SPM Biology 4 Chemical Composition of the Cell Part 5 Organic Compounds in the Cell - Nucleic Acids

1. Macromolecules containing carbon, hydrogen, oxygen, nitrogen, and phosphorus.

2. The building blocks (monomers) of nucleic acids are called nucleotides.

3. Each nucleotide consists of three parts:

• A 5-carbon sugar or pentose
• A phosphate group
• A nitrogenous base

Structure of nucleotide

4. 2 types of pentose sugars

• ribose
• deoxyribose

5. Nitrogenous base

• adenine (A)
• guanine (G)
• cytosine (C)
• thymine (T)
• uracil (U)

6. Importance: store & transmit hereditary (genetic) information.

7. There are 2 types of nucleic acids:

• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)

Deoxyribonucleic acid (DNA)

1. DNA contains deoxyribose sugar. 

2. Nitrogenous base groups for DNA - A, T, G, C

3. Consists of 2 polynucleotide strands twisted around each other in the form of a double helix.

4. DNA is found in the nucleus, mitochondrion & chloroplast.

5. Importance: carries the genetic code; to store genetic information

Ribonucleic acid (RNA)

1. RNA contains ribose sugar.

2. Nitrogenous bas groups for RNA - A, U, G, C

3. Consists of single-stranded polynucleotide chain, shorter than DNA.

4. RNA is found in nucleus & cytoplasm.

5. 3 types of RNA:

• messenger RNA (mRNA)
• ribosomal RNA (rRNA)
• transfer RNA (tRNA)

6. Importance: involve in protein synthesis

RNA and DNA structures

Formation of chromosomes

Formation of chromosomes

STPM Biology Biological Molecules Part 20 Osmotic, Turgor, Wall Pressure and Water Potential

Osmotic Pressure

• When a solution is separated from pure water by semi-permeable membrane, there will be net water moving across into the solution.
• The minimum pressure that has to be exerted by the solution to prevent water from moving in is called the osmotic pressure of the solution.

Osmotic pressure examples

Turgor Pressure

• Turgor pressure = the pressure of cytoplasm exerted against the walls of a turgid cell.
• This pressure is counteracted by the wall pressure.

Wall Pressure (Ψ p)

• Wall pressure = the pressure of the cell wall exerted against the cytoplasm of the plant cell.
• The wall pressure is also known as pressure potential (Ψ p) for plant cells.
• Pressure potential usually has a positive value.

The relationship between turgor pressure and wall pressure

Water Potential (Ψ)

• Water potential = the potential of water to move out of a solution by osmosis.
• The water potential of a cell is the potential of water to move out of a cell through osmosis.
• Symbol = (Ψ) ; Unit = kPa (kiloPascal; 1kPa = 1000Pa) or MPa (MegaPascal), 1MPa = 100,000Pa)
• Pure water has the highest water potential. The water potential of pure water is 0 kPa at atmosphere pressure (101325 kPa).
• The water potential of a plant cell (Ψ) = solute potential (Ψ s) + pressure potential (Ψ p)

The water movement from a dilute to a concentrated solution

Solute Potential (Ψ s)

• Solute potential = the potential of a solution to take in water by osmosis due to the presence of solute materials.
• Solute potential is also known as osmotic potential.

Water Potential for Solution (Ψ sol)

• (Ψ sol) = the potential of water to move out of a solution by osmosis.
• The water potential of a solution is negative in value.
• This is because water potential for pure water is 0 kPa and pure water has the highest water potential.
• Solution with larger negative water potential value have low water potential.
• For example, cell A with water potential of -0.5 kPa has higher water potential than cell B with water potential value of -0.9 kPa.  Thus, water will flow from A to B.

The movement of water through different types of solution

STPM Biology Biological Molecules Part 19 Mineral Ions and Vitamins

• Mineral ions and vitamins are generally needed in minute amounts. 
• Lack of them in diet can lead to a variety of disorders.
• The importance of mineral ions and vitamins are shown in the tables below.

Mineral ions

Vitamins

SPM Biology 4 Chemical Composition of the Cell Part 4 Organic Compounds in the Cell - Lipids

1. Contain carbon, hydrogen, oxygen.

2. Proportion of oxygen is lower than in carbohydrates. For example: stearic acid C₁₈H₃₆O₂.

3. Insoluble in water (non-polar molecule), but dissolve in other lipids and non-polar solvents (ether, ethanol, etc.).

4. Four main types of lipids:

• Fats and oils (triglycerides)
• Waxes
• Phospholipids
• Steroids

5. Importance:

• Store large amount of energy
• Sources of energy
• A major part of the structure of cell membranes

Fats and Oils (triglycerides)

Fats and oils

1. Fats are solid at room temperature (20ºC).

2. Oils are liquid.

3. Triglyceride is formed from a condensation reaction between 1 molecule of glycerol and 3 molecules of fatty acids. The bonds formed are called ester bonds.

Formation of triglyceride

4. Fats often contain only saturated fatty acid (single bond).

5. Oils usually contain unsaturated fatty acid (double bond).

Diagrammatic representation of fats

Structure of saturated and unsaturated fats

6. Importance of fats and oil:

• Function as energy reserve & storage materials. They provide 38kJ per gram, while carbohydrates provide only 17kJ per gram.
• Fats act as an insulator against the loss of heat. 

7. Types of fats

Similarities and differences of saturated fat and unsaturated fat

Waxes

1. Similar to triglycerides.

2. Produced by both plants & animals.

3. Usually hard solids at room temperature.

Waxes

4. Importance of waxes:

• Used to waterproof the external surfaces of plants & animals. E.g: cuticle of leaf, protective covering on an insect’s body.
• Also a constituent of the honeycomb of bees.

Phospholipids

• Major component of plasma membranes
• Made up of 1 glycerol, 2 fatty acid and 1 phosphate

See SPM Biology 3 Movement of Substances Across the Plasma Membrane Part 1 Structure of Plasma Membrane

Steroids

1. Complex ring structure. Do not contain fatty acids.

2. Occur in plants and animals.

3. Examples: 

Steroids

STPM Biology Biological Molecules Part 18 Nucleic Acids - DNA and RNA

DNA - the hereditary material of life

Structure

1. A DNA molecule consists of 2 polynucleotide chains coiled to form a double helix. 
2. The 2 chains are held together by hydrogen bonds between complementary bases. (T and A are complementary bases; while G and C are another complementary bases).
3. Each complete turn of the double helix is 3.4nm long and contains 10 pairs of bases.
4. The diameter of each helix is 1.0nm.
5. The polynucleotide chains of DNA molecule are anti-parallel (the 5'end of one chain lies next to the 3' end of the other chain).
   
6. the polynucleotide chain is made up of deoxyribonucleotides that are linked together by phosphodiester bonds.

Structure of DNA molecule

Complementary base pairing

1. Due to its structure, only purine bases can pair with pyrimidine bases.
2. Adenine (A, a purine) pairs with thymine (T, a pyrimidine) with 2 hydrogen bonds.
3. Guanine (G, a purine) pairs with cytosine (C, a pyrimidine) with 3 hydrogen bonds.

Complementary base pairing

RNA

1. RNA is a polynucleotide. The monomer of RNA is ribonucleotide.

2. RNA molecule consists of one polynucleotide chain.

3. There are three types of RNA in cells:

• ribosomal RNA (rRNA)
• messenger RNA (mRNA)
• transfer RNA (tRNA)

Ribosomal RNA (rRNA)

1. More than 80% of RNA in the cell is rRNA.

2. rRNA is found in ribosome. A ribosome is constructed from rRNA (50%) and protein (50%).

3. Functions of rRNA:

• Main component of ribosome.
• Bind mRNA molecule to ribosome during protein synthesis.

Messenger RNA (mRNA)

1. The longest RNA molecules which contains 70 to 3,000 nucleotides.

2. mRNA molecules are long uncoiled molecules.

3. Function of mRNA:

• Carry genetic information from gene into the cytoplasm for protein synthesis.

Transfer RNA (tRNA)

1. The shortest RNA molecules.

2. tRNA makes up about 10% to 15% of RNA in cells.

3. The polynucleotide chain is folded to form a 'clover-leaf'.

4. The anticodon of tRNA contains 3 bases which are complementary to the codon for the amino acid it carries.

5. Function of tRNA:

• Transfer a specific amino acid to ribosome for polypeptide synthesis.

rRNA, mRNA, tRNA

Differences between RNA and DNA

SPM Biology 4 Chemical Composition of the Cell Part 3 Organic Compounds in the Cell - Proteins

Food that contain protein

1. Consists of carbon, hydrogen, oxygen and nitrogen.

2. Sometime Sulphur and phosphorus may be present in some protein.

3. All proteins are made up of subunits called amino acids.

4. Each amino acid carries 2 functional groups:

• carboxyl group (-COOH)
• amino group (-NH₂)

Amino acids basic structures

5. Human need 20 types of amino acids to synthesize proteins.

6. 2 amino acids can combine to form a dipeptide by condensation reaction.

condensation reaction

7. Long chains of amino acids are called polypeptides.

8. Proteins act as enzymes, hormones, antibodies, etc.

9. Changes in pH, temperature and salt concentration can cause proteins to lose their shapes and functions. This process is known as denaturation.

10. Importance:

• as building blocks of many structural components of the cell.
• form enzymes, hormones and antibodies.

Types of amino acids

The 20 amino acids needed by humans can be divided into 2 groups:

(a) Essential amino acids (11)

• cannot be synthesized by human body.
• for examples: leucine, lysine, histidine.

(b) Non-essential amino acids (9)

• can be synthesized by human body.
• for examples: alanine, glutamine, glycine.

Protein structures

There are 4 different structures of protein:

SPM Biology 4 Chemical Composition of the Cell Part 2 Organic Compounds in the Cell - Carbohydrates

Organic compounds - chemical compounds that contain carbon (C) elements.

Monomers - building blocks for polymers

Polymers - materials made of long, repeating chains of molecules.

Organic Compounds in the Cell - Carbohydrates

Foods that contain carbohydrates

• Made up of carbon, hydrogen & oxygen
• Ratio of hydrogen atoms to oxygen atoms in one molecule of carbohydrate is 2:1
• Importance: as storage and supply of energy
• 3 main types of carbohydrates: monosaccharides, disaccharides, polysaccharides

3 main types of carbohydrates

Monosaccharides (Simple Sugar)

• General formula: (CH₂O)_n , where n = 3 , 5 / 6 carbon atoms in the molecule
• Most common = 6-carbon sugar / hexoses (C₆H₁₂O₆)
• Soluble in water, sweet, and form crystals
• Can combine with protein & lipids to form glycoproteins & glycolipids (part of plasma membrane)
• All monosaccharides are reducing sugar!!
• Examples:

Monosaccharides

Disaccharides

• 2 monosaccharides form disaccharides, by removing a molecule of water (condensation)
• Formula: C₁₂H₂₂O₁₁
• It can be broken down to monosaccharides by adding water (hydrolysis)
• Water soluble, sweet, form crystals
• Maltose and lactose are reducing sugar, sucrose is not !!
• Examples:

Disaccharides

Polysaccharides

• Polymers that consisting of chains of monosaccharides
• General formula: (C₆H₁₀O₅)_n , where n varies from 40 to several thousands
• Can be hydrolyzed to monosaccharides by heating with acid / enzymatic reactions
• Insoluble in water, ✗ sweet, cannot be crystallized
• Iodine solution is used to test for the presence of starch
• Examples:

Polysaccharides

Condensation and hydrolysis 

★ Reducing Sugar ★ [Any carbohydrate whose structure contains an aldehyde, or a hemiacetal in equilibrium with an aldehyde]

Define: sugars that can act as reducing agents.

Examples of reducing sugar's structure

Test for a reducing sugar: Benedict’s solution

• When sugar solution is heated with Benedict’s solution, formation of a brick-red precipitate indicates a reducing sugar is present.

Benedict`s test

SPM Biology 4 Chemical Composition of the Cell Part 1 Inorganic Compounds in the Cell - Water

SPM Biology 4 Mind Map

Properties of water and its importance in a cell

1. Polarity of water

• Water is inorganic compound.
• Consist of hydrogen and oxygen elements.
• Polar molecules - produce hydrogen bonds and allow water to act as universal solvent.
• Allow solutes such as glucose to be transported into cells.

Structure of water

2. Cohesive force and adhesive force of water

• Cohesive force: Water molecules are attached to each other.
• Adhesive force: Water molecules are attached to other surfaces.
• Both forces produce capillary action (allow water to move along narrow spaces, eg. xylem tube).

3. Specific heat capacity of water 

• Water has a high specific heat capacity (4.2kJ/kg/°C) - 4.2kJ of heat energy required to raise the temperature of one kg of water by 1°C.
• Water absorbs a lot of heat energy with a small rise in temperature. This helps to maintain the body temperature of organisms.

STPM Biology Biological Molecules Part 17 Nucleic Acids

1. The 2 nucleic acids in the cells are:

• DNA (deoxyribonucleic acid)
• RNA (ribonucleic acid)

2. Nucleic acids are natural polymers. Nucleic acid monomers are nucleotides.

3. A nucleotide has 3 components:

• 5-carbon sugar (pentose)
• Organic base / nitrogenous base
• Phosphoric acid

Structure of nucleotide

4. The pentose of nucleotides are ribose or deoxyribose. 

5. Nucleotide containing ribose is called ribonucleotides (RNA monomers).

6. Nucleotide containing deoxyribose is called deoxyribonucleotide (DNA monomers).

Structure of ribose and deoxyribose

7. Nucleotide has one of these five organic bases:

• adenine (A)
• guanine (G)
• thymine (T)
• cytosine (C)
• urasil (U)

8. These bases can be divided into 2 group:

• Purines (double-ringed molecule): Adenine, Guanine
• Pyrimidine (single-ringed molecule): Thymine, Cytosine, Uracil

5 organic bases

Formation of nucleotides and nucleic acid

1. In formation of nucleotide, a nitrogenous base is first linked to pentose by condensation reaction to form nucleoside.
2. Phosphate group is then added to the nucleoside to form a nucleotide.
3. Nucleic acids are polynucleotides. Polynucleotides are formed by linking nucleotides together.
4. Two nucleotides are linked together through condensation reaction to form dinucleotides.
5. Further addition of nucleotides to dinucleotides will form polynucleotides.
6. Nucleotides in polynucleotides are linked together in phosphodiester bonds.
   
   

   

   Formation of phosphodiester bond

   
   
7. A nucleotide chain has 5' end and a 3' end. The 5' end of the polynucleotide chain is the end with the free phosphate group.

5' end and 3' end of nucleotide chain