1. Molecular Biology (Work in Progress) updated copy
     Molecular mechanism of GENE activity  

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)

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

15. MOLECULAR APPROACH IN DEVELOPMENTAL BIOLOGY

new entries

Cross-species transmission

Ribosome

Evolution of sexual reproduction

Expressed sequence tag

DNA replication

Sequencing

Transcription (genetics)

Mollicutes

Viral evolution

Cohesin

Argonaute

Cis-natural antisense transcript

XIST (gene)

Plasmid

Minicircle

G banding

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