topic 1 chemistry of life

8/13/2019 Topic 1 Chemistry of Life

1/31

INTRODUCTION

All living organisms, from microbes to mammals, are composed of chemicalsubstances from both the inorganic and organic world, that appear in roughly thesame proportions, and perform the same general tasks. Hydrogen, oxygen,nitrogen, carbon, phosphorus and sulphur normally make up more than 99% ofthe 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 elementsand compounds that are found in cells. You are specifically going to studyoxygen, carbon dioxide and water as simple molecules that play many importantroles for living organisms. You will then explore macromolecules lipids,carbohydrates, protein and nucleic acid.

TTooppiicc

11

Chemistry ofLife

By the end of this topic, you should be able to:

1. List examples of elements and compounds found in living cells;

2. Explain the differences between element and compound;

3. Discuss the properties of water and its importance to organisms;

4. Differentiate between the biochemistry of lipid, carbohydrate and fat;

5. Discuss the process of protein; and

6. Explain the functions of enzymes in living systems.

LEARNING OUTCOMES


2/31

TOPIC 1 CHEMISTRY OF LIFE2

CHEMICAL COMPOSITION IN CELLS

The cells of animals, plants and microorganisms have a similar chemicalcomposition. A cell contains several thousand substances that are involved in avariety of chemical reactions. Some elements are present in cells in relativelylarge quantities while others are in small quantities. The four elements that arepresent in large quantities are oxygen, carbon, nitrogen and hydrogen (98%).Sulphur, phosphorus, chlorine, potassium, magnesium, sodium, calcium andiron together comprise 1.9%. All other elements are present in the cell in smallamounts (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 fiveelements, together with examples of the structures of simple compoundsinvolving the elements in which the bonds are represented by lines linking theatoms together.

Table 1.1:Examples of Important Elements in Cells

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

1.1


3/31

TOPIC 1 CHEMISTRY OF LIFE 3

Carbon has a special place in the chemistry of life because with its four bonds, itcan link with other carbon atoms to form chains, loops and networks providingthe 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 elementand a compound? The difference between an element and a compound is that anelement is a substance made of the same type of atoms, whereas a compound ismade of different elements in definite proportions. Iron, copper, hydrogen andoxygen 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 substanceswhose molecules contain one or more carbon atoms covalent bonded withanother element or radical (including hydrogen, nitrogen, oxygen, halogens aswell as phosphorus, silicon and sulphur). A few exceptions are carbon monoxide,carbon dioxide, carbonates, cyanides, cyanates, carbides and thyocyanates, whichare considered inorganic. Examples of organic compounds are carbohydrates,lipids, proteins and nucleic acids.

Inorganic compounds are extracted from non-living things. They are anycompound not containing carbon atoms. Inorganic compounds have salt formingcapacity while organic compounds do not form salts.

Next, we are going to explore the important elements and their uses. Here, wewill 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. Elementsare listed in order of decreasing abundance, with the most common element (bymass) listed first. Approximately 96% of body weight consists of only fourelements oxygen, carbon, hydrogen and nitrogen. Calcium, phosphorus,magnesium, sodium, potassium and sulphur are macronutrients or elementswhich the body needs in a significant amount.

Find out more about covalent, ionic and hydrogen bonds. You coulduse any chemistry textbook as reference.

ACTIVITY 1.1


4/31


1.1.1 Oxygen (O2)

Oxygenis a colourless, odourless and tasteless gaseous chemical element whichappears in great abundance on Earth, trapped by the atmosphere. Many peopleare familiar with oxygen, because it is a vital component of the respirationprocess; without oxygen, most organisms will die within minutes.

The atomic number of oxygen is eight, and it is identified by an O symbol on theperiodic table of elements. It is a key catalystin many chemical reactions.Oxidationis one such reaction, and it occurs when oxygen mixes with otherelements 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 moreatomsof hydrogen in your body than oxygen, each oxygen atomis 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 onlystop when we die. We inhale oxygen and exhale carbon dioxide. Thisprocess is the same for other living things such as animals, plants and

bacteria.

(b) When plants and animals die and decompose, oxygen is used.

(c) When you burn a fire, it uses oxygen.

(d) When metals are rusting, oxygen is used.

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


5/31


Figure 1.1:Oxygen CycleSource:http://www.exploringnature.org

1.1.2 Carbon (C)

All living organisms contain carbon, which forms the basis of all organicmolecules in the body. Carbon is the second most abundant element in thehuman body, accounting for 18% of body weight.

All organic molecules (fats, proteins, carbohydrates, nucleic acids) containcarbon. Carbon is also found as carbon dioxide. You inhale air that containsabout 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 inwater, which functions to transport nutrients, remove wastes, lubricate organsand joints, and regulate body temperature.


6/31


Hydrogen is also important in energy production and use. The H+ion can beused 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, nucleicacids and other organic molecules contain nitrogen. Nitrogen gas is found in thelungs, 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 theskeletal 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 isimportant 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 animportant mineral in all cells. It functions as an electrolyte and is particularlyimportant for muscle contraction and conducting electrical impulses.


7/31


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 formsskin, hair and nails. It is also needed for cellular respiration, allowing cells to useoxygen.

1.1.9 Sodium (Na)

Approximately 0.10% to 0.15% of your body mass is made up of the elementsodium. Sodium is an important electrolyte in the body. It is an importantcomponent of cellular fluids and is needed for the transmission of nerveimpulses. 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 thebody's magnesium is found in the bones. Magnesium is important for numerousbiochemical reactions. It helps regulate heartbeat, blood pressure and bloodglucose levels. It is used in protein synthesis and metabolism. It is needed tosupport the immune system as well as muscle and nerve functions.

Draw lines to match each chemical element to its function in yourbody.

Element FunctionMg Forms skin, hair and nails.

K Builds and maintains bones and teeth.

Ca Transmits nerve impulses.

Na Functions as an electrolyte and regulates fluidvolume, temperature and blood pressure.

S Regulates heartbeat and blood pressure.

SELF-CHECK 1.1


8/31


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. Allcompounds 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 ofsmall 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 theuniverse. It has only three atoms one carbon and two oxygen atoms (see Figure1.2).

Figure 1.2: The atoms of carbon dioxideIt 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 fourmore before it is filled up. In the same way, the outer shell of an oxygen atom hasonly six electrons in it, leaving room for two more to make eight. When twooxygen atoms share their electrons with one carbon atom, all three of the atomscan fill up their shells the carbon atom has four electrons of its own, plus fourmore that it shares with the oxygen atoms, and each oxygen atom has sixelectrons of its own, plus two more that it shares with the carbon atom. We callthis a covalent bond.

1.2


9/31


Plants make their cells mostly out of carbon. The way plants get carbon is bybreathing in carbon dioxide and breaking off the oxygen, which they then breatheout 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, thecarbon in it returns to the air, where it mixes with oxygen to become carbondioxide again.

In the last hundred years or so, carbon dioxide emission has become a bigproblem for everyone on Earth. We have been burning hydrocarbons as gasolinefor cars, heating oil for houses and coal for factories that a lot of carbon has beenreleased 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 theEarth, 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) Carbon dioxide is found in the atmosphere. About 0.03% of the air is

carbon dioxide; and

(ii) It is found in lakes, ponds, streams and oceans.

(b) Where does it come from?(i) It is produced by almost all living organisms, both plants and

animals. Plants release carbon dioxide mostly at night;(ii) It is released into the air every time we exhale;

(iii) Even organisms without lungs or gills, such as insects, plants andbacteria, release carbon dioxide into the environment; and

(iv) All aquatic organisms release carbon dioxide into the water. This gaseither bubbles to the surface or dissolves in the water. Most of thecarbon dioxide found in the water is produced by the decompositionof dead organisms, mostly bacteria.

(c) Carbon dioxide and plants a nest relationship(i) Most of the plant material in an aquatic environment is made up of

algae;

(ii) 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 carbondioxide. This process is called respiration; and


10/31


(iv) All dead plants use a lot of oxygen and give off a lot of carbon dioxideas they rot and decay.

(d) Carbon dioxide and animals another exciting relationship!(i) All animals use oxygen and give off carbon dioxide; and

(ii) Dead animals continue to use oxygen and give off carbon dioxide asthey rot and decay.

See Figure 1.3 for the carbon cycle.

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

1.2.2 Water

Did you know that 90% of cellular contents is made of water? Thus, withoutwater, there would be no life! Water, along with carbohydrates and fat, areimportant sources for life (see Figure 1.4).

1. What are the important functions of carbon dioxide?

2. What are the major suppliers of carbon dioxide to theatmosphere?

SELF-CHECK 1.2


11/31


Figure 1.4: The important sources for life water, carbohydrates and fatWateris a stable medium for most of the biochemical reactions in living things.In addition, it acts as the intercell and intracell transporter for most dissolvednutrients. Heat is also transported through water. From the evolutionary point ofview, 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 othermolecules. You will be amazed by the special features of water and understandwhy it is so important to living things.

Figure 1.5: Features of water


12/31


(a) Water is bipolarOne molecule of water consists of two hydrogen atoms and one oxygenatom (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 aweak negatively charged oxygen atom are present in a water molecule. Theresult 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 cometogether through a weak hydrogen bond. Water molecules appearcollectively. This is the reason why water is a stable matter.

(c) Water is in liquid state at room temperatureWater has a higher boiling and melting point in comparison with othermatters that have the same relative molecular mass. It means more energy is

needed to break down the hydrogen bonds in the water. Thus, water canappear in liquid state at room temperature.

(d) Water is the universal solventBipolarity in water makes water a good solvent with most charged solutes.When water meets charged solutes (for example, Na+ Cl ), an electrostaticreaction between the molecules will happen. Non-charged solutes like oilwill not form any reaction with water.

(e) Water has low viscosityWater can flow easily. This beneficial feature allows water to enter and leavecells efficiently.

(f) Water has a high surface tension (high adhesion)Due to this reason, water molecules stick together. It explains why you couldobserve rain water in the form of droplets. For plants, high adhesion helpsthrough the capillary action. Thus, absorbed water can be distributed well inplants via transpiration.


13/31


(g) Water has a high specific heat capacityHigh specific heat capacity means more energy is needed to increase thetemperature (1C) of 1kg of water. As a result, fluid temperature is very

stable in all the cells of our body.

(h) Water density is maximum at 4CHave you ever wondered why an ice cube floats in a glass of water? Whydoes it not sink? The answer is very simple ice has a lower densitycompared to water. To undertand, you have to recall the molecular structureof water. This feature helps aquatic organisms to survive during winter

because only the upper layer of the lake is frozen (0C) while the temperatureinside the lake would be slightly warmer at 4C.

MACROMOLECULES

Macromolecules are big molecules which are the building blocks of cells.Macromolecules are generally built by combining many single units ormonomers into larger units called polymers. All cells are composed of fourgeneral types of macromolecules, which are lipids, carbohydrates, proteins andnucleic acids.

In this section, you will learn about the four types, how they are formed andbroken down and how they are used in cells.

1.3

1. Which has a higher boiling point, pure water or Na+Clcontaminated water?

2. Water has a good surface tension. Is that an advantage for aquaticinsects?

3. Draw a collective of at least five water molecules with hydrogenbonds.

ACTIVITY 1.2


14/31


1.3.1 Lipid: Pure FatFatty Acid and GlycerolWhat 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:

The ratio between oxygen and hydrogen atom is 1:2. Lipid does not dissolve inwater because it is hydrophobic. Nevertheless, it is dissolvable in other solventslike warm alcohol.

(a) Triglyceride (pure fat) fatty acid and glycerolThe general structure of pure fat is shown in Figure 1.7. Pure fat is an esterformed by amolecule of glycerol(a kind of alcohol) and three molecules offatty acid(an acid). The process of esterificationcan be seen in Figure 1.8.

Figure 1.7: General structure of triglyceride

Lipidis an organic matter composed of C, H and O.


15/31


Figure 1.8: Esterification in triglycerideSource: http://www.elmhurst.eduFrom Figure 1.8, you can observe that the general molecular formula for fattyacid 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 fattyacid with one or more double-bonded bonds is called unsaturated fatty acid.Stearic acid (C17H35COOH) and oleic acid (C17H33COOH) are examples ofsaturated fatty acid and unsaturated fatty acid respectively.

Do you know the difference between oil and fat? The main difference is thatoil exists as liquidand fat exists in solid stateat room temperature. Secondly,oil is unsaturated fat while fat belongs to the saturated fatgroup.How about essential and non-essential fatty acids? Maybe you could make aguess before we continue further. Basically, our body cannot produceessential fatty acids at a sufficient basis. It can only be synthesised from ourdaily diet. Linoleic acidis an example of an essential fatty acid. For the non-essential fatty acid, it could be synthesised from our body. Thus, it is notneeded for food consumption.


16/31


(b) PhospholipidsPhospholipids are very much like triglycerides but with one importantdifference 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 toa chemically confused (solubility-challenged) molecule. When exposed toan aqueous (water) environment, phospholipids form unique assembliescalled 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 allface 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 isan important barrier and defines the boundaries of living and non-livingportions of a cell.

Hydrogen bonds form between the phospholipid heads and the wateryenvironment inside and outside of the cell in which the hydrophobicinteractions force the tails to face inward. Phospholipids are not bonded toeach other, which makes the double layer fluid.

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


17/31


(c) SteroidsAnother major class of lipids is steroids, which have structures totallydifferent from the other classes of lipids. The main feature of steroids is the

ring system of three cyclohexanes and one cyclopentane in a fused ringsystem. There are a variety of functional groups that may be attached. Themain feature, as in all lipids, is the large number of carbon-hydrogenswhich 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 (seeFigure 1.10 for structure of cholesterol). Cholesterol is formed in brain

tissues, nerve tissues and the blood stream. It is also the major compoundfound in gallstones and bile salts. Cholesterol contributes to the formationof deposits on the inner walls of blood vessels. These deposits harden andobstruct the flow of blood. This condition, known as atherosclerosis, resultsin various heart diseases, stroke and high blood pressure.

Figure 1.10:Structure of cholesterolSource:http://chemwiki.ucdavis.edu


18/31


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 energyCarbohydrateis 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 themolecule.

1. In your opinion, which one is more healthful; saturated orunsaturated fat?

2. Lipid is important to maintain body temperature duringwinter. Do you agree with this statement?

1. What are the unique features of water?2. State the groups that form carbohydrate.

3. Explain the differences between oil and fat.

ACTIVITY 1.3

SELF-CHECK 1.3


19/31


We eat carbohydrates every day. As Malaysians, we eat rice and bread as themain sources of carbohydrate. Do you know the functions of carbohydrate in our

body? At the cellular level, carbohydrate is important because:

(a) Simple carbohydrate is the main energy sourcefor cells;(b) Long-chained carbohydrate can keep more energy; and(c) 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 threegroups (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 incarbohydrate. Under monosaccharide, two classifications could be used togroup all the simple sugars. The first classification is based on the numberof carbon atoms in the structure (see Table 1.2).

Table 1.2:First Classification of MonosaccharidesMonosaccharide Function(s)

Triose (3C) Inter-product that is important for respiration andphotosynthesis

Pentose (5C) Supports the structure of DNA and RNA

Hexose (6C)Supplies instant energy to animals and plants (glucose)Provides sweetness (fructose) for fruits, thus encouragingseed dispersal


20/31


The second classification is based on the functional group in the molecularstructure (see Table 1.3). Here, we are just looking at the most basicmonosaccharide sugar (triose). Both aldose and ketone (triose) possess a

similar molecular formula but the atomic arrangement is different. Thisphenomenon is called structural isomer. Monosaccharides with an aldosegroup and a ketose group are called aldose sugar and ketose sugarrespectively.

Table 1.3: Second Classification of Monosaccharides

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

1. Predict the molecular structure for pentose sugar based on thefunctional group of aldose.

2. State one example for disaccharide and polysaccharide.

ACTIVITY 1.4


21/31


1.3.3 Amino Acid and Peptide

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

Figure 1.13: Basic structure of amino acidThere 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)

(b) Amino acid with polarised R group Example: serine (Ser)

(c) Amino acid with acidic R group (negatively charged) Example: aspartic acid (Asp)

(d) Amino acid with basic R group (positively charged) Example: lysine (Lys)

When one amino acid is combined with another amino acid, condensationwilloccur. As a result, a peptide bondwill be formed between the amino acids. Thenew molecule is called dipeptide (see Figure 1.14). A dipeptide might formtripeptide with another amino acid. When this continues, a polypeptide mightform. Proteinis the combination of polypeptides.


22/31


Figure 1.14:Formation of a peptide bondSource:Cooper (2000)You might ask the number of polypeptides that can be formed here. Twentyamino acids can form unlimitedtypes of polypeptides.Protein is a complex macromolecule. It contains thousands of atoms in itsstructure. One molecule of protein is made from C, H, O and N. Rarely, it alsoconsists of S and P. Protein is made from amino acids.

Three-dimensional protein structures are organised into four levels (seeFigure 1.15), namely:

(a) Primary Polypeptide chain that is composed of amino acid linearsequences;

(b) Secondary Folding and coiling of polypeptide chain;(c) Tertiary Folding of -helix (shaped like telephone wire) polypeptide to

form packed globular protein molecules; and

(d) Quartenary The arrangement of more than one polypeptide chain to forma protein molecule.We can use structureor compositionto classify proteins. At a high temperature(40C), protein denaturalisation might happen. The structures of our body aremade from proteins. These also act as hormones and enzymes.


23/31


Figure 1.15: Four levels of protein structure

1.3.4 Nucleotides and Nucleic AcidWhat is nucleic acid? Nucleic acidis a complex molecule made of C, H, O, P andN. Two important nucleic acids are deoxyribonucleic acid(DNA) and ribonucleicacid (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 andnitrogenous base. There are four types of nucleotides in a DNA and RNA thymine is substituted by uracil (U):


24/31


(a) Adenine (A)} Purine-based group

(b) Guanine (G)(c) Thymine (T)

} Pyrimidine-basedgroup(d) Cytosine (C)

Figure 1.16: A unit of nucleotideSource:http://faculty.uca.eduBy now, you should be clear that DNA and RNA are composed of units ofnucleotides. How about their structures? Figure 1.17 shows a portion of the DNAstructure (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).


25/31


26/31


UCUUCCUCA } SerineUCGAGUAGC

Figure 1.19: The combination that forms SerineIn mRNA, there is also a type of codon or genetic codes, named stop codon. Itacts as the termination signal in protein synthesis. You will understand morewhen we move on to the next subtopic. In short, genetic code is present in tripletform and consists of three nucleotides.

1.3.5 Protein Synthesis

The function of protein synthesis is to generate protein as the end product. Itbegins with DNA which contains all the genetic materials. It means, DNAensures that protein-made components in our body are sufficient and availablewhen needed.

Protein synthesis takes place in the rRNA. mRNA is a template or copy of theDNA (DNA is the genetic material and protein synthesis can only be done frommRNA). tRNA (anticodon) is needed to transfer amino acids to each of thematching codons in the mRNA. The synthesis process will be terminatedautomatically when the stop anticodon has reached rRNA. Then, the synthesis ofthe desired protein is complete.

1. Based on your understanding, can we pair Adenine (A) withGuanine (G)? Give a valid reason.

2. State one genetic code for stop codon. You may get the answer fromreference books or Internet sources.

ACTIVITY 1.5


27/31


In summary, transcriptionoccurs in the nucleus and involves making a template(mRNA) for a particular DNA site. The goal of translationis to get the protein asan end product. It takes place in the cytoplasm and involves three main stages:

initiation, elongation and termination.

1.3.6 Enzyme

Thousands of intercellular (extracellular) and intracellular reactions might beaffected if there is no enzyme. So, what is enzyme?

Lets take a look at these three characteristics of enzyme. First, the basic functionof 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 asubstrate)to produce products. The third and most remarkable characteristic is thatenzymes 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 inlarge part to the unique set of some 3,000 enzymes that it is geneticallyprogrammed to produce. If even one enzyme is missing or defective, the result

can be disastrous.Examples of enzymes are lactase, diastase and sucrose.

Enzyme is a protein molecule that is a biological catalystwith threecharacteristics.

Which of the following can potentially appear in mRNA?

(i) ACUUCGGCUCUG

(ii) UGCUCAACGGUT

(iii) ACGUAGUCTUCU

(iv) AGCCGCCCGAAG

(v) ACUGGAUUGGGA

A. i, ii and iv D. ii and iiB. i, iv and v E. i, iii, iv and vC. ii, iii and iv

ACTIVITY 1.6


28/31


Figure 1.20 shows a typical enzymatic reaction. As you can see, enzyme facilitatessubstrates by changing the shape of its active site. The enzyme is larger than itssubstrate. 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

Chemical compositions of all living cells are similar. They are made up ofvarious elements and compounds.

Elements are made up of one kind of atom, while compounds are made oftwo or more different atoms combining with a covalent or an ionic bond.

Carbon dioxide and water are examples of inorganic compounds found inliving cells.

Lactase breaks down lactose, lipase breaks down fats and proteasebreaks down starch. What do you think the functions of the following

enzymes are?(a) Sucrase

(b) Cellulase

(c) Amylase

(d) Maltase

ACTIVITY 1.7


29/31


Carbon dioxide is produced by all living things when they respire. Plants alsotake in carbon dioxide to make food through photosynthesis.

Water is the most stable and the most abundant in living cells. It has severalunique physical and chemical characteristics.

Lipid is an organic matter composed of C, H and O and the ratio betweenoxygen and hydrogen atoms are 1:2.

Triglycerides, phospholipids and steroids are examples of lipid.

Triglycerides is an ester formed by a molecule of glycerol and threemolecules of fatty acid.

Phospholipids are very much like triglycerides but with one importantdifference. A phosphate functional group is substituted for one of the threefatty acids.

Steroids have a ring system of three cyclohexanes and one cyclopentane in afused ring system. Cholesterol is one example of steroid.

There are three main groups of carbohydrates: monosaccharide, disaccharideand polysaccharide.

Amino acid is the basic unit for protein. Protein is the main source for cellulardevelopment and repair in living organisms.

The basic unit for nucleic acid is called nucleotide. One unit of nucleotideconsists of pentose sugar, phosphate group and nitrogenous base.

The two types of nucleic acid are deoxyribonucleic acid (DNA) andribonucleic acid (RNA).

The four bases in DNA are adenine, thymine, cytosine and guanine, while thebases 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 upchemical reaction in our cells.


30/31


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)


31/31


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 SdnBhd.

Cooper, G. M. (2000). The cell: A molecular approach (2nd ed.). Sunderland:Sinauer Associates.

Diffen Contributers. (2013). Compounds vs. Elements. Retrieved fromhttp://www.diffen.com.

Elmhurst College. (2008). Elmhurst College. Retrieved fromhttp://www.elmhurst.edu.

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: PenerbitFajar Bakti Sdn Bhd.

Mountain Empire Community College. (n.d.). Carbon dioxide. Retrieved fromhttp://water.me.vccs.edu

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

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

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

topic 1 chemistry of life

Documents