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