C4 Composition

transcript

Chapter 4Chemical Composition of the Cell

4.1 Chemical composition of the cell

4.2 Carbohydrates-loq-ferissa

4.3 Lipids-aishah-foto

4.4 Proteins-mariah-gigi kilat

4.5 Enzymes-kecil-reena-tak datang adlina

4.6 Nucleic Acids-2 tangan-zabreeee

4.7 Water-minah-idzmir

4.1Chemical composition of the cell

- Elements & chemical compounds

- Importance of Organic compounds, Inorganic compounds (water)

Element = a substance that composed of

only 1 type of atom

Most common elements found in living cells 96%

Other elements in cells

Trace elements

< 0.01%

C - Carbon

H - Hydrogen

O - Oxygen

N - Nitrogen

S – Sulphur

K – Potassium*

Na – Sodium*

Cl – Chlorine*

Mg – Magnesium*

Ca – Calcium*

P - Phosphorus

Fe – Ferum / Iron*

Cu – Copper

I – Iodine

Zn - Zinc

* Mineral ions - Exist as ions in the cell

25 essential elements which are important to living organisms

Chemical compounds= consist of >1 types of atoms

• Common elements combined with each other to form various chemical compounds in the cell.

• Divided into:– organic compounds & inorganic compounds.

Chemical compounds

Inorganic compound

Organic compounds

Carbohydrates

C, H, O

Lipids

C, H, O

Nucleic Acids

C, H, O, N, P

Proteins

C, H, O, N, (S)

Contain carbon

Does not contain carbon

Obtained from external environment

Synthesized by living cells

Handouts

1. Function of elements in animal cell and plant cell

2. Importance of chemical compounds in the cell

Importance of water

1. Universal solvent2. Medium for biochemical reactions3. As transport medium4. Maintain body temperature5. Provide support6. Maintain osmotic pressure & turgidity7. High surface tension & cohesion8. Provide moisture & lubrication

Organic compounds

• Carbohydrate

• Lipid

• Nucleic acid

• Protein – Enzyme

Monomer

• Monomer = small molecules that build a polymer.= cannot be broken down into smaller units.

• Examples of monomer:Monosaccharide, amino acid, glycerol, fatty acid

• Process of condensation to produce polymer is known as polymerization.

Polymer

• Consists of repeating units of monomers joined together by chemical bonds

through condensation / polymerisation.

Class Monomer Dimer Polymer

Nucleic acids Nucleotide - Polynucleotide

Carbohydrates Monosaccharide Disaccharide Polysaccharide

Proteins Amino acid Dipeptide Polypeptide

Fat / Oil / Lipids

Fatty acid, Glycerol

- Triglyceride / Fats / Lipids

Carbohydrate

4.2 Carbohydrates

- Elements in carbohydrates

- Types of carbohydrates:

Monosaccharides, Disaccharides, Polysaccharides

- Formation and Breakdown of Disaccharides and Polysaccharides

Carbohydrates

• Elements: C : H : O

• Ratio: 1 : 2 : 1

• Empirical formula: (CH2O)n , n≥3

Carbon Water

4 types of Carbohydrates

1. Monosaccharide

one sugar

2. Disaccharide

two sugar

3. Oligosaccharide

3-7 sugar

4. Polysaccharide

multiple sugar

Class of carbohydrates

Examples Characteristics Importance /Functions

Monosaccharide

(also known as simple sugars)

GlucoseFructose

Galactose

• Soluble in water• Tastes sweet

• All are reducing sugar(able to reduce Cu II

sulphate into Cu I oxide)

• Instant source of energy• Building block (as monomers) of

carbohydrates

Disaccharide

(also known as complex sugars)

MaltoseLactoseSucrose

• Soluble in water• Tastes sweet

• All are reducing sugarexcept sucrose

• No specific function• As intermediate

substances in digestion of carbohydrates

Oligosaccharide

GlycoproteinGlycolipid

• Found on the plasma membrane of the cell

• As a marker for cell recognition &

cell communication

Polysaccharide

Starch

Glycogen

Cellulose

• Insoluble in water• Not sweet-tasting

• All are non-reducing sugar

• Food (Energy) storage in plant cell

• Food (Energy) storage in animal cell

• Structural component in the plant cell wall

Monosaccharides

Examples: Glucose, Fructose, Galactose

Characteristics:

• Soluble in water•Tastes sweet•All are reducing sugar

(able to reduce Cu II sulphate into Cu I oxide)

Monosaccharide

Importance:

•Instant source of energy•Building block (as monomers) of carbohydrates

Test for Reducing Sugar

1. Glucose solution

For solid food sample - add distilled water- crushed using mortar & pestle

2. Benedict’s

solution

3. Heat in water bath

Blue Brick red precipitate

Copper (II) sulphate Copper (I) oxide

Cu 2+ Cu + + e-

from glucose

DISACCHARIDES

Examples of disaccharides:

• Glucose + Glucose Maltose + Water

• Glucose + Galactose Lactose + Water

• Glucose + Fructose Sucrose + Water

• Disaccharides are formed through a process called condensation where one water molecule is produced / expelled.

Monomer

+ Dimer

Condensation

Hydrolysis

Monosaccharide

+Disaccharides

Condensation

HydrolysisMonosaccharide

+ Water

2 units of sugar

WORD EQUATION

2 units of monomer

CARBOHYDRATES

Test for Non-Reducing Sugar

1. Sucrose solution

4. Benedict’s

solution

5. Heat in water bath

Blue Brick red precipitate

Copper (II) sulphate Copper (I) oxide

Cu 2+ Cu +

2. HCl

Sucrose Glucose + Fructose

3. Sodium bicarbonate

To neutralise the excess acid + e-

from glucose &fructose

Sucrose

Glycosidic linkage

D-glucose D-Fructose

Linkages depending on how the –OH group on the anomeric carbon is oriented.

Glycosidic linkage

POLYSACCHARIDES

• Storage polysaccharides

= Starch, Glycogen.

• Structural polysaccharides

= Cellulose, Chitin.

Polyccharides

Starch

Glycogen

Cellulose

Lipids

4.3 Lipids

• Elements in lipids• Types of lipids• Components of Fats and Oils• Formation and Breakdown of Triglyceride• Saturated Fat and Unsaturated Fat

Lipids

• Elements: C : H : O

- no fixed ratio

Unsaturated fat - Double bond between C=C

Saturated fat - Single bond between C-C

Types of LipidsLipid Function

Fats & Oils Energy storage, insulation, protection

Wax A waterproof layer on the cuticle of leaves

Phospholipid Main component of plasma membrane

Steroid

1. Cholesterol

2. Hormone

Make plasma membrane more rigid

Controls secondary sex characteristics

Glycerol + Triglyceride

Condensation

Hydrolysis

3 Fatty acid + 3 Water

Examples of Lipids

Structure of Lipids

1. Textbook pg 68Figure 4.8

– Condensation and hydrolysis of triglycerides

2. Textbook pg 69Figure 4.9

- Saturated & unsaturated fatty acids

Fats & Oils

• Saturated fat contains saturated fatty acids condensed with glycerol.

• Saturated fatty acid

= fatty acid with single bond between carbon atoms

• Unsaturated fat contains unsaturated fatty acids condensed with glycerol.

• Unsaturated fatty acid

= fatty acid ≥ 1 double bonds between carbon atoms.

Nucleic acid

Monomer of DNA = Nucleotide

DNA – Deoxyribose

RNA - Ribose

DNA – A, T, G, C

RNA – A, U, G, C

DNA = Deoxyribonucleic acid

• Monomer = Nucleotide• Polymer =Polynucleotide

• Nitrogen bases:Adenine

Thymine

Guanine

Cytosine

Uracil

DNA = Deoxyribonucleic acid RNA = Ribonucleic acid

Double stranded polynucleotide Single stranded polynucleotide

Nucleotide consists of: Deoxyribose + Phosphate group + Nitrogenous base.

Nucleotide consists of:

Ribose + Phosphate group + Nitrogenous base.

Found in nucleus, mitochondrion, chloroplast

Found in nucleus, cytoplasm, ribosome

Function:

1. Store genetic information of an organism

Function:

1. Copies information carried by DNA for the use of protein synthesis.

2. Genetic material in some viruses.

1 type of DNA 3 types of RNA

2 types of Nucleic Acids

Polymer = Polynucleotide

Sugar is joined to phosphate group forming the backbone of the polynucleotide molecule.

Pairing of bases is specific.

Double helix DNA is like a twisted ladder.Sugar-phosphate backbone makes the sides of the ladder.

Base pairs are held by hydrogen bonds makes the steps of the ladder.

1. mRNA = messenger RNA

2. rRNA = ribosomal RNA

3. tRNA = transport RNA

3 types of RNA- involved in Protein Synthesis

Protein synthesisstage 1 – Transcription: genetic codes of DNA are copied into mRNA

stage 2 – Translation: tRNA amino acids

Translation of mRNA into Amino acids by tRNA

3 bases = 1 genetic code

= 1 codon

codes for 1 amino acid

•mRNA bind to ribosome.

•Ribosome can read the genetic codes on mRNA.

•tRNA transport suitable amino acids

Proteins

4.4 Proteins

• Elements, Structure

• Formation & Breakdown of Dipeptides

• Amino acids: Essential, Non-Essential

Proteins

• Elements: C, H, O, N, S

• Monomer = Amino acid

• Polymer = Polypeptide = Protein (linear, 2D)

Amino acid

R = (CH3)n = Methyl group

Carboxylic group

- acidic

Amino group

- basic

Monomer Monomer+Dimer

Condensation

Hydrolysis

Dipeptide

Condensation

Hydrolysis

+ Water

2 units of amino acids

WORD EQUATION

2 units of monomer

PROTEINS

Amino acid

Formation of Dipeptide

• Amino acids are joined together by

peptide bond through condensation process.

Word equation: Amino acid + Amino acid Dipeptide + Water

Structural equation:

Peptide bond

Refer: Textbook pg66 • 20 types of amino acids required by human

Types of Amino acids

Essential amino acids

Non-essential amino acids (11)

Must be obtained from food / diet.

Not necessary to be obtained from diet.

Reason: Can be derived from other amino acids.

Cannot be synthesized by the body / cell.

Can be synthesized by the body / cell.

Examples:

Leucine, Isoleucine, Lysine

Examples:

Alanine, Asparagine, Aspartic acid

4 Levels of the Structures

of Proteins

Draw in Notebook Textbook pg 66Figure 4.7

Structure of Protein1. Primary structure = Linear structure

2. Secondary structure:a) Coiled structure = Alpha-helix

α - helixb) Folded structure = Beta-pleated sheets

β – pleated sheets

3. Tertiary structure = 3 Dimensional shape - 1 polypeptide chain folded or coiled into 3D shape - example: Hormone, enzyme, antibodies.

4. Quarternary structure- ≥2 tertiary chains joined together- example: Haemoglobin

Tertiary structure

• 1 polypeptide coiled & folded

into 3-dimensional structure

with specific function.

• Examples:

Enzyme, antibodies, plasma protein

Enzymes

4.5 Enzymes• Definition, Naming, Characteristics, Roles

• Synthesis of enzymes : – Intracellular & Extracellular Enzymes

• Mechanism of Enzyme Reaction: – Lock-and-Key Hypothesis

• Factors that affect the Activity of Enzymes

• Uses of Enzymes in Industry

Definition of Enzyme

Enzyme = Biocatalyst

= Protein produced by living cells which can

speed up biochemical reactions.

Naming of enzymes

• Most enzymes have a name derived by adding the suffix –ase at the end of the name of their substrates.

Substrate Enzyme

Lactose Lactase

Sucrose Sucrase

Maltose Maltase

Lipid Lipase

2. Enzymes lower the activation energy needed by the biochemical reactions to occur,

thus speed up biochemical reactions.

Characteristics of Enzymes

3. Remained unchanged at the end of the reactions, thus can be reused.

4. Small amount of enzymes can catalyzed large amount of substrates. Reason: (3)

Mechanism of enzyme reaction

Lock-and-Key Hypothesis

5. Highly specific – each enzyme can catalyze 1 type of reaction or 1 type of substrate. Reason: Specific active site of enzyme only binds to specific substrate.

6. Most reactions catalyzed by enzymes are reversible (forward & backward).

6. Many enzymes require cofactor (helper molecule) to function.

7. Enzyme activities can be slowed down or stopped by inhibitors (heavy metals like mercury Hg, lead Pb).

• Enzyme has a 3-D shape which is highly-specific.

• Polypeptide chains folded to form a pocket called active site.

• Active site has a distinctive shape and charges that complement to its substrate.

Lock-and-Key Hypothesis

E + S ES E + P

Enzyme + Substrate Enzyme + ProductEnzyme-Substrate complex

• The way an enzyme binds to its substrate can be explained by the “lock-and-key” hypothesis.

• Lock represents enzyme; Key represents substrate.

1. A specific substrate molecule arrives at the active site of the enzyme molecule.

2. Substrate molecule binds to the active site to form an enzyme-substrate complex, like a key fits into a lock. E-S complex is unstable.

3. - Enzyme catalyses the substrate to form products.- Products leave the active site of enzyme.- Enzyme is free to bind to another substrate and catalyze another reaction (can be reused).

Biochemical Reactions in living cell / organism

• Metabolism = all biochemical reactions occurring in living cells.

• Most of these biochemical reactions are catalyzed by enzymes.

• Metabolism includes:1. Anabolism

= Synthesis of large complex molecules from smaller, simpler molecules Requires / Absorbs energy

2. Catabolism= Breakdown of large complex molecules into smaller, simpler molecules Release energy

Intracellular Enzyme Extracellular Enzyme= Enzymes which are

produced & retained in the cell for the use of the cell

itself.

= Enzymes which are produced in the cell but secreted from the cell to

function externally.

These enzymes are found in:

Cytoplasm, nucleus, mitochondrion, chloroplast

These enzymes are found:

Outside the cell

(tissue fluid, blood)

Example:

Oxidoreductase catalyses biological oxidation &

reduction in the mitochondrion.

Example:

Digestive enzymes secreted by pancreas but not used by

pancreas cells.

These enzymes are transported to duodenum which is the actual site of

enzymatic reaction.

Synthesis of Enzymes

• Intracellular enzyme

• Extracellular enzyme

1. mRNA = messenger RNA

2. rRNA = ribosomal RNA

3. tRNA = transport RNA

3 types of RNA- involved in Protein Synthesis

Protein synthesisstage 1 – Transcription: genetic codes of DNA are copied into mRNA

stage 2 – Translation: tRNA amino acids

Translation of mRNA into Amino acids by tRNA

3 bases = 1 genetic code

= 1 codon

codes for 1 amino acid

•mRNA bind to ribosome.

•Ribosome can read the genetic codes on mRNA.

•tRNA transport suitable amino acids

Factors that affect activity of enzymes

1. Temperature2. pH3. Concentration of substrate4. Concentration of enzyme

* Refer handouts Essay

1. Temperature

• Optimum temperature = temperature at which an enzyme catalyses a reaction at the maximum rate.

• Most human enzymes have an optimum temperature at around 37oC.

• Most plants enzymes have an optimum temperature at around 25oC.

Textbook Pg 73 – Figure 4.12

• At low temperature, enzymes are inactive and reaction takes place slowly.

• Rate of reaction doubles with every 10oC.

• Rate of reaction increases proportional to the temperature increase until the optimum temperature.

• Rate of reaction is the highest at the optimum temperature.

Denaturation

• Textbook pg73 – Figure 4.12

• Beyond the optimum temperature (>37 oC), increase in temperature will no longer increase the rate of reaction.

• At 40 oC, rate of reaction decreases due to denaturation of enzymes.

• At 60 oC, rate of reaction = 0 (stop)

Reason: All enzymes are denatured.

At high temperature:

1. Chemical bonds that hold enzyme together begin to break.

2. 3D shape of enzymes are altered.

3. Active sites are destroyed.

4. Substrates can no longer fit in the active site.

5. Enzymes are denatured Irreversible

• As a result, rate of reaction = 0

2. pH• Optimum pH

= pH at which the rate of reaction is at the maximum.

• Optimum pH for most enzymes ranges between pH 6-8.

• Effect of pH on enzymes are normally reversible.

Trypsin

Rate of reaction

Change of pH can:

1. Alter the charges on the active sites.2. Reduce the ability of enzyme & substrate

to bind with each other.

• As a result, rate of reaction decreases

• When pH reverts to optimum, charges on active sites are restored, enzyme can resume its normal function = Reversible

3. Enzyme concentration

4. Substrate concentration

Uses of EnzymesZymase Convert sugar to ethanol in beer / wine-making industry

Protease Tenderizes the meat in food processing industryRemove the skin of fishin detergent / washing powder – remove stain by breaking down proteins

Amylase Break down starch to sugar in syrup makingin detergent / washing powder - remove starch which is used as stiffener of fabrics.

Lipase Ripening of cheese (dairy products)

Rennin Solidify milk proteins in making dairy products

Trypsin Remove hair from animal hides in leather- making

Cellulase Breakdown cellulose of seed coat from cereal grainsBreakdown cell wall to extract agar from seaweed

C4 Composition

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