STPM BIOLOGY Basic Chemistry of A Cell

Basic chemistry of a cell Properties of water – – –

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Life on Earth began in water and evolved there for 3 billion years before spreading onto land. Modern life, even terrestrial life, remains tied to water. All living organisms require water more than any other substance. Human beings for example, can survive for quite for a few weeks without food, but only a week or so without water.

Water is deceptively simple. It is shaped something like a wide V, with its two hydrogen atoms joined to the oxygen atom by single covalent bond. Because oxygen is more electronegative than hydrogen, the electrons of the covalent bonds spend more time closer to oxygen than to hydrogen; in other words, they are polar covalent bonds. The uneven distribution of electrons of water molecules makes it an universal solvent.

In overall, water has four emergent properties: Cohesion 1. Water molecules stay close each other as a result of hydrogen bonding. 2. Although the arrangement of molecules in a sample of liquid water is constantly changing, at any given moment many of the molecules are linked by multiple hydrogen bonds. 3. These linkages make water more structured than most other liquid. 4. Collectively, the hydrogen bonds hold the substance together, a phenomenon called cohesion. 5. Cohesion means the hydrogen bonding between the water molecules that can form a continuous water column against the gravity without breaking. 6. Besides cohesion, water molecules can also perform adhesion between water molecules and cell walls by hydrogen bonds. 7. Both cohesion and adhesion are important in the transport of water in plants.

8. Related to cohesion is surface tension, a measure of how difficult it is to stretch or break the surface of a liquid. 9. At interface of water and air is an ordered arrangement of water molecules, hydrogen-bonded to one another and to the water below. 10. This makes the water behave as though coated with an invisible film. 11. You can observe the surface tension of water by slightly overfilling a drinking glass; the water will stand above the rim. 12. In a more biological example, some animals can stand, walk or run on water without breaking the surface.

Moderation of temperature 1. The ability of water to stabilize temperature stems from its relatively high specific heat capacity. 2. The specific heat capacity of water is 4200 JoC-1kg-1 which means 4200 J of heat energy is required to raise the temperature of 1 kg of water by 1oC . 3. Therefore, water acts as a thermal buffer. 4. The heat of vaporization of water is also high. The high amount of energy required to vaporize water has a wide range of effects. 5. On a global scale, for example, it helps moderate Earth’s climate. 6. On organismal level, water plays an important role in homeostasis. 7. Water acts like a cooling agent. When body temperature deviates from normal range, sweat is produced to cool the body down. The heat energy produced by body can be eliminated by the evaporation of water (sweat) from the surface of skin. Insulation of bodies of water by floating ice 1. Water is one of the few substances that are less dense as a solid than as a liquid. In other word, ice floats in liquid water. 2. At 4oC, the density of water is the greatest. Below this point, water begins to expand and cause the density of water to become lower. 3. A layer of ice on the surface of seas, lakes and ponds during winter prevents the whole volume of water to freeze. Thus, the aquatic organisms can still survive from the insulation of the floating ice.

The solvent of life 1. Water is a versatile solvent which can dissolve many solutes. 2. Therefore, water is a good medium for most of the biochemical reactions. 3. Water can act as a lubricant. Mucus, synovial fluid, pericardial fluid are the examples of lubricants composed mainly of water. 4. Water is a good medium for transport and removal of substances and wastes. 5. Some animals also depend on water to support their body and for locomotion by the hydrostatic skeleton. 6. Water is a dispersal agents for seeds of land plants such as coconut trees and also aid the fertilization of some plants such as Marchantia sp.. Carbohydrates – –

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Carbohydrate composes of carbon, hydrogen and oxygen in the ratio of 1:2:1. The basic formula for carbohydrate is CX(H2O)Y where x and y are constant variables. In cell, carbohydrate is the main source of energy, food storage compounds and structural components. Carbohydrates can be divided into three main clasees: 1. Monosaccharide 2. Disaccharide 3. Polysaccharide

Monosaccharides Trioses

Pentose

Glyceraldehyde

ribose

Dihydroxyacetone

ribulose

Hexose

Aldoses

Glucose

Ketoses

Fructose

Galactose

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Monosaccharides generally have molecular formulas that are some multiple of unit CH2O. Glucose, the most common monosaccharide, is the central of importance in the chemistry of life. The molecule has a carbonyl group and multiple hydroxyl groups. Depending on the location of carbonyl group, a sugar is either an aldose or a ketose. Glucose, for example is an aldose; fructose, a structural isomer of glucose, is a ketose. Generally, monosaccharide have the following properties: 1. Taste sweet 2. Polar 3. Dissolve easily in water 4. Form white crystal readily 5. Reducing sugar For glucose, there are two isomers called alpha-glucose and beta-glucose.

The only difference is the position of hydroxyl group in carbon atom one. Beta-glucose is mainly found in cellulose while alpha-glucose is the main repeating units of starch and glycogen.

Linear and ring forms

Disaccharides – – –

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Disaccharide is made up of two monomers by mean of condensation reaction. The two monomers are joined by a glycosidic linkage, a covalent bond formed between two monomers. The two molecules of monomers which are bound by a glycosidic bond in disaccharide are called residues.

There are three common disaccharides: 1. Maltose(malt sugar) -- glucose + glucose (bound by 1,4 glycosidic bond) 2. Sucrose(intermediate product in photosynthesis) – glucose + fructose (bound by 1,2 glycosidic bond) 3. Lactose(milk sugar) – glucose + galactose (bound by 1,4 glycosidic bond) All the disaccharides reducing sugar except for sucrose.

Condensation reaction in the synthesis of maltose

Condensation reaction in the synthesis of sucrose

Polysaccharide –

Polysaccharides are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages,

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Some polysaccharides serve as storage material, hydrolysed as needed to provide sugar for cells. Other polysaccharides serve as building materials for structures that protect the cell or the whole organism. Polysaccharides is suitable to be storage material because: 1. It is highly branched and thus saves space. 2. It contains a lot of energy-rich bonds. 3. It is osmotically inactive which does not affect the water potential of cell.

Storage polysaccharide – – – – –

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Both plants and animals store sugars for later use in the form of storage polysaccharides. Plants store starch, a polymer of glucose monomers, as granules within cellular structures known as plastids, which include chloroplast. Synthesizing starch enables the plants to stockpile surplus glucose. The sugar can later be withdrawn from this carbohydrate “bank” by hydrolysis. Most of the glucose monomers in starch are joind by 1, 4 glycosidic linkage. The angle of these bonds makes the polymer helical. There are two types of starch: amylose and amylopectin. Amylopectin has more branched as compared to amylose.

Animals store a polysaccharide called glycogen, a polymer of glucose that is like amylopectin but more extensively branched. This fuel cannot sustain an animal for long because glycogen stores are depleted in about a day unless they are replenished by consumption of food.

Structural polysaccharides – – – – – –

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Organisms build strong materials from structural polysaccharides. For example, the polysaccharide called cellulose is a major component of the tough walls that enclose plant cells. Like starch, cellulose is a polymer of glucose, but the glycosidic linkages in these two polymers differ. Instead of using alpha-glucose, cellulose is made up of beta-glucose, making every other glucose monomer upside down with respect to its neighbours. The differing glycosidic linkages in starch and cellulose give the two molecules distinct three-dimensional shapes. Cellulose is never branched and some hydroxyl groups on its glucose monomers are free to hydrogen-bond with the hydroxyls of other cellulose molecules lying parallel to it. In plant cell walls, parallel cellulose molecules held together in this way are grouped into units called microfibrils. These cable-like microfibrils are a strong building material for plants.

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Other compounds closely related to polysaccharides: 1. Chitin is a structural polysaccharide. It is found in some fungi for the replacement of cellulose. It is also an essential part of the exoskeleton particularly for arthropods. 2. Murein (peptidoglycan) is a polysaccharide which is found in the capsule of some coated bacteria.

Lipids –

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Lipids are the one class of large biological molecules that does not include true polymers, and they are generally not big enough to be considered macromolecules. Unlike glucose, its oxygen to hydrogen ratio is much smaller. Lipids are hydrophobic organic compounds that are insoluble in water but can dissolve in organic solvents. The most biologically important types of lipids: triglycerides, phospholipids and steroids.

Triglycerides – –

Triglyceride is an ester formed from the condensation reaction of one molecule of glycerol and three molecules of fatty acids. The process is known as esterification. During esterification, the glycerol donates H from its hydroxyl group and the fatty acid donates OH from its carboxyl group to form water.

Fatty acids – – –

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Fatty acids can be divided into saturated fatty acids and unsaturated fatty acids. Saturated fatty acids contain the maximum number of H atoms and do not have any double bond. Unsaturated fatty acids contain at least one double bond. It is called “unsaturated” because the fatty acid can be still inserted some more H atoms to make it saturated. Triglyceride formed from saturated fatty acids is normally solid at room temperature due to its compact shape and it is called fat. Triglyceride formed from unsaturated fatty acids is liquid at room temperature due to the kinks caused by double bond and prevent triglyceride to form compact shape. It is called oil. Oil can be converted to fat by the process of hydrogenation.

Phospholipids – –

Cells could not exist without another type of lipid – phospholipids. Phospholipids are essential for cells because they make up cell membranes.

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Phospholipids contain one glycerol and two molecules of fatty acid and a phosphate group. Additional small molecules, which are usually charged or polar, for example choline, can be linked to the phosphate group to form a variety of phospholipids. Lecithin is the common phospholipid which forms the cell membrane.

The two ends of phospholipids show different behaviour toward water. The hyrocarbon tails are hydrophobic and are excluded from water while the phosphate groups and its attachments form a hydrophilic head that has an affinity for water. When phospholipids are added to water, a micelle is formed where all the hydrophobic tails point to a point. If phospholipids is in excess, a phospholipid bilayer is formed that shield their hydrophobic portions from water.

Steroids –

Many hormones, as well as cholesterol are steroids which are lipid characterized by a carbon skeleton consisting of four fused rings.

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Different steroids vary in the chemical groups attached to this ensemble of rings. Cholesterol is a common component of animal cell membranes and is also the precursor from which other steroids are synthesized. In vertebrates, cholesterol is synthesized in the liver, Many sex hormones are steroids produced from cholesterol.

oestrogen

testosterone

progesterone

Proteins – –

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Nearly every dynamic function of a living being depends on proteins. Some proteins speed up chemical reactions, while others play a role in structural support, storage, transport, cellular communication, movement and defense against foreign substances. Proteins may be composed of one or more polypeptide chains. Each polypeptide chain is a polymer consisting of many basic units of amino acids linked together, by peptide bonds, through condensation reactions.

Amino acids –

All amino acids share a common structure. The only different is the variable R groups which determine the types of amino acids.

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There are about 20 types of amino acids. Amino acids are organic molecules possessing both carboxyl and amino groups. When dissolve in water, amino acids dissociate to form zwitterions, carrying a positive charge on the amino part and negative charge on the carboxyl group. Thus, amino acids show bipolar property. This amphoteric property allows amino acids to function as a pH buffer to maintain the pH level in blood. Amino acids can be grouped into essential and non-essential. The essential amino acids are the amino acids which cannot be synthesized by our body and is needed to obtain from the daily diet. The non-essential amino acids are the amino acids which can be synthesized by our body. The task is completed by liver by mean of transamination.

Polymerization of amino acids –

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When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, they can become joined by a dehydration reaction, with the removal of a water molecule. The resulting covalent bond is called a peptide bond. Repeated over and over, this process yields a polypeptide, a polymer of many amino acids linked by peptide bonds. The polypeptide chain may coil and fold into a particular structure as a result of hydrogen bonds, disulphide bonds, Van de Waal’s forces or hydrophobic interaction and ionic bonds.

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These bonds determine the behavior of proteins and thus give rise to four separate levels of structure.

Protein structure and function –

There are four levels of protein structures: primary, secondary, tertiary and quaternary.

Primary structure of protein – –

Primary structure of a protein is its unique sequence of amino acids in a linear polypeptide chain. The sequence of amino acids in a linear polypeptide chain is determined genetically by DNA.

Secondary structure of protein – –

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Secondary structure of a protein is the coiling and folding of a polypeptide chain that contribute to the protein’s overall shape. One such secondary structure is alpha-helix, a delicate coil held together by hydrogen bonding between every fourth amino acids. The other main type of secondary structure is the beta-pleated sheet, a folded sheet held together by hydrogen bonding between two or more regions of a pair of parallel polypeptides chain lying side by side. Example: keratin, fibroin and silk.

Tertiary structure of protein – – – –

Superimposed on the patterns of secondary structure is a protein’s tertiary structure. Tertiary structure of protein is three dimensional, compact and globular. The structure is maintained by the interaction of hydrogen bonds, disulphide bonds, ionic bonds and hydrophobic interaction. Example: hormones, enzymes, antibodies and plasma proteins.

Quaternary structure of protein – –

Quaternary structure is the overall protein structure that results from the aggregation of several tertiary structures of proteins. Example: haemoglobin, collagen.

Classification of proteins Structurally, proteins can be classified into three groups: – – – – – – – – –

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1. Fibrous proteins Examples: collagen, keratin, fibrin and myosin Have secondary structure Insoluble in water Helical structures or pleated sheets held together by hydrogen bond A stable protein structure 1. Globular proteins Examples: globulin, enzymes, antibody and hormone Have tertiary structures Tightly coiled and folded to form sphere Structure maintained by various bonds Easily soluble in water 1. Intermediate proteins Example: fibrinogen Basically a fibrous protein but soluble in water

If classified according to their composition, proteins are placed into two groups. – –

Simple proteins are considered pure proteins which do not contain any other substances except amino acids. Conjugated protein is considered complex compound which contains protein part and a non-protein component known as prosthetic group.

Properties of proteins Colloid formation – –

Globular proteins are soluble but being macromolecules, they do not dissolve completely in water but form a colloidal solution. The electrical charges found on the bonding of the proteins prevent them from settling down and thus, they remain suspended in water.

Denaturation of proteins –

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Denaturation of proteins involves the loss of their specific three-dimensional shape and is usually irreversible. This is caused by the breaking of the bonds which hold the shape of the proteins. Heat is the main factor that contributes to the denaturation of proteins. Other than that, there are several factors which may denature proteins: 1. Strong acids and alkalis 2. Organic solvents and detergents 3. Heavy metals 4. Radiation

Nucleic acids – –

The amino acid sequence of a polypeptide is programmed by a unit of inheritance known as gene. Genes consists of DNA, a polymer belonging to the class of compounds known as nucleic acids.

Roles of nucleic acids –

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The two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), enable living organisms to reproduce their complex components from one generation to the next. DNA is the genetic material that organisms inherit from their parents. Each chromosome contains a long DNA molecule, usually carrying several hundred or more genes. RNA is the intermediate between DNA and proteins which involves in the synthesis of proteins from the codes in DNA.

Structure of nucleic acids –

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Nucleic acids are macromolecules that exist as polymers called polynucleotide. As indicated by the name, each polynucleotide consists of monomers called nucleotides. A nucleotide itself composed of three parts: a phosphate group, a nitrogenous base and a five-carbon sugar (pentose). The portion of this unit without the phosphate group is called a nucleoside.

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The only difference between DNA and RNA is the loss of one oxygen atom on the pentose sugar.

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There are five types of bases present in the nucleotide. Three are single ringed called the pyrimidine and two are double-ringed called purine.

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The nitrogenous bases found in DNA are adenine, guanine, cytosine and thymine. In RNA, the nitrogenous bases are adenine, guanine, cytosine and uracil instead of thymine. Adenine is always paired with cytosine in DNA and uracil in RNA. On the other hand, cytosine is always paired with guanine in both DNA and RNA. The phosphate group is derived from the phosphoric acid and it gives the acidic property to nucleic acid.

Deoxyribonucleic acid (DNA) –

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Each DNA molecule is a double-stranded polynucleotide held antiparallel to each other by hydrogen bonds between the nitrogenous bases on both strands. One strand runs from 5’ end to 3’ end direction and the other strand runs from 3’ end to 5’ end. The bonding between one nucleotide and the other in a strand is called the phosphodiester bond. The backbone of DNA is made up of phosphate groups and pentose sugars. 5’ end and 3’ end mean that the fifth carbon and third carbon of the pentose sugar.

From X-ray diffraction, it is found that the diameter of DNA helix is 2nm. The distance between base pairs is 0.34nm and a complete turn of the DNA consists of 10 base pairs with a distance of 3.4nm.

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The number of hydrogen bonds formed between adenine with thymine or uracil and cytosine and guanine are two and three respectively.

Ribonucleic acid (RNA) – – – –

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RNA molecule is a single strand of polynucleotide chain which is much shorter than DNA. There are three types of RNA: messenger RNA (mRNA), transfer RNA (tRNA) and ribosomal RNA (rRNA). Messenger RNA is a linear single strand polynucleotide. It is found during protein synthesis. It consists of a nucleotide sequence transcribed from triplet codes of the DNA in the nucleues. Ribosomal RNA is synthesized in nucleolus. It is one of the structural components of ribosome. Transfer RNA is a folded polynucleotide strand. It helps in the protein synthesis. DNA

RNA

Definition

A nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms

RNA, single-stranded chain of alternating phosphate and ribose units with the bases adenine, guanine, cytosine, and uracil bonded to the ribose. RNA molecules are involved in protein synthesis and sometimes in the transmission of genetic information.

Bases and sugars

DNA is a long polymer with a deoxyribose and phosphate backbone and four different bases: adenine, guanine, cytosine and thymine

RNA is a polymer with a ribose and phosphate backbone and four different bases: adenine, guanine, cytosine, and uracil

Differences

1.Found in nucleus 2. sugar is deoxyribose 3. Bases are A,T,C,G

1.Found in nucleus and cytoplasm 2.sugar is ribose. 3. Bases are A,U,C,G

Location

Nucleus and cytoplasm

Nucleus

Length

Shorter

Longer

Diversity

Three types of RNA: tRNA, Only one type of DNA mRNA and rRNA

Role

Medium of long-term storage and transmission of genetic information

Transfer the genetic code need for the creation of proteins from the nucleus to the ribosome. This prevents DNA having to leave nucleus.