Topic

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1. 2. 3. 4. 5. 6.

Chemistry of Life

LEARNING OUTCOMES
By the end of this topic, you should be able to: List examples of elements and compounds found in living cells; Explain the differences between element and compound; Discuss the properties of water and its importance to organisms; Differentiate between the biochemistry of lipid, carbohydrate and fat; Discuss the process of protein; and Explain the functions of enzymes in living systems.

INTRODUCTION

All living organisms, from microbes to mammals, are composed of chemical substances from both the inorganic and organic world, that appear in roughly the same proportions, and perform the same general tasks. Hydrogen, oxygen, nitrogen, carbon, phosphorus and sulphur normally make up more than 99% of the mass of living cells, and when combined in various ways, form virtually all known organic biomolecules. In this topic, you will be exposed to the study of the different types of elements and compounds that are found in cells. You are specifically going to study oxygen, carbon dioxide and water as simple molecules that play many important roles for living organisms. You will then explore macromolecules lipids, carbohydrates, protein and nucleic acid.

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1.1

CHEMICAL COMPOSITION IN CELLS

The cells of animals, plants and microorganisms have a similar chemical composition. A cell contains several thousand substances that are involved in a variety of chemical reactions. Some elements are present in cells in relatively large quantities while others are in small quantities. The four elements that are present in large quantities are oxygen, carbon, nitrogen and hydrogen (98%). Sulphur, phosphorus, chlorine, potassium, magnesium, sodium, calcium and iron together comprise 1.9%. All other elements are present in the cell in small amounts (less than 0.01%). The key factor in the reactivity of the atoms of various chemical elements is the number of bonds they can form with other atoms. Table 1.1 shows the five elements, together with examples of the structures of simple compounds involving the elements in which the bonds are represented by lines linking the atoms together.
Table 1.1: Examples of Important Elements in Cells

Source: http://www.greenspirit.org.uk/resources/LifeChemistry.shtml

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Carbon has a special place in the chemistry of life because with its four bonds, it can link with other carbon atoms to form chains, loops and networks providing the structural basis for complex compounds that may contain many thousands of carbon atoms. Cells are also made up of compounds. What is the difference between an element and a compound? The difference between an element and a compound is that an element is a substance made of the same type of atoms, whereas a compound is made of different elements in definite proportions. Iron, copper, hydrogen and oxygen are examples of elements. Examples of compounds include water (H2O) and salt (Sodium Chloride NaCl). There are two types of compounds organic and inorganic. Organic compounds are extracted from living organisms. These substances whose molecules contain one or more carbon atoms covalent bonded with another element or radical (including hydrogen, nitrogen, oxygen, halogens as well as phosphorus, silicon and sulphur). A few exceptions are carbon monoxide, carbon dioxide, carbonates, cyanides, cyanates, carbides and thyocyanates, which are considered inorganic. Examples of organic compounds are carbohydrates, lipids, proteins and nucleic acids. Inorganic compounds are extracted from non-living things. They are any compound not containing carbon atoms. Inorganic compounds have salt forming capacity while organic compounds do not form salts.

ACTIVITY 1.1
Find out more about covalent, ionic and hydrogen bonds. You could use any chemistry textbook as reference.

Next, we are going to explore the important elements and their uses. Here, we will discuss carbon dioxide and water, and move on to organic compounds in detail. We will look at the elements that are present and their uses in the cells. Elements are listed in order of decreasing abundance, with the most common element (by mass) listed first. Approximately 96% of body weight consists of only four elements oxygen, carbon, hydrogen and nitrogen. Calcium, phosphorus, magnesium, sodium, potassium and sulphur are macronutrients or elements which the body needs in a significant amount.

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1.1.1

Oxygen (O2)

Oxygen is a colourless, odourless and tasteless gaseous chemical element which appears in great abundance on Earth, trapped by the atmosphere. Many people are familiar with oxygen, because it is a vital component of the respiration process; without oxygen, most organisms will die within minutes. The atomic number of oxygen is eight, and it is identified by an O symbol on the periodic table of elements. It is a key catalyst in many chemical reactions. Oxidation is one such reaction, and it occurs when oxygen mixes with other elements and compounds. Oxygen also plays a role in combustion. By mass, oxygen is the most abundant element in the human body. If you think about it, this makes sense, since most of the body consists of water or H2O. Oxygen accounts for 61-65% of the mass of the human body. Even though there are many more atoms of hydrogen in your body than oxygen, each oxygen atom is 16 times more massive than a hydrogen atom. Oxygen has many uses, as shown below: (a) We use oxygen for respiration and it is an ongoing process which will only stop when we die. We inhale oxygen and exhale carbon dioxide. This process is the same for other living things such as animals, plants and bacteria. When plants and animals die and decompose, oxygen is used. When you burn a fire, it uses oxygen. When metals are rusting, oxygen is used.

(b) (c) (d)

Oxygen is needed for processes all over the world. The composition of oxygen is maintained at about 20% in the air by the oxygen cycle (see Figure 1.1).

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Figure 1.1: Oxygen Cycle Source: http://www.exploringnature.org

1.1.2

Carbon (C)

All living organisms contain carbon, which forms the basis of all organic molecules in the body. Carbon is the second most abundant element in the human body, accounting for 18% of body weight. All organic molecules (fats, proteins, carbohydrates, nucleic acids) contain carbon. Carbon is also found as carbon dioxide. You inhale air that contains about 20% oxygen. The air that you exhale contains much less oxygen but is rich in carbon dioxide.

1.1.3

Hydrogen (H)

Hydrogen accounts for 10% of the mass of the human body. Since around 60% of your body weight is water, much of the hydrogen exists in water, which functions to transport nutrients, remove wastes, lubricate organs and joints, and regulate body temperature.

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Hydrogen is also important in energy production and use. The H+ ion can be used as a hydrogen ion or proton pump to produce adenosine triphosphate (ATP) and regulate numerous chemical reactions. All organic molecules contain hydrogen in addition to carbon.

1.1.4

Nitrogen (N2)

Approximately 3% of the mass of the human body is nitrogen. Proteins, nucleic acids and other organic molecules contain nitrogen. Nitrogen gas is found in the lungs, since the primary gas in air is nitrogen.

1.1.5

Calcium (Ca)

Calcium accounts for 1.5% of human body weight. Calcium is used to give the skeletal system its rigidity and strength. Calcium is found in bones and teeth. The Ca2+ ion is important for muscle function.

1.1.6

Phosphorus (P)

About 1.2% to 1.5% of your body consists of phosphorus. Phosphorus is important for bone structure and is part of the primary energy molecule in the body, ATP. Most of the phosphorus in the body is in the bones and teeth.

1.1.7

Potassium (K)

Potassium makes up 0.2% to 0.35% of the adult human body. Potassium is an important mineral in all cells. It functions as an electrolyte and is particularly important for muscle contraction and conducting electrical impulses.

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1.1.8

Sulphur (S)

Sulphur makes up 0.20% to 0.25% of the human body. Sulphur is an important component of amino acids and proteins. It is present in keratin, which forms skin, hair and nails. It is also needed for cellular respiration, allowing cells to use oxygen.

1.1.9

Sodium (Na)

Approximately 0.10% to 0.15% of your body mass is made up of the element sodium. Sodium is an important electrolyte in the body. It is an important component of cellular fluids and is needed for the transmission of nerve impulses. It helps regulate fluid volume, temperature and blood pressure.

1.1.10 Magnesium (Mg)

The metal magnesium comprises about 0.05% of body weight. About half of the body's magnesium is found in the bones. Magnesium is important for numerous biochemical reactions. It helps regulate heartbeat, blood pressure and blood glucose levels. It is used in protein synthesis and metabolism. It is needed to support the immune system as well as muscle and nerve functions.

SELF-CHECK 1.1
Draw lines to match each chemical element to its function in your body.
Element Mg K Ca Na S Function x x x x x Forms skin, hair and nails. Builds and maintains bones and teeth. Transmits nerve impulses. Functions as an electrolyte and regulates fluid volume, temperature and blood pressure. Regulates heartbeat and blood pressure.

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1.2

SMALL BIOLOGICAL MOLECULES

A molecule is formed when two or more atoms join together chemically. A compound is a molecule that contains at least two different elements. All compounds are molecules but not all molecules are compounds. So are hydrogen (H2), oxygen (O2), nitrogen (N2), water (H2O), carbon dioxide (CO2) and methane (CH4) molecules or compounds? In this section, we are going to explore carbon dioxide and water as examples of small molecules. They may be small but they are very important to us.

1.2.1

Carbon Dioxide

Carbon dioxide (CO2) is one of the simplest and commonest molecules in the universe. It has only three atoms one carbon and two oxygen atoms (see Figure 1.2).

Figure 1.2: The atoms of carbon dioxide

It is easy for carbon atoms to combine with oxygen atoms because the outer shell (valence shell) of a carbon atom has only four electrons in it, leaving room for four more before it is filled up. In the same way, the outer shell of an oxygen atom has only six electrons in it, leaving room for two more to make eight. When two oxygen atoms share their electrons with one carbon atom, all three of the atoms can fill up their shells the carbon atom has four electrons of its own, plus four more that it shares with the oxygen atoms, and each oxygen atom has six electrons of its own, plus two more that it shares with the carbon atom. We call this a covalent bond.

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Plants make their cells mostly out of carbon. The way plants get carbon is by breathing in carbon dioxide and breaking off the oxygen, which they then breathe out again. So the carbon in carbon dioxide is what all plants are made of, and the oxygen becomes the oxygen we breathe. When a plant dies, decays or burns, the carbon in it returns to the air, where it mixes with oxygen to become carbon dioxide again. In the last hundred years or so, carbon dioxide emission has become a big problem for everyone on Earth. We have been burning hydrocarbons as gasoline for cars, heating oil for houses and coal for factories that a lot of carbon has been released into the air, where it makes a lot more carbon dioxide than usual. Carbon dioxide is good for plants but it acts like a warm blanket around the Earth, trapping heat on Earth instead of releasing the heat into space. This is the main cause of global warming. (a) Where is it found? (i) (ii) (b) Carbon dioxide is found in the atmosphere. About 0.03% of the air is carbon dioxide; and It is found in lakes, ponds, streams and oceans.

Where does it come from? (i) (ii) It is produced by almost all living organisms, both plants and animals. Plants release carbon dioxide mostly at night; It is released into the air every time we exhale;

(iii) Even organisms without lungs or gills, such as insects, plants and bacteria, release carbon dioxide into the environment; and (iv) All aquatic organisms release carbon dioxide into the water. This gas either bubbles to the surface or dissolves in the water. Most of the carbon dioxide found in the water is produced by the decomposition of dead organisms, mostly bacteria. (c) Carbon dioxide and plants a nest relationship (i) (ii) Most of the plant material in an aquatic environment is made up of algae; During daylight, all plants use carbon dioxide and release oxygen. This process, which requires light, is called photosynthesis;

(iii) At night, the opposite happens. Plants use oxygen and give off carbon dioxide. This process is called respiration; and

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(iv) All dead plants use a lot of oxygen and give off a lot of carbon dioxide as they rot and decay. (d) Carbon dioxide and animals another exciting relationship! (i) (ii) All animals use oxygen and give off carbon dioxide; and Dead animals continue to use oxygen and give off carbon dioxide as they rot and decay.

See Figure 1.3 for the carbon cycle.

Figure 1.3: Carbon cycle Source: http://water.me.vccs.edu/exam_prep/carbondioxide.html

SELF-CHECK 1.2
1. 2. What are the important functions of carbon dioxide? What are the major suppliers of carbon dioxide to the atmosphere?

1.2.2

Water

Did you know that 90% of cellular contents is made of water? Thus, without water, there would be no life! Water, along with carbohydrates and fat, are important sources for life (see Figure 1.4).

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Figure 1.4: The important sources for life water, carbohydrates and fat

Water is a stable medium for most of the biochemical reactions in living things. In addition, it acts as the intercell and intracell transporter for most dissolved nutrients. Heat is also transported through water. From the evolutionary point of view, life started from water. In fact, most organisms live in the aquatic system. Water has several unique physical and chemical characteristics (see Figure 1.5). Its molecules are small, polarised and form hydrogen bonds with other molecules. You will be amazed by the special features of water and understand why it is so important to living things.

Figure 1.5: Features of water

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(a)

Water is bipolar One molecule of water consists of two hydrogen atoms and one oxygen atom (see Figure 1.6a). The structure of water forms an angle of 104.5 (see Figure 1.6b). As a result, weak positively charged hydrogen atoms and a weak negatively charged oxygen atom are present in a water molecule. The result is a biopolarised molecule.

Figure 1.6: Molecular shape of water

(b)

Water molecules are networked through hydrogen bonds Water molecules bond when hydrogen meets oxygen. The molecules come together through a weak hydrogen bond. Water molecules appear collectively. This is the reason why water is a stable matter. Water is in liquid state at room temperature Water has a higher boiling and melting point in comparison with other matters that have the same relative molecular mass. It means more energy is needed to break down the hydrogen bonds in the water. Thus, water can appear in liquid state at room temperature. Water is the universal solvent Bipolarity in water makes water a good solvent with most charged solutes. When water meets charged solutes (for example, Na+ Cl), an electrostatic reaction between the molecules will happen. Non-charged solutes like oil will not form any reaction with water. Water has low viscosity Water can flow easily. This beneficial feature allows water to enter and leave cells efficiently. Water has a high surface tension (high adhesion) Due to this reason, water molecules stick together. It explains why you could observe rain water in the form of droplets. For plants, high adhesion helps through the capillary action. Thus, absorbed water can be distributed well in plants via transpiration.

(c)

(d)

(e)

(f)

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(g)

Water has a high specific heat capacity High specific heat capacity means more energy is needed to increase the temperature (1C) of 1kg of water. As a result, fluid temperature is very stable in all the cells of our body. Water density is maximum at 4C Have you ever wondered why an ice cube floats in a glass of water? Why does it not sink? The answer is very simple ice has a lower density compared to water. To undertand, you have to recall the molecular structure of water. This feature helps aquatic organisms to survive during winter because only the upper layer of the lake is frozen (0C) while the temperature inside the lake would be slightly warmer at 4C.

(h)

ACTIVITY 1.2
1. Which has a higher boiling point, pure water or Na+Cl contaminated water? Water has a good surface tension. Is that an advantage for aquatic insects? Draw a collective of at least five water molecules with hydrogen bonds.

2.

3.

1.3

MACROMOLECULES

Macromolecules are big molecules which are the building blocks of cells. Macromolecules are generally built by combining many single units or monomers into larger units called polymers. All cells are composed of four general types of macromolecules, which are lipids, carbohydrates, proteins and nucleic acids. In this section, you will learn about the four types, how they are formed and broken down and how they are used in cells.

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1.3.1

Lipid: Pure Fat Fatty Acid and Glycerol

What is lipid? This term might be confusing if you have never learned about fats before. We normally say fat, instead of lipid. Lipid is a broader term than fat. Lipid can be subdivided into three groups, namely, triglyceride (pure fat), phospholipid and steroid. Lipid can be defined as the following: Lipid is an organic matter composed of C, H and O. The ratio between oxygen and hydrogen atom is 1:2. Lipid does not dissolve in water because it is hydrophobic. Nevertheless, it is dissolvable in other solvents like warm alcohol. (a) Triglyceride (pure fat) fatty acid and glycerol The general structure of pure fat is shown in Figure 1.7. Pure fat is an ester formed by a molecule of glycerol (a kind of alcohol) and three molecules of fatty acid (an acid). The process of esterification can be seen in Figure 1.8.

Figure 1.7: General structure of triglyceride

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Figure 1.8: Esterification in triglyceride Source: http://www.elmhurst.edu

From Figure 1.8, you can observe that the general molecular formula for fatty acid is RCOOH. When the hydrocarbon chain of the fatty acid is maximised by the number of hydrogen atoms, it is called saturated fatty acid. A fatty acid with one or more double-bonded bonds is called unsaturated fatty acid. Stearic acid (C17H35COOH) and oleic acid (C17H33COOH) are examples of saturated fatty acid and unsaturated fatty acid respectively. Do you know the difference between oil and fat? The main difference is that oil exists as liquid and fat exists in solid state at room temperature. Secondly, oil is unsaturated fat while fat belongs to the saturated fat group. How about essential and non-essential fatty acids? Maybe you could make a guess before we continue further. Basically, our body cannot produce essential fatty acids at a sufficient basis. It can only be synthesised from our daily diet. Linoleic acid is an example of an essential fatty acid. For the nonessential fatty acid, it could be synthesised from our body. Thus, it is not needed for food consumption.

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(b)

Phospholipids Phospholipids are very much like triglycerides but with one important difference a phosphate functional group is substituted for one of the three fatty acids. The most important feature of phospholipids structure is that the fatty acid "tails" are non-polar, while the phosphate "head" is very polar. This leads to a chemically confused (solubility-challenged) molecule. When exposed to an aqueous (water) environment, phospholipids form unique assemblies called bilayers. The polar heads of P-lipids turn towards water molecules (hydrophilic), while non-polar tails hide from water molecules (hydrophobic). Please refer to Figure 1.9. The structure that surrounds each of your cells (plasma or cell membrane) is formed from a phospholipid bilayer. The polar heads of phospholipids all face the aqueous environments of the outside, and the inside of the cell, while the non-polar tails form a fatty layer on the inside. This structure is an important barrier and defines the boundaries of living and non-living portions of a cell. Hydrogen bonds form between the phospholipid heads and the watery environment inside and outside of the cell in which the hydrophobic interactions force the tails to face inward. Phospholipids are not bonded to each other, which makes the double layer fluid.

Figure 1.9: Lipid bilayer of cell membrane Source: http://www.biologycorner.com

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(c)

Steroids Another major class of lipids is steroids, which have structures totally different from the other classes of lipids. The main feature of steroids is the ring system of three cyclohexanes and one cyclopentane in a fused ring system. There are a variety of functional groups that may be attached. The main feature, as in all lipids, is the large number of carbon-hydrogens which make steroids non-polar. Steroids include well-known compounds such as cholesterol, sex hormones, birth control pills, cortisone and anabolic steroids. The best known and most abundant steroid in the body is cholesterol (see Figure 1.10 for structure of cholesterol). Cholesterol is formed in brain tissues, nerve tissues and the blood stream. It is also the major compound found in gallstones and bile salts. Cholesterol contributes to the formation of deposits on the inner walls of blood vessels. These deposits harden and obstruct the flow of blood. This condition, known as atherosclerosis, results in various heart diseases, stroke and high blood pressure.

Figure 1.10: Structure of cholesterol Source: http://chemwiki.ucdavis.edu

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ACTIVITY 1.3
1. In your opinion, which one is more healthful; saturated or unsaturated fat? Lipid is important to maintain body temperature during winter. Do you agree with this statement?

2.

SELF-CHECK 1.3
1. 2. 3. What are the unique features of water? State the groups that form carbohydrate. Explain the differences between oil and fat.

1.3.2

Carbohydrate

Before we go any further in discussing carbohydrate, let us take a look at Figure 1.11.

Figure 1.11: Carbohydrate as source of energy

Carbohydrate is an organic matter that consists of C, H and O in the ratio of 1:2:1. Its molecular formula is (CH2O)n, where n is the number of carbon in the molecule.

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We eat carbohydrates every day. As Malaysians, we eat rice and bread as the main sources of carbohydrate. Do you know the functions of carbohydrate in our body? At the cellular level, carbohydrate is important because: (a) (b) (c) Simple carbohydrate is the main energy source for cells; Long-chained carbohydrate can keep more energy; and Long-chained carbohydrate forms the structure of living things, especially in cell walls (plants).

Based on the complexity or structure of carbohydrate, it can be divided into three groups (refer to Figure 1.12).

Figure 1.12: The three groups of carbohydrates

(a)

Monosaccharide This is the simplest sugar. It is the basic unit that forms complex sugar in carbohydrate. Under monosaccharide, two classifications could be used to group all the simple sugars. The first classification is based on the number of carbon atoms in the structure (see Table 1.2).
Table 1.2: First Classification of Monosaccharides Monosaccharide Triose (3C) Pentose (5C) Hexose (6C) Function(s) Inter-product that is important for respiration and photosynthesis Supports the structure of DNA and RNA Supplies instant energy to animals and plants (g glucose) Provides sweetness (fructose) for fruits, thus encouraging seed dispersal

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The second classification is based on the functional group in the molecular structure (see Table 1.3). Here, we are just looking at the most basic monosaccharide sugar (triose). Both aldose and ketone (triose) possess a similar molecular formula but the atomic arrangement is different. This phenomenon is called structural isomer. Monosaccharides with an aldose group and a ketose group are called aldose sugar and ketose sugar respectively.
Table 1.3: Second Classification of Monosaccharides

In short, monosaccharide is sweet, easily dissolves in water and forms white crystals.

ACTIVITY 1.4
1. Predict the molecular structure for pentose sugar based on the functional group of aldose. State one example for disaccharide and polysaccharide.

2.

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1.3.3

Amino Acid and Peptide

Amino acid is the basic unit that forms protein. All amino acids have the same basic structure but differ only at the side group (-R group). Look at Figure 1.13 to have a clear picture of the structure of amino acid.

Figure 1.13: Basic structure of amino acid

There are 20 types of amino acids. Amino acids are classified into four groups according to their side group. The four groups are: (a) Amino acid without polarised R group Example: glysine (Gly) Amino acid with polarised R group Example: serine (Ser) Amino acid with acidic R group (negatively charged) Example: aspartic acid (Asp) Amino acid with basic R group (positively charged) Example: lysine (Lys)

(b)

(c)

(d)

When one amino acid is combined with another amino acid, condensation will occur. As a result, a peptide bond will be formed between the amino acids. The new molecule is called dipeptide (see Figure 1.14). A dipeptide might form tripeptide with another amino acid. When this continues, a polypeptide might form. Protein is the combination of polypeptides.

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Figure 1.14: Formation of a peptide bond Source: Cooper (2000)

You might ask the number of polypeptides that can be formed here. Twenty amino acids can form unlimited types of polypeptides. Protein is a complex macromolecule. It contains thousands of atoms in its structure. One molecule of protein is made from C, H, O and N. Rarely, it also consists of S and P. Protein is made from amino acids. Three-dimensional protein structures are organised into four levels (see Figure 1.15), namely: (a) (b) (c) (d) Primary Polypeptide chain that is composed of amino acid linear sequences; Secondary Folding and coiling of polypeptide chain; Tertiary Folding of -helix (shaped like telephone wire) polypeptide to form packed globular protein molecules; and Quartenary The arrangement of more than one polypeptide chain to form a protein molecule.

We can use structure or composition to classify proteins. At a high temperature (40C), protein denaturalisation might happen. The structures of our body are made from proteins. These also act as hormones and enzymes.

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Figure 1.15: Four levels of protein structure

1.3.4

Nucleotides and Nucleic Acid

What is nucleic acid? Nucleic acid is a complex molecule made of C, H, O, P and N. Two important nucleic acids are deoxyribonucleic acid (D DNA) and ribonucleic acid (RNA). What is the basic unit for nucleic acid? It is called nucleotide (see Figure 1.16). One unit of nucleotide consists of pentose sugar, phosphate group and nitrogenous base. There are four types of nucleotides in a DNA and RNA thymine is substituted by uracil (U):

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(a) (b) (c) (d)

Adenine (A) } Purine-based group Guanine (G) Thymine (T) } Pyrimidine-based group Cytosine (C)

Figure 1.16: A unit of nucleotide Source: http://faculty.uca.edu

By now, you should be clear that DNA and RNA are composed of units of nucleotides. How about their structures? Figure 1.17 shows a portion of the DNA structure (two-dimensional). You may notice that eight nucleotides are present. The bases pairing should be always adenine (A)-thymine (T) and guanine (G)cytosine (C).

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Figure 1.17: Two-dimensional DNA fragment

Basically, DNA consists of two antisense (5' to 3' and 3' to 5') strands. It coils and forms a double helical shaped molecule. As for the RNA, it stands as a single strand. It can appear in three forms ribosomal RNA (rRNA), messenger RNA (mRNA) and transfer RNA (tRNA). Next, we are going to see what genetic code is all about. We have learnt that there are 4 types of nucleotides and 20 types of amino acids. Generally, the codes are a combination of three nucleotides from one type of amino acid. Figure 1.18 below shows one type of amino acid known as Valine (found in DNA) can be formed through four combinations of nucleotides. CAA CAG } Valine CAT CAC
Figure 1.18: The combination that forms Valine

Next, we will take a look at an example of codon in the mRNA. Serine is formable from six combinations of nucleotides. Thus, Codon is the triplet genetic code found only in the mRNA. However, take note that genetic codes in DNA and mRNA are different (refer to Figure 1.19).

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UCU UCC UCA } Serine UCG AGU AGC

Figure 1.19: The combination that forms Serine

In mRNA, there is also a type of codon or genetic codes, named stop codon. It acts as the termination signal in protein synthesis. You will understand more when we move on to the next subtopic. In short, genetic code is present in triplet form and consists of three nucleotides.

ACTIVITY 1.5
1. Based on your understanding, can we pair Adenine (A) with Guanine (G)? Give a valid reason. State one genetic code for stop codon. You may get the answer from reference books or Internet sources.

2.

1.3.5

Protein Synthesis

The function of protein synthesis is to generate protein as the end product. It begins with DNA which contains all the genetic materials. It means, DNA ensures that protein-made components in our body are sufficient and available when needed. Protein synthesis takes place in the rRNA. mRNA is a template or copy of the DNA (DNA is the genetic material and protein synthesis can only be done from mRNA). tRNA (a anticodon) is needed to transfer amino acids to each of the matching codons in the mRNA. The synthesis process will be terminated automatically when the stop anticodon has reached rRNA. Then, the synthesis of the desired protein is complete.

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In summary, transcription occurs in the nucleus and involves making a template (mRNA) for a particular DNA site. The goal of translation is to get the protein as an end product. It takes place in the cytoplasm and involves three main stages: initiation, elongation and termination.

ACTIVITY 1.6
Which of the following can potentially appear in mRNA? (i) ACUUCGGCUCUG (ii) UGCUCAACGGUT (iii) ACGUAGUCTUCU (iv) AGCCGCCCGAAG (v) ACUGGAUUGGGA A. B. C. i, ii and iv i, iv and v ii, iii and iv D. E. ii and ii i, iii, iv and v

1.3.6

Enzyme

Thousands of intercellular (extracellular) and intracellular reactions might be affected if there is no enzyme. So, what is enzyme? Enzyme is a protein molecule that is a biological catalyst with three characteristics. Lets take a look at these three characteristics of enzyme. First, the basic function of an enzyme is to increase the rate of a reaction. Most cellular reactions occur about a million times faster than they would in the absence of an enzyme. Second, most enzymes act specifically with only one reactant (called a substrate) to produce products. The third and most remarkable characteristic is that enzymes are regulated from a state of low activity to high activity and vice versa. Gradually, you will appreciate that the individuality of a living cell is due in large part to the unique set of some 3,000 enzymes that it is genetically programmed to produce. If even one enzyme is missing or defective, the result can be disastrous. Examples of enzymes are lactase, diastase and sucrose.

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Figure 1.20 shows a typical enzymatic reaction. As you can see, enzyme facilitates substrates by changing the shape of its active site. The enzyme is larger than its substrate. This helps increase the rate of biochemical reaction and produce the expected products. The enzyme is substrate-specific.

Figure 1.20: A biochemical reaction catalysed by an enzyme

ACTIVITY 1.7
Lactase breaks down lactose, lipase breaks down fats and protease breaks down starch. What do you think the functions of the following enzymes are? (a) (b) (c) (d) Sucrase Cellulase Amylase Maltase

Chemical compositions of all living cells are similar. They are made up of various elements and compounds. Elements are made up of one kind of atom, while compounds are made of two or more different atoms combining with a covalent or an ionic bond. Carbon dioxide and water are examples of inorganic compounds found in living cells.

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Carbon dioxide is produced by all living things when they respire. Plants also take in carbon dioxide to make food through photosynthesis. Water is the most stable and the most abundant in living cells. It has several unique physical and chemical characteristics. Lipid is an organic matter composed of C, H and O and the ratio between oxygen and hydrogen atoms are 1:2. Triglycerides, phospholipids and steroids are examples of lipid. Triglycerides is an ester formed by a molecule of glycerol molecules of fatty acid. and three

Phospholipids are very much like triglycerides but with one important difference. A phosphate functional group is substituted for one of the three fatty acids. Steroids have a ring system of three cyclohexanes and one cyclopentane in a fused ring system. Cholesterol is one example of steroid. There are three main groups of carbohydrates: monosaccharide, disaccharide and polysaccharide. Amino acid is the basic unit for protein. Protein is the main source for cellular development and repair in living organisms. The basic unit for nucleic acid is called nucleotide. One unit of nucleotide consists of pentose sugar, phosphate group and nitrogenous base. The two types of nucleic acid are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The four bases in DNA are adenine, thymine, cytosine and guanine, while the bases in RNA are adenine, cytosine, guanine and uracil. Protein synthesis takes place in the cytoplasm and involves three main stages: initiation, elongation and termination. Enzyme is a protein molecule that is a biological catalyst that speed up chemical reaction in our cells.

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CHEMISTRY OF LIFE

Adenine (A) Aldose sugar Anticodon Antisense Amino acid Bipolar Carbohydrate Catalyst Codon Cytosine (C) Denaturalisation Deoxyribonucleic acid (DNA) Disaccharide Elongation Enzyme Esterification Fat Fatty acid Glycerol Guanine (G) Hexose Hydrogen bond Initiation

Ketose sugar Ligase enzyme Lipid Monosaccharide Nucleotide Pentose Polymerase chain reaction (PCR) Polysaccharide Protein Ribonucleic acid (RNA) Saturated fat Stearic acid Steroid Substrate-specific Termination Thyamine (T) Transcription Translation Triglyceride Triose Unsaturated fat Uracil (U)

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Amsel, S. (2013). Oxygen cycle. Exploring Nature Educational Resource. Retrieved from http://exploringnature.org.

Chemical composition of the human body. (2013). Elements in the human body.
Retrieved from http://chemistry.about.com Chen, P. (1992). Biologi STPM Jilid 2. Kuala Lumpur: Penerbit Fajar Bakti Sdn Bhd. Cooper, G. M. (2000). The cell: A molecular approach (2nd ed.). Sunderland: Sinauer Associates. Diffen Contributers. (2013). Compounds vs. Elements. http://www.diffen.com. Elmhurst College. (2008). http://www.elmhurst.edu. Retrieved from Retrieved from

Elmhurst

College.

Hardman, J. (n.d.). The lipid bilayer. Retrieved from http://www.fastbleep. com/biology-notes/31/170/969 Lee, S. C., & Liew, S. L. (2000). Biologi STPM Jilid 1. Kuala Lumpur: Penerbit Fajar Bakti Sdn Bhd. Mountain Empire Community College. (n.d.). Carbon dioxide. Retrieved from http://water.me.vccs.edu

Phospholipids. (n.d.). Retrieved from http://bioweb.wku.edu

Schirber, M. (2009). The chemistry of life: The human body. Retrieved from http://www.livescience.com

Steroids. (2010). Retrieved from http://chemwiki.ucdavis.edu