Chapter 9 - Mechanisms Flashcards
What are the 4 catalytic principles?
covalent catalysis
acid base catalysis
catalysis by approximation
metal ion catalysis
what is covalent catalysis?
an enzyme makes a covalent bond by itself
the covalent bond will need to break to not use up all the energy in for the enzyme to continue its reaction
what is acid base catalysis?
enzyme is acting as an acid or base or both in the process of catalysis
not an acid base reaction but the enzyme is an acid by donating a proton and accepts a proton and is a base
what is catalysis by approximation?
the distance and the orientation is very specific
what is metal ion catalysis?
enzymes use metal ion as prosthetics
How many catalytic principles do enzymes usually follow>
they use at least one but most use more than one
proteases hydrolyze what bond?
the peptide bond
how are protease families divided?
They are divided by what they do
which enzymatic principle is involved in all enzymes?
catalysis by approximation
what is the other substrate involved in a proteases hydrolysis?
the peptide bond (is the implied one)
water
what are the products for a proteases hydrolosis?
carbonyl containing product
amine containing product
how do we classify enzymes?
by what they do
what group is a protease? And what does that class do?
proteases are a class of enzymes
cut peptide bonds
if you hydrolyze a peptide bond what are you?
a protease
what does the term family mean?
they have a common ancestor (similar by genealogical evolutionary relation)
what makes you a member of a family?
where you come from
what makes you a protease?
cut peptide bonds
or what you do
in order to be a member of the class of proteases you need to be able to do what?
hydrolyze a peptide bond
what are some of the families of proteases?
serine
how is the serine protease family “related”?
because they are inhibited by certain irreversible competitive inhibitors.
have homologous tertiary structures (because of having homologous primary structure)
Because the serine protease family has homology in tertiary structure what is that due to?
having homology in there primary structure
What makes a serine protease part of this family?
they have varying substrate specificity but use the same catalytic mechanism
What are two examples of a serine protease?
Chymotrypsin and Trypsin
they are digestive enzymes in your gut
how is chymotrypsin and trypsin similar and how are they different?
similar:
- active site
- they use the same mechanisms
- use covalent catalysis
differences:
- trypsin has an aspartic acid in the active site
- chymotrypsin cuts after an aromatic amino acid (Phenylalanine, tryptophan, tyrosine)
- trypsin with its negative charge cuts after the basic amino acids (lysine or arginine, (positively charged))
What 3 amino acids are in the active site that is conserved in all serine proteases?
aspartic acid
histidine
serine
Which amino acid allows the serine protease to participate in the catalytic principle of acid base chemistry?
histidine
pulls and extracts a proton making it positively charged
What is the catalytic triad?
- aspartate (that interacts with and changes the PKA of a histidine)
2.histidine (that then becomes a strong enough base that it get protonated and changes the nucleophilicity of a serine) - serine (the now strong enough nucleophilicity of the serine attacks the first reactant making a covalent bond with it)
Which catalytic principles do serine proteases use? Which do they not use?
acid base chemistry
covalent catalysis
approximation
DON’T USE: Metal Ion
What comes after the catalytic triad?
first product is released the second reactant comes in splits (through hydrolysis) the acyl enzyme covalent structure releasing the second product
what are the other 3 protease families named?
cysteine proteases
aspartyl proteases
metalloproteases
which catalytic principles does cysteine proteases use?
thiol will make a covalent interaction with the substrate (covalent catalysis)
approximation (because everyone does)
NO to acid base because the histidine does not get protonated.
which catalytic principle does aspartyl proteases use?
acid base catalysis (extracts a proton from the water, aspartate acting as a base and the water will attack the amide bond)
approximation (everyone has it)
which catalytic principle does metalloproteases use?
metal ion catalysis (zinc will manipulate the nucleophilicity of a water molecule which can attack the second substrate and end with two products)
approximation (everyone does)
what is the other substrate other than aspartate in a aspartyl protease?
water
What does chelate or chelation mean?
an interaction between a metal ion or metal atom and an organic molecule through more than one coordination sphere
How does carbonic anhydrase catalyze? And what does it catalyze?
it does this by using a zinc dependent mechanism
It catalyzes the formation of carbonic acid
what is the carbon dioxide hydration?
carbon dioxide + water -> hydrated carbon dioxide (carbonic acid) -> bicarbonate ion + Hydrogen
what enzyme catalyzes the carbon dioxide hydration?
carbonic anhydrase
what do all carbonic anhydrases have in common?
they all use a zinc assisted catalytic mechanism
how does the zinc ion catalysis mechanism work?
has three histidines chelating the zinc ion
which interacts with one of the two substrates (water) making it a better nucleophile so that it will attack the carbon dioxide and hydrate it
what catalytic principles are involve din the zinc ion catalysis?
metal ion catalysis
approximation
why are there three different families of carbonic anhydrase?
because of the convergent evolution
are all carbonic anhydrases related?
no, they are not homologous but because they all use chelated zinc ions that are chelated by histidines (using the same mechanism) but they did not arrive to that evolution with a common ancestoral chain
what is convergent evolution?
when molecules seem to have the same mechanisms or parts but they did not form from the same common ancestor and are not homologous making the same ending not the same start.
Restriction enzymes do what to DNA? How do they do it?
hydrolyze
in a sequence specific manner using a magnesium dependent mechanism
What catalytic principles does restriction enzymes show?
metal ion catalysis (Mg)
approximation
what are the three important types of phosphate related enzymes?
kinases
phosphorylases
phosphatases
what does phosphate related mean?
that the substrate and the product both have phosphate in them
all of the phosphorous appear in humans as what?
phosphate PO4
what is the most important type of phosphate related enzymes?`
kinases then phosphorylases then phosphatases
what does a kinase do?
what does a phosphorylase do?
what does a phosphatase do?
kinases transfer phosphates
phosphorylases join together phosphates to organic molecule
phosphatases take phosphates off
of the three which will you see the most?
kinases
what is an example of a kinase?
NMP and ATP transfers a phosphate to get NDP and ADP
what is the p in p loop family?
phosphase
why is the p loop family important?
shows dramatic induced fit
why is something in the p loop family?
has a central beta sheet
and at least two flanking alpha helices that are homologous
a little random coil piece that interacts with the phosphate as a substrate product or both (phosphate binding loop)
what is the relationship between enzyme class and protein family?
protein families are defined as being evolutionary related
enzyme classes are defined by the reaction they catalyze
there is no relationship between enzyme class and protein family.
most phosphate related enzymes use what?
magnesium
what do phosphate related enzymes do when using magnesium?
they break a phospho ester bond
what do p loop family members use?
approximation catalysis
metal ion catalysis
dependent on the enzyme they could use the other two but by defintion they use the above two
which enzymes uses zinc as part of there metal ion catalysis?
metalloproteases
carbonic anhydrase
which enzymes use magnesium as part of there metal ion catalysis?
restriction enzymes
p loop family members
