotides DNA structure and function Points RNA structure and function Protein structure an...

A Review ON Nucleic acids & Proteins Prelims: MLS 420 JOHN MARKE B. BERNARDO, RMT, MSMT  The Central Dogma of Mol Bio Learning Nucleotides DNA structure and function Points RNA structure and function Protein structure and function The Central Dogma Nucleic Acids  Nucleoside Nucleotide Nitrogenous base + Pentose SUGAR NucleoSIDE + PhosphaTe (N-glycosidic linkage) (EsTer bond) PuGA = Purines, Guanine & Adenosine (in DNA and RNA) CUTiePy = Pyrimidines, Cytosine, Uracil (RNA), & Thymine (DNA)  Ribose Deoxyribose D-ribose sugar in RNA 2’-deoxy D-Ribose sugar in DNA  Building blocks of nucleic acids (DNA/RNA) Other functions: Function Carriers of activated intermediates Structural component of coenzymes of Second messengers in signal transduction pathways Nucleotides Principal biologic transducers of free energy Regulatory compounds in pathways Synthetic analogues as drugs Deoxyribonucleic acids (DNA)  History 1. Composition of DNA was known 2. Erwin Chargaff’s experimental finding: Chargaff’s Rule 3. Rosalind Franklin obtained X-ray crystallography images of DNA 4. James Watson and Francis Crick created the two-strand, double-helix model *Recommended watch: “The Secret of Photo 51”  Made up of nucleotides held together by 3’ – to 5’ phosphodiester bonds Consists of 2 chains Structure Complementary & Properties Antiparallel Hydrogen bonded by the bases Right-handed double helix (usually) 10.5 base pairs per turn (usually)  Base Hydrophobic Interactions Stacking Van der Waals forces  A-DNA B-DNA Z-DNA No. of BP per turn 11 10 12 Morphology Broad and short Long and thin Long and thin Screw sense Right-handed Right-handed Left-handed In low humidity and In 5’ end of Features Most common form high salt conditions chromosomes  LEVELS of DNA ORGANIZATION 1 2 nm DNA double helix First level organization of DNA Made of nucleosomes 2 10 nm chromatin fibril separated by linker DNA DNA wrapped 1.75x over a histone octamer (left-handed)  30 nm 3 chromatin fibril (solenoid) 4 Supercoiled structure Promotes packing DNA into compact structures Condensation of DNA during prophase of mitosis 5 Chromosome 23 pairs of chromosomes (46 total) 22 pairs autosomes 1 pair of sex chromosomes HETEROCHROMATI N Condensed, darker on EM Sterically inaccessible Transcriptionally inactive ↑ Methylation, ↓ Acetylation EUCHROMATIN Less condensed, lighter on EM Sterically accessible Transcriptionally active HeteroChromatin = Highly Condensed Euchromatin = Expressed Ribonucleic Acids (RNA)  Similar to DNA with purine and pyrimidine bases Single stranded FUNCTIONS depend on the type and can be: Coding Non-coding  Protein-coding: mRNA “MESSENGER RNA” Most heterogenous RNA (5% of total RNA) mRNAs are magkakaiba mRNA Conveys information from DNA to the translation machinery (ribosomes) Template for protein synthesis mRNA  Protein-coding: mRNA “MESSENGER RNA” In eukaryotes, it has a methylguanosine cap at the 5’ end and a poly(A) tail at the 3’ end mRNA Primary transcript undergoes splicing prior to protein synthesis mRNA  NONProtein-coding: rRNA “Ribosomal RNA” Most abundant RNA (80% of total RNA) Ang rami-raming rRNA! mRNA Contributes to the formation and function of ribosomes mRNA  NONProtein-coding: rRNA Contain many loops and extensive base-pairing Molecules differ in their sedimentation coefficients: Prokaryotes: 50S and 30S subunits, made up of3 types of RNA: 16S, 23S, and 5S mRNA Eukaryotes: 60S and 40S subunits, made up of 4 types of cytosolic rRNA: 18S, 28S, 5S, and 5.8S mRNA  NONProtein-coding: tRNA “Transfer RNA” Smallest RNA (15% of total RNA) Tiny tRNA mRNA Adapter molecules that translate nucleotide sequences of mRNA into specific amino acids mRNA  NONProtein-coding: tRNA 74 to 95 nucleotides with high % of unusual bases At least 20 different species mRNA Contains an anticodon Cloverleaf appearance in 2D (Acceptor arm terminates the nucleotides –CCA and receives the tRNA-appropriate amino acid)mRNA  NONProtein-coding: snRNA “Small nuclear RNA” Functions in mRNA processing and rRNA processing mRNA Splice together the exons to form the mature mRNA mRNA  NONProtein-coding: miRNA “micro-RNA” Interact with the 3’ untranslated region of mRNA mRNA to induce mRNA degradation and translational repression mRNA  NONProtein-coding: siRNA “silencing RNA” Double-stranded RNA (20-24 bp) Interfere with the expression of genes that have complementary nucleotide sequence mRNA to that of siRNA Induces mRNA degradation mRNA  NONProtein-coding: lncRNA “long non-coding RNA” Non-coding transcripts of >200 nt Involved in regulation of mRNA cell differentiation & development, and maintenance of telomere length (TERC and TERRA) mRNA  DNA RNA Sugar moiety Deoxyribose Ribose Purines Adenine & Guanine Pyrimidines Cytosine & Thymine Cytosine & Uracil Structure Double-stranded Single-stranded Chargaff’s rule Applies Does NOT apply Unstable Stable Can by hydrolyzed by Not hydrolyzed by alkali Stability alkali to 2’, 3’-cyclic d/t absence of 2’ hydroxyl diesters of the group mononucleotides PROTEINS  Most abundant and functionally diverse molecules in living systems Linear polymers of amino acids N-CX-COOH (X: variable R group) Linked together by peptide bonds  Between 100-1000 AAs in length Protein sequence can be determined by removing one AA at a time (Edman e.g. degradation) OXYTOCIN  Regulate metabolism Facilitate muscle contraction Provide structural framework PROTEIN FUNCTIONS Shuttles molecules in the bloodstream Components of the immune system  STRUCURAL ORGANIZATION OF PROTEINS 1 o PRIMARY STRUCTURE Determined by the AA sequence Has an N (NH3) and a C (COOH) terminus N = eNtry (targeting signals) C = Contain (retention signals) Peptide bonds attach the α–amino group of one to the α–carbonyl group of another Partial double-bond character Trans-configuration Can be disrupted by hydrolysis 2 o Secondary STRUCTURE The folding of short (3-30 residues) segments of polypeptide into geometrically ordered units Stabilized by hydrogen bonds Motifs – supersecondary structures produced by packing of sidechains from adjacent secondary structural elements  ALPHA HELIX Most common secondary structure Spiral with polypeptide backbone core and side chains extending outward ~3.6 AAs per turn  BETA SHEET AA residues form zigzags or a pleated pattern R groups of adjacent residues project in opposite directions Can be parallel or antiparallel 3 o TERTIARY STRUCTURE Overall 3D shape of the protein Stabilized by: Hydrophobic clustering force Disulfide bridges (Cysteine) Hydrogen bonds Ionic interactions van der Waals forces  Protein Folding The AA sequence holds all the info needed Proteins fold into a conformation of lowest energy Most proteins fold to a single Molecular chaperones assist in protein folding but stable conformation are NOT the determinants of the final structure 4 o QUATERNARY STRUCTURE 2 or more polypeptide chains forming one macromolecule Not all proteins have a corresponding quaternary structure Hemoglobin Clinical Correlate: Sickle Cell Disease  Due to a point mutation (missense) in both genes coding for the β-chain Change from a Glu  Val at position 6 Homozygous recessive disorder EFFECTS on RBCs Polymerization and decreased solubility of the deoxy form of Hb in low oxygen tension Distortion of RBC membrane Sickling of RBCs Occlusion of capillaries  Treatments Clinical Hydration Manifestations Analgesics Antibiotics* Anemia Transfusions Tissue anoxia Hydroxyurea L-glutamine Painful crises Crizanlizumab Voxcelotor  A Review ON Nucleic acids & Proteins