Biochemistry Biochemistry aims to explain biological form and function in chemical terms.

Biochemistry explains life in terms of atomic structures of biological molecules.

Biochemistry of Carbohydrate
Carbohydrates (CHO) are the most abundant biomolecules in nature
CHO are the photosynthesis product nCO2 +H2O (CH2O)n + nO2 light Originally thought to have the formula (CH2O)n. Now known that only simple monosaccharides obey this rule. Carbohydrate- polyhydroxy aldehyde or ketone or a larger molecule which can be hydrolyzed to a polyhydroxy aldehyde or ketone.

Functions of Carbohydrates
1. 2. 3. 4. 5. Energy source for plants and animals Source of carbon in metabolic processes Storage form of energy Structural elements of cells and tissues Some CHO participate in recognition and adhesion between cells and mediate some forms of inter cellular communications

Classes of Saccharides
Monosaccharides
= single polyhydroxy aldehyde or ketone unit, (eg. 6-carbon glucose, most abundant in nature)

Oligosaccharides
= short chain of 2- ~20 monosaccharides joined by glycosidic bonds (eg. disaccharide sucrose = glucose-fructose) - oligosaccharides > 3 residues are usually joined to protein or lipid in glycoconjugates

Polysaccharides
- chains > ~ 20 to 1000s of monosaccharides in length - linear: eg. cellulose (glucose)n or chitin (N-acetylglucosamine)n - branched: eg. glycogen & starch (glucose) - depending on the sugar residues in a polysaccharide and the linkages between them, polysaccharides can have very different biological roles

Monosaccharides
- Backbone = unbranched carbon chains in which all C atoms are linked by single bonds - Colorless, crystallin, solid freely soluble in water, insoluble in organic solvents - If it has keto group as the most oxidized functional group = Ketose - If it has aldehyde group as the most oxidized functional group = aldose According to the number of carbon atoms

- 3 C = triose, 4 C = tetrose, 5 C = pentose, 6 C = hexose (eg. aldo- or ketohexoses) Simplest monosaccharides are 3 carbon...
Common monosaccharides are 6 carbon...

Aldotriose

ketotriose...

D and L configurations of monosaccharides

- Stereoisomers of monosaccharides > 3 C divided into 2 groups: differ in the configuration about the chiral center most distant from the carbonyl C In biochemistry, we use the D-L system (similar principle to the R-S system usually used in organic, but everything is compared with glyceraldehyde

- Most of the hexoses in living organisms are D-isomers

Joining of sugars via glycosidic bonds

reducing

Non-reducing

reducing

Polysaccharides:

are polymers of monosaccharides units of medium to high molecular weight.

Homopolysaccharides contain only a single type of monomers, as starch, glycogen, cellulose Heterpolysaccharides contain two or more different kinds monomers, as glycosaminoglycans Polysaccharides could be branched or unbranched Function: storage of energy, structural elements, animal exoskeleton and provide support

- Important cell surface components, eg. in holding cells together in tissues - Important in molecular recognition events

Polysacchs. usually dont have precisely defined molecular weights, unlike proteins

Storage polysaccharides: glycogen and starch

Glycogen: polymer of (14) linked glucoses with (16) branches (one every 8-12 glucoses), average mol. wt. = several millions. Can be 7 % wet wt. of liver

Starch: = mixture of amylose, a linear polymer of (14) linked glucoses, and amylopectin, a linear polymer of (14) linked glucoses with (16) branches (one every 4-30 glucoses)

Liver cells (hepatocytes) store glycogen equivalent to a [glucose] of 0.4 M

Storage polysaccharides are essentially insoluble in the cell, so they dont raise the intracellular [glucose], which would set up a very high [glucose] gradient.

Lipids
Defined on the basis of solubility.

Lipids: heterogeneous group of water insoluble (hydrophobic) organic molecules, they are chemically diverse compound but have one feature: water insoluble

Many distinct chemical species in a lipid fraction

Functions
-The biological functions of lipids are divers as their chemistry

Lipids perform three biological functions:

1. Lipids in form of a bilayer are essential components of biological membranes.

2. Lipids containing hydrocarbon side chains serve as energy stores.

3. Many intra-and intercellular signaling events involve lipid molecules.

Lipid Classification
1. Storage lipids Triglycerides, Waxes and Fatty acids. Fats and oils are stored forms of energy and are derivatives of fatty acids. 2. Structural lipids in membranes Glycerophospholipids, Sphingolipids, Sterols. are major structural elements in biological membranes 3. Lipids as signals, cofactors and pigments. These lipids presents in small quantities but play crucial roles -Phosphatidylinositols, Eicosanoids - Prostaglandins. - Thromboxanes. - Leukotrienes. - Steroid hormones carry messages between tissues. - Vitamins A and D are hormone precursors. - Vitamins E and K are oxidation-reduction cofactors.

Storage Lipids
Fats and oils are derivatives of Fatty acids. Fatty acids (F.A) are carboxylic acids with long hydrocarbon chain ranging from 4-36 carbon atom 16- and 18-C long are most abundant. -Even number of carbons, 16, 18 the odd are also present but rare. -the hydrocarbon chain can be fully saturated (without double bonds), or with one, two or three double bonds (cis-configuration only) - usually they are unbranched, some cases have methyl, hydroxyl, or three-carbon ring as branch

Triacylglycerols or Triglycerides
Fatty acid triesters of glycerol Most contain two or three different types of fatty acid residues triglycerides are non-polar and hydrophobic molecules (the polar groups of both glycerol and F. A are linked in ester linkage non-polar molecule )

Fats and oils

* Plant oils are usually richer in unsaturated fatty acids residues than animal fats * Fats and oils are complex mixtures of triacylglycerols *Triacylglycerols can be found in most eukaryotic cell as oily droplets in the aqueous cytosol serving as metabolic fuel *In vertebrates specialized cells called Adipocytes (fat cell) store amounts of triglycerides as fat droplets that fill the cell. Triglycerides also stored as oil in the seeds of many types of plants . *Adipocytes contain lipases catalysis the hydrolysis of stored triglycerides releasing F.A for export to sites where they can be used as fuel. *Two advantages for using the triglycerides as stored fuel rather than polysaccharides as glycogen and starch:

1- the carbon atoms of F.A are more reduced than that of carbohydrates oxidation of triglycerides yields more than twice as much energy (gm/gm) as the oxidation of CHO 2- triglycerides are hydrophobic unhydrated, the organism that carries fat as fuel does not have to carry the extra weight of water of hydration that is associated with stored polysaccharides (2gm water/1gm polysaccharides

Polar vs. Nonpolarlipids

Non-Polar Lipids Energy storage Polar lipids are the basis of Bilayers Biological membranes feature: double layer of lipid

act as barrier to the passage of polar molecules and ions. Amphipathic: one end of the molecule is hydrophobic and the other is hydrophilic The hydrophobic interactions between molecules and the hydrophilic interactions with water direct their packing into sheets called membrane bilayer

Glycerophospholipids
Glycerophospholipidsare the major lipid component of biological membranes -amphiphilicmolecules with non-polaraliphatic tails and polar phosphoryl-X heads Phosphoglycerides: two F. A are attached in ester linkage to the first and decond carbons of glycerol and a highly charged group is attached through a phosphodiester linkage to the thrid carbon

Sphingolipids are major membrane components, with polar head and non-polar tail) They are derivatives of the C18 amino alcohol sphingosine The double bond in sphingosine is trans C1, C2, C3 of sphingosine molecule are structurally similar to the three carbons of glycerol in phospholipids N-acyl fatty acid derivatives of sphingosine are known as ceramides Ceramides are the parent compounds of the more abundant sphingolipids . Sphingolipids are major lipids in mylene sheath and CNS lipids

Sphingolipids

General structure of Sphingolipids, if X is H, the compound is Ceramide

3-Sterols
Structural lipids present in the membranes of some eukaryotic cells. Characterized by the steroid nucleus consisting of four fused rings three rings with 6 C atoms and one ring with 5 C atoms, the steroid nucleus is relatively rigid and planar Cholesterol is the major sterol in animal tissues and it is amphipathic with a polar head (the OH group), and the non-polar body is the steroid nucleus Similar sterols are present in eukaryotes: Stigmasterol plants Ergosterol fungi

Functions
-membrane constituents -precursors of different product with vital biological activities (steroidal hormones that regulate the gene expression) -bile acids are derivatives of cholesterol that act as emulsifying agent in the intestine

Amino Acids Amino acids are building blocks of proteins. - There are more than 300 a. a. found in the nature, only 20 are found in mammalian proteins and these are coded for by DNA -The nature of the side chain decides the role of an amino acids in a protein - Amino acids can be classified according to the properties of their side chains All the amino acids found in the proteins are L-configuration
At physiologic pH

Side chain is distinctive for each amino acid

All the amino acids found in the proteins are L-configuration

Hydrophobic (nonpolar) R groups

-Non polar side chains don't bind or give off protons or participate in hydrogen or ion bonds. So they are oily or lipid like material

Hydrophobic (nonpolar) R Group

- Proline: the side chain of proline and -amino group form a ring structure and it differs from other amino acids that it contains an imino group

-Location of amino acids in proteins: proteins found at the aqueous solutions, the side chain of non-polar amino acids tend to cluster together in the interior of the protein. The hydrophobic interaction is important in stabilizing protein structure.
Hydrophobic Amino acids

Hydrophilic Amino acids

Hydrophilic (polar) R Group

Uncharged side chains. These amino acids have zero net charge at neutral pH

Some side chains act as sites of attachment for the compounds: serine, threonine and tyrosine contain polar hydroxyl group that can serve as site of attachment: phosphorylation. Side chain of serine residue is an important component of the active sites of many enzymes. The OH of serine and threonine can be linked to oligosaccharide in glycoprotein

Uncharged side chains. These amino acids have zero net charge at neutral pH

Hydrophilic R Groups with Formal Charge

Basic R Groups Acidic R Groups

These amino acids have positive charge at neutral pH

These amino acids are proton acceptor at neutral pH

Disulfide bond formation

Disulfide bond: the cysteine contains a sulfhydryl group (-SH), which is also an important component of the active site at many enzymes. The two SH become oxidized to form a dimer cystine which contain a covalent cross-link disulfide bond

Essential Amino Acids

10 amino acids not synthesized by the body arg, his, ile, leu, lys, met, phe, thr, trp, val Must obtain from the diet

Amino acid Nonpolar R groups: Glycine Alanine Valine Leucine Isolecine Phenylalanine Tryptophan Methionine Proline Polar, uncharged R: Serine Threonine Tyrosine Cysteine Asparagine Glutamine

Abbreviated name Gly Ala Val Leu Ile Phe Trp Met Pro

One-letter symbol G A V L I F W M P

Ser Thr Tyr Cys Asn Gln

Asp Glu Lys His Arg

S T Y C N Q
D E K H R

Acidic R groups: Aspartate Glutamate

Basic R groups: Lysine Histidine Arginine

Amino Acids as Acids and Bases

Ionization of the NH2 and the COOH group Zwitterion has both +ve and ve charge Zwitterion is neutral overall NH2CH2COOH glycine + H3NCH2COO Zwitterion of glycine

pH and ionization of amino acids

H+ OH + H3NCH2COO zwitterion neutral pH H2NCH2COO Negative ion High pH

+ H3NCH2COOH
Positive ion Low pH