Chapter 16 Chemistry: Amino Acids, Proteins, and Enzymes

Proteins

• in the body are polymers made from 20 different amino acids

• differ in characteristics and functions that depend on the order of amino acids that make up the protein

what do proteins form?

Form structural components such as cartilage, muscles, hair, and nails

How do proteins function?

Function as enzymes to regulate biological reactions such as digestion and cellular metabolism

Such as hemoglobin and myoglobin transport oxygen in the blood

Amino acids

the molecular building blocks of proteins

What do amino acids have?

• Have a central carbon atom called the a-carbon bonded to two functional groups: an ammonium group (— NH₃⁺ ) and a carboxylate group (—COO^- )

• Have a central carbon atom bonded to a hydrogen atom and R group or side chain in addition to the carboxylate and ammonium groups

How are amino acids classified?

as

• nonpolar (hydrophobic ) with hydrocarbon side chains

• polar (hydrophilic) with polar or ionic side chains

How are amino acids nonpolar?

when the R group is H, alkyl, or aromatic

Glycine (Gly, G)

nonpolar amino acids with H as R group

Alanine (Ala, A)

non polar amino acid with alkyl as R group

Valine (Val, V)

nonpolar amino acid with alkyl as R group

Leucine (Leu, L)

nonpolar amino acid with alkyl as R group

Isoleucine (Ile, I)

nonpolar amino acid with alkyl as R group

Phenylalanine (Phe, F)

nonpolar amino acid with aromatic as R group

Methionine (Met, M)

nonpolar amino acid with alkyl as R group

Proline (Pro, P)

nonpolar amino acid with alkyl as R group

Tryptophan (Trp, W)

nonpolar amino acid with aromatic as R group

How is an amino acid polar?

when the R group is hydroxyl, a thiol, or an amide

Serine (Ser, S)

polar amino acid with hydroxyl as R group

Threonine (Thr, T)

polar amino acid with hydroxyl as R group

Tyrosine (Tyr, Y)

polar amino acid with hydroxyl as R group

Cysteine (Cys, C)

polar amino acid with thiol as R group

Asparagine (Asn, N)

polar amino acid with amide as R group

Glutamine (Gln, Q)

polar amino acid with amide as R group

How is an amino acid acidic?

When the R group is a carboxylate

Aspartate (Asp, D)

polar acidic amino acid with carboxylate as R group

Glutamate (Glu, E)

polar acidic amino acid with carboxylate as R group

How is an amino acid basic?

When the R group is an amine, which ionizes to give an ammonium ion

Histidine (His, H)^b

polar basic amino acid with amine as R group

Lysine (Lys, K)

polar basic amino acid with amine as R group

Arginine (Arg, R)

polar basic amino acid with amine as R group

Structural Formulas of Amino Acids

has

• an a-carbon atom that is attached to three components:

— NH₃⁺ , — COO^- , and —H

• a fourth component, an R group that differs for each particular amino acid

• a three-letter or one-letter abbreviation derived from its name

Proteins: Primary structure

A peptide bond is an amide bond that forms when the —COO^- group of one amino acid reacts with the —NH₃ ⁺ group of the next amino acid.

The linking of two or more amino acids by peptide bonds forms a peptide

Peptides formed from

• Two amino acids are called dipeptides

• Three amino acids are called tripeptides

• four amino acids are called tetrapeptides

A peptide bond

• is an amide bond

• forms between the —COO^- group of one amino acid and the —NH₃ ⁺ group of the next amino acid

Formation if dipeptide

A peptide bond between glycine and alanine forms the dipeptide glycylalanine

Naming Peptides

With the exception of the C-terminal amino acid, the names of all the other amino acids in a peptide end with yl.

Essential Amino Acids

Of the 20 amino acid used to build the proteins in the body, only 11 can be synthesized in the body

• only 11 can be synthesized in the body

• the other 9 amino acids are essential amino acids that must be obtained from the proteins in the diet

Primary structure of Proteins

A protein is a polypeptide of 50 or more amino acids that has biological activity.

The primary structure of a protein is the particular sequence of amino acids held together by peptide bonds.

Insulin

was the first protein to have its primary structure determined

Insulin structure

• has a primary structure of two polypeptide chains linked by disulfide bonds

• has a chain A with 21 amino acids and a chain B with 30 amino acids

Enkephalins and endorphins

are natural painkillers produced in the body. They are polypeptides that bind to receptors in the brain to give relief from pain

Enkephalins

are found in the thalamus and the spinal cord, are pentapeptides, the smallest molecules with opiate activity

What are two hormones produced by the pituitary gland?

nonapeptides oxytocin and vasopressin

Oxytocin

stimulates uterine contractions in labor

Vasopressin

is an antidiuretic hormone that regulates blood pressure by adjusting the amount of water reabsorbed by the kidneys.

Alpha helix structure

is similar to that of a spiral staircase

acquires a coiled shape from hydrogen bonds between the oxygen of the C=O group and the hydrogen of the N—H group in the next turn.

Secondary structure of alpha helix

• hydrogen bonds form between the oxygen of the C=O groups and the hydrogen of N—H groups of the amide bonds in the next turn of the a helix

• the formation of many hydrogen bonds along the polypeptide chain gives the helical shape of a spiral staircase

secondary structure of a beta-pleated sheet

hydrogen bonds form between the carbonyl oxygen atoms and hydrogen atoms in the amide groups bending the polypeptide chain into a sheet

Secondary structure of a triple helix

• Three polypeptide chains are woven together

• hydrogen bonds hold the chains together, giving the polypeptide the added strength typical of collagen, connective tissue, skin, tendons, and cartilage

• Collagen fibers are triple helices of polypeptide chains held together by hydrogen bonds

In an Alzheimer’s brain..

beta-amyloid plaques and neurofibrillary tangles damage the neurons and interfere with nerve signals

Tertiary structure of a protein

is an overall three-dimensional shape caused by interactions of different parts of the chain, causing it to bend and twist

How is the tertiary structure of a protein determined?

by cross-links, the attractions and repulsions between the side chains (R groups) of the amino acids in a peptide chain

Sections of a protein interact to create the tertiary structure of a protein due to

• hydrophobic interactions between two nonpolar amino acids

• hydrophilic interactions between the external aqueous environment and the R groups of polar amino acids

• salt bridges, ionic bonds between ionized R groups of basic and acidic amino acids

• hydrogen bonds between H of a polar R group and the O or N of another amino acid

• disulfide bonds —S—S— between the —SH groups of cysteine amino acids

Quaternary Structure

• is the combination of two or more protein units

• consist of four polypeptide chains as subunits in hemoglobin

• is stabilized by the same interaction found in tertiary structures

Denaturation of proteins

involves the disruption of bonds in the secondary, tertiary, and quaternary protein structures

Heat and organic compounds in denaturation

break apart H bonds and disrupt hydrophobic interaction

Acids and bases in denaturation

break H bonds between polar R groups and disrupt ionic bonds

Heavy metal ion in denaturation

react with S — S bonds to form solids

Agitation in denaturation

whipping, that stretches peptide chains until bonds break

Enzymes

• are proteins that act as biological catalysts. On the surface of an enzyme, a small region called an active site binds a substrate and catalyzes a specific reaction for that substrate

• increase the rate of reaction by lowering the energy of activation

The name of an enzyme

• is derived by replacing the end of the name of the reaction or reacting compound with the suffix ase

• could be a common name, particularly for the digestion enzymes, such as pepsin and trypsin

What does the name of an enzyme identify?

the reacting substance—for example, sucrase catalyzes the reaction of sucrose

What does the name of an enzyme describe?

the compound or the reaction that is catalyzed— for example, oxidase catalyzes an oxidation reaction

Active site

• is a region within an enzyme that fits the shape of the reacting molecule called a substrate

• releases products when the reaction is complete

What does the active site contain?

amino acid R groups that bind the substrate

Enzyme-catalyzed reaction

• a substrate attaches to the active site

• an enzyme-substate (ES) complex forms

• reaction occurs and products are released

• an enzyme is used over and over

Lock and key model

• active site has a rigid, nonflexible shape

• enzyme binds only substrates that exactly fit the active site like a lock

• substrate is the key that fits the lock

induced-fit model

• enzyme structure is flexible, not rigid, and adjusts to the shape of the active site in order to bind to substrate

• the range of substrate specificity increases

• shape changes improve catalysis during reaction- lowers the activation energy of the reaction

Isoenzymes

• are different forms of an enzyme that catalyze the same reaction in different cells or tissues of the body

what do isoenzymes consist of?

quaternary structures with slight variations in the amino acids in the polypeptide subunits

The activity of an enzyme

describes how fast an enzyme catalyzes the reaction that converts a substrate to product

What affects the activity of an enzyme?

temperature, pH, and the presence of inhibitors

When are enzymes most active?

optimum temperature (usually 37 C in humans)

show little activity at low temperatures

At what temperature do enzymes lose activity?

above 50 C as denaturation occurs with loss of catalytic activity

What pH are enzymes most active?

• at optimum pH

• contain R groups of amino acids with proper charges at optimum pH

At what pH do enzymes lose activity?

in low or high pH as tertiary structure is disrupted

What is the optimum pH for enzymes in the body?

about 7.4

Enzyme inhibitors

• are molecules that cause a loss of catalytic activity

• prevent substrates from fitting into the active sites

Competitive inhibitor

• Has a structure that is similar to that of the substrate

• competes with the substrate for the active site

• has its effect reversed by increasing substrate concentration

Noncompetitive inhibitor

• Has a structure that is much different than that of a substrate

• binds to an enzyme at a site other than the active site and distorts the shape of the enzyme by altering the shape of the active site

• prevents the binding of the substrate

• cannot have its effect reversed by adding more substrate

Irreversible inhibitor

• is a molecule that causes the enzyme to lose all activity

• is often a toxic substance that destroys enzymes

• usually forms a covalent bond with an amino acid side chain preventing catalytic activity

• may be a nerve gas, an insecticide, or an antibiotic