BMMB 110 Lecture 1 - Atomic Theory PDF

SCHOOL OF MEDICINE & HEALTH SCIENCES LECTURE 1. ATOMIC STRUCTURE BMMB 110 Medical Biology Lecturer: Mr. Musona (PhD Cand. - Microbiology) Motivational Corner Proverbs 3: 5 - 6 “Trust in the Lord (your God) with all...

SCHOOL OF MEDICINE & HEALTH SCIENCES LECTURE 1. ATOMIC STRUCTURE BMMB 110 Medical Biology Lecturer: Mr. Musona (PhD Cand. - Microbiology) Motivational Corner Proverbs 3: 5 - 6 “Trust in the Lord (your God) with all your heart, and lean not on your own understanding; in all your ways acknowledge him, and he will make your paths straight”. It’s God who gives you the breath of life, strength and mental abilities to learn and pursue your medical career. To effectively go further in your studies, be humble; remember your Creator and present your plans before him. You will succeed. Welcome into the School of Medicine  TOPIC: ATOMIC STRUCTURE Objectives:  Explain and apply the Aufbau principle, Pauli Exclusion Principle, and Hund's Rule to determine the electron configurations of elements.  Define and describe the four quantum numbers (n, l, ml, and ms) and their significance in determining the location and energy of electrons in an atom.  Identify and describe the shapes and orientations of s, p, d, and f orbitals, and explain how these shapes influence chemical bonding and molecular  ATOMIC THEORY I. Introduction: Elements in Living Things:-  The Earth generally made of 92 naturally occurring elements  Element, a substance that cannot be split into simpler substances by any chemical means  Living, non-living & the dead, all made of elements  Out of 92, only 21 naturally occurring elements are important to living organisms  Most common elements in Living Organisms:-  Carbon  Oxygen  Hydrogen  Nitrogen Occurring in smaller amounts: phosphorus (P), potassium (K), sulphur (S), calcium Ca), iron (Fe), magnesium (Mg), sodium (Na), chlorine (Cl)  Biological Organisation 1. Atoms Make Elements  Atoms: The smallest units of matter, consisting of protons, neutrons, and electrons.  Elements: Pure substances made of only one type of atom (e.g., Hydrogen (H), Oxygen (O), Carbon (C)). 2. Elements Make Molecules  Molecules: Formed when two or more atoms bond together (e.g., H₂O, CO₂).  Chemical Bonds: Atoms in molecules are held together by covalent or ionic bonds.  A bond is the means by which atoms of different (or similar) elements can be chemically held together 3. Molecules Make Biomolecules  Biomolecules: Large, complex molecules essential for life, such as carbohydrates, proteins, lipids, and nucleic acids. Examples:  Carbohydrates: Sugars and starches (e.g., glucose).  Proteins: Made of amino acids (e.g., enzymes, hemoglobin).  Lipids: Fats and oils (e.g., triglycerides, phospholipids).  Nucleic Acids: DNA and RNA. 4. Biomolecules Make Cell Components  Cell Membrane: Composed of phospholipids, proteins, and carbohydrates, providing structure and regulating transport.  Organelles: Specialized structures within cells (e.g., mitochondria, ribosomes) made from various biomolecules. 5. Biomolecules make a functional unit called a Cell o Cells: Basic units of life, consisting of cytoplasm enclosed within a membrane and containing organelles. o Types of Cells: 2 - Prokaryotic (without a nucleus) and Eukaryotic (with a nucleus). 6. Cells Make Tissues  Tissues: Groups of similar cells that perform a specific function.  Types of Tissues: Epithelial, connective, muscle, and nervous tissue. 7. Tissues Make Organs  Organs: Structures composed of two or more tissue types that work together to perform specific functions (e.g., heart, liver). 8. Organs Make Body Systems  Body Systems: Groups of organs that work together to perform complex functions. Examples:  Circulatory System: Heart, blood, blood vessels.  Digestive System: Stomach, intestines, liver.  Nervous System: Brain, spinal cord, nerves. 9. Systems Make Entire Living Organisms o Organisms: Individual living entities that can carry out all basic life processes. o Examples: Humans, animals, plants, bacteria.  VISUAL SUMMARY The following hierarchical organization illustrates how simple atomic structures build up to form complex living organisms, each level contributing to the overall function and life of the organism. 1. Atoms → Elements 2. Elements → Molecules 3. Molecules → Biomolecules 4. Biomolecules → Cell Components 5. Cell Components → Cells 6. Cells → Tissues 7. Tissues → Organs 8. Organs → Body Systems 9. Body Systems → Organisms There are 11 organ systems in the human body: the integumentary, skeletal, muscular, nervous, cardiovascular, lymphatic, respiratory, digestive, urinary, endocrine, and reproductive systems.  II. ATOMIC STRUCTURE Atom:  An element is made up of atoms  A single atom is the smallest amount of any element that can exist  Atoms, too small to be seen with an ordinary microscope  Structure and function of whole organism depends on the structures of the atoms they contain  Atoms combine in different ways to form thousands of materials  ATOMIC STRUCTURE – WHY LEARN???  Knowing about atoms helps us understand the basic building blocks of all living things. It is crucial for understanding biochemical processes in medical biology.  Understanding atoms helps explain how medicines interact with our cells. It helps explain how molecules like drugs interact with cellular components, aiding in the study of pharmacology and drug design  3. Knowing atomic structure is important for using medical tools and creating new treatments. Knowledge of atomic structure is foundational for using advanced diagnostic tools (like MRI and CT scans) and for developing new therapies in medical science.  4. Learning about atoms helps us know how cells work and do their jobs. Structure: Atoms are the fundamental units of matter, consisting of three main subatomic particles:  Protons: Positively charged particles found in the nucleus (mass:1)  Neutrons: Neutral particles found in the nucleus with no charge (mass: 1).  Electrons: Negatively charged particles orbiting the nucleus in regions called electron clouds (1/1836, neglible).  The atomic number (Z) represents the number of protons in an atom and defines the element.  The mass number (A) is the sum of protons and neutrons in the nucleus.  Quantum Numbers Quantum numbers are values that describe the properties and behaviors of electrons in atoms. There are four main quantum numbers: Principal Quantum Number (n): Indicates the energy level and size of the orbital where the electron is located. Higher n values mean the electron is further from the nucleus. Angular Momentum Quantum Number (l): Describes the shape of the orbital. It can have values from 0 to n-1. Each value corresponds to a different orbital shape (s, p, d, f). Magnetic Quantum Number (m-l): Indicates the orientation of the orbital in space. It can have values from -l to +l. Spin Quantum Number (m-s): Represents the direction of the electron's spin, either +1/2 or -1/2. This describes the two possible spin states of an electron within an orbital. VIDEO – QUANTUM NUMBERS Shells, Subshells, and Orbitals Shells:  Shells (or energy levels) are layers around the nucleus where electrons are likely to be found.  They are designated by principal quantum numbers (n=1, 2, 3,...).  The capacity of each shell to hold electrons is given by the formula 2𝑛2 Subshells  Subshells are subdivisions of the shells.  Subshells are labeled as s, p, d, and f: o s-subshell (1 orbital): Can hold 2 electrons. o p-subshell (3 orbitals): Can hold 6 electrons. o d-subshell (5 orbitals): Can hold 10 electrons. o f-subshell (7 orbitals): Can hold 14 electrons. Orbitals: Orbitals are regions within subshells where there is a high probability of finding an electron. Each type of subshell has a specific number of orbitals: o s-orbital: 1 orbital. o p-orbital: 3 orbitals. o d-orbital: 5 orbitals. o f-orbital: 7 orbitals. Each orbital can hold a maximum of 2 electrons with opposite spins. Division of the Periodic Table According to Orbitals: The periodic table can be divided into blocks based on the subshell in which the last electron resides:  s-block: Groups 1 and 2 (alkali and alkaline earth metals).  p-block: Groups 13 to 18 (includes non-metals, metalloids, and some metals).  d-block: Groups 3 to 12 (transition metals).  f-block: Lanthanides and actinides (inner transition metals).  ATOMIC STRUCTURE & ELECTRONIC CONFIGURATION The four key principles or rules guiding electron distribution in atomic structure are: 1. Aufbau Principle: determines the E.C.  Explanation: Electrons fill atomic orbitals in order of increasing energy levels.  This means electrons occupy the lowest energy orbitals available before filling higher energy orbitals.  For example, the 1s orbital is filled before the 2s orbital, which is filled before the 2p orbitals, and so on. The Aufbau Principle states that electrons will fill in an atom in a specific order. One energy subshell must be completely filled before a new subshell begins to fill in. 2. Pauli Exclusion Principle  Explanation: Each orbital can hold a maximum of two electrons, and these electrons must have opposite spins.  This principle ensures that no two electrons in an atom can have the same set of four quantum numbers (n, l, ml, and ms). This is represented in an orbital filling diagram, a square represents an orbital, while arrows represent electrons. An arrow pointing upward represents one spin direction, while an arrow pointing downward represents the other spin direction. 3. Hund's Rule  Explanation: When electrons occupy degenerate orbitals (orbitals of the same energy), they first fill each orbital singly with parallel spins before pairing up.  This minimizes electron-electron repulsion and results in a more stable electron configuration. Hund's rule states that: Every orbital in a sublevel is singly occupied before any orbital is doubly occupied. All of the electrons in singly occupied orbitals have the same spin (to maximize total spin) 4. Heisenberg Uncertainty Principle  Explanation: It is impossible to simultaneously know both the exact position and exact momentum (velocity) of an electron  This principle implies that electrons are described in terms of probabilities rather than exact locations, leading to the concept of electron clouds or orbitals where electrons are likely to be found.  ELECTRON DISTRIBUTION Bromine has an electronic configuration ending in 4P5 Meaning:  4 means the fourth shell/period/energy level  P means found in the “P” block of elements  5 means the fifth element in the block Electron Distribution in Selected Elements: 1. Carbon (C):  Atomic number 6, so it has 6 protons and 6 electrons.  Electron configuration: 1s² 2s² 2p².  Four valence electrons in the 2nd shell. 2. Hydrogen (H):  Atomic number 1, so it has 1 proton and 1 electron.  Electron configuration: 1s¹.  One valence electron in the 1st shell. 3. Oxygen (O):  Atomic number 8, so it has 8 protons and 8 electrons.  Electron configuration: 1s² 2s² 2p⁴.  Six valence electrons in the 2nd shell. 4. Nitrogen (N):  Atomic number 7, so it has 7 protons and 7 electrons.  Electron configuration: 1s² 2s² 2p³.  Five valence electrons in the 2nd shell. 5. Phosphorus (P):  Atomic number 15, so it has 15 protons and 15 electrons.  Electron configuration: 1s² 2s² 2p⁶ 3s² 3p³.  Five valence electrons in the 3rd shell. 6. Sodium (Na):  Atomic number 11, so it has 11 protons and 11 electrons.  Electron configuration: 1s² 2s² 2p⁶ 3s¹.  One valence electron in the 3rd shell. 7. Chlorine (Cl):  Atomic number 17, so it has 17 protons and 17 electrons.  Electron configuration: 1s² 2s² 2p⁶ 3s² 3p⁵.  Seven valence electrons in the 3rd shell. Detailed Composition and Function of Orbitals: s-Orbital  Composition: Spherical shape, centered around the nucleus.  Function: Basic orbital that holds up to 2 electrons. Found in every principal energy level.  Role: Fundamental in forming the electron cloud around the nucleus. s – orbital: 1 p-Orbital:  Composition: Dumbbell-shaped, oriented along x, y, and z axes (px, py, pz).  Function: Each of the three p-orbitals can hold 2 electrons, for a total of 6 electrons in the p-subshell.  Role: Important in forming covalent bonds and molecular shapes. The p-orbital consists of three degenerate orbitals, which are labeled as Px, Py, and Pz. Each of these orbitals has a specific orientation along one of the three spatial axes: 1.Px - Orbital: Oriented along the x-axis. 2.Py - Orbital: Oriented along the y-axis. 3.Pz - Orbital: Oriented along the z-axis.  These orbitals are shaped like dumbbells and are symmetrical around their respective axes  Each p-orbital can hold a maximum of two electrons, leading to a total of six electrons that can occupy the three p-orbitals in a given energy level p – orbital: 3 d-Orbital:  Composition: More complex shapes (cloverleaf and other shapes), with 5 orbitals in each d-subshell.  Function: Each d-orbital can hold 2 electrons, for a total of 10 electrons in the d-subshell.  Role: Significant in the chemistry of transition metals, influencing their bonding and magnetic properties. d – orbital: 5 f-Orbital:  Composition: Even more complex shapes, with 7 orbitals in each f- subshell.  Function: Each f-orbital can hold 2 electrons, for a total of 14 electrons in the f-subshell.  Role: Crucial for the chemistry of lanthanides and actinides, affecting their magnetic and optical properties. f - orbital III. HYBRIDIZATION: What is Hybridization?  Hybridization is the concept of mixing atomic orbitals to form new hybrid orbitals that are suitable for the pairing of electrons to form chemical bonds in molecules. Purpose of Hybridization:  Shape and Geometry: Hybridization helps explain the shapes and bond angles of molecules.  Bond Formation: It allows atoms to form stable bonds with the correct geometry.  Energy Consideration: Hybridized orbitals have lower energy than pure atomic orbitals, leading to more stable bonding configurations. Types of Hybridization:  sp Hybridization: Mixing of one s and one p orbital, forming two sp hybrid orbitals (linear geometry).  sp2 Hybridization: Mixing of one s and two p orbitals, forming three sp2 hybrid orbitals (trigonal planar geometry).  sp3 Hybridization: Mixing of one s and three p orbitals, forming four sp3 hybrid orbitals (tetrahedral geometry).  sp3d and sp3d2 Hybridization: Mixing of one s, three p, and one or two d orbitals, forming five (trigonal bipyramidal) or six (octahedral) hybrid orbitals, respectively.  Examples of Hybridisation  Understanding atomic structure, shells, subshells, and orbitals provides a foundation for explaining the periodic table and chemical bonding.  Hybridization further refines this understanding by describing the shapes and stability of molecules sp Hybridization  Example: Acetylene (C₂H₂)  Structure: Each carbon in acetylene has two sp hybrid orbitals forming sigma bonds, one with hydrogen and one with the other carbon.  The remaining two unhybridized p-orbitals on each carbon form two π-bonds (a triple bond between the carbons). sp² Hybridization  Example: Ethylene (C₂H₄)  Structure: Each carbon in ethylene has three sp² hybrid orbitals forming sigma bonds, two with hydrogen atoms and one with the other carbon.  The remaining unhybridized p-orbital on each carbon forms a π-bond (a double bond between the carbons). sp³ Hybridization  Example: Methane (CH₄)  Structure: The carbon atom in methane has four sp³ hybrid orbitals, each forming a sigma bond with a hydrogen atom, resulting in a tetrahedral structure. sp³d Hybridization  Example: Phosphorus pentachloride (PCl₅)  Structure: The phosphorus atom in PCl₅ has five sp³d hybrid orbitals forming sigma bonds with five chlorine atoms, resulting in a trigonal bipyramidal structure. sp³d² Hybridization  Example: Sulfur hexafluoride (SF₆)  Structure: The sulfur atom in SF₆ has six sp³d² hybrid orbitals forming sigma bonds with six fluorine atoms, resulting in an octahedral structure.  Thank You for Your Attention. Any Questions? Bibliography (References) Clegg, C.J. and Mackean, D.G. (2008). Advanced Biology: Principles and Applications, Second Edition. Hodder Education. London. Craig, N.L., Cohen-Fix, O., Green, R., Greider, C., Storz, G. and Welberger, C. (2014). Molecular Biology: Principles, of Genome Function. Oxford University Press. Oxford. Raven, P.H., Johnson, G.B., Mason, K.A., Losos, J.B. and Singer, S.R. (2014). Biology, 10th Edition. McGraw-Hill Co. Soper, R., Taylor, D.J., Green, N.P.O. and Stout, G.W. (2017). Biological Science 1 & 2. Cambridge University Press.