Topic 5 Flashcards
Nitrogen fixation
N2 + 3H2 > NH3
At what environments do industrial processes do N fix?
~200 atmospheres and 400 degrees Celcius
At what environments do bacteria fix N?1
Atmospheric pressure, ambient temperature
2 ways a reaction can be accelerated?
Adding heat
Adding catalyst
3 ways enzymes are proteins?
- primary, secondary, tertiary, quaternary structure
- typically globular
- structure determined by same forces
3 ways enzymes are catalysts?
- accelerate reaction rates
- regenerate at the end of reaction
- highly specific (no side reactions)
Enzyme Nomencclature
end in -ase
substrate (or product) chemical rxn
A reaction will only proceed if…
free E of products is less than free E of reactants
When G is negative
Reaction is exergonic, thermodynamically favourable, spontaneous
When G is positive
Reaction is endergonic, thermodynamically unfavourable, and non-spontaneous
how is the speed of a biochemical reaction determined?
activation energy barrier
At what point in the reaction is there highest free energy?
Transition state
T/F do enzymes affect G of reaction
FALSE, enzymes do not affect
How do enzymes reduce free energy? (4)
- remove substrates from aqueous solutions
- proximity and orientation
- taking part in reaction mechanism
- stabilizing transitions state
Active sites (4)
- where catalysis occurs (small portion of protein)
- key amino acids located in active site (binding and catalysis)
- determines affinity, speciality and rate
- complementary to substrate/transition state (shape, hydrophobic interactions, H bonds, ion pairs)
Where is the active site in a lysosome?
3D cleft/crevice
Lock and Key model
active site matches shape of substrate contributing to affinity and specificity
Desolvation
exclusion of water,
3 advantages of desolvation
- removal of water shell accelerates reactions
- enhances polar interactions
- prevents side reactions
Induced Fit Model
enzymes change shape when substrate binds
closes off active site
brings catalytic groups together
orientation
chemical reactions only occur if substrates come together in right orientation
proximity
active sites bind substrates close to each other
3 types of catalysis
acid/base, covalent, metal ion
how are catalysis reactions acheived
amino acids or cofactors
Acid/Base catalysis
R groups of amino acids act as acids or bases depending on state of protonation
Covalent catalysis
de-protonated R groups of amino acids act as nucleophiles
Review classification of cofactors tree
and examples btw
holoenzyme
prosthetic group and tertiary structure
apoenzyme
tertiary structure without prosthetic group
3 ways transition state is stabilized
- binding TS lowers G
- parts of protein interact with unstable transition state
- enzyme active sites
the more tightly an enzyme binds to TS ….
the greater the catalytic activity of the enzyme
TS analogs are ____ inhibitors
potent
potent inhibitors
binds to enzyme with higher affinity compared to substrate
rational basis for drug design
Km gets ___ as affinity ____
smaller, increases
Mechanisms that affect intrinsic activity of enzyme
competitive inhibition, allostery, reversible covalent modification, ionic signals
Allostery (allosteric enzymes)
modify metabolic processes with allosteric effectors because enzyme activity may be cooperative
Reversible covalent modification
modify proteins in tertiary amino acid residue, increase or decrease activity of target
mechanisms that change amount of enzyme available,
regulation of gene expression, changes in sub cellular localization (regulate access of enzyme and substrate)
competitive inhibitors
bind reversibly
resemble substrate or TS but DO NOT react
physically block = less active sites, lower reaction rate, increase in Km
how to overcome inhibition
increase substrate concentration (no change in Vmax)
Competitive inhibitors decrease _____ affinity (increase Km)
decrease
T state
low activity, allosteric inhibitor favours
R state
high activity, allosteric activators favours
most common type of reversible modification
phosphorylation
Phosphorylation
increases size, polarity, and charge
____ catalyze phosphoryaltion
protein kinase
______ catalyze dephosphorylation by ____
protein phosphatase, hydrolysis
which amino acids are usually phosphorylated (ones with OH)
ser, tyr, thr
