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Samenvatting biochemie
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Summary of 53 pages for the course biochemie at Hanze (biochemistry)
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BiochemieUnification
Enzymes
Naamgeving van enzyme en soorten enzymen
-eindiggen meestal op -ase
-bij hydrolases: naam afgeleid van het substraat: urea wordt urease
-andere enzyme worden vernoemd naar het substraat en het type reactie: lactaat
dehydrogenase, pyruvaat decarboxylase
Enzym katalyse in 4 stappen
o vorming van enzym-substraat complex (E-S)
o E-S* is de transition state (overgangstoestand)
o E-P is het enzym-product complex
o Enzymen stabiliseren het transitie-stadium (intermediair), waardoor Eact verlaagd
wordt
Enzym mechanisme
Hoe stimuleert een enzym versnelling van een reactie?
o Door vorming van het E-S complex kan er spanning (“stress”) op een binding komen
o Orienteren en bij elkaar brengen van reactanten
o Locale pH-modificatie
Transferase = verplaatst een groep Subklassen: transaminases, kinases (fosfaat groep), …
Kinase = een transferase enzym voor de fosfaat groep: PO4 3-
Hydrolase = hydrolyse, breekt binding d.m.v H2O. Subklassen: phosphatases, peptidases,
lipases,…
Lyase = additie of verwijdering van een klein molecuul (H2O, NH3, CO2) aan/van een dubbele
binding. Subklassen: (de)carboxylases, (de)hydratases,….
Isomerase = conversie van isomeren Subklassen: mutases, cis-trans isomerases
Ligase = maken van een C-O, C-C, C-S of
C-N binding BELANGRIJK: ook O-P binding (mist in het boek)
,The enzyme
Active site = the active site consist of the binding site and the catalytic site
o (Hydrofobe) pocket of spleet
o Het substraat wordt gebonden met vele niet-covalente interacties (zout-
bruggen, H-bruggen, van der Waals interacties, hydrophobe interacties)
o De vorm complementeert het substraat
o De catalytic site bevat de aminozuren die de eigenlijke katalyse verzorgen
Binding site = De plek waar het substrate bind
Catalytic site = De plek waar de catalyse plaatsvind
The binding and catalytic site together make up the active site where the substrate reacts
Lock-and-key model = het substraat past als sleutel in het enzym (Slot)
Induced-fit model = De enzymen verranderen van vorm wanneer ze een susbtraat binden
(als een handschoen)
Mayor properties of enzyme active sites
Enzyme active sites are pockets in the surface of an enzyme that inculde R
groups involved in binding and R groups involved in catalysis. The shape
of the active site is complementary to the shape of the substrate. Thus,
the conformation of the active site determines the specificity of the
enzyme. Enzyme-substrate binding involves weak, noncovalent
interactions.
Although enzyme active sites are small, the other portions of the protein
are also
important. It is the precise three-dimensional conformation assumed by
these sequences that holds the active site in the correct shape.
The enzyme active site is responsible for the specificity of an enzyme
The induced fit model assumes that the enzyme is flexible. Both the
enzyme and the substrate are able to change shape to form the enzyme-
substrate complex. The lock-and-key model assumes that the enzyme is
inflexible (lock) and the substrate (key) fits into a specific rigid site
(active site) on the enzyme to form the enzyme-substrate complex.
The size, shape, and charge distribution of the active site of an enzyme is
complementary to those of the substrate
Enzym interactions
Bindings-specificiteit = Enzym verbreekt/vormt 1 type binding en de omgeving moet aan
bepaalde voorwaarden voldoen
,Absolute specificiteit = katalyse van 1 substraat
Groep-specificiteit = Substraten hebben vergelijkbare structuur; bij de reactie is een functionele
groep betrokken (bijv. Fosfaat)
Stereochemische specificiteit= enzym herkent maar 1 van de twee enantiomeren
water-soluble vitamins are required by the body for the synthesis of
coenzymes that are required for the function of a variety of enzymes..
A coenzyme transiently binds to an enzyme and accepts chemical groups from
or donates chemical groups to the substrate in a biochemical reaction.
A proteolytic enzyme catalyzes the cleavage of the peptide bond that
maintains the primary protein structure. (chymotrypsin etc)
Co-enzym=
-organisch molecuul gebonden door zwakke interacties zoals H-bruggen
-tijdelijke interactie met enzym
-veelal dragers van chemische groepen of e- (pincetten v.d. cel)
-veelal bestaande uit gemodificeerde vitamines.
Protease = hydrolyseren peptide bindingen van eiwitten (spijsvertering/afbraak defecte
eiwitten).
-Chymotrypsine = Hydrolyseert de peptide binding na de volgende aminozuren:
phenylalanine, Tryptophaan, Tyrosine
-Trypsine = hydrolyseert peptide binding na de volgende aminozuren: lysine en arginine
(basisch)
-Elastase = hydrolyseert peptide binding na de volgende aminozuren: glycine of alanine
Enzyme regulation
Regulatie enzym activiteit
1. Alleen enzym maken wanneer nodig (vnl bacterien)
2. compartimenten (bv lysosoom)
3. Allosterische enzymen: regulatie door binding van een molecuul op een andere
plaats dan de active site. Activatie / inhibitie.
Feedback inhibitie: eindproduct van een biochemisch pad remt het eerste enzym
4. Inactief pro-enzym (pepsine/trypsine)
5. Eiwit modificatie (aan/uit)
-Een chemische groep wordt covalent gebonden aan het enzym of juist
‘weggeknipt’
, -eiwit modificatie zet enzym aan of uit
-meest gebruikte groep: fosfaat
-geschikte aminozuren voor deze modificatie: Serine, Threonine en Tyrosine (OH-
groepen)
Enzym inhibitie
-sommige moleculen binden aan enzymen en verminderen hun activiteit
classificatie:
1 irreversible inhibitors : binden zeer stevig (meestal covalent) aan het enzym /
vaak in de active site / hierdoor kan substraat niet meer binden of wel maar
reactie blokkeert/ veelal vergif: arseen/zenuwgassen.
2 reversibele inhibitors: binden reversibel in de active site. Stof lijkt vaak op
substraat/ binding aan active site voorkomt binding substraat.
3 reversible non-competative inhibitors: binden reversible maar niet in de active
site. Zorgt
voor een conformatie verandering = allosterische regulatie
a. Feedback inhibition is a phenomenon in which the end product of a
biochemical
pathway inhibits the entire pathway for its biosynthesis.
b. Feedback inhibition occurs because one of the early enzymes in the
pathway is an
allosteric enzyme having as its effector the molecule that is the end
product of the
pathway.
c. Feedback inhibition is an example of negative allosterism because
effector binding
inhibits activity of the enzyme.
A cofactor helps maintain the shape of the active site of an enzyme.
A structural analog is a molecule that has a structure and charge
distribution very similar to that of the natural substrate of an enzyme.
Generally, they are able to bind to the enzyme active site. This inhibits
enzyme activity because the normal substrate must compete with the
structural analog to form an enzyme-substrate complex.
A structural analog resembles the size, shape, and charge distribution
of the normal substrate for an enzyme. Because of this resemblance, it is
able to bind to the active site. However, when the structural analog binds
to the active site, no reaction occurs. Thus the enzyme is inhibited by
formation of the enzyme-structural analog complex.
An irreversible inhibitor binds very tightly, often covalently, to an enzyme,
thereby
permanently inactivating the active site. A reversible, noncompetitive inhibitor
binds
much more weakly to the enzyme. Enzyme activity is restored when the inhibitor
dissociates from the enzyme
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