Fundamental Building Blocks: Chemistry, Water, and pH

1. Chapter 2 Fundamental Building Blocks:Chemistry, Water, and pH

2. Chemistry’s Building Block: The Atom • All objects in the universe are made of matter (= anything that occupies space and has mass). • The fundamental unit of matter is the atom. • The three basic parts of an atom are: • protons (p+) • neutrons • electrons (e-)

3. Protons, Neutrons, and Electrons Protons have a positive (+) electrical charge, neutrons have no charge, and electrons have a negative (-) charge. Protons and neutrons exist in the atom’s nucleus, while electrons move around the nucleus.

4. electron (negative charge) electron shell proton (positive charge) nucleus neutron (no charge) Hydrogen (H) Helium (He) Figure 2.2

5. The Element • An element is any substance that cannot be reduced to any simpler set of substances through chemical means. • Each elem. is defined by the number of protons in its nucleus. • An elem. has its own unique chemical properties. • An atom is the smallest unit that retains the properties of a particular elem.

6. Matter is Transformed Through Chemical Bonding • Atoms can link to one another through chemical bonding. • When two or more atoms are linked together, it forms a molecule. • Covalent bonds form when atoms share one or more pairs of e-’s. • Ionic bonds can form when atoms gain or lose e-’s.

7. Formation of a Molecule hydrogen (H) atom hydrogen (H) atom hydrogen (H) atom hydrogen (H) atom oxygen (O) atom oxygen (O) atom (a) Two hydrogen atoms and one oxygen atom (b) One water molecule Figure 2.8

8. Covalent Bond • Atoms of different elements differ in their power to attract e-’s. • If the attraction of two atoms is similar, they can share e-’s equally, resulting in a nonpolar covalent bond • The elec. charge is spread equally across the mol.

9. Polar Bonding • If atoms attract e-’s differently, they can form a polar covalent bond • The e-’s are not shared equally and “prefer” one atom over the other • The mol. is polar (= one end is slightly pos. while another end is slightly neg.)

10. Ions • An atom with equal numbers of p+’s and e-’s is neutral (= has no net charge because the pos. charges perfectly cancel out the neg. charges). • But atoms can gain or lose one or more e-’s and become ions (the number of p+’s remains the same). • Positive ions have lost e-’s and negative ions have gained e-’s.

11. Ions

12. Ionic Bonding • The charge differences between pos. and neg. ions can link the ions together into a molecule. • This type of attraction is an ionic bond.

13. Hydrogen Bonding • H-bonds are not true chemical bonds because they do not form molecules • Instead they help shape a mol. or attract 2 mol.’s together • Hydrogen bonds form between a partially pos. hydrogen atom and a second partially neg. atom. • H-bonds are very weak by themselves but, in large numbers, can be very strong.

14. Hydrogen Bonding hydrogen bond Figure 2.11

15. Water and Life • Water is a polar mol. and has several qualities that strongly affect life on Earth. • Water is a powerful solvent, with the ability to dissolve polar and ionic substances in greater amounts than any other liquid. • A solution is a uniform mixture of two or more kinds of molecules, atoms, or ions. • The mol. dissolved in solution is the solute; whatever is doing the dissolving is the solvent.

16. Water’s Structure Gives It Many Unusual Properties • Because ice is less dense than liquid water, bodies of water do not freeze solid in winter. • Allows life to flourish under the ice. • Water has a great capacity to absorb and retain heat. • Because of this, the oceans act as heat buffers for the Earth, thus stabilizing Earth’s temperature, and the water in your cells does the same for your body.

17. Hydrophobic and Hydrophilic • Non-polar molecules do not interact well with water and are called hydrophobic. • Water cannot break down hydrophobic molecules (which is why oil and water don’t mix). • Molecules that are polar or carry an electric charge will interact with water and are called hydrophilic.

18. Acids and Bases Are Important to Life • Water (H2O) can dissociate (fall apart) into a hydrogen ion (H+) and a hydroxide ion (OH-) • The pH scale measures the concentration of H+’s that a given solution has and determines how basic or acidic that solution is. • This scale runs from 0 to 14, with 0 most acidic,14 the most basic (or alkaline), and 7 neutral.

19. Acids and Bases Are Important to Life • An acid is any substance that yields H+ when put in a liquid solution. • A base is any substance that accepts H+’s in solution. • The pH of a solution (or cell or body) is very important, affecting the chemical reactions that can occur.

20. REMINDER • Health/Safety regulations prohibit food and drink in lab classrooms, so please NO FOOD OR DRINK IN CLASS

21. Chapter 3 Life’s Components:Biological Molecules

22. Molecules of Life • Living cells produce several categories of biologically important molecules: • Carbohydrates • Lipids • Proteins • Nucleic acids

23. Why is Carbon Central to Life? • Biol. import. mol.’s usually are organic (consisting primarily of carbon and hydrogen atoms) – water (H2O) is an exception (it’s import. but not organic). • The carbon atoms bond covalently with up to four other atoms, often in long chains or rings called the carbon backbone of the mol. • Attached to the backbone are a variety of functional groups (clusters of atoms that provide special properties to the mol.)

24. Functional Groups Table 3.1

25. Structure and Function • The three-dimensional shape of a molecule is important as it determines its function. • If the shape of the mol. is altered/destroyed, so is its function.

26. Building Organic Molecules • Complex organic mol.’s are often very large and are called macromolecules. • Usually they are built by joining multiple sub-units, or monomers, into larger polymers. • Joining monosaccharides produces carbohydrates • Joining amino acids produces proteins • Joining nucleotides produces nucleic acids

27. Monomers vs. Polymers

28. Carbohydrates • Functions: • Source of quick energy • Transportable/storable forms of energy • Structural components • Simple sugars are monosaccharides used for a particular purpose • Complex carbs, or polysaccharides, are polymers of monosacc.’s

29. Complex Carbohydrates • Four polysaccharides are critical in the living world: • starch – stores energy in plants • glycogen – stores energy in animals • cellulose – used to build plant and algal cells • chitin – used to build fungi and some animal cells

30. Four Complex Carbohydrates (a) Potato (b) Liver (c) Algae (d) Tick Starch Glycogen Cellulose Chitin Figure 3.6

31. Lipids • Lipids do not readily dissolve in water (= are non-polar and hydrophobic). • Functions include: • Store more energy than other types of molecules • Structural components • Used to build cell membranes • Lipids are not built of monomers like other biological molecules.

32. Lipids • Triglycerides have three fatty acid chains and comprise most of the fat in our diets • Steroids have a core of four carbon rings and include cholesterol, testosterone, and estrogen • Phospholipids have two fatty acid chains and a phosphate group; these form the outer membrane of cells • Waxes are composed of a single fatty acid linked to a long-chain alcohol and are widely used as waterproofing and lubrication

33. The Triglyceride Tristearin glycerol fatty acids Figure 3.9

34. Steroids (a) Four-ring steroid structure (b) Side chains make each steroid unique testosterone cholesterol estrogen Figure 3.12

35. Phospholipids (a) Phospholipid structure — variable group phosphate group polar head nonpolar tails (b) Phospholipid orientation “like attracts like” nonpolar hydrophobic tails (fatty acids) exposed to oil phospholipids oil (nonpolar) polar hydrophilic heads exposed to water water (polar) Figure 3.14

36. Waxes Figure 3.15

37. Proteins • Proteins are an extremely diverse group of molecules composed of around 20 different amino acids. • Sequences of amino acids are strung together to produce polypeptide chains, which then fold up into working proteins. • Proteins are used in transportation, communication, and defense in the body and as structural units and enzymes.

38. Types of Protein Table 3.3

39. Four Levels of Protein Structure • The primary structure is the order in which amino acids join to form a polypeptide chain. • The secondary struct. is formed by folding the prim. struct. • The tertiary struct. forms by packing the sec. struct. more tightly. • The quaternary struct. results from two or more tert. struct.’s joining together. • The sec., tert., and quat. struct.’s are held by H – bonds.

40. Beginnings of a Protein The linkage of several amino acids . . . ala gln ile ala gln ile A typical protein would consist of hundreds of amino acids . . . produces a polypeptide chain like this: Figure 3.18

41. Levels of Protein Structure Four Levels of Structure In Proteins (a) Primary structure The primary structure of any protein is simply its sequence of amino acids. This sequence determines everything else about the protein’s final shape. amino acid sequence (b) Secondary structure Structural motifs, such as the corkscrew-like alpha helix, beta pleated sheets, and the less organized “random coils” are parts of many polypeptide chains, forming their secondary structure. alpha helix random coil beta pleated sheet (c) Tertiary structure These motifs may persist through a set of larger-scale turns that make up the tertiary structure of the molecule folded polypeptide chain (d) Quaternary structure Several polypeptide chains may be linked together in a given protein, in this case hemoglobin, with their configuration forming its quaternary structure. two or more polypeptide chains Figure 3.20

42. Why is Protein Structure So Important? • Protein structure determines function. • A single amino acid substitution can cause a serious change in function (e.g. sickle cell anemia). • A protein can denature, or unfold and lose its 3-dimensional shape, altering/destroying its function. • Denaturation can be caused by changes in pH or temperature and by exposure to certain chemicals (e.g. detergents).

43. Nucleic Acids • Nucleic acids are polymers composed of nucleotides. • DNA is a double – stranded molecule which encodes the genetic information of all living things. • The information in the DNA molecule is converted into a second type of nucleic acid called RNA (which are single – stranded). • Various types of RNA convert this information into proteins.

44. Nucleotide Functions • Nucleotides can have other functions – some function in metabolism and others as chemical messengers. • Perhaps the most important is ATP – a nucleotide with three attached phosphate groups. • ATP is used as the “energy currency” in a cell. • When a phosphate group is removed, it releases energy that the cell can use.

45. ATP as an Energy Source

46. Biological Molecules Table 3.4

47. Chapter 4 Life’s Home:The Cell

48. Cells are the Fundamental Units of Life • The cell theory states: • The cell is the smallest unit that retains the properties of life. • Every form of life on Earth consists of one or more cells. • Cells only arise through the growth and division of pre-existing cells.

49. What is a Cell? • All cells have a plasma membrane (PM), cytosol, DNA, and ribosomes.

50. What is a Cell? • The PM is the boundary layer separating the inside of the cell from the outside environment. • The cytosol is a jelly-like fluid filling the interior of the cell. • DNA codes for the genetic info. • Ribosomes are structures that produce proteins.