Protein are polymers of -amino acidsThe amino acids used to make proteins are2-aminocarboxylic acids.The (alpha) carbon is the carbon to which afunctional group is attached.
Properties of amino acids:structure and chemical functionalitychiralityacid-base propertiescapacity to polymerize
Proteins in the Diet9 of the 20 amino acids must be obtained from thediet. These are referred to as the essential aminoacids. Histidine Isoleucine Leucine Lysine Methionine Phenylalanine Threonine Tryptophan Valine Proteins are also the major source of nitrogen in thediet
Properties of amino acids:Aliphatic chains: Gly, Ala, Val, Leu, and Ile HydrophibicityHydroxyl or sulfur side chains: Ser, Thr, Cys, MetAromatic: Phe, Trp, TyrBasic: His, Lys, ArgAcidic and their amides: Asp, Asn, Glu, Gln
Amino acids Classified according to their capacity to interact with water 4 classes: NON POLAR, POLAR, ACIDIC AND BASIC Non polar amino acids contain hydrocarbon R groups R groups do not have (+) or (-) charges and interact poorly with water 2 types of hydrocarbon chains: aliphatic and aromatic
Non-Polar Side Chains: Side chains which have pure hydrocarbon alkyl groups (alkane branches) or aromatic (benzene rings) are non-polar. Examples include valine, alanine, leucine, isoleucine, phenylalanine. The number of alkyl groups also influences the polarity. The more alkyl groups present, the more non-polar the amino acid will be. This effect makes valine more non-polar than alanine; leucine is more non-polar than valine.
Polar Side Chains:Side chains which have various functional groups such asacids, amides, alcohols, and amines will impart a more polarcharacter to the amino acid.The ranking of polarity will depend on the relative ranking ofpolarity for various functional groupsIn addition, the number of carbon-hydrogens in the alkane oraromatic portion of the side chain should be considered alongwith the functional group.
>Example: Aspartic acid is more polar than serine because anacid functional group is more polar than an alcohol group.
>Example: Serine is more polar than tyrosine, since tyrosinehas the hydrocarbon benzene ring.
Acid - Base Properties of Amino Acids: Acidic Side Chains: If the side chain contains an acid functional group, the whole amino acid produces an acidic solution. Normally, an amino acid produces a nearly neutral solution since the acid group and the basic amine group on the root amino acid neutralize each other in the zwitterion. If the amino acid structure contains two acid groups and one amine group, there is a net acid producing effect. The two acidic amino acids are aspartic and glutamic
Basic Side Chains: If the side chain contains an amine functional group, the amino acid produces a basic solution because the extra amine group is not neutralized by the acid group.Amino acids which have basic side chains include:lysine, arginine, and histidine.
Hydrophobic Amino Acids (aliphatic)
Hydrophobic Amino Acids (aromatic) all very hydrophobic Some contain aromatic group Absorb UV at 280 nm
Sulfur Containing Amino AcidsMethionine (Met, M) startamino acid, very hydrophobicCysteine (Cys,C) sulfur inform of sulfhydroyl, importantin disulfide linkages, weak acid,can form hydrogen bonds.
Charged Amino Acids Asp and Glu are acidic amino acids Contain carboxyl groups Negatively charged at physiological pH, present as conjugatebases Hydrophillic nitrogenous bases Carboxyl groups function as Positively charged at nucleophiles in some enzymatic physiological pH reactions Histidine imidazole ring protonated/ionized, only amino acid that functions as buffer in physiol range. Lysine - diamino acid, protonated at pH 7.0 Arginine - guianidinium ion always protonated, most basic amino acid
Polar Amino Acids 1
Polar Amino Acids 2
Classification of Amino Acids by Polarity POLAR Acidic Neutral Basic Asp Asn Ser Arg Tyr Cys His Glu Gln Thr Lys Gly POLAR Ala Ile Phe Trp NON- Val Leu Met Pro Polar or non-polar, it is the bases of the amino acid properties. Juang RH (2003) Biochemistry
Functional significanceHydrophobic amino acids: encountered in the interiorof proteins shielded from direct contact with waterHydrophillic amino acids: generally found on theexterior of proteins as well as in the active centers ofenzymesImidazole group: act as either proton donor oracceptor at physiological pH Reactive centers of enzymesPrimary alcohol and thiol groups: act as nucleophilesduring enzymatic catalysis Disulfide bonds
Stereochemistry Note that the R group means that the -carbon is a chiral center. All natural amino acids are L-amino acids.
L-Form Amino Acid StructureCarboxylic group - COO Amino group + H3 N H H = Glycine R group CH3 = Alanine Juang RH (2004) BCbasics
Mirror Images of Amino Acid Mirror image Same chemical properties Stereo isomers Juang RH (2004) BCbasics
THE ACID-BASE BEHAVIOUR OF AMINO ACIDS Amino acids are zwitterions: An amino acid has both a basic amine group and an acidic carboxylic acid group.
There is an internal transfer of a hydrogen ion from the -COOH group to the -NH2 group to leave an ion with both a negative charge and a positive charge. This is called a zwitterion.
Adding an alkali to an amino acid solution increase the pH of a solution of an amino acid by adding hydroxide ions, the hydrogen ion is removed from the -NH3+ group The amino acid would be found to travel towardsthe anode (the positive electrode).
Adding an acid to an amino acid solution decrease the pH by adding an acid to a solution of an amino acid, the -COO- part of the zwitterion picks up a hydrogen ion. the amino acid would move towards thecathode (the negative electrode).
Shifting the pH from one extreme to the other Suppose you start with the ion weve just produced under acidic conditions and slowly add alkali to it. That ion contains two acidic hydrogens - the one in the -COOH group and the one in the -NH3+ group. The more acidic of these is the one in the -COOH group, and so that is removed first - and you get back to the zwitterion.
So when you have added just the right amountof alkali, the amino acid no longer has a netpositive or negative charge. That means that it wouldnt move towards either the cathode oranode during electrophoresis. The pH at which this lack of movement duringelectrophoresis happens is known as theisoelectric point of the amino acid. This pHvaries from amino acid to amino acid.
If you go on adding hydroxide ions, you will get the reaction weve already seen, in which a hydrogen ion is removed from the -NH3+ group.
You can, of course, reverse the whole processby adding an acid to the ion weve just finishedup with. That ion contains two basic groups - the -NH 2group and the -COO- group. The -NH2 group isthe stronger base, and so picks up hydrogenions first. That leads you back to the zwitterionagain.
. . . and, of course, you can keep going by then adding a hydrogen ion to the -C