Biochem Exam 3

Different enzymes that catalyze the same reaction are known as _____.

isozymes

Hexokinase catalyzes the formation of glucose-6-phosphate through the transfer of Pi to glucose and is therefore categorized as a _____.

transferase

How does a catalyst increase the rate of a reaction?

it allows reacting molecules to more easily form the transition state

Which type of enzyme catalyzes the following reactions?

a. oxidoreductase b. ligase

How does the addition of an enzyme to a chemical reaction affect each of the following parameters?

Standard free energy of the reaction = No effect Activation energy of the reaction = decrease Initial velocity of the reaction = increase

Glu-His-Ser would be a suitable variant for the catalytic triad of chymotrypsin.

True

To which class do the enzymes that catalyze the following reactions belong?

Isomerase

To which class do the enzymes that catalyze the following reactions belong?

Lyase

To which class do the enzymes that catalyze the following reactions belong?

Oxidoreductases

Which free energy diagram describes a fast reaction? A slow reaction?

The reaction on the left is fast; the reaction on the right is slow.

Which of the following amino acid side chains may participate in acid-base catalysis?

Tyr His Glu

Which of the following amino acid side chains may participate as a nucleophile?

Lys Cys Ser

The mechanism of a steroid hydrolase was recently determined. The enzyme has potential industrial applications in the large-scale production of cholesterol-lowering drugs. The first step of the mechanism, very similar to that of chymotrypsin, is shown below. Match the roles (below) to the active site amino acid side chains? a. Tyr 170, b. Lys 60, and c. Ser 57.

Tyr 170 - acts as a base catalyst to abstract a proton from the Ser 57. Lys 60 - has a positively charged side chain that stabilizes the negatively charged phenolate anion on Tyr 170 by forming an ion pair. Ser 57 - acts as a nucleophile.

Transition state analogs effective as drugs.

True

The specificity pocket of a hypothetical serine protease contains the side chain shown here. This enzyme most likely catalyzes hydrolysis of what peptide bond? Hint: The N-terminal amino acid will be in the specificity pocket (i.e. if the answer choice is His-Arg the His would be found in the specificity pocket).

Glu—Ser

Most enzymes are globular rather than fibrous.

True

The model that best describes a conformational change in enzyme structure upon binding substrate is referred to as:

The induced-fit model

Which of the following statements about different types of enzyme inhibition are correct?

Competitive inhibition occurs when the substrate and the inhibitor compete for the same active site on the enzyme. Noncompetitive inhibition of an enzyme cannot be overcome by adding large amounts of substrate. Competitive inhibitors are often similar in chemical structure to the substrates of the inhibited enzyme.

Which of the following is/are true for a competitive inhibitor?

it increases the apparent Km it raises the substrate concentration required for the rate to be 1/2 of Vmax

With respect to enzymes, (select all that apply):

Kcat varies with enzyme concentration The efficiency of an enzyme is defined as kcat/Km

For each inhibitor type below indicate if it would increase, decrease, either increase or decrease, or have no effect on the apparent Km of the enzyme.

Competitive - increase Non-competitive - no effect Uncompetitive - decrease Mixed - increase or decrease

If the enzyme-catalyzed reaction E + S ⇋ ES ⇋ E + P is proceeding at or near the V​max​, what can be deduced about the relative concentrations of S and ES?

S is abundant, [ES] is at its highest point

Which statement is correct about the Michaelis-Menten constant, Km?

It is numerically equal to the substrate concentration required to achieve one half the maximum velocity.

What are the units for the Michaelis constant Km?

moles/liter

A graph of reaction velocity as a function of substrate concentration would yield a ______ curve for a Michaelis-Menten enzyme.

Hyperbolic

What relative values of K​M and k​cat​ would describe an enzyme with a low catalytic efficiency?

High K​M and Low k​cat

Determine the Km using the plot of velocity versus substrate concentration shown in the figure below.

0.5

Brain glutaminase has a Vmax of 1.1μmol∙min-1 ∙mL-1 and a KM of 0.6mM. What is the substrate concentration when the velocity is 0.3μmol∙min-1 ∙mL-1?

0.2 mM

The steady-state kinetics of an enzyme are studied in the absence and presence of an inhibitor (Inhibitor B). The initial rate is given as a function of substrate concentration and plotted below. Determine the Vmax in the absence and presence (Vmaxapp)of Inhibitor B. [S] has units of mmol/L and v has units of mmol L-1 min -1 . A. Vmax =5.13 mmol L−1 min−1, Vmaxapp = 5.38 mmol L−1 min−1 B. Vmax =0.1951 mmol L−1 min−1, Vmaxapp = 0.1861 mmol L−1 min−1 C. Vmax =5.38 mmol L−1 min−1, Vmaxapp = 5.13 mmol L−1 min−1 D. Vmax = Vmax app = 0.2 E. None of the above are correct.

A

Alcohol dehydrogenase is inhibited by numerous alcohols. Using the data given in the table below, determine which of the alcohols is most easily metabolized by alcohol dehydrogenase. A. Ethanol B. 1-Butanol C. 1- Hexanol D. 12-Hydroxydodecanoate E. I did not study well enough for this exam

D

The KM and kcat for fumarase with fumarate as a substrate are 5 x 10-6 M and 8 x 102 s-1 , respectively. When malate is the substrate the KM and kcat are 2.5 x 10-5 M and 9 x 102 s-1 , respectively. What do these data tell you about the operation of this enzyme. A. Fumarase approaches the diffusion limit with both substrates and is thus highly efficient. B. Fumarase is not an efficient enzyme. C. Fumarase can process fumarate but not malate. D. There is not enough information to solve this problem. E. Both B and C

A

The following data were obtained in a study of an enzyme known to follow Michaelis-Menten kinetics (assume [S] >> Km at the end of the experiment): The Km for this enzyme is approximately: A) 1 mM. B) 1,000 mM. C) 2 mM. D) 4 mM. E) 6 mM.

C

Examine the following five sugar structures:

contain or are pentoses = A is the disaccharide sucrose = B is a monosaccharide containing a B-anomeric carbon = E is a ketose monosaccharide = C

Consider the aldopentoses shown below. Name the types of stereoisomers represented by each pair.

A and B are = C-3 epimers B and C are = diastereomers A and C are = enantiomers

Use the Haworth projection of beta-D-altrose to place labels on the pyranose ring. The anomeric carbon is shown. Labels may be used more than once.

1 = OH 2 = H 3 = OH 4 = H 5 = H

Which two polysaccharides share all of their glycosidic linkage types in common?

Glycogen and amylopectin

In a Fischer projection, which chiral carbon determines whether the sugar is the D- or the L-isomer?

highest numbered asymmetric carbon atom

Use the Fischer projection below to describe the sugar:

The sugar shown is a ketohexose and is a D enantiomer and has 3 chiral centers and has 8 possible stereoisomers.

Of the four monosaccharides shown below, which are ketoses?

B C

Which of the following are reducing sugars?

A B D

When sugars form ring structures the additional chiral carbon is called this:

anomeric

The reactive carbonyl group on an aldose is always at position number;

1

In β-D-glucose the hydroxyl group at C1 is pointing _____ in the Haworth projection.

Up

Of the two monosaccharides shown below, which has the greatest number of stereoisomers?

C

Which type of isomer is represented by the pair of sugars shown below?

Epimer

Name the two small metabolites at the "crossroads" of metabolism.

pyruvate Acetyl-CoA

Match the characteristic/phrase to its association with either catabolic or anabolic reactions below.

reduction of NAD+ = catabolic reactions makes covalent bonds = anabolic reactions oxidation of NADH = anabolic reactions

Which of the following molecules is involved with the oxidation of glucose, synthesis of fatty acids and oxidation of fatty acids?

acetyl-CoA

The oxidized form of NADH is _____.

NAD+

The conversion of a carbohydrate into CO 2 is a(n) _______ process; the conversion of CO 2 into a carbohydrate is a(n) _______ process.

Oxidative; Reductive

Catabolic pathways relate to a(n) ____ of free energy and anabolic pathways to a(n) ______ of free energy.

release: input

Which of the following does not represent the biochemical standard state?

37°C temperature

When a reaction is at equilibrium, the G is equal to _____.

0

If the following two reactions were coupled, what would be the overall ΔG°? Glucose + Pi --> Glucose-6-Phosphate ΔG° = 13.8 kJ/mol ATP + H20 --> ADP + Pi ΔG° = -30.5 kJ/mol

-16.7 kJ/mol

Generally speaking, ATP is produced by _____ reactions and used by _____ reactions.

catabolic; anabolic

A reaction from the alcoholic fermentation pathway, a catabolic process:

The reactant is being reduced.

A reaction associated with the citric acid cycle, which plays an important role in catabolism:

The reactant is being oxidized.

A reaction associated with the anabolic pentose phosphate pathway:

The reactant is being oxidized.

Cells control or regulate flux through metabolic pathways by:

Cells can use all of these ways to control flux through metabolic pathways.

Ways to increase the rate of chemical reactions:

Increasing the temperature. Increasing the concentrations of the reacting substances. Adding a catalyst, a substance that participates in the reaction yet emerges at the end in its original form.

Enzymes vs non-biological catalysts

Most enzymes are proteins. Enzymes contain a specific fraction of the structure where reactions take place – active site. Most enzymes work at mild conditions. Activity of many enzymes are regulated.

There are seven major classifications of enzymes

The sign of ΔG indicates the spontaneity of a reaction

Enzymes lower the activation energy for a reaction

Enzymes often use cofactors to aid in catalysis

Three kinds of chemical catalytic mechanisms used by enzymes:

Acid-base catalysis, in which a proton is transferred between the enzyme and the substrate. This mechanism of catalysis can be further divided into acid catalysis and base catalysis. Covalent catalysis, in which a covalent bond forms between the catalyst and the substrate during the formation of the transition state. Metal ion catalysis, in which metal ions mediate oxidation-reduction reactions or promote the reactivity of other groups in the enzyme’s active site through electrostatic effects.

Acid-base catalysis

Some amino acids can play a role in acid-base catalysis

Covalent catalysis

ALWAYS has 2 transition states

Amino acids that act as covalent catalysts

Metal ions as catalysts

Stabilize the transition state

The catalytic triad of chymotrypsin

The hydrogen-bonded arrangement of the Asp, His, and Ser residues of chymotrypsin and other serine proteases is called the catalytic triad. Histidine --> acid/base catalysis part Serine --> nucelophile Chymotrypsin also has a covalent catalysis part

Lock-and-key model and its limitations

The lock-and-key model was proposed to suggest that the substrate is precisely aligned in the active site and fits the enzyme like a key in a lock. Enzymes, like other proteins, are not rigid molecules but instead can—and must—flex while binding substrates.

Enzymes stabilize the transition state

Formation of a low-barrier hydrogen bond during catalysis by chymotrypsin

Induced fit model

Conformational flexibility is a key feature of enzyme-catalyzed reactions, from binding substrates to repositioning them in the active site, forming the transition state, and releasing products. By sequestering substrates in the active site from the solvent, an enzyme can eliminate the energy barrier imposed by the ordered water molecules, thereby accelerating the reaction. Upon binding substrates, some enzymes undergo a pronounced conformational change so that they almost fully enclose the substrates. This phenomenon was called induced fit.

Specificity pockets of serine proteases

The varying specificities of these enzymes are largely explained by the chemical character of the so-called specificity pocket, a cavity on the enzyme surface at the active site that accommodates the residue on the N-terminal side of the scissile peptide bond.

Zymogens

In many organisms, the activity of proteases is limited by the action of protease inhibitors and by synthesizing the proteases as inactive precursors (called zymogens) The enzyme becomes maximally active only when it can efficiently bind its substrates and stabilize the transition state.

Reaction velocity can be thought of as concentration vs. time

Many enzymes react with substrates in a nonlinear fashion

A unimolecular reaction

A bimolecular reaction

Assume steady state equilibrium

Many enzymes obey Michaelis–Menten kinetics

The Michaelis-Menten Equation

gives hyperbolic curve

The Michaelis–Menten equation is hyperbolic

kcat/KM indicates catalytic efficiency

concentration reaching 10^8 = limit of diffusion = perfect enzyme

The Lineweaver–Burk plot: Linearizes Michaelis–Menten kinetics data

The Lineweaver–Burk plot: Graphical form

Not all enzymes fit the Michaelis– Menten model: Two substrates

1. Ordered Mechanism - substrate 1 binds first, then substrate 2 2. Random Mechanism

Some inhibitors act irreversibly

suicide inhibitors, they bind covalently

Competitive inhibitors bind to the same site as the substrate

- The most common form of reversible enzyme inhibition - Overcome competitive inhibition by increasing the substrate concentration - Increase the Km, but no affect to Vmax (inc Km = dec enzyme affinity for substrate)

A Lineweaver–Burk plot for competitive inhibition

Transition state analogs often make better ______ than substrate analogs

inhibitors

(Pure) Noncompetitive inhibitors appear to decrease Vmax

Km stay the same

Mixed inhibitors affect both Vmax and KM

Km and Vmax both change Vmax always dec, Km inc or dec

Uncompetitive inhibitors reduce Vmax and KM by roughly the same amount

ONLY multisubstrate ONLY bind substrate-enxyme complex parallel lines on lineweaver-burke plot

Some mechanisms for regulating enzyme activity

Monosaccharides made from aldehydes form aldoses

Monosaccharides made from ketones form ketoses

Some Common Monosaccharides

Stereoisomers

Cyclization of Sugars

Fischer --> Haworth

Derivatives of Monosaccharides

alpha and beta anomers - if the anomeric carbon still has OH = reducing sugar - if anomeric carbon does not have OH = nonreducing sugar - can tell if reducing sugar on fischer projections if they still have the carbonyl group on anomeric carbon

What is the most stable form of glucose?

Chair conformation where all heavy groups (-OH) are equitorial

Phosphorylated monosaccharides

Nucleic Acid monosaccharides

Lactose

galactose + glucose

Carbohydrate chains are called

glycans

Sucrose

glucose + fructose

Starch STORAGE - plants

Amylose - linear --> alpha 1-4 linkages Amylopectin - branched --> linear: alpha 1-4, branched: alpha 1-6 --> branches occur every 24-30 glucoses

Glycogen STORAGE - animals

Branched --> linear: alpha 1-4, branched: alpha 1-6 --> branches occur every 12 glucose (bc animals need the sugar for energy since we move meanwhile plants are not)

Cellulose STRUCTURAL

Beta 1-4 linkages, linear

Chitin STRUCTURAL

Beta 1-4 glucose, modified glucose --> N-acetylglucosamine

Biofilm

attached to a prokaryote, created by a community of bacteria, protection

Glycoproteins functions

1. protection of a cell 2. identify and recognition

N-linked or O-linked glycoproteins

Proteoglycans

found often in joints, highly hydrophilic molecules, shock absorbers and bc of negative charges they bounce back to normal because of repelling forces

Peptidoglycan

bacterial support systems - cross-linked CHO chains, surround plasma membrane of a cell and determine overall shape

Overview of Metabolism

Starchy foods are hydrolyzed by _____

amylases

Proteins are hydrolyzed by _____

proteases

Fatty acids are hydrolyzed by ______

lipases

In order to transport some fatty acids:

- some FA are linked to cholesterol (LDL, HDL, etc) - chylomicrons (lipoprotein)

It's easier for us to store ____

lipids bc they do not require any water (CHOs do) --> so we have adipocytes that hold triacylglycerols

Glycogen

Breakdown of glycogen

occurs bc of phsophorolysis

Most of our energy comes from ___ and ____

carbohydrates and lipids

Lysosome

hydrolytic enzymes - recycles amino acids in the cell

Proteasome

multiprotein complex think like a food processor

Ubiquitin

protein added to old/damaged proteins as a signal that a protein needs to go to the proteasome

Protein Degradation by the Proteasome

none of the metabolic pathways act in

isolation

Some Intermediates of Glucose Metabolism

G3P Pyruvate Acetyl-CoA

Some major metabolic pathways share a few common intermediates

Many metabolic pathways include oxidation-reduction reactions