User:RIT RAJARSHI/Books/Molecular Biology (Work in Progress) updated copy

Molecular mechanism of GENE activity

 * 1. ABOUT MOLECULAR BIOLOGY
 * 1.1. the subject
 * Molecular biology


 * 1.2. the features of genetic system
 * Genetic variation
 * Heredity
 * Inheritance


 * 2. CLASSIFICATION OF LIVING FORMS, CELL-STRUCTURE DIVERSITY
 * 2.1. introduction
 * Organism


 * 2.2. those in border of living and nonliving
 * Non-cellular life
 * Prion
 * Viroid
 * Virus
 * Virusoid


 * 2.3.virus-bit more detail
 * Virus classification
 * Baltimore classification


 * 2.4. viroid-bit more detail
 * Pospiviroidae
 * Avsunviroidae


 * 2.5. prion-bit more detail
 * Proteopathy
 * Amyloidosis
 * Neurofibrillary tangle
 * Transmissible spongiform encephalopathy
 * PRNP
 * Amyloid
 * Amyloid beta
 * Amyloid precursor protein
 * Fungal prion


 * 2.6. prokaryotes
 * Prokaryote


 * 2.7. eubacteria
 * Bacteria


 * 2.8. archebacteria
 * Archaea


 * 2.9. eubacteria-bit more details
 * 2.10. archebacteria bit more details
 * Crenarchaeota
 * Euryarchaeota
 * Methanobacteria
 * Methanococci
 * Haloarchaea
 * Thermoplasmata
 * Thermococci
 * Archaeoglobi
 * Methanopyri


 * 2.11. eukaryote
 * Eukaryote


 * 2.12. NOTE 1. Few-cellular eukaryotes=PROTISTA; Other groupings(PROTOZOA,SLIME-MOULDS,FUNGI,ALGAE)are highly INTERMIXED. Blue-Green-algae (=Cyanophyta/ Cyanobacteria)are prokaryotic(Eubacteria)
 * 2.12. Eukaryotes Are Very Similar to Archaebacteria
 * 2.13. endosymbiotic theory OF Origin of some organelles
 * 2.13.1. General features
 * Symbiogenesis
 * Endosymbiont
 * Hydrogen hypothesis


 * 2.13.1. NOTE 1. Present-Day example of FORMATION of intracelluler symbiosis
 * Root nodule


 * 2.13.1. NOTE 2. Some examples of endosymbiosis other than mitochondria and plastid
 * 2.13.2. mitochondria
 * Mitochondrion


 * 2.13.3. plastid
 * Plastid
 * Chloroplast


 * 2.14. protista
 * Protist


 * 2.15. Protozoa
 * Protozoa


 * 2.16. Animals
 * Animal


 * 2.17. slime moulds
 * Slime mold


 * 2.18. fungi
 * Fungus


 * 2.19. algae
 * Algae


 * 2.20. plants
 * Plant


 * 2.21. classification ... eukaryotes
 * Bikont
 * Plants+HC+SAR megagroup
 * Plants+HC clade
 * Archaeplastida
 * Glaucophyte
 * Red algae
 * Viridiplantae
 * Prasinophyceae
 * Charophyta
 * Charales
 * Hacrobia
 * Haptophyte
 * Cryptomonad
 * Centrohelid
 * Telonemia
 * SAR supergroup
 * Halvaria
 * Heterokont
 * Ochrophyta
 * Bigyra
 * Pseudofungi
 * Alveolate
 * Ciliate
 * Myzozoa
 * Apicomplexa
 * Dinoflagellate
 * Rhizaria
 * Cercozoa
 * Retaria
 * Foraminifera
 * Radiolaria
 * Excavate
 * Euglenozoa
 * Percolozoa
 * Loukozoa
 * Collodictyon
 * Diphylleia rotans
 * Jakobid
 * Metamonad
 * Malawimonas
 * Unikont
 * Apusomonadida
 * Apusomonas
 * Amastigomonas
 * Apusozoa
 * Ancyromonas
 * Spironemidae
 * Amoebozoa
 * Lobosea
 * Conosa
 * Phalansterium
 * Breviata
 * Opisthokont
 * Holozoa
 * Mesomycetozoea
 * Dermocystida
 * Ichthyophonida
 * Filozoa
 * Filasterea
 * Capsaspora
 * Ministeria vibrans
 * Choanoflagellate
 * Codonosigidae
 * Salpingoecidae
 * Acanthoecidae
 * Eumetazoa
 * Bilateria
 * Cnidaria
 * Ctenophora
 * Mesozoa
 * Dicyemida
 * Orthonectida
 * Parazoa
 * Placozoa
 * Sponge
 * Holomycota
 * Dikarya
 * Ascomycota
 * Basidiomycota
 * Glomeromycota
 * Zygomycota
 * Blastocladiomycota
 * Chytridiomycota
 * Neocallimastigomycota
 * Microsporidia
 * Rozellida
 * Nucleariid
 * Nuclearia
 * Micronuclearia
 * Rabdiophrys
 * Pinaciophora
 * Pompholyxophrys
 * Fonticula
 * Incertae sedis
 * Corallochytrium
 * Kamera lens
 * Picozoa


 * 3. CELL-STRUCTURE ... THE LOCATION OF GENETIC MACHINARY IN CELLS
 * 3.1. general topics
 * Cell (biology)


 * 3.2. prokaryotic cell
 * 3.2. nucleoid
 * Nucleoid


 * 3.3 plasmid (prokaryotic)
 * Plasmid
 * Minicircle


 * 3.4. prokaryotic ribosome
 * 3.5. other features in prokaryotes
 * 3.6. eukaryotic cell
 * 3.7. nucleus of cell
 * Cell nucleus


 * Nucleus- structure
 * Nuclear membrane
 * Nuclear pore
 * Nuclear lamina
 * Nuclear matrix
 * Nucleoplasm
 * Nucleolus
 * Nuclear dots
 * Cajal body


 * nucleus- number, placement, shape etc.
 * 3.8. eukaryotic cytoplasmic ribosome
 * 3.9. plastidial DNA
 * 3.10. plastidoribosome
 * 3.11. mitochondrial DNA
 * 3.12. mitochondrial ribosome
 * 3.13. Eukaryotic plasmid
 * 3.14. organellar & nuclear genome : HORIZONTAL GENE TRANSFER IN ORGANELLAR ENDOSYMBIOSIS
 * Numt


 * 3.14. NOTE 1.See also: Horizontal Gene Transfer (any organism), Inter-species gene transfer, Vertical gene transfer, Transformation, Conjugation, Transformation, Agrobacterium-mediated gene-transfer
 * 3.15. See Also: 3-Genomes in eukaryotic cells, Jumping-Genes, Transposition
 * 4. BIOCHEMISTRY OF SMALL COMPOUNDS FOR GENETIC MACHINARY
 * 4.1. Alkaloids & Biological Nitrogenous Bases
 * Amine
 * Imine
 * Ammonium
 * Iminium
 * Chemical classification
 * Alkaloid
 * Heterocyclic amine
 * Biogenic amine
 * B vitamins
 * Pyrrolidine
 * Pyrrole
 * Imidazole
 * Piperidine
 * Pyridine
 * Pyrimidine
 * Pyrazine
 * Pyrrolizidine
 * Quinolizidine
 * Quinoline
 * Isoquinoline
 * Pteridine
 * Indolizidine
 * Indole
 * Purine
 * Phenanthrene
 * Aporphine
 * Morphinan
 * Quinuclidine
 * Tropane
 * Pseudopelletierine
 * Anatoxin-a
 * Nucleobase


 * 4.2. amino acids
 * Amide
 * Amino acid
 * Proteinogenic amino acid
 * Non-proteinogenic amino acids


 * Standard-20-aminoacid
 * Glycine
 * Alanine
 * Valine
 * Leucine
 * Isoleucine
 * Serine
 * Threonine
 * Tyrosine
 * Cysteine
 * Methionine
 * Aspartic acid
 * Asparagine
 * Glutamic acid
 * Glutamine
 * Arginine
 * Lysine
 * Histidine
 * Tryptophan
 * Phenylalanine
 * Proline


 * Special aminoacids found in protein
 * Selenocysteine
 * Pyrrolysine


 * Non-protein amino acids and related compound
 * Urea
 * Acylurea
 * Ornithine
 * Citrulline


 * 4.3. Sugars
 * 4.4. glycosidic linkage
 * 4.5. phosphates
 * 4.6. nucleic acid components
 * Nucleotide


 * 4.7. nucleic acid structure
 * Nucleic acid
 * RNA
 * DNA


 * 4.8. protein structure
 * 4.9. proteins as enzyme. different other works for protein
 * 4.10. Nucleic Acids as Enzyme
 * Ribozyme
 * Deoxyribozyme


 * 4.11. Nucleotide Metabolism
 * Nucleotide salvage


 * 4.12. Amino Acid Metabolism
 * 5. SEQUENTIAL PATTERNS OF BIOMOLUCULES OF GENETIC MACHINARY
 * sequence and pattern-overall
 * Polymer
 * Monomer
 * Polymer architecture
 * Copolymer
 * Cross-link
 * Polymerization
 * Addition polymer
 * Condensation polymer
 * Biopolymer
 * Sequence (biology)
 * Nucleic acid sequence
 * Peptide sequence
 * Directionality (molecular biology)
 * Antiparallel (biochemistry)
 * Complementarity (molecular biology)
 * Base pair
 * Direct repeat
 * Inverted repeat
 * Palindromic sequence
 * Conserved sequence


 * sequence and patterns - DNA
 * Complementary DNA
 * Repeated sequence (DNA)


 * sequence and patterns - RNA
 * Antisense RNA


 * 6. DIFFERENT TYPES OF NUCLEIC ACID
 * Different type of DNA
 * Gene
 * Intergenic region
 * Exon
 * Intron
 * Cistron
 * Operon
 * Structural gene
 * Regulator gene
 * Regulatory sequence
 * Pseudogene
 * Noncoding DNA
 * Tandem repeat
 * Satellite DNA
 * Centromere
 * Centric heterochromatin
 * Beta satellite
 * Minisatellite
 * Microsatellite
 * Selfish DNA
 * Transposable element
 * Simple transposon
 * Conservative transposition
 * Replicative transposition
 * Insertion sequence
 * Composite transposon
 * Tn3 transposon
 * Tn10
 * P element
 * Ac/Ds Activator/Dissociation Transposable Element
 * Retrotransposon
 * Long terminal repeat
 * Long interspersed nuclear element
 * Interspersed repeat
 * CRISPR
 * Secondary constriction
 * Nucleolus organizer region
 * Telomere
 * Euchromatin
 * Heterochromatin


 * Different type of RNA
 * MicroRNA
 * Small interfering RNA
 * Small nuclear RNA
 * Small nucleolar RNA
 * Molecular genetics
 * Small conditional RNA
 * Transfer-messenger RNA
 * Non-coding RNA
 * Long non-coding RNA
 * Guide RNA
 * Transfer RNA
 * Piwi-interacting RNA
 * Telomerase RNA component
 * Messenger RNA
 * Ribosomal RNA


 * 7. CENTRAL DOGMA AND RELATED PROCESS
 * 8. ENZYMOLOGY OF CENTRAL DOGMA AND RELATED PROCESS
 * Protein Motifs
 * DNA-binding domain
 * Zinc finger
 * Leucine zipper
 * Helix-turn-helix
 * Basic helix-loop-helix
 * DNA clamp
 * Rossmann fold


 * Enzymes and Enzyme Complex
 * Ligase chain reaction
 * DNA polymerase
 * Polymerase chain reaction
 * DNA ligase
 * Ribonuclease


 * 9. TOPOLOGY OF CENTARL DOGMA, AND TOPOLOGICAL ENZYMES
 * Tus (biology)
 * Ter protein


 * 10. CELL DIVISION
 * 11. GENE EXPRESSION AND REGULATION- PART 1
 * 12. DETERMINATION OF SEX
 * 13. BIOMOLECULAR SYSTEMS- THE OMICS APPROACH
 * 13. GENE AND PROTEIN FAMILIES
 * 13.1. types of homology : ORTHOLOGS & PARALOGS
 * Homology (biology)
 * Protein isoform


 * 14. GENE EXPRESSION AND REGULATION-PART 2 : BIOSIGNALING
 * 14.1. general discussion
 * Cell signaling
 * Signal transduction


 * 14.2. Components
 * Regulatory machines
 * Regulatory enzyme


 * Receptors
 * Receptor (biochemistry)
 * Cell surface receptor
 * Nuclear receptor
 * Immune receptor


 * first messenger
 * Ligand (biochemistry)


 * synthesiis of first messengers - 1
 * transport of first messengers
 * Juxtacrine signalling
 * Paracrine signalling
 * Autocrine signalling
 * Endocrine system
 * Intracrine
 * Gap junction
 * Connexon
 * Ephaptic coupling
 * Electrical synapse
 * Chemical synapse
 * Hormone
 * Neurotransmitter
 * Neurohormone


 * Second messenger
 * (first-second-messenger, second-second-messenger, third-second-messenger erc).
 * Not "third messenger"
 * Second messenger system


 * 14.3. Mechanisms
 * Proteolysis
 * Phosphorylation
 * Protein kinase
 * Dephosphorylation
 * Protein phosphatase
 * Allosteric regulation
 * Allosteric enzyme
 * Allosteric modulator


 * 14.4. More details about receptor & other components
 * G protein–coupled receptor
 * G protein
 * GTPase
 * Small GTPase
 * GTPase-activating protein
 * GTP-binding protein regulators
 * Arrestin
 * Heterotrimeric G protein
 * G alpha subunit
 * G beta-gamma complex
 * Regulator of G protein signaling
 * Hedgehog signaling pathway
 * Wnt signaling pathway
 * Patched
 * Smoothened
 * Enzyme-linked receptor
 * Receptor tyrosine kinase
 * Tyrosine kinase
 * Receptor tyrosine phosphatase
 * Protein tyrosine phosphatase
 * Cytokine receptor
 * Cytokine
 * JAK-STAT signaling pathway
 * Janus kinase
 * STAT protein
 * Receptor protein serine/threonine kinase
 * Serine/threonine-specific protein kinase
 * Guanylyl cyclase
 * Guanylate cyclase-coupled receptor
 * Biological functions of nitric oxide
 * Nitric oxide
 * Histidine kinase
 * Two-component regulatory system
 * Mitogen-activated protein kinase
 * MAPK/ERK pathway
 * Tumor necrosis factor receptor
 * Tumor necrosis factors
 * Toll-like receptor
 * Lipid signaling
 * Phosphoinositide phospholipase C
 * Phospholipase C
 * Phosphoinositide 3-kinase
 * Diglyceride
 * Inositol trisphosphate
 * Inositol trisphosphate receptor
 * Ceramide
 * Sphingomyelin
 * Ceramide kinase
 * Sphingosine-1-phosphate
 * Ganglioside
 * Notch signaling pathway
 * Notch proteins
 * Delta-like 1


 * 15. MOLECULAR APPROACH IN DEVELOPMENTAL BIOLOGY
 * new entries
 * Ribosome
 * G banding
 * Cis-natural antisense transcript
 * Argonaute
 * Evolution of sexual reproduction
 * Expressed sequence tag
 * Cross-species transmission
 * DNA replication
 * Sequencing
 * Transcription (genetics)
 * Mollicutes
 * Viral evolution
 * Cohesin
 * XIST (gene)