Understanding Atoms, Elements, and Compounds in Biology

1. Chapter 6 – Chemistry in Biology UNIT 2 – THE CELL

2. Section 1 – Atoms, Elements & Compounds • Everything we see, are and experience comes from stardust

3. Atoms • Chemistry is the study of matter • Atoms are building blocks of matter • Although discussion began in the 5th century B.C., evidence was not in place until the 1800’s for the existence of the “atom”

4. Atoms are made up of even smaller particles • Nucleus (made up of p+’s and n0’s • Protons (+) • Neutrons (0) • Electrons (-) • Move around the nucleus • Atom is a result of attraction between particles • Overall charge on an atom is zero

5. Examples of “H” and “O” Atoms

6. Elements • Pure substance that cannot be broken down by physical or chemical means • Collected in the periodic table • Atomic mass • Chemical & physical behavior/characteristics • State • 92 naturally occurring • Horizontal rows called periods & vertical columns called groups/families

8. Isotopes • When atoms have different # of neutrons • Isotopes will have the same chemical characteristics

9. Radioactive Isotopes • Changing the number of neutrons can affect the stability of the nucleus • Radiation can be given off as a result • Ages can be taken by measuring the rate of decay in these radioactive isotope

10. Compounds • Two or more different elements combined • i.e. water, sodium chloride, methane • Must be in a fixed ratio • Are chemically & physically different from the elements that make them up • Cannot be broken down by physical means • Can be separated by chemical means (i.e. electrolysis

11. Chemical Bonds • Force that holds substances together • Energy levels & electrons control bonding • Forming chemical bonds stores energy while breaking them provides energy for life processes • There are two types • Covalent • ionic

12. Covalent Bonds • Share electrons in the outer shell • Majority of compounds in a living organism • Called a molecule • Can have single, double or triple bonds

13. Covalent Bond Example

14. Ionic Bond • Higher melting points • Give or take an electron • Electrical attraction • Most dissolve in water • Called ions most solid at room temperature • Helps maintain homeostasis in organisms • Transmits signals

15. Ionic Bond Example

17. Van de Waal Forces • Attraction between molecules • Dutch physicist named Johannes • Depends on the size, shape & ability to attract electrons • Not as strong as covalent or ionic • Key role in biological processes • This is why water droplets form

18. HOMEWORK 6-1 • Find a covalent (molecule) & ionic (ion) example not mentioned in the text or in class. Give the formula and explain the bond in picture form or words • Write a poem about the difference between ionic & covalent. Have at least one line dedicated to Van de Waals forces (no examples from class or text)

19. Section 2 – Chemical Reactions • This is why we grow, develop, reproduce & adapt • Reactant & products • Chemical reactions (i.e. rust) • Creates a new substance (change in color, production of heat or light, formation of new gas, liquid or solid)

20. Chemical equation • reactants on the left → products on the right • “→” meaning yields or reacts to form • Balanced equations – conservation of mass – use of coefficients Unbalanced Balanced

21. Energy of Reactions • Most compounds cannot undergoes chemical reactions without energy • Activation energy – the minimum amount of energy that it takes for reactions to occur (high or low) • Example: a candle will not light without a flame

22. Energy change in chemical reactions • Exothermic – releases energy in the form of heat (i.e. candle) • Endothermic – it absorbs heat energy (i.e. internal body homeostasis)

23. Enzymes • All living functions require numerous chemical reactions • Catalyst – a substance that lowers the activation energy & does NOT get used up in the reaction

24. Enzymes or biological catalysts will speed up biological processes, are essential to life & can be reused. • i.e. amylase that is found in saliva • Most enzymes are specific to one reaction • Substrates (reactants that bind to enzyme) • Active site is where the substrates attach themselves (like puzzle pieces) • Once binding occurs, active site changes to an enzyme-substrate complex • pH, temperature & other substances can affect the enzyme

25. Example of Enzyme as catalyst

26. Substrate at Active Site of Enzyme

28. 6-2 Homework • Apple Lab pg. 159 at home. Create a table to record findings and take photographs (possible groups of 2) • Give an example of enzyme not mentioned in book or class and tell me name and function of said enzyme • Balance equations on the handout and list products and reactants • Other than book or class topics, let me know a specific example (real world please) of an endothermic and exothermic reaction.

29. Section 3 – Water and Solutions

30. Water’s Polarity • Is water covalent or ionic? • Unequal distribution of electrons in the water molecule • Polar molecules (i.e. tug o war) • Opposites attract (electrostatic attraction) – in water this is called a hydrogen bond (F,O,N) – Van de Waal force • So what is the formula for water? What is it made of? What is the formula for ice? For water vapor?

31. Mixtures • Combo of two or more substance • Homogeneous (solution) • Solvent & solute • Heterogeneous • Suspension • colloid

32. Acids & Bases • Acids (release H+ ions when dissolved in H₂O) • Bases (release OH- ions when dissolved in H₂O)

33. pH & Buffers • Biological processes carried out in pH range of 6.5 to 7.5 • Buffers are mixtures that react with acid & bases to keep pH in that safe range

34. 6-3 Homework • Paragraph on H₂O importance in the body • Examples (that were not mentioned in class or text) of a solution, a colloid, a suspension and a homogenous mixture with the reasons why.

35. Section 6-4 The Building Blocks of Life (Carbon based)

36. Organic Chemistry • Study of organic compounds (containing C) • Can be a straight, branched or ringed molecule – which leads to diversity of life on the planet

37. Macromolecules • Large molecules formed by joining smaller organic molecules together • Also called polymers which are large molecules made up of repeated molecules called monomers • There are 4 types of macromolecules/polymers • Carbohydrates • Lipids • Proteins • Nucleic acids

38. Carbohydrates (see pg. 168)

39. Carbohydrates • Stores energy, provides structure • Made up of 1 C, 2 H’s, 1 O (CH₂O)n • Where “n” is 3 – 7 then the carb. is a simple sugar ( see glucose illustration) • When 2 monosaccharides are put together (ex. Sucrose or lactose) it is called a disaccharide • Even longer chained monosaccharides are called polysaccharides • Makes up plants mass, exoskeletons, ect.

40. Lipids • Store energy, provide barriers • Fats, oils & waxes • Fatty acids, glycerol & other compounds • Prevents water loss from plants • Needed to carry out body functions • Saturated (will not accept H’s) & unsaturated (will accept H’s) • Polyunsaturated can accept more H’s • Phospholipids – responsible for structure and function of cell membrane since lipids are hydrophobic they create wonderful barriers between cells • Steroids • Cholesterol & hormones

41. Proteins • Transport substances, speed reactions, structural support, hormones • Made up of amino acids (C,N,O,H and sometimes S) • Bonds covalently with H, amino group (-NH₂), carboxyl (-COOH) & variable(-R) • There are 20 variables • Peptide bonds amino acids together forming proteins • Makes up 15% of body mass

42. Amino Acids Making a Protein

43. Protein Shapes

45. Nucleic acids • Store and transmit genetic information • Made up of nucleotides (C, N, O, P, H) • 6 major nucleotides (all have) • A phosphate • A nitrogenous base • A ribose sugar • DNA & RNA (deoxyribonucleic acid & ribonucleic acid) • ATP (Adenosine triphosphate)

46. Nucleic Acids

47. 6-4 Homework • Comprehension Sentences • Handout • Tutorials • Awesome grade on test