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Unit 1B
Structure and properties of biologic molecules.
29
Biochemistry
Graduate
09/04/2011
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Term
Valine (V), leucine (L), and isoleucine (I) Characteristics
 Definition
 referred to as "branched-chain amino acids."
 Their metabolism is altered in maple syrup urine disease.
Term
Proline (P) Characteristics
 Definition
 has a cyclized side chain joined back to its α-amino group to form an "imino" acid.
 It functions as a helix breaker in the secondary structure of proteins.
 It is also hydroxylated to hydroxyproline after incorporation into collagen, a reaction that requires vitmin c or ascorbic acid.
Term
Phenylalanine (F), tyrosine (Y) and tryptophan (W) Characteristics
 Definition
 the bulkiest amino acid, are aromatic amino acids.
 Phenylalanine is increased in the serum and tissues of patients with phenylalanine hydroxylase deficiency (phenylketonuria; PKU), characterized by an inability to synthesize tyrosine from phenylalanine.
 Tyrosine is a precursor to dopamine and the catecholamines and, in proteins, can be phosphorylated by the action of tyrosine kinases.
 Tryptophan serves as a precursor for serotonin and melatonin and can be converted to niacin.
 The aromatic amino acids are the primary sites of cleavage by the protease, chymotrypsin in proteins.
Term
Methionine (M) Characteristics
 Definition
 sulfur-containing amino acid.
 It is always the first amino acid incorporated into polypeptides, but it may be removed afterward.
 S-adenosyl methionine serves as a single carbon donor. Methionine is the site of cyanogen bromide cleavage in proteins.
Term
Alanine (A) and glycine (G) Characteristics
 Definition
 the smallest amino acid, have the small side chains.
 Glycine lacks a side chain, which makes it compatible with hydrophobic environments.
 Alanine is prominent in the transport of nitrogen from muscle to liver during fasting (alanine cycle).
Term
Cysteine Characteristics
 Definition
 hydrophobic counterpart methionine,
 one of two sulfur-containing amino acid.
 Its thiol group can undergo enzyme-catalyzed oxidation, but it is also sensitive to oxidation by air, forming cystine, two cysteine residues linked by a disulfide bond.
 Cysteine is a component of glutathione, a recyclable antioxidant in cells.
 It can form covalent disulfide crosslinks that stabilize the structure of proteins, especially secreted proteins.
Term
Aspartate (D), asparagine (N), glutamate (E) and glutamine (Q) Characteristics
 Definition
 the acidic amino acids and their corresponding amides.
 Both aspartate and glutamate carry a negative charge at pH 7;
• aspartate is interconverted with oxaloacetate by aspartate aminotransferase (AST),
• glutamate is interconverted with -ketoglutarate by alanine aminotransferase (ALT).
 Asparagine and glutamine are polar, neutral amino acids.
 Glutamine is formed by glutamine synthetase action in the brain and liver to detoxify ammonia, and it also serves as a donor of amide nitrogen in the biosynthesis of purines and pyrimidines.
Term
Lysine (K), histidine (H) and arginine(R) Characteristics
 Definition
 the basic amino acids and they carry a positive charge at pH 7.
 Lysine and arginine are the site of cleavage by the protease, trypsin in proteins;
• both are present at high concentration in histones.
 Histidine is only weakly basic and is uncharged at pH 7.
• Histidine forms one of the six coordination bonds with Fe2+ in the heme prosthetic group of hemoglobin and myoglobin.
 Arginine (pK3 ∼14) always has a positive charge at neutral pH;
 it has an important role in the binding of anionic molecules, such as nucleic acids.
Term
Serine (S) and threonine (T Characteristics
 Definition
 the primary and secondary hydroxyl-containing amino acids.
 Both can be phosphorylated by the action of various serine and threonine kinases.
 Serine serves as a single carbon donor to tetrahydrofolate (THF) to produce N5,N10-methylene THF and glycine.
Term
Amylose
 Definition
(-1,4 linkages) has only a linear structure.

Starch
Term
Sucrose
 Definition
glucose + fructose; table sugar
Term
Lactose
 Definition
glucose + galactose; milk sugar
Term
Maltose
 Definition
glucose + glucose; product of starch digestion
Term
Amylopectin
 Definition
(-1,4 linkages + -1,6 linkages) has a branched structure; a branch point occurs every 25-30 glucose residues.

Starch
Term
 Glycogen
 Definition
has a structure like amylopectin except that it is more highly branched (every 8-12 residues of glucose).
Term
 Cellulose
 Definition
(β-1,4 linkages) has an unbranched structure and is the structural polysaccharide of plant cells. It is an important source of fiber in the diet; not hydrolyzed by digestive enzymes and has no caloric value
Term
 Sugar acids
 Definition
Oxidation of glucose at carbon 1 produces "onic" acids, such as gluconic acid, and oxidation at carbon 6 produces "uronic" acids, such as glucuronic acid.
Term
 Uronic acids
 Definition
contribute a negative charge to polysaccharide chains, which promotes binding of cations.
Term
 Glucuronic acid
 Definition
is conjugated with bilirubin in the liver.
Term
 Ascorbic acid
 Definition
• a product of glucuronic acid metabolism, except in primates, guinea pigs.
Term
 Deoxy sugars
 Definition
Reduction of ribose at carbon 2 produces 2-deoxyribose.
Term
 Sugar alcohols
 Definition
Also called polyols, they have no carbonyl groups.
• The aldehyde or keto group of aldoses or ketoses is reduced, yielding a non-reducing polyol.
Term
 Amino sugars
 Definition
Replacement of the hydroxyl group on carbon 2 by an amino group produces glucosamine and galactosamine.
• The amino group is usually acetylated, yielding a neutral sugar.
Term
 Sugar esters
 Definition
Reaction of phosphoric acid with one or more hydroxyl groups
• produces sugar esters such as glucose 6-phosphate.
Term
o Pseudouracil
 Definition
contributes to the tertiary structure of tRNA.
Term
o Methylation protects polynucleotides
 Definition
from nuclease digestion
Term
 B-form DNA
 Definition
is the predominant, natural form;
• 10 base pairs per right-handed turn and a periodicity of 34 Å per turn.
Term
 A-form DNA
 Definition
is produced by dehydrating purified DNA;
• 11 base pairs per right-handed turn and a periodicity of 26 Å.
Term
 Z-form DNA
 Definition
is favored by long stretches of alternating C and G;
• 12 base pairs per left-handed turn and a periodicity of 57 Å
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