exam 2 Flashcards
enzyme
biological catalyst
with the exception of some RNAs,
enzymes are proteins
reaction rate is increased/decreased by enzymes?
increased up to 10^20 fold
most enzymes are so specific they..
catalyze reactions of only 1 stereoisomer of a given substrate
what can also catalyze a reaction?
temperature and it increases rate
activation energy
delta G with the temp sign and the lil cross thing
delta G is lowered/increased by
enzymes
in an enzyme catalyzed reaction…
enzyme binds substrate (S) which is the reactant
after enzyme binds substrate,
ES complex is formed
after ES complex forms,
transition-state species forms
after transition-state species is formed,
product is released from enzyme
substrate binds to the
active site
the active site is where a
small portion of enzyme where the substrate binds
active site is bound by what kind of forces?
non-covalent forces (so that easy separation can occur)
the delta G of a rxn doesn’t tell us..
anything about the rate at which a reaction will occur
what does delta G tell us?
if a reaction will proceed and release energy
rate of rxn usually expressed in terms of
delta in reaction or delta in product in a given time
rxn rate at low substrate…
slow rxn rate
substrate increases…
initial rate of rxn increases
what happens to enzyme binding sites when substrate becomes larger?
enzyme binding sites become filled to limit of Vmax (max rate of rxn)
beyond this limit, the enzyme is…
saturated with substrate and the reaction rate ceases to increase
Vo =
initial velocity (product formed/time)
S =
substrate concentration
as more substrate is added, rxn rate…
increases
at higher substrate, rxn rate changes…
very little
max rxn rate is reached when..
enzyme is saturated with substrate
Vmax =
maximum velocity
Km is also known as…
Michaelis-Menten constant
Km =
substrate concentration when Vo is 1/2 Vmax
Km is substrate that
leads to half-maximal velocity
when substrate gets large, Vmax is the…
max velocity
Km (Michaelis-Menten constant) is the..
dissociation constant for ES complex
a small Km indicates…
high enzyme/substrate affinity, meaning Vmax will be reached more quickly at lower S
from a hyperbolic curve, Vmax is…
- difficult to determine
- hyperbolic curve can be transformed into a straight line by taking the reciprocal of each variable
Michaelis-Menten
V = Vmax [S] / Km + [S]
lineweaver-burk plot
1/V = Km / Vmax x 1/[S] + 1/Vmax
in simpler words… y = m times x + b
plot of 1/V vs 1/[S] will give a straight line with
slope of Km/Vmax, y intercept of 1/Vmax, x intercept of -1/Km (absolute values)
rxn rate is also dependent on…
[S] at low concentration
reaction also reaches max velocity..
at high [S]
allosteric enzymes have a….
sigmoidal shape
allosteric behavior manifests as..
subtle changes at one site of enzyme affects substrate binding
allosteric enzymes are always multi-subunit
example of allosteric enzymes
oxygen binding of hemoglobin
multimeric
each chain has 1 heme group that can bind O2 (hemoglobin can bind up to 4 O2)
O2 binding curve for myoglobin is a…
hyberbolic curve
O2 binding curve for hemoglobin is…
sigmoidal (allosteric!!!!!)
O2 binding to myoglobin shows
steady rise until complete saturation
O2 binding to hemoglobin indicates
binding of 1st O2 which helps binding of next O2 (allosteric effect)
positive cooperativity
enzyme inhibition
competitive inhibitor and noncompetitive inhibitor
competitive inhibitor binds to the
active (catalytic) site and blocks access to it by substrate
noncompetitive inhibitor
- binds to a site other than the active site
- inhibits the enzyme by changing its conformation
competitive inhibitor is comprised of
- substrate competing with inhibitor for the active site
- more substrate needed to ‘outcompete’ inhibitor
changes in competitive inhibition variables
slope and x-int change, y doesn’t
y int –> Vmax doesn’t change
x int –> Km does change (apparent Km)
in competitive inhibition, inhibitor is directly…
- competing with the substrate active sites on enzymes
- apparent Km increases (you will need more substrate to get the same 1/2 Vmax)
- vmax doesn’t change
in noncompetitive inhibition, the inhibitor does not…
- interfere with binding of substrate to the active site, Km is unchanged
- increasing [S] can’t overcome noncompetitive inhibition
noncompetitive inhibition variables
slope and y-int change, x-int does not change
Vmax changes (apparent Vmax)
Km does not change
in noncompetitive inhibition, inhibitor does not bind..
the active site, binds allosterically
substrate cannot win binding race (rxn will not occur as fast as it could - apparent Vmax decreases)
in noncompetitive inhibition, the overall rxn will..
not occur as fast as it could ; Vmax decreases
allosteric enzymes are..
an oligomer whose bio activity is affected by other substances binding to it
substances binding to allosteric enzyme can..
change the enzyme’s activity by altering the conformations of the quaternary structure
allosteric effector is a…
subtance that modifies the behavior of an allosteric enzyme
components of allosteric effectors…
allosteric activator and allosteric inhibitor
allosteric inhibitor means that..
the formation of product inhibits its continued production (aka feedback inhibition or end-product inhibition)
allosteric enzymes are single or multi subunit?
multi-subunit ; meaning multiple conformations of the enzyme exist
allosteric effector is..
a substance that modifies the quarternary structure of an allosteric enzyme (can be homotropic or heterotropic)
models for allosteric enzyme behavior
concerted model or sequential model
concerted model
enzyme has two conformations
conformations of the concerted model
R (relaxed) - binds substrate tightly (active form)
T (tight) - binds substrate less tightly (inactive)
when there’s no substrate in the concerted model, most enzyme molecules are in the…
T (inactive) form
in the presence of substrate in the concerted model,
equilibrium shifts T form to R form
- inactive to active
- simultaneous
changing from T to R and vice versa, all subunits change…
conformation simultaneously in the concerted model
allosteric activator binds and stabilizes…
R form (active)
allosteric inhibitor binds and stabilizes…
T form (inactive)
sequential model’s main features are the
- binding of substrate induces conformational change from T to R form
- change in conformation is induced by the fit of substrate to enzyme (induced-fit model)
- REPRESENTS cooperativity
in the sequential model…
- R form is favored by the allosteric activator
- T form is favored by allosteric inhibitor
main difference between concerted and sequential models
concerted - all subunits change simultaneously
sequential - subunits change in sequence (not at the same time)
allosterism and pharmaceuticals
- beta blockers
- binds to beta-adrenergic receptors
- used to treat chance of 2nd heart attack
another example of allosterism and pharmaceuticals…
valium
- binds to allosteric site on GABA receptors
- leads to CNS depressant effects
control of enzyme activity
side chain (-OH groups) of serine, threonine, tyrosine can form phosphate esters
the phosphorylation by ATP converts inactive precursor into active enzymes
phosphorylation - protein kinases are…
proteins that catalyze phosphorylation rxns
other ways to control enzymes (way 1)
zymogen - inactive precursor of an enzyme
- cleavage of one or more covalent bonds transforms it into an active enzyme
2nd way to control enzymes
chymotrypsinogen
- synthesized and stored in the pancreas
- when secreted into the small intestine, the digestive enzyme trypsin cleaves it to give pi-chymotrypsin
chymotrypsin is..
alpha-chymotrypsin is enzymatically active bc of its tertiary structure
- was inactive b/c of its tertiary structure
common types of catalytic mechanism
general acid base catalysis
lewis acid/base rxns
coenzyme is…
a nonprotein substance bound covalently or non-covalently to an enzyme
- takes part in an enzymatic rxn and is regenerated for further rxn
- organic compounds, many of which are vitamins or are metabolically related to vitaminds
cofactors are…
metal ions that behave as coordination compounds (Zn2+, Fe2+)
coenzyme (NAD+)
nicotinamide adenine dinucleotide (NAD+) is used in many redox rxns (precursor is niacin - B3)
- redox rxns provide energy
coenzymes (NADH)
NADH is formed from the reduction of NAD+, a two-electron oxidizing agent
lipids are organic compounds that are….
insoluble in water and are nonpolar
have SOME ampipathic qualities
open chain forms (fatty acids)
triacylglycerols
phosphoacylglycerols
sphingolipids
glycolipids
lipid-soluble vitamins
prostaglandins
leukotrienes, and thromboxanes
cyclic forms of lipids - sterols
cholesterol
steroid hormones
bile salts
fatty acids qualities
- unbranched-chain carboxylic acids
- length of chain plays a role in chemical character
- most commonly 12 - 20 carbons
- usually even #s of carbons
- C=C is UNSATURATED
- C-C is SATURATED
most unsaturated fatty acids have a (x) isomer
cis
unsaturated fatty acids have a (x) melting point than their saturated counterparts
lower (greater degree of unsaturation, lower melting point)
- think: oils
triglycerides are..
- an ester of glycerol w/ 3 fatty acid chains
- more energy per gram than carbs or proteins
- can be saturated or unsaturated
trans-fatty acids are made from…
hydrogenation process makes trans bonds
- trans fat leads to heart disease
- high LDL = not good
phospholipids are…
one alcohol group of glycerol esterified by a phosphoric acid
rather than by a carboxylic acid
phospholipids are found in
biological membranes
- can be saturated or unsaturated fatty acid chains
lipid bilayer is found in the
biological membrane
the lipid bilayer is made of
predominantly phospholipids
polar head groups get in contact w/ water
nonpolar tails buried within (hydrophobic)
can be rigid (lots of saturated fatty acids) or fluid (lots of unsaturated FA)
membrane layers
both layers contain mixtures of lipids
- asymmetric (compositions on inside/outside of lipid bilayer can be different)
- exterior usually has more bulky lipids
unsaturated FA in membranes put…
a kink in chain
- causes disorder in packing
- disorder increases fluidity
cholesterol prevents…
extremes in temperature in membrane
- stabilizes extended chain conformations in FA (hydrophobic interactions)
- reduces fluidity on inside
cholesterol also disrupts..
the tight packing of phospholipids so FA chains can’t come together
- increases fluidity outside cell
fluid mosaic model
lateral motion of various components in membrane that exist side-by-side as separate entities
(lipid bilayer w/ proteins, glycolipids, glycoproteins, sterols)
membrane proteins
peripheral proteins (electrostatic interactions)
integral proteins (hydrophobic interactions)
membrane protein functions
- transport substances across membranes
- act as receptor sites
- sites of enzyme catalysis
glycoproteins on cell surface are involved in
- cell identification
- receptor sites
- immune function
glycolipids are important for
- membranes
- brain
- nervous systems
gangliosides are glycolipids with…
complex carbohydrate moiety that contains more than 3 sugars
membrane is selectively…
permeable
types of transport
passive & active
active transport requires…
energy
passive transport doesn’t…
require energy
- moves down a concentration gradient
simple diffusion is..
passive
- movement of a molecules across membrane from higher to lower concentration
facilitated diffusion is…
passive
uses a carrier protein or channel protein
active transport is linked to…
hydrolysis of ATP or any other high-energy molecule
membrane receptors are responsible for…
the binding of a biologically active substance to a receptor initiates an action within the cell
types of lipoproteins
low density lipoprotein (LDL)
high density lipoprotein (HDL)
LDLs are…
- LDLs carry cholesterol and phosphoglycerides along w/ protein in blood
- excess of cholesterol inhibits synthesis of LDL receptor which keeps cholesterol in blood
HDL transports…
cholesterol back to liver
vitamins are separated by
lipid soluble and water soluble
vitamin A
site of primary photochemical reaction in vision
- often found in cell membrane
- vitamin A (retinol) occurs only in the animal world
vitamin D regulates
calcium and phosphorus metabolism
vitamin E
serves as an antioxidant
may be necessary for reproduction in humans and rats
vitamin K
important for blood clotting
vitamin A is found in the…
plant world as a group of pigments called carotenes
- enzyme catalyzed cleavage of beta-carotene followed by reduction gives 2 molecules of vitamin A
vitamin A’s active molecule is…
retinal
- helps to form visual pigment rhodopsin
vitamin D is mostly found in the
circulatory system
vitamin E is often found in the
cell membrane
reducing agent
electron donor
oxidizing agent
electron acceptor
