Biological molecules and Enzymes Flashcards by Jennifer Shin

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

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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.

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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.

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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.

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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

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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.

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What is the reciprocal of the Michaelis-Menten equation?

1/V = (Km/Vmax)(1/S) + (1/Vmax)

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At what pH do the pancreatic enzymes work the best?

In alkaline conditions

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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

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Lipids - Number of carbon formula

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what does amphiphatic mean

both polar and non-polar

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how many rings does a steroid have

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eicosanoids

how many carbons and what are their functions

20 C

usually local hormones, paracrine hormones like prostaglandins

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What are lipoproteins?

What do they look like?

Composed by phospholipids and apoproteins

Hydrophobic core and hydrophilic shell

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carbohydrates

formula

Cn(H2O)n

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Type of linkage in glycogen

alpha glycosidic linkage

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starch (amylopectin and amylose) linkage

difference between amylopectin and amylose

both have alpha linkage

amylopectin is branched but amylose can be branched or unbranched

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cellulose linkage

beta

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method of glucose absorption in the digestive tract and kidney cells

secondary active down the Na+ concentration gradient

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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

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what organs are capable of absorbing glucose without insulin?

brain and liver

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List basic amino acids

HAL

histidine

arginine

lysine

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List acidic amino acids

aspartate

glutamate

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List non-polar amino acids

VIP AL PH MALT Glycine

valine
Isoleucine
Proline

Alanine

Methionine
Leucine
Trptophan

Phenylalanine

Glycine

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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?

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!