Biochemistry

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Biochemistry of Water

  • Most reactions occur in an aqueous environment in cells.
  • The O-H bond in water is highly polar because the Oxygen atom is very electronegative (pulls shared electrons towards itself).
  • This makes Hydrogen slightly positive.
  • The separation of charge is called a dipole.
  • Adjacent Oxygen atoms on other water molecules are attracted to +ve hydrogen atoms.
  • This is called a hydrogen bond, the strongest intermolecular force.
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Biochemistry of Water (cont)

(http://chemtools.chem.soton.ac.uk/projects/emalaria/page_imgs/content/water.gif)

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Properties of Water

  • Ice is less dense than liquid water, so ice will float on water. Therefore ice can support life and allow it to flourish.
  • Water has a high specific heat capacity (or capacity to absorb water). This allows water to maintain a fairly constant temperature .
  • Water acts as an excellent solvent. Water can form hydrogen bonds or other intermolecular forces with other polar substances. 
  • Non-polar groups will associate to avoid water, forming a colloidal suspension. 
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Properties of Water (cont)

  • Water has a high surface tension, so acts like it has a thin 'skin' on top of it.
  • This is because of the strong H-bonding between water molecules. This is very important in plant transport systems and life at surface of ponds. 
  • Water is amphoteric- it acts as an acid (proton donor) or a base (proton acceptor).
  • Therefore pH inside cell is buffered, and so won't change too much. 
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General Saccharides

  • Organic compounds contain carbon, hydrogen and oxygen. They also sometimes contain sulphur, nitrogen and phosphorus. 
  • Single units (monomers) can join together in two's to form dimers or in a long chain to form a polymer. 
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Monosaccharides

  • Monosaccharides have the general formula (CH2O)n 
  • They are simple sugars, for example carbohydrates.
  • Triose- n=3, found in mitochondria.
  • pentose- n=5, found in DNA and RNA
  • hexose- n=6, found in glucose, galactose and fructose. 
  • The most important monosaccharide is glucose, a hexose sugar. 
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Glucose

  • Glucose has the molecular formula C6H12O6.
  • There are two main structural isomers of glucose: alpha glucose and beta glucose.
  • In alpha glucose, the -OH group attached to C-1 and the CH2OH group on C-5 lie on opposite planes (a trans arrangment).
  • In beta glucose these groups are on the same plane (a cis arrangement).
  • Other isomers include galactose, mannose and fructose. 
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Glucose (cont)

     (http://2.bp.blogspot.com/-RlMSy4ukvs0/TeZ6QkDeYUI/AAAAAAAAAMc/2I-8F68rEJ4/s1600/alpha+and+beta+glucose.jpg)

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Disaccharides

  • A disaccharide is formed when 2 monosaccharides join together.
  • This is done by a condensation reaction, where water is removed and the two monosaccharides are joined by a common oxygen.
  • This is called a glycosidic bond.
  • Hydrolysis (addition of water) breaks the glycosidic bond. 
  • Disaccharides have the general formula (C6H12O5)n.
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Disaccharides (cont)

  • Sucrose- stored in plants, glucose + fructose.
  • Lactose- found in milk, glucose + galactose.
  • Maltose- found in germinating seeds eg barley, glucose + glucose.

(http://www.mansfield.ohio-state.edu/~sabedon/069malto.gif)

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Polysaccharides

  • Polysaccharides consist of many monosaccharides linked together with gylcosidic bonds.
  • They are often used for storage in cells.
  • Starch is made from amylose and amylopectin, both of which are made up of alpha glucose. 
  • Starch is a very compact molecule, and is not very soluble. 
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Polysaccharides (cont)

  • Amylose is made from alpha glucose joined by 1,4 glycosidic bonds. It is an unbranched, spiralled polysaccharide, which is very compact.
  • Amylopectin is made from alpha glucose joined by 1,6 glycosidic bonds. It is a branched polymer with many ends. 
  • Glycogen is made from alpha glucose joined by 1,4 and 1,6  glycosidic bonds. it is a branched polymer.
  • The branched nature of glycogen and amylopectin makes them ideal for fast release energy, while amylose is better for slow release energy storage.
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Cellulose

  • Cellulose is made from beta glucose joined by 1,4 glycosidic bonds. It is the polysaccharide that makes up a plant cell wall.
  • Each glucose monomer is 180 degrees inverted to the following glucose monomer.
  • The outlying -OH groups form hydrogen bonds with other cellulose molecules, which strengthens the cell wall.
  • This is called cross-linking. 
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Amino Acids

  • All amino acids have the same basic structure: central carbon atom joined to- R group, hydrogen, amino group, carboxyl group. 
  • The R group varies between amino acids, and affects the way amino acids bond with others to form a protien. 
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Amino Acids (cont)

(http://legacy.owensboro.kctcs.edu/gcaplan/anat/notes/amino_acid_structure_2.jpg)

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Amino Acids (cont)

  • A polypeptide is a sequence of amino acids joined together by peptide bonds. 
  • 2 amino acids are joined together by a condensation reaction between the amino group of one amino acid and the carboxyl group of the other.
  • Bonds between amino acids in different polypeptides include: hydrogen bonds, ionic bonds and sulphur bridges.
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Amino Acids (cont)

        (http://revisionworld.co.uk/sites/default/files/rw_files/dipeptide.jpg)

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Protein Structure

  • Primary- linear sequence of amino acids joined by peptide bonds.
  • Secondary- A repeating pattern in the structure of peptide chains eg alpha helix or beta pleated sheet.
  • Tertiary- 3D structure/folding of the secondary structure, with previously named bonds holding all the folds together.
  • Quaternery- 3D arrangement of more than 1 tertiary structure joined together.
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Types of Protein

  • Fibrous proteins- have no tertiary structure, stop at secondary. They are long parallel polypeptides with some cross-linkage (bonds). They are insoluble in water and very tough.
  • Globular proteins- have a complex tertiary structure, that is folded into a globular (blob) shape. They form a colloid in water.
  • Conjucated proteins- are proteins that join with a non-protein molecule eg a glycoprotein (protein + carbohydrate). 
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Lipids

  • Lipids are an important energy storage as they provide more energy per gram than carbohydrates.
  • They are important in thermal and electrical insulation, protection of body organs, and they allow aquatic animals to float.
  • Examples of lipids are oils and fats. 
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Triglyceride Formation

  • A triglyceride consists of 3 fatty acids and a glyceride. To form a tryglyceride there is a condensation reaction between the carboxyl group of each fatty acid and each OH group of a glyceride.
  • This is called esterification.
  • [Note: 2 fatty acids + phosphate = phospholipid]
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Nucleotides

  • DNA and RNA contain deoxyribose and ribose sugars respectively.
  • The sugars are modified with nitrogenous bases plus a phosphate group to make a nucleotide.
  • DNA contains 2 sets of nitrogenous base: Pyrimidine: C and T..... Purine: A and G.
  • RNA contains U instead of T.
  • Nucleotides are subunits of nucleic acids.
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Building DNA

  • The structure of the nucleotides means hydrogen bonds can form between bases, linking together 2 strands of DNA.
  • This linkage of strands forms a stable double helix structure.
  • The bonds between nucleotides in a single strand are phosphodiester bonds.
  • These bonds can be broken down by enzymes relatively easily for DNA replication. 
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Building DNA (cont)

                       (http://asingaporeanbiologist.files.wordpress.com/2011/10/nucleotide.jpg)

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