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

SPM Biology 3 Movement of Substances Across the Plasma Membrane Part 3 3 Types of Solution & the Effects of Different Concentrations of Solution on Cells

The direction of movement of substances across the plasma membrane in the cell depends on the concentration of the solution around it.

There are 3 types of solution:

1. Hypertonic solution = solution with higher concentration of solutes than the cell. (lower water concentration)
2. Hypotonic solution = solution with lower concentration of solutes than the cell. (higher water concentration)
3. Isotonic solution = solution with equal solute concentration.

**osmosis happen when the water diffuse across the membrane from hypotonic solution to hypertonic solution***

Three types of solution

In hypertonic solution, red blood cells undergo crenation (water diffuse out from cell, cell shrivel and die). Plant cells undergo plasmolysis (plant cell loses water and shrivels, cell becomes flaccid, cause plant wilt). 

In hypotonic solution, red blood cells undergo hemolysis (the cell gain water and swell, finally burst because they no cell wall). Plant cells become turgid (vacuole gain water, expands and exerts pressure outwards on the cell wall).

In Isotonic solution, water diffuses into and out of the cell by osmosis at the same rate. The cells maintain their normal shape.

***terms hemolysis & crenation only for red blood cell.

Blood condition in different solutions

STPM Biology Biological Molecules Part 16 Amino Acids - Properties of Protein

1. Protein is amphoteric.

• Its structure has basic and acidic group.
• Amino group, NH2 is basic; while carboxyl group, COOH is acidic.

Structure of amino acid

2. Protein is an important buffer in biological systems.

• The amphoteric nature of protein allows it to function as a buffer.
• Amino groups of protein removes excess acids in the system.
• Carboxyl groups neutralize the excess bases in the system.

Protein as buffer in biological system

3. The colloidal nature of proteins allow it to exist as individual molecules in solution.

• Colloids are particles not soluble in water but remain suspended in the solution.
• Colloidal particles are usually 1nm to 100nm in diameter.
• Most globular proteins are soluble in water due to the small size of its molecule and existing polar groups such as -COOH.
• Globular protein with larger molecules will from colloidal suspensions in water.
• The colloidal nature of protein provides a larger surface are for biochemical reactions in cells.

Differences between solution, colloidal solution and suspensions

4. Protein denaturation.

• The change of structure and shape of the protein molecule due to the breaking down one or more bonds maintaining the structure of protein molecule is called protein denaturation.
• It can be caused by acids, bases, heat, pH and ultraviolet light.

Protein denaturation

STPM Biology Biological Molecules Part 15 Amino Acids - Levels and Composition of Protein Structure

Levels of protein structure

1. Primary structure

• Primary structure is structure showing the number and sequence of amino acids in its molecule.

Primary structure of insulin

2. Secondary structure

• Secondary structure is the structure showing the coiling of polypeptides to become helix or the folding of polypeptide to become pleated-sheet.
• Secondary structures are maintained and stabilized by hydrogen bonds.

Secondary structure of protein

3. Tertiary structure

• Tertiary structure of protein is the structures showing how a single polypeptide chain (helix) is folded form a globular structure.
• This structure is maintained by various bonds; among which are disulphide bonds, electrovalent bonds or hydrogen bonds.

Tertiary structure of protein

4. Quaternary structure

• Quaternary structures of protein is the structure showing how two or more polypeptide chains are bound together.
• Examples of protein with quaternary structure are hemoglobin.

Quaternary structure of protein

Four levels of protein structure

Composition and structures of protein

1. Proteins can be classified according to its composition or structure.

2. Based on composition, proteins can be grouped into:

• simple protein
• conjugated protein

3. Based on structure, proteins can be divided into:

• Fibrous protein
• globular protein

Simple protein

• Proteins that contain amino acids only.
• For examples: albumin, globulin, and histone.

Conjugated protein

• Protein bounds to non-protein groups.
• Non-protein groups which bound to proteins are known as prosthetic groups.
• For example: hemoglobin.

Structure of hemoglobin

Fibrous protein

(a) Fibrous protein consists of long and parallel polypeptide chains.

(b) The polypeptide chain in fibrous protein is usually coiled to form α-helix.

(c) Neighboring helical chains are usually cross-linked by hydrogen bonds, electrovalent bonds, or disulphide bonds.

(d) Fibrous protein are not soluble in water and are very strong.

(e) Examples of fibrous protein:

• Collagen - in tendons, cartilages, bones and skin.
• Myosin - structural protein in muscles.
• Keratin - structural protein in hairs, nails, feathers and horns.
• Elastin - found in ligaments.
• Sclerotin - combines with chitin to form the exoskeleton of insects.

(f) Collagen is the most common protein in mammals.

• This protein is a main structural component of connective tissues (cartilage, skin, tendons and ligaments).
• The basic structure of collagen is a tropocollagen helix which consists of three polypeptide chains (helixes) twisted together.
• The chains are stabilized by hydrogen bonds between the protein chains.

Collagen fiber

Globular protein

(a) In globular proteins, the polypeptides (helixes) are folded into globular structures.

(b) The globular structure is maintained and stabilized by hydrogen bonds, disulphide bonds and electrovalent bonds.

(c) Some globular proteins are soluble in water; some of them form suspension, and the rest are insoluble in water.

(d) Globular proteins are easily denatured. This is because the hydrogen bonds and disulphide bond in the molecule can easily be broken.

Denaturation of protein

(e) Examples of globular protein:

• Hemoglobin
• Myoglobin
• Hormones
• Enzymes