-------- Basic Metabolism --------
- - - Principles - - -
dynamic equilibrium;
enzyme reaction diagram;
exergon, endergon; reversible, irreversible;
Some definitions of life:
a process far away from thermodynamic equilibrium [Eigen]
reproduction, metabolism and evolution [one possibility]
life is a daring adventure - or nothing [Helen Keller]
- - - a) Carbohydrates - - -
Glycolysis
glucose enz-glyc1: hexokinase, glucokinase
glucose-6-phosphate enz-glyc2: phospho-gluco-isomerase
fructose-6-phosphate enz-glyc3: 6-phospho-fructo-kinase pfkA pfkB
fructose-1,6-biphosphate enz-glyc4: fructose-bi-phosphate aldolase
dihydroxyacetone-phosphate +
glycerinaldehyd-3-phosphate enz-glyc5: glyceryladehyd-3-phosphate DH
1,3-bi-phospho-glycerate enz-glyc6: 3-phospho-glycerate-kinase
3-phospho-glycerate enz-glyc7: phospho-glycerate-mutase
2-phospho-glycerate enz-glyc8: enolase
phospho-enol-pyruvat enz-glyc9: pyruvat-kinase
(other direction: phospho-enol-pyruvate-synthase)
pyruvate end-glyc
Entner-Doudoroff
6-phospho-gluconate enz-EntD1: phospho-gluconate-dehydratase
2-dehydro-3-deoxy enz-EntD2: 2-dehydro-3-deoxy
6-phospho-gluconate gluconate aldoalse
pyruvate +
glyceraldehyde-3-phosphate end-EntD There are additions branching off !
Pentose phosphate cycle
glucose-6-phosphate enz-Pent1: glucose-6-phosphate DH
6-phospho-1,5-gluconolactone enz-Pent2: 6-phospho-gluconolactonase
6-phospho-gluconate enz-Pent3: phospho-gluconate DH
ribulose-5-phosphate enz-Pent4: ribose-phosphate-isomerase
xylulose-5-phosphate +
ribose-5-phosphate enz-Pent5: Transketolase
seduheptulose-7-phosphate +
glyceraldehyd-3-phosphate
glyceraldehyd-3-phosphate +
fructose-6-phosphate enz-Pent5: Transketolase
erythrose-4-phosphate +
xylulose-5-phosphate
erythrose-4-phosphate
fructose-6-phosphate + enz-Pent6: Transaldolase
seduheptulose-7-phosphate +
glyceraldehyd-3-phosphate
Note different elementary modes for pentosephosphate cycle
Citric acid cycle
synonym: TCA (tricarboxylic acid) cycle
oxalacetate + enz-Citr1: citrate synthase
Acetyl-CoA
citrate enz-Citr2: aconitase
isocitrate enz-Citr3: isocitrate DH
+CO2
2-ketoglutarate enz-Citr4: 2-ketoglutarate DH
+CO2
succinyl-CoA enz-Citr5: succinate-thiokinase
succinat enz-Citr6: succinat DH
fumarate enz-Citr7: fumarase
malate enz-Citr8: malate DH
oxalacetate end-Citr
polysaccharids
cellulose gluc b(1-4)
glycogen gluc a(1-4) and a(1-6) (branching every 30th or so)
Note: Regulation of glycogen synthesis
starch
amylose gluc a(1-4) CHK
amylopectin gluc a(1-4) and a(1-6) CHK
- - - b) Amino Acids - - -
ammonia assimilation
glutamate +NH3 +ATP enz-AA1 : glutamine synthetase glnA
glutamine +ADP
glutamine +NADPH
+ alpha-ketoglutarate enz-AA2 : glutamate synthetase gltBD
2 glutamate + NADP
NH3 + alpha-ketoglutarate
+ NADPH enz-AA3 : glutamate dehydrogenase gdhA
glutamate + NADP
further nitrogen metabolizing
oxalacetate + glutamate enz-AA4 : aspartate transaminase aspC, tyrB
alpha-ketoglutarate
+ aspartate
aspartate + glutamine + ATP enz-AA5 : glu-dependent asparagine asnB
asparagine + glutamate + ADP synthetase
aspartate + NH3 + ATP enz-AA6 : ammonia dependent asparagine asnA
asparagine + ADP synthetase
pyruvate + glutamate enz-AA7 : glutamic-pyruvic alaB?
L-alanine transaminase
+ alpha-keto-glutarate
valine + pyruvat enz-AA8 : alanin-valine transaminase avtA
+ alpha-ketoisovalerate
+ L-alanine
L-alanine to D-alanine enz-AA9 : alanine racemase alr
L-alanine to D-alanine enz-AA0 : alanine racemase dadX, dadB
urea cycle
arginine
- urea enz :
ornithine
+ carbamoyl-P enz :
citrullin
+ asparagin enz :
argininosuccinat
- fumarat enz :
arginine
Common aromatic amino acid pathway
phosphoenolpyruvate + enz-Arom1: 3-deoxy-D-arbino-heptulosonate-
erythrose 4-phosphate 7-phosphate-synthase aroF,G,H
3-deoxy-D-arabino-heptuloso-
nate-7-phosphate enz-Arom2: 3-Dehydroquinate synthase aroB
3-Dehydroquinate
- H20 enz-Arom3: 3-Dehydroquinate dehydratase aroD
3-dehydroshikimate +NADPH,H+ enz-Arom4: Shikimate dehydrogenase
Shikimate + NADP enz-Arom5: Shikimate kinase I,II aroE
Shikimate 3-phosphate+PEP enz-Arom6: 5-Enolpyruvoylshikimate- aroK,L
5-Enolpyruvoylshikimate- 3-phosphate synthase aroA
3-phosphate enz-Arom7: Chorismate synthase aroC
Chorismate + P end-Arom
Phenylalanine biosynthesis
Chorismate enz-Phe1 : Chorismate mutase pheA
Prephenate enz-Phe2 : Prephanate dehydratase pheA
- CO2 - H2O
Phenylpyruvate enz-Phe3 : Tyrosine aminotransferase tyrB
+ Glu
Phenylalanine
+ alpha-Ketoglutarate
Tyrosine biosynthesis
Prephenate enz-Tyr1 : Prephenate dehydrogenase tyrA
4-Hydroxyphenylpyruvate enz-Phe3 : Tyrosine aminotransferase tyrB
+ Glu
Tyrosine
+ alpha-Ketoglutarate
in man CHK:
phenylalanine enz-Tyr2 : Phenylalaninehydroxylase
tyrosine
lack of it Phenylketonuria;
toxic phenyl-acetic acid ?
Tryptophan biosynthesis
Chorismate + Glutamine enz-Trp1 : Anthranilate synthase trpE
Glutamate +
Anthralinate enz-Trp2 : Anthranilate phosphoribosyl
+ phosphoribosyl transferase trpD
pyrophosphate
Phosphoribosyl enz-Trp3 : Phosphoribosyanthranlinate trpC
anthranlinate isomerase
1-(o-carboxyphenylamino)-1-
deoxyribulose-5-phosphate enz-Trp4 : Indoleglycerol phosphate trpC
- CO2 synthetase
Indoleglycerol phosphate enz-Trp5 : Tryptophan synthase trpA,B
+ Serine
Tryptophan
+ glyceraldehyd
3-phosphate
- - - c) Lipids - - -
carriers
carnithin-cycle (carnithin amphoter, derived from lysine)x:
acyl-CoA (cytosol)
acyl-carnithin (mitochondrial membrane)
acyl-CoA (mitochondrial matrix)
fatty acid synthesis
- unsaturated fatty acids:
ketone bodies
acetoacetate
3-hydroxy-butyrate CHK
Note: Condition e.g. in diabetes
fatty acid oxidation
- - - d) Nucleotide metabolism - - -
pyrimidine synthesis
OTP
UTP
TTP
purine synthesis
ITP
ATP
GTP
- - - e) Other - - -
Vitamins
watersoluble:
B1, B2, B6, B12, Ascorbic acid
lipohilic:
A
D hydroxycholecalciferol, UV, activated
E
K gamma carboxylation of glutamic acid, important in blood clotting
factors
-------- Higher level regulation --------
- - - a) in a cell - - -
DNA synthesis
DNA polymerase III (main enzyme in eucaryotes CHK)
Note: 3'-5' exonuclease activity CHK
Toxins: Cytostasis; DNA gyrase inhibitor
Transcription
RNA polymerase II
Translation
Seondary messengers
cAMP
Regulatory structures in DNA
DNA types: A,B,Z
procaryotes:
operons
regulons
eucaryotes:
histones CHK
nucleosomes
enhancers
hox genes
cell division control:
-cell cycle genes:
cdc 2
-apoptosis genes:
p53
Regulatory RNA and higher RNA metabolism
mRNA, tRNA, rRNA; cyoplasmic RNAs: 7SL RNA, 7K RNA; viral RNA;
nuclear RNAs: snRNAs, snoRNAs;
splicing variants: self splicing introns (type I, type II)
ATAC introns;
regulatory elements:
- in mRNA: IREs, se-cys-RNAs,
catalytic RNAs:
hammerheads
ribozymes
RNAse P
telomerase
Chylomicrones: Resorption of fatty acids in illeum; rich in cholesterol;
IDL : Intermediate density lipids in the liver;
VLDL : Very low density lipids, transport to adipose tissues
LDL : Low density lipids, transport from the adipose tissue
into the periphery (lipids, cholesterol)
HDL : Heavy density lipids: scavengers of cholesterol from tissue
degradation protective;
enzyme: Aryltransferase CHK
enz: Lipase
- - - b) Global metabolic changes in yeast - - -
Diauxic shift (from glucose rich to glucose poor)
look at Brown lab(Stanford) for more results on this.
710 mRNAs increased more than 2x, 183 mRNAs more than 4x
1030 mRNAs decreased more than 2x, 203 mRNAs more than 4x
Gene families (well known):
+ aerobic ethanol utilization (aldehyd-DH, alcohol-DH, citric acid cycle,
pyruvate carboxylase, glyoxylate cycle, cytochromes)
+ mitochondrial ribosomal genes (for mitochondria growth)
+ carbohydrate storage (gycogen, trehalose)
+ gluconeogenesis
- pyruvate decarboxylase, glycolysis
- protein synthesis (ribosomal proteins, tRNA synthetase,
translation, elongation, intiation)
Gene families (before not considered in the diauxic shift):
+ (late but strong, 9x induction): Glucose repressed genes with CSRE-sites
as common activator for transcription
+ genes with STRE-sites as common activator for transcription (e.g. one
putative glutathione peroxidase, a putative transaldolase)
+ genes with Hap2,3,4 transcription factor binding site (cytochrome c related
genes, Hap4 itself is 9x induced)
- 7 ribosomal proteins regulated by upstream activating sequence, recognized
by transcription factor RAP1 (which is 4,4x repressed)
+ Only other transcription factor gene more than 3x induced
(of a total of 149 factors measured here):
SIP4 (interacts with Snf1, a master regulator of glucose repression)
------------------------------------------------------------------------------
DH indicates dehydrogenase; CSRE carbon source response element;
STRE stress response element (sequence CCCCT);
HAP (a heterotrimeric transcription activator complex, binding site CCAAT);
Effect of a transcription factor on the complete genome:
Tup1 deletion:
+ 34 genes involved in glucose utilization and also induced by the
diauxic shift (e.g. Suc2, hexose transporters)
+ a-glucosidases, mating-type specific genes MFA1,MFA2;
DNA damage inducible RNR2, RNR4;
genes involved in floculation (6 from 13 have TUP1 binding site),
cell wall mannoproteins;
Yap1 overexpression:
+ 17 genes more than 3x (5 are aryl-acohol-dehydrogenease
- sugar permeases
_________________________________________________________________
tup1 (co-repressor with Mig1); SUC2 gene for invertase;
- - - c) In tissues and organs - - -
Blood:
Antibody production
Complement Cascade
see cartoon
Complement system and regulators
antigen-antibody complex ->
-> several Fc fragments as part of a multivalent
antibody-antigen complex
find the C1q tips
-> activating of zymogen C1r ->
activating of zymogen C1s
-> C4 -> C2 -> C3 -> C5
->C5b forms complex with C6, C7 and C8, penetrating
the antigen carrying membrane
-> about 16 molecules C9 dock to this
lysis of the alien cell
Blood clotting
Blood clotting cascade
see cartoon
Blood coagulation and fibrinolysis
Hemoglobine
cooperative or Bohr effect
see porphyrine synthesis
see iron metabolism
globin synthesis
regulation of glycogen storage
independent activating and de-activating cascade
of kinases;
Regulation of levels of lipoproteins
Aging
cellular programs:
- four genetic complementation groups for first cell division stop signal.
- second, more final stop by telomer chopping;
aging by random processes:
- free radical attack
see redox protection
see glutathion reductase / peroxidase
see catalase / superoxid dismutase
- aging of DNA / repair of DNA
enzymes: helicase involved in Werner's syndrom
Death: thermodynamic equilibrium is close (compare with start)