BIO 2, Lecture 3

1. BIO 2, Lecture 3 – O H H THE CHEMISTRY OF LIFE I: ATOMS, MOLECULES, AND BONDS + + H2O

2. Matter is made up of elements • A substance that cannot be broken down to other substances by chemical reactions • 92 naturally-occurring elements (periodic table) • A compoundis a substance consisting of two or more elements in a fixed ratio (e.g. NaCl, MgCl2) • A compound has characteristics different from those of its elements

3. Sodium Chloride Sodium Chloride

4. About 25 of the 92 naturally-occurring elements are essential to living organisms on Earth

6. Dwarfing of plants due to nitrogen deficiency Goiter due to iodine deficiency

7. An element’s chemical behavior and properties depend on the structure of its atoms • Each element consists of unique atoms • An atom is the smallest unit of matter that still contains the behavior and properties of an element • Atoms are composed of a nucleus containing protons (+) and (usually) neutrons, and electrons (-) that inhabit defined energy shells around the nucleus

8. Cloud of negative charge (2 electrons) Electrons Nucleus (b) (a)

9. Atoms of the various elements differ in number of subatomic particles they contain • An element’s atomic numberis the number of protons in its nucleus • An element’s mass number is the sum of protons plus neutrons in the nucleus • Atomic mass, the atom’s total mass, can be approximated by the mass number (since electrons are so light)

10. All atoms of an element have the same number of protons but may differ in number of neutrons • Isotopesare two atoms of an element that differ in number of neutrons • Radioactive isotopesdecay spontaneously, giving off particles and energy

11. Isotopes of hydrogen: • Symbol Name # protons # neutrons Half-life • 1H Protium 1 0 Stable • 2H Deuterium 1 1 Stable • 3H Tritium 1 2 12.3 yrs • 4H Lab only 1 3 Very low* • 5H Lab only 1 4 Very low* • 6H Lab only 1 5 Very low* • 7H Lab only 1 6 Very low* • * less than 10-22 seconds

12. Some applications of radioactive isotopes in biological research are: • Dating rocks and fossils • Tracing atoms through metabolic processes to learn about those processes • Diagnosing medical disorders

15. Compounds including radioactive tracer (bright blue) Incubators 1 3 2 20ºC 10ºC 15ºC Human cells 5 6 4 30ºC 25ºC 35ºC Human cells are incubated with compounds used to make DNA. One compound is labeled with 3H. 1 9 7 8 50ºC 40ºC 45ºC The cells are placed in test tubes; their DNA is isolated; and unused labeled compounds are removed. DNA (old and new) 2

16. The test tubes are placed in a scintillation counter. 3

17. Optimum temperature for DNA synthesis 30 Counts per minute ( 1,000) 20 10 0 40 20 30 50 10 Temperature (ºC)

18. Cancerous throat tissue

19. Energy is the capacity to do work (fight entropy) • Atoms have mass and therefore have potential energy; E = mc2 • Part of this energy is stored in the nucleus of the atom and part is stored in the energy levels of the electrons • An electron’s state of potential energy is called its energy level, or electron shell

20. (a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons (b) Third shell (highest energy level) Second shell (higher energy level) Energy absorbed First shell (lowest energy level) Energy lost Atomic nucleus

21. The chemical behavior of an atom is determined by the distribution of electrons in electron shells • The periodic table of the elements shows the electron distribution for each element • Valence electrons are those in the outermost shell, or valence shell • Elements with filled valence shells are inherently stable and don’t readily combine with other elements

22. Helium 2He Hydrogen 1H Atomic number 2 He 4.00 Atomic mass Element symbol First shell Electron- distribution diagram Lithium 3Li Beryllium 4Be Fluorine 9F Boron 5B Nitrogen 7N Neon 10Ne Carbon 6C Oxygen 8O Second shell Chlorine 17Cl Sodium 11Na Aluminum 13Al Silicon 14Si Argon 18Ar Magnesium 12Mg Phosphorus 15P Sulfur 16S Third shell

23. An orbitalis the three-dimensional space where an electron is found 90% of the time • Each electron shell consists of a specific number of orbitals • 1S (1 orbital; 2 electrons) • 2S (1 orbital; 2 electrons) • 2P (3 different oribitals; 6 electrons) • The shell is designated by the number, the orbitals by the letter • Atoms seek filled shells above all else

24. Neon, with two filled shells (10 electrons) (a) Electron-distribution diagram First shell Second shell (b) Separate electron orbitals y x z 1s orbital 2s orbital Three 2p orbitals (c) Superimposed electron orbitals 1s, 2s, and 2p orbitals

25. Atoms with incomplete valence shells can share or transfer valence electrons with certain other atoms • These interactions usually result in atoms staying close together, held by attractions called chemical bonds • A covalent bond is the sharing of a pair of valence electrons by two atoms • In a covalent bond, the shared electrons count as part of each atom’s valence shell

26. Hydrogen atoms (2 H) Both atoms unstable (unfilled valence shells) e- e- e- e- e- Atoms stable, share electrons so both have filled valence shells e- Hydrogen molecule (H2)

27. A moleculeconsists of two or more atoms held together by covalent bonds • A single covalent bond, or single bond, is the sharing of one pair of valence electrons • A double covalent bond, or double bond, is the sharing of two pairs of valence electrons

28. Lewis Dot Structure and Structural Formula Space- filling Model Name and Molecular Formula Electron- distribution Diagram (a) Hydrogen (H2) COVALENT BONDS (b) Oxygen (O2) (c) Water (H2O) (d) Methane (CH4)

29. Covalent bonds can form between atoms of the same element or atoms of different elements • A compound is a combination of two or more different elements • Bonding capacity is called the atom’s valence

30. Electronegativityis an atom’s attraction for the electrons in a covalent bond • The more electronegative an atom, the more strongly it pulls shared electrons toward itself • In a nonpolar covalent bond, the atoms share the electron equally • In a polar covalent bond, one atom is more electronegative, and the atoms do not share the electron equally

31. Unequal sharing of electrons causes a partial positive or negative charge for each atom or molecule (e.g. water) – The oxygen nucleus has more protons and attracts the shared electrons more strongly than the hydrogen nuclei O H H + + H2O

32. Rather than sharing electrons, atoms sometimes transfer electrons to their bonding partners because it fills their valence shells (makes them stable) • An example is the transfer of an electron from sodium to chlorine • After the transfer of an electron, both atoms have charges • A charged atom (or molecule) is called an ion • Ions with opposite charges attract to form ionic bonds

33. Cl Na Na Cl Cl– Na Cl Na+ Chloride ion (an anion) Sodium ion (a cation) Sodium atom Chlorine atom Sodium chloride (NaCl) IONIC BOND

34. Compounds formed by ionic bonds are called ionic compounds, or salts • Salts, such as sodium chloride (table salt), are often found in nature as crystals because they stack easily Na+ Cl–

35. Most of the strongest bonds in organisms are covalent bonds that form a cell’s molecules • Weak chemical bonds, such as ionic bonds and hydrogen bonds, are also important • Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other

36. A hydrogen bond forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom • In living cells, the electronegative partners are usually oxygen or nitrogen atoms • Hydrogen bonding is important in water, DNA and RNA, proteins, and many other molecules important for life

37.  + Water (H2O) HYDROGEN BOND +  Ammonia (NH3) + + +