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.