Biochemistry Exam 1

How would each of the following treatments contribute to protein denaturation? (A) Heat (B) Addition of the hydrophobic detergents (C) Large changes in pH

(A) Heat would increase the thermal energy of the chain. The weak bonds holding the chain in its correct 3-D structure would not be able to withstand the wiggling of the backbone and the tertiary structure would be lost. Often, the denatured chains would interact with each other, forming large complexes that precipitate out of solution. (B) Detergents would denature the protein by essentially turning it inside out. The hydrophobic residues in the interior of thee protein would interact with the detergent, whereas the hydrophilic residues would interact with one another and not with the environment. (C) All ionic interactions, including hydrogen bonds, would be disrupted, resulting in protein denaturation.

What does p stand for

-log

What is G at equilibrium?

0

What are general characteristics of enzyme active sites?

1. 3-D cleft or crevice 2. the active site takes up a small part of the total volume of the enzyme 3. active sites are unique micro-environments 4. substrates are bound to enzymes by multiple weak attractions 5. the specificity of binding depends on precisely defined arrangement of atoms in an active site

What is the LIneweaver Burk equation?

1/v = (Km/Vmax)(1/[S]) + 1/Vmax

What is the rate of diffusion?

10^8-10^9 s^-1 M^-1

Calculate the axial length of an a helix that is 120 Amino acids long. How long would the polypeptide be if it were fully extended?

120 x (5.4/3.6) = 180

What are disulfide links

2 Cysteine = cystine. Redox reaction, important for maintaining structure of some proteins

What is a DNA double helix?

2 polymer strands, opposite orientations, bases pair up

What is the pKa of COOH?

2.18

How many different polypeptides of 50 amino acids in length can be made from the 20 common amino acids?

20^50

What is reverasible inhibition?

3 main types: competitive, uncompetitive and mixed inhibitors

What are active site features?

3D cleft or crevice to bind small portion of total protein volume Unique microenevionrment - nonpolar binds substrates with many weak attractions specificity depends on precise arrangement of a toms in active site

How many amino acids are in a reverse beta turn?

4, carbonyl of first residue hydrogen bonds to NH of fourth

What are the pH and pOH of distilled water?

7

What is the pKa of N3H+?

8.95

Differentiate between a first-order rate constant and a second-order rate constant.

A first-order rate constant is a proportionality constant for reactions having only one reactant; it relates the rates of a reaction to the concentration of the sole reactant. First-order rate constants have the units s^-1. A second-order rate constant is a proportionality constant for reactions having two reactants; it relates the rate of a reaction to the concentrations of both reactants. Second-order rate constants have the units M^-1s^-1.

Kcat/Km

A measure of enzyme effinciency

What is a pseudo-first order reaction?

A second-order reaction that appears to be first-order. If the concentration of one reactant is much greater than that of the second, the velocity will appear to be first order with respect to the reactant present in the lower concentration.

Define the term side chain in the context of amino acid or protein structure?

A side chain is the functional group (R group) attached to the alpha carbon atom of an amino acid.

Sequential reaction

A ternary complex is formed

Which four statements are true about amino acids? A. the val side chain does not form hydrogen bonds with other amino acids B. Der and Gln are polar amino acids C. The can undergo oxidation to form Tyr D. Methionine is a thiol E. The form of glycine used by the human body is D-glycine F. Threonine has more than one stereocenter G. Leucine has an overall charge at phsyioligcal pH

A, B, C, F

Differentiate between amino composition and amino acid sequence?

AA composition refers simply to the amino acids that make up the protein. The order is not specified. Amino acid sequence is the same as the primary structure - the sequence of amino acids from the amino terminal to the carboxyl terminal of the protein. Different proteins may have the same AA composition, but AA sequence identifies a unique protein.

What is lyase?

Adds or removes atoms or functional groups to double bounds

What is Alanine?

Ala, A

How do allosteric and Michaelis-menton enzymes differ?

Allosteric enzymes are regulated so they do not rise as rapidly. Both eel out because sites are saturated.

What is Asparagine?

Ans, N

What is Arginine?

Arg, R

What is secondary structure?

Arrangment of local regions of the polypeptide backbone , driven by hydrogen bonding and sterics

what is Aspartate?

Asp, D

Which amino acids are negatively charged?

Aspartate and glutamate

Which amino acids have a charge at the physiological pH?

Aspartic acid and glutamic acid are negative and lysine, arginine and histidine are negative

What is the biochemical advantage of having a Km approximately equal to the substrate concentration normally available to an enzyme?

At [S] near the Km, the enzyme displays significant catalysis yet is sensitive to changes in [S].

What are alpha helices?

Backbone hydrogen bonding parallel to helix axis, right handed, tightly packed, side chains point out

How does competitive inhibition work with bacteria?

Bacteria take PABA and use it to make folic acid. Antibiotics look very similar structurally to PABA so it binds in the active site an and EI formation reduces ES formation. Adding more substrate creates competition so Substrate saturation means we can still reach the same Vmax

Why would the specificity constant be high?

Because of either Kcat or binding

What is a transition state analog?

Biding stabilizes the transition state, transition state analogs are typically tight binding inhibitors that bind higher than substrates so the substrate cannot bind

What is the connected model of allosterism?

Binding S induces conformation change in other subunits

What limits k1 (dissociation)

Binding, so diffusion

What is mixed inhibition?

Binds to free enzyme and EI, influences conformation and reduces ability to form product. EI formation affects the formation of EIS

Uncompetetivw

Binds to the enzyme-substrate complex only. Lowers Vmax and KMapp. Roundup.

What is the zwitterion form?

Both a + and a - charge

What is sequential binding?

Both substrates bust bind e before reaction can occur. A tertiary complex forms (ES1S2)

How are buffers prepared?

By mixing the required amounts of weak acid and its conjugate base or by neutralizing some of the weak acid with strong g base to generate the conjugate base

How is the 3D Structure of a protein determined?

By the order of the amino acids

Select the true statements about protein structure a. in a B-pleated sheet, the side chains are located between adjacent segments b. peptide bonds stabilize secondary structure c. the secondary level of protein structure refers to the spatial arrangement of short segments of the protein d. in an a-helix the side chains are located on the outside of the helix e. the a-helix is held together by hydrogen bonds between N-H and C=O

C, d, e

psi angle

C-Ca bond

phi angle

Ca-N bond

What is an amide?

Carboxylic + amine, peptide bond, neutral

What is k2?

Catalytic, chemistry step

What are suicide inhibitors?

Chemically modified substrates that provide researchers with he most opseicif means of modifying gan enzymes active site. Binds to the enzyme as a substrate and is initially processed by the normal catalytic mechanism. The mechanism of catalysis then generates a chemically reactive intermediate that inactivates the enzyme through covalent modification. Participates in its own irreversible inhibition

What caused a "burst" of activity followed by a steady-state reaction when chymotrypsin was studied in the milliseconds subsequent to mixing the enzyme and substrate?

Chymotrypsin cleaves peptide bonds in a two-step reaction, in which the first step, the formation of the acyl-enzyme intermediate, is faster than the second step, hydrolysis.

If chymotrypsin is such an effective protease, why doesn't it digest itself?

Chymotrypsin recognizes large hydrophobic groups, which are usually buried in the enzyme's core owing to the hydrophobic effect.

What kind of inhibitors are transition state analogs usually classified as?

Competitive inhibitors

What is a buffer?

Consists of a weak acid base conjugate pair and resists changes in pH

What is Cystein?

Cys, C

Which amino acids are polar and neutral?

Cysteine, asparagine, glutamine

What is replication?

DNA-DNA

What is transcription?

DNA-RNA

Michaelis-Menten equation

Describes the kinetics of simple one-substrate reactions

The shape of hair is determined in part by the pattern of disulfide bonds in keratin, its major protein. How can curls be induced?

Disulfide bonds in hair are broken by adding a thiol-containing reagent and applying gentle heat. The hair is curled, and an oxidizing agent is added to re-form disulfide bonds to stabilize the desired shape.

What is regulation?

Don't want all pathways and reactions occurring all the time, regulated enzymes act as stop lights or traffic signals in a busy city

Lineweaver-Burk equation

Double-reciprocal plot

Why is hydrophobic effect useful?

Drives many biological processes such as protein folding. Interor of proteinsa rehydrophibic/nonpolar, coming together helps fold

What is a positive Gibbs free energy?

Endergonic

What is the hydrophobic effect driven by?

Entropy driven

What is a holoenzyme?

Enzyme + CoE

What is an apoenzyme?

Enzyme - CoE

What are enzymatic reactions?

Enzyme alter the raeaction path to lower Each by inserting intermediates. Binding involves weak intermolecular forces and reacting groups are bought into close proximity

What is covalent catalysis?

Enzyme has reactive group that covalently bonds to substrate which is often a nucleophile and temporarily modified the enzyme so it can be isolated and characterized. Water is the reactant in the second step

Rheumatoid arthritis (RA) is an autoimmune disease marked by inflammation and cartilage destruction. Although the causes are not known, it may be linked to lysosomal proteases (protein‑digesting enzymes). How may lysosomal proteases be linked to RA?

Excess lysosomal proteases are produced and released extracellularly, where they degrade collagen.

What is negative Gibbs free energy?

Exergonic, equilibrium favors this

Which metals are often used for metal ion catalysis?

Fe, Cu in redox reaction because they have two oxidation states. Switching means they are gaining and losing electron which can go to and from substrates. This helps metals bind transition states

What does G depend on?

Free energy of reactants and products, do not depend on the path

What is Gibbs free energy change equation?

G = Go + RTlnQ Go = -RT ln(Keq) Keq = e ^ (-Go/RT)

What is Glutamine?

Gln, Q

What is Glutamate?

Glu, E

Identify the groups in a protein that can form hydrogen bonds or electrostatic bonds with an arginine side chain at pH 7.

Glutamate, aspartate, and the terminal carboxylate can form salt bridges with the guanidinium group of arginine. In addition, this group can be a hydrogen-bond donor to the side chains of glutamine, asparagine, serine, threonine, aspartate, glutamate, and tyrosine and to the main-chain carbonyl group. At pH 7, histidine also can hydrogen bond with arginine.

What is glycine?

Gly, G

Glycine is a highly conserved amino acid residue in the evolution of proteins. Why?

Glycine has the smallest side chain of any amino acid. Its size is often critical in allowing polypeptide chains to make tight turns or to approach one another closely.

Which amino acids are hydrophobic?

Glycine, alanine, valine, leucine, isoleucine, methionine, proline

What are the four key types of irreversible inhibitors that can be used to study enzyme function?

Group-specific inhibitors; affinity analogs; suicide inhibitors; transition-state analogs.

What is a prosthetic group?

Groups that are permanently bound to the enzyme Tighlty bound coenzyme

What is a hydrogen bond donor?

H attached to N, O or F

What is water dissociation?

H2O hydrogen bonded to H2O can become H3O+ and OH-

What is Histidine?

His, H

How do we handle 2 substrates?

Hold one stand while varying ht other (keep it high)

Differentiate between homotropic and heterotropic effectors.

Homotropic effectors are the substrates of allosteric enzymes. Heterotropic effectors are the regulators of allosteric enzymes. Homotropic effectors account for the sigmoidal nature of the velocity vs. [S] curve, whereas heterotropic effectors alter the midpoint of Km of the curve. Ultimately, both types of effectors work by altering the T/R ratio.

What isa carbonyl?

Hydrogen bond acceptor

papain and trypsin are proteases. What type of reaction do they catalyze?

Hydrolysis, water is being used to break bond

What are lipids?

Hydrophobic molecules, not polymers Fuel storage Barriers

How can group-specific reagents be used to determine the mechanism of action of an enzyme?

If a particular amino acid side chain is suspected of participating in a catalytic mechanism, covalent modification of the residue by a group-specific reagent may alter it sufficiently that the enzyme activity is altered or inhibited.

What is Isoleucine?

Ile, I

How does handiness compare between individual strands and bundles

In keratin 2 right handed alpha helices create a left handed supercoil, collagen has left handed turns and a right handed overall structure

Double displacement (ping-pong) reaction

Includes a substituted enzyme intermediate

noncompetetive

Inhibitor and substrate can bind simultaneously. KM remains unchanged but Vmax is lower. Doxycycline.

What are beta sheets?

Inter strand hydrogen bonding, side chains alternate above and below the plane of the sheet

Why is this important to biochemists?

Interaction of many proteins are nonpolar, stronger interactions within the protein

Is the attraction of Na+ to Cl- stronger in water or oil? Explain

It is stronger in oil because the dielectric constant. water has a higher dielectric constant so it interacts well with charges and diminishes charges with each other

What is Kcat?

K2, rate of catalytic step (chemistry step)

How is KM related tot he rate constants?

Km = k-1 + k2 / k1

How do pure inhibitors affect lineweaver burk double reciprocal plots?

Km is not altered, binding to E and ES has the same fafinity

Which amino acids are proteins?

L isomers

How are lipids used for fuel storage?

Less oxidized than carbohydrates and less hydrated than carbohydrates. More energy per mass and volume

What is Leucine?

Leu, L

What are backbone conformations?

Limited by steric constrains, trans is more stable, glycine can exist in cis

What are polysaccharides?

Linear or branched, structural roles (cellulose and chitin), easily mobilized energy storage (glycogen and starch)

When is hydrogen bonding strongest?

Linear orientation In the absence of water because water can compete with hydrogen bonding within and between other molecules

What are proteins?

Linear polymers of amino acid building blocks.

What are the features of proteins?

Linear, amino acid polymer

What is hydrogen bonding?

Lone pair on N, O or F of one atom and hydrogen attached to N, O or F of another

What are loops?

Longer than 4 residues, typically contain polar residues on the outside when exposed to solvent

Many of the loops on the proteins that have been described are composed of hydrophilic amino acids. Why?

Loops invariably are on the surface of proteins, exposed o the environment. Because many proteins exist in aqueous environments, the exposed loops are hydrophilic so as to interact with water.

What is a cosubstrate?

Loosely associated and used by a variety of enzymes

What can you say about the pH and pOH of acidic and basic solutions?

Low pOH = more OH = more basic High pOH = more H = less basic Low pH = more H = more acidic High pH = more OH = less acidic

What is Lysine?

Lys, K

Which amino acids are positively charged?

Lysine, Arginine, Histidine

What does ionic bond strength depend on?

Magnitude of charge, distance between charges, the polarity of the solvent

What are eukaryotes?

Membrane enclosed internal compartments Ex: animal, plant, fungi

What is Methionine?

Met, M

What is metal ion catalysis?

Metals carry a positive charge so they are able to accept electron density and are considered electrophilic Can help generate nucleophiles by increasing acidity of nearby group, metal helps stabilizize negative care creating b better nucleophile

What is an example of restriction enzymes involving Mg ions?

Mg+2 reacts with Asp and helps activate water (restriction enzymes dehydrolysis). Water attacks backbone of nucleic acid so oxygen is more negative and is therefore a better nucleophile. Mg also stabilizes the negative charge on phosphate making it easier to bring water in and the metal ion helps with proximity

What is ES?

Michaelis complex

what is KM?

Michaelis constant, amount of substrate required to half fill the active sites measure of [S] required for significant catalysis approximates [S]in vivo for the natural substrate

What are group specific reagents?

Modify specific R groups of amino acids Ex: DIPF: modifies only one of the 28 series residues in the protein implying that this serine residue is especially active.

What are affinity labels/substrate analogs?

Molecules that covalently modify active site residues and re structurally similar to an enzyme's substrate. They are more specific for an enzyme's active site than group specific. Ex: TPCK is an affinity label for chymotrypsin, it binds at the active site and reacts irreversibly with a histidine residue at that site, inhibition the enzyme

What direction are amino acids read in?

N-C

What are prokaryotes?

No membrane enclosed internal compartments. Ex: bacteria, archaebacteria

What is uncompetitive inhibition?

Only binds after enzyme binds subside causing a conformational change. Inhibitor binds and blocks product from being released and the enzyme is stuck and cannot do its job. This forms a ternary complex. Only bind ES and ESI formation occurs

What are coenzymes?

Organic cofactor derived from vitamins

An enzyme that requires the coenzyme nicotinamide adenine dinuclotide belongs to which enzyme class? (NAD+)

Oxidoreductase

What is Phenylalanine?

Phe, F

How is cytosolic pH maintained

Phosphate

What are peptide bond?

Planar, resonance, partial double bond, partial charges

What is an enzyme?

Powerful biological catalyst, typically protein, highly specific, contain an active site, may require cofactor

What are van Der Waals interactions?

Present between all interacting substance because all matter has protons and electrons. Due to fluctuations in electron clouds. "Exposed" nuclei attracted to regions of excess electrons

What are the levels of protein structure? Describe the type of bonds characteristic of each lelvel

Primary structure - peptide bond; secondary structure - local hydrogen bonds between components of the polypeptide backbone; tertiary structure - various types of noncovalent bonds between R groups that are far apart in the primary structure; quaternary structure - various noncovalent bonds between R groups on the surface of subunits

What is Proline?

Pro, P

What are the primary biological molecules

Proteins, carbohydrates, nucleic acids and lipids

What is general acid base catalysis?

Proton transfer by a group other than water, usually an amino acid side chain such as His

What are the two conformations of allosterism?

R and T

Consider the partial sequence of a peptide. I L W A N R M S H V L F A V E A Select all amino acid residues likely to be on the solvent‑exposed surface once the peptide folds into its native conformation.

RHE Because they have charged side chains so they are more likely to be found at the surface of the protein and N and S because they are polar

What is Translation

RNA-protein

What ate BME and DTT?

Reagents that can remove disulfide linkages by reacting with the SHs instead

The α and ß subunits of hemoglobin bear a remarkable structural similarity to myoglobin. However, in the subunits of hemoglobin, residues that are hydrophilic in myoglobin are hydrophobic. Why?

Recall that hemoglobin exists as a tetramer, whereas myoglobin is a monomer. Consequently, the hydrophobic residues on the surface of hemoglobin subunits probably take part in van der Waals interactions with similar regions of the other subunits and are shielded from the aqueous environment by these interactions.

What is the R conformation?

Relaxed, open, easy substrate access to active site, high binding

What enzymes are used in the central dogma?

Replication - DNA polymerase Transcription - RNA polymerase Translation - ribosomes

What are turns and loops?

Required to obtain a compact globular structure

Which of the following best describes and alpha helical region of a polypeptide?

Right handed, 3.6aa/turn

What is induced fit model?

Sbstrate binds to the enzyme with many weak interactions, the enzyme backbone adjust to position the interacting amino acids better to prevent side reactions.

What is the defining characteristic for an enzyme catalyzing a sequential reaction? A double-displacement reaction?

Sequential reactions are characterized by the formation of a ternary complex consisting of the enzyme and both substrates. Double-displacement reactions always require the formation of a temporarily substituted enzyme intermediate.

What are oligosaccharides?

Short chains, often attached to proteins or lipids, diverse structures via branching, recognition signals

What are allosteric enzymes?

Sigmoidal plots, contain more than one binding site (allosteric site), multiple subunits and conformations.

What is RNA?

Single stranded, folds back on itself

What are the structural features of RNA?

Single stranded, ribose backbone, contains the base uracil

What is a cofactor?

Small molecules needed to catalysis that provide chemical reactive groups

Most proteins have hydrophilic exteriors and hydrophobic interiors. Would you expect this structure to apply to proteins embedded in the hydrophobic interior of a membrane? Explain.

Some proteins that span biological membranes are "the exception that prove the rule" because they have the reverse distribution of hydrophobic and hydrophilic amino acids.

What is heterotrophic regulation?

Something else (ex: feedback inhibitor) causes shift in curve

What is competitive inhibition?

Structurally similar to substrate, binds only to enzyme's active site and prevents enzyme from binding substrate I only binds free E, EI formation prevents ES formation

What are the functions of proteins?

Structure: cytoskeleton Transport: hemoglobin Signaling: insulin Signal receptors: insulin receptor catalysist: enzyme

What is the threshold effect?

Substrate binding shifts the equilibrium to favor R state. The activity of allosteric enzymes is more sensitive to substrates near KM then Michaelis-Menten enzymes with the same Vmax Like an on off switch

Michaelis constant (Km)

Substrate concentraion that yields 1/2 Vmax

What is the t conformation?

Taught, closed, poor substrate access to active site, low binindg

Proteins that span biological membranes often contain α helices. Given that the insides of membranes are highly hydrophobic, predict what types of amino acids will be in such a helix. Why is an α helix particularly suitable for existence in the hydrophobic environment of the interior of a membrane?

The amino acids will be hydrophobic in nature. An α helix is especially suitable for crossing a membrane because all of the amide hydrogen atoms and carbonyl oxygen atoms of the peptide backbone take part in intrachain hydrogen bonds, thus stabilizing these polar atoms in a hydrophobic environment.

What is the turnover number?

The catalytic rate constant, measures how fast the chemical step can proceed Measures amount of product made per enzyme in given time How many reactions enzymes can do in a given time Vmax=k2[E] or k2 = Vmax/[E]

What is the catalytic triad and what are the roles of the individual components in chymotrypsin activity?

The catalytic triad, composed of the amino acids serine 195, histidine 57, and aspartate 102, resides at the active site of chymotrypsin. The histidine residue serves to position the serine side chain and to polarize its hydroxyl group so that it is poised for deprotonation. In the presence of the substrate, histidine 57 accepts the proton from the serine-195 hydroxyl group. The withdrawal of the proton from the hydroxyl group generates an alkoxide ion, which is a much more powerful nucleophile than a hydroxyl group is. The aspartate residue helps orient the histidine residue and make it a better proton acceptor through hydrogen bonding and electrostatic effects.

A mutation that changes an alanine residue in the interior of a protein into valine is found to lead to a loss of activity. However, activity is regained when a second mutation at a different position changes an isoleucine residue into a glycine. How might this second mutation lead to a restoration of activity?

The first mutation destroys activity because valine occupies more space than alanine does, and so the protein must take a different shape, assuming that this residue lies in the closely packed interior. The second mutation restores activity because of a compensatory reduction of volume; glycine is smaller than isoleucine.

List some of the differences between an a helix and a B strand

The helix is a condensed, coiled structure, with the R groups bristling outward from the axis of the helix. The distance between two adjacent amino acids is 1.5 Å. The strand is a fully extended polypeptide chain and the side chains of adjacent amino acids point in opposite directions. The distance between adjacent amino acids is 4.5 Å. Both structures are stabilized by hydrogen bonding between components of the polypeptide backbone.

What is feedback inhibition? Why is it a useful property?

The inhibition of an allosteric enzyme by the end product of the pathway controlled by the enzyme. Prevents the production of too much end product and the consumption of substrates when product is not required.

Poly-L-leucine in an organic solvent such as dioxane is α helical, whereas poly-L-isoleucine is not. Why do these amino acids with the same number and kinds of atoms have different helix-forming tendencies?

The methyl group attached to the ß-carbon atom of isoleucine sterically interferes with α-helix formation. In leucine, this methyl group is attached to the y-carbon atom, which is farther from the main chain and hence does not interfere.

Suppose that a mutant enzyme binds a substrate 100 times as tightly as does the native enzyme. What is the effect of this mutation on catalytic rate if the binding of the transition state is unaffected?

The mutation slows the reaction by a factor of 100 because the activation free energy is increased by 53.22kJ mol^-1. Strong binding of the substrate relative to the transition state slows catalysis.

Predict the effect of mutating the aspartic acid at the active site of chymotrypsin to asparagine.

The negative charge on the aspartic acid helps orient histidine 57 so that it acts as a general base catalyst to assist in the formation of the reactive alkoxide ion on serine. Asparagine, lacking a charge, would be less effective at orienting histidine 57. Indeed, chymotrypsin with this mutation has 10,000-fold lower activity than that of the wild-type enzyme.

What is meant by the term polypeptide backbone?

The nitrogen - alpha carbon - carbonyl carbon repeating unit

What is the purpose of the oxyanion hole in chymotrypsin?

The oxyanion hole is a structure at the active site of chymotrypsin that stabilizes the tetrahedral intermediate in the proteolysis reaction and facilitates the formation of the acyl-enzyme intermediate.

List some of the benefits of knowing the primary structure of a protein?

The primary structure determines the tertiary structure. Knowing it helps to elucidate the function of the protein.

What is double displacement?

The product is related before the second substrate binds, only a binary complex forms, enzyme ping pongs back and forth and is temporarily modified

What is the buffering region

The range of pH in which the solution resists change in pH

Aspartate transcarbamoylase (ATCase) is an allosteric enzyme that regulates the synthesis of uridine triphosphate (UTP) and cytidine triphosphate (CTP). It can be separated into regulatory subunits and catalytic subunits. If isolated regulatory and catalytic subunits of ATCase are mixed, the native enzyme is reconstituted. What is the biological significance of the observation?

The reconstitution shows that the complex quaternary structure and the resulting catalytic and regulatory properties are ultimately encoded in the primary structure of individual components.

Kinetics

The study of reaction rates

Many isolated enzymes, if incubated at 37°C, will be denatured. However, if the enzymes are incubated at 37°C in the presence of substrate, the enzymes are catalytically active. Explain this apparent paradox.

The three-dimensional structure of an enzyme is stabilized by interactions with the substrate, reaction intermediates, and products. This stabilization minimizes thermal denaturation.

How do irreversible inhibitors map the active site?

They modify functional groups which can then be midnetified. If treatment with an irreversible inhibitor results in a loss of enzymatic activity, then this loss suggest that the modified group is retried fo enzymatic activity.

Why are buffers not composed of strong acids and bases?

They will fully dissociate

What is the central dogma of biology?

Transcription is the process of synthesizing RNA from DNA. Translation is the process of synthesizing an amino acid sequence from RNA

Transition state analogs, which can be used as enzyme inhibitors and to generate catalytic antibodies, are often difficult to synthesize. Suggest a reason.

Transition states are very unstable. Consequently, molecules that resemble transition states are themselves likely to be unstable and hence difficult to synthesize

What is Tryptophan?

Trp, W

What is an antiparallel B Sheet?

Two peptide strands running in opposite directions, the Hydrogen bonds between the strands are straight and stronger.

What is Valine?

Val, V

Which of the following amino acids re likely to be found on the interior of a protein? a. valine b. aspartic acid c. Leucine d. lysine

Valine and Leucine

What interactions can contribute to the intrinsic binding energy during enzymatic catalysis?

Van der Waals interactions, electrostatic interactions, and hydrogen bonding.

How do uncompetitive inhibitors affect lineweaver burk double reciprocal plots?

Vmax is lowered and Km is lowered. Slope remains constant

How do mixed inhibitors affect lineweaver burk double reciprocal plots?

Vmax is lowered, Km is raise for stays the same

How do competitive inhibitors affect lineweaver burk double reciprocal plots?

Vmax remains the same and Km is larger

Competitive inhibition

Vmax remains the same but the KMapp increases. Sulfanilamide. Inhibitor binds at the active site.

What is 0 order?

Vmax, no substrate left

What is the hydrophobic effect?

Water molecules more ordered around the non polar molecule than in the bulk solution. When the nonpolar molecule associate water is displaced which increases entropy and more favorable water:water interactions

What are simple sugars?

Water soluble, mobile energy source via combusion

What are the four basic catalytic strategies used by many enzymes?

What are the four basic catalytic strategies used by many enzymes? Covalent catalysis; general acid-base catalysis; metal ion catalysis; catalysis by approximation and orientation.

What are the two properties of enzymes that make them especially useful catalysts?

What are the two properties of enzymes that make them especially useful catalysts? 1. They facilitate the formation of the transition state which enhances the rate of reaction 2. their specificity

The p𝐾a of lactic acid is 3.86, and its conjugate base is lactate. Which form of lactic acid predominates at pH 7.4? lactate lactic acid neither; lactic acid and lactate are equimolar

When acid's pKA is below the pH, the acid is more li kely to be deprotonated

What is feedback inhibition?

When the product of a reaction near the end of a chain of reactions inhibits the function of an enzyme in an earlier reaction of the chain. Prevents build up of intermediates that are not needed

What is a spontaneous reactioN/

Will proceed toward products if provided sufficient energy to get reaction started

What is Kw?

[H][OH]=10^-14

Binding of a ligand to protein X affects the binding properties of another site on X. This is an example of which of the following phenomena? a. allosteric regulation b. competitive inhibition c. noncompetitive inhibition d. induced fit e. transition state stabilization

a

R groups in a B strand a. alternate between one side of the strand and the other b. are on one side of the strand only c. are incompatible with he B strand d. must be charged

a

The characteristic that distinguish and uncompetitive enzyme inhibitor from other types of inhibitors is a. the inhibitor binds only to the ES complex b. the inhibit binds to bot the E and the ES complex c. that binding of the inhibit decreases Vmax d. that inhibit binding increases Km e. that high concentration of substrate can overcome inhibiton

a

The kinetic parameter Kcat/Km provides a measures of what property of an enzyme? a. catalytic efficient b. concentration c. diffusion rate d. substrate-binding affinity e. turnover number

a

Which of the choices best describes a biological membrane? a a bilayer containing lipids with hydrophilic head groups oriented toward the solvent (extracellular fluid and cytosol) and hydrophobic tail groups pointing inward b a bilayer containing lipids with hydrophobic head groups oriented toward the solvent (extracellular fluid and cytosol) and hydrophilic tail groups pointing inward c a bilayer containing lipids with hydrophilic head groups pointing inward and hydrophobic tail groups oriented toward the solvent (extracellular fluid and cytosol)

a

Which of the following best describes the arrangement of amino acid side chains in an alpha helix? a. the side chains point outward away from the helical axis b. the side chains point inward toward the center of the helix c. the side chains point toward the nearest beta sheet

a

Which of the choices are components of biological membranes? Select all that apply. a proteins b lipids c nucleic acids

a and b

Select all the choices that correctly describe the Golgi apparatus of the cell. a. proteins are modified by this organelle and repackaged into transport vesicles b. proteins are produced by this organelle c. aerobic respiration is carried out by this organelle, which produces ATP d. this organelle is made up of flattened sacs of membrane

a and d

Which of the statements about peptide bonds are true? a. the formation of a peptide bond involves a dehydration reaction b. a terapeptide contains five amino acid residues c. peptides are polymers of proteins d. peptide bonds are ester linkages e. a tripeptide contains three amino acid residues

a and e

Wolman disease is a lysosomal storage disease that results in the buildup of lipids (fats) in the spleen, liver, bone marrow, small intestine, adrenal glands, and lymph nodes. Which is the probable cause?

a gene mutation results in a shortage of lipid digesting enzymes in the lysosome

What is a titration curve

a graph that shows how pH changes when an acid or base is added to a solution

What are characteristics of allosteric enzymes? a. They may have binding sites for regulatory molecules that are separate from active sites b. They tend to have a sigmoidal curve of V vs S c. They undergo conformational changes as a result of modulator binding d. They conform to Michaelis-Menten kinetics e. They are generally small single subunit proteins

a, b, c

Which of the following statements about enzymes are true? Choose all that apply a.) an enzyme yields a specific product, whereas a nonbiologival catalyst may produce more than one product, and side reactions may occur. b.) generally, an enzyme is specific for a substrate. for example, thrombin catalyzes the hydrolysis of the peptide bond between Arg and Gly. c.) a substrate must bind to the active site before a reaction occurs. d.) reactions occur at the active site, which usually consists of a crevice on the surface of the enzyme e.) nonbiological catalysts and enzymes tend to have a similar degree of reaction specificity.

a, b, c, d

Select the three true statements A.Placing a hydrophobic molecule into water disrupts some of the water-water hydrogen bonds. B. Forming an ordered network of water around hydrophobic molecules increases the entropy of water C. Polar molecules with small nonpolar regions (e.g. acetic acid) readily form micelles. D. The bilayer of a cellular membrane is primarily composed of amphipathic (amphiphilic) lipids E. The tendency of hydrophobic molecules to aggregate in water is called hydrophobic effect.

a, d, e

Which of the following amino acids would likely disrupt an a helix? a. Tryptophan b. Phenylalanine c. Glycine d. Proline

a,b,d - they're bulky/cyclic

Select the descriptions that apply to the ribosome

a. a membrane-enclosed organelle that stores DNA b. a cellular structure that is composed of both RNA and protein c. a membranous network associated with protein production d. a membrane-bound organelle that stores digestive enzymes e. a cellular structure that is responsible for the synthesis of protons

Which direction is activation?

above the sigmoid curve

What is refolding driven by?

aggregation of hydrophobic residues, formation of local secondary structures

What is keratin?

alpha helical, 2 stranded coiled coil, disulfide cross links. Disulfide bonds form between neighboring cysteins

Which orientation of a beta sheet is more stable?

antiparallel because the hydrogen bonds are straight

How does pH affect reaction conditions?

as pH changes protonation changes which changes the activity of the protein. active site residues in correct ionization sate, subunit dissociation or protein denaturation. Mechanism for regulating enzymatic activity. Protein side chains aka usually around 3

Which of the following most accurately describes a mechanism by which enzymes catalyze reactions involving multiple substrates? a. In double displacement reactions, product formation b. In double displacement reaction mechanisms, one or more products are always released before all lustrates bind to the enzyme c. In sequential displacement reaction mechanism the enzyme always relates the products in a random order d. In sequential displacement reaction mechanisms, the enzyme generally undergoes temporary modification as a substituted enzyme intermediate e. In sequential displacement reaction mechanisms, the substrates always bind to the enzyme in a particular order

b

Which of the phrases best describes the hydrophilic region of a phospholipid? a repelled by water b interacts with water c floats in nonpolar compounds d has an affinity for high salt concentrations

b

Which statement describes the action of a buffer composed of citric acid (H3C6H5O7) and sodium citrate (NaH2C6H5O7) ? a Sodium citrate neutralizes added base, and citric acid neutralizes added acid. b Citric acid neutralizes added base, and sodium citrate neutralizes added acid. c Both components, citric acid and sodium citrate, neutralize added acid. d Both components, citric acid and sodium citrate, neutralize added base.

b

Why does oil not dissolve in water? a Hydrogen bonds form between oil molecules, causing them to aggregate. b Water molecules form hydrogen bonds with each other and exclude oil molecules. c Water molecules form stronger associations with other polar molecules than with oil. d Oil is less dense than water, which causes it to separate from water instead of dissolving

b and c

Select the descriptions that apply to the smooth endoplasmic reticulum a. a membrane enclosed organelle that stores DNA b. an organelle that is reposnviel for the detoxification of drugs c. a network of membranes associated with protein production d. a membranous organelle with the nucleus that does not produce proteins e. a membranous complex which produces secretory vesicles

b and d

Identify the true statements regarding disulfide bridges (disulfide bonds). Include all that apply. a. Disulfide bridges are important to primary and tertiary structure, not quaternary b. Disulfide bridges have a stabilizing effect on proteins c. A disulfide bridge forms between two cysteine residues. d. Disulfide bridges can exist between two amino acid residues on the same chain. e. Disulfide bridges are formed by an irreversible oxidation reaction.

b, c, d

Which statements accurately describe the polarity and electronegativity of water? a. Water has polar bonds and a linear symmetrical shape, so it is polar. b. Covalent bonds in a water molecule bind its oxygen atom to its two hydrogen atoms. c. Water molecules are polar and thus associate with each other through hydrogen bonds. d. Strong covalent bonds are formed between two or more water molecules. e. The oxygen atom in a water molecule is strongly electronegative.

b,c, and e

Which direction is inhibition?

below the sigmoid curve

How is blood pH maintained?

bicarbonate

What is the role of binding energy in enzyme catalysis?

binding energy is maximized when an enzyme interacts with the transition state, thereby facilitating the formation of the transition state and enhancing the rate of reaction.

What are the features of glycogen?

branched, glucose polymer

R groups of amino acid residues in an a helix a. participate in hydrogen bonds that stabilize the helix b. are located in the interior of the helix c. Bristol out from the axis of the helix d. are incompatible with helix formation

c

The binding of a positive allosteric effector to an allosteric enzyme typically a. induces an R state to a T state conversion b. decreases the Vmax c. decrease the Km for its substrate d. results in hyperbolic reaction kinetics e. induces subunit dissociation

c

Which of the following statements is least accurate? a. peptide bonds tend to form a planar structure b. peptide bonds are thermodynamically unstable, but kinetically stable c. favored confirmation of peptide bond is with the sequential alpha carbons in the cis position d. water is released during the formation of peptide bonds e. at equilibrium the peptide bond forming reaction favors hydrolysis

c

Select the phrases that describe the plasma membrane a. separates the nucleus and the cytosol b. provides a rigid structures that allows the cell to hold its shape c. maintains the correct ion concentration inside the cell d. creates a barrier between the inside and outside of the cell

c and d

The mitochondrion a. contains digestive enzymes that break down cellular waste and debris b. is a system of membranous channels on which ribosomes produce proteins c. contains unique DNA that is different form the cell's nuclear DNA d. has a double membrane, with ATP synthesis occurring at the inner membrane e. is a series of proteins necessary for cell structure and movement

c and d

What are the functional groups in amino acids?

carboxylic acid and amino

Rank the constituents of eukaryotic cells form largest to smallest

cell nucleus > mitochondrion > ribosome > protein > amino acid > water molecule > proton

What is ph>pKa

comopund is mainly basic

What is ph<pKa

compound is more acidic

If a solid line represents a covalent bond and a dotted line represents intermolecular attraction, which of the choices shows a hydrogen bond? a H−H b H2O⋅⋅⋅⋅⋅⋅H−CH3 c H4C⋅⋅⋅⋅⋅⋅H−F d H3N⋅⋅⋅⋅⋅⋅H−O−H

d

What is quaternary structure?

describes the interactions between polypeptide chains, symmetry is often present, hydrophobic patches complementary shapes and specific interactions help stabilize binidng

what dictates how fast enzyme reaction can occur?

difusion

What are the structural features of DNA?

double stranded, deoxyribose backbone, contains the base thymine

Which of the following contributes most tot the theromdynamic stabilization of a protein's native structure? a. coiled-coil interactions b. alpha helix dipole interactions c. disulfide bonds d. electrostatic interactions e. hydrophobic interactions

e, in attempt to maximize water-water reaction, driven by enthalpy and entropy

What is the fundamental mechanism by which enzymes enhance the rate of chemical reactions?

enzymes facilitate the formation of the transition state

What is catalysis by proximity and orientation?

enzymes help bring together and help orient them. They are held in place by groups with opposite charges

What is collagen?

helical but not alpha helical, three stranded helix, 1/3 Gly. high pro/hyp

what is the pKa of amino groups?

high because they are basic

How does temperature affect reaction conditions?

higher temperature means higher Brownian motion which is necessary for interactions but if it gets too hot then denaturation will occur

Which amino acids are essential?

histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine

What is a nitrogen?

hydrogen bon donor

What is tertiary structure driven by?

hydrophobic effect

What are metal ions?

inorganic cofactors, form coordination complexes, + charge so - charges can interact

What is ligase?

joins 2 molecules in a reaction powered by ATP hydrolysis

Turnover number

k2 or kcat

What is the specificity constant?

kcat/KM Rate constant or interaction of S and E

What is Coulomb's law?

law stating that like charges repel and opposite charges attract, with a force proportional to the product of the charges and inversely proportional to the square of the distance between them.

What is a hydrogen bond acceptor?

lone pair on N, O or F

What is the pKa of carboxylic acids?

low because they are acidic

What are amino acids?

monomer building blocks of proteins

When do spontaneous reactions occur?

negative G

What are the dihedral angles in an alpha helix

o = -57, w = -47

What are the dihedral angles in an antiparallel beta sheet?

o=-119, w=120

what are the dihedral angles in a parallel beta sheet?

o=-139, w=-135

what is pseudo first order?

one concentration is much higher so its concentration does not significantly change.

What is primary structure?

order of covalently bound amino acids

What is tertiary structure?

overall fold of a single polypeptide chain, proteins have felixlbe structures, interior lacks free hydrogen bonding sites, minimized van der waals,

What is oxidoreductase?

oxidation-reduction reactions Electron transfers

What is 10^-14

pH scale

How does a titration curve determine the pKa of a weak acid?

pKa is a pH at which the concentration of weak acid and its conjugate base will be in equimolar concentrations

Why is rotation around the peptide bond prohibited and what are the consequences of the lack of rotation?

partial double bond character which prevents rotation. this lack of rotation constrains the conformation of the peptide backbone and limits possible structures

How does penicillin irreversibly inactivate a key enzyme in bacterial cell wall synthesis

penicillin mimics a normal substrate and enters the active site. It creates cross links between the tsrapeptides and pentaglycines and forms an acyl intermediate which reacts with the amino group of the terminal glycine in another peptide to form the cross link. Upon binding to the transpeptidase, the serine residue at the active site attacks the carbonyl carbon atom of the lactic ring to form the peniclloyl serine derivative. This enzyme does not react rather, it is irreversibly inhibited and cell wall synthesis cannot take place

which amino acids are hydrophobic aromatics?

phenylalanine and tryptophan

Proteins are thermodynamically unstable. The ^G of the hydrolysis of proteins is quite negative, yet proteins can be quite stable. Explain this apparent paradox. What does it tell you about protein synthesis?

protein hydrolysis has a large activation energy. Protein synthesis must require energy to proceed.

What is max velocity?

rate constant x how much enzyme, first order with relation to enzyme, doubling the enzyme will double the rate Vmax = k2[E]

What is isomerase?

rearrangement of atoms

What does KM depend on?

substrate and environmental conditions: pH, temp, ionic strength

What is homotrophic regulation?

substrate influences another substrate, this accounts for sigmoidal character

Why does the activation energy of a reaction not appear in the final ^G of the reaction

the energy required to reach the transition state (the activation energy) is returned when the transition state proceeds to the product.

What is meant by the term binding energy?

the free energy released when two molecules bind together, such as when an enzyme and substrate interact.

What is the structural basis for enzyme specificity?

the intricate three-dimensional structure of proteins allows the construction of active sites that will recognize only specific substrates

What is the equivalence point?

the point in a titration where the amount of titrant added is enough to completely neutralize the analyte solution.

What would be the result of an enzyme having a greater binding energy for the substrate than for the transition state?

there would be no catalytic activity. if the enzyme-substrate complex is more stable than the enzyme transition state complex, the transition state would not form and catalysis would not take place

What are irreversible inhibitors?

tightly bound to the enzyme, either covalently or noncovalently.

What is transferase

transfers functional groups between molecules

What is a Parallel B Sheet?

two peptide strands running in the same direction held together by diagnoal hydrogen bonds between the strands.

What id denaturation?

unfolding, caused by changes in pH, heating, addition of chaotropic reagents, organic solvents, and detergents, often reversing

What is Chymotrypsin?

uses Serine as covalent catalysis Asp takes H and His is deprotonated and takes one from serene making it more negative and a better nucleophile

What is the rate equation for first order?

v=k[A]

What is the rate equation for second order?

v=k[A]^2 or v=k[A][B]

What is the Michaelis-Menten equation?

vo = Vmax[S]/[S]+KM

What is feed forward activation?

when a product of an earlier reaction stimulates or prepares a later reaction by activating it

What goes on each axis of a titration curve?

y = ph x = OH added

What is hydrolase?

•Hydrolysis Hydrolase cleaves C‐O, C‐N, or C‐S bonds by addition of water. • Most digestion and lysosomal enzymes are hydrolases. • Hydrolase names indicate the substrate or bonds on which they act, which include peptidase, lipases, esterases and phosphatases.