Chapter 1

Learning outcomes:• State the elements in the cell• List the chemical compounds in the cell• Explain the importance of organic

compounds in the cell• Explain the importance of water in the cell.

UNDERSTANDING THE CHEMICAL COMPOSITION OF THE CELL

UNDERSTANDING THE CHEMICAL COMPOSITION OF THE CELL

ELEMENT IN THE CELL

• All living and non living things are made of substances called element

• The four most common elements (96%) 1) Carbon (C)2) Oxygen (O)3) Hydrogen (H)4) Nitrogen (N)

• Chief element (4%) Calcium (Ca) Potassium (K) Phosphorus (P) Sulphur (S) Chlorine (Cl) Magnesium (Mg)

• Trace element (0.01%) Copper (Cu)Iodin (I)Iron (Fe)

Is substances composed of only one kind of atom which cannot be broken into simpler substance by chemical reaction.

Element Functions

Animal cells Plant cells

Hydrogen,carbon,oxygen,nitrogen

Synthesis of organic compound, for example, protein,lipids and nucleic acids

Sulphur Component of some proteins

Sodium •regulates osmotic in cells•helps in transmission of nerve impuls

•not required

Magnesium •Involved in protein synthesis.•As a cofactors for some enzymes

•required for the synthesis of chlorophyll•activate enzymes in cells

Ferum •involved in the synthesis of red blood cells and synthesis of respiratory enzymes

•synthesis of chlorophyll•act as an electron carrier during photosythesis and respiration

Calcium •required for formation of strong bones and teeth•Helps in contraction of muscle cells•Promotes blood clotting

•Synthesis of cell walls(cellulose)•Helps maintain the semi-permeable plasma membranes.

Phosphorus •Formation of bones and teeth.•Helps in the contraction of muscle sells•Synthesis of ATP •An essential component of nucleic acids(DNA/RNA)

•Promotes cell division•Synthesis of ATP and nucleic acids•Induces the formation of flowers and seeds

Pottassium •Required in muscle contractions and transmission of nerve impulses

•Synthesis of carbohydrates•Activates certain enzymes

Chlorine •Synthesis of HCl by gastric glands in the stomach which destroys pathogens and maintains pH of the stomach

•Photolysis of water during light reaction in photosynthesis

THE IMPORTANCE OF CHEMICAL COMPOUND

COMPOUNDS IMPORTANCE

Carbohydrates •A primary source of energy in cells•Starch is the main energy store of carbohydrates in plant cells•Glycogen is the main energy store of carbohydrates in animal cells•Cellulose forms the main constituent of the cell wall



Protein •The basic unit of proteins are amino acid•Function : build new cells for growth and repair damaged tissues•Required in the synthesis of enzyme, antibody and hormone•Form structural components such as keratin in skin, collagen in bones and skin and myosin in muscle fibres•Important components of the plasma membrane•Involved in the synthesis of haemoglobin in red blood cells



Lipids

Examples :

Fat, oil, waxes, phospholipids and steroid

15% of protoplasm is made up of lipids

•Fats and oils are important source of energy•The layer of adipose tissue underneath the skin insulates the bodies of animal against low temperature •Act as a solvent for fat soluble vitamins such as Vitamin A, D, E , K•Phospholipids form a major constituent of the plasma membrane•Wax prevent water loss in plants and infection by pathogens



Nucleic acids• nucleotide is a building block of nucleic acids• 2 type of nucleic acids :

i) deoxyribonucleic acids (DNA)

ii) ribonucleic acids (RNA)

•Store genetic information •Consists of a nitrogenous base, a pentose sugar and a phosphate group•DNA – double stranded polynucleotide, twisted around each other to form double helix. Found in nucleus, chloroplast and mitochondria•RNA – found in cytoplasm, ribosome and nucleus, copies information carried by DNA for use in protein synthesis, a single stranded of polynucleotide

Phosphate group

Pentose sugar

Nitrogenous base

DNA Structure

DNA consists of two molecules that are arranged into a ladder-like structure called a Double Helix.

A molecule of DNA is made up of millions of tiny subunits called Nucleotides.

Each nucleotide consists of:1. Phosphate group2. Pentose sugar3. Nitrogenous base

Nucleotides

Phosphate

PentoseSugar

NitrogenousBase

Nucleotides

The phosphate and sugar form the backbone of the DNA molecule, whereas the bases form the “rungs”.

There are four types of nitrogenous bases.

Nucleotides

A

Adenine

T

Thymine

G

Guanine

C

Cytosine

Nucleotides

Each base will only bond with one other specific base.

Adenine (A)Thymine (T)

• Cytosine (C)Guanine (G)

Form a base pair.

Form a base pair.

DNA Structure

Because of this complementary base pairing, the order of the bases in one strand determines the order of the bases in the other strand.

DNA Structure

To crack the genetic code found in DNA we need to look at the sequence of bases.

The bases are arranged in triplets called codons.

A G G - C T C - A A G - T C C - T A G

T C C - G A G - T T C - A G G - A T C

DNA Structure

A gene is a section of DNA that codes for a protein.

Each unique gene has a unique sequence of bases.

This unique sequence of bases will code for the production of a unique protein.

It is these proteins and combination of proteins that give us a unique phenotype.

Protein

DNA

Gene

Trait

Your Task

Draw a flow chart to show how to get from:

The important of

in the cell

Medium of biochemical reactions

Universal solvent

Transport medium

Maintaining body temperature

Support

Maintaining osmotic balance andturgidity

Lubrication

High surface andcohesion

The importance of water

Solvent • Water is the universal solvent of many biological

molecules because the properties of its molecules

Maintaining osmotic balance and turgidity • It helps in maintaining the osmotic balance

between the blood and interstitial fluid• In plants, it helps the cells to be turgid,

turgidity provides support in plants


Moisture • Water provides moisture to respiratory

surface• This enables respiratory gasses to

dissolve

Lubrication

• Mucus (composed mostly of water)assits the movement of food substances in the intestinal tract

• Synovial fluid lubricates the joint


Maintaining body temperature• It helps to keep a relatively constant body

temperature for optimum enzymatic activities

Medium for biochemical reaction

• Water act as a medium for biochemical reaction


Transport medium• It is an agent for transport medium in blood,

lymphatic, excretory and digestive systems• It helps to remove waste products

CARBOHYDRATES

Diagram A

Diagram C

Diagram B

Glucose + Glucose Maltose + Water

Glucose + Fructose Sucrose + Water

Glucose + Galactose Lactose + Water

Two monosaccharides joined together through condensation

Condensation Reaction

Condensation

Condensation

Condensation

Each of the condensation reactions involves the removal of one water molecule

Maltose + Water Glucose + Glucose

Sucrose + Water Glucose + Fructose

Lactose + Water Glucose + Galactose

Hydrolysis Reaction

Hydrolysis

Hydrolysis

Hydrolysis

Disaccharides can be broken down to their constituent monosaccharides through hydrolysis

Hydrolysis is a chemical reaction that involves the breaking up of large molecules

by adding water to them

Sugar Observation Inference

Glucose A brick-red precipitate is formed

Glucose is reducing sugar

Sucrose (without dilute hydrochloric acid)

The colour of the Benedict’s solution remains unchanged

Sucrose is non-reducing sugar

Sucrose (boiled with dilute hydrochloric acid)

A brick-red precipitate is formed

A positive result with Benedict’s solution can only be obtained if the sucrose solution is first boiled with dilute hydrochloric acid

Differentiating between REDUCING and NON-REDUCING

SUGAR

PROTEINS

• Basic units of proteins – amino acids

• Long chains of amino acids – polypeptides

• Function :-– Build new cells for growth– Renew damaged tissues– Required in the synthesis of enzymes,

antibodies, hormones, haemoglobin– Form keratin (skin), collagen (bones), myosin

(muscle tissues)– Components of the plasma membrane

A very short polypeptide chain

Amino acids

Peptides bond

TYPES OF PROTEIN STRUCTURE

TYPES OF PROTEIN STRUCTURE

PRIMARY STRUCTURE

TERTIARY STRUCTURE

QUARTERNARY STRUCTURE

SECONDARY STRUCTURE

• linear sequence of amino acids in a polypeptides chain

• the polypeptides chain that is

coiled to form

• an alpha helix (a-helix) chain or

• folded into beta pleated (B-pleated)

• hold together by hydrogen bonds

• the helix chains or the beta pleated sheets are coiled or folded into three dimensional shape of a polypeptide chain

• enzymes, hormones, plasma proteins, antibodies

• 2 or more tertiary structure polypeptide chains are arrange to form a functional and complex protein molecule

• Haemoglobin (4 polypeptide chains)

PROTEIN STRUCTURE

LIPIDS

* Complex organic

compound

* Cholesterol

* Sex hormones

(testosterone,

oestrogen, progesteron

e)

Structure of triglycerides

• Triglycerides is an ester

• Formed through 1 molecule of glycerol and 3 molecules of fatty acids

• Fatty acids are either saturated or unsaturated

• Fats and oils

Unsaturated Fats• The fatty acids in unsaturated fats have at least one double bonds between the carbon atoms

Saturated Fats• The fatty acids do not have any double bonds between the carbon atoms Saturated

fats

Saturated fats

Saturated fats

Saturated Fats

Unsaturated Fats

•Solids at room temperature (butter)

• Raises the levels of LDL (bad cholesterol) in the blood

• Lower the levels of HDL (good cholesterol) in the blood

• Liquid at room temperature (corn oils)

• Lower the levels of LDL (bad cholesterol) in the blood

• Increases the levels of HDL (good cholesterol) in the blood

Learning Objectives• State what enzymes are• Explain why enzymes are needed in life processes• List the general characteristics of enzymes• Relate the name of enzyme to substrate• State sites where enzymes are synthesized• State the meaning of intracellular enzymes and extracellular enzymes• Explain the involvement of specific organelles in the production of

extracellular enzymes• Explain the effects of pH, temperature, enzyme concentration and substrate

concentration• Explain the mechanism of enzyme action• Relate the mechanism of enzyme action with pH, temperature, enzyme

concentration and substrate concentration• Explain the uses of enzymes in daily life and industry using examples

What is enzyme?

Have you seen these products?

http://www.southernlion.com.my/en/product/biozip_powder.html

http://www.southernlion.com.my/en/product/biozip_powder.html

What is enzyme?

Enzyme is biological catalyst that regulate cellular

reactions and speed up biochemical reaction

What is biochemical reaction?

• Biochemical reaction is called metabolism

• Biochemical reactions occur in a cell simultaneously at all times

• Metabolic reaction :

Reaction

Substrate Product

Type of metabolic reaction

Anabolism Catabolism

Build complex molecules Example : photosynthesis

Breakdown complex moleculesExample : digestion

Naming of enzyme

• According to the name of the substrate it catalyses

• Adding the suffix …ase at the end of the name of their substrates

• Example

Substrate Enzyme

Lactose Lactase

Sucrose Sucrase

Lipid Lipase

Example :

Sucrose + water glucose + fructoseSucrase

Substrate

Enzyme

Products

Pepsin Trypsin Rennin

Enzymes that were named before a systematic way of naming enzymes

was formulated

The general characteristics of enzyme

• All enzymes are protein • Enzymes speed up biochemical

reactions• Enzymes are not changed or destroyed

by the reactions • Enzymes are highly specific (can only

catalyse specific substrate only, have specific site)

• Enzymes are needed in small quantities

• Most of metabolic reaction by enzyme are reversible

• Enzyme activities can be slowed or completely stopped by inhibitor

• Enzymes require helper molecules called cofactor (inorganic or organic)

Temperature Temperature

Enzyme concentration


Substrate concentrationSubstrate

concentration

pHpH

Factor affecting enzyme activity

Factor affecting enzyme activity

Temperature

• Temperature low, enzyme reaction slow• Temperature increase, more collisions

between enzyme and substrate molecules, the reaction is accelerated

• Every 10°C rise in temperature, the rate of reaction is doubled

• up to the optimum temperature, the enzyme reaction at maximum rate

• Beyond the optimum temperature, enzyme is denatured

Temperature

pH

• Different enzymes, different optimum pH

• pH changes, protein (enzyme) conformation changes, the charge at active site is altered

• The ability to bind is reduced

• Optimum pH : the reaction at maximum rate

pH

Substrate concentration

• Substrate concentration is high, the reaction is high

• More substrate are available to bind active site of enzyme

• The reaction is rise to maximum rate until not enough enzyme supply

• Thus, the enzyme becomes a limiting factor

• To increase the reaction is increase the concentration of enzyme

Substrate concentration


• Enzyme concentration is high, the reaction is high

• More enzyme molecules are available• The reaction will increase till a

maximum rate is reached• After maximum rate, the concentration

of substrate become a limiting factor• The rate of reaction will increase if

there is more substrates supply


The sites of enzyme synthesis

• Ribosomes is the site of enzyme synthesis

• The information is carried by DNA

• The different sequences of bases in DNA are codes to make different protein

Types of enzymes

• Synthesised and retained in the cell for the use of the cell itself • Found in the cytoplasm, nucleus, mitochondria and chloroplast• Example : oxidoreductase catalyses

Synthesised in the cell but secreted

from the cell to work externally

Intracellular enzymes Extracellular enzymes

Production of extracellular enzymes

Mitochondria

Secretory vesicle

Transport vesicle

Ribosome

Nucleus

Rough endoplasmic reticulum

Golgi apparatus

Where are the location of enzyme production?

Protein synthesis in

ribosome

Transport vesicle

Rough ER

Golgi apparatus

Plasma membrane

Secretory vesicle

Production of extracellular enzymes

Protein are synthesised in the ribosomes

Protein are transported through the space between rough ER

Protein depart from rough ER and wrapped in vesicle

The vesicle fuse with the membrane with Golgi apparatus and empty their content

into membranous of Golgi apparatus

The protein are further modified during their transport in Golgi apparatus

The protein then will wrapped with secretory vesicle

The secretory vesicles bud off from Golgi apparatus and travel to the plasma membrane

The vesicles fuse with plasma membrane before releasing the protein outside the cell as enzyme

The mechanism of enzyme


Enzyme Enzyme-substrate

complexEnzyme Products Substrate + +

‘LOCK AND KEY’ HYPOTHESIS

Substrate molecule represents the ‘key’Enzyme molecule represents the ‘lock’

A specific substrate arrives at active site of enzyme molecule

The substrate molecule binds to the active site to form an enzyme-substrate complex

The enzyme catalyses the substrate to form products, which then leaves the active site

The enzyme molecule is now free to bind more substrate molecules


The Uses of Enzymes in Daily life and Industry

• Enzyme technology: the use of enzymes in industrial processes

• It can be isolated from cells and function outside the cell.

• It can be obtained from plants and animals mostly from bacteria and fungi in large quantities

Baking industry

Baking industry

Dairy product Dairy product

Fish & meat industry

Fish & meat industry

Medical analysis

Medical analysis

Processing food

Processing food

Paper industryPaper industry

Leather tanning industry

Leather tanning industry

Textile industryTextile industry

Biological detergent

Biological detergent

Brewing industry

Brewing industry

The uses ofenzymes

The uses ofenzymes

87

UsesType of Industry Enzymes used

Protease

Cellulase

Amylase

Tenderises meat

Removes the skin of fish

Softening vegetables

Extracts agar jelly fromseaweed

Removal of seed coatsfrom cereal grains

Production of sweets,beverages and chocolates

Foodprocessingindustry

88


Foodprocessingindustry

Detergents

Rennin

Lactase

Protease

Solidifies milk proteins

Hydrolyses lactose to makeice-cream

Dissolve protein stains inclothes

89


Amylase

Pancreatictrypsin

Microbialtrypsin

Trypsin

Removes starch that isused as stiffeners fromfabrics

Treats inflammation

Dissolves blood clots

Removal of hair from animalhides

Textile industry

Medicalindustry

Leatherproducts

Education

Chapter 1