If the alcohol moiety is derived from another sugar, the product is a glycone, whereas if it is derived from a non-sugar such as glycerol, sterol, nucleotide, etc., the product is an aglycone. The –OH groups on the non-anomeric C atom of the monosaccharides can be methylated or ethylated.
DISACCHARIDES
Cellobiose also has a 1:4 glycosidic bond, but it is of the β-type instead of the α-bond in maltose. Mutarotation of fructose causes reversal of the optical rotation of the original solution from (+) 66.5o to (-) 28.2o; thus sucrose is also called an "invert" sugar.
OLIGOSACCHARIDES
POLYSACCHARIDES (= GLYCANS)
It is a large polymer, composed of alternating β-glucuronate (GlcA) and N-acetyl-glucosamine (GlcNAc) units, joined by β-1:3 glycosidic linkages. It is a variably sulfated GAG composed of sulfated derivatives of iduronic/glucuronic acid and glucosamine joined by a combination of α- and β-glycosidic 1:4 linkages.
GLYCOCONJUGATES
They extend from the surface of the proteins and their rapidly fluctuating conformations are difficult to visualize in a static 3-D structure. Glycophorin A on RBC membrane: 16 oligosaccharide units (green) are present on the extracellular domain of the protein.
CARBOHYDRATES
Pause for a moment to consider these numbers: if 20 different monosaccharide subunits are used to construct oligosaccharides, then 1.44 x 1015 different hexameric oligosaccharides are possible. Compare this to 206 different hexapeptides possible with 20 common amino acids and 46 different hexanucleotides with the four nucleotide subunits.
Section 2 LIPIDS
Simple lipids: Esters of fatty acids with alcohols; sub-groups are fats (fatty acids + glycerol) and waxes (fatty acids + monohydric alcohols of high molecular weight)
- FATTY ACIDS
- GLYCERIDES (= fats/acylglycerols)
- WAXES
- PHOSPHOLIPIDS
- GLYCOLIPIDS
- STEROIDS
- OTHER POLYPRENOIDS
- LIPID ASSEMBLIES
The carboxylic group is written on one side and is carbon atom 1. The C atom adjacent to the functional group –COOH, can also be designated as α, followed by β, γ,…etc. The length and degree of unsaturation of the hydrocarbon chain determines many of the properties of fatty acids. Water solubility decreases with increasing chain length and degree of unsaturation of fatty acids.
Thus, oleic acid can have 15 possible positional isomers, depending on the location of the double bond in the chain. Changes in hydrocarbon chain shape in C-18 fatty acids resulting from: (A) and (B) saturated versus unsaturated chains (Source: Nelson and Cox, 2005, pg 345 fig 10-1). Oxidation of double bonds in unsaturated fatty acids gives hydroxy, aldehydic and ketone derivatives that undergo polymerization in resins.
To avoid ambiguity, the carbon atoms in the glycerol backbone of the TGs are numbered in the order shown above. Comparison of the structures of (A) phosphatidylethanolamine and ethanolamine plasmalogs and (B) phosphatidylcholine and lysolecithin (the modified groups are indicated in pink). Conventionally, a transorientation of the hydrogen atom at C-5 is not represented in the structural formula.
The properties of the constituent lipids are responsible for both stability and flexibility of the membranes.
LIPIDS
Hydrophobic molecules such as the TGs and other lipids are included in water-soluble lipoprotein complexes and transported by blood to various tissues of the body. The polar heads are oriented towards the aqueous medium of the intra- and extracellular fluids (fig 2.2.15B). The fatty acyl chains of phospholipids and the steroid core of sterols are directed toward the interior of the bilayer, and their hydrophobic interactions provide stability. Fatty acyl chains possess freedom of movement that favors a disordered, fluid state in the interior of the membrane, especially if the chains are unsaturated or the temperature is high.
Glycosphingolipids with their long saturated fatty acyl chains form transient clusters in the outer leaves. These bonds are compact and more stable than those of glycerophospholipids with their shorter and often unsaturated acyl chains. Sphingomyelins and phosphatidylcholines are mainly located in the outer leaflet of membranes, while phosphatidylethanolamines, phosphatidylserines and phosphatidylinositols are mainly in the inner leaflet.
The permeability of the membranes to ions and other small molecules is limited by their hydrophobic/electrostatic interactions with surface lipids. Their non-polar, hydrophobic nature and low reactivity are suitable for their primary role as energy storage in the body.
Section 3 PROTEINS
- AMINO ACIDS
- Influence of R groups of the amino acids on proteins
- Isomerism
- Amino acids as zwitterions
- Titration of an amino acid
- Chemical reactivity of the amino acids
- Formation of the Peptide Bond
- PEPTIDES
- PROTEINS
- Colloidal nature
- Charged state
- Solubility and precipitation
- Binding of ligands
- Denaturation
- PROTEIN CONFORMATIONS
- Secondary structure refers to local conformations formed by neighbouring amino acids in polypeptide chains. These patterns are repeated in diverse proteins and are enabled by extensive
- PROTEOMICS
Each amino acid has its own specific pI, which varies according to the nature of the medium. Specific reactions of amino and carboxyl groups are important in the body and in protein analysis. The most important biological reaction of an amino acid is the formation of a peptide bond.
Two amino acids can be condensed to form a unique amide bond between the α-carboxyl group of the first amino acid and the α-amino group of the second. Free rotation is not allowed between the carbonyl C (Co) of one amino acid and the α-amino N (Nα) of the other in the chain, i.e. The linear sequence of amino acids represents the primary structure of the peptide and can be indicated using abbreviations for the components e.g.
The charge on a protein molecule is the sum of the charges on its constituent amino acids. Therefore, a protein can be cationic, zwitterionic or anionic, depending on the pH of the medium. The PI of many body proteins is lower than the physiological pH, and therefore many cellular proteins exist as anions. The protein molecule at a given pH can simultaneously lose.
Covalent peptide bonds tightly hold the genetically programmed sequence of amino acids together in the protein backbone, laying the foundation for the protein's possible conformation.
PROTEINS
Proteins with significant similarity in primary sequence or demonstrable similarity in structure and function are grouped into one family. Two or more families with little similarity in primary sequence, but with similarity in some major motif and function, are merged into the same superfamily, e.g. The emerging field of proteomics is the collective study of the entire complement of proteins in an organelle/cell/organism.
It differs from conventional protein chemistry in that it deals with large numbers of proteins at once. Unlike the genome which is identical in all somatic cells, the proteome varies from cell to cell and from time to time depending on the organism's requirements and responses to its internal and external environment. Because the synthesis of proteins is strictly determined by genes, proteomics indirectly and reliably gives us a clear picture of how the genome works in cells.
Protein conformations depend on the nature of the constituent amino acids, the characteristic properties of the peptide bond, and non-covalent interactions between different parts of the same or different polypeptide chains. The new science of proteomics deals collectively with the large number of proteins in a single cell or organism.
Section 4 NUCLEIC ACIDS
NUCLEOSIDES AND NUCLEOTIDES
The general structural formula of purine and the two purines found in nucleic acids, adenine and guanine. Nucleoside derivatives of these molecules contain ribose (in this case they are called ribonucleosides) or deoxyribose sugars (in this case they are called deoxyribonucleosides) linked to a purine ring via an N-glycosidic bond at N-9. The main pyrimidines found in nucleic acids are cytosine and uracil in RNA and cytosine and thymine in DNA (Figure 2.4.3).
As with purine derivatives, the pyrimidine nucleosides or nucleotides contain either the ribose or deoxyribose sugar linked through their C-1 to the pyrimidine through an N-glycosidic bond at N-1. The general structural formula of a pyrimidine and the three pyrimidines found in nucleic acids, cytosine, uracil and thymine. In nucleosides and nucleotides, the pentose residue is present in the non-planar furanose form.
Nucleotides with the sugar ribose are written in the unmodified form, such as AMP, ADP or ATP, whereas deoxy forms are indicated with the prefix d (eg dAMP, dADP or dATP). The concentrations of ribonucleotides in the cell far exceed the concentrations of the deoxyribonucleotides except at the time of DNA synthesis, when their levels rise markedly.
STRUCTURE OF DNA
The six-membered rings of the bases are numbered counterclockwise, starting with a nitrogen atom. The sugar-phosphate backbones of the helix are not evenly spaced along the helix axis. This leads to the formation of empty spaces, called grooves, between the atoms of the two chains.
The double helix breaks during any transformation of the molecule such as DNA replication, transcription, repair and recombination. The ions suppress the electrostatic repulsion between the negatively charged phosphate groups on the complementary strands of the helix, stabilizing it. This is called renaturation or renewal (Figure 2.4.11) and requires the rejoining of the strands in a double helix.
The degree of hybridization is a measure of the sequence similarity or relatedness between the two species. The relaxed state of the double helix has no turns in it other than the double helical turns.
TYPES OF RNA
The first step in processing is the addition of a cap to the initiating (5') nucleotide of the primary transcript. Each cloverleaf consists of four H-bonded segments - three loops and the stem where the 3' and 5' ends of the molecule meet. Indeed, any two codons of the type NNPyr (N = any base; Pyr = pyrimidine) encode a single amino acid and are decoded by a single tRNA with G in the first (wobble) position of the anticodon.
For example, four of the six codons for leucine (CUA, CUC, CUU, and UUA) are all recognized by the same tRNA with the anticodon 3'-GAI-5'; the inosine in the wobble position forms non-standard base pairs with the third base in the four codons. In the case of the UUA codon, a non-standard G·U pair is also formed between position 3 of the anticodon and position 1 of the codon. Although A is theoretically possible in the wobble position of the anticodon, it is almost never found in nature.
The smallest RNA component of the large subunit, present in almost all types of ribosome, is 5 S rRNA. The function of rRNA is to provide a mechanism for decoding mRNA into amino acids (in the center of the small ribosomal subunit) and to interact with tRNAs during translation by providing peptidyltransferase activity (large subunit).
NUCLEIC ACIDS
These machines then self-assemble into two complex folded structures (the large and small subunits) in the presence of 70-80 ribosomal proteins.
