BIO270H1 Lecture Notes - Lecture 3: Glycogen Synthase, Beta Sheet, Glycosylation

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2 Oct 2015

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Lecture 3 (september 30, 2015): biochemical basis of psychology continued. Energy storage cells store energy in two forms: reducing energy oxidized, high energy molecules. Made of multiple polypeptides ex: hemoglobin: most proteins can fold by themselves, but some need multi-protein complexes (molecular chaperones) proteins are a last ditch effort for the body to get energy. More energy can be produces when there is o2 present: more so than glycolysis can produce produces lots more atp. 2 redox shuttle remove nadh from the cytoplasm to allow glycolysis to continue: one shuttle turns into fadh2, other shuttle turns into nad, in the absence of o2. Krebs cycle acetyl coa goes in, 3 nadh, 1 fadh2, and 1 gtp comes out it is an anabolic and catabolic pathway it is regulated by the amount and activity of enzymes and the concentration of reactants.

Related Questions

describe the definitions of substrate, enzyme active site and its general characteristics, and apoand

holo-enzymes.

Â· describe the fact that enzyme catalysis is specific in terms of the type of reaction and the exact

substrate structure.

Â· Explain the difference in the âlock-and-keyâ model and the induced fit model of enzyme

substrate interaction.

Â· describe that reaction rate constant thus reaction rate is dependent on the activation energy.

Â· describe the relationship between the energy of the transition state and the activation energy.

Â· describe the relative binding affinity of a substrate and its transition state to the enzyme.

Â· Explain how enzymes speed up reaction rate, i.e., how do enzymes lower the activation

energy. Note: Factors other than preferential stabilization of transition state also contribute to increased

reaction rate. They include 1) enzymes placing one substrate (reactant) next to the other substrate (reactant)

so that the reaction is no longer dependent on the collision rate of the two substrates; 2) enzymes sequester the

substrate(s), minimizing solvent competition thus speeding up the reaction; 3) in enzyme complexes with each

enzyme catalyzing one step in a multi-step reaction sequence, the product of one reaction is fed to the active site

of another enzyme for the next step without the product diffusing away from the enzyme complex thereby

increasing reaction rate.

Â· describe the Michaelis-Menten equation relating the initial velocity to total substrate

concentration.

Â· describe the assumptions that went into the derivation of the Michaelis-Menten equation. ([E]

is constant, steady state assumption, etc)

Â· describe the relationship between Vmax and kcat and the fact that kcat is a constant for a given

enzyme and substrate at a given temperature and solution condition; whereas Vmax can differ

for a given enzyme and substrate at a given temperature and solution condition, depending

on the enzyme concentration.

Â· describe the definition of Kd (equilibrium dissociation constant for ES into E and S).

Â· describe the relationship between Kd and the affinity of substrate for the enzyme, i.e., the

higher the Kd, the weaker the binding between E and S.

Â· describe the relationship between Kd and Km, i.e., in general, the higher the Kd, the higher theKm.

Â· Use the Michaelis-Menten equation and the relationship between Vmax and kcat to do

calculations.

Â· describe the other names for the catalytic rate constant, kcat (i.e., the turn over number; also

called krelease) and why it is so called (kcat reports on per unit time per enzyme molecule the

number of product molecules formed/released, thus the name turnover number or krelease).

Â· Determine Vmax and Km using both the Michaelis-Menten plot (initial velocity versus [S]) and

the Lineweaver-Burk Plot (the double reciprocal plot), given the data of initial velocity and

[S].

Â· Draw the Michaelis-Menten plot AND the double reciprocal plot (Lineweaver Burk), given

the Vmax and Km values.

Â· describe the fact that the term kcat/Km is the best parameter for measuring the catalytic

capability (efficiency) of an enzyme.

Â· describe the existence of irreversible enzyme inhibition and the general mechanisms of

irreversible inhibition.

Â· describe the different types of reversible inhibitions, namely the competitive, uncompetitive,

and mixed inhibitions (noncompetitive inhibition is a special case in which the inhibitor

binds E and ES with equal affinity therefore Î± is equal to Î±â â Km is not affected).

Â· Describe each type of inhibition in terms of inhibitor binding site (active site or other than

the active site), how the inhibitor affects vmax and Km and the quantitative relationship of

each parameter with and without the inhibitor present and their relationship with [I] and KI

or KI

Â· Show the characteristics of each type of inhibition on a Michaelis-Menten plot (initial

velocity versus total substrate concentration), i.e. draw the curves with and without the

competitive inhibitor.

Â· Show the characteristics of each type of inhibition on a double reciprocal plot (LineweaverBurk

Plot) by drawing the lines with and without the competitive inhibitor.

Â· Given the Michaelis-Menten or double reciprocal plot with and without the inhibitor,

determine the type of inhibitor.

Â· describe the fact that transition state analogs are potent inhibitors.

Â· Explain why transition state analogs are potent inhibitors.

Â· describe that not all enzymes obey Michaelis-Menten kinetics.

Â· describe situations when an enzyme will not obey Michaelis-Menten kinetics (when the enzyme

catalyzes reactions with multiple substrates or when the enzyme is allosteric, i.e. binding of

the substrate at one active site affects the other active site(s) for the same substrate).

Â· Name the four types of catalytic mechanisms. (electrostatic catalysis, general/specific acid

base catalysis, metal ion catalysis, covalent catalysis)

Â· Contrast acid/base catalysis to general acid/base catalysis, i.e., comment on their similarity

and difference.

Â· Name the eight common general acid/base pairs in proteins and write the formula of the

acid and base form for each pair (hint: consider the eight amino acids that have ionizable

side chainsâ¦)

Â· describe the meaning of covalent catalysis.

Â· describe the reaction catalyzed by chymotrypsin and the three catalytic residues in

chymotrypsin.

Â· Draw the interactions among the three catalytic residues (catalytic triad).

Â· State the catalytic role of each of the catalytic residues and how they accomplish that.

Â· describe the steps in the formation of the acyl-enzyme intermediate, and the substrate and

products in this first part of the chymotrypsin mechanism.

Â· Draw the transition state structure for the formation of the acyl-enzyme intermediate and

indicate by drawing how it is preferentially stabilized.

Â· describe the steps in the regeneration of chymotrypsin (deacylation), the substrates and

product of this second part of the chymotrypsin mechanism.

Â· Draw the transition state for deacylation and explain how it is preferentially bound to or

stabilized by the enzyme.

Â· Explain what general acid and base catalysis refers to and what groups act as the general acid

and base in the chymotrypsin mechanism.

Â· Explain what covalent catalysis refers to in the chymotrypsin mechanism.

Â· Explain the basis for the substrate specificity of chymotrypsin (consider the composition of

the active site â chymotrypsin specifically cleaves peptide bonds adjacent to aromatic

residues)

Â· Explain the term âserine proteaseâ. Answer: these are proteases (enzymes that

hydrolyze peptide bonds) that have serine as a catalytic residue (that acts as a

nucleophile, which can attack the carbonyl carbon of the peptide bond).

Â· Key features of Hexokinase, enolase and lysozyme mechanisms that were discussed in class

(specific methods of catalysis utilized by these enzymes; general description of overall

catalytic transformation)

Â· describe the four regulatory strategies of enzyme catalysis

Â· describe the definition of feedback inhibition (mechanism of cellular regulation that regards an

enzyme that catalyzes the production of a given substance that then inhibits the cell when

concentration of that substance has reached an appropriate level â this balances/regulates

amount of product provided with amount needed)

Â· describe the most common type of covalent modification and the types of enzymes

responsible for the addition and removal of the chemical group in this covalent

modification.

Â· Explain the general mechanism of phosphorylation in regulating enzyme activity.

Â· describe the general naming scheme for active and inactive proteases.

Â· describe that protease inhibitors exist to inhibit protease.

Â· describe that enzymes are regulated through covalent and non-covalent processes.

Â· Noncovalent regulation

o Describe noncovalent modification in general terms. Elaborate on the relation

among enzyme activity, allostery, effector molecules (small molecules) and control

proteins.

o Concerning allosteric regulation, some enzymes have multiple active sites for the

same substrate and the binding of the substrate increases the activity of the enzyme

by stabilizing the R (more active) state over the T (relatively inactive) state. (Lecture

13: âNoncovalent Modification: Allosteric Regulatorsâ)

Ã Draw a curve for the initial reaction velocity versus substrate concentration.

Ã describe and explain the specific shape of the v0 vs. [S] plot.

Ã Draw on the same graph above a v0 vs. [S] curve for the enzyme in the

absence of allostery. and how th i.e., in the absence of conformational change

upon substrate binding. Comment on the shape of this curve.

Ã Comment on the benefit of allosteric activation.

Ã When an inhibitor is present for such an allosteric enzyme, the v0 versus [S]

plot will shift. Draw a v0 vs. [S] curve with and without the inhibitor.

Ã When an activator is present for such an allosteric enzyme, the v0 versus [S]

plot will shift. Draw a v0 vs. [S] curve with and without the inhibitor.

Ã When an activator is present for such an allosteric enzyme, the v0 versus.

Ã describe the relationship between feedback inhibition and allosteric regulation

and the reason behind the term âfeedback inhibitionâ.

Â· Covalent regulation

o describe the most common covalent modification, the enzymes that catalyze the

modification and the removal of that modification, respectively and the amino acid

residues that tend to be the site of this modification.

o Write the structure of the added group bonded to those residues and the reaction for

this covalent modification.

o Rationalize the effectiveness of phosphorylation on altering the activity of an

enzyme.

o describe the mechanism of chymotrypsinogen activation to chymotrypsin (cleavage of

zymogen by trypsin).

Enzyme Activity

1. Briefly explain the principle of spectrophotometry.

2. Which of the following statements is true about enzymes?(check all correct answers)

		__ enzymes act on (are specific for) one or just a fewsubstrates
		__ enzymes can be denatured (loose their tertiary/quaternarystructure and activity) by extreme conditions such as heat, high orlow pH,or presence of organic solvents
		__most enzymes are DNA
		__ enzymes are protein
		__enzymes perform best at specific conditions of temperature, pHand salt concentration 5. Which enzymes break the following macromolecules? Match the following with their correponding answers: ___ Nucleic acids A. proteases or proteinases such as pepsin ___ Cellulose B. none ___ Triglycerides C. lipases ___ Proteins D. amylases ___ Starch E. nucleases 6.Match the following enzymes totheir products. Answers ___ pepsin, trypsin and other digestive proteases A.Nucleotides ___ salivary and pancreatic amylases and other enzymes B. AminoAcids ___ lipases C. Monosaccharides ___ nucleases D. fatty acids and glycerol 7. Based on experiments, what is the effect of extremeconditions of pH and temperature (boiling tube) on enzymeactivity? 8. ATP stores energy in the form of___ ___ Chemical energy ___ Kinetic energy ___ Thermal energy ___ Activation energy 9. An allosteric site in anenzyme is____ __ the site where reactions occur __ the site that binds aregulator __ the site that binds thesubstrate __ the site that binds the product 10. Enzymes increase the rate of reactions by making thetransition state less stable. __ True __ False 11. Enzymes increase the rate of reactions by placing reactingparts of the molecule in favorable positions. __ True __ False 12. Which of the followingis a mechanism for regulation of enzymes? __ covalent modification __ feedback inhibition __ allosteric regulation __ all of the above 13. Which of the following represents a correct order of eventsin an enzyme catalytic cycle? 1.enzyme changes shape 2.substrate binds to active site 3.substrate is converted to products 4. products are released from activesite __ 1>2>3>4 __ 2>1>3>4 __ 3>2>1>4 __ 2>4>3>1

cyancicada301

QUESTION 10

If you can drink milk as an adult, it means that you have inherited a mutation in the promoter of your lactase gene (the gene that encodes the enzyme you need to break down lactose). Predict the effect of this mutation:

		The mutation changes the number of domains in the enzyme, which makes it work more efficiently
		The mutation changes the amino acid sequence of the lactase protein
		The mutation increases the number of copies of the lactase gene that will be found in your genome
		The mutation changes whether the lactase sequence is found in an intron or exon
		The mutation affects the expression of the lactase gene

1.2 points

QUESTION 11

A competitive inhibitor is decreasing the activity of an enzyme. Predict the effect of adding more substrate to the reaction.

		The substrate will increase the reaction rate by binding to the allosteric site
		The substrate will increase the reaction rate by competing with the inhibitor for the active site
		The reaction rate will not change unless the inhibitor can be removed
		The enzyme adjusts its shape so that the substrate, but NOT the competitive inhibitor, can bind
		The substrate will bind to the competitive inhibitor and block its ability to bind to the enzyme

1.2 points

QUESTION 12

What determines where in the genome a transcription regulator will bind?

		Transcription regulators bind to the 5' UTR region of a gene
		Regulators bind via complementary base-pairing to certain DNA molecules
		Covalent bonds form between the transcription regulator and the atoms of the DNA backbone
		Every eukaryotic gene has a different transcription regulator that will bind to the 5' end of the gene
		Transcription regulators bind to specific DNA sequences via multiple weak non-covalent interactions

1.2 points

QUESTION 13

What is the basic premise of cell theory?

		DNA -> RNA -> protein
		All cells arise from pre-existing cells
		DNA provides the complete instructions to create a cell
		The identity of a cell is determined through gene expression patterns
		All cells contain the same four basic macromolecules

1.2 points

QUESTION 14

What is the benefit of using BOTH the lac activator and the lac repressor to control gene expression?

		Using both an activator and repressor enables cells to more accurately determine the amount of lactose available in the environment
		Enzymes to digest lactose are only made when energy is low and lactose is available
		The activator can override the inhibition of the lac operon by the repressor
		The repressor can control the enhancer, while the activator can control the promoter
		When neither the lac activator or repressor is present, expression of the lac operon is too high

1.2 points

QUESTION 15

What is the histone code used for?

		Phosphorylation and acetylation of DNA affect its ability to be compacted
		Changes to the sequence of DNA change whether DNA will wrap around histone proteins
		Covalent modifications of histones affect the ability of the transcription initiation complex to form
		Histones provide the codon sequences needed for translation to occur
		The histone code affects which amino acids will get added to a polypeptide

BIO270H1 Lecture Notes - Lecture 3: Glycogen Synthase, Beta Sheet, Glycosylation

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