chapter_2 powerpoint for high school AP.

Anatomy and physiology slide

1. The Chemical Level of Organization Raritan Valley Community College Dr. Ahmed Katsha [email protected]

2. Disclosure This course is using Open Education Resources (OER) mainly from OpenStax . This OpenStax ancillary resource is © Rice University under a CC-BY 4.0 International license; it may be reproduced or modified but must be attributed to OpenStax , Rice University and any changes must be noted. Images in these slides are from OpenStax textbook unless otherwise noted. Text is a mix from OpenStax text and Dr. Ahmed Katsha own explanation.

3. Chapter 2: CHEMICAL LEVEL OF ORGANIZATION Learning Objects: Describe the fundamental composition of matter Identify the three subatomic particles Identify the four most abundant elements in the body Explain the relationship between an atom’s number of electrons and its relative stability Distinguish between ionic bonds, covalent bonds, and hydrogen bonds Explain how energy is invested, stored, and released via chemical reactions, particularly those reactions that are critical to life Explain the importance of the inorganic compounds that contribute to life, such as water, salts, acids, and bases Compare and contrast the four important classes of organic (carbon-based) compounds—proteins, carbohydrates, lipids and nucleic acids—according to their composition and functional importance to human life

4. Why do we need to understand Chemistry? Understanding the building blocks of human body helps in understanding how does it work Changes at the atom levels significantly affect homeostasis and causes no responsiveness in neurons and muscles. Changes in pH causes malfunctioning in proteins and intervene with oxygen transport and hormone functions. Understanding chemistry and biochemistry helps to determine the most effective solutions to use to treat dehydration and fluid loss.

5. Videos about chemistry A playlist of several videos about chemistry https://www.youtube.com/watch?v=thnDxFdkzZs&list=PLlpyoea1FfWtrHPtHqtisoyAfTpW3ZnJk

6. Basic Chemistry: Matter Matter is anything that occupies space and has mass. Wood, Air and Water are few examples of matter. Matter is made out of elements. Elements are a substance that is distinguished from all other matter by the fact that it cannot be created or broken down by ordinary chemical means. Easy Concept

7. Matter, Elements and Atoms Matter Elements Atoms Protons Neutrons Electrons

8. Matter, Elements and Atoms Four elements form the bulk of the body: Oxygen, Carbon, Hydrogen, and Nitrogen There are other 9 essential elements There are other 11 important elements Easy Concept

9. Atoms Elements are composed of atoms. Atoms are smallest quantity of an element that retains the unique properties of that element an atom of hydrogen is a unit of hydrogen—the smallest amount of hydrogen that can exist. Atoms are referred to by one or two letters coming from their names “H” for Hydrogen, “O” for oxygen, “C” for carbon Some symbols come from Latin names: “Na” ( natrium ) is sodium; “K” ( kalium ) is potassium Easy Concept

10. Atomic structure Atoms are made up of three subatomic particles: Protons Positively charged (+) Have 1 atomic mass unit (1 amu ) Neutrons No charge (neutral) Have 1 amu Electrons Negatively charged (  ) Are so tiny they have virtually no weight (1/2000 amu ) Easy Concept

11. Atoms structure Atoms are neutral since the number of protons equal the number of electrons. Since protons and neutrons are heavy, they are located in the center of the atom which is the nucleus. Since electrons are lighter, they constantly spin around the nucleus The positive proton attracts them to stay around but not within the nucleus. Easy Concept

12. Atoms Different elements contain different numbers of subatomic particles. Each atom has a unique number of neutron. Electrons spin around the nucleus in energy levels called electron shells. Electron shells have different number of electrons.

13. Atoms The far the electron from the nucleus, the more energy it has and the easiest to separate from the atom. Atoms can have up to 7 electron shells. We will study only three. Each shell can hold limited number of electrons: 1 st shell holds up to 2 electrons 2 nd shell holds up to 8 electrons 3 rd shell holds up to 18 electrons Electrons fill the lower shell before moving to higher one

14. Role of Electrons The outer shell is called the valence shell. Atoms are most stable when they have 8 electrons in their valence shell. This is known as the octet rule. Since electrons tend to leave the atom, they control the ability of the atom to participate in chemical reactions. The atoms are neutral since the number of protons equal the number of electrons. Any changes in electron number will change the charge of the atom.

15. Role of Electrons Most of the atoms do not have 8 electrons in their valence shell. Because of the octet rule, atoms engage in chemical reactions to either gain, lose or share electron(s) and have 8 electrons in their valence shell.

16. Compounds and Molecules Atoms when react they form chemical bond. A bond is a weak or strong electrical attraction that holds atoms in the same vicinity. Bonds are energy relationships between the atoms and not physical connection. When two identical atoms form a bond they form a molecule . Example of molecules is O 2 and H 2 If the atoms are different, they form a compound. Because of the octet rule, atoms engage in chemical reactions to either gain, lose or share electron(s) and have 8 electrons in their valence shell. Easy Concept

17. Chemical Bonds Three main types of chemical bonds Ionic bonds Covalent bonds Hydrogen bonds

18. Ionic bonds When atoms lose or gain electrons they become Ions In ions the number of protons and electrons is not equal Atoms lose or gain electron to have 8 electrons in their valence shell. If the atom loses an electron or more it becomes a cation. Cations are positively charged ions. If the atom gains an electron or more it becomes an anion . Anions are negatively charged ions.

19. Ionic bonds A classical example of ionic bond is the table salt or NaCl . Na donates its lonely electron in its valence shell to have only 8 electrons in the 2 nd level (the new valence shell). Na will become a cation. Cl accepts the donated electron to have 8 in its valence shell and becomes an anion. The opposite charges of anion and cation result in attraction between the two atoms. This attraction is the Ionic Bond.

20. Ionic bonds Salts in general are results of ionic bond. Salts are crystals when dry. Salts are easily disassociate in water and ions will be released. The Na + and Cl - once disassociated they remain ions (Na does not get its electron back!) +

21. Covalent bonds Molecules formed by a covalent bond share electrons in a mutually stabilizing relationship. The atoms do not lose or gain electrons permanently. Electrons spin around the two atoms endlessly so each atom feel having 8 electrons in its valence shell. Two types: Polar. Nonpolar. https://www.youtube.com/watch?v=0HfN3CvXP2M

22. Covalent bonds Sharing 2 electrons results in a single bond H2 molecule Sharing 4 electrons is a double bond Oxygen molecule CO2 compound Sharing 6 electrons is a triple bond Nitrogen molecule (N 2 )

23. Covalent bonds: Polar vs Nonpolar Nonpolar covalent bonds Electrons spend equal time at each atom. Electrons shared equally. Gives neutral nonpolar compounds such as CO 2 Polar covalent bonds Electrons spend more time around one atom. Electrons shared unequally. Gives in electrically polar molecules (one end positive and the other is negative) Atoms have different electron-attracting abilities, leading to unequal sharing.

24. Polar covalent bonds H2O is a classical example of polar molecule Oxygen has more attraction force (electronegative) for the electrons, so it pulls the shared electrons from the 2 hydrogen atoms. O will display partial 2 ( d − ) negative charges and each H will display a partial 1 ( d + ) positive charge. Electrons spend more time around the oxygen atom and less time around the hydrogen atom. Water as a molecule has no charge.

25. Hydrogen bonds Formed when a weakly positive hydrogen atom already bonded to one electronegative atom (for example, the oxygen in the water molecule) is attracted to another electronegative atom from another molecule. In other words, hydrogen bonds always include hydrogen that is already part of a polar molecule. https://www.youtube.com/watch?v=aH2IbYs_XjY

26. Chemical Reactions Chemical reactions are results of chemical bonds formation, rearrangement, or breakage. Scientists developed chemical equations to write the reactions in symbolic forms. Reactants : one or more substances that enter into the reaction Product(s) : one or more substances produced by a chemical reaction The numbers indicate the amounts of reactants and products 2A + B A 2 B

27. Types of Chemical Reactions Three main types of chemical reactions: Synthesis (chemical reaction that results in the synthesis (joining) of components that were formerly separate Results in larger molecule. Building process (anabolism) uses synthesis reaction A + B  AB Easy Concept Amino acids joined together in a synthesis reaction to form a protein

28. Types of Chemical Reactions Decomposition chemical reaction that breaks down or “de-composes” something larger into its constituent parts) Breaks the large molecule to smaller molecules Catabolism reaction uses decomposition reaction AB  A + B Easy Concept Proteins can be broken down by certain enzymes to their amino acids

29. Types of Chemical Reactions (cont.) Exchange reactions are chemical reaction in which both synthesis and decomposition occur, chemical bonds are both formed and broken, and chemical energy is absorbed, stored, and released AB + C  AC + B and AB + CD  AD + CB Easy Concept Na H OH Cl + Na H OH Cl +

30. Reversibility of Chemical Reactions In general chemical reactions are reversible. They can move in both direction till equilibrium. A + B AB Many chemical reaction in living things are not reversible Due to the high energy needed to reverse the reaction or the availability of the products. Easy Concept

31. Rate of Chemical Reactions The speed of chemical reactions can be affected by: Properties of the Reactants: the greater the surface area of the reactants, the more readily they will interact. Temperature: The higher the temperature, the more likely they are to react. Concentration and Pressure: chemists can speed up chemical reactions by increasing the concentration of particles—the number of particles in the space—and/or decreasing the volume of the space, which would increase the pressure. Particle size: smaller particles usually increase rate. Enzymes and Other Catalysts: catalyst is a substance that increases the rate of a chemical reaction without itself undergoing any change. An enzyme is a catalyst composed of protein or ribonucleic acid (RNA) Enzymes are biological catalysts Easy Concept

32. Chemistry of Biological Systems (Biochemistry) Biochemistry is the part that studies chemical composition and reactions within living biological systems. Depending on the composition, chemicals can be organic or inorganic Inorganic compounds: is a substance that does not contain both carbon and hydrogen. Water , salts , and many acids and bases Organic compounds: is a substance that contains both carbon and hydrogen. Carbohydrates, fats, proteins, and nucleic acids

33. Inorganic Compounds Water As much as 70 percent of an adult’s body weight is water. This water is contained both within the cells and between the cells that make up tissues and organs. Its several roles make water indispensable to human functioning. Water as a Heat Sink Water as a Component of Liquid Mixtures Water as a Lubricant and Cushion Role of Water in Chemical Reactions

34. Water Water as a Heat Sink A heat sink is a substance or object that absorbs and dissipates heat but does not experience a corresponding increase in temperature . In the body, water absorbs the heat generated by chemical reactions without greatly increasing in temperature. Water can absorb the same amount of heat that will warm other substances without significant change in its temperature Heat Heat

35. Water Water as a Component of Liquid Mixtures A mixture is a combination of two or more substances, each of which maintains its own chemical identity. Example: Oil and water There are three types of liquid mixtures, all of which contain water as a key component. These are solutions, colloids, and suspensions

36. Solutions Consists of a solvent that dissolves a substance called a solute. Solutions are homogeneous; the solute molecules are distributed evenly throughout the solution. Solutions do not precipitate (settle down) over time. Water is considered the “universal solvent” Example of solutions: sugar and water, salt and water, blood sugar – glucose is solute, and blood (plasma) is solvent. Easy Concept

37. Solutions Water molecules are polar, with regions of positive and negative electrical charge, water readily dissolves ionic compounds and polar covalent compounds. Polar molecules are hydrophilic (water-loving) and can dissolve easily in water. Nonpolar molecules are hydrophobic (water-hating) and can not dissolve in water. Easy Concept

38. Concentration of solutions We can express concentration in three ways Percentage: Number of solute particles in 100 parts of a solution. Example: 2% milk means 2 parts fat to 98 parts of milk Milligrams per deciliter (mg/dl) Deciliter equals 1/10th of a liter Example: normal fasting blood glucose levels are between 70-99 mg/dl Molarity (M) which is moles (M) of the molecules per liter (L)

39. Colloids A colloid is a mixture that is somewhat like a heavy solution. The solute particles consist of tiny clumps of molecules large enough to make the liquid mixture opaque (not transparent). Colloid do not settle down or takes long time to settle. Examples: milk, mayonnaise, whipped cream. Polar molecules are hydrophilic (water-loving) and can dissolve easily in water. Easy Concept

40. Suspensions Liquid mixture in which a heavier substance is suspended temporarily in a liquid, but over time, settles out. Examples: water and sand, blood. Easy Concept

41. Lubricant : Water is a major component of many of the body’s lubricating fluids. Water in synovial fluid lubricates the actions of body joints Cushioning: Water also protects cells and organs from physical trauma. cushioning the brain within the skull and protecting the delicate nerve tissue of the eyes. Water as a Lubricant and Cushion

42. Two types of chemical reactions involve the creation or the consumption of water: Dehydration Synthesis . Hydrolysis . These reactions are reversible, and play an important role in the chemistry of organic compounds. Water in Chemical Reactions

43. In dehydration synthesis, one reactant gives up an atom of hydrogen and another reactant gives up a hydroxyl group (OH) in the synthesis of a new product. In the formation of their covalent bond, a molecule of water is released as a byproduct . Water in Chemical Reactions

44. In hydrolysis, a molecule of water disrupts a compound, breaking its bonds. The water is itself split into H and OH. One portion of the severed compound then bonds with the hydrogen atom, and the other portion bonds with the hydroxyl group. Water in Chemical Reactions

45. Salts Formed from ionic bonds Dissociates completely in water The positive and negative regions on the water molecule (the hydrogen and oxygen ends respectively) attract the negative chloride and positive sodium ions, pulling them away from each.

46. Salts These ions are electrolytes; they are capable of conducting an electrical current in solution. critical to the function of ions in transmitting nerve impulses and prompting muscle contraction. Ions plays essential role in homeostasis

47. Acids and Bases Acids and bases, like salts, dissociate in water into electrolytes. Acids and bases can very much change the properties of the solutions in which they are dissolved.

48. Acids A substance that releases hydrogen ions (H+) in solution Hydrogen ions are protons since they have no electrons. In solution, H+ are very likely to participate in chemical reaction. Examples of acids HCl (hydrochloric acid): strongest acid. H 2 CO 3 (carbonic acid): weak acid, important in human body

49. Bases A substance that accepts H+ already present in solution Basic substances combine with H+ present to form a water molecule, thereby removing H+ and reducing the solution’s acidity. In many cases when a base dissolved in water it releases OH – Example: NaOH → Na + + OH – Important bases Bicarbonate ion (HCO 3 – ) and ammonia (NH 3 )

50. pH: Acid-base concentration The relative acidity or alkalinity of a solution can be indicated by its pH. pH measures the concentrations of H+. Acidic solutions have lower pH and high concentrations of H+. pH range: 0-6.99 Basic solutions have higher pH and low H+ concentrations pH range: 7.01-14 Neutral solutions have pH of 7.

51. Acids and Bases (cont.) Acids and bases can easily get into a reaction. The result is water and salt pH will turn into middle range depending on the pH of each solution. If strong acid and base reacts they neutralize each other (pH=7) Example: NaOH (pH=14)+ HCl (pH=0) gives salt NaCl and H2O (pH=7) NaOH + HCl → NaCl + H 2 O

52. A solution of a weak acid and its conjugate base. Buffers prevent large changes in pH Can gives hydrogen ions to prevent pH increase Can takes hydrogen ions to prevent pH decrease In human body the Carbonic acid–bicarbonate system is the most important buffer system of blood Buffers H 2 CO 3                                            HCO - 3 + H + Act as an acid by giving H + Act as a base by taking H +

53. Organic Compounds Organic molecules contain carbon and hydrogen Major organic compounds : Carbohydrates. Lipids. Proteins. Nucleic acids.

54. Carbohydrates A carbohydrate is a molecule composed of carbon, hydrogen, and oxygen; in most carbohydrates, hydrogen and oxygen are found in the same two-to-one relative proportions they have in water. Main function is to provide energy Three classes Monosaccharides : one single sugar Monomers: smallest unit of carbohydrate Disaccharides : two sugars Polysaccharides : many sugars Polymers are made up of monomers of monosaccharides

55. A monosaccharide is a monomer of carbohydrates. Usually referred to as simple sugars. Monomers of carbohydrates Essential monosaccharides in human body Hexose sugars; have 6 carbon atoms Glucose (blood sugar), fructose, and galactose Pentose sugars; have 5 carbon atoms Ribose and deoxyribose Monosaccharides

56. Disaccharides A disaccharide is a pair of monosaccharides. formed via dehydration synthesis. glucose + fructose → sucrose + water Important disaccharides Sucrose; table sugar, maltose; malt sugar, lactose; milk sugar Body breaks them through hydrolysis in order to digest them.

57. Polysaccharides Polysaccharides can contain a few to a thousand or more monosaccharides. Important polysaccharides Starch: polymers of glucose. In plant-based foods and are relatively easy to digest. Glycogen: polymers of glucose in animals’ tissues especially in muscles and liver. Cellulose: is the component of plant food referred to as “fiber”. In humans, cellulose/fiber is not digestible; however, dietary fiber has many health benefits

58. Lipids A lipid is made up mostly of hydrocarbons (C and H). Contains O and P sometimes. All lipids hydrophobic In water, lipids do not form a true solution, but they may form an emulsion; a mixture of solutions that do not mix well. Main types: Triglycerides or neutral fats Phospholipids Steroids

59. Most abundant in body tissues. Composed of three fatty acids and one glycerol molecule Main functions Major fuel source for the body. Assists the absorption and transport of the nonpolar fat-soluble vitamins A, D, E, and K. Protects and cushions the body’s bones and internal organs, and acts as insulation to retain body heat. Triglycerides or Neutral Fats

60. Saturated fatty acids: have no double carbon bonds. These straight, rigid chains pack tightly together and are solid or semisolid at room temperature Butter and lard are examples Increase the risk of heart disease Unsaturated fatty acids: have one double carbon bond. Liquid at room temperature. Olive oil and Omega-3 are examples Reduce the risk of heart disease Triglycerides or Neutral Fats

61. Phospholipids Phospholipid is a bond between the glycerol component of a lipid and a phosphorous molecule. Two fatty acid chains and glycerol attached to a phosphate group. The nonpolar fatty acids and the polar phosphate group creates two distinct ends in the phospholipid molecule. Head (the phosphor group) is hydrophilic Tails (the fatty acids) are hydrophobic Important in cell membrane structure

62. Steroids The most important contribution to human structure and function is cholesterol Cholesterol is an important component of bile acids, compounds that help emulsify dietary fats. Building block of many hormones. Found in the cell membrane

63. Proteins An organic molecule composed of amino acids linked by peptide bonds. critical components of all tissues and organs. Serve wide variety of functions Structural and support, enzymes and hormones, contraction and protection Proteins are polymers made up of nitrogen-containing monomers called amino acids.

64. Proteins An amino acid is a molecule composed of an amino group and a carboxyl group, together with a variable side chain. 20 different amino acids contribute to nearly all of the thousands of different proteins important in human structure and function.

65. Amino Acids and Peptide Bonds Proteins are made by dehydration synthesis reaction. Water molecule will be removed from two amino acids The carboxyl group of one amino acid binds to the amino group of the second amino acid. This covalent bond is called peptide bond. New amino acids are added to the peptide in the same way

66. Shape of Proteins Protein’s shape is essential to its function Proteins are not functional till they have a 3D shape that makes them specific. As a key that opens one lock because of its groves, the 3D structure enables the protein to bind to its target. A protein’s shape is determined by the sequence of amino acids of which it is made. The sequence is called the primary structure of the protein.

67. Shape of Proteins The secondary structure, which can take the form of an alpha-helix or a beta-pleated sheet, is maintained by hydrogen bonds between amino acids in different regions of the original polypeptide strand.

68. Shape of Proteins The tertiary structure occurs as a result of further folding and bonding of the secondary structure. Some small proteins are functional at this level.

69. Shape of Proteins The quaternary structure occurs as a result of interactions between two or more tertiary subunits. The example shown here is hemoglobin, a protein in red blood cells which transports oxygen to body tissues.

70. Protein Denaturation Denaturation is a change in the structure of a molecule through physical or chemical means. Extreme heat, acids, bases, and certain other substances Denatured proteins lose their functional shape and are no longer able to carry out their jobs. Example: the curdling of milk when acidic lemon juice is added. Boiling an egg

71. Proteins Function as Enzymes Enzymes : proteins that catalyse chemical reactions There is a specifically matched enzyme for each substrate and, thus, for each chemical reaction Substrate should match the 3D shape of the active site (key and lock/jigsaw puzzle)

72. Proteins Function as Enzymes Enzymes work by lowering the activation energy required for a given chemical reaction to occur. This increases the speed of the chemical reactions.

73. Nucleotides Nucleotide is composed of three subunits: one or more phosphate groups a pentose sugar: either deoxyribose or ribose a nitrogen-containing base: adenine, cytosine, guanine, thymine, or uracil Nucleotides can be assembled into nucleic acids (DNA or RNA) or the energy compound adenosine triphosphate. Deoxyribose (in DNA) Ribose (in RNA)

74. Nucleic Acids The nucleic acids differ in their type of pentose sugar. Deoxyribonucleic acid (DNA) is nucleotide that stores genetic information. Ribonucleic acid (RNA) is a ribose-containing nucleotide that helps manifest the genetic code as protein. Deoxyribose (in DNA) Ribose (in RNA)

75. DNA Two strands of DNA coil around each other to form double helix structure. DNA is strictly located in cell nucleus Nitrogen base is one of four : Adenine (A), Guanine (G), Cytosine (C) or Thymine (T) A pairs with T. C pairs with G.

76. RNA RNA consists of a single strand of sugar-phosphate backbone studded with bases. Located mainly outside nucleus Thymine is replaced with Uracil

77. DNA vs RNA Characteristic DNA RNA Site within cell Nucleus Cytoplasm Function Holds genetic material and direct protein synthesis Carries the genetic instruction for protein synthesis Sugar Deoxyribose Ribose Bases G,C,A,T G,C,A,U Structure Double strand coiled in a double helix Single strand

78. ATP: Adenosine Triphosphate Is composed of a ribose sugar, an adenine base, and three phosphate groups ATP is classified as a high energy compound because the two covalent bonds linking its three phosphates store a significant amount of potential energy. Structure of ATP Adenine-containing RNA nucleotide with two additional phosphate groups

79. ATP When a phosphate group is cleaved from ATP, the products are adenosine diphosphate (ADP) and inorganic phosphate (Pi). ATP usage in the body Muscle contraction Transport of substances and ions in and out of cells Anabolic chemical reactions