Volledige samenvatting van het OPO 'Biochemie' gebaseerd op de blokwijzer en de lessen. Alle hoofdstukken worden duidelijk toegelicht in eigen woorden. Voldoende om het examen te slagen samen met de samenvatting 'Moleculaire biologie'.
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
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
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