Molecules for life

Chemistry of life

All living organisms are made up of atoms, which combine chemically to form molecules, and these make up the basic units of life - cells.

Cells, tissues, and organs:

Plant and animal cells, the basic structural and functional units of living organisms, have a complex organisation that enables them to carry out the seven basic characteristics of life.

Movement

Respiration

Sensitivity

Growth

Reproduction

Excretion

Nutrition

Cells are differentiated and form tissues that perform certain functions. Tissues are organised into organs that are specialised to perform particular functions.

Molecules for Life

Chemical compounds are divided into 2 groups: inorganic and organic.

Inorganic Compounds

Inorganic compounds are chemical compounds that do NOT contain the element carbon (C) and are not produced by living organisms.

Water

The most important inorganic compound for living organisms.

NO WATER = NO LIFE.

H2O = 2 hydrogen molecules and 1 oxygen atom.

Functions of water:

1. Solvent

   Mineral salts in the soil dissolve in water so that the roots of the plant can absorb them.

   O2 & CO2 must be dissolved in water before they can enter or leave the body cells.

2. Medium in which chemical reactions occur

   All chemical reactions in living organisms occur in water.

3. Reagent during hydrolysis

   Water breaks polymers (larger macro-/giant molecules) down into their monomers (smaller building blocks).

4. Transporting agent

   Digested nutrients, metabolic waste products, gases (CO2 & O2 in blood), as well as mineral salts are transported in water.

5. Lubricant

   • Makes chewing and swallowing easier.

   • Aids in the movement of food through the rest of the alimentary canal.

   • Water fluids surround the eyeballs and joints to prevent friction.

6. Regulates body temperature

   • water loss through sweat, which evaporates and cools the body.

7. Gives shape and rigidity

   • Animals such as earthworms and jellyfish have hydrostatic skeletons that give their bodies shape and rigidity.

   • Water in the vacuoles of plant cells causes an internal pressure that pushes against the cell wall - this pressure is known as turgor pressure and keeps plant cells firm.

Mineral salts

Minerals are inorganic substances/metals/elements that are present in rocks and soil, but are essential for all living organisms.

Minerals combine with other elements and compounds to form mineral salts, which can be absorbed by plant roots from the soil.

Humans and animals obtain mineral salts from their food and water.

Importance of mineral salts in plants and animals:

Macronutrients:

Micronutrients:

Phosphates (PO4) and nitrates (NO3) are also mineral compounds.

In humans, a lack of nitrogen-containing protein results in the deficiency disease kwashiorkor.

• Kwashiorkor mainly results in stunted growth.

In plants, a lack of nitrate ions causes the deficiency disease chlorosis, where the leaves become yellow due to a shortage of chlorophyll.

Fertilisers and eutrophication:

In over-utilised soils, where crops are grown and harvested regularly, the soil becomes depleted of mineral salts. Fertilisers are continuously worked into the soil to counteract this mineral deficiency. Fertilisers containing mostly nitrogen, potassium, and phosphates are added to the soil in large quantities.

Many of these minerals are leached (washed away) during heavy rains, ending up in rivers and dams. The phosphates cause a drastic increase in the growth of freshwater algae, known as an algal bloom. The increase in algae blocks sunlight from other photosynthesising organisms, which results in the death of many water plants. Dead organic material leads to an increase in decomposer bacteria. Decomposition requires oxygen, and this large-scale decomposition process depletes the oxygen supply to the water. Large numbers of fish and other water organisms die as a result of an oxygen shortage. This phenomenon is known as eutrophication.

Organic Compounds

Organic compounds are chemical compounds that contain the element carbon (C) and are produced by living organisms.

Organic compounds are composed of carbon, hydrogen (H), and oxygen (O)

Some also contain nitrogen (N), phosphorus (P), and sulfur (S).

Carbohydrates:

Made up of the elements: carbon, hydrogen, and oxygen.
H atoms : O atoms = 2 : 1

Carbohydrates are made up of ring-shaped units know as saccharides.

Mono - and disaccharides are sugars because they taste sweet and are water soluble.

Polysaccharides are not sugars as they do not taste sweet and are insoluble in water.

Monosaccharides are single-ring structures.

• glucose

• fructose

• galactose

(Glucose is the base building block of all carbs)

A disaccharide is formed when 2 monosaccharides are joined.

One water molecule is removed to form a disaccharide.

This reaction is known as a condensation reaction.

• maltose

• sucrose

• lactose

Polysaccharides are long chains of monosaccharides that bind to one another by a condensation reaction.

• starch

• glycogen

• cellulose

• chitin

Starch is the form in which glucose is stored in the plant. When the plant needs energy, the starch is broken down and the glucose is released.

Glycogen is the form in which excess glucose is stored in the liver and skeletal muscles of humans and animals. When energy is needed, glycogen is converted back to glucose.

Cellulose forms the structural component of plant cells.

Chitin forms the structural component of cell walls in fungi and exoskeletons in arthropods and molliucs. Under extreme pressure, chitin becomes limestone and marble.

Importance of carbs in animals and plants:

1. Main source of energy

   • Most important fuel molecule.

   • During respiration, energy is released from glucose while CO2 and H2O are formed as waste products.

2. Source of reserve energy

3. Structural component

   • Plant cell walls consist of cellulose, which strengthens the cell wall.

The test for the presence of glucose we use the Benedict’s solution (a deep blue liquid)
Iodine on the food.

1. Prepare a water bath. Take a heat-resistant beaker, fill it with water, and heat it over a Bunsen Burner.

2. Pour ± cm3 of Benedict’s solution into a test tube.

3. Add about 10 drops of the test solution (Energade, Oros, or fruit juice) to the Benedict’s solution.

4. Place the test tube into the water bath and examine the solution after 4 mins

5. The results can be presented as follows:

Blue - no glucose present

Green - low concentration of glucose

Yellow

Orange

Brink

To test for starch:

1. Take a piece of test material (bread or potato) and place it in a saucer.

2. Drop 2-3 drops of yellow-brown iodine solution onto it.

3. If the test material turns a blue-black colour, starch is present.

Lipids (fats and oils)

Lipids are made up of the same 3 elements as carbs: carbon, hydrogen, and oxygen.

The ratio of H : O, lipids contain more than double the number of H atoms that O atoms.

Lipid molecules consist of 2 types of building blocks - glycerol and fatty acids.

Lipids are:

• insoluble in water

• soluble in ether and alchol

• hydrophobic - water-repelling

However, too much saturated fat can raise cholesterol levels in the blood. Cholesterol travels in the blood as either LDL (bad) or HDL (good). HDL removes excess cholesterol, while high LDL levels increase the risk of cardiovascular disease by causing fatty deposits (plaque) in arteries. This leads to a narrowing called atherosclerosis, where blood clots may form.

The coronary artery supplies the heart's muscle tissue with oxygen-rich blood. If it becomes completely blocked by a clot, the heart muscle is deprived of oxygen, and a heart attack occurs. If the artery is only partially blocked, the heart gets less oxygen, leading to chest pain (called angina) and tiredness during physical or emotional stress.

Importance of lipids in animals and plants:

1. Source of energy

   • A large amount of energy is released when fat molecules are broken down

2. Insulating material

   • Fat is a poor conductor of heat. Marine mammals (whales, dolphins and seals) have a layer of blubber (fat) under the skin that insulates their body heat from the cold sea water. This layer of bubbler also helps them to float.

3. Shock absorption

   • Kidneys and eyes are surrounded by a layer of fat to protect them from mechanical injury.

4. Structural component of cell membranes

   • Cell membranes consist of a double layer of phospholipid molecules with a protein layer on either side

5. Waterproofing

   • A fatty substance, cutin, forms a cuticle that covers the epidermal cells of plants. The cuticle prevents excessive water loss. Birds have oil glands that secrete oil to make their feathers waterproof.

6. Absorption of vitamins

   • Fat-soluble vitamins A, D, E, and K can only be absorbed when dissolved in fat

7. Source of water

   • Animals that hibernate in cold weather, or others that survive in hot, dry conditions, store fat that is broken down to CO2 and H2O during cellular respiration.

   • The camel, which thrives in desert areas, is an animal that survives using metabolic water.

We test for fats using ether:

1. Grind the test material (eg, peanuts) to a fine consistency.

2. Place a small amount in a test tube.

3. Add 5 cm3 of ether and shake the test tube well.

4. Allow the test tube to stand for approximately half an hour.

5. Filter the ether (finely ground peanuts will stay behind).

6. Allow a drop of the filtrate (liquid that filtered through) to fall onto a clean filter paper.

7. The ether will evaporate quickly.

8. If any fats are present, a translucent, greasy spot will form on the filter paper.

Proteins

A protein is a polymer (a large molecule) with amino acids as monomers.

Amino acids are made up of the elements carbon (C), hydrogen (H), oxygen (O), and nitrogen (N). In some amino acids, phosphorus (P), sulphur (S), and iron (Fe) are also present.

There are only 20 different amino acids.

The sequence and type of amino acids determines the type of protein.

The bond/link formed between 2 amino acids is known as a peptide bond.

• Dipeptide: 2 amino acids linked by a peptide bond

• Tripeptide: 3 amino acids linked by peptide bonds

• Polypeptide: long chain of amino acids linked by peptide bonds

• Protein: 51+ amino acids linked by peptide bonds

Every protein has its own particular shape. The long chains of amino acids form folds and loops that can fold back onto themselves. The number of amino acids, sequence of amino acids, and specific shape of a protein determines its function.

Importance of proteins in animals and plants:

1. Structural component of protoplasm

   • About 15% of protoplasm consists of protein

2. Building materials

3. Structural component of cell membranes

   • Together with phospholipids, it forms the cell membrane that surrounds a cell.

4. Plays a role in the permeability of cell membranes

   • Proteins act as carrier molecules that transport other molecules through the cell membrane.

5. Source of reserve energy

   • Excess amino acids are broken down into urea and glucose.

6. Hormones regulate processes in the body

   • Some hormones, like insulin and adrenaline, are proteins and act as chemical messengers

7. Haemoglobin transports O2 and CO2 in the blood

8. Protect the body against disease

   • Antibodies are blood proteins that respond to antigens and fight bacteria and viruses.

9. Chromosomes carry hereditary material

   • Chromosomes are made up of proteins and DNA

10. Act as buffers

    • Proteins keep the pH of body fluids constant as they can release hydrogen atoms (to an alkaline solution) and take up hydrogen atoms (from an acidic solution).

11. Enzymes control metabolic processes in the body

    • Enzymes are proteins that accelerate chemical reactions.

Test for proteins: (The Biuret test)

1. Grate or grind the test material (beans) or use soup powder or milk powder. Add a little water and boil until it forms a thin soup.

2. Pour about 5 cm3 of soup into a test tube and add 2 - 3 drops of dilute copper sulphate solution (light blue)

3. Add 5 - 10 cm3 of sodium-hydroxide solution (clear) to the mixture.

4. Shake the test tube gently.

5. Heat the mixture over a Bunsen burner to obtain a deeper colour.

6. Blue = no protein present

   Purple/violet = protein present

Enzymes

Enzymes are proteins that accelerate chemical reactions inside living cells. Without them, vital reactions essential for life would take place too slowly to sustain life.

Substances that accelerate chemical reactions are known as catalysts.

Enzymes are, therefore, biological catalysts.

In order for a chemical reaction to occur, the reaction needs activation energy to initiate the reaction.

Chemical reactions that take place in living cells are known as metabolic reactions.

During the digestion of food, complex molecules (larger macromolecules) are broken down into simple molecules (smaller, soluble molecules) by adding H2O.

This catabolic process is known as hydrolysis.

Enzyme action:

1. During a chemical reaction, a substance/s is/are changed from one form to another.

2. The substance on which the enzyme acts is known as the substrate.

3. The substance formed during the reaction is the product.

4. Enzymes are proteins, and each protein has a particular shape to enable it to perform its specific function.

5. Enzymes are substrate-specific; in other words, a specific enzyme can only act on a specific substrate.

6. There is a region on the enzyme known as the active site. The substrate molecule fits into the enzyme’s active site as a key fits into a lock. This ensures the specificity of the enzyme.

7. A temporary enzyme-substrate complex is formed.

8. The enzyme lowers the activation energy for the reaction.

9. The substrate changes chemically and leaves the active site.

10. The enzyme remains unchanged during the reaction and it ready to bind with the next substrate molecule.

Influence of temperature and pH on enzyme action:

Temperature:

• Enzymes are very sensitive to temperature changes

• Low temperatures make enzymes temporarily inactive

• The temperature at which most enzymes work the best is known as their optimum temperature

• At high temps, usually above 45’C, the shape of the enzyme begins to change and the substrate no longer fits into the active site. The enzyme loses its structure and function - it has denatured.

• At lower temperatures, enzymes become inactive. If enzymes freeze, they also denature.

pH:

• Each enzyme has a narrow pH range within which it can function. This is known as the optimum pH.

• Some enzymes work optimally in acidic medium, whereas others work better in neutral or alkaline medium.

• Enzymes denature at extreme pH levels.

Properties of enzymes:

• Enzymes are spherical proteins.

• Enzymes are sensitive to changes in temperature - high temperatures denature enzymes, whereas lower temperatures make them temporarily inactive.

• Enzymes are sensitive to changes in pH - enzymes denature if the pH changes drastically (too acidic/alkaline)

• Enzymes are substrate-specific

• Enzymes can be used over and over again

• A small amount of enzyme can change a large amount of substrate.

Enzymes in everyday life

Biological washing powders contain enzymes that break up/remove biological stains. These enzymes usually act on proteins and are known as proteases.

Stains caused by blood, egg yolk, and sweat consist of proteins and are difficult to remove from clothes. The enzymes in washing powder break the proteins into smaller, soluble molecules that are easily removed by cleaning agents in the washing powder.

Lactose-free milk and meat fertiliser are also examples of products that contain enzymes.

Nucleic acids

Nucleic acids are made up of the elements carbon (C), hydrogen (H), oxygen (O), nitrogen (N) and phosphorus (P). Monomers of nucleic acids are called nucleotides.

There are 2 types of nucleic acids:

Vitamins

Vitamins are essential for normal metabolism, growth and development of the human body.

They are needed in small quantities and are produced by plants.

Vitamins must be in solution to perform their functions. Vitamins can be classified as water-soluble or fat-soluble.

Insufficient vitamins cause deficiency diseases.