THE CHEMISTRY OF LIFE

THE CHEMISTRY OF LIFE CHEMICAL ELEMENTS AND WATER 3.1

3.1.1 State that most frequently occurring chemical elements in living things are carbon, hydrogen, oxygen, and nitrogen • Elements are the basic units of pure substances • An atom is the smallest part of an element that can take part in a chemical change. • At the centre of an atom is a nucleus of protons (positively charged particles), and usually also neutrons (uncharged particles). Around the nucleus are tiny particles called electrons (negatively charged). • A molecule is a group of like or different atoms held together by chemical forces. • A compound contains two or more elements chemically combined together. • If an atom gains or loses an electron an ion is formed.

Chemical elements • Life requires about 25 elements. Four of these – Oxygen (O), Carbon ( C), Hydrogen (H), and Nitrogen (N)- make up about 96% of human body, as well as most other living organisms. • These four elements are the main ingredients of biological molecules such as proteins, sugars and fats. • Why do these four elements predominate in living things?

- • The elements carbon, hydrogen, and oxygen predominate because living things contain large quantities of water, and also because most other molecules present in cells and organisms are compounds of carbon combined with hydrogen and oxygen, including the carbohydrates and lipids. • The element nitrogen is combined with carbon, hydrogen, and oxygen in compounds called amino acids from which proteins are constructed.

Human body • Hydrogen -63% • Oxygen -25.5% • Carbon -9.5% • Nitrogen -1.4% • Calcium -0.31% • Phosphorus -0.22%

3.1.2 State that a variety of other elements are needed by living organisms, including sulfur, calcium, phosphorus, iron and sodium • Sodium (Na), potassium(K), calcium (Ca), phosphorus (P), sulfur (S), chlorine (Cl), and Magnesium (Mg) account for the remaining 4% of the human body. These elements are involved in such important functions such as bone formation, nerve signaling and DNA synthesis.

3.1.3 State one role for each of the element mentioned in 3.1.2 • Needed to make 2 of the 20 amino acids that proteins contain. Found in protein molecules Role in Prokaryotes • Some prokaryotes use a chemical reaction involving sulfur as their source of energy (chemo-autotrophs) Role in Plants and animals • Plant and animals require sulfur to produce some of the amino acids that are part of enzymes they need • In some Vitamins

Calcium • Important for healthy bones and teeth; helps muscles relax and contract; important in nerve functioning, blood clotting, blood pressure regulation, immune system health. Regulates processes inside the cell including transcription. Role in Prokaryotes Involved in maintaining the cell structure and movement Co-factor for certain enzymes Contributes to heat resistance of bacterial endospores

Calcium Role in Plants Component of cell walls and cell membranes Co-factor for certain enzymes Role in animals Constituent of bones Muscle contraction Blood clotting Co-factor for certain enzymes

Phosphorus • Part of the phosphate group in ATP and DNA molecules. Important for healthy bones and teeth; found in every cell; part of the system that maintains acid-base balance • Role in Prokaryotes • Synthesis of nucleotides, ATP • Role in plants • Synthesis of nucleotides, ATP • Role in animals • Synthesis of nucleotides, ATP, constituent of bones

Iron • Iron is needed to make hemoglobin in many animals. Vital for energy processing and transporting oxygen in your blood. Role in Prokaryotes • Constituent of electron transport molecules • Chlorophyll synthesis in photosynthetic prokaryotes

Role of iron in plants and animals • In plants • Constituent of electron transport molecules (e.g. cytochromes) • Chlorophyll synthesis • In animals • Constituent of electron transport molecules • (e.gcytochromes and haem part of hemoglobin)

Sodium • Needed for proper fluid balance, nerve transmission, and muscle contraction. Pumped into the cytoplasm to raise solute concentration and cause water to enter by osmosis. • Role in Prokaryotes • Involved with potassium in membrane function • Indirectly helps move the flagellum

-- • Role in plants • Involved with potassium in membrane function • In some plants (C4 plants) sodium can help bind carbon dioxide for photosynthesis • Role in animals • Membrane function along with potassium. • nerve impulse transport. • Aids glucose transport across membranes

Trace elements (less than 0.01%) : Boron, chromium, cobalt, copper, fluorine, iodine, iron, manganese, molybdenum, selenium, silicon, vanadium and zinc. • Iodine - Essential element of thyroxinehormone • Manganese-Mn is an antioxidant, activates numerous enzymes and has roles in protein, carbohydrate and fat metabolism. It is necessary for blood sugar regulation, healthy nerves and brain, sex hormone production, normal skeletal development, production of mother's milk and a healthy immune system. • Magnesium- in chlorophyll- in green plants and certain prokaryotes.

For all the elements mentioned above make a table with the names of elements and their functions in plants, animals and prokaryotes.

3.1.4 Draw and label a diagram showing the structure of water molecules to show their polarity and hydrogen bond formation

Structure of water molecule • Water molecules consist of two hydrogen atoms bonded to an oxygen atom. The hydrogen atoms have slight positive charge and the oxygen atom has a slight negative charge. So water molecules have two poles- a positive hydrogen pole and a negative oxygen pole. This feature of a molecule is called polarity. • Covalent bonds (sharing of electrons) keeps the atoms together. • The structure of water molecule is fixed: the small hydrogen atoms bond to the larger oxygen atom at a fixed angle as shown in the figure.

-- • Positive and negative charges attract, there will be an attraction force (hydrogen bond) between the (slightly positive) hydrogen of one water molecule and the (slightly negative) oxygen of the adjacent molecule. • Due to the water molecule having a slightly positive and a negative side we can say it has two poles: a positive and a negative pole. • That means water is polar and polar solutes are likely to dissolve in t, whereas non-polar molecules will not.

Hydrogen bonding in water is a result of polarity. • Hydrogen bonds are not complete chemical bonds. There is no sharing or transferring of electrons. Instead, it is an attraction force between a slightly positive hydrogen atom and a slightly negative oxygen atom. Hydrogen bonds are much weaker than covalent or ionic bonds. They are significant and are quite common. A lot of hydrogen bonds together are strong. For example the bonds between complementary bases keep the two strands of DNA double helix together .

Hydrogen bonds in DNA Hydrogen bonds attract water molecules to charged particles or charged surface. Refer to the water molecule and the hydrogen bond it forms from IB By C.J. Clegg page number 39

--- • The hydrogen and oxygen atoms in a single water molecule are held together by a type of bond called a polar covalent bond. Polar covalent bond results from unequal sharing of electrons. In water, the single oxygen atom is bonded to two different hydrogen atoms. Each oxygen-hydrogen bond is a polar covalent bond and results in slight negative charge at the oxygen end of the molecule and a slight positive charge at the end with the two hydrogen atoms. • (In molecules of one element like oxygen and hydrogen, the two identical atoms exert an equal pull on the electrons. The covalent bonds in such molecules are said to be non polar because the electrons are shared equally between the atoms. • Water is composed of atoms with very different electronegativity. Oxygen is one of the most electronegative of the elements. Oxygen attracts the shared electrons in water much more strongly than does hydrogen, so that the shared electrons spend more time near the oxygen atom than near the hydrogen atoms. This unequal sharing of electrons produces what is called polar covalent bond)

A bond can form between the positive pole of one water molecule and the negative pole of another. This is called a hydrogen bond. In liquid water many of these bonds form, giving water properties that make it very useful substance for living organisms. The diagram above shows hydrogen bond between two water molecules.

3.1.5 outline the thermal, cohesive and solvent properties of water • Thermal Properties • Water has a large heat capacity- large amounts of energy are needed to raise its temperature. The energy is needed to break some of the hydrogen bonds. • Water has a better ability to resist temperature change than most other substances. Because of this property Earth’s giant water supply moderates temperatures, keeping them within limits that permits life.

Thermal Properties • High specific heat • Water requires a lot of energy to warm up and gives off a lot of energy when cooled down. • Transport • Blood can carry heat to colder places in our body, your nose goes red when you are skiing or skating • High heat of vaporization • Water requires a lot of energy to change from a liquid into a gas due to cohesion. • Coolant • Both plants and animals evaporate water which has a cooling effect- a little will take up a lot of energy to evaporate

Heat energy and the temperature of water • A lot of heat energy is required to raise the temperature of water. This is because much energy is needed to break the hydrogen bonds that restrict the movements of water molecules. This property of water is its specific heat capacity. The specific heat capacity of water is the highest of any known substance. • As a result aquatic environments like streams and rivers, ponds, lakes and seas are very slow to change temperature when the surrounding air temperature changes. • Aquatic environments have much more stable temperatures than terrestrial environments do.

Latent heat of vaporisation • The hydrogen bonds between water molecules make it difficult for them to be separated and vaporised. This means that much energy is needed to turn liquid water into water vapor (gas). This amount of energy is the latent heat of vaporisation, and for water it is very high. • As a result, the evaporation of water in sweat on the skin, or in transpiration from green leaves, causes marked cooling. The escaping molecules take a lot of energy with them. You experience this when you stand under a fan after vigorous exercise.

Latent heat of Fusion • The amount of heat energy that must be removed from water to turn it to ice is very great, as is that needed to melt ice. This amount of energy is the latent heat of fusion, and is very high for water. • As a result, both the contents of cells and the water in the environment are always slow to freeze in extreme cold.

The density of ice • Water reaches it maximum density at 4 ̊C. So as water freezes, the ice formed is less dense than the cold water around it. As a result, ice floats on tope of very cold water. The floating layer of ice insulates the water below. The consequence is that lakes rarely freeze solid; aquatic life can generally survive a freeze-up.

Cohesive Properties of water • Water molecules are highly cohesive. Cohesion is when molecules of the same type are attracted to each other. This attraction is due to the polar covalent bonding. Whenever two water molecules are near each other the positive end of one attracts the negative end of another. • When water cools below the freezing point, molecular motion has slowed to the point where these polar attractions become locked into place and an ice crystal forms.

Surface Tension • Hydrogen bonds give water unusually high surface tension, making it as though it were coated with an invisible film. The insect called a water spider, takes advantage of the high surface tension of water. It strides across ponds without breaking the surface.

Solvent Properties • Water is polar and will dissolve many polar solutes and this property helps the xylem in plants to transport water and minerals • Phloem to transport water and sugar • Animals to transport oxygen, glucose, urea through blood • Reactions involving polar molecules can take place in water as water is the medium for all metabolic reactions

Some common aqueous solutions in which specific biochemical reactions take place • Cytoplasm – glycolysis/protein synthesis • Nucleoplasm – DNA Replication/transcription • Stroma – light-independent reaction of photosynthesis Blood plasma – loading and unloading of gases

3.1.6 Explain the relationship between the properties of water and its uses in living organisms as a coolant, medium for metabolic reactions and transport medium • A large body of water can store a large amount of heat from the sun during warm periods. At cooler times, heat given off from the gradually cooling water can warm the air. That’s why coastal areas have milder climates than inland regions. • Water’s resistance to temperature change also stabilizes ocean temperatures, creating a favorable environment for marine life. • Blood, which is mainly composed of water, can carry heat from warmer parts of the body to cooler parts. Blood is used as a transport medium for heat

The boiling point of water is high, because to change it from liquid to gas all of the hydrogen bonds between the water molecules have to be broken. • Water is below boiling point almost everywhere on Earth, and in most areas it is above freezing point. As a liquid, rather than a solid or a gas it can act as the medium for metabolic activities. • Another way water moderates temperatures is by evaporative cooling. When a substance evaporates, the surface of the liquid remaining behind cools down as the molecules with the greatest energy leave. Evaporative cooling helps prevent land-dwelling organisms from overheating.

Evaporation from a plant’s leaves keeps them from becoming too warm in the sun, just as sweating helps to dissipate our excess body heat. • The evaporation of surface waters cools tropical seas. • Solvent properties: • Many different substances dissolve in water because of its polarity. Inorganic particles with positive or negative charges dissolve, for example sodium ions. Organic substances with polar molecules dissolve, for example glucose. Enzymes also dissolve in water,

-- • Most chemical reactions in living organisms take place with all of the substances involved in the reactions dissolved in water. Water is the medium for metabolic reactions. • The solvent properties of water allow many substances to be carried dissolved in water in the blood of animals and the sap of plants. Water can be used as transport medium. • Xylem carries water and dissolved minerals up from the root system to the leaves of a plant. Phloem then transports dissolved sugars from the leaves to the stems, roots and flowers of a plant. • Blood is the common transport medium in animals and is largely made up of water.

- • Tree depend on cohesion to help transport water and nutrients from their roots to their leaves. (water is used as a transport medium in the xylem of plants) • The evaporation of water from leaves exerts a pulling force on water within the veins of a leaf. Because of cohesion, the force is relayed through the veins all the way down to the roots. As a result water raises against the force of gravity.

Reference • Made use of IB Biology By Alan Damon, Minca, C. J. Clegg

THE CHEMISTRY OF LIFE