SBI4U BIOCHEMISTRY Atoms, Bonding & Molecular Polarity Ms. Lefebvre

ATOMS, BONDING, AND MOLECULAR POLARITY

ElementSymbolAtomic # % of human body weight OxygenO865.0 CarbonC618.5 HydrogenH19.5 NitrogenN73.3 CalciumCa201.5 PhosphorusP151.0 PotassiumK190.4 SulfurS160.3 SodiumNa110.2 ChlorineCl170.2 MagnesiumMg types of atoms make up 99% of all living organisms Naturally Occurring Elements in the Human Body

Atoms and Elements Matter is any substance in the universe that has mass and occupies space All matter is composed of extremely small particles called atoms, which is the smallest unit of any given element. Every atom has the same basic structure: Subatomic Particles Core nucleus of protons and neutrons Orbiting cloud of electrons

The Atom The atom has three parts: 1) Protons 2) Neutrons 3) Electrons – 3D particle

The element carbon - 6 th element in the periodic table C Carbon Atomic Number = # of protons = # electrons Symbol Mass Number = protons + neutrons

Bohr model of a hydrogen and oxygen atom Subatomic Particles Nucleus Shell

Isotopes are atoms of the same element that vary in the number of neutrons. Because they have the same number of electrons, all isotopes of an element have the same chemical properties.

Radioiostopes are isotopes of certain elements that are unstable and emit radiation as they decay; constant proportion of radioisotope breaks down during a given time interval. The process may be quick or slow depending on the isotope The radiation emitted can be harmless or lethal Alpha Particles Naturally occurring in the environment. (ex. by uranium-238, radium-226) during mining processes Beta Particles Many uses, especially in medical diagnosis, imaging, and treatment (ex. Iodine-131) Gamma Rays Irradiation of food. (High energy breaks chemical bonds in molecules that are vital for cell growth and integrity; as a result microbes die). Types of Radiation

Half-Life the amount of time required for half of the nuclei in a radioisotope to decay Ex. A by product of forming uranium for nuclear reactors is radium-226 which has a half-life of years. If your sample is initially 25g, how much would remain after one half-life? Five half-lives?

Radioactive Tracers Used to investigate a variety of reaction mechanisms and biochemical processes First used to study photosynthesis, then DNA and later other biochemical processes Currently used in nuclear medicine for diagnosis and treatment Iodine-131 Used to diagnose and treat thyroid disease Cobalt-60 Used in gamma knife radiosurgery to remove cancerous tumours

Why are electrons so important? The chemical behaviour of an atom is determined by its electron configuration – that is, the distribution of electrons in the atom’s electron shells. The chemical behaviour of an atom depends mostly on the number of electrons in its outermost shell. (= valence electron/shell) All atoms with incomplete valence shells are chemically reactive.

Octet Rule = atoms tend to gain, lose or share electrons so as to have 8 electrons C would like to N would like to O would like to H would like to Gain 4 electrons Gain 3 electrons Gain 2 electrons Gain 1 electron

Atoms bond to form compounds Compounds are made up of at least 2 different kinds of atoms (e.g., H 2 O) Bonds are formed by the sharing or transfer of electrons 2 Types of Chemical Bonds Ionic Bonds Covalent bonds

Ionic Bonds – occur when one atom donates or gives up one or more electrons Opposite charges attract to form ionic bonds Ionic Compound ( Na + Cl - )Salt crystals

Covalent Bonds – involve a sharing of a pair of valence electrons between atoms.

Single covalent bond ( 2 shared electrons) Double covalent bond (4 shared electrons) Four single covalent bonds Two single covalent bonds Triple covalent bond (6 shared electrons)

Covalent Bonds Polar Covalent Unequal sharing of electrons Non-Polar Covalent Equal sharing of electrons 2 types of covalent bonds Determined by the atoms ELECTRONEGATIVITY

Electronegativity the measure of the relative abilities of bonding atoms to attract electrons (Pauling Scale) In a non-polar covalent bond, there is no electronegative difference. Electrons are shared equally. E.g., O 2 oxygen atoms have the same electronegativity In a polar covalent bond, there is an electronegative difference. Electrons are shared unequally. E.g., H 2 O oxygen atom is more electronegative than the hydrogen atoms Electronegativity = Stronger pull of shared electrons

increasing

Shared electrons spend more time near the oxygen nucleus As a result, the oxygen atom gains a slightly negative charge and the hydrogen atoms become slightly positive Water is a polar molecule because oxygen is more electronegative than hydrogen, and therefore electrons are pulled closer to oxygen.

Molecular Shapes When atoms react to form covalent bonds, their valence electron orbitals undergo a process called hybridization that changes the orientation of the electrons. Hybridization is a complex process (better suited to a chemistry course).

The Valence Shell Electron Pair Repulsion (VSEPR) theory, is an easier way to predict molecular shape. VSEPR theory states that, since electrons are all negatively charged, valence electron pairs repel one another and will move as far apart as possible VSEPR

Molecular Polarity Symmetrical molecular structures produce nonpolar molecules (whether the bonds are polar or not) Asymmetrical molecular shapes produce nonpolar molecules if the bonds are all nonpolar, and they produce polar molecules if at least one bond is polar

Polar Molecules (like water) have an unequal distribution of charge. Since water is polar, it can attract other water molecules. The attraction between water molecules are called hydrogen bonds. Hydrogen bonds are weak forces between molecules

van der Waals forces – in addition to the intramolecular forces that exist within a molecule, there are forces of attraction between molecules. Hydrogen bonding in water Determine the physical state of molecular substances at a given temperature and pressure Weaker than intramolecular ionic and covalent bonds

van der Waals forces

Water- it’s importance to the human body

Water Water is a colourless, tasteless, odourless substance that can exist as a solid, liquid, or gas in the temperature ranges normally found near Earth’s surface. Its physical and chemical properties are a direct result of its simple composition and structure. Water’s polar covalent bonds and asymmetrical structure create a highly polar molecule.

Solubility of Substances in Water Due to water’s polarity, it is a great solvent. More substances dissolve in water than in any other liquid. Nearly all chemicals of biological interest occur in a water medium. What is happening in the example below? Water is great at dissolving both ionic (+,-) compounds and polar (partial positively, partial negatively charged molecules) molecules. Cl - Water Na + Cl - Water Na +

Solubility of Substances in Water Hydrophilic (water-loving): having an affinity for water; the tendency of ionic and polar molecules to dissolve in water (Ex. Salt and sugar dissolve in water) Hydrophobic (water-fearing): having an aversion to water; the tendency of nonpolar molecules that do not interact with water because they cannot form hydrogen bonds (ex. Fats do not dissolve in water)

Water- Properties water attracted to other water molecules because of polar properties Cohesion water attracted to other materials Adhesion water is pulled together creating the smallest surface area possible Surface Tension

Capillary Action Because water has both adhesive and cohesive properties, capillary action is present. Capillary Action = water’s adhesive property is the cause of capillary action. Water is attracted to some other material and then through cohesion, other water molecules move too as a result of the original adhesion. ex: think water in a straw ex: water moves through trees this way

Surface Tension

High Heat Capacity In order to raise the temperature of water, the average molecular speed has to increase. It takes much more energy to raise the temperature of water compared to other solvents because hydrogen bonds hold the water molecules together! Water has a high heat capacity. “The specific heat is the amount of heat per unit mass required to raise the temperature by one degree Celsius.” Did you know? High heat capacity helps organisms maintain a constant body temperature! You’ll see why this is so important when we talk about enzymes.

Density Water is less dense as a solid! This is because the hydrogen bonds are stable in ice – each molecule of water is bound to four of its neighbors. Solid – water molecules are bonded together – space between fixed Liquid – water molecules are constantly bonding and re-bonding – space is always changing

Solid Water molecules are bonded together – space between fixed Liquid Water molecules are constantly bonding and re-bonding – space is always changing Gas Water molecules have the most energy; greatest space between particles

The Atom: Just because it’s small doesn’t mean it’s insignificant! Behold… the future!