Chemistry of Life

Molecular genetics, biochemistry

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Topic themes :
adhesion: · Cadherins · cellular adhesion · cellular adhesion molecules (CAM) · cytokines · focal adhesion kinases · Immunoglobulins · Integrins · Rho GTPases · second messengers · Selectins · signal transduction · two-component systems ·  Cell Adhesion Molecules  Cell signaling  Immune Cytokines  Second Messengers 

chromosomes : abasic site ~ AP site : centromere : chromosome ~ chromatid, chromatin, chromosome : constitutive heterochromatin : DNA : euchromatin : facultative heterochromatin ~heterochromatin : kinetochore : nucleosome : : :

damage/repair DNA : abasic site : DNA ~ DNA RNA ~ DNA damage C to T C to U ~ DNA damage by ROS : DNA repair : double strand breaks : oxidative stress and DNA damage : : : : :

decay : nonsense-mediated decay : nonstop decay : ~ targetted genetic repair ~ : : : : :

enzymes : ~ cofactor : DNA polymerases : oxoG repair : RNA polymerase : AP endonuclease : base excision repair : DNA glycosylase : DNA ligase : DNA polymerases : DNA repair : Fen1

energy :anaplerotic reactionsbeta-oxidationcatabolismchloroplastselectron transfer chainglycolysisglyoxylate cycleKrebs cyclemitochondrionoxidative phosporylation •:


protein : helicases : hOGG1: nucleotide excision repair : oxoG : replication : reverse transcriptase : RNA polymerase : ribozymes : ribozymes in repair of RNA and DNA : : : : :

evolution : allele ~ Basic mechanisms of evolution ~ Biological Evolution ~ Beyond Darwin and Neo-Darwinism ~ Bottleneck ~ Conjugation ~ Conserved & Consensus ~ Deletion
~ Duplication ~ Epistasis ~ Genetic drift ~ Gene flow ~ genome and proteome ~ Founder effect ~ Horizontal Gene Transfer ~ Insertion ~ Inversion ~ Meiosis ~ Mendel's Laws ~ mispairing ~ Modern synthesis ~ Non-disjunction ~ Persistence of functional gene duplicates ~ Phyletic gradualism ~ Population Genetics and Formulae ~ Punctuated equilibria ~ Recombination ~ Speciation ~ Substitution ~ Transduction ~ Transformation ~ Translocation ~

genome : allele : codon : conserved & consensus, consensus sequence : DNA : enhancer : exon : genes : genome : insulator : intron : LINEs ~ long interspersed elements ~ long terminal repeats ~ LTRs : Okazaki fragments : open reading frame ORF : promoters : repressor : response elements : self-splicing : silencers : short interspersed elements ~ silencers ~ SINEs ~ splice-sites : spliceosome : transposable elements :

processing : capping : polyadenylation : pre-mRNA splicing : RNA processing : pre-mRNA splicing : : : : : :

regulation : alternative splicing : epigenetics : gene regulation : nonsense-mediated decay : nonstop decay : response elements : RNA processing : spliceosome : transcription : transcription factors : transcription initiation : termination of transcription

repair : base excision repair : DNA repair : mismatch repair : nucleotide excision repair : oxoG repair : ribozymes in repair of RNA and DNA : SSOs : targetted genetic repair :

RNAs : RNA : mRNA : nuclear speckles : miRNAs : pre-mRNA : tRNA : ribozymes in repair of RNA and DNA : snoRNAs : trans-splicing ribozymes and therapeutics : : :: : :

replication : helicases : meiosis : mitosis

research : Research techniques : Research Articles :
RNAs : RNA : mRNA : nuclear speckles : miRNAs : pre-mRNA : tRNA : ribozymes in repair of RNA and DNA : snoRNAs : trans-splicing ribozymes and therapeutics : : :

signaling :CELL SIGNALINGchemotaxis ~ GPCRsGPCR familieshormonesNitric Oxideneurotransmissionneuronal interconnectionsphosphotransfer-mediated signaling pathwaysProtein Kinase Signaling Networkssignaling gradients • • signal transductiontwo-component systems •~ ERKs ~ MAP Kinase ~ PKA, protein kinase A ~ PKC ~ protein kinase A ~ protein kinase C ~ protein tyrosine kinases ~ PTKs ~ receptor tyrosine kinases ~ Rho GTPases ~ RTKs ~ signaling gradientstwo-component systems • ~ ~

splicing : alternative splicing : cis versus trans-acting factors : epigenetics : pre-mRNA splicing : self-splicing : splice-site : spliceosome : : : :

transcription : basal transcription factors : capping : DNA to mRNA : epigenetics : general transcription factors ~ GTFs : inducible transcription factors : Okazaki fragments : polyadenylation : RNA polymerase : transcription : termination of transcription : upstream transcription factors :

translation : open reading frame ORF : RNA polymerase :


Specific Enzymes/Types : ·· A · adenylyl (adenylate) cyclaseallosteric enzymes · allosteric enzymes · AP endonuclease (Ape1) ·· C · cAMP-dependent protein kinase · cyclin-dependent kinases ·· D · DAGKs · diacyl glycerol kinases · DNA glycosylase · DNA ligase · DNA Ligase I · DNA polymerases · DNA polymerase I · DNA polymerase beta · DNase IV · · E · exonuclease 1 · exosome ·· F · focal adhesion kinases (FAKs) · Fen1 · Flap Endonuclease FEN-1 · G · guanylate cyclases · guanyl cyclase ·· H · hOGG1 · hOGG1 oxoG repair ·· I · inducible transcription factors ·· L · LigIII · · M · MAP kinase · mitogen activated protein kinases · Msh2-Msh3 · MutS, MutL, and MutH ·· O · 8-oxoguanine glycosylase · oxoG repair hOGG1 ·· P · PCNA · phosphatases · phosphodiesterases · phospolipases · phospholipase C-gamma · PLC-G · protein kinase A · protein kinase C · protein tyrosine kinases (PTKs) · receptor tyrosine kinases · R · RNA polymerase · Replication factor C · reverse transcriptase · ribozymes · RNA polymerase II · RTKs ·· S · serine/threonine kinases · spliceosomal-mediated RNA trans-splicing · SMaRT ·· T · trans-splicing ribozymes ·· U · UvrD ·· X · XRCC1 ·

Specific proteins/types : ·· C · cAMP receptor binding protein · cofactor · core histones H2A, H2B, H3, and H4 · CRE-binding protein CREB · cytokines ·· E · elongation factor EF ·· G · general transcription factors ·· H · helicases : Helicase II · heterochromatin · histone · HP1 · I · inducible transcription factors · L · · LexA repressor ·· M · mCAT2 receptor · motor proteins ·· N · nucleosome ·· P · PcG proteins · PCNA · Polycomb group · proteome ·· R · RecA · regulatory proteins · repressor proteins · Receptor Tyrosine Kinases (RTKs) · ribosomes · RPA ·· S · serine rich (SR) splicing factors · silencers · Ski7p · small nuclear ribonucleoproteins (snRNPs) · spliceosome · SR (serine rich) splicing factors ·· T · TATA binding protein · TBP · trans-acting factors · trithorax group (trxG) ·· U · ubiquitin (Ub) · UPF1 UPF2 · upstream transcription factors ·

:~ BIOCHEMISTRY ~ Biochemistry overview ~ amines ~ amino acids ~ amphipathic~ enzyme ~ heterocyclic ~ hydrogen bond ~ hydrophilic ~ hydrophobic ~ peptide~ phospolipid ~ proteins ~ thermochemistry ~ zinc fingers ~

Special Functions : ··· Cellular Adhesion Molecules · cadherins · catenins ·
immunoglobulin superfamily · integrins · selectins · focal adhesion kinases (FAKs) ··· Cellular Stress Response · chaperones · hsp40 · hsp60 · hsp70 · hsp90 · TCP1 · cnp60 · molecular chaperones ··· Chemotaxis ··· Cytokines · TNF · cytokine receptors ··· Protein Degradation · proteasome · ubiquitin (Ub) ···Regulation · cellular differentiation · gene regulation · metabolic regulation ··· Second messengers · cAMP · cGMP · calcium ions ·· DAG · diacylglycerol · IP3 ·
·· Signal Transduction ·· A · AKAPs ·· C · cAMP receptor binding protein · cellular signal transduction · chemotaxis · cytokines . cytokine receptors ·· D · DAG . DAGKs . diacylglycerol . diacyl glycerol kinase ·· E · ERKs ·· F · focal adhesion kinases (FAKs) ·· G · G-proteins · GPCRs · GPCR families · guanylate cyclases · guanyl cyclase ·· H · hormones ·· K · kinases ·· M · MAP kinase · mitogen activated protein kinases ·· N · Nitric Oxide · neurotransmission · neuronal interconnections ·· P · PDZ domain · PKA, protein kinase A · phospholipase C-gamma . PLC-G · phosphorylation · PKC · protein kinase A · protein kinase C · protein tyrosine kinases · phosphotransfer-mediated signaling pathways · Protein Kinase Signaling Networks ·· R · Ras · receptor tyrosine kinases · RTKs ·· S · second messengers · serine/threonine kinases · signaling · signaling gradients · signal transduction · two-component systems · zinc fingers .

 Cell Adhesion Molecules  Cell signaling  Electron Transport Chain vs Oxidative Phosphorylation  Enzymes Function Krebs Cycle  Enzymes Cofactors of Krebs Cycle  Gene Regulation in E.coli  Immune Cytokines  Regulatory Proteins Sequences  Receptor Tyrosine Kinases(RTK)  Second Messengers  Phosphate-handling Enzymes  Second Messengers .

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. . . transcription begun 10/06/06