Term
| which hypothesis did Daniel Koshland come up with in 1958 regarding the ES complex? |
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Definition
the Induced Fit
here the substrate isn't a perfect fit for the active site but it wriggles its self in to make an ES complex through an induced fit |
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Term
| what is the name of the region that binds the substrate and any cofactors known as? |
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Definition
the active site
amino acids in the active site come from different locations in the primary amino acid sequence |
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Term
| what kind of interactions do substrates bind the active site by? |
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Definition
weak interactions such as electrostatic and van der waals interactions
the active site is usually a 3-d pocket or groove in the structure of the enzyme and it also contains amino acids involved in catalysis. these are found in the catalytic loop |
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Term
| mitogen activated protein kinase uses phosphate from ATP to phosphorylate other proteins targets. Name the three mains binding sites/loops found on the protein kinase |
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Definition
ATP binding site
substrate binding site
catalytic loop |
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Term
| what do mechanisms of catalysis do and name the three main mechanisms used |
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Definition
they hold substrate in place, establish substrate specifictiy and increase catalytic efficiencey
entropy effect
orbital steering
induced fit |
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Term
| entropy effect, orbital steering and induced fit are the 3 main mechanism of catalysis. what do they do? |
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Definition
entrophy effect - substrates held near each other or catalytic groups for increased time to > chance of binding
orbital steering - best orientation of substrate relative to catalytic groups
induced fit - maximal binding involves changes to conformation of E and S. this promotes formation of transition state |
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Term
| if substrates were held next to each other or catalytic groups for increased lengths of time to increased the oppurtunity of ES complexes forming which mechanism of catalysis would this be? |
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Definition
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Term
| this mechanism of catalysis involves maximal binding and involves changes to confomration of E and S. This mechanism also promotes formation of transition state |
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Definition
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Term
| which mechanism of catalysis invovles the best orientation of the substrate relative to catalytic groups? |
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Definition
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Term
some enzymes need a non-protein component - a cofactor
what do cofactors do? |
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Definition
they extend the range of chemical reactions that enzymes can catalyse
protein alone = inactive apoenzyme
protein + cofactor = active haloenzyme
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Term
Cofactors are non protein components that can be organic or metal ions. what is an organic cofactor called?
what do you call a cofactor that binds irreversibly to the enzyme? |
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Definition
an organic cofactor is called a coenzyme
cofactors that bind irreversibly to enzyme are called prosthetic group |
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Term
| which cofactors assist in substrate binding and orientation? |
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Definition
metal ions
they act in acid-base catalysis, serving as an electrophile to stabilise negative charge.
an electrophile is electron deficient thus is able to accept an electron to stabilise negative charge |
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Term
metal ions such as Cu (II), Fe (II), Zn (II) can also take part in oxidation-reduction reactions for which amino acids are not suited to.
what do you call a metal ion that is strongly bound?
what do you call a metal ion that is weakly bound? |
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Definition
strongly bound metal ion called metalloenzyme
weakly bound metal ion called metal-activated enzyme |
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Term
| what happens in covalent catalysis? |
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Definition
well, the active site contains a reactive group (usually a nucleophile) that becomes covalently modified during the reaction
eg double displacement reactions
amino acids commonly involved are:
serine -OH
Cysteine -SH
Histidine -imidazole ring
Lysine -NH3 |
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Term
| name 2 types of catalysis that enzymes use |
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Definition
| covalent catalysis and general aid-base catalysis |
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Term
| when does acid-base catalysis occur? |
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Definition
when a molecule other than water plays a role as a proton donor or acceptor
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Term
| how do enzymes increase reaction rates? |
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Definition
hold substrates together - entropy/orbital steering
promote formation of transition state - induced fit
contribute reactive groups - amino acid side chains and cofactors |
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