Chem110 - Ch 12

Larger oligopeptides are known by common names. give examples

(a) Leucine-enkephalin, a pentapeptide, is a naturally occurring pain reliever found in the brain. (b) Oxytocin, a nonapeptide, is a hormone that induces labor during pregnancy.

Which statements accurately describe a noncompetitive inhibitor? (a) It denatures the enzyme. (b) It changes V max for the enzyme. (c) It catalyzes the hydrolysis of the normal substrate for the inhibited enzyme. (d) It changes KM for the enzyme.

(b) It changes V max for the enzyme.

Which statements accurately describe a competitive inhibitor? (a) It denatures the enzyme. (b) It changes V max for the enzyme. (c) It catalyzes the hydrolysis of the normal substrate for the inhibited enzyme. (d) It changes KM for the enzyme.

(d) It changes KM for the enzyme.

Examples of proteins that contain some d-amino acid residues include: ....

- Some d-amino acid residues are used by bacteria to build cell walls -and a number of bacteria-produced antibiotics are d-amino acid residues.

D-Alanine, and L-Alanine Fischer projections

-Alanine contains one chiral carbon atom and can exist as a pair of enantiomers, d-alanine and l-alanine. -Fischer projections are drawn with the carbon atoms running vertically and the carboxyl group at the top. -In this orientation, d-amino acids have -NH2 on the right and l-amino acids have -NH2 on the left.

Explain what is meant by the term denaturation, and list some of the ways to denature a protein.

-Denaturation is any disruption to the native conformation that destroys protein activity -Denaturation is caused by factors that disrupt noncovalent forces, including: Change in temperature Change in pH Agitation Use of detergents or soaps -"Mild" denaturation can be reversed Denaturation keeps the primary structure of the protein intact

The binding of oxygen to hemoglobin is cooperative. Explain this term.

-Hemoglobin has quaternary structure and contains four subunits 2 α ( 141) and 2 β (146) -Each subunit contains a heme groups and can transport one oxygen molecule -The subunits are cooperative so that when one oxygen molecule has bound to a heme, additional oxygens bind more easily

summarize the flowchart above

-Hydrophobic: have nonpolar side chains or R, such as alkyl groups or aromatic groups. -Hydrophilic—neutral: contain polar R, such as hydroxyl, -OH and sulfhydryl, -SH, groups. -Hydrophilic—acidic: have R containing carboxylic acid, -COOH, groups. -Hydrophilic—basic: have R containing amine, -NH2 groups.

Name the covalent and noncovalent forces responsible for each level of structure.

-Primary structure is held together by peptide bonds -secondary structure by hydrogen bonds between atoms in the polypeptide backbone, -tertiary structure by interactions between side chains hydrogen bonding, the hydrophobic effect, ionic bonds, and disulfide bonds, -quaternary structure by the same forces responsible for tertiary structure.

primary structure of protein

-Primary structure refers to the sequence of amino acid residues in a peptide or protein. When applied to oligo- or polynucleotides, primary structure is the sequence of deoxyribonucleotide (in DNA) or ribonucleotide (in RNA) residues.

The amino acids in the preceding tables are shown as they exist at physiological pH = 7

-The COOH is deprotonated to yield COO- -The NH2 is protonated to yield NH3+

Collagen

-is a structural protein found in tendon, cartilage, bone, blood vessels, and teeth -Each chain coils into an extended helix -Three helices then coil around each other to form a triple helix (next slide) -Parallel triple helices will pack together to form strong collagen fibers

Ala-Gly-Val

-primary structure and, -reading from the N-terminus -consists of an alanine residue, a glycine residue, attached to a valine residue. -Five other tripeptides can be constructed from these three amino acids.

secondary structure of protein

-secondary structure to common structural features α-helix and β-sheet).

Distinguish between absolute specificity, relative specificity, and stereospecificity.

Enzymes display varying degrees of specificity: -Absolute specificity :means that the enzyme accepts only one specific substrate(reactant)for example Urease -Relative specificity: refers to those enzymes that will react with a range of substrates having the same functional group (alcohol dehydrogenase) -Stereospecific enzymes: will react with or produce a particular stereoisomer only (desaturase)

Polar-neutral amino acids

Do not have charged.

Describe how pH affects the net charge on a peptide.

Each peptide contains a basic N-terminal amino group and an acidic C-terminal carboxyl group. Carboxyl groups appear as -CO2H at pHs less than 7 and as -CO2− at pH 7 or higher. Amino groups appear as -NH3+ at pH 7 or lower and as -NH2 at pHs greater than 7. Acidic and basic groups present in the side chains of amino acid residues exhibit the same behavior.

Protein Structure

Fibrous proteins exist as long fibers or strings. These proteins, including collagen (in skin) and keratin (in hair), are usually tough and water insoluble. Globular proteins are spherical in shape, highly folded, and tend to be water soluble.

What happens to amino acid after hydrolysis?

For the amino acid residues in a peptide or protein, hydrolysis of the peptide bond restores their amino and carboxyl groups to their original state

Glycine (Gly)

Glycine is the only amino acid which does not have a chiral carbon

Nonpolar amino acids

Have mainly Carbon and Hydrogen bonds.

describe the bond that joins amino acid residues in these compounds.

In an oligo- or polypeptide the amino acid residues are joined to one another by peptide (amide) bonds.

Explain what is meant by feedback inhibition and covalent modification.

In feedback inhibition the product of a metabolic pathway prevents its own overproduction by inactivating one or more of the enzymes responsible for its synthesis. In covalent modification an enzyme is switched "on" or "off" by the making or breaking of covalent bonds to or within the enzyme. Phosphorylation/dephosphorylation and zymogens are examples of covalent modification.

which level does Insulin fall into?

Insulin, a protein involved in glucose metabolism, contains 51 amino acid residues.

Calculate the isoelectric point for the example

Mathematically, isoelectric point, pI, for glycine is calculated using the formula

classification of amino acid

Only differences in the side chain or R group, the atom or group of atoms also attached to the α carbon atom, distinguish one amino acid from another

quaternary structure of protein

Quaternary structure is the combination of more than one polypeptide chain that may be required to produce an active protein.

tertiary structure of protein

Tertiary structure is the overall three-dimensional shape of a protein or a polynucleotide, including the contribution of secondary structure.

N-terminus

The amino end (normally protonated as NH3+) is called the N-terminus

Hydrophobic effect

The attraction of non-polar groups for one another when they are placed in an aqueous solution.

C-terminus

The carboxyl end (normally deprotonate COO- is called the C-terminus

Covalent modification-from powerpoint

The enzyme undergoes making or breaking of the bond. For example When Glycogen Phosphorylase, an enzyme needed for the breakdown of glycogen to glucose It has 2 forms it changes between forms depending on its activity.

Isoelectric point

The isoelectric point, or pI, is the pH at which an amino acid has a net charge of zero.

how are amino acids classified?

The nature of the side chain (the atom or group of atoms also attached to the α carbon) is used to classify amino acids as one of the following: nonpolar, polar-acidic, polar-basic, or polar-neutral.

isoelectric point

The pH at which an amino acid has a net charge of zero is called the isoelectric point (pI)

Polypeptide backbone

The series of alternating alpha carbon atoms and peptide groups present in a polypeptide.

In an aqueous environment, the native form of a globular protein typically has its nonpolar amino acid side chains folded into the hydrophobic interior and its polar side chains on the hydrophilic surface. Why is this most stable arrangement?

This folding rule, known as "nonpolar in, polar out," is the most stable arrangement because it allows polar side chains on the surface of the protein to interact with water molecules and allows nonpolar side chains to avoid water.

Native

This term refers to the biologically "active" form of a protein.

zwitterion

When an amino acid (such as glycine at the right at pH=7) carries one positive charge and one negative charge, the species is called a zwitterion

β-sheet

a sheet-like arrangement forms between different segments of a polypeptide chain. β-sheets can be parallel or antiparallel. Also known as a β-pleated sheet. Held together by hydrogen bonds between amide N-H and C=O groups along the backbone.

define affinity in chemistry

affinity is the electronic property by which dissimilar chemical species are capable of forming chemical compounds. Chemical affinity can also refer to the tendency of an atom or compound to combine by chemical reaction with atoms or compounds of unlike composition.

To which functional group from organic chemistry do peptide bonds belong?

amide group

Polar-basic amino acids

are electrically charged on the R group, have gained proton/s

Polar-acidic amino acids

are electrically charged on the R group, have given away proton/s

Give an example of Isoelectric point (pI) of amino acids

as we add hydroxide ions—in other words, raise the pH—different charged forms of glycine exist. Form B has a net zero charge and is called a zwitterion. Form A has a net charge of +1, and form C has a net charge of -1.

what different shapes and colors

blue arrows representing β-sheets, red coils representing α-helices, and the yellow rope representing other twists and turns of the polypeptide chain.

alpha helix (α-helix)

polypeptide coils into a helical shape that is held in place by hydrogen bonds between amide N-H and C=O groups from different parts of the polypeptide backbone.

Which level of structure determines which folding pattern to be selected?

primary structure ultimately determines which folding pattern is selected, so both secondary structure and tertiary structure depend on primary structure.

Identify the steps required for a typical Michaelis-Menten enzyme to convert a substrate into a product.

step 1-Substrate binding E + S = ES The Michaelis constant KM measure the strength of the attraction between E and S step 2-Product release ES → E + P Vmax is the maximum velocity rxn rate) that a given concentration of enzyme can produce

Protein

A polypeptide containing more than fifty amino acid residues.

Simple protein

A protein that does not require a prosthetic group for biological activity.

Conjugated protein

A protein that requires a prosthetic group for biological activity.

Globular protein

A protein whose structure is spherical and highly folded. Typically, a globular protein is water soluble.

Fibrous protein

A protein whose structure resembles long fibers or strings. Typically, fibrous proteins are tough and water insoluble.

Competitive inhibitor

A reversible enzyme inhibitor that competes with a substrate at the active site of an enzyme, changes KM , and has no effect on V max.

Allosteric effector

Allosteric effectors are ions or molecules that regulate allosteric enzymes Effectors bind at sites other than the active site thereby altering the subunit shape and affecting its ability to bind substrate Note that Km and V max do not apply in this concept.

Allosteric enzyme

Allosteric enzymes typically have quaternary structure and display cooperativity Binding of substrate to the active site of one subunit affects the binding of substrate to other subunits.

Describe allosteric enzymes and the role that effectors play in the ability of these enzymes to catalyze reactions.

Allosteric enzymes usually consist of more than one polypeptide chain, and the binding of substrate to the active site on one subunit affects the binding of substrate at other subunits. Allosteric enzymes are controlled by positive effectors which increase reaction velocity) and negative effectors which decrease it).

Distinguish between oligopeptides, polypeptides, and proteins.

Amino acids are the building blocks used to produce oligopeptides (2-10 amino acid residues) and polypeptides (more than 10 residues). A protein is a polypeptide with more than 50 amino acid residues.

Describe the structure of amino acids

Amino acids contain an amino group and a carboxyl group, and in α-amino acids the amino group is attached to the carbon atom α to the carboxyl group. Because both amines and carboxylic acids have acidic and basic forms, amino acid structure is pH dependent.

Positive effector

An allosteric effector that enhances substrate binding and increases the rate of an enzyme-catalyzed reaction.

Negative effector

An allosteric effector that reduces substrate binding and slows the rate of an enzyme-catalyzed reaction.

L-amino acid

An amino acid that belongs to one particular family of stereoisomers. When drawn in a Fischer projection with the carboxyl group pointing up and the side chain pointing down, the alpha amino group points to the left in an l amino acid.

D-amino acid

An amino acid that belongs to one particular family of stereoisomers. When drawn in a Fischer projection, with the carboxyl group pointing up and the side chain pointing down, the alpha amino group points to the right in a d amino acid.

Polar-acidic amino acid

An amino acid whose side chain contains a carboxyl group.

Polar-basic amino acid

An amino acid whose side chain contains an amino group or another basic nitrogen-containing group.

Nonpolar amino acid

An amino acid whose side chain is an alkyl group, an aromatic ring, or another nonpolar collection of atoms.

Polar-neutral amino acid

An amino acid whose side chain is polar and neutral, typically an alcohol, a phenol, or an amide.

Reversible inhibitor

An enzyme inhibitor whose effect is not permanent (is reversible) because the inhibitor is loosely bound to the enzyme and can dissociate, restoring the enzyme to its original state.

Irreversible inhibitors.

An enzyme inhibitor whose effect is permanent.

Zymogen

An inactive enzyme precursor.

Tripeptide

An oligopeptide that consists of three amino acid residues.

Dipeptide

An oligopeptide that consists of two amino acid residues.

Tetrapeptide

An oligopeptide that contains four amino acid residues.

peptide bond

Another name for the amide bond that connects amino acid residues in a peptide or a protein.

Inhibitor

Any substance that reduces an enzyme's ability to act as a catalyst.

Cooperativity

Attachment of a ligand to a binding site on a protein that impacts binding at other sites.

Oligopeptide

A compound consisting of from two to ten amino acid residues.

Polypeptide

A compound consisting of more than ten amino acid residues.

structure of amino acids

A compound that contains one or more carboxyl groups and one or more amino groups. Amino acids are the building blocks used to construct peptides and proteins.

Binding site

A crevice on the surface of a globular protein where molecules or ions attach.

Covalent modification

A form of control over the activity of an enzyme, in which the making or breaking of covalent bonds within the enzyme activates or deactivates it.

Feedback inhibition

A form of control over the activity of an enzyme, in which the product of a metabolic pathway inhibits one or more of the enzymes responsible for the product's synthesis.

Noncompetitive inhibition

A form of enzyme inhibition in which a reversible inhibitor that attaches to an enzyme at a site other than the binding site, changes V max, and has no effect on KM.

Peptide

A general name given to oligo- and polypeptides.

α-amino acid

A molecule containing an amino group and a carboxylic acid group that are separated by one carbon

Prosthetic group

A nonpeptide component that contributes to protein tertiary structure.