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Structure of the Atom Dr. Kamal Omer, Associate Professor of Biochemistry & Molecular Biology Physical and Chemical sciences alone may not completely explain the nature of life, but they at least provide the essential framework for such an explanation. Thus, for understanding of nature of life all students of Health Sciences must have a fundamental understanding of organic chemistry and biochemistry. Organic chemistry is the study of Carbon compounds. Organic compounds, are compounds composed primarily of a carbon skeleton. • All living things are composed of organic compounds. • The atom is the fundamental component of all chemical substances including the protoplasm (the living substance). • Atoms have mass and space thus, they are matter. The name atom comes from the Greek word ἄτομος (atomos, "indivisible") from ἀ- (a-, "not") and τέμνω (temnō, "I cut"), which means indivisible, something that cannot be divided further. The concept of an atom as an indivisible component of matter was first proposed by early Indian and Greek philosophers. th 18 th 19 In the and centuries, chemists provided a physical basis for this idea by showing that certain substances could not be further broken down by chemical methods, and they applied the ancient philosophical name of atom to the chemical entity. th 19 th 20 During the late and early centuries, physicists discovered sub-atomic components and structure inside the atom, thereby demonstrating that the chemical "atom" was divisible and that the name might not be appropriate. However, the name atom was retained. An atom is one of the basic units of matter. Atoms form the building blocks of the simplest substances, the chemical elements. Nearly everything on earth is made up of atoms. Each element consists of one basic kind of atom. • Protoplasm, the living substance of cells is termed living matter. • Understanding of the atom is essential for the understanding the nature of protoplasm. 1. Methane 2. DNA 1. Methane with 1 Carbon atom 3. Glucose 2. DNA with tens of Billions of Carbon atoms • Atom is very very small, less than billionth of an inch in diameter. • Atoms have sizes on the order of 1-5 A (1 angstrom = 10-10 m) and masses on the order of 1-300 atomic mass unit (amu). • Thus, an atom can’t be seen with light microscope. This unit is much more convenient to use than grams for describing masses of atoms. It is defined so that both protons and neutrons have a mass of approximately 1 amu. Physical nature of atoms is complex, its structure is similar to the solar system in which several planets continuously circle around the sun in certain orbits. Most atoms consist of three basic particles: protons (with a positive electrical charge), electrons (with a negative electrical charge), and neutrons (with no electrical charge) Protons and neutrons are bundled together in the center of the atom, called the nucleus. The electrons move around the nucleus, each in its own orbit like the moon around the earth. Each atom of the same element is characterized by a certain number of protons in the nucleus. • This atomic number identifies the elements. The list of elements (ranked according to an increasing number of protons) is called the Periodic Table. • Protons and neutrons are held together rather closely in the center of the atom. Together they make up the nucleus, which accounts for nearly all of the mass of the atom. • Electrons move rapidly around the nucleus and constitute almost the entire volume of the atom. Although quantum mechanics are necessary to explain the motion of an electron about the nucleus, we can say that the distribution of electrons about an atom is such that the atom has a spherical shape. • An atom is similar to the solar system consists of one or more electrons. • Electrons like planets orbiting a nucleus (like the sun). • Orbiting electrons are arranged in regular sequence, each in its own shell. Atoms in the protoplasm are different and are called elements (eg. hydrogen, oxygen, nitrogen, phosphorous). • The nucleus contains a definite number of protons & neutrons. • The interaction of electrons, protons & neutrons gives each atom its distinctive chemical properties. • Even though the number of protons in the nucleus is the same for all atoms of a particular element, the number of neutrons in the nucleus can differ for different atoms of the same element. Atoms of an element that contain the same number of protons, but different numbers of neutrons, are called isotopes of the element. Isotopes are identified by adding the number of protons and neutrons together, a number which is referred to as the mass number. • The number of electrons is equal to the number of protons. • e.g. H: 1e¯ & 1p⁺. O: 8e¯ & 8p⁺. • Neutron is neutral. • The atom is electrically neutral. When an atom loses an (e¯) it becomes positive charged (cation) & when it gains an e¯ it becomes negatively charged (anion). Cations & anions are called ions. • The electrons of an atom are bound to the nucleus by the electromagnetic force. Likewise, a group of atoms can remain bound to each other by chemical bonds based on the same force, forming a molecule. Atomic number & atomic weight The atomic number is equal to the positive charges or the number of electrons or to the ordinal number of the element in the periodic table. • The atomic weight is equal to the total number of protons & neutrons. The extra-nuclear electrons: • Chemical substance depends on interaction between the outer extra-nuclear electrons of the atoms combining together. • The chemical properties of an atom depend on the arrangement of the extra-nuclear electrons. • Eg. Each element in group one of the Period. Table has one electron in the outer most orbit. • The total number of electrons that can occupy any shell is given by the formula 2n². n is the principal quantum number (KLMNOPQ or 1-7). ie group: • 1. Li 2. 1; Na 2.8.1; K 2.8.8.; Ag 2.8.18.18.1 • Group 2. Be 2.2; Mg 2.8.2; Ca 2.8.8.2. An atom is classified according to the number of protons and neutrons in its nucleus: the number of protons determines the chemical element, and the number of neutrons determines the isotope of the element. • A unit of mass called the atomic mass unit (amu) is much more convenient to use than grams for describing masses of atoms. It is defined so that both protons and neutrons have a mass of approximately 1 amu. Protons and neutrons have almost the same mass, while the electron is approximately 2000 times lighter. Protons and electrons carry charges of equal magnitude, but opposite charge. Neutrons carry no charge (they are neutral). • Chemical reactions involve either the transfer or the sharing of electrons between atoms. Therefore, the chemical reactivity/ properties of an element are primarily dependent upon the number of electrons in an atom of that element. • Protons also play a significant role because the tendency for an atom to either lose, gain or share electrons are dependent upon the charge of the nucleus. Therefore, we can say that the chemical reactivity of an atom is dependent upon the number of electrons and protons, and independent of the number of neutrons. • The mass and radioactive properties of an atom are dependent upon the number of protons and neutrons in the nucleus. Atoms’ properties • Combine with one another through chemical bonds to form molecules. e.g. the ions of Na⁺ and Cl⁻ form an ionic bond. The result is NaCl (1 molecule). • Water: H₂O (H-O-H covalent bonds). • Hydrogen bonds are formed between molecules of water to give clusters. Extra-nuclear Electrons Electrons are arranged around the nucleus in different orbits. Orbits have different energies. • The transfer of electrons from one orbit to an other leads to absorption or emission of energy. • Electrons rotate on their selected orbits do not radiate energy (stationary states, least energy). • In any other state, the atom is said to be excited. • Various energy levels (orbits) are labeled by quantum numbers. These are: 1. The principle quantum Number: (PQN) This is referred to stationary or circular orbits (1-7; or K-Q ) the first one is that near to the nucleus 1 or K. • Each PQN represents a shell (a group) of orbits. • Total Number of electrons that can occupy any shell is given by the formula 2n². n is the PQN. 2. Subsidiary QN, which represents the various orbits within a shell (1,2,3,4 or s,p,d,f). The number of SQN in any shell is limited. 3. Magnetic QN: The L (2) PQN can contain a max. of 8e¯. Two of them with opposite spin↕ will be in 2S level. The remaining 6e¯ are different (the 2P orbits are divided into 3 levels, 2px, 2py & 2px). 3d into 3d₁-3d₅ (∑10e¯). The f subsidiary orbit is divided into 7 levels. • The subdivision of the SQNs into 3p, 5d & 7f is called MQN. 4. Spin QN: Each 2e⁻ in any levels of 3d, 5p & 7f rotate in opposite directions, this refers to as spin QN Thank You