SAMENVATTING
BOUWSTENEN VAN HET LEVEN
Door: Claire Snel
12 OKTOBER 2020
,Inhoudsopgave
1 Elements & Energies ...................................................................................................................................... 3
1.1 Some Relevant Elements ...................................................................................................................... 3
1.2 Energy ........................................................................................................................................................... 6
1.2.1 Internal energy (inwendige energie) .................................................................................................... 6
1.2.2 Enthalpy ................................................................................................................................................ 6
1.2.3 Entrophy ............................................................................................................................................... 7
1.2.4 Gibs free energie .................................................................................................................................. 8
1.3 Interactions................................................................................................................................................... 9
2 Protein Structure & Dynamics ..................................................................................................................... 10
2.1 AminoAcids ................................................................................................................................................. 10
2.2 Protein structure ......................................................................................................................................... 13
2.2.1 Primaire structuur .............................................................................................................................. 13
2.2.2. Secundaire structuur ......................................................................................................................... 14
2.2.3 Tertiaire structuur .............................................................................................................................. 17
2.2.4 Quartaire structuur ............................................................................................................................. 18
2.3 Protein Dynamics ........................................................................................................................................ 19
2.3.1 Eiwit vouwing ..................................................................................................................................... 19
3.3.2 Eiwitstabiliteit ..................................................................................................................................... 22
2.3.3 Eiwitbeweging .................................................................................................................................... 23
3 Protein function .......................................................................................................................................... 24
3.1 Fluorescent Proteins ................................................................................................................................... 24
3.2 Shuttle Proteins: Globins ............................................................................................................................ 28
3.2.1 Myoglobin ........................................................................................................................................... 28
3.2.2 Hemoglobine ...................................................................................................................................... 29
3.3 Structural Proteins ...................................................................................................................................... 33
3.1 Collagen ................................................................................................................................................. 34
3.2 Elastin .................................................................................................................................................... 36
4 Enzymes ...................................................................................................................................................... 39
4.1 Enzyme Catalysis ........................................................................................................................................ 39
4.1.1 Specifity .............................................................................................................................................. 39
4.1.2 Activation Energy ................................................................................................................................ 41
4.1.3 Acceleration ........................................................................................................................................ 42
4.1.4 Mechanism: How Enzymes Do It ........................................................................................................ 43
4.1.5. Michaelis & Menten: How Fast Enzymes Do It .................................................................................. 47
4.1.6 Cofactors: Mother’s Little Helpers ...................................................................................................... 50
4.2 Enzyme Regulatie ....................................................................................................................................... 52
4.2.1 Irreversible Regulation by Covalent Modification .............................................................................. 52
4.2.2 Reversible Regulation by Covalent Modification ................................................................................ 53
4.2.3 Reversible, Non-covalent Inhibition ................................................................................................... 55
4.2.4 Cooperativity and Allostery ................................................................................................................ 58
5 Biological Membranes ................................................................................................................................. 60
5.1 Lipids ........................................................................................................................................................... 60
5.2 Bilayer ......................................................................................................................................................... 62
5.2.1 Building Membranes........................................................................................................................... 62
1
, 5.2.2 Membrane Function and Dynamics .................................................................................................... 63
5.3 Membrane Proteins .................................................................................................................................... 68
5.4 Membrane Transport ................................................................................................................................. 70
5.4.1 Fundamentals of Membrane Transport ............................................................................................. 70
5.4.2 Membrane-active Antibiotics ............................................................................................................. 72
5.4.3 Transport of Small Molecules ............................................................................................................. 75
6 Cellular Metabolism .................................................................................................................................... 86
6.1 Fundamentals ............................................................................................................................................. 86
6.2 Metabolic Routes........................................................................................................................................ 92
6.2.1 Glycolysis ............................................................................................................................................ 92
6.2.2 Pyruvate Decarboxylation .................................................................................................................. 96
6.2.3 Fermentation ...................................................................................................................................... 97
6.2.4 TCA-cyclus ........................................................................................................................................... 98
6.3 Electron Transport Chain ............................................................................................................................ 99
6.3.1 Mitchell’s Postulates: Membranes: de stuwdam ............................................................................... 99
6.3.2 Mitchell’s Postulates: Electron Transfer Chain (ETC) .......................................................................... 99
6.3.3 Mitchell’s Postulates: Proton Pumping ............................................................................................ 105
6.3.4 ROS production ................................................................................................................................. 107
6.3.5 Bacterial Respiration......................................................................................................................... 108
6.3.6 Heat production................................................................................................................................ 109
6.4 ATP synthesis ............................................................................................................................................ 110
6.4.1 The Coupling Factor .......................................................................................................................... 110
6.4.2 F1 ....................................................................................................................................................... 111
6.4.3 Rotations........................................................................................................................................... 111
6.4.4 F0: en dit is de aandrijf ...................................................................................................................... 113
2
, 1 Elements & Energies
1.1 Some Relevant Elements
Atomen:
- kern + elektronen daaromheen
- hebben verschillend aantal protonen en elektronen
- atoomnummer = aantal protonen (en elektronen) in de kern
- atoommassa = protonen + neutronen
De buitenste schil van sommige atomen is niet vol, we noemen deze elementen dan reactief
In moleculen zijn atomen verbonden met covalente bindingen
> covalente bindingen:
Een paar elektronen worden gedeeld door twee atomen
Carbon (C)
- heeft 4 elektronen in de buitenste schil --> 4 opnemen of 4
afstaan om de buitenste schil te verzadigen
- heeft een bijzondere rol in cellen: kan sterke covalente
bindingen vormen met andere carbon-atomen
>> met 1 covalente binding kunnen de groepen vrij rond bewegen rond elkaar
>> met meerdere covalente bindingen kan dit niet, liggen ineen vlak
>> carboxyl(zuur)-groepen kunnen proton >> veel CN-bindingen in proteines/ eiwittten
afstaan en negatief geladen worden >> amine = NH2
>> amide = CONH
Fosfaatgroepen:
- Hydroxyy groep (alcohol) + fosfaatgroep → fosfaatester
>> bij hydrolyse wordt de binding verbroken waardoor energie vrijkomt
3
BOUWSTENEN VAN HET LEVEN
Door: Claire Snel
12 OKTOBER 2020
,Inhoudsopgave
1 Elements & Energies ...................................................................................................................................... 3
1.1 Some Relevant Elements ...................................................................................................................... 3
1.2 Energy ........................................................................................................................................................... 6
1.2.1 Internal energy (inwendige energie) .................................................................................................... 6
1.2.2 Enthalpy ................................................................................................................................................ 6
1.2.3 Entrophy ............................................................................................................................................... 7
1.2.4 Gibs free energie .................................................................................................................................. 8
1.3 Interactions................................................................................................................................................... 9
2 Protein Structure & Dynamics ..................................................................................................................... 10
2.1 AminoAcids ................................................................................................................................................. 10
2.2 Protein structure ......................................................................................................................................... 13
2.2.1 Primaire structuur .............................................................................................................................. 13
2.2.2. Secundaire structuur ......................................................................................................................... 14
2.2.3 Tertiaire structuur .............................................................................................................................. 17
2.2.4 Quartaire structuur ............................................................................................................................. 18
2.3 Protein Dynamics ........................................................................................................................................ 19
2.3.1 Eiwit vouwing ..................................................................................................................................... 19
3.3.2 Eiwitstabiliteit ..................................................................................................................................... 22
2.3.3 Eiwitbeweging .................................................................................................................................... 23
3 Protein function .......................................................................................................................................... 24
3.1 Fluorescent Proteins ................................................................................................................................... 24
3.2 Shuttle Proteins: Globins ............................................................................................................................ 28
3.2.1 Myoglobin ........................................................................................................................................... 28
3.2.2 Hemoglobine ...................................................................................................................................... 29
3.3 Structural Proteins ...................................................................................................................................... 33
3.1 Collagen ................................................................................................................................................. 34
3.2 Elastin .................................................................................................................................................... 36
4 Enzymes ...................................................................................................................................................... 39
4.1 Enzyme Catalysis ........................................................................................................................................ 39
4.1.1 Specifity .............................................................................................................................................. 39
4.1.2 Activation Energy ................................................................................................................................ 41
4.1.3 Acceleration ........................................................................................................................................ 42
4.1.4 Mechanism: How Enzymes Do It ........................................................................................................ 43
4.1.5. Michaelis & Menten: How Fast Enzymes Do It .................................................................................. 47
4.1.6 Cofactors: Mother’s Little Helpers ...................................................................................................... 50
4.2 Enzyme Regulatie ....................................................................................................................................... 52
4.2.1 Irreversible Regulation by Covalent Modification .............................................................................. 52
4.2.2 Reversible Regulation by Covalent Modification ................................................................................ 53
4.2.3 Reversible, Non-covalent Inhibition ................................................................................................... 55
4.2.4 Cooperativity and Allostery ................................................................................................................ 58
5 Biological Membranes ................................................................................................................................. 60
5.1 Lipids ........................................................................................................................................................... 60
5.2 Bilayer ......................................................................................................................................................... 62
5.2.1 Building Membranes........................................................................................................................... 62
1
, 5.2.2 Membrane Function and Dynamics .................................................................................................... 63
5.3 Membrane Proteins .................................................................................................................................... 68
5.4 Membrane Transport ................................................................................................................................. 70
5.4.1 Fundamentals of Membrane Transport ............................................................................................. 70
5.4.2 Membrane-active Antibiotics ............................................................................................................. 72
5.4.3 Transport of Small Molecules ............................................................................................................. 75
6 Cellular Metabolism .................................................................................................................................... 86
6.1 Fundamentals ............................................................................................................................................. 86
6.2 Metabolic Routes........................................................................................................................................ 92
6.2.1 Glycolysis ............................................................................................................................................ 92
6.2.2 Pyruvate Decarboxylation .................................................................................................................. 96
6.2.3 Fermentation ...................................................................................................................................... 97
6.2.4 TCA-cyclus ........................................................................................................................................... 98
6.3 Electron Transport Chain ............................................................................................................................ 99
6.3.1 Mitchell’s Postulates: Membranes: de stuwdam ............................................................................... 99
6.3.2 Mitchell’s Postulates: Electron Transfer Chain (ETC) .......................................................................... 99
6.3.3 Mitchell’s Postulates: Proton Pumping ............................................................................................ 105
6.3.4 ROS production ................................................................................................................................. 107
6.3.5 Bacterial Respiration......................................................................................................................... 108
6.3.6 Heat production................................................................................................................................ 109
6.4 ATP synthesis ............................................................................................................................................ 110
6.4.1 The Coupling Factor .......................................................................................................................... 110
6.4.2 F1 ....................................................................................................................................................... 111
6.4.3 Rotations........................................................................................................................................... 111
6.4.4 F0: en dit is de aandrijf ...................................................................................................................... 113
2
, 1 Elements & Energies
1.1 Some Relevant Elements
Atomen:
- kern + elektronen daaromheen
- hebben verschillend aantal protonen en elektronen
- atoomnummer = aantal protonen (en elektronen) in de kern
- atoommassa = protonen + neutronen
De buitenste schil van sommige atomen is niet vol, we noemen deze elementen dan reactief
In moleculen zijn atomen verbonden met covalente bindingen
> covalente bindingen:
Een paar elektronen worden gedeeld door twee atomen
Carbon (C)
- heeft 4 elektronen in de buitenste schil --> 4 opnemen of 4
afstaan om de buitenste schil te verzadigen
- heeft een bijzondere rol in cellen: kan sterke covalente
bindingen vormen met andere carbon-atomen
>> met 1 covalente binding kunnen de groepen vrij rond bewegen rond elkaar
>> met meerdere covalente bindingen kan dit niet, liggen ineen vlak
>> carboxyl(zuur)-groepen kunnen proton >> veel CN-bindingen in proteines/ eiwittten
afstaan en negatief geladen worden >> amine = NH2
>> amide = CONH
Fosfaatgroepen:
- Hydroxyy groep (alcohol) + fosfaatgroep → fosfaatester
>> bij hydrolyse wordt de binding verbroken waardoor energie vrijkomt
3
