Biochem 2: Enzymes Flashcards
an enzyme is a
biological catalyst
-proteins (with the exception of some RNAs that catalyze their own splicing, all enzymes are proteins)
enzymes can increase the
rate of a reaction by a factor of up to 10^20 over an uncatalyzed reaction
the rate of a reaction depends on its
activation energy (delta G)
enzymes do what to activation energy
an enzyme provides an alternative pathway with a lower activation energy
substrate
reactant binds to active site of an enzyme
active site
the small portion of the enzyme surface where the substrate(s) is bound
enzyme substrate complex (ES) is held together by
hydrogen bonding, electrostatic attractions, van der Waals attractions
what two models have been developed to describe formation of the enzyme-substrate complex
- lock and key model
2. induced fit model (most enzymes follow this model)
in the lock and key model, the
substrate binds to that portion of the enzyme with a complementary shape
in the induced fit model, the
binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit
the rate of a catalyzed reaction depends on
substrate concentration
concentration of an enzyme is usually much _____ than the concentration of substrate
lower
what occurs at saturation
all enzyme is bound to substrate, it is working at maximum rate
list of things that can affect the rate of a reaction
- temperature
- pH
- enzyme concentration
- substrate concentration
- presence of controlling molecules
pH influences ______ of the functional groups
ionization
example of how pH affects enzyme function
at low pH (high H+), COO- may react with H+ to form COOH which is no longer charged
-this affects folding and thus enzyme function
increasing temperature will _____ reaction rate
increase
at high temperature what bonds begin to break?
non-covalent
what happens with denaturation and around what temperature
enzymes can lose tertiary structure and become denatured, usually occurs around 50-55 degrees C
what occurs when the enzyme is saturated
the rate of the reaction is maximal and cannot increase
the rate of the reaction is _____ proportional to the enzyme concentration
directly
as long as substrate does not run out
the rate and observed kinetics of an enzymatic reaction depends on
substrate concentration
at low substrate concentration, adding more substrate will
increase the rate of reaction
a constant rate Vmax is reached when
the enzyme is completely saturated with substrate
Km is the
michaelis constant
the higher the value for Km, the ____ the affinity for substrate
lower
the lower the Km value, the ____ the affinity for substrate
higher
how can you liberalize the michaelis-menten equation
with the lineweaver-burke plot (y=mx + b) form
lineweaver-burke plot is of ___ versus ____
slope=
y intercept=
1/V versus 1/[S] which gives a straight line
slope: Km/Vmax
y intercept: 1/Vmax
what is a reversible inhibitor and what types are there
a substance that binds to an enzyme to inhibit it, but can be released
-competitive and noncompetitive
reversible inhibitor:
competitive
binds to the active (catalytic) site and blocks access to it by substrate
reversible inhibitor:
noncompetitive
binds to a site other than the active site
-inhibits the enzyme by changing its conformation
irreversible inhibitor
a substance that causes inhibition that cannot be reversed
-usually involves formation or breaking of covalent bonds to or on the enzyme
list of things important to enzyme regulation
-feedback inhibition allosteric regulation -covalent modification: phosphorylation -proteolytic activation -regulatory proteins
feedback inhibition
formation of product inhibits its continued production
allosteric enzyme
an oligomer whose biological activity is affected by other substances binding to it
how do allosteric enzymes work
these substances change the enzyme’s activity by altering the conformation(s) of its 4 quaternary structure
allosteric effector
a substance that modifies the behavior of an allosteric enzyme
-may be an allosteric inhibitor or allosteric activator
a _____ shape of curve describes allosteric behavior
sigmoidal
the side chains -OH groups of ___, ___, an d___ can form phosphate esters
Ser, Thr, Tyr
what changes can phosphorylation by ATP cause
can convert an inactive precursor into an active enzyme
what is a zymogen
an inactive precursor of an enzyme where proteolytic cleavage of one or more covalent bonds transforms it into the active enzyme
common examples of zymogens
digestive enzymes, complement proteins, blood clotting factors and capsizes in apoptosis
chymotrypsinogen
- synthesized and stored in the pancreas
- a single polypeptide chain of 245 amino acid residues cross linked by 5 disulfide bonds
- when secreted into the small intestine, the digestive enzyme trypsin cleaves a 15 unit polypeptide from the N-terminal end to give pi-chymotrypsin
apoptosis is a
programmed form of cellular suicide in which the cell participates actively in its own death
what is a prearranged signaling pathway of cell death triggered by a variety of special extracellular and intracellular signals
apoptosis
why is apoptosis useful
it is a self-defense mechanism to destroy cells infected with pathogens or those with genomic alterations
events of apoptosis
- cell detaches from its neighbors
- chromatin is digested by enzymes that cut DNA between nucleosomes
- forms membraneous lobes called “blebs” that break into fragments
- surrounding living cells ingest remains of the dead cell and recycle the contents
signals that initiate apoptosis:
- hormones
- growth factors
- viral infections
- toxins
- extensive DNA damage
apoptotic signals: what do the pathways affect?
some affect: mitochondria, increasing permeability of the membranes, ATP production stops and the cell dies
proteases called _____ may be activated in apoptosis
caspases
what do capsases do
they hydrolyze membrane proteins in nuclear and cell membranes and nucleosomes
G proteins are activated during
signal transduction once a hormone binds its receptor and the receptor activates the G-protein (found in cAMP cascade)
what is transducer and what is it involved in?
transducin is a G-protein in retinal rods and cones that is involved in transduction of the visual signal
what is an isozyme?
isozymes are enzymes that catalyze the same reaction but have different properties, such as optimal temperatures
enzyme differences in humans vs. bacteria
enzymes in humans have higher optimal temperature than enzymes in most bacteria- a fever can denature the bacterial enzymes
types of non protein “partners” of enzymes
- prosthetic groups
- inorganic cofactors
- coenzymes
prosthetic groups
non-amino acid groups bound to enzymes
inorganic cofactors
ions permanently bound to enzymes
coenzymes
small carbon-containing molecules, not permanently bound
NAD is a type of
coenzyme- carries electrons/protons
NAD+ facts
nicotinamide adenine dinucleotide, used in many redox reactions in biology
contains: nicotinamide ring, adenine ring, 2 sugar-phosphate groups
NAD+ is a ___ ___ ____ ____ and reduced to what?
two-electron oxidizing agent
-reduced to NADH
where on NAD does the reduction-oxidation occur
nicotinamide ring
B6 vitamins are
coenzymes involved in amino group transfer from one molecule to another
-important in amino acid biosynthesis
