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LOWER SIX PUSAT TUISYEN KASTURI PREPARED BY BIOLOGY LESSON 1
T.K. LEONG
TOPIC: BASIC CHEMISTRY OF A CELL (1)INTRODUCTION
Biochemistry is the study of the chemicals of living organisms.
Its importance lies in the fundamental understanding it gives us the way in which biological system work.
Living organisms are made of a limited number of types of atom, which combine to form molecules, the building block of life.
These molecules vary enormously in size from simple molecules such as carbon dioxide and water to macromolecules such as proteins.
WATER
1. Of the smaller molecules, water is the most abundant, typically making up between 60-95% of the fresh mass of an organism.
2. They are the kind of molecules which biologist speculate could have been made in the “primeval soup” of chemicals which is thought to have existed in the early history of the planet, before life itself appeared.
3. Water is important for two reasons;
(a) It is a vital chemical constituent of living cells.
(b) It provides an environment for those organisms that live in water 4. It is worthwhile, then, looking at some of its chemical and physical
properties.
5. The two most important properties of water are; (i) Polarity
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Water Molecule is Polar
The water molecule is deceptively simple. Its two hydrogen atoms are joined to the
oxygen atom by single covalent bond.
In water, one part, or pole, of the molecule is slightly positive and the other slightly negative. This is known as a dipole.
It occurs because the oxygen atom has greater electron-attracting power
(electronegativity) than the hydrogen atoms. As a result, the oxygen atom tends to attract the single electrons of the hydrogen atoms, this result opposite ends of the molecule have opposite charges. (Dipole molecule or polar molecule)
Water molecules therefore have a weak attraction for each other, with opposite charges coming together and causing them to behave as if they were “sticky”.
These attractions are not as strong as normal ionic or covalent bonds and are called
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Hydrogen Bonds
Hydrogen bond is the electrostatic attraction between a positively charged region
of one molecule and a negatively charged region of another. They are constantly being formed, broken and reformed in water.
Although individually weak, their collective effect is responsible for many unusual physical properties of water.
The two diagrams above explain why the density of ice is much lower than the water that allows ice cube floated.
Under room temperature, water molecules exist in the form of liquid and only 20% of such hydrogen bonds are formed. But as temperature decreased to 0ºC, all water molecules are involved in forming the three-dimensional structure of ice.
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Biological Importance of Water
SOLVENT PROPERTIES
Water is an excellent solvent for polar substances. These include ionic substances like salts, which contain charged particles (ions), and some non-ionic substances like sugars hat contain polar groups (slightly charged) such as the slightly negative
hydroxyl group (-OH).
On contact with water, the ions and the polar groups are surrounded by water molecules which separate (dissociate) the ions or molecules from each other. This is happens when a substance dissolves in water.
Once a substance is in solution its molecules or ions can move about freely, thus making it more chemically reactive than if it were solid. Thus the majority of the cell’s chemical reactions take place in aqueous solutions.
By contrast, non-polar molecules, such as lipids, are repelled by water and usually group together in its presence, that is non –polar molecules are hydrophobic (water-hating). Such hydrophobic interactions are important in the formation of membrane and help to determine the 3D structure of many protein molecules, nucleic acids and other cell structures.
Water’s solvent properties also mean that it acts as a transport medium, as in blood, lymphatic and excretory systems, the alimentary canal and in xylem and phloem.
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The specific heat capacity of water is the amount of heat required to raise the temperature of 1kg of water by 1C.
Water has a high heat capacity. This means that a large increase in heat energy results in a relatively small rise in temperature.
This is because much of the energy is used in breaking the hydrogen bonds which restrict the movement of the molecules.
Temperature changes within water are minimised as a result of it high specific heat capacity. Biochemical processes therefore operate over smaller temperature range, proceeding at more constant rates and are less likely to be inhibited by extremes of temperature.
HIGH HEAT OF VAPORISATION
Latent heat of vaporisation is a measure of the heat energy required to vaporise a
liquid that is to overcome the attractive forces between its molecules so that they can escape as a gas.
A relatively large amount of energy is needed to vaporise water. This is due to the hydrogen bonding. As a result, water has an unusually high boiling point for such a small molecule.
Its significant physiological roles include; (a) Enable many invertebrate to survive. (b) Cooling effect when we sweat.
(c) Panting helps to rid the body excessive heat such as dog
(d) Transpiration helps lower temperature in the plants during hot day.
DENSITY AND FREEZING PROPERTIES
The density of water decreases below 4C and ice therefore tends to float.
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Since ice floats, it forms at the surface first and the bottom last. If ponds froze from the bottom upwards, fresh water life could not exist in temperate or arctic climates. Ice insulates the water below it, thus increasing the chances of survival of organisms in the water.
HIGH SURFACE TENSION AND COHESION
Cohesion is the force whereby individual molecules stick together. At the surface of
the liquid, a force called surface tension exists between the molecules as a result of cohesive forces between the molecules.
These cause the surface of the liquid to occupy the least possible surface area. (ideally a sphere)
Water has a higher surface tension than any other liquid. The high cohesion of water molecules is important in cells and in translocation of water through xylem in plants. At a less fundamental level, many small organisms rely on surface tension to settle on water or to skate over its surface. Example: water skaters.
MACROMOLECULES
Simpler organic molecules often associate to form larger molecules. A
macromolecule is a giant molecule made from many repeating units. Molecules
built like this are known as polymers. The individual units are known as monomers. The units are joined by a chemical process known as condensation.
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There are three important types of macromolecule in biology; I. Polysaccharides
II. Proteins III. Nucleic acids
CARBOHYDRATES
Carbohydrates are substances which contain the elements carbon, hydrogen and oxygen and have the formula Cx(H2O)y. Their name is derived from the fact that hydrogen and oxygen are present in the same proportions as in water.
They have the following properties; All are aldehydes or ketones
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Monosaccharides
Monosaccharides are single sugar units. Their general formula is (CH2O)n. There are
classified according to the number of carbon atoms as trioses (3C), tetroses (4C),
pentoses (5C), hexoses (6C) and heptoses (7C).
Aldoses and ketoses
In monosaccharides, all the carbon atoms except one have a hydroxyl group
attached. The remaining carbon atom is either part of an aldehydes group, in which
case the monosaccharide is called an aldose or aldo sugar, or is part of a keto
group, when it is called a ketose or keto sugar. Example:
The two simplest monosaccharides are the trioses glyceraldehydes and
dihydroxyacetone.
In general, aldoses, such as ribose and glucose, are more common then ketoses, such as ribulose and fructose.
A suitable monosaccharide to study in more detail is glucose, the most common monosaccharide. It is a hexose, and therefore has the formula C6H12O6.
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Figure above shows glucose as having either an ‘open chain’ or ring structure. The open chain form can be straight, but because of the bond angles between carbon atoms it is possible for sugars with 5 or 6 carbon atoms to bend and form stable ring structures.
In glucose, the 1C combines with the O on 5C to give a six-membered ring as shown above.
The ring structures of pentoses and hexoses are the usual forms, with only a small proportion of the molecules existing in the open chain form at any one time. The ring structure is the form used to make disaccharides and polysaccharides. Glucose can exist in two possible ring forms, known as alpha (α) and beta (β) forms. α glucose is used to make the polysaccharide starch and β glucose the
