In-Class Quiz 2

How do aldoses and ketoses differ?

Aldoses are monosaccharides that contain aldehydes

Ketoses are monosaccharides that contain ketones

Define: Triose

Monosaccharides with three carbons (the simplest monosaccharides are trioses)

Define: Epimer

Diastereomers that differ at only one carbon atom

Define: Anomer

Differ at which asymmetric carbon is involved in ring closure

Define: Diastereoisomers

Isomers that are not mirror images

Define: Enantiomers

Isomers that are non-superimposable mirror images

Define: anomeric center

The location at which aldehyde/ketone groups react with alcohol groups to form a ring

What is the term for a 6 figured ring?

Pyran

What is the term for a 5 figured ring?

Furan

How do alpha-anomers and beta-anomers differ?

On anomeric carbon:

A - OH group below

B - OH group above (Or OH group on the same side as carbon 6 - large group)

When does the pyranose form of fructose dominate?

When fructose is free in solution

When does the furanose form of fructose dominate?

In many fructose derivatives

Draw the open chain forms of glucose, galactose, mannose, ribose, and fructose

Define: Glycosidic bond

Bond formed between the anomeric carbon of one monosaccharide to the alcohol of a carbohydrate, protein, or lipid.

What is the chemical name of sucrose?

a-D-glucopyranosyl-B-D-fructofuranose

What is the chemical name of maltose?

a-D-glucopyranosyl-(1-4)-a-D-glucopyranose

What is the chemical name of Lactose?

B-D-galactopyranosyl-(1-4)-a-D-glucopyranose

Draw sucrose, maltose, and lactose

Define: Reducing sugar

Sugars with open forms that can react with oxidizing agents via interactions with their aldehyde group. (Ketoses can tautomerize to aldoses to react)

Both glucose and fructose are reducing sugars, why isn’t sucrose a reducing sugar?

The anomeric centers of both glucose and fructose are in a glycosidic bond, making it so that they cannot convert to their open chain forms and act as reducing sugars

Describe: Glycogen

A glucose homopolymer, used for energy storage

* a-1,4 glycosidic bond backbone
* a-1,6 glycosidic bond branching every 10 glucose units

What are the two starches?

Amylose and Amylopectin, these are the nutritional reservoir in plants

Describe: Amylose

A glucose homopolymer

* a-1,4 glycosidic bond backbone
* Linear, no branching

Describe: Amylopectin

A glucose homopolymer

* a-1,4 glycosidic bond backbone
* a-1,6 glycosidic bond branching every 30 glucose units

Describe: Cellulose

A glucose homopolymer, structural role in plants

* B-1,4 glycosidic bond backbone
* Linear, no branching
* Hydrogen bonds join chains
* Rigid structure

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No human enzymes can break the B-1,4 bond

Describe: O-linked glycosylation

Carbohydrates attached to side chain hydroxyl oxygen of SERINE or THREONINE

Describe: N-linked glycosylation

Carbohydrates attached to side chain amide nitrogen of ASPARAGINE

How are carbohydrates attached to proteins?

Catalyzed by an enzyme called glycosyltransferase

Which features of carbohydrate chemistry make carbohydrates information rich molecules?

* Complex structure allows for a number of glycosidic bonds, and the adding of many monosaccharides
* Different anomers
* Attached to proteins in many ways

How does glycosylation change the properties of proteins?

Additional chemical information for a variety of functions

What are the three classes of glycoproteins?

Glycoproteins

Proteoglycans

Mucins

Summarize: Glycoproteins

* More protein than carb by weight
* N or O linked glycosylation

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Ex) EPO: glycosylation improves the stability of protein in blood

Summarize: Proteoglycans

* More carb than protein by weight
* Attached to glycosaminoglycans

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Ex) Aggrecan: glycosaminoglycans have a (-) charge that absorbs water

Summarize: Mucins

* More carb than protein by weight
* O-linked glycosylation

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Ex) MUC2: glycans bind water, form gel, lubricate/protect intestines

Define: Lectins

Proteins that specifically bind carbs by non-covalent interactions

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(Hemagglutinin promotes interactions between cells)

Define: Selectins

A type of lectin that helps the immune system bind to sites of energy by recognizing and binding carbs

What does a - or + value of G mean?

(+) Non-spontaneous reaction

(-) Spontaneous reaction

How do enzymes affect reactions?

They speed up the rate of reaction by decreasing activation energy (G) (this is done by stabilizing the transition state)

Do enzymes alter the equilibrium of a reaction?

No, enzymes only affect rate

What are some features of an enzyme active site?

1. Residues forming the active site come from different positions of the primary sequence
2. Make up a small volume of the total protein
3. Unique microenvironment
4. Forms many weak interactions with substrates
5. Specificity depends on the precise arrangement of active site residues

Define: Co-factor

Non-protein compounds that bind to proteins and are needed for biological activity.

* Co-enzymes are organic molecules derived from vitamins
* Metals (Zinc/Iron)

Define: Apo-enzyme

An enzyme without the cofactor

Define: Halo-enzyme

An enzyme with the cofactor

Define: Prosthetic group

A cofactor that is very tightly bound to the enzyme

Define: Co-substrate

A cofactor that is loosely bound to the enzyme

Describe: The Lock and Key Model

A perfect fit exists between enzyme and substrate

Describe: The Induced Fit Model

Dynamic recognition of substrate causes a conformational change in the enzyme

Define: Initial velocity

The moles of product made per second when time = 0

What is Vmax dependent on?

Vmax is directly dependent on enzyme concentration.

When the concentration of substrate is much smaller than Km, what happens to velocity?

Velocity will be directly proportional to the concentration of substrate (Vmax = \[S\]/Km, V0 = Vmax X \[S\]/Km)

When the concentration of substrate is much larger than Km, what happens to velocity?

Velocity will be equal to Vmax, and the rate is zero order (V0 = Vmax)

When the concentration of substrate is equal to Km, what happens to velocity?

Km is equal to the \[S\] at which the reaction rate is half its maximal value (V0 = Vmax/2)

What is Km?

The concentration of substrate at which half of the enzyme molecules are bound to substrate

What does Km depend on?

Substrate, pH, temperature, and ionic strength

How can you determine Km from the X intercept?

Km = (-1)/Intercept

How can you determine Vmax from the Y intercept?

Vmax = (1)/Intercept

How can you determine slope?

Slope = Km/Vmax

What is Kcat?

The turnover number, or the number of substrate molecules that the enzyme can turn into product per unit time when fully saturated with substrate

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Kcat=Vmax/\[E\]t

A 10^-6 M solution of carbonic anhydrase catalyzes the \n formation of 0.6 M H 2CO3 per second when the \n enzyme is fully saturated with substrate. What is the \n kcat?

Kcat=Vmax/\[E\]

Kcat=(0.6M/s)/(10^-6 M)

Kcat=6x10^5 sec^-1

What is the specificity constant?

Kcat/Km

A measure of catalytic efficiency because it takes into account turnover number (Kcat) and the nature of the substrate-enzyme interaction (Km)

Define: Sequential reactions

Characterized by formation of a tertiary complex consisting of the two substrates and the enzyme.

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May be ordered or random in terms of how substrates bind

Define: Double Displacement (Ping-Pong) reactions

Characterized by the formation of a substituted enzyme intermediate.

One or more products are released before all substrates bind the enzyme.

Allosteric Enzymes

Allosteric enzymes are enzymes that regulate the flux of biochemicals through metabolic pathways • They catalyze the “committed step” of metabolic pathways

Define: Feedback inhibition

Inhibitors bind the regulatory site on the enzyme, which inhibits activity

True or False: Allosteric Enzymes can recognize both inhibitory and stimulatory molecules

True, allosteric enzymes can be affected by feed forward (stimulatory) or feed backward (inhibitory) activation

How do the curves of Michaelis-Menten enzymes and allosteric enzymes differ?

Michaelis-Menten enzymes have a standard curve

Allosteric enzymes form sigmoidal curves

Which form of allosteric enzymes catalyzes reactions?

Relaxed form

Which form of allosteric enzymes is stable and most common?

Tense form

What is the allosteric constant?

T/R = L0 (usually in the hundreds)

What is the symmetry rule?

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All active sites must be in the same state (R or T)

Does substrate binds more readily to R or T enzymes?

R, this is why relaxed enzymes catalyze reactions

Describe the Concerted Model for Allosteric Enzymes

When \[S\] is low: More T than R, L0 is very large

As \[S\] increases it binds an active site on R, trapping all other active sites in R (symmetry rule)

More enzymes in R state makes it easier for substrate to bind and more active sites become R formed

How does the binding of substrate effect T-R equilibrium?

The binding of substrate disrupts the T-R equilibrium in favour of R, this is called COOPERATIVITY

Describe the threshold effect

Allosteric enzymes are more sensitive to \[S\] near KM than Michaelis-Menten enzymes with the same Vmax

* Acts as a lightswitch to dramatically change velocity as \[S\] changes

Define: Heterotrophic effects

__Regulators__ shift sigmoidal curve left (activator) or right (inhibitor)

Describe: Homotrophic effects

Effects of __substrate__ on allosteric enzyme (sigmoidal curve)

Describe: Sequential Model for Allosteric Enzymes

Binding of substrate to one active site influences the binding of substrate to a neighbouring active site

What are the 4 catalytic strategies?

* Covalent catalysis
* General Acid-Base Equilibrium
* Metal Ion Catalysis
* Catalysis by approximation and orientation

Describe: Covalent Catalysis

The active site contains a reactive group that becomes temporarily covalently modified

Describe: General Acid/Base Catalysis

A molecule other than water plays the role of a proton donor/acceptor

Describe: Metal Ion Catalysis

* Stabilize negative charge on intermediate
* Generate a nucleophile by increasing acidity of a nearby molecule (like water)
* Increase binding energy through interaction with substrate

Describe: Approximation/Orientation Catalysis

Who substrates are brought into close proximity and correct orientation when bound to the enzyme

What are the types of reversible enzyme inhibitors?

* Competitive
* Uncompetitive
* Noncompetitive

Describe: Competitive Inhibition

* Inhibitor resembles the substrate and binds to the active site


* As the concentration of inhibitor increases, higher concentrations of substrate are required to obtain a particular velocity
* The inhibitor has no effect on Vmax, but increases KM

Describe: Uncompetitive Inhibition

* The inhibitor binds to the ES complex


* The enzyme-substrate-inhibitor (ESI) complex does not form any product
* With uncompetitive inhibitors both KM and Vmax decrease
* ESI complex decreases active enzyme (decreases Vmax)
* Inhibitor shifts E+S-ES equilibrium towards ES, which increases K and decreases Km

Describe: Noncompetitive Inhibition

* The substrate binds to the enzyme alone or the enzyme-inhibitor complex
* The enzyme-inhibitor (EI) and enzyme-substrate-inhibitor (ESI) complexes do not form any product
* With noncompetitive inhibitors Vmax decrease and KM is unchanged
* Decreases active enzyme (decreases Vmax)
* No effect on substrate binding to E, so Km is unchanged

What are the types of irreversible inhibitors?

* Group specific
* Affinity label
* Transition state analog
* Suicide inhibitor (mechanism based)

Describe: Group Specific Inhibitors

Modify specific R groups of amino acids and deactivate enzymes

Describe: Affinity Label Inhibitors

* Covalently modify active site residues
* Structurally similar to substrate
* Specific to enzymes

Describe: Transition-State Analog Inhibitors

Molecules that inhibit an enzyme by binding the active site and mimicking the transition state

Describe: Suicide Inhibitors

* Chemically modified substrate that binds and is initially processed by the enzyme
* Mechanism of catalysis results in chemically reactive intermediate that inactivate enzyme through covalent modification

What are the seven classes of enzymes, what is the role of each?

* Oxidoreductases - transfer electrons, REDOX
* Transferases - transfer functional groups between molecules
* Hydrolases - cleave molecules by addition of H2O
* Lyases - add or remove atoms/functional groups to add/remove double bonds
* Isomerases - move function groups within a molecules
* Translocases - join molecules (ATP powered)
* Ligases - catalyze movement of ions/molecules accross membranes

Describe the mechanism of chymotrypsin

Cleaves on the carboxyl side of bulky hydrophobic amino acids (Phe, Met, Trp)

Define: Catalytic Triad (of Chemotrypsin)

His 57 acts as a general base and accepts a proton from Ser 195 → Creates a powerful nucleophile (alkoxide ion)

Asp 102 orients His 57 in the correct orientation to serve as a general base

What class of enzyme is chymotrypsin?

Hydrolase

What is the function of the oxyanion hole?

The oxyanion hole stabilizes the negative charge on the tetrahedral intermediate. These interactions contribute to binding energy

What are the substrates of peptide hydrolysis by chymotrypsin?

Peptide (with C-terminal and N-terminal)

Water

What are the products of peptide hydrolysis by chymotrypsin?

C-Terminal end of a peptide

N-terminal end of a peptide

What is the prosthetic group of hemoglobin?

Heme groups

What is the role of heme groups in myoglobin and hemoglobin

Myoglobin and Hemoglobin bind oxygen in heme groups