Inhoudsopgave
1 Biomoleculen .....................................................................................................................................................5
1.1 Aminozuren ...............................................................................................................................................5
1.2 Indeling der aminozuren volgens eigenschappen zijketens ......................................................................5
1.3 Suikers .......................................................................................................................................................9
1.3.1 Monosachariden en disachariden: belangrijke sachariden ...............................................................9
1.3.2 Polysachariden (=polymeer suikers)................................................................................................11
1.3.3 Glycoconjuganten (conjugaat suiker met ‘iets anders’) ..................................................................12
1.3.4 Glycolipiden .....................................................................................................................................13
1.3.5 Lectines/Selectines ..........................................................................................................................13
Eiwitten: passieve rol.......................................................................................................................................15
1.4 Vetten ......................................................................................................................................................15
Vetzuren ..........................................................................................................................................................15
Triglyceriden ....................................................................................................................................................15
Glycerofosfolipiden .........................................................................................................................................15
Sfingolipiden ....................................................................................................................................................16
Sterolen ...........................................................................................................................................................16
Lipiden: actieve rol ..........................................................................................................................................17
Fosfatidylinositols ............................................................................................................................................17
Eicosanoids ......................................................................................................................................................17
Steroiden .........................................................................................................................................................17
2 Basisbegrippen van bio-energetica .................................................................................................................18
2.1 Inleiding ...................................................................................................................................................18
2.2 Soorten arbeid die cel moet verrichten: energie nodig ..........................................................................18
2.3 Energie/moleculaire omzettingen voor cellulaire arbeid ........................................................................18
2.4 Tijdelijke energie-opslag in cel ................................................................................................................19
2.5 Ongunstige reacties toch doorgaan ........................................................................................................19
2.6 Spontane reacties met hoge Ea sneller verlopen ....................................................................................19
2.7 Thermodynamisch systeem als levend organisme ..................................................................................19
2.8 Nut ‘Vrije Energie’....................................................................................................................................20
2.9 Hoge-energieverbindingen ......................................................................................................................20
2.9.1 Wat? ................................................................................................................................................20
2.9.2 ATP ...................................................................................................................................................20
2.9.3 Verbindingen met nog hogere energie dan ATP .............................................................................20
2.10 Oxidatie voedingsmoleculen ...................................................................................................................21
2.10.1 Waarom? .........................................................................................................................................21
2.10.2 Moleculen als carriers: Moleculen als goede dragers e- .................................................................22
3 Eiwitten............................................................................................................................................................22
1
, 3.1 4 niveaus van eiwitstructuur ...................................................................................................................22
3.1.1 Primaire structuur ...........................................................................................................................22
3.1.2 Secundaire structuur .......................................................................................................................22
3.1.3 Tertiaire structuur ...........................................................................................................................24
3.1.4 Quaternaire structuur .....................................................................................................................26
3.2 Hoe vouwen eiwitten op? .......................................................................................................................26
3.2.1 Voorgeschiedenis: Denaturatie-renaturatie experimenten van Anfinsen ......................................26
3.2.2 Krachten ..........................................................................................................................................26
3.2.3 Spontaniteit van het vouwen: hulp door andere eiwitten ..............................................................27
3.2.4 Foutief vouwen ................................................................................................................................28
3.3 Werking eiwitten .....................................................................................................................................29
3.3.1 Binding aan ligand ...........................................................................................................................29
3.3.2 Myoglobine & hemoglobine ............................................................................................................29
3.3.3 Antistoffen .......................................................................................................................................31
3.3.4 Chemische energie van motereiwitten: beweging in cel ................................................................31
4 Enzymen ..........................................................................................................................................................32
4.1 Wat zijn enzymen? ..................................................................................................................................32
4.1.1 Hoe zijn enzymen opgebouwd? ......................................................................................................32
4.1.2 Hoe worden enzymen onderverdeeld? ...........................................................................................33
4.2 Bevordering enzymreacties .....................................................................................................................34
4.3 Via welke mechanismen voeren enzymen hun katalytische functie uit? ...............................................34
4.4 Enzym kinetica .........................................................................................................................................35
4.4.1 Invloed op reactiesnelheid ..............................................................................................................35
4.4.2 Michaelis-Menten vergelijking ........................................................................................................35
4.5 3 vormen van inhibitie.............................................................................................................................36
4.6 Regeling van enzymwerking ....................................................................................................................36
4.7 Wat is het klinische belang van enzymen? ..............................................................................................38
4.7.1 Enzymbepaling voor meting van weefselbeschadiging ...................................................................38
4.7.2 Detectoren van moleculen ..............................................................................................................38
4.7.3 Enzymen als doelwitten...................................................................................................................38
4.7.4 Enzymen als geneesmiddel..............................................................................................................38
4.7.5 Ontstaan ziektes door mutaties in enzymcoderende genen ..........................................................39
5 Glycolyse & fermentatie ..................................................................................................................................40
5.1 Glycolyse ........................................................................................................................................................40
5.1.1 Algemene glycolyse .........................................................................................................................40
5.1.2 Stappen glycolyse in detail ..............................................................................................................41
5.1.3 Energieopbrengst glycolyse .............................................................................................................43
5.1.4 Verdere omzetting van pyruvaat .....................................................................................................43
2
, 5.2 Andere suikers (dan glucose) als brandstof glycolyse .............................................................................44
5.2.1 Monosachariden ..............................................................................................................................44
5.2.2 Poly & disachariden .........................................................................................................................44
6 Acetyl-CoA-productie & krebscyclus ...............................................................................................................46
6.1 Cellulaire respiratie .................................................................................................................................46
6.2 Moleculen voor vorming Acetyl-CoA.......................................................................................................46
6.2.1 Uit Pyruvaat (uit glycolyse) ..............................................................................................................46
6.2.2 Uit vetzuren .....................................................................................................................................48
6.2.3 Uit ketogene aminozuren ................................................................................................................49
6.2.4 Uit ethanol .......................................................................................................................................49
6.3 De Krebscyclus .........................................................................................................................................49
6.3.1 Krebscyclus werking ........................................................................................................................50
6.3.2 Energieopbrengst – conservatie ......................................................................................................51
6.3.3 Waarom oxidatie acetaat zo complex? ...........................................................................................51
6.3.4 Aminozuur afbraak via krebscyclus .................................................................................................52
6.3.5 Anaplerotische reacties = peil houden krebscyclus-intermediairs..................................................52
6.3.6 Regeling Krebs cyclus.......................................................................................................................53
6.3.7 Regeling pyruvaat dehydrogenase complex (PDH-complex) ..........................................................53
7 Elektronen transport & oxidatieve fosforylatie...............................................................................................54
7.1 Opbouw mitochondria ............................................................................................................................54
7.2 Mitochondriale ATP-productie ................................................................................................................54
7.2.1 Oorsprong & bestemming e- ...........................................................................................................55
7.2.2 Mitochondriën = batterijen .............................................................................................................55
7.3 ET & Oxidatieve fosforylering: algemeen ................................................................................................55
7.3.1 Elektronen gegenereerd in Krebscyclus ..........................................................................................55
7.3.2 Pad van e- doorheen ET-keten ........................................................................................................55
7.3.3 Gebruik van gepompte protonen = elektrochemische protonen gradiënt .....................................56
7.4 ET & Oxidatieve fosforylering: detail .......................................................................................................56
7.4.1 Redoxpotentialen ............................................................................................................................56
7.4.2 Complexen in ET ..............................................................................................................................56
7.4.3 ET complexen: koppeling ET aan pompen van H+ ..........................................................................57
7.4.4 Terugstroom protonen in matrix = ATP synthase aandrijven .........................................................58
7.4.5 Cytosolische elektronen (NADH) in mitochondria: Hoe? ................................................................59
7.5 Regeling & ontregeling ET en oxfosmechanismen (ATP-producerende pathways) ................................60
7.5.1 Regeling via pathways die leiden naar ET & oxfos die NADH en FADH2 regelen............................60
7.5.2 Ontregelen ET en oxfos door verschillende moleculen...................................................................60
8 Celcyclus: celproliferatie en celdood ...............................................................................................................61
8.1 Ziekten .....................................................................................................................................................61
3
, 8.1.1 Kanker ..............................................................................................................................................61
8.1.2 Neurodegeneratieve ziekten (alzheimer, Parkinson, AIDS) ............................................................61
8.2 Celcyclus & regeling .................................................................................................................................62
8.2.1 4 fasen in celcyclus ..........................................................................................................................62
8.2.2 Centrale regelaar(s) van celcyclus ...................................................................................................62
8.2.3 Centrale regel-machanismen ..........................................................................................................62
8.2.4 Celcyclusregeling: Cycline afhankelijke kinases...............................................................................63
8.2.5 Faling celcylus regeling & therapeutische aangrijpingspunten .......................................................66
8.3 Apoptosis en haar regeling ......................................................................................................................67
8.3.1 Celdood & apoptosis vs. Necrosis ...................................................................................................67
8.3.2 Celdood verbonden met functioneren levend organisme ..............................................................67
8.3.3 Basismechanismen ..........................................................................................................................68
8.3.4 Experimenten ..................................................................................................................................69
8.3.5 Caspasen als centrale factoren apoptosis .......................................................................................69
8.3.6 Signalen die leiden tot apoptosis ....................................................................................................69
8.3.7 Remming apoptosis .........................................................................................................................71
8.3.8 P53 in respons op cellulair stress ....................................................................................................73
8.3.9 Celdood niet altijd via caspasen ......................................................................................................74
8.3.10 Ubiquitine en proteasoom ..............................................................................................................74
4
,Biochemie
1 Biomoleculen
1.1 Aminozuren
De persoonlijkheid van biomoleculen = functionele groepen
o D en L-vorm (mensen, zoogdieren)
o Hydrofiel/hydrofoob
o Naamgeving: 3 letter code/1 letter code
o Pkr waarden = lading van AZ afhankelijk van Ph
1.2 Indeling der aminozuren volgens eigenschappen zijketens
Nonpolair, alifatische zijketens
- Niet asymmetrisch
- Grote conformationele
flexibiliteit
(kunnen roteren rond de -C-
binding
- Inert en alifatisch
- Nonpolair, hydrofoob
- Geen functionele groepen
- Zijketens clusteren samen
In vitro mutagenesis (alanine)
: Het bepalen van belangrijke AZ -
zijketens bij een bepaalde binding
➔ Alle eiwitten (leucine) in een
plasmide (drager)
DNA + codons -> codon vervangen ->
RNA -> nieuw eiwit (alanine)
= ‘afknippen van zijketens’
5
, AZ met aromatische R-groepen
- Zeer hydrofoob
- Apolair
- Weinig reactief
- OH-groep
- Intermediair polair
Deelname aan H-bruggen
- Functionele groep in enzymen
= fosforylatieplaats
➔ Fosfaat inplanten op eiwit
- Intermediair polair (N)
- Zeldzaam
- Structurele studies
Lichttechniek: meten van hoeveelheid eiwitten in
bijvoorbeeld medicatie
- Licht door een monochromator
- Licht met een bepaalde intensiteit uitgezonden,
door cuvette met vloeistof (eiwitten)
- Hoeveelheid opgenomen/uitgezonden licht
gemeten (absorbantie) = hoeveelheid eiwitten
6
, AZ met polaire, ongeladen R-groepen
- SH-groep
- Polair
- pKa: 8
- OXIDATIE: cystine vorming
- Disulfidebrug eiwit = 3D vorm
Belangrijke groep ih katalytisch
centrum enzyme:
: S aanval op enzym -> CoA los
- OH groep
- Polair
- Kunnen worden
gefosforyleerd
- Nemen deel aan H-bruggen
- Amiden
- Polair
- H-brugvorming
- Geen deelname aan H-
bruggen
- Cyclisch
- Gematigd polair
- Rigide vanwege ringvorm
Knikvorming ter hoogte van prolines
in peptideketen
➔ Bochtvorming binnen
eiwitketens (2 AZ verbonden
door peptide binding)
➔ TRANS configuratie is
gunstigst bij alle AZ
! Proline heeft CIS configuratie
= knikvorming ipv zigzagvorm
7
1 Biomoleculen .....................................................................................................................................................5
1.1 Aminozuren ...............................................................................................................................................5
1.2 Indeling der aminozuren volgens eigenschappen zijketens ......................................................................5
1.3 Suikers .......................................................................................................................................................9
1.3.1 Monosachariden en disachariden: belangrijke sachariden ...............................................................9
1.3.2 Polysachariden (=polymeer suikers)................................................................................................11
1.3.3 Glycoconjuganten (conjugaat suiker met ‘iets anders’) ..................................................................12
1.3.4 Glycolipiden .....................................................................................................................................13
1.3.5 Lectines/Selectines ..........................................................................................................................13
Eiwitten: passieve rol.......................................................................................................................................15
1.4 Vetten ......................................................................................................................................................15
Vetzuren ..........................................................................................................................................................15
Triglyceriden ....................................................................................................................................................15
Glycerofosfolipiden .........................................................................................................................................15
Sfingolipiden ....................................................................................................................................................16
Sterolen ...........................................................................................................................................................16
Lipiden: actieve rol ..........................................................................................................................................17
Fosfatidylinositols ............................................................................................................................................17
Eicosanoids ......................................................................................................................................................17
Steroiden .........................................................................................................................................................17
2 Basisbegrippen van bio-energetica .................................................................................................................18
2.1 Inleiding ...................................................................................................................................................18
2.2 Soorten arbeid die cel moet verrichten: energie nodig ..........................................................................18
2.3 Energie/moleculaire omzettingen voor cellulaire arbeid ........................................................................18
2.4 Tijdelijke energie-opslag in cel ................................................................................................................19
2.5 Ongunstige reacties toch doorgaan ........................................................................................................19
2.6 Spontane reacties met hoge Ea sneller verlopen ....................................................................................19
2.7 Thermodynamisch systeem als levend organisme ..................................................................................19
2.8 Nut ‘Vrije Energie’....................................................................................................................................20
2.9 Hoge-energieverbindingen ......................................................................................................................20
2.9.1 Wat? ................................................................................................................................................20
2.9.2 ATP ...................................................................................................................................................20
2.9.3 Verbindingen met nog hogere energie dan ATP .............................................................................20
2.10 Oxidatie voedingsmoleculen ...................................................................................................................21
2.10.1 Waarom? .........................................................................................................................................21
2.10.2 Moleculen als carriers: Moleculen als goede dragers e- .................................................................22
3 Eiwitten............................................................................................................................................................22
1
, 3.1 4 niveaus van eiwitstructuur ...................................................................................................................22
3.1.1 Primaire structuur ...........................................................................................................................22
3.1.2 Secundaire structuur .......................................................................................................................22
3.1.3 Tertiaire structuur ...........................................................................................................................24
3.1.4 Quaternaire structuur .....................................................................................................................26
3.2 Hoe vouwen eiwitten op? .......................................................................................................................26
3.2.1 Voorgeschiedenis: Denaturatie-renaturatie experimenten van Anfinsen ......................................26
3.2.2 Krachten ..........................................................................................................................................26
3.2.3 Spontaniteit van het vouwen: hulp door andere eiwitten ..............................................................27
3.2.4 Foutief vouwen ................................................................................................................................28
3.3 Werking eiwitten .....................................................................................................................................29
3.3.1 Binding aan ligand ...........................................................................................................................29
3.3.2 Myoglobine & hemoglobine ............................................................................................................29
3.3.3 Antistoffen .......................................................................................................................................31
3.3.4 Chemische energie van motereiwitten: beweging in cel ................................................................31
4 Enzymen ..........................................................................................................................................................32
4.1 Wat zijn enzymen? ..................................................................................................................................32
4.1.1 Hoe zijn enzymen opgebouwd? ......................................................................................................32
4.1.2 Hoe worden enzymen onderverdeeld? ...........................................................................................33
4.2 Bevordering enzymreacties .....................................................................................................................34
4.3 Via welke mechanismen voeren enzymen hun katalytische functie uit? ...............................................34
4.4 Enzym kinetica .........................................................................................................................................35
4.4.1 Invloed op reactiesnelheid ..............................................................................................................35
4.4.2 Michaelis-Menten vergelijking ........................................................................................................35
4.5 3 vormen van inhibitie.............................................................................................................................36
4.6 Regeling van enzymwerking ....................................................................................................................36
4.7 Wat is het klinische belang van enzymen? ..............................................................................................38
4.7.1 Enzymbepaling voor meting van weefselbeschadiging ...................................................................38
4.7.2 Detectoren van moleculen ..............................................................................................................38
4.7.3 Enzymen als doelwitten...................................................................................................................38
4.7.4 Enzymen als geneesmiddel..............................................................................................................38
4.7.5 Ontstaan ziektes door mutaties in enzymcoderende genen ..........................................................39
5 Glycolyse & fermentatie ..................................................................................................................................40
5.1 Glycolyse ........................................................................................................................................................40
5.1.1 Algemene glycolyse .........................................................................................................................40
5.1.2 Stappen glycolyse in detail ..............................................................................................................41
5.1.3 Energieopbrengst glycolyse .............................................................................................................43
5.1.4 Verdere omzetting van pyruvaat .....................................................................................................43
2
, 5.2 Andere suikers (dan glucose) als brandstof glycolyse .............................................................................44
5.2.1 Monosachariden ..............................................................................................................................44
5.2.2 Poly & disachariden .........................................................................................................................44
6 Acetyl-CoA-productie & krebscyclus ...............................................................................................................46
6.1 Cellulaire respiratie .................................................................................................................................46
6.2 Moleculen voor vorming Acetyl-CoA.......................................................................................................46
6.2.1 Uit Pyruvaat (uit glycolyse) ..............................................................................................................46
6.2.2 Uit vetzuren .....................................................................................................................................48
6.2.3 Uit ketogene aminozuren ................................................................................................................49
6.2.4 Uit ethanol .......................................................................................................................................49
6.3 De Krebscyclus .........................................................................................................................................49
6.3.1 Krebscyclus werking ........................................................................................................................50
6.3.2 Energieopbrengst – conservatie ......................................................................................................51
6.3.3 Waarom oxidatie acetaat zo complex? ...........................................................................................51
6.3.4 Aminozuur afbraak via krebscyclus .................................................................................................52
6.3.5 Anaplerotische reacties = peil houden krebscyclus-intermediairs..................................................52
6.3.6 Regeling Krebs cyclus.......................................................................................................................53
6.3.7 Regeling pyruvaat dehydrogenase complex (PDH-complex) ..........................................................53
7 Elektronen transport & oxidatieve fosforylatie...............................................................................................54
7.1 Opbouw mitochondria ............................................................................................................................54
7.2 Mitochondriale ATP-productie ................................................................................................................54
7.2.1 Oorsprong & bestemming e- ...........................................................................................................55
7.2.2 Mitochondriën = batterijen .............................................................................................................55
7.3 ET & Oxidatieve fosforylering: algemeen ................................................................................................55
7.3.1 Elektronen gegenereerd in Krebscyclus ..........................................................................................55
7.3.2 Pad van e- doorheen ET-keten ........................................................................................................55
7.3.3 Gebruik van gepompte protonen = elektrochemische protonen gradiënt .....................................56
7.4 ET & Oxidatieve fosforylering: detail .......................................................................................................56
7.4.1 Redoxpotentialen ............................................................................................................................56
7.4.2 Complexen in ET ..............................................................................................................................56
7.4.3 ET complexen: koppeling ET aan pompen van H+ ..........................................................................57
7.4.4 Terugstroom protonen in matrix = ATP synthase aandrijven .........................................................58
7.4.5 Cytosolische elektronen (NADH) in mitochondria: Hoe? ................................................................59
7.5 Regeling & ontregeling ET en oxfosmechanismen (ATP-producerende pathways) ................................60
7.5.1 Regeling via pathways die leiden naar ET & oxfos die NADH en FADH2 regelen............................60
7.5.2 Ontregelen ET en oxfos door verschillende moleculen...................................................................60
8 Celcyclus: celproliferatie en celdood ...............................................................................................................61
8.1 Ziekten .....................................................................................................................................................61
3
, 8.1.1 Kanker ..............................................................................................................................................61
8.1.2 Neurodegeneratieve ziekten (alzheimer, Parkinson, AIDS) ............................................................61
8.2 Celcyclus & regeling .................................................................................................................................62
8.2.1 4 fasen in celcyclus ..........................................................................................................................62
8.2.2 Centrale regelaar(s) van celcyclus ...................................................................................................62
8.2.3 Centrale regel-machanismen ..........................................................................................................62
8.2.4 Celcyclusregeling: Cycline afhankelijke kinases...............................................................................63
8.2.5 Faling celcylus regeling & therapeutische aangrijpingspunten .......................................................66
8.3 Apoptosis en haar regeling ......................................................................................................................67
8.3.1 Celdood & apoptosis vs. Necrosis ...................................................................................................67
8.3.2 Celdood verbonden met functioneren levend organisme ..............................................................67
8.3.3 Basismechanismen ..........................................................................................................................68
8.3.4 Experimenten ..................................................................................................................................69
8.3.5 Caspasen als centrale factoren apoptosis .......................................................................................69
8.3.6 Signalen die leiden tot apoptosis ....................................................................................................69
8.3.7 Remming apoptosis .........................................................................................................................71
8.3.8 P53 in respons op cellulair stress ....................................................................................................73
8.3.9 Celdood niet altijd via caspasen ......................................................................................................74
8.3.10 Ubiquitine en proteasoom ..............................................................................................................74
4
,Biochemie
1 Biomoleculen
1.1 Aminozuren
De persoonlijkheid van biomoleculen = functionele groepen
o D en L-vorm (mensen, zoogdieren)
o Hydrofiel/hydrofoob
o Naamgeving: 3 letter code/1 letter code
o Pkr waarden = lading van AZ afhankelijk van Ph
1.2 Indeling der aminozuren volgens eigenschappen zijketens
Nonpolair, alifatische zijketens
- Niet asymmetrisch
- Grote conformationele
flexibiliteit
(kunnen roteren rond de -C-
binding
- Inert en alifatisch
- Nonpolair, hydrofoob
- Geen functionele groepen
- Zijketens clusteren samen
In vitro mutagenesis (alanine)
: Het bepalen van belangrijke AZ -
zijketens bij een bepaalde binding
➔ Alle eiwitten (leucine) in een
plasmide (drager)
DNA + codons -> codon vervangen ->
RNA -> nieuw eiwit (alanine)
= ‘afknippen van zijketens’
5
, AZ met aromatische R-groepen
- Zeer hydrofoob
- Apolair
- Weinig reactief
- OH-groep
- Intermediair polair
Deelname aan H-bruggen
- Functionele groep in enzymen
= fosforylatieplaats
➔ Fosfaat inplanten op eiwit
- Intermediair polair (N)
- Zeldzaam
- Structurele studies
Lichttechniek: meten van hoeveelheid eiwitten in
bijvoorbeeld medicatie
- Licht door een monochromator
- Licht met een bepaalde intensiteit uitgezonden,
door cuvette met vloeistof (eiwitten)
- Hoeveelheid opgenomen/uitgezonden licht
gemeten (absorbantie) = hoeveelheid eiwitten
6
, AZ met polaire, ongeladen R-groepen
- SH-groep
- Polair
- pKa: 8
- OXIDATIE: cystine vorming
- Disulfidebrug eiwit = 3D vorm
Belangrijke groep ih katalytisch
centrum enzyme:
: S aanval op enzym -> CoA los
- OH groep
- Polair
- Kunnen worden
gefosforyleerd
- Nemen deel aan H-bruggen
- Amiden
- Polair
- H-brugvorming
- Geen deelname aan H-
bruggen
- Cyclisch
- Gematigd polair
- Rigide vanwege ringvorm
Knikvorming ter hoogte van prolines
in peptideketen
➔ Bochtvorming binnen
eiwitketens (2 AZ verbonden
door peptide binding)
➔ TRANS configuratie is
gunstigst bij alle AZ
! Proline heeft CIS configuratie
= knikvorming ipv zigzagvorm
7
