The Chemical Nature of Cells Biology, Unit 3 Area of Study 1

Water: A unique compound Water is the most abundant compound in our bodies and is the main solvent for many of the organic molecules present. Water makes the ideal medium for chemical reactions that take place in the body. The sum total of these reactions is called metabolism.

Water: A unique compound Although a water molecule has an overall neutral charge, the oxygen at the end of a covalent bond is slightly negative and the hydrogen atoms are slightly positive areas. Individual molecules of water are highly attracted to each other such that the negative oxygen of one molecule of water is attracted to the positive hydrogen of another water molecule.

Water: A unique compound they tend to stick together, held by hydrogen bonds, which are weaker than covalent bonds.

Water: A unique compound Although water molecules are attracted to each other, the hydrogen bonds that hold them together are relatively weak and continually breaking. At the same time, hydrogen bonds are continually rejoining. As the temperature of water falls, the rate of molecule movement decreases, and at 4°C there is no longer sufficient movement to break the hydrogen bonds. If the temperature of fluid water increases significantly to 100C, the movement of water molecules increases to a point where hydrogen bonds no longer hold them together.

Water is a versatile solvent Water is the predominant solvent in living organisms. Its versatility as a solvent is due to its cohesive nature.

Acid or alkaline? Pure water has a pH of 7 and is a neutral solution. pH is a scale that provides a measure of hydrogen ions in a solution. The range of the pH scale is from 0 to 14. pH of body fluids is kept relatively constant because hydrogen ions are continually being produced and used in cells.

Organic molecules Carbon-containing compounds present in living matter. large molecules made of smaller sub units (monomers) that are bonded together (polymers) in various ways. MonomersPolymers sugars (monosaccharides ) polysaccharides amino acidsproteins fatty acidsfats, lipids, membranes nucleotidesnucleic acids

Carbohydrates The basic unit is a sugar molecule, a monosaccharide. Carbohydrates containing one or two sugar units are referred to simple carbohydrates; those containing many sugar molecules are called complex carbohydrates. Carbohydrates play an important role as a source of energy for plants and animals, as food storage in the form of starch for plants and glycogen in animals, and as structural elements in plants.

Classification of carbohydrates

Simple carbohydrates Simple carbohydrates have:

Monosaccharides Usually has formula C 6 H 12 O 6 Some monosaccharides have the same molecular formula - their different properties arise from their differences in structural formula - the way their atoms are arranged within the molecule.

Disaccharides Example: sucrose, the sugar used in tea/coffee. Sucrose is the form in which carbohydrate is transported in plants, and is formed from the combination of glucose with fructose.

Structure and function of some simple sugars

Polysaccharides Most common sugar component is glucose. starch, glycogen and cellulose are all composed of glucose, yet their structure and properties are different from one another. insoluble in water.

Polysaccharide - Glycogen When carbohydrates are digested, glucose is absorbed into the bloodstream that carries it to the liver and then to all cells of the body. Excess to body requirements is converted into glycogen by the liver for storage. The liver is able to sore about 100 gram of glycogen. Glycogen is also stored in muscle tissue (upto 300 g) a circular molecule that has a protein as its ‘starting point’ (the protein is called a primer) and lots of branches each containing the same number of sugar units.

Starch Glucose is distributed around a plant in the form of sucrose, and while some plants do store excess requirements in this form, starch is the chief form of storage by most plants. storage can occur in a number of different sites, eg: potatoes and ginger store in a modified stem sweet potatoe stores in modified roots onions store in modified leaves seeds store in their endosperm and provide from the young plant until it becomes established.

Cellulose structural polysaccharide (C 6 H 10 O 5 )n molecules are long and unbranched

Proteins although water is the main compound in living cells, more than half of the remainder, about 18%, is protein. there are thousands of different proteins in each cell and many of these control all metabolic processes within cells.

The building blocks of proteins Humans are unable to make all 20 amino acids and must rely on their food for the nine they are unable to make. the general formula of an amino acid is:

The building blocks of proteins two amino acids join together as a dipeptide when a peptide bond forms between the amino groups of one amino acid and the carboxyl group of another amino acid. each type of protein has its own particular sequence of amino acids. polypeptide chains become folded in different ways depending on their function.

The structure and shape of proteins protein structure is described at four different levels of organisation.

The structure and shape of proteins Primary structure - the specific linear sequence of amino acids in the protein. Different proteins have different primary structures and different functions. The sequence of amino acids in a protein is determined by the genetic material in the nucleus. Secondary structure -

The structure and shape of proteins Tertiary structure - the total irregular folding held together by ionic or hydrogen bonds forming a complex shape, eg: myoglobin. The bonds form between side chains of amino acids to from a complex internal structure. Quaternary structure - two or more polypeptide chains interact to form a protein. The resulting structure can be, for example, globular as in haemoglobin or fibrous as in collagen, the most common of animal proteins.

Examples of proteins and their function Type of proteinFunctionExample structuralfibrous support tissue in skin, bone, tendons, cartilage, blood vessels, heart valves and cornea of the eye collagen, keratin enzymecatalyse reactionsATP synthase contractilemuscle movementmyosin, actin immunoglobulindefence against diseaseantibodies hormoneregulate body activityinsulin Receptorrespond to stimuliinsulin receptors transportcarry other moleculeshaemoglobin

Conjugated proteins With some proteins, the chains of amino acids conjugate with other groups, esp. proteins in the nucleus (nucleoproteins - contain protein and nucleic acid) Example of a conjugated protein: haemoglobin

Non-active to active molecule Although a molecule may be made from a number of molecules linked together by sulfide or other bonds, they may derive from the same initial inactive protein.

What is a proteome? In living organisms, proteins are involved in one way or another in virtually every chemical reaction. They may be the enzymes involved, they may be the reactants or the products, or they may be all three.

Lipids composed of C, H, O. carry more energy per molecule than either carbohydrates or proteins.

Fats triglycerides are a common form of fats - has a single glycerol molecule to which three fatty acid molecules are attached. hydrophobic

Phospholipids Have a phosphate group attached to the glycerol and other small groups attached to the phosphate to make different kinds of phospholipids.

Nucleic Acids There are two kinds of nucleic acid: deoxyribonucleic acid (DNA) - located in chromosomes in the nucleus of eukaryotic cells. It is the genetic material that contains hereditary information and is transmitted from generation to generation. ribonucleic acid (RNA) - is formed against DNA which acts as the template.

DNA a polymer of nucleotides Each DNA molecule consists of two chains of nucleotides that are complementary to each other and held together by hydrogen bonds. the sugar and phosphate parts are the same in each nucleotide.

DNA The nucleotide sub-units are assembled to form a chain in which the sugar of one nucleotide is bonded with the phosphate of the next nucleotide in the chain. Each DNA molecule contains two chains that bond with each other because the bases in one chain pair with the bases in another. The base pairs between the two stands, ie A with T, and C with G, are complimentary pairs.

DNA Chromosomes reside in the nucleus of a cell and the DNA they contain carries genetic instructions that control all functions of the cell.

How does DNA control all functions within cells? Proteins are formed from polypeptide chains – chains of amino acids

How does a DNA molecule directly influence the production of a polypeptide chain? The sequence of nitrogen bases along one of the chains of nucleotides in a DNA molecule carries a set of information. This information controls the production of all the polypeptide chains for which that molecule of DNA is responsible, and can be thought of as a code.

How does the DNA code work? The total process is quite complex and involves action both in the nucleus of a cell and in the cytosol. The DNA code comprises the four bases in the four nucleotides that make up the DNA structure, represented by the letters A (adenine), T (thymine), C (cytosine) and G (guanine).

How does the DNA code work? A particular set of three letters together in a molecule of DNA codes for a particular amino acid. For example: – the sequence AAA in a molecule of DNA results in the amino acid phenylalanine being added into the polypeptide chain for which the particular DNA molecule is responsible – the sequence GTA results in histidine being added and the sequence GCA results in arginine and so on.

How does the DNA code work? If a mutation occurs in a DNA molecule and leads to a change in the order of bases, there is likely to be a change in the amino acids in the polypeptide chain. Example: a change in a sequence from AAA  AGA, the amino acid added is serine and not phenylalanine. A change in amino acid sequence in a polypeptide chain may result in a non-functional protein, or a protein that may act in a way that causes harm to a cell. It is generally suggested that many cancers arise as a result of changes in the genetic material.

RNA Ribonucleic acid (RNA) is also a polymer of nucleotides. In RNA, each nucleotide consists of a ribose sugar part, a phosphate part and an N-containing base. It differs from DNA in that it is an unpaired chain of nucleotide bases. Each RNA molecule consists of a single strand of nucleotides.

RNA

RNA RNA exists in three different forms, all are produced in the nucleus against DNA as a template: The strand of nucleotides in each of the RNAs is folded in a different way.