amino_acids.docx

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1. Proteins

Proteins are biochemical compounds consisting of one or more polypeptides typically folded

into a globular or fibrous form in a biologically functional way. A polypeptide is a single linear

polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino

groups of adjacent amino acid residues.

Amino acids

 Definition: an amino acid is an organic compound containing an amino group and an

acidic group (usually, but not always, a carboxylic acid).

 This description fits a very large number of compounds, most of which are non-

physiological. In addition, many physiologically important amino acids are not used in

proteins.

 However, in biochemistry, the term “amino acid.” generally refers to one of the 20 types of

monomeric units that are constituents of proteins.

Biological roles:

1. Amino acids can be metabolized to produce energy. This is especially important during

fasting, when the breakdown of muscle protein is a major energy source.

2. Some amino acids act as neurotransmitters, and some act as starting materials for the

biosynthesis of neurotransmitters, hormones, and other important biochemical compounds.

3. Amino acids are the primary building blocks for proteins

4. General structure of Amino Acids

 The amino acids that constitute proteins are all α-amino acids. The “α-carbon” is bonded to

four different groups: an amino group, a carboxylic acid, hydrogen, and the side-chain.

 Because there are four different chemical groups, the α-carbon is chiral. Physiological

amino acids are almost exclusively L stereochemistry.

 The reason for the specifically L-stereochemistry is not known; in principle D-

stereochemistry would also be possible.

 Experiments performed using a chemically synthesized protein made from D-amino acids

showed the resulting protein to be fully functional, although folded into the mirror image of

the normal protein.

 In the above paragraph, it is stated that physiological amino acids are almost exclusively L-

stereochemistry. A few exceptions exist.

 Glycine is non-chiral, and therefore has no stereochemistry. In addition, some organisms

use small amounts of D-amino acids for specific purposes.

 However, the protein synthesis machinery cannot use D-amino acids, and therefore protein

synthesis results in proteins comprised of L amino acids and glycine.

 Finally, two of the standard amino acids, isoleucine and threonine, have chiral centers at

both the α and β carbons.

 Physiological forms of these two amino acids always have the L-stereochemistry at the α-

carbon, and have a set stereochemistry at the β-carbon as well; unless specifically stated

otherwise, you should assume the correct stereochemistry at both carbons.

 The α-amino group and carboxylic acid are normally ionized at physiological pH, forming a

zwitterion. Note that if both groups are fully ionized, the overall net charge of the amino

acid (ignoring the side chain) is zero.

 Structurally, the standard amino acids (with the exception of glycine) can be considered to

be derivatives of alanine. (Note: these amino acids are not synthesized from alanine;

instead, looking at the amino acids as alanine derivatives is merely an aid to understanding

the structures.)

 The “first” carbon of the amino acid is the carboxylate carbon. The next carbon is called

the α-carbon, because it is in the position α to the first carbon.

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1. Proteins Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form in a biologically functional way. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. Amino acids  Definition: an amino acid is an organic compound containing an amino group and an acidic group (usually, but not always, a carboxylic acid).  This description fits a very large number of compounds, most of which are nonphysiological. In addition, many physiologically important amino acids are not used in proteins.  However, in biochemistry, the term “amino acid.” generally refers to one of the 20 types of monomeric units that are constituents of proteins. Biological roles: 1. Amino acids can be metabolized to produce energy. This is especially important during fasting, when the breakdown of muscle protein is a major energy source. 2. Some amino acids act as neurotransmitters, and some act as starting materials for the biosynthesis of neurotransmitters, hormones, and other important biochemical compounds. 3. Amino acids are the primary building blocks for proteins 4. General structure of Amino Acids  The amino acids that constitute proteins are all α-amino acids. The “α-carbon” is bonded to four different groups: an amino group, a carboxylic acid, hydrogen, and the side-chain.  Because there ar ...
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