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Chapter 2 Molecules of Life

Chapter 2 Molecules of Life. The Atom Fundamental unit of matter Nucleus Protons : Positive charge; mass of 1 Neutrons : No charge; mass of 1 Electrons Spin around the nucleus in orbitals (shells) Negative charge; No mass

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Chapter 2 Molecules of Life

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  1. Chapter 2 Molecules of Life

  2. The Atom • Fundamental unit of matter • Nucleus • Protons: Positive charge; mass of 1 • Neutrons: No charge; mass of 1 • Electrons • Spin around the nucleus in orbitals (shells) • Negative charge; No mass • Electrically negative: # of protons = # electrons http://www.yourdictionary.com/ahd/a/a0501900.html

  3. Electrons • Electrons carry energy. How?? • Electrons are negatively charged as such, they are attracted to the positive charge in the nucleus. Meanwhile, electrons repel other electrons. • REMEMBER… OPPOSITES ATTRACT and SAME REPELS • Electrons spin around the nucleus at various levels. They are attracted to the nucleus but repel each other, therefore it takes work to keep them in orbit. • Example is an apple in your hand.

  4. Electron Orbitals Volumes of space that surround the nucleus Electrons move in orbitals

  5. Electron shells and electron orbitals Constants: The 1st shell in any atom can hold 2 electrons The 2nd shell in any atom can hold 8 electrons The 3rd shell in any atom can hold 8 electrons Shell # of electrons each shell can hold First shell 2 Second shell 8 Third shell 8 P + N

  6. Electron Movement • Electron shells = energy levels • Electron orbital = Volume of space around a nucleus where an electron is most likely to be found • Useful Analogy: • planets (electrons) ORBITING around the sun (nucleus)

  7. Why is it necessary to understand how electron orbitals work? This isn’t a Chemistry class, right?? Electrons and the energy they posses (their energy state) determine the chemical behavior of atoms thus, the losing, gaining or sharing of electrons is the BASIS FOR CHEMICAL REACTIONS IN WHICH CHEMICAL BONDS FORM (chemical bonds include hydrogen bonding, ionic bonding and covalent bonding).

  8. If electrons couldn’t lose or gain other electrons, or share with other electrons, chemical bonds would NOT form! Example, H2O

  9. Element a substance that cannot be reduced into a simpler component substance through a chemical process

  10. http://cougar.slvhs.slv.k12.ca.us/~pboomer/chemlectures/textass2/secondsemass.htmlhttp://cougar.slvhs.slv.k12.ca.us/~pboomer/chemlectures/textass2/secondsemass.html

  11. How to Read the Periodic Table • Elements are arranged: LEFT to RIGHT and TOP to BOTTOM in order of increasing atomic mass. • Rows are arranged in periods Ex. H and He are in period 1 C and O are in period 2 • The period number of an element = highest energy level an electron in that element occupies in an unexcited state • Therefore, • H and He have 1 electron shell • C and O have 2 electron shells

  12. Columns represent groups and families. • Each element symbol has 2 numbers listed: atomic number and atomic mass. Atomic Number Number of protons in the nucleus 6 C 12 Atomic Mass Number of protons and neutrons in the nucleus

  13. Fig. 3.3

  14. Carbon • Carbon Facts: • 6 protons (Atomic # is 6) • 6 neutrons (Atomic mass is 12…so, how do you get 6?) N = Atomic Mass - P • 6 electrons (Atomic # is 6) • Is the first electron shell full (inactive)? • Is the second electron shell full? • How many unpaired orbitals does C have? Yes No 4

  15. Carbon • Carbon Facts: • How many chemical bonds can Carbon form with other atoms? 4 Can an element ever have a variable number of neutrons?

  16. Isotopes • Same atom but with a different # of neutrons, thus a different atomic mass • Atomic number = # protons in the nucleus • Atomic mass = # protons + # neutrons • Having a different number of neutrons in the nucleus DOES NOT change the chemical properties of an element BUT it DOES change the stability of the element!!

  17. Isotope Atomic # # protons # protons # protons 6 6 6 Atomic Mass # P + # N #P + # N # P + # N 6 + 6 = 12 6 + 7 = 13 6 + 8 = 14

  18. Medical Uses of Radioactive Isotopes • Short-lived isotopes are used clinically to diagnose pathological abnormalities/disease • Ex. Use of 99Tc for renal scan • 99 Tc (tracer) is introduced through your bloodstream • Kidney cells take up the radioactive tracer (isotope of Tc = 99Tc) • A camera detects emissions from the tracer and records them. • What makes 99Tc specific for kidney cells?

  19. The isotope is specific for a protein unique to kidney cells. Remember, electrons are the basis for chemical reactions!! So… if 99Tc has a different number of neutrons in its nucleus, the stability of the electrons in the other shell of that 99Tc atom are changed. There are 43 isotopes of Technitium! It just so happens that the particular stability of 99Tc seeks to form a chemical bond with this unique kidney protein.

  20. Matter • Any substance in the universe that has mass and occupies space • Matter is transformed through chemical bonding • Conservation of Matter = Matter cannot be created or destroyed but… it can be transformed • Use of an equation to show how matter is transformed: • Reactants Products • Sodium + Chloride Sodium chloride Na+ + Cl- NaCl

  21. Important Bonds in Biological Membranes • Way in which atoms link to one another to form molecules • Links are formed through the exchange of electrons • Atoms are driven to react to become more stable • Atomic stability is achieved by filling an outer electron shell • Non-reactive elements have full outer shells = INACTIVE • Types of chemical bonding • Ionic bonding • Covalent bonding • Hydrogen bonding

  22. Ionic Bonding • Creates ions (charged atoms): one atom loses electrons and becomes a (+) charged ion while another gains electrons and becomes (-) charged • Note: in charged atoms, the # of protons DOES NOT equal the # of electrons!!!! # Protons = # Electrons • Formed when atoms are attracted to each other by opposite electrical charges (i.e. magnet) • Two key properties of ionic bonding: • They are strong bond (although NOT the strongest) • They are non-directional

  23. Ionic Bonding Example: Table salt Reactants: Sodium atom has 1 lone electron in its outer orbital (Ax) + Chloride atom has 7 electrons in its outer orbital (Ax) Products: Sodium ION that has given up an electron from its outer shell + Chloride ION that has accepted an electron from Sodium and has included it in its outer shell

  24. Fig. 3.8

  25. Both the sodium ion and the chloride ion are electrically attracted because of the opposite charges incurred by the altered electron orbitals. This electrical attraction results in the formation of an elaborate matrix resulting in a crystal of table salt.

  26. Covalent Bonds • Electrons are shared between atoms • Two key properties of covalent bonding: • VERY STONG!!! (strongest type of bond) • Directional • Carbon ALWAYS forms a covalent bond!!!!! • 2 types: • Non-polar Covalent: electrons are equally shared • Generates hydrophobic molecules (“water hating”) • Polar Covalent: electrons are unequally shared • Generated hydrophilic bonds (”water loving”)

  27. Non-Polar Covalent Bond: Methane (CH4) H H H H

  28. Non-Polar Covalent Bond: Methane (CH4) H H H H

  29. Polar Covalent Bonding: H2O

  30. Hydrogen Bonding • Links a polar covalent molecule to another polar covalent molecule • Results in VERY WEAK bonding BUT because so many are formed, the complex as a whole is VERY STONG

  31. Hydrogen Bonding

  32. Solutions • A homogenous mixture of 2 or more substances • Solute = ingredient being dissolved • Solvent = substance that does the dissolving • Example. You make a solution of water and salt. Which is the solute and which is the solvent? Solute = Salt Solvent = Water • Components of solutions Acids Bases Salts pH

  33. Components of Solutions, continued • Acids • A substance that puts hydrogen ions (H+ )into a solution • Example: Hydrochloric Acid placed in water • HCl + H2O Cl- + H+ • Water HCl dissolved in water H H H H H H H H

  34. Components of Solutions, continued • Bases • A substance that puts hydroxide ions (OH-) into solution • Example: Sodium Hydroxide dissolved in water • NaOH + H2O Na+ + OH- • Water NaOH dissolved in water OH OH OH OH OH OH OH OH

  35. Components of Solutions, continued • Salts • A substance that puts other ions into solution (ions other than H+ and OH-) • Example: Sodium chloride dissolved in water • NaCl + H2O Na+ + Cl- + H2O Cl Na Na Na Cl Cl Cl Na Na Cl Na Na Cl Cl Na Cl

  36. Salts are formed when acids and bases are added to each other; this results in neutralization of the acid and base. • HCl + NaOH NaCl + H2O • (Acid) (Base) (Salt) (Water)

  37. Components of Solutions, continued • pH • A logarithmic scale that measures the acidity of alkalinity (basicity) of a solution • Note: the difference between 2 units on the pH scale is 10, therefore, the difference between 3 pH units is… 100 • pH scale • Neutral : pH = 7 • Acidic : pH < 7 • Basic : pH > 7 • Buffers keep pH within normal limits

  38. pH scaleAcidicNeutralBasic

  39. The Importance of Water to Life • Three quarters of the Earth’s surface is water • Two thirds of the human body is composed of water • All organisms require water • Since water is an essential part of life, it’s surprising that the bond that 2 atoms of H make with 1 atom of O is so weak. Actually, the bond that forms a single H20 molecule (which is what type of bond??) lasts only 1 / 100,000,000,000 of a second! • However, water molecules form extensive lattices with other water molecules. This occurrence leads to the important physical properties of water!

  40. Water • Water is a polar covalently bonded molecule that forms hydrogen bonds with other polar covalently bonded water molecules. • Universal solvent • Ice (solid water) is less dense than liquid ice. • Ex. Ice floats in liquid water • 4. Water has a high capacity to store heat. Water stabilizes Earth’s temperature (Remember, water comprises ¾ Earth’s surface. • 5. Adhesion and cohesion

  41. Properties of Water • Bonds to hydrophilic substances and repels hydrophobic ones • Stabilizes temperature • Expands when it freezes • Cohesive • Dissolves substances

  42. Cohesion Since water is polar, it is attracted to other polar molecules. Cohesion occurs when the other polar molecule is water. Surface Tension Created by cohesion and due to the strong hydrogen bonding between the polar water molecules.

  43. Chemistry:Macromolecules

  44. Forming Macromolecules • Organic molecule • Formed by living organisms • Carbon-based core with functional groups attached • Functional group • Groups of atoms with special chemical properties • Confer specific chemical properties on the molecules that posses them • Ex. • Macromolecules • Potentially large molecules (Macro-) that are the building materials of cells. They are the material that makes up the body of cells and the machinery that runs within cells • Thousands of different types in an organism BUT the body is made of 4 types (protein, nucleic acid, carbohydrates, lipids)

  45. Five Principle FunctionalGroups Figure 3.17

  46. More on Macromolecules • Polymer: a molecule made of MANY chains of a similar subunit • Monomer: a single molecule that is the BASIC building block of a macromolecule • Monomers can combine to form a polymer View animation on Polymer formationhttp://science.nhmccd.edu/biol/dehydrat/dehydrat.html

  47. Dehydration Synthesis • The process of FORMING a macromolecule • Forms a COVALENT bond between two subunits: • A hydroxyl (OH) group is removed from one subunit • A hydrogen (H) is removed from the other subunit • Small molecule + small molecule large molecule + H20 • View animation

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