Chapter 3: Amino Acids

Arginine

Arg, R

Asparagine

Asn, N

Aspartate

Asp, D

Cysteine

Cys, C

What is acid-base catalysis?

The ability to donate or accept protons is called acid-base catalysis and is an important chemical reaction for many enzymes

What are the two negatively Charged Amino Acids that Have Acidic Side Chains

aspartate and glutamate

Amino acids that cannot be generated in the body must be supplied by the diet and are termed

essential amino acids (there are nine of them)

Lysine and arginine have long side chains that terminate with groups that are _________ charged at _______ pH

positively; neutral

Amino acids are the building blocks of

proteins

_____ kinds of side chains varying in....... Many of these properties are conferred by _______ ______. The amino acid functional groups include...... Most of these groups are chemically ________

-20 -size, shape, charge, hydrogen-bonding capacity, hydrophobic character, and chemical reactivity are commonly found in proteins. -functional groups -alcohols, thiols, thioethers, carboxylic acids, carboxamides, and a variety of basic groups. -reactive

Proteins, as well as biochemicals in general, derive their amazing array of functions from the ability to form ______ ________

3D structures

With a pKa value near ____, the imidazole group of histidine is unique in that it can be

6, uncharged or positively charged near neutral pH, depending on its local environment

The zwitterionic form predominates near physiological pH, approximately

7.4

______ of the 20 amino acids—..........—have readily ionizable side chains. These seven amino acids are able to

7; tyrosine, cysteine, arginine, lysine, histidine, and aspartic and glutamic acids; form ionic bonds as well as to donate or accept protons to facilitate reactions.

The dipolar form persists until the pH approaches ___, when the ________ _______ _______ loses a proton.

9; protonated amino group

Alanine

Ala, A

List the nonessential amino acids

Alanine, Arginine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Proline, Serine, and Tyrosine

Glycine

Gly, G

Glutamine

Gln, Q

Glutamate

Glu, E

Histidine

His, H

Isoleucine

Ile, I

Explain an α-amino acid

It consists of a central carbon atom, called the α carbon, which is bonded to an amino group, a carboxylic acid group, a hydrogen atom, and a side chain, called the R group. Each kind of amino acid has a different R group.

Only _____ amino acids are constituents of proteins

L

Leucine

Leu, L

lysine

Lys, K

Fun facts about lysine:

Lysine is an essential amino acid which means that human beings cannot synthesize lysine and must obtain it in the diet. In experimental animals, kept on a cereal-based diet, inadequate dietary lysine increased stress-induced anxiety. Recent studies suggest that this response to lysine deprivation may be true for human beings, too.

Methionine

Met, M

Phenylalanine

Phe, F

Proline

Pro, P

Serine

Ser, S

The three amino acids that contain hydroxyl (-OH) groups

Serine, threonine, and tyrosine

Name the Polar Amino Acids Have Side Chains That Contain an Electronegative Atom

Serine, threonine, tyrosine, cysteine, asparagine, glutamine

What is the basis for the preference for L amino acids?

The answer is not known, but evidence shows that pure L or D amino acids are slightly more soluble than a stable DL crystal. Consequently, if simply by chance, there were a small excess of the L amino acid, this small solubility difference could have been amplified over time so that the L isomer became dominant in solution.

Explain the hydrophobic effect

The hydrophobic amino acids, particularly the larger aliphatic and aromatic ones, tend to cluster together inside the protein away from the aqueous environment of the cell. This tendency of hydrophobic groups to come together is called the hydrophobic effect and is the driving force for the formation of the unique three-dimensional architecture of water-soluble proteins. The different sizes and shapes of these hydrocarbon side chains enable them to pack together to form compact structures with little empty space.

Talk about glycine

The simplest amino acid is glycine, which has a single hydrogen atom as its side chain. With two hydrogen atoms bonded to the α-atom, glycine is unique in being achiral.

The importance of amino acids in the diet (usually ingested as proteins) is illustrated by kwashiorkor, a particular form of malnutrition. Explain kwashiorkor

This condition was first defined in the 1930s in Ghana. Kwashiorkor means "the disease of the displaced child" in the Ga language, a Ghanaian dialect; that is, the condition arises when a child is weaned because of the birth of a sibling. It is a form of malnutrition that results when protein intake is not sufficient. Initial symptoms of the disease are generalized lethargy, irritability, and stunted growth. If treated early enough, the effects of the disease are reversible. However, if not corrected early enough, many physiological systems fail to develop properly, including the brain. For instance, children will suffer from various infectious diseases because their immune systems, composed of many different proteins, cannot be constructed to function adequately. Likewise, the lack of protein prevents the complete development of the central nervous system, with resulting neurological problems. The most common characteristic of a child suffering from kwashiorkor is a large protruding belly (Figure 3.8). The large belly is a sign not of excess calories but of edema, another result of the lack of protein. Edema is swelling that results from too much water in tissue. Insufficient protein in a child's blood distorts the normal distribution of water between plasma and surrounding capillaries. Although the swollen belly is most obvious, the limbs of a child suffering from kwashiorkor also are often swollen. Such suffering children are a devastating display of the centrality of protein to life. Note the swollen belly. This swelling (edema) is due to fluid collecting in the tissues because there is not enough protein in the blood

Threonine

Thr, T

Tryptophan

Trp, W

What are also classified as hydrophobic?

Two amino acids with simple aromatic side chains are also classified as

Tyrosine

Tyr, Y

Valine

Val, V

When is the visualization of the shape of the molecule most important? What are used in such instances?

When emphasis is on the molecule's function; stereochemical renderings

Explain a Fischer projection

When visualizing the constituent atoms of a molecule (such as carbons and hydrogens) is more important than seeing the shape of the molecule, we use a depiction called a Fischer projection. In a Fischer projection, every atom is identified and the bonds to the central carbon atom are represented by horizontal and vertical lines. By convention, the horizontal bonds are assumed to project out of the page toward the viewer, whereas the vertical bonds are assumed to project behind the page away from the viewer.

Explain Monosodium glutamate (MSG)

a glutamate with sodium bound to an acid group, commonly used as a taste enhancer. In fact, the taste of glutamate and aspartate (called umami, from the Japanese word for "deliciousness") is one of the five primary tastes, the others being sweet, sour, bitter, and salty.

Negatively Charged Amino Acids Have ______ Side Chains. There is a negative charge on their side chains. In some proteins, these side chains accept protons, which ______ the negative charge. This ability is often functionally important

acidic, neutralize.

Indeed, histidine is often found in the........ where the imidazole ring can bind and release ______ in the course of _________ __________

active sites of enzymes, protons, enzymatic reactions

Lysine is topped by an ________ group and arginine by a _________ group

amino; guanidinium

What does histidine contain

an imidazole group, an aromatic ring that also can be positively charged

All amino acids are precursors to other _________, such as

biomolecules; hormones, nucleic acids, lipids, and, as just mentioned, proteins.

Note that the R groups of lysine and arginine have dual properties which means the

carbon chains constitute a hydrocarbon backbone, similar to the amino acid leucine, but the chain is terminated with a positive charge.

As the pH is raised, the _______ _______ is the first group to give up a proton, because its pKa is near _____

carboxylic acid, 2

With four different groups connected to the tetrahedral α-carbon atom, α-amino acids are _____

chiral

Describe Phenylalanine

contains a phenyl ring attached in place of one of the methyl hydrogen atoms of alanine.

What are disulfide bonds?

covalent bonds that are particularly important in stabilizing some proteins

Under physiological conditions, amino acids exist in the ________ _______

dipolar form

Free amino acids in solution at neutral pH exist predominantly as

dipolar ions (also called zwitterions).

Pairs of sulfhydryl groups in close proximity may form __________ _________

disulfide bonds

Although there are many ways to classify amino acids, we will assort these molecules into ____ groups, on the basis of the general chemical characteristics of their ___ groups:

four; R 1. Hydrophobic amino acids with nonpolar R groups 2. Polar amino acids with neutral R groups but the charge is not evenly distributed 3. Positively charged amino acids with R groups that have a positive charge at physiological pH (pH ≈ 7.4) 4. Negatively charged amino acids with R groups that have a negative charge at physiological pH

Name the Hydrophobic Amino Acids That Have Mainly Hydrocarbon Side Chains:

glycine, alanine, valine, leucine, isoleucine, methionine, proline, phenylalanine, and tryptophan

Describe Tryptophan

has an indole ring joined to a methylene (—CH2—) group; the indole group comprises two fused rings and an NH group.

List the essential amino acids

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

Positively Charged Amino Acids Are _____________

hydrophilic

The hydroxyl groups on serine, threonine, and tyrosine make them more _______ and ________ than their respective nonpolar counterparts,

hydrophilic, reactive; alanine, valine, and phenylalanine.

The amino acids having side chains consisting only of hydrogen and carbon are

hydrophobic

Proline markedly influences protein architecture because

its ring structure makes it more conformationally restricted than the other amino acids.

Proline also has an aliphatic side chain, but it differs from other members of the set of 20 in that

its side chain is bonded to both the α-carbon and the nitrogen atom

Name the Positively Charged Amino Acids That Are Hydrophilic

lysine, arginine, histidine

Most _________ can synthesize the entire basic set of 20 amino acids, whereas human beings can make only ____ of them.

microorganisms, 11

The sulfhydryl group is much _____ reactive than a hydroxyl group and can completely lose a _____ at slightly _____ pH to form the _______ ________ ________

more; proton, basic; reactive thiolate group

The electrons in the O—H bond are attracted to the ______ atom, making it partly _______, which in turn makes the ________ partly _________

oxygen, negative, hydrogen, positive

The ionization state of an amino acid varies with

pH

The different sizes and shapes of these hydrocarbon side chains enable them to

pack together to form compact structures with little empty space.

In the dipolar form, the amino group is _______ and the carboxyl group is ___________

protonated (NH3+); deprotonated (COO−).

In acid solution (e.g., pH 1), the amino group is _______ and the carboxyl group is ______ ___________

protonated (NH3+); not dissociated (—COOH).

Cysteine is structurally similar to _______ but contains a _______________ group in place of the ________ group.

serine; sulfhydryl, or thiol (—SH), hydroxyl

Some amino acids function as ________ _________, such as _____________

signal molecules; neurotransmitters

Stereochemical renderings also _____ the diagram, thereby making the function of a molecule clearer. Carbon and hydrogen atoms are not explicitly shown unless they are important to the activity of the molecule. In this way, the functional groups are easier to identify. To illustrate the correct stereochemistry of tetrahedral carbon atoms, _______ are used to depict the direction of a bond _____ or __ of the plane of the page. A solid wedge denotes a bond coming out of the plane of the page _____ the viewer. A dashed wedge represents a bond going _____ from the viewer and behind the plane of the page. The remaining two bonds are depicted as _____ ______

simplify; wedges; into; out, toward; away; straight lines

In addition, the set of polar amino acids includes asparagine and glutamine, which contain a ___________ __________

terminal carboxamide.

An L isomer is where

the amino group is on the left

Now talk about alanine

the next simplest amino acid, has a methyl group (—CH3) as its side chain

What does it mean that α-amino acids are chiral?

they may exist in one or the other of two mirror-image forms, called the L isomer and the D isomer

Methionine contains a largely aliphatic side chain that includes a ______ group.

thioether (—S—)

Larger aliphatic side chains are found in the branched-chain amino acids

valine, leucine, and isoleucine.