General remarks

  1. Enzymes are shown in blue. The "Recommended Names" in the "Enzyme Nomenclature 1984" (Academic Press, Orlando etc.) and its supplements (Eur.J. Biochem. 157,1 (1986) and 179, 489 (1989) are used. Enzymes not listed there are printed in parentheses.
  2. Coenzymes are shown in red, other reaction participants in black.
  3. Color of the arrows shows type of organism in which the reaction was obseved or is likely to occur:
    • general biochemical pathways
    • higher plants
    • animals
    • unicellular organisms + fungi
    Dashed arrows are used for catabolic pathways, continuous lines for anabolic and bidirectional (amphibolic) pathways. Points on both ends of arrows indicate reversibility. An orange arrow alongsite of it shows the preferred direction.
  4. Regulatory effects are shown in orange. Metal ions and similar activators are located next to the reaction arrow, Effactors with a “fast“ regulation of the flow (e. g. by allosteric mechanisms) have a contiuos orange arrow coming from thr side,those with a “slow“ regulation (e.g. induction or repression of the enzyme synthesis) a dashed orange arrow. = increase, = decrease of enzymatic activity. Roman numerals indicate, that that only one of multiple enzyems is regulated this way.Regulators shown in parentheses are effective in only one group or species of organisms.
  5. Compounds enclosed in black lined, sharp edged boxes occur in several places in the chart. Coenzymes or compounds with very simple structures are not in boxes
  6. Boxes with rounded corners are sometimes used in part 2 to indicate enzymes (inactiv in black, active in blue). Protein sequences are abbreviated by
  7. Compound names in orange boxes indicate excretory or end- products of metabolism.
  8. For ionized compounds, the name of the salt is used to correspond with enzyme names. Structural formulas, however, show the free acid or base, since frequently at physiclogical pH different grades of ionization occur simultaneously. Therefore, participation of H+ or OH- is not shown (except in NADH+H+ and NADPH+H+).
  9. Organic phosphate is abbreviated to -P, inorganic phosphate to Pi, pyrophosphate to PPi.
  10. All amino acids can be attached to their respective tRNAs by the appropriate ligases. Some of this reactions are shown here as examples.
  11. Cellular surface membranes, membranes of the endplasmic reticulum, of the Golgi apparatus etc. have approximately the same thickness. For graphical raesons, however, they have been drawn in part 2 with different widths.
  12. While notations for genes are written with small letters (e.g. raf.), the respective gene products (proteins) are written with captalized first letters (e.g. Raf.). Another way of designating them is p 74c-raf, indicating the molecular weight (in kD) and the origin (c = cellular, v = virus).

Abbreviations Used in Complement System

C1..9,B,Dcomplement factors (mostly written in boxes. Activated forms shown in blue)
H,Ifactor C3b and C4b inactivators
C4bpfactor C4 binding protein
C8bpfactor C8 binding protein = HRF (homologous restriction factor)
C1-Inhcomplement factor 1 inhibitor
CR1complement receptor typel
DAFdecay accelerating fact
MCPmembrane cofactor protein
formulabinding to hydroxy- or amino groups at serum or membrane proteins

Abbreviations Used in DNA Metabolism, Transcription, Translation and Receptor Systems

(Many abbreviations are those used by the first authors)
aaamino acid (unspecified). For specified amino acids, see "Genetic Code" (square OP 7- 8).
A,C,G,Tadenosine, cytidine, guanosine, thymidine ribo- or deoxyribo-nucleotides
A-3,5-MP(cyclic) adenosine-3',5'-monophosphate = cAMP
ARSautonomously replicating sequence
bp,kbpbase pair,kilobase pair
CAPproteincatabolite gene activator protein (=CRP)
CBPCAP binding protein
c-Fos,c-Mybnuclear proteins involved in transcriptional regulation (proto-oncogenes)
CREBA-3',5' -MP (cAMP) responsive element binding protein
CTFCAAT-binding transcription factor (mammal.)
DNAdeoxyribonucleic acid
DnaAprotein binding to DNA information of the initiation complex
DnaCprotein asssociated with DNA helicase
eEF1α,flelongation factors (transport of aminoacyl-tRNA to ribosome)
EF-Gelongation factor for translocation
EF-Tu,EF-Tselongation factors for translation
EGFepidermal growth factor
eIF-2,3,4,5,6eukaryotic initiation factors for translation (abbrev. to I2..)
ERendoplasmic reticulum
eRFeukaryotic release factor
fMetN-formylmethionine
Gα i,o,s,PLC,t,kG-proteins
GAPGTPase activating protein
GEFguanyl nucleotide exchange factor
G-3,5-MP(cyclic) guanosine-3',5' -monophosphate = cGMP
HER-2receptorlike protein related to EGFreceptor
5-HETE(5S)-hydroxy(6,8,11,14)-eicosatetraenoic acid
5-HPETE(5S)-hydroperoxy(6,8,11,14)eicosatetraenoic acid
HU proteinstimulation protein for initiation of DNAreplication
IGF-1insulin-like growth factor
kbkilobases (1000 bases)
MAP-2large microtubule-associated protein (brain)
mRNAmessenger ribonucleic acid
MutH, Senzymes for repair of replication errors in DNA synthesis
Nnucleoside(s) (unspecified)
n,n'protein components of primase complex
NBPNLS binding protein
NLSnuclear location signal
NtrB, Cgene activator proteins for nitrogen metabolism
PIIregulatory subunit of NtrB protein
PCNAproliferating cell nuclear antigen (increases processivity of DNA polymerase δ)
PDE1phosphodiesterase 1
PDGFplatelet derived growth factor
RF-I,II,IIIeubacterial release factors
RF-A,RF-Creplication factors (RF-C: ATPase, stimulated by PCNA)
RNAribonucleic acid
rRNAribosomal ribonucleic acid
SSvedberg units (sedimentation rate)
SecA,E,Ypreprotein export system
SecB"chaperone" protein (antifolding activity)
sp1stimulatory protein 1 (transcription factor)
SRFserum responsive factor
ssbsingle strand binding protein
SSRsignal sequence receptor (at ER membrane)
TFI B,Ctranscription factors for RNA polymerase I
TFII A,B,D, ...transcription factors for RNA polymerase II
TFIII A,B,Ctranscription factors for RNA polymerase III
tRNAtransfer ribonucleic acid
U1... 6 = snRNPsmall nuclear ribonucleoprotein particles (mammalian only)
UBFupstream binding factor (to RNA polymeraseI)
UvrA, B, Cenzymes for repair of UV damage to DNA

Abbreviatons Used in Coagulation

(Index a = Activated, Index i = Inhibited)
Proteinases and Preccursors
II/IIafactor II, prothrombin/thrombin
VII/VIIafactor VII, proconvertin/convertin
IX/IXafactor IX, Christmas factor
X/Xafactor X, Stuart-Prower factor
XI/XIafactor XI (=PTA, plasma-thrombin antecedent)
XII/XIIafactor XII, Hageman factor
KKplasma kallikrein (activated PK)
PC/aPCprotein C/ Ca
PKplasma prekallikrein(Fletcher factor)
PLGplasminogen
sctPA/tctPAsingle/ two chain tissue-type plasminogen activator
scuPA/tctPAsingle (=prourokinase)/ two chain urokinase-type plasminogen activator
Proteinase Inhibitors
α1PIα1-proteinase inhibitor
α2APα2-antiplasmin
α2Mα2-macroglobulin
ATIIIantithrombin III
C1-INHcomplement factor 1 inhibitor
HCIIheparin cofactor II
PAI-1,2,3plasminogen activator inhibitor
PCIProtein C inhibitor (=PAI-3)
PN-2protease nexin 2
TFPItissuefactor pathway inhibitor (=EPI,LACI)
Cofactors and Receptors
V/Va/Vaifactor V,proaccelerin
VIII/VIIIa/VIIIaifactor VIII,antihemophilic globulin
BE"binding epitope" on fibrin surface
BS"binding site"
HK/HKihigh mol. weightkininogen (Fitzgerald factor)
HRGPhistidin-rich glycoprotein
PF3plateletfactor 3,platelet microvesicles
PLphospholipid
PS/PSiphospholipid
TFtissue factor (apoprotein), thromboplastin
TMthrombomodulin
TSPthrombospondin
VWFvon-Willebrandfactor (factor VIII related antigen)
Others
XIII/XIIIafactor XIII, fibrin stabilizing factor (subunits in parentheses)
C4BPcomplementfactor 4b binding protein
F1, F2activation peptide (formed by thrombin activation)
FDPfibrin degradation products
fibrin In/IInpolymerized fibrin (soluble)
FPA, FPBfibrinopeptides A,B (generated by thrombin)
PAFplatelet activation factor
Platelet Surface Receptors (Important for Activation of Adhesion)
αV/IIavitronectin receptor
CD9responsible for G-protein mediated activation
GMP140α-granule membran protein exposed
(=PADGEM)on the platelet surface during secretion
GPIa/IIacollagen receptor
GPIb/IXreceptor for von-Willebrand factor
GPIc/IIafibronectin receptor
GPIIb/IIIafibrinogen receptor
GPIIIbactivation signal transducing binding site (formerly:thrombospondin receptor)
GP Vthrombin receptor (split by thrombin)
GP 53Iysosomal membrane protein exposed during activation

Notes for this map

  1. Lipopolysaccharides (IPS) are antigenic determinants. They are used in Kauffmann-White classification of Salmonellae.
  2. Protein A of Staphylococcus aureus binds to the Fc part of antibodies.
  3. M protein is an antigenic determinant. It is used in Lancefield classification of Streptococci.
  4. Attachment of the starting fMet-tRNA or later, of the peptide-loaded tRNA occurs at the high-affinity P-site of the ribosome. The next aminoacid-loaded tRNA attaches to the A-site.
  5. Translation of mRNA is achieved by many ribosomes lined up at the mRNA in polysomes.
  6. Bacteria start translation at AUG, but also at GUG or UUG codons. These are preceded by a ribosome binding site (Shine-Delgarno box, consensus sequence UAAGGAGG)complementary to the 3'-end of the 16 S rRNA.
  7. tRNA and rRNA contain many modified nucleotides.
  8. mRNA turnover is high in bacteria. Its half life is in the range of minutes.
  9. Commonly, termination is effected by an "intrinsic" DNA sequence (GC rich). Alternativeiy, factor scans RNA in 5' to 3' direction with concomitant ATP hydrolysis and terminates transcription when it reaches the RNA polymerase.
  10. In elongation mode, antitermination factors (e.g. NusA) bind to RNA polymerase in order to prevent emature termination.
  11. tRNAs are L-shaped in their tertiary structure. Here, the two-dimensional clover-leaf and a more simplified representation is used.
  12. Ribosome assembly is a sequential process: Some proteins bind at distinct sites of the rRNA and thus create proper binding sites for other ribosomal proteins.
  13. Alternative σ factors recognize different promoter types. E.g., at elevated temperatures, σ32 factor recognizes "heatshock" promoters.
  14. Bacterial genes are usually organized in operons. They are transcribed into polycistronic mRNAs (coding for all the proteins of an operon). The proteins, however, are translated separately.
  15. Bacterial DNA replication is started at a single site (origin). Overlapping replication initiation may take place before the first replication cycle is completed, resulting in many simultaneous replication forks.
  16. All bacterial DNA polymerases exhibit 3'->5' exonuclease activity required for postsynthetic proofreading. In addition, DNA polymerase I exhibits 5'->3' exonuclease activity required in 'nick translation' and for removal of RNA primers from Okazaki fragments.
  17. ATP hydrolysis takes place accompanying the DNA helicase, primase, gyrase reactions, the activation of DNA polymerase III etc.
  18. HU protein stimulates the initiation of DNA replication.
  19. Gyrase / topoisomerase removes superhelical tension generated by DNA unwinding during replication (decatenation).
  20. The activated complement components bind covalently to hydroxy or amino groups of serum or membrane proteins. Many activated C3 or C4 molecules, however, do not bind but simply hydrolyze.
  21. After being attached to receptors, anaphylotoxins C5a and C3a cause inflammatorv responses, vascular permeabilityn changes, smooth muscle contraction, induce phagocytosis or opsonin adherence etc. They are rapidly degraded by arginine carboxypeptidase (serum carboxy-peptidase N).
  22. Binding of one molecule C3b is a prerequisite for starting the amplification loop, which leads to further deposit of C3b
  23. Solubilization of immune complexes and their coating with C3b are prerequisites for their elimination by monocytes / macrophages.
  24. Prevention of immunoprecipitation (formation of soluble immune complexes) also occurs at earlier stages of the classical complement pathway.
  25. Binding of only 1 lgM molecule to the antigen-carrying structure is sufficient foy complement activation. With lgG, a higher concentration is required in order to achieve binding of 2 lgG molecules in close proximity to each other. Thereafter, binding of C1 to the Fc-region of the immunoglobulins occurs.
  26. Antigen-bound C3b may be inactivated to iC3b, which binds to CR3.
  27. The general pattern of enzymatic splitting of immunglobulins is shown. The cleavage sites differ somewhat among lg isotypes.
  28. Typical examples of surface-assocated 0-glycosylated proteins are mucines, LDL-receptor, glycophorin etc.
  29. Secretion is either constitutive (in all cells) or is regulated by extracellular signals (in secretory cells).
  30. The mannose 6-P receptor recognizes mannose 6-P containing glycoproteins and transports them to lysosomes. The receptor returns to the Golgi network.
  31. The Golgi apparatus consists of stacks of compartments (cisternae / dictyosomes), which are functionally different. Transport between them is performed by vesicles.
  32. The mechanism in mammals is shown. In yeast and green plants, mannose is the first sugar being attached to the serine or threonine moieties of the protein. This takes place in the endoplasmic reticulum.
  33. The SRP (signal recognition particle) attaches to the ribosome possibly at the A site. The subunit SRP 54 binds to the signal peptide.
  34. Binding of SRP to the ribosome stops translation until SRP becomes attached to its receptor at the membrane of the endoplasmic reticulum.
  35. The reactions shown are those for a single-pass protein with an extracellular C terminus. By other mechanisms, extracellular N termini, multiple pass proteins etc. are formed. The signal peptide is split off by a specific signal peptidase. Proteins may also be transferred to glycolipid anchors (see at left).
  36. The transmembrane portion of the proteins usually assumes the configuration of an -helix, symbolized by a cylinder.
  37. The procedure shown is the glycosylation at asparagine residues. These proteins might additionally be glycosylized at serine or threonine residues.
  38. Puromycin causes premature chain termination by acting as an analogue of aminoacyl-tRNA.
  39. eEF1 transports and positions aminoacyl-tRNA to the ribosome and corresponds to a combination of prokaryotic factors EF-Tu and EF-Ts.
  40. Only ribosomes synthesizing membrane- bound or secreted proteins become attached to the endoplasmic reticulum.
  41. Factor eIF3 (abbreviated to I3) prevents reassociation of ribosomes in the absence of an initiation complex and finds the AUG triplet closest to the 5'end. eIF4A is an ATPdriven factor searching for AUG. eIF5 induces release of eIF3 and eIF4 after the pairing at AUG by triggering hydrolysis of GTP bound to eIF2.
  42. Initiation of eukaryotes starts mostly at the first AUG codon with Met-tRNA (contrary to fMet-tRNA in prokaryotes).
  43. The poly-A tail is shortened in the cytoplasm.
  44. The situation in mammals is shown. In addition, several minor snRNPs (U7...U14) with a variety of functions are present.
  45. U1 snRNP binds to the 5' splice site.
  46. Some mRNAs without poly(A)-tails, e.g., histone mRNAs, can also be effective templates for protein synthesis.
  47. Termination of transcription occurs at 0.5 ...2 kb distance beyond the polyA site (polyadenylation signal). No conserved termination regions have yet been identified.
  48. RNA polymerase II also transcribes genes for many small proteins, such as snRNA 1...5.
  49. Enhancers can be located in either orientation within genes, upstream or downstream up to several kb distance.
  50. Not all genes have TATA-boxes. Transcriotion of these genes is regulated by factors like Sp I (mammalian).
  51. Eukaryotic tRNAs contain a large variety of modified (e.g., methylated) nucleotides for fine-tuning of activity, fidelity and stability (cf. prokaryotic tRNA).
  52. RNA polymerase III also transcribes genes for various other small RNAs (5 S RNA, snRNA 6 etc.).
  53. Export of ribosomal subunits takes place through nuclear pores resembling those used for protein import.
  54. 5S rRNA is only exported when bound to TF IIIA or ribosomal protein L5.
  55. In each ribosome, about 100 nucleotides are methylated at 2'-OH of ribose and more than 100 uridines isomerize to pseudo-uridines (cf. square 04).
  56. TF-IIIA binds to an internal control region (ICR) of the 5S RNA gene(s).
  57. In the nucleolus, genes for 28 S, 18 S and 5.8 S rRNA are clustered and tandemly repeated.
  58. Other types of DNA damage repair in mammalian cells are base excision, reversal of alkylation etc. Similar mechanisms exist in bacteria.
  59. Reverse transcriptase is a multifunctional enzyme, containing RNA- and DNA-directed DNA polymerase and RNase H activities.
  60. Retroviral DNA is transcribed only when integrated in the host genome.
  61. A nucleosome contains 200 base pairs of DNA (of which 146 base pairs form 1 ⅔ lefthanded turns) and 2 molecules each of histones H2A, H2B, H3 and H4 (core). Histone H1 is bound to the outside of the core and also to the 'linker DNA' between the nucleosome cores. Structures of higher order are looped solenoids and nucleosome helices.
  62. After uncoating of the SV 40 virus, T antigen is being expressed. The virus replication depends on it. It recognizes the origin, has helicase activity and enhances transcription. 'Late genes' (especially for structure proteins) are being expressed simultaneously to DNA replication.
  63. DNA topoisomerase II is also required for segregation of daughter molecules and is a nuclear scaffolding protein.
  64. During DNA replication, the nuclear membrane is dissolved. Up to 100 replication forks are operating simultaneously on a mammalian chromosome during S-phase of the cell cycle.
  65. At least 100... 200 function of yeast ARS (autonomously replicating sequences).
  66. The graph shows only the most important factors in a schematized way.
  67. DNA polymerase γ is responsible for replication of mitochondrial DNA.
  68. Replication factor RF-C is an ATPase. It is stimulated by PCNA and influences DNA polymerases α and δ.
  69. The genetic information for immunoglobulins is modified twice before the translation step takes place: by somatic recombination at the DNA level and by different ways of RNA splicing.
  70. Damage of the endothelial cell layer, exposing a surface ('subendothelial matrix'), allows binding and activation of the contact factors. The activating surface consists mostly of negatively charged sulfated carbohydrates.
  71. These complexes are short lived and represent an intermediate state.
  72. The mechanism of autoactivation is not fully elucidated yet.
  73. The protease nexin-2 is present in plasma or on the surface of modulated platelets. It inhibits XIa strongly.
  74. Factor fI-XIIa (XIIf) cannot bind to surfaces and has another reactivity than α-XIIa.
  75. The activation of factor XII by α-XIIa or KK proceeds by identical reactions, KK being much more reactive. The repciprocal activation of XII by KK and of PK by α-XIIa is the main reaction at the onset of contact activation.
  76. The "binding site" at the surface of cellular membranes is composed of negatively charged phospholipids and/ or a binding protein. The occurence of BS mostly results from an activation process (see notes 78 and 85).
  77. The main physiological activator of factor VII is not known. The activation proceeds mostly with TF-complexed factor VII and increases VII activity by about 100 fold.
  78. Tissue factor is a "binding site", which is exposed by blood vessel damage. AIso, effector proteins like tumor necrosis factor induce its de novo-synthesis and its transport to the cell surface of endothelial cells and monocytes.
  79. The upper and lower sequences are the so-called 'intrinsic' and 'extrinsic' pathways of coagulation. These terms should be avoided because of crossovers in the reaction schemes and inducibility of the tissue factor inside the blood vessels.
  80. Factor VIII is stabilized in plasma as a complex with von-Willebrand-factor. Release from the complex and subsequent activation is catalyzed by thrombin.
  81. Activation of factor X may also proceed by activated monocytes, which have expressed the receptor protein MAC-1 on their surface.
  82. While factor Xa causes the primary activation of prothrombin, a supporting activation is effected by factor XIa inside the growing clot.
  83. C4BP-bound protein S does not promote protein C activation.
  84. In the thrombomodulin / thrombin complex, the activity of thrombin is changed from a pro- to an anticoagulant by inhibition of the thrombin reaction with fibrinogen or plateIets and by allowing activation of protein C.
  85. Blood platelets (thrombocytes) play an important role in blood coagulation. Their activation occurs at tissue lesions or by natural agonists, e.g., thrombin, collagen, ADP, epinephrine, PAF. The activated platelets aggregate, activate surface receptors for fibrinogen, collagen etc. and secrete activating agonists from intracellular granules.
  86. Synthesis and release of both tPA and PAI-1 are modulated by numerous stimulators and processes (venous occlusion, physical exercise, hormones, small blood peptides, such as bradykinin, cytokines, growth factors, thrombin).
  87. uPA is produced as a proenzyme with low activity. After activation, its main function is tissue-related proteolysis (e.g. degradation of extracellular matrix, tumor invasiveness, tissue remodeling). Binding of uPA to specific urokinase receptors is important for plasminog activation.
  88. Traces of plasmin convert proteolytically the native GIu- to Lys-plasminogen, which has higher activity towards fibrin.
  89. Fibrin is both target and trigger of the physiological fibrinolytic process. In absence of fibrin, tPA is a very poor activator of plasminogen. Polymerization of fibrin monomers stimulates tPA activity. Fibrin provides the binding epitopes for plasminogen and sc-/tc-PA.
  90. The 110 kD activator apparently connects the contact activation system with fibrinolysis.
  91. The synthesis of the LDL-receptor is regulated by the blood cholesterol concentration. In familial hypercholesterolemia, this regulation is defective.
  92. In presence of the phosphatidylinositol-P2 binding protein profilin, phospholipase C γ1 can split the inositol derivative only after being phosphorylated at a tyrosine residue by EGF- or PDGF-receptors with bound agonists.
  93. Phospholipase C, being activated by ligand binding to receptors, splits 1-phosphatidyl-1-D-myo-inositol 4,5-P2 to 1-D-myo-inositol (1,4,5)-P3 (which causes Ca++ release from the endoplasmatic reticulum) and to 1,2-diacylglycerol (which converts, in combination with Ca++, protein kinase C to its active form).
  94. Cholera toxin causes ADP-ribosylation of the subunits Gαs-GTP, Gαf-GTP or Gαt-GTP, preventing their dephosphorylation to the respective GDP complexes and keeping them permanently active.
  95. In yeast, Ras.GTP also activates adenylate cyclase, thus exerting a large number of effects.
  96. There are different Gα / Gβ / Gγ protein trimers, varying in their Gα moiety. They are activated by different hormone-receptor complexes. The various Gα .GTP moieties exert different actions.
  97. Pertussis toxin causes ADP-ribosylation of the Gαt .GDP / Gβ, Gαi .GDP / Gβ / Gγ and Gα .GDP / Gβ / Gγ protein trimers, preventing their activation by hormone-receptor complexes.
  98. Inositol pentakisphosphate decreases O2 affinity of hemoglobin in birds, similar to the 2,3-bisphosphoglycerate effect in other animals.
  99. The pathway of inositol phosphorylation to phytate in higher plants is unknown.
  100. The release of Ca++ from the endoplasmic reticulum is regulated by the inositol-P3 pathway shown. Ca++ release from the sarcoplasmic reticulum is initiated by depolarization of the cell membrane.
  101. Activated inositol 3-kinase also initiates the movement of GLUT 4 transporter to the cell surface, enhancing / enabling glucose input
  102. Overexpression of receptors or continuous presence of ligands (e.g. α-TGF) may cause cell proliferation / transformation.
  103. The oncogenic v-ErbB protein (from avian erythroblastosis virus) is similar to the EGF receptor and has enhanced tyrosine kinase activity
  104. The oncogenic v-Fms protein (of feline sarcoma virus) is similar to the CSF 1 receptor and has enhanced tyrosine kinase activity.
  105. In yeast, the lra-1 and lra-2 proteins play a similar role as the mammalian c-Ras protein.
  106. After binding of EGF, an EGF receptor combines either with another EGF- or with a HER 2-receptor, forming a homo- or heterodimer, respectively.This is the prerequisite for starting the activation cascade.
  107. Similar to the pathway leading to Erk, JNK is formed, catalyzing the phosphorylation of Jun as a prerequisite of dimerization with Fos.
  108. A similar function as GAP is ascribed to the NF1 gene product.
  109. Excitons characterize excited states of molecules. They are transferred to neighboring molecules via resonance interactions (here from the antenna pigments to the reaction center).
  110. Possible combinations of electron donor and acceptor reactions can be taken from the redox scale.
  111. The redox potential of flavin enzymes may differ up to 200mV from the values of the free coenzymes.
  112. Fe++ oxidation occurs mostly in strongly acidic medium (pH ca. 2) by periplasmic enzymes, while Fe3+ reduction may also take place at approximately neutral pH. Additionally, Fe3+ might be reduced nonenzymatically.
  113. Instead of succinate dehydrogenase, nitrate or nitrite reductases etc. may accept the electrons.
  114. Protons and electrons can also be supplied to the ubiquinone pool by glycerol 3-phosphate-, choline- and acyl- CoA dehydrogenases.
  115. In case of anaerobic bacterial growth on substrates with a more positive redox potential than NAD+ (e.g., succinate), 'reverse electron flow' takes place, reducing NAD+.
  116. In E.coli, protons and electrons can also be supplied to the ubiquinone pool by glycerol-3-phosphate-, D- and L-lactate dehydrogenases etc.
  117. There are 2 terminal oxidases in E.coli, operating at medium (D complex) and high (O complex) O2 pressurre.
  118. All photosynthetic bacteria are able to grow with reduced sulfur compounds as electron source (photolithotrophy). The most common reactions are oxidation of sulfide or thiosulfate to sulfate. The electrons are transferred to the light-driven electron cycle by specific cytochromes.
  119. Rhodobacter sphaeroides and most other purple bacteria contain 2 types of antenna complexes composed of bacteriochlorophyII- and carotenoid-carrying polypeptides.
  120. 'Reverse electron flow' from ubiquinol to NAD+ is driven by the electrochemical proton gradient across the plasma membrane (which is generated by cyclic electron flow through the reaction center and the cytochrome bc1 complex). The NADH dehydrogenase (ubiquinone) is similar to the mitochondrial enzyme.
  121. The membrane-spanning succinate dehydrogenase (ubiquinone) is similar to the mitochondrial enzyme. During photoheterotrophic growth of bacteria it supplies electrons for NAD(P)+ reduction, transferring them to the quinone pool (see note 120).
  122. Further metabolism of glyoxylate proceeds to glycolate (in peroxysomes, see part 1).
  123. The CO2 pumping system occurs only in (mostiy tropical) C4 plants. It enhances the local CO2 concentration, thereby reducing photorespiration.
  124. The insulin receptor with a bound ligand initiates a Ras cascade (similar to the EGF receptor cascade) as well as a direct activation sequence for glycogen synthesis.
  125. The antenna complexes comtain peptide-bound chlorophyll a, chlorophyll b and carotenoids (about 200 chlorophyll molecules per reaction center in photosytem I, about 250 chlorophyII molecules in photosystem II).
  126. P-680, the primary photoreceptor, is probabiy a chlorophyII a dimer.
  127. Plastoquinol (in chloroplasts) or ubiquinol (in purple bacteria) at the B site exchange with quinone from the quinone pool in the membrane.
  128. The 'special pair' P700 of 2 chlorophyIIs a transmits electrons to 2 further pairs of chlorophyII a, then to a pair of phyIIoquinones (A1), followed by 4 Fe4S4 centers (FX , FA , FB ).
  129. The reaction centers of chloroplast photosystem I and of green sulfur bacteria (e.g. Chlorobium limicola) are homologous to each other.
  130. The RNA primer at the 5'-end of the Okazaki fragments is removed and the gap is closed by DNA polymerase and DNA ligase.
  131. Topoisomerase removes positive superhelical tension, which is induced in the DNA template ahead of the replication fork.