Biological molecules and Enzymes Flashcards
How do enzymes affect equilibrium constant and Gibb’s free energy?
How does it affect the rate of reaction?
How does it affect the intermediate state?
doesn’t change equilibrium or Gibb’s free energy
It lowers the activation energy without being used up in the reaction. Increase both the forward and reverse rate of reaction equally.
allow more molecules to overcome the energy barrier to achieve the intermediate state, making the intermediate state more stable
Effect of temperature and pH on enzymes
Optimal temperature is 37C and optimal pH is 7.4.
The rate of enzyme reaction increases linearly until 37C and drops rapidly fast after 37C reaching 0 rate of reaction at 50C.
The rate of enzyme reaction increases steadily and linearly upto pH of 7.4 and drops linearly and steadily down till reaching 0 at pH of 12 for most enzymes. For some enzymes like pepsin, optimal pH is at 2. So it really depends on the enzyme.
Does Michaelis-Menten enzyme kinetics apply to allosterically regulated enzymes? What is an allosteric regulation? Give an example.
Nope. An example of allosteric regulation is hemoglobin and oxygen which has a sigmoidal curve. Allosterically regulated enzymes have multiple binding sites where other binding sites regulate the activation or deactivation of the enzyme by changing its conformation.
If a forward rate constant is greater than the reverse rate constant at equilibrium, what does it imply about the concentration of products and reactants at equilibrium?
It implies that the concentration of products is higher than the concentration of reactants.
What is the Michaelis-Menten equation?
Take the two most important factors: Vmax and Km
Add both of them to S, and divide. Vmax on top and Km at the bottom
V = (Vmax + S) / (S + 1/2Vmax)
1/2Vmax = Km
When does Km, the substrate concentration at half the max velocity, indicate affinity of the enzyme to the substrate? When Km is indicative of the affinity, what is the equation of Km? What portion of the Michaelis-Menten graph is this instance?
When rate constant of ES dissociation is greater than the rate constant of product (E + P) formation. In this case, Km = rate constant ES dissociation/ rate constant E+P formation
This instance represents the linear portion of the Michaelis-Menten graph, the first order part of the graph.
What is the reciprocal of the Michaelis-Menten equation?
1/V = (Km/Vmax)(1/S) + (1/Vmax)
At what pH do the pancreatic enzymes work the best?
In alkaline conditions
Michaelis Constant, Km
1/2 Vmax
indicates how high substrate concentration must be to speed up the reaction. Km is inversely related to enzyme-substrate affinity.
lower the Km, better the enzyme is working when the substrate concentration is low
Lipids - Number of carbon formula
2n
what does amphiphatic mean
both polar and non-polar
how many rings does a steroid have
4
eicosanoids
how many carbons and what are their functions
20 C
usually local hormones, paracrine hormones like prostaglandins
What are lipoproteins?
What do they look like?
Composed by phospholipids and apoproteins
Hydrophobic core and hydrophilic shell
carbohydrates
formula
Cn(H2O)n
Type of linkage in glycogen
alpha glycosidic linkage
starch (amylopectin and amylose) linkage
difference between amylopectin and amylose
both have alpha linkage
amylopectin is branched but amylose can be branched or unbranched
cellulose linkage
beta
method of glucose absorption in the digestive tract and kidney cells
secondary active down the Na+ concentration gradient
glucose absorption method in most cells and how insulin increases the rate of absorption
facilitated diffusion
insulin increases the rate of facilitated diffusion by making more channels
what organs are capable of absorbing glucose without insulin?
brain and liver
List basic amino acids
HAL
histidine
arginine
lysine
List acidic amino acids
aspartate
glutamate
List non-polar amino acids
VIP AL PH MALT Glycine
valine
Isoleucine
Proline
Alanine
Methionine
Leucine
Trptophan
Phenylalanine
Glycine
cysteine vs. cystine
cystine dimers (bonding or linkage of two cysteine amino acids) - represents the whole entity of two amino acids linked together
cysteine (polar amino acid)
proline and the secondary conformation
creates kinks in alpha helix and beta pleated sheets (secondary structure of proteins)
denaturation
loss of secondary, tertiary, and quaternary structure of proteins
information for proper conformation of a protein
primary
urea denaturation
hydrogen bonding
mercaptoethanol denaturation
cystine dimers
salt or change in pH denaturation
electrostatic charges
organic solvent denaturation
non-polar
heat denaturation
all of the bonds
What is a major component of cytochrome?
What does a prosthetic mean in biology? what does a conjugated protein mean? What is a prosthetic enzyme?
prosthetic heme
prosthetic means non-proteineous so a proteins with a prosthetic groups is called conjugated proteins
Prosthetic enzyme is a coenzyme with a covalently bonded component that comes out unchanged during a reaction
What is a turnover number?
number of substrate molecules “one active site” can work one at a time when the solution is saturated with substrate
How is Km related to ES affinity?
inversely related to ES affinity
How does Km change when enzyme concentration has changed?
What does this mean?
Km does not change when enzyme concentration changes. It doesn’t matter if more enzymes are added. The Km will remain the same.
This means that Km indicates an intrinsic fit between the substrate and the enzyme
What is a cofactor?
What are the two types of cofactors? and how are they different?
a non-protein component of enzyme needed for catalysis
coenazymes or metal ions (organic or non-organic)
coenzymes are organic, metal ions are not
what is a coenzyme
what are the two types of coenzymes?
what’s the difference between the two?
coenzymes are a type of cofactor that are organic carrier molecules that hold onto something to make catalysis happen like transfer one thing to another
cosubstrate and prosthetic
prosthetic is covalently bonded to the enzyme, cosubstrate is not
what is an apoenzyme
Is it functional?
enzyme without a cofactor.
completely non-functional
uncompetitive inhibitor
what does it bind to?
Effect on Km and Vmax
inhibitor binds only to the ES complex forming ESI
ES remain bound, so Km decreases
Vmax also decreases
can uncompetitive inhibitor be overcome by adding more substrate?
nope, therefore, Vmax decreases
mixed inhibitor
what does it bind to?
how is it different from a non-compeitive inhibitor
effect on Km and Vmax
it can bind to either enzyme alone, or ES complex.
it differs from a non-competitive inhibitor in that it has a preference for enzyme alone or ES complex
Vmax always decreases but Km depends on the preference of the inhibitor
non-competitive inhibitor
what does it bind to?
how is it different from a mixed inhibitor
it can bind to either enzyme alone or ES complex
it differs from the mixed inhibitor in that it was NO preference. 50-50
V max always decreases, but Km stays the same
holoenzyme
enzyme with a cofactor - functional
how do control proteins function?
control board on an enzyme that act like activators and repressors of transcription
subunit associated with the enzyme, initiating or inhibiting a reaction
examples are calmodulin or G-proteins
lyase vs ligase
ligase - link molecules through condensation reaction
lyase - remove double bond by adding functional group or create double bond by removing functional group
effect of enzyme on gibbs free energy of the transition state
lowers the gibbs free energy of the transition state but the overall Gibbs free energy remains the same
assuming that the enzyme concentration remains constant, the rate of the reaction can be increased by increasing the substrate concentration. in this case, what happens to the equilibrium constant K?
why is this so?
the equilibrium constant stays the same
the equilibrium constant reflects the environment
T/F: in order for a Vmax to exist, the enzyme concentration must be constant
True
how does change in enzyme concentration affect Vmax, Km, equilibrium constant K, and G?
increase in E, increase Vmax
Km, equilibrium constant, and G stay the same regardless of enzyme concentration
what is the steady-state assumption in enzyme kinetics?
it assumes that the rate of formation of ES is equal to the loss of ES
this assumption derives the Michaelis Menten Equation
the reverse reaction of ES E + P is negligible. so we assume that all the ES complexes undergo reaction to form E + P
what is turn over number or kcat?
how is Vmax and turnover number related?
kcat in sec- so a 1/kcat would give the time for each catalytic round of an active site
Vmax = kcat * [Etotal]
kcat = Vmax / [Etotal] kcat = Vmax / [E] + [ES]
what is the equation for catalytic efficiency?
kcat / Km
the reaction rate is directly related to catalytic efficiency
how is kcat (turn over number) and Km related?
inversely related
homotropic vs. heterotropic activator and inhibitor
homotropic - regulator and substrate are the same molecule
heterotropic - regulator and substrate are different
What is the maximum number of carbons in a fatty acid?
24
Do all proteins have secondary structures?
Nope, some proteins remain in their primary structure
T/F: 5 forces acting on the tertiary structure also acts on the quaternary structure
TRUE
What is a cytochrome?
“Colored cells” that can’t function without blood related non-proteinceous protein (prosthetic heme)
What is the difference between glycoproteins and proteoglycans?
Proteoglycans are generally 50% protein and 50% carbohydrates
Slope of the reverse Michaelis-Menten graph
Km/Vmax
Do temperature and pH affect Km?
YES!
