CHAPTER 4: CHEMICAL COMPOSITION OF CELL

4.5 Enzymes

Enzymes are proteins which act as biological catalysts. They speed up biochemical reactions in the cell.

The substance whose reactivity is increased by an enzyme is known as substrate.

Example:

substrate —enzyme–> products

sucrose + water —sucrase–> glucose + fructose

Thousands of simultaneous biochemical reactions occur in living cells. Without enzymes, these biochemical reactions would be too slow to sustain life.

General characteristics of enzymes

1. Enzymes work very rapidly

• One molecule of enzyme can turn thousands or millions of substrate molecules into products per minute. For example, catalyse can transform approximately six million hydrogen peroxide molecules into oxygen and water molecules per minute.

2. Enzymes are not destroyed by the reactions which that catalyse

• Since enzymes are not altered by the reactions they catalysed, they can be used again. A smaill concentration of enzymes can bring about a large amount of biochemical reactions

3. Enzyme-catalysed reactions are reversible

•  lactose + water —lactase–> glucose + galactose
•  lactose + water <–lactase— glucose + galactose

• The enzyme which catalyses a reaction works in such a way that the reaction can proceed from left to right or from right to left, depending on circumstances. Note the two way arrows.

4. Enzymes are extremely specific

• Most enzymes are specific to one particular substrate molecule. Thus,  a given enzyme will catalyse only one reaction or one type of reaction. Maltase, for example, acts only on maltose.

5. Enzymes are denatured by high temperature

• An enzyme inactive at very low temperature. As temperature rises, its activity increases until the optimum temperature is reached. The optimum temperature is around 40′ C. Above the optimum temperature, the rate of reaction decline rapidly, ceasing altogether at about 60′ C. This is because enzymes are made of protein, so they are denatured at high temperature. When an enzyme becomes denatured, the bonds are broken and the polypeptide chains open up. The enzyme loses its normal shape and becomes inactive.

6. Enzymes are sensitive to pH

• Every enzymes has its own optimum pH in which it functions best. Small changes in the pH of the medium will denature the enzyme and render its activity. Alterations in the ionic charges of the acidic and basic groups of the enzyme change the shape of the enzyme.

Naming of enzymes based on the substrate

• An enzyme is named by attaching the suffix -ase to the name of the substrate on which it acts. For example, maltase acts on maltose, sucrase on sucrose and cellulase on cellulose.
• The ‘-ase‘ rule does not apply to enzymes discovered before the ‘-ase‘ idea was introduced. For example, pepsin rennin, ptyalin and trypsin.

Intracellular and extracellular enzymes

• Enzymes can be divided into two groups: intracellular and extracellular.
• Enzymes formed and retained in the cell are known as intracellular enzymes, and occur in the cytoplasm, organelles or the nucleus. Examples of intracellular enzyme are DNA polymerase, RNA polymerase and ATP synthetase.
• Extracellular enzymes are produced in the cell then packed and secreted from the cell, Extracellular enzymes caralyse their reactions outside the cell. Most digestive enzymes are extracellular enzymes. For example, amylase, cellulase and zymase.

Site of Enzyme Synthesis

• Since enzymes are made of proteins, they are synthesised by ribosomes.
• Intracellular enzymes are synthesised on ‘free’ ribosomes.
• Extracellular enzymes are synthesised on ribosomes attached to the endoplasmic reticulum.

Formation and secretion of extracellular enzymes:

1. The instruction for making the extracellular enzyme is transcribes from deoxyribonucleic acid (DNA) to ribonucleic acid (RNA) in the nucleus.
2. The RNA then leaves the nucleus through the nuclear pore and attaches itself to the ribosome located on the endoplasmic reticulum.
3. When the enzyme synthesis has completed, it is extruded into the interior of the endoplasmic reticulum.
4. The enzyme is then encapsulated in a transport vesicle.
5. The transport vesicle fuses with the Golgi apparatus, releasing the enzyme into the Golgi apparatus.
6. In the Golgi apparatus the enzyme is further modified before packing the enzyme in a secretory vesicle.
7. The secretory vesicle transports the enzyme to the plasma membrane.
8. The secretory vesicle membrane fuses with the plasma membrane and the enzyme is release outside the cell.

Mechanism of enzyme action

• Each enzyme molecule has a region with very precise shape called the active site.
• The substrate molecule fits into the active site of the enzyme like a key into a lock.
• Various types of bonds including hydrogen bonds and ionic bonds hold the substrate(s) in the active site to form a enzyme-substrate complex.
• The enzyme then changes the substrate(s) either by splitting it apart (for example, hydrolysis) or linking them together (for example, condensation)
• Once formed, the products no longer fit into the active site and escape into the surrounding medium, leaving the active site free to receive further substrate molecules.

enzyme+substrate —enzyme-substrate complex–> enzyme+product

• The explanation of enzyme action is known as the ‘lock and key hypothesis’, where the substrate is like a key whose shape is complementary to the enzyme or lock.
• The ‘lock and key’ hypothesis is able to explain why enzymes are specific and why any change in enzyme shape alters its effectiveness.

Factors afftecting enzymes

1. pH

• Most enzymes are effective in only a narrow pH range.

• The optimum pH is the particular pH at which the rate of reaction is the highest.

• Deviations from the optimum pH decrease the rate of reaction because bonds maintaining the tertiary shape of the enzyme are broken.

• The active site loses its shape and the enzyme-substrate complex can no longer be formed. The enzyme is denatured.

2. Temperature

• Initially an increase in temperature leads to an increase in the rate of reaction because the kinetic energy of the enzyme and substrate molecules produce more collisions, and therefore more enzyme-substrate complexes are formed.

• The rate of reaction will increase up to a maximum, known as the optimum temperature.

• After the optimum temperature, the rate of reaction falls quickly because the bonds maintaining the structure of the enzyme start to break and the active site loses its shape.

• The enzyme-substrate complexes can no longer form and the enzyme is denatured.

Substrate Concentration

• Initially an increase in substrate concentration increases the chance of enzyme-substrate collisions, and the rate of reaction increases.

• Eventually all the active sites are filled at any one time and the rate remains constant The reaction has reached its maximum rate, Vmax.

• Further addition of substrate will not increase the rate of reaction anymore because the constant enzyme concentration becomes the limiting factor.

4. Enzyme Concentration

• As the concentration of the enzyme increases there are more chances of enzyme-substrate collisions. The rate of reaction increases linearly as long as no other factors are limiting.

• As more active sites are available, more substrates can be converted to products.

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4.4 Lipids

Posted by 5 people in Chapter 4: Chemical Composition of the Cell on September 9, 2011

Lipids are a diverse group of substances that contain carbon, hydrogen and oxygen. The proportion of oxygen is lower than that in carbohydrates. For example, the general formula of stearic acid is C18H36O2.

All lipids are insoluble in water.

Lipids dissolve readily in other lipids and in organic solvents such as ether and ethanol.

The main types of lipids are:

• Fats
• Oils
• Waxes
• Phospholipids
• Steroids

Fats and Oils

Fats are solid at room temperature (20′ C), whereas oil are liquid.

Each molecule of fats or oils is made up of one glycerol combined with three fatty acids which may be the same or may be different. Three molecules of water are removed in this condensation reaction.

Click on the link below to watch a short explanation video of condensation of a lipid.

http://nutrition.jbpub.com/resources/animations.cfm?id=10&debug=0

If the process is inversed, the process is called hydrolysis.

These molecules of fats and oils are known as triglycerides.

Fats often contain only saturated fatty acids and oils usually contain unsaturated fatty acids

In a saturated fatty acid, the carbon atoms are bonded to the maximum number of other atoms. Saturated fatty acid has only single bond and the hydrocarbon chain is relatively straight.

Unsaturated fatty acids has double bonds in the form of -CH=CH- in the hydrocarbon chain. Fatty acids with one double bond are called monounsaturated fatty acid; those with two or more double bonds are called polyunsaturated fatty acids.

Fats and oils function efficiently as energy storage material. Fats and oils provide 38kJ per gram, while carbohydrates can provide only 17kJ per gram.

Waxes

Waxes are similar to triglycerides, but the fatty acids are bonded to long-chain alcohols rather than glycerol.

Waxes are usually hard solids at room temperature.

Waxes are used to waterproof the external surfaces of plants and animals. The cuticle of a leaf and the protective covering on an insect’s body are made of waxes.

Wax is also a constituent of the honeycomb of bees.

Phospholipids

Phospholipids have a similar structure to triglucerides but one of the fatty acids is replaced by a phosphate group.

The end of the phospholipid molecule containing the phosphate group is hydrophilic (water-loving). The other end containing the hydrocarbon chains of the fatty acids is hydrophobic (water-hating).

The hydrophilic end is soluble in water while the hydrophobic end is insoluble in water.

Phospholipid bilayers (double layers) form the basis of all cell membranes.

Steroids

A steroid molecule has a complex ring structure.

Steroids occur in plants and animals.

Examples of steroids are cholesterol, testosterone, oestrogen and progesterone.

• Cholesterol – Strengthens the cell membrane at high temperatures.
• Testosterone – Male reproductive hormone
• Oestrogen, progesterone – Female reproductive hormones

Saturated and Unsaturated Fats

Animal fats such as lard, butter and cream are examples of saturated fats

Vegetable oils such as olive oil, corn oil and sunflower oil are examples of unsaturated fats.

fats and oils, Lipids, Phospholipids, Saturated and Unsaturated Fats, Steroids, Waxes

4.3 Proteins

Posted by 5 people in Chapter 4: Chemical Composition of the Cell on September 8, 2011

About two-thirds of the total dry mass of a cell is composed of proteins.

Proteins contain carbon, hydrogen, oxygen and nitrogen. Sulphur is often present and sometimes phosphorus and other elements too.

Amino acids are the monomers of all proteins.

A dipeptide consists of 2 molecules of amino acids that are linked together by a peptide bond through condensation. Conversely, a dipeptide can be broken down into amino acids by means of hydrolysis.

Amino acid + amino acid —condensation–> dipeptide + water

Dipeptide + water —hydrolysis–> amino acid + amino acid

Long chains of amino acids are called polypeptides. A protein consists of one or more polypeptide chains twisted and folded in an appropriate way.

Protein Structures

1. Primary Structure

• The linear sequence of amino acids in a protein molecule. The first protein to have its sequence of amino acids determined was the hormone insulin.

2. Secondary Structure

• Peptide chain becomes folded or twisted forming a helix or pleated sheet. The structure is maintained by hydrogen bonding.

3. Tertiary Structure

• Bending and twisting of the polypeptide helix into a compact structure. Structure is maintained by ionic, disulphide and hydrogen bonding. Myoglobin, a protein found in muscles, has the tertiary structure. Enzymes, antibodies and many hormones have this structure as well.

4. Quaternary Structure

• Different polypeptide chains combine with associated non-protein groups forming a large complex protein molecule. Haemoglobin, an oxygen-binding protein, has a quaternary structure.

The peptide bond can be broken by hydrolysis with heat, dilute acids or by enzymes.

The loss of the three-dimensional structure of a protein molecule is known as denaturation. Denaturation can be caused by changes in temperature, pH and salt concentration.

Heating proteins usually denatures the protein irreversibly. For example, the transparent egg white irreversibly solidifies and becomes opaque on boiling.

Essential and non-essential amino acids

• In the digestive tract, protein is broken down into its amino acid subunits by hydrolysis.
• Humans can synthesise 11 of the 20 different amino acids used in protein synthesis. These 11 amino acids are known as non-essential amino acids.
• The remaining 9 amino acid cannot be synthesised in human. They must be included in the diet. They are known as essential amino acids.
• Examples of essential amino acids are lysine, valine, leucine and tryptophan.
• Examples of non-essential amino acids are proline, glycine and glutamic acid.

Amino acids, Essential and non-essential amino acids, Proteins, proteins structures

4.2 Carbohydrates

Posted by 5 people in Chapter 4: Chemical Composition of the Cell on September 8, 2011

1. The carbohydrates are made up of carbon, hydrogen and oxygen. The ratio of hydrogen to oxygen atoms in the molecules is usually 2 : 1.

2. Many carbohydrates have the general formula Cx (H2O)y, where x is approximately equal to y.

3. The three basic types of carbohydrates are monosaccharides, disacharides and polysaccharides.

Monosaccharides

1. Monosaccharides are also called simple sugars.
2. The common monosaccharides are six-carbon sugars with a molecular formula of C6H12O6.
3. Examples of monosaccharides are glucose, fructose (fruit sugar) and galactose.
4. Glucose is the most common monosaccharides and respiratory substrate.
5. Monosaccharides are sweet-tasting crystalline substances which are soluble in water.

Disacharides

1. Disacharides are formed from two monosaccharides molecules combining together with the elimination of a molecule of water. The chemical reaction of the formation is known as condensation.
2. The general formula of a disacharide is C12H22O11.
3. Disacharides are also called double sugars.
4. Disacharides can be broken down to their constituent monosaccharides by a chemical reaction involving the addition of water. The reaction is known as hydrolysis.
5. Like monosaccharides, they are sweet-tasting crystalline substances that are soluble in water.
6. The most common disacharides are maltose, lactose and sucrose.

Polysaccharides

1. Many monosaccharides molecules can be added by a series of condensation reactions to form a very large molecule (macromolecule).
2. Polysaccharides are polymers of monosaccharide monomers.
3. Polysaccharides have a general formula of (C6H10O5)n, where n is the number of monomers.
4. The large size of polysaccharides makes them more or less insoluble in water. They are not sweet and cannot be crystallised.
5. The common polysaccharides are starch, glycogen and cellulose.
6. The addition of iodine solution to a solution containing starch yields a blue-black colour.

Carbohydrates, Disaccharides, Monosaccharides, Polysaccharides

4.1 Chemical Composition of the Cell

Posted by 5 people in Chapter 4: Chemical Composition of the Cell on September 8, 2011

Chemical compounds in the cell can be divided into two major groups: Organic and Inorganic compounds

Organic compounds are chemical compounds that contain the element carbon. Organic compounds in the cell include carbohydrates, protein, lipids and nuclei acids. Some of these compounds are synthesised by the cell itself.

Water is an inorganic compound which is composed of hydrogen and oxygen. It is an important compound in the cell.

Percentage of Body Weight	Element	Usage
65%	Oxygen	This element is obviously the most important element in the human body. Oxygen atoms are present in water, which is the compound most common in the body, and other compounds that make up tissues. It is also found in the blood and lungs due to respiration.
18.6%	Carbon	Carbon is found in every organic molecule in the body, as well as the waste product of respiration (carbon dioxide). It is typically ingested in food that is eaten.
9.7%	Hydrogen	Hydrogen is found in all water molecules in the body as well as many other compounds making up the various tissues.
3.2%	Nitrogen	Nitrogen is very common in proteins and organic compounds. It is also present in the lungs due to its abundance in the atmosphere.
1.8%	Calcium	Calcium is a primary component of the skeletal system, including the teeth. It is also found in the nervous system, muscles, and the blood.
1.0%	Phosphorus	This element is common in the bones and teeth, as well as nucleic acids.
0.4%	Potassium	Potassium is found in the muscles, nerves, and certain tissues.
0.2%	Sodium	Sodium is excreted in sweat, but is also found in muscles and nerves.
0.2%	Chlorine	Chlorine is present in the skin and facilitates water absorption by the cells.
0.06%	Magnesium	Magnesium serves as a cofactor for various enzymes in the body.
0.04%	Sulfur	Sulfur is present in many amino acids and proteins.
0.007%	Iron	Iron is found mostly in the blood since it facilitates the transportation of oxygen.
0.0002%	Iodine	Iodine is found in certain hormones in the thyroid gland.

The Importance of Organic Compounds in the Cell

1. Carbohydrates

• Supply energy for cell processes
• A means of storing energy
• Give structural support to cell walls

2. Lipids

• Store large amounts of energy over long periods of time
• Act as an energy source
• Play a major role in the structure of the cell membranes
• Act as a source of metabolic water
• Reduce the loss of water by evaporation

3. Proteins

• Act as building blocks of many structural components of the cell ; required for growth
• Form enzymes which catalyse chemical reactions
• Form hormones which control growth and metabolism

4. Nucleic acids

• Contain the genetic information of cells
• Play a vital role in protein synthesis

The importance of water in the cell

• Water is important for life because its chemical and physical properties allow it to sustain life.
• Water is a polar molecule which consists of 2 hydrogen atoms and 1 oxygen atom. A polar molecule is a molecule with an unequal distribution of charges. Each molecule has a positively charged and a negatively charged end. Polar molecules attract one another as well as ions. Because of this property, water is considered the solvent of life.
• It is the transport medium in the blood
• It acts as a medium for biochemical reactions.
• Water helps in the maintenance of a stable internal environment within a living organism. The concentration of water and inorganic salts that dissolve in water is important in maintaining the osmotic balance between the blood and interstitial fluid.
• It helps in lubrication.
• Water molecules have very high cohesion. Water molecules tend to stick to each other and move in long unbroken columns through the vascular tissues in plants.

Chemical Composition of the cell, inorganic compounds, organic compounds

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Elements in the Cell

Posted by 5 people in Chapter 4: Chemical Composition of the Cell on September 8, 2011

Elements in the cell

1. Elements are the basic units of matter.
2. Out of the 92 stable elements found on the Earth, only 25 are found in living things.
3. Elements known to be of universal importance to living things include hydrogen (H), oxygen (O), carbon (C), nitrogen (N), calcium (Ca), phosphorus (P), potassium (K), sulphur (S), chlorine (Cl), sodium (Na), magnesium (Mg) and iron (Fe).

Major constituents

• Hydrogen – Component of water and organic molecules
• Carbon – Backbone of organic molecules
• Nitrogen – Component of proteins and nucleic acids
• Oxygen – Required for cellular respiration

Trace elements

• Sodium – Important in functioning of nerves
• Magnesium – Constituent of chlorophyll
• Phosphorus – Constituent of nucleic acids and of bones and teeth
• Sulphur – Component of certain proteins and vitamins
• Chlorine – Principal anion in fluids outside the cell
• Potassium – Important in functioning of nerves
• Calcium – Cofactor of enzymes, triggers muscle contraction and component of bones, teeth and plant cell walls

Ultratrace element

• Iron – Cofactor of many enzymes and constituent of haemoglobin

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CHAPTER 3: MOVEMENT OF SUBSTANCES ACROSS PLASMA MEMBRANE

1. Uniqueness of Plasma Membrane (also known as cell membrane):

PLASMA MEMBRANE

• it is a semi-permeable cell membrane
• it allows water and certain substances to move in and out of the cell.

2. Importance of Plasma Membrane:

• - cells obtain nutrients and gases
• cells excrete metabolic wastes
• cells can maintain pH for enzyme activity
• cells can maintain ionic concentration of the cells for enzyme activity
• control the types and the amount of substances
• allow useful substance (hormones/enzymes) to secrete from cells
• protect cells
• a boundary between the inside and outside of cell.

3. Structure of the basic unit of plasma membrane

• Phospholipid molecule:
  ‘Head’ – hydrophilic: a polar phosphate molecule (philic~loves water / attracted to water)
  ‘Tail’ – hydrophobic: two non-polar fatty acids (phobic~hates water / repelled to water)
• Formation:
  Hydrophilic heads pointing outwards
  Hydrophobic tails pointing inwards
  (Bilayer phospolipid)

Fluid Mosaic Model (Protein embedded in the bilayer)

Carrier protein

• carrier for some molecules (glucose, amino acids, proteins and nucleic acids)
• controls the movement of ions and particles (Na⁺, Ca²⁺ and K⁺)
• Glycoprotein

Glycolipid

• combination of lipids and polysaccharides

4. Permeability

Permeable (allow to pass through)

• small non-polar molecules (vitamins A, D, E, K, fatty acids, glycerol and steroids)

Impermeable (not allow to pass through but with help of carrier protein and cellular energy, it is allow to pass through)

• large polar molecules (glucose, amino acids, mucleic acids and polysaccharides)
• charged ions (H⁺, Na⁺, K⁺, Cl^- and Ca²⁺)

Substances that are allowed to move in the cell:

• CO₂
• O₂
• excess H₂O
• waste: nitrogenous

Substances that are allowed to move out of the cell:

• CO₂
• O₂
• amino acids
• ionic salts
• glucose

Materials must be able to move through the plasma membrane in order for the cell cytoplasma to interact with the external environment. Therefore, the movement of soluble substances can occur in several mechanisms:

• A. Process of Passive Transport
• B. Process of Active Transport

A. Passive Transport

i) Simple Diffusion

• not selective: lipid-soluble molecules, gases and water.
• not control by cell.
• movement of the molecules from a region of higher concentration to a region of lower concentration.
• Factors affecting the rate of diffusion are temperature, size of molecules/ions, diffusion gradient, surface area and diffusion medium.
• example: diffusion of oxygen and carbon dioxide at the alveolus.

ii) Osmosis:

• only water molecules.
• not control by cell.
• movement of water from a region of higher concentration to one of lower concentration and often occurs across a semipermeable membrane.
• strong sucrose solution = less water molecule = low water potential.
• weak sucrose solution = more water molecule = high water potential.
• example: absorption of water by root hairs.

iii) Facilitated Diffusion:

• very specific: glucose, nucleic aicds, amino acids, protein and mineral ions.
• control by cell.
• transport of molecules (only certain molecules) across the outer membrane of living cell by a process of carrier protein (hydrophilic group) / channel protein (Ions: Na⁺, Ca²⁺, K⁺) within the cell membrane.
• normally take place from a region with higher concentration of molecules to a region of lower concentration.
• example: absorption of digested food in the villus.

B. Process of Active Transport

• very specific: minerals ions and amino acids.
• control by cell.
• This process needs carrier proteins and energy (due to against concentration gradient) from a region of lower concentration to a region of higher concentration).
• Cell must expend energy that derived from ATP (adenosine triphosphate)
• example: human nerve cells (sodium ions are constantly transport out of the cell) / ions intake by root hairs of a plant.

PASSIVE AND ACTIVE TRANSPORT

Type of Solution

1. Hypotonic
2. Isotonic
3. Hypertonic

1) Hypotonic

• Solute concentration in the external solution is lesser than solute concentration inside the cell.
• Water concentration outside the cell is higher than the water concentration inside the cell.

2) Isotonic

• Solute concentration in the external solution is equal to the solute concentration inside the cell.
• Water concentration inside and outside of the cell is the same.

3) Hypertonic

• Solute concentration in the external solution is greater than solute concentration inside the cell.
• Water concentration outside the cell is lower than the water concentration inside the cell.

Types of solutions:

ANIMAL CELL IN HYPO, ISO AND HYPERTONIC SOLUTION

Type of Solution	Hypotonic	Isotonic	Hypertonic
Animal Cell	The cell inflates due to the water molecules enter the cell. Eventually it bursts(thin plama membrane). Example: red blood cell in distilled water.	No change in the size of cell. Net movement of water is zero. Example: red blood cell in 0.85% sucrose solution.	The cell shrinks and becomes soft anddehydrated due to the water molecule leave the cell. Example: red blood cell in 5% sodium chloride solution.
Plant Cell	The cell expands and becomes firm / turgid due to the water molecules enter the cell. The rigidcellulose cell wall expands slightly and prevents cell from bursting. Example: strip of potato in distilled water.	No change in the size of cell. Net movement of water is zero. Example: strip of potato in 5% sucrose solution.	The cell becomes flaccid(plasmolysis occurs), vacuole and cytoplasmashrink due to the water molecules leave the cell. Example: strip of potato in 30% sucrose solution.

PLANT CELL IN HYPO, ISO AND HYPERTONIC SOLUTION

Application

1. Food is soaked in a concentrated salt solution to prevent bacteria and fungus to survive.
2. Chemical fertiliser (dissolved ions) increases solute concentration (decrease water molecules) in soil. Therefore, water leaves from the cell sap of the plant which result the plant wither.

IKAN MASIN

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