BIOO211 Biochemistry for Complementary Therapists

Transcription

1 BIOO211 Biochemistry for Complementary Therapists Session #1 Introduction to Chemistry Department of Bioscience

2 Introduction to Biochemistry for Complementary Therapists o Subject outline and aims o Assessment o Teaching resources o Scientific method o Chemistry: the study of matter Endeavour College of Natural Health 2

3 The scientific method o The scientific method is a set of general principles that helps to describe how a scientist thinks. o Make observations about nature and ask questions about what you observe. o Propose a hypothesis, which states a possible explanation of the observations. o Several experiments (method and materials) may be done to test the hypothesis. o When results of the experiments are analyzed, a conclusion is made as to whether the hypothesis may be true or false. o Endeavour College of Natural Health 3

4 Using scientific method o The hypothesis is modified if the results of the experiments do not support it. o The scientific method develops conclusions using observations, hypotheses, and experiments Pearson Education, Inc Endeavour College of Natural Health 4

5 How matter is organised o Matter is anything that has mass and occupies space. o Mass is the amount of matter in any object. o Weight is the force of gravity acting on matter. o In outer space, weight is close to zero, but mass remains the same as on Earth. Figure 2.4 (c) Brass is a homogeneous mixture of copper and zinc atoms (Timberlake, 2013, p. 56) Endeavour College of Natural Health 5

6 Classification of Matter 2016 Pearson Education, Inc Endeavour College of Natural Health 6

7 Elements o Elements are pure substances that cannot be separated into simpler substances by ordinary laboratory processes. o There are at least 118 elements known today. o These elements can be identified by physical properties o Shape, color, density, conduction electricity and heat Endeavour College of Natural Health 7

8 Element symbols from Latin Names Some symbols (not all!) are derived from Latin names as shown below: Cu, copper (cuprum) Au, gold (aurum) Fe, iron (ferrum) Ag, silver (argentum) Diagrams from Table 3.2 (Timberlake, 2013, p. 84) and Table 2.2 (Timberlake, 2007) Endeavour College of Natural Health 8

9 Compounds and mixtures Compounds o Contain two or more elements in a definite ratio: o Salt (NaCl) o Table sugar (C 12 H 22 O 11 ) o Water (H 2 O) Mixtures o Two or more substances that are physically mixed, not chemically combined in different proportions. o Substances that can be separated by physical methods o Two types: homogeneous and heterogeneous Endeavour College of Natural Health 9

10 Atoms Dalton s Atomic Theory Are tiny particles of matter. Of an element are similar and different from other elements. Of two or more different elements combine to form compounds. Are rearranged to form new combinations in a chemical reaction. Atoms are never created or destroyed during a chemical reaction. Aluminum foil consists of atoms of aluminum Endeavour College of Natural Health 10

11 Structure of an Atom An atom consists of a nucleus that contains protons and neutrons. electrons in a large, empty space around the nucleus. Fig 4.10 Q. Why can we say that an atom is mostly empty space? (Timberlake, 2016, p. 144) Endeavour College of Natural Health 11

12 Charges of Subatomic Particles Protons have a positive (+) charge. Electrons have a negative (-) charge. Like charges repel and unlike charges attract. Neutrons are neutral. Animation of an atom < Fig 4.8 Like charges repel, and unlike charges attract Timberlake, 2016, p. 144) Endeavour College of Natural Health 12

13 Atomic Mass Scale On the atomic mass scale for subatomic particles 1 atomic mass unit (amu) is defined as 1/12 of the mass of the carbon-12 atom. A proton has a mass of about 1 (1.007) amu. A neutron has a mass of about 1 (1.008) amu. An electron has a very small mass, amu. Fig 2.1 How are the electrons of carbon distributed between the first and second shells? (Tortora and Derrickson, 2012, p. 31) Endeavour College of Natural Health 13

14 Atomic Number and Protons The atomic number Is specific for each element. Is the same for all atoms of an element. Is equal to the number of protons in an atom. Appears above the symbol of an element. Atomic Number Symbol 11 Na Endeavour College of Natural Health 14

15 Number of Electrons in An Atom An atom of an element is electrically neutral; the net charge of an atom is zero. has an equal number of protons and electrons. number of protons = number of electrons For example: aluminum has 13 protons and 13 electrons. The net charge is zero. 13 protons (13+) + 13 electrons (13 -) = 0 Endeavour College of Natural Health 15

16 Mass Number The mass number Represents the number of particles in the nucleus. Is equal to the Number of protons + Number of neutrons (Timberlake, 2016, p. 147) Endeavour College of Natural Health 16

17 Isotopes Isotopes are atoms of the same element that have different mass numbers. Have the same number of protons, but different numbers of neutrons, as a result the mass number is going to be different Mg is the atomic symbol. Table 3.7 (Timberlake, 2013, p. 98) Endeavour College of Natural Health 17

18 Atomic mass of an element The atomic mass of an element is often listed below the symbol of each element on the Periodic Table gives the mass of a weighted average atom of each element compared to C-12 is not the same as the mass number in amu; since it is a weighted average, it is a decimal (Timberlake, 2016, p. 151) Endeavour College of Natural Health 18

19 Concept Map: Atoms & Elements Endeavour College of Natural Health 19

20 Periodic Table Periodic table is an arrangement of elements by increasing atomic number. Vertical column Group Horizontal row Period A group contains elements with similar chemical and physical properties. Each group is identified by a group number at the top of the column. Endeavour College of Natural Health 20

21 Elements and the periodic table Fig 3.1 What is the symbol and name of the alkali metal (group 1A) in Period 3? (Timberlake, 2013, p. 86, 2016 p. 137) Light blue: Metals, tend to lose electron Light green: metalloid Yellow: non-metal, tend to gain electrons Endeavour College of Natural Health 21

22 Electron Arrangements in Atoms o Electrons with similar energies are grouped in an energy level (shell) there is a maximum of 7 energy levels o Energy level closest to the nucleus contain electrons with the lowest energies o Energy level further away from the nucleus contain electrons with higher energies o Each energy level can hold different number of electrons 2n 2 = the maximum No. of electrons that can be placed onto a energy level o Energy level 1 2 e -, Energy level 2 8 e -, Energy level 3 18 e -, Energy level 4 32 e -, etc. Endeavour College of Natural Health 22

23 o Sublevel s : houses electrons with the lowest energy within one particular energy level Sublevels o o Sublevel p Sublevel d o Sublevel f : houses electrons with the highest energy within one particular energy level o Orbital Each sublevel consists of a specific number of orbitals; is a region around the nucleus where an electron is most likely to be found. o Each sublevel can hold a specific No. of electrons: o Sublevel s holds 2 e - o Sublevel p can hold 6 e - o Sublevel d takes up 10 e - o Sublevel f holds a maximum of 14 e - Endeavour College of Natural Health 23

24 Electronic configuration o Describes how the electrons occupy in the orbitals o Orbitals fill in the order of increasing energy from lowest to highest o Each orbital can hold up to two electrons o E.g: carbon atomic number is 6, has 6 electron and the electronic configuration is; 1S 2, 2S 2 2P 2 Endeavour College of Natural Health 24

25 Electronic Arrangement and the Position of an Element in the Periodic Table (the Periodic Law) o What does the electron arrangement tell us about an elements location in the Periodic Table? Elements that have the same electron arrangement in their outer shells, belong to the same group and have similar chemical properties. The number of the outermost shell indicates the Period to which an A block element of A block belongs. Electrons in outermost shell are referred to as valence electrons. Group number = number of valence electrons Endeavour College of Natural Health 25

26 Electron-Dot (Lewis) Symbols An electron-dot symbol Indicates valence electrons as dots around the symbol of the element. Magnesium has two valence electrons (Group 2A), shown as single dots on the side of the symbol Mg.. Mg or Mg or Mg or Mg Groups 5A to 7A use pairs and single dots. P : O Endeavour College of Natural Health 26

27 Formation of Ions o What are ions and how do they form? An ion is a charged form of an atom, formed by losing or gaining electron to acquire eight electrons in the outer energy level (electron configuration of the nearest noble gas). An atom which loses electrons from its valence shell, forms a positively charged ion (cation) An atom that gains electrons in its valence shell, forms a negatively charged ion (anion) Polyatomic ions contain more than one type of atom Fig 2.4 Ions and Ionic bond formation (Tortora and Derrickson, 2012, p. 34) Endeavour College of Natural Health 27

28 Metals Form Positive Ions o Metals form positive ions by a loss of their valence electrons; o They prefer to have the electron configuration of the nearest noble gas. Positive ions have more protons than electrons. Group 1A(1) metals ion 1+ Group 2A(2) metals ion 2+ Group 3A(3) metals ion 3+ Endeavour College of Natural Health 28

29 Transition Metals form Positive Ions o Most transition metals (3-12) and Group 4A (14) metals form 2 or more positive ions, except Zn 2+, Ag +, and Cd 2+, which form only one ion. Endeavour College of Natural Health 29

30 Formation of Sodium Ion, Na + o Sodium forms an octet by losing its one valence electron. Na Na + + 1e- 1s 2 2s 2 2p 6 3s 1 1s 2 2s 2 2p 6 (= Ne) o Sodium has 1 electron in the outer shell loses that electron to become stable o Na +, a positive ion forms with a +1 charge. Sodium atom, Na 2e-,8e-,1e- 11 p+ 11 p+ 11e- 10 e- Sodium ion, Na + 2e-, 8e- 0 charge overall 1 + charge overall 2016 Pearson Education, Inc. Endeavour College of Natural Health 30

31 Formation of Chloride Ion, Cl - o In ionic compounds, nonmetals achieve an octet arrangement. gain electrons. form negatively charged ions with 3 -, 2 -, or 1 - charges, ( 8 Group number) o E.g. Chlorine (electron arrangement 2e-, 8e-, 7e-) 2016 Pearson Education, Inc. Endeavour College of Natural Health 31

32 Ionic Charge from Group Numbers The charge of a positive ion is equal to its Group number. Group 1A(1) = 1+ Group 2A(2) = 2+ Group 3A(3) = 3+ The charge of a negative ion is obtained by subtracting 8 or 18 from its Group number. Group 6A(16) = 6-8 = 2 - or = 2 - Endeavour College of Natural Health 32

33 Some Ions in the Body Timberlake 2016, p. 220 Endeavour College of Natural Health 33

34 Ions, molecules and compounds o o o Ions are formed by ionisation are charged an atom that gave up or gained an electron written with its chemical symbol and (+) or (-) Molecule electrically neutral element or compound when atoms share electrons eg H 2 or H 2 O written as molecular formula showing the number of atoms of each element (H 2 O) Compound electrically neutral in the crystal (solid) Compound = atoms bonded together that are not the same element Endeavour College of Natural Health 34

35 Ionic and Covalent Bonds Atoms form octets To become more stable. By losing, gaining, or sharing valence electrons. By forming ionic or covalent bonds. Metal, M, loses electrons; Non-metal, Nm gains electrons in an Ionic Bond Nm-Nm, non-metals form covalent bonds

36 Covalent bonds and dot diagrams o Carbon is in Group IVA and needs 8-4 = 4 covalent bonds to be stable o Nitrogen is in Group VA and needs 8-5 = 3 covalent bonds to be stable o Oxygen is in Group VIA and needs 8-6 = 2 covalent bonds to be stable o Octet number subtract group number = # bonds for a stable compound 2016 Pearson Education, Inc Endeavour College of Natural Health 36

37 Chemical Bonds and o Electronegativity is a measure of the attraction an atom has for the electrons it shares in a chemical bond o Electronegativity increases from left to right across the Periodic Table decreases from top to bottom o O and N very electronegative compared to H atom this will be important when properties of H 2 O are studied Electronegativity 2016 Pearson Education. Inc Endeavour College of Natural Health 37

38 Lewis Model of Bonding and the Octet Rule o What is the Octet Rule? o Applies strictly to elements 1 to 20 only. Hydrogen (element 1) achieves stability by filling or emptying its first energy shell. o Elements in Groups I to VIIA of the Periodic Table tend to react in ways which achieve a full outer shell, usually with eight valence electrons. o They achieve this by losing (metals), gaining (non-metals) and sharing of electrons (non-metals) o Noble gases (which already possess this stable, outer shell electron arrangement) are chemically unreactive. Group VIIIA Endeavour College of Natural Health 38

39 Polyatomic ions o A polyatomic ion is a group of two or more atoms that has an overall ionic charge, but is bonded covalently o Some examples of polyatomic ions in foods, remedies and in the body are: o NH 4 + o OH - o SO 4 2- o NO 3 - ammonium hydroxide Sulphate nitrate NO 2 - nitrite CO carbonate HCO 3 - hydrogen carbonate (bicarbonate) PO phosphate othe formula of an ionic compound has overall charge equal zero (0, balanced out). Refer to Table 6.7,p.229, Timberlake, 2016 Na + and NO 3- NaNO 3 Endeavour College of Natural Health 39

40 Naming Simple Chemical Compounds Endeavour College of Natural Health 40

41 Learning Check, ionic compounds If ionic bonding: Name the Metal ion first, use the name of the element Non-metal ion uses the name of the element but ends in ide, or if a polyatomic ion, named accordingly Endeavour College of Natural Health 41

42 Naming covalent compounds o If covalent, name the first element plus a prefix - if needed o The second name uses a syllable from the element s name but ends in ide. o Use a prefix on the second name as there are other compounds with the same elements (mono = one; di = two; tri = three; tetra = four o E.g.: CO 2 (carbon dioxide), SO 3 (Sulphur trioxide) o Refer Table 6.10 Timberlake 2016, p.233. o Some covalent compounds have special names e.g. water, methane, ammonia Learning check: o o o The correct name for the covalent compound N 2 O 3 is: A) nitrogen oxide. B) nitrogen trioxide. C) dinitride trioxide. D) dinitrogen oxide. E) dinitrogen trioxide. Answer: E It is important when naming covalent compounds, to use prefixes to distinguish e.g. N 2 O 3 from N 2 O (laughing gas or nitrous oxide or dinitrogen oxide) Endeavour College of Natural Health 42

43 Concept Map: Compounds & Their Bonds Endeavour College of Natural Health 43

44 Post-Session summary 1. Define chemistry and matter. /revision questions 2. Define chemical & physical change. 3. Describe the concept of an atom and describe electrical charge, and the location of the proton, neutron and electron. 4. Define atomic mass, atomic number, ions and isotopes 5. Write the correct symbol for the major elements in the human body. 6. Define the octet rule and electron levels. 7. Describe the different between ionic and covalent compounds. 8. Describe polar and non-polar compounds 9. Name ionic and molecular compounds. 10. Table 6.7 Names and formulas of some common polyatomic ions important in physiological processes : learn hydroxide, ammonium, carbonate, hydrogen carbonate, CH 3 COO - acetate (ethanoate), phosphate, hydrogen phosphate and dihydrogen phosphate Endeavour College of Natural Health 44

45 References & Diagrams Timberlake, KC 2016, General, organic, and biological chemistry, 5 th edn, Pearson, Boston. Timberlake, KC 2013, General, organic, and biological chemistry, 4 th edn, Pearson Benjamin Cummings, Boston. Timberlake, KC 2010, General, organic and biological chemistry, 3 rd edn, Pearson Benjamin Cummings Timberlake, KC 2007, General, organic and biological chemistry,2 nd edn, Pearson Benjamin Cummings Tortora, G. and Derrickson, B 2012, Principles of anatomy and physiology, 13 th edn, John Wiley & Sons, Inc, Hoboken, NJ. Endeavour College of Natural Health 45

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