BIO-UP! CHEMISTRY FOR BIOLOGY CLASSES FALL 2017

Transcription

1 BIO-UP! CHEMISTRY FOR BIOLOGY CLASSES FALL 2017

2 Welcome! Agenda How to read your textbook How does learning work The atom Water Carbon Molecules of life

3 How to Read Use Your Textbook Don t read front to back 1. Go to the questions at the end first. 2. Read the final summary of the chapter. 3. Look at the headings and subdivision of the chapter. 4. Read the chapter introduction Read for Big Ideas Read for Key Details Read the book once but your notes multiple times

4 How Does Learning Work? We Learn 10% of what we hear 15% of what we read 20% of what we see and hear 40% of what we discuss 80% of what we experience and practice 90% of what we attempt to teach What does this mean for you? How can you use this to help direct your study? Information from

5 THE ATOM All elements listed on the periodic table are made up of atoms. An atom is the smallest particle of an element.

6 Dalton's Atomic Theory The idea of atoms did not become scientific theory until John Dalton ( ) developed an atomic theory proposing that atoms were responsible for the combinations of elements in compounds.

7 Dalton's Atomic Theory 1. All matter is made up of tiny particles called atoms. 2. All atoms of a given element are identical to one another and different from atoms of other elements. 3. Atoms of two or more different elements combine to form compounds. A particular compound is always made up of the same kinds of atoms and the same number of each kind of atom. 4. A chemical reaction involves the rearrangement, separation, or combination of atoms. Atoms are never created or destroyed in a chemical reaction.

8 Atoms Atoms are the building blocks of everything around us too small to see with the naked eye Image of Platinum & Nickel atoms

9 Subatomic Particles in an Atom By the end of the 1880s, experiments with electricity showed that atoms were composed of tiny particles, called subatomic particles which included protons, neutrons, and electrons it was shown that some subatomic particles in an atom have charge

10 Electrical Charges in an Atom Electrical charges can be positive or negative. two positive charges repel each other two negative charges repel each other unlike charges attract each other

11 The Structure of an Atom In 1897, J.J. Thomson discovered the electron using cathode ray experiments. He proposed the plum pudding model of an atom. In this model electrons and protons are uniformly mixed throughout the atom.

12 The Structure of an Atom In 1911, Ernest Rutherford tested J. J. Thomson s hypothesis using his gold foil experiment. This findings were not consistent with Thomson s model. Rutherford proposed the planetary model of the atom. Which states there is: a small region in the center with positive charge called the nucleus a region of space around the center of the atoms occupied by electrons

13 The Structure of an Atom In 1932, James Chadwick discovered that the nucleus of the atom also contained neutral particles called neutrons.

14 The Structure of an Atom In an atom, the protons and neutrons that make up almost all the mass of the atom are packed into the tiny volume of the nucleus. The rapidly moving electrons (negative charge) surround the nucleus and account for the large volume of the atom.

15 Mass of the Atom The mass of the atom is due to the protons and neutrons in the nucleus. Electrons have a much smaller mass. Chemists use a unit called atomic mass unit (amu), defined as one-twelfth of the mass of the carbon atom with 6 protons and 6 neutrons. The mass of all elements in the periodic table is compared to the mass of this carbon atom. On the amu scale, the mass of a proton and a neutron have a mass of about 1 amu.

16 THE PERIODIC TABLE

17 ATOMIC NUMBER The atomic number is specific for each element and the same for all atoms of that element is equal to the number of protons in an atom typically appears above the symbol of an element

18 ATOMIC NUMBERS AND PROTONS Hydrogen has atomic number 1; every H atom has 1 proton. Carbon has atomic number 6; every C atom has 6 protons. Copper has atomic number 29; every Cu atom has 29 protons. Gold has atomic number 79; every Au atom has 79 protons.

19 ATOMIC MODELS

20 LEARNING CHECK State the number of protons in each atom. 1. A nitrogen atom (a) 5 protons (b) 7 protons (c) 14 protons 2. A sulfur atom (a) 32 protons (b) 16 protons (c) 6 protons 3. A barium atom (a) 137 protons (b) 81 protons (c) 56 protons

21 SOLUTION State the number of protons in each atom. 1. A nitrogen atom (b) 7 protons 2. A sulfur atom (b) 16 protons 3. A barium atom (c) 56 protons

22 Atoms Are Neutral An atom of any element is electrically neutral; it has a net charge of zero has an equal number of protons and electrons A neutral atom of calcium, atomic number 20, contains 20 protons and 20 electrons. It has zero net charge.

23 Mass Numbers The mass number represents the number of particles in the nucleus is equal to the number of protons + number of neutrons does not appear on the periodic table because it applies to a single atom only

24 Calculate Number of Neutrons We calculate the number of neutrons in an atom from its mass number and atomic number: - Potassium has a mass number of 39 and an atomic number of 19. To find the number of neutrons, subtract the atomic number from its mass number. 39 (mass number) 19 ( atomic number) = 20 neutrons

25 Composition of Elements 1 8

26 Learning Check An atom of zinc has a mass number of How many protons are in the nucleus? (a) 30 (b) 35 (c) How many neutrons are in the nucleus? (a) 30 (b) 35 (c) What is the mass number of a zinc atom that has 37 neutrons? (a) 37 (b) 65 (c) 67

27 Solution An atom of zinc has a mass number of How many protons are in the nucleus? (a) How many neutrons are in the nucleus? (b) What is the mass number of a zinc atom that has 37 neutrons? (c) 67

28 Learning Check An atom has 14 protons and 20 neutrons. 1. Its atomic number is (a) 14 (b) 16 (c) Its mass number is (a) 14 (b) 16 (c) The element is (a) Si (b) Ca (c) Se

29 Solution An atom has 14 protons and 20 neutrons. 1. Its atomic number is (a) Its mass number is (c) The element is (a) Si

30 Isotopes ISOTOPES are atoms of the same element that have different mass numbers have the same number of protons, but different numbers of neutrons most elements have two or more isotopes that contribute to the atomic mass of that element.

31 Atomic Symbols An atomic (nuclear) symbol represents a particular isotope of an element gives the mass number in the upper left corner and the atomic number in the lower left corner mass number atomic number 24 Mg 12 Chemical Symbol

32 Atomic Symbols, Subatomic Particles The atomic symbol indicates the number of protons, neutrons and, electrons in a specific isotope of an element O 15P Zn 8 protons 15 protons 30 protons 8 neutrons 16 neutrons 35 neutrons 8 electrons 15 electrons 30 electrons

33 Atomic Mass Atomic mass is the average of all the naturally occurring isotopes of that element. The atomic mass of an element is listed below the symbol of each element on the periodic table calculated based on the weighted average of all naturally occurring isotopes based on its comparison to the mass of 12 C not the same as the mass number 11 Na Atomic Mass 22.99

34 VALENCE ELECTRONS Electrons orbit the nucleus in various energy levels or shells. Electrons in the outermost energy shell are called valence electrons. All elements in the same group have the same number of valence electrons. An elements valence electrons determines the chemical properties Atoms transfer or share valence electrons in order to obtain a stable electron configuration. Typically, eight or zero valence electrons.

35 Ions Ions, which have electrical charges, form when atoms lose or gain electrons to form a stable electron configuration. Metals lose valence electron to form ions with positive charge. Non-metals gain valence electrons to form ions with negative charge.

36 Positive Ions: Loss of Electrons A sodium atom (Na) will lose its valence electron to form a sodium ion (Na + ). Positively charged ions of metals are called cations.

37 Positive Ions: Loss of Electrons Magnesium, a metal in Group 2A (2), obtains a stable electron configuration by losing two valence electrons, forming an ion with a 2 + charge.

38 Negative Ions: Gain of Electrons An atom of chlorine with seven valence electrons gains one electron to form an octet. Because it now has 18 electrons and not 17 electrons, it becomes a chloride ion (Cl ) with a charge of 1. Negatively charged ions of nonmetals are called anions.

39 Transfer of Electrons The metal transfers its valence electron(s) to the non-metal.

40 Formula and Names of Some Common Ions

41 Ionic and Molecular Compounds

42 Electronegativity We can use the periodic table to predict the relative electronegativity value for each element. Electronegativity increases from left to right going across a period on the periodic table decreases going down a group on the periodic table 2014 Pearson Education, Inc.

43 Electronegativity Figure 10.1 The electronegativity values of the representative elements in Group 1A (1) to Group 7A (17), which indicate the ability of atoms to attract shared electrons, increase going across a period from left to right and decrease going down a group Pearson Education, Inc.

44 Polar and Nonpolar Covalent Bonds Figure 10.2 In the nonpolar covalent bond of H 2, electrons are shared equally. In the polar covalent bond of HCl, electrons are shared unequally Pearson Education, Inc.

45 Dipoles and Bond Polarity Bonds become more polar as the difference in electronegativity increases. A polar covalent bond that has a separation of charges is called a dipole. The positive and negative ends are represented by the Greek letter delta, with a + or charge. Arrows can also be used to represent dipoles Pearson Education, Inc.

46 Summary of Important Concepts General Rules = = = = For Atoms = =

47 Water The compound, water makes up a majority of most organisms and is a critical component making the processes of life possible. Water is known by other names including Oxidane Hydrogen oxide Dihydrogen monoxide Hydric acid, etc Water consists of two hydrogen atoms covalently bonded to one oxygen atom.

48 Water: Polarity Oxygen has a greater attraction for electrons than does hydrogen due to electronegativity. The oxygen atom gains a slight excess of negative charge (partial negative charge), and the hydrogen atoms become slightly positive (partial positive charge). An individual water molecule has a bent shape therefore the dipoles do not cancel. Water is polar thus having positive & negative partial charges on its ends.

49 Solvency Solvency - ability to dissolve other chemicals Solvent - the part of a solution present in the largest amount Solute - the substance that is present in a solution in a smaller amount and is dissolved by the solvent Hydrophilic (charged, ionic or polar substances) dissolve easily in water - salt Hydrophobic (neutral or non-polar substances) do not easily dissolve in water - oil Water = universal solvent

50 Water as a Solvent Water is a versatile solvent due to its polarity. It can form aqueous solutions. The different regions of the polar water molecule can interact with ionic compounds called solutes and dissolve them. Negative oxygen regions of polar water molecules Na are attracted to sodium + + cations (Na + ). Positive hydrogen regions of water molecules cling to chloride anions (Cl ). Cl Na + Cl

51 Water Hydrogen Bonds The slightly negative oxygen atom of one water molecule is attracted to the slightly positive hydrogen atoms of nearby water molecules, forming hydrogen bonds. Each water molecule can form hydrogen bonds with up to four neighbors. Hydrogen bonds hold water molecules together. They form, break, and reform with great frequency. Extraordinary Properties that are a result of hydrogen bonds: Cohesive and adhesive behavior Resists changes in temperature High heat of vaporization Expands when it freezes Versatile solvent

52 Carbon Carbon is a central element to life because most biological molecules are built on a carbon framework. The complexity of living things is facilitated by carbon s linkage capacity. Carbon has great bonding capacity due to its tetrahedral structure. Carbon s outer shell has only four of the eight electrons necessary for maximum stability in most elements. Carbon atoms are thus able to form stable, covalent bonds with a wide variety of atoms, including other carbon atoms.

53 Organic vs Inorganic Compounds Compounds which contain carbon carbon bonds are called organic molecules. Contain carbon and hydrogen. Contains single, double, or triple covalent bonds. Examples methane, ethane, sugar, lipids Compounds which do not contain carbon carbon bonds are called inorganic. Examples water, oxygen, ammonia, salt

54 Organic Compounds always contain carbon and hydrogen, and sometimes oxygen, sulfur, nitrogen, phosphorus, or a halogen occur in nature and are also found in fuel, shampoos, cosmetics, perfumes, and foods are the foundation for understanding biochemistry have low melting and boiling points are not soluble in water and are less dense than water undergo combustion, burning vigorously in air Formulas for organic compounds are written with carbon first, followed by hydrogen and then other elements.

55 Hydrocarbons Hydrocarbons are organic compounds that contain only carbon and hydrogen. Saturated hydrocarbons contain only single carbon-carbon bonds.

56 Molecules of Life

57 Monomers and Polymers Biological molecules are made by monomers bonding to form polymers Monomers Molecules that are building blocks for larger molecules Simple sugars, fatty acids, amino acids, nucleotides Polymers Molecules that consist of multiple monomers Carbohydrates, lipids, proteins, nucleic acids Polymers are made by dehydration synthesis (removal of water) Polymers are broken apart by hydrolysis (addition of water).

58 Monomers and Polymers Dehydration of Synthesis Hydrolysis

59 Carbohydrates Carbohydrates are formed from the building blocks or monomers of simple sugars, such as glucose. Some simple sugars have the same chemical formula but are arranged differently, such as glucose and fructose. These are called isomers. These monomers can be linked to form larger polymers, which are known as disaccharides polysaccharides (complex carbohydrates).

60 Carbohydrates - Disaccharides Disaccharides are two simple sugars bonded together. Some examples include: Sucrose = glucose + fructose Table sugar Lactose = glucose + galactose Milk sugar Maltose = glucose + glucose Found in germinating grains, malt products

61 Carbohydrates - Polysaccharides Polysaccharides are made up of many monomers joined together. Four polysaccharides are critical in the living world: Starch Glycogen Cellulose Chitin nutrient storage form of carbohydrates in plants nutrient storage form of carbohydrates in animals rigid, structural carbohydrate found in the cell walls of many organisms tough carbohydrate that forms external skeleton of arthropods.

62 Carbohydrates - Polysaccharides

63 Lipids The defining characteristic of all lipids is that they do not readily dissolve in water. Lipids do not possess the monomers-to-polymers structure seen in other biological molecules; no one structural element is common to all lipids. Lipids include Triglycerides Steroids Phospholipids Waxes Lipids are used for Storing energy Insulating and cushioning Hormones - steroids Waterproofing Cell membranes

64 Lipids - triglycerides Among the most important lipids are the triglycerides, composed of a glyceride and three fatty acids. Most of the fats that human beings consume are triglycerides. Saturated fats are triglyceride molecules that have only single bonds. Unsaturated fats are triglyceride molecules that have at least one double bond. The two types of unsaturated fats are: Cis fat naturally occurring configuration of double bond Trans fat artificially created configuration of double Hydrogenated fats are artificially created saturated fats made from cis fats.

65 Lipids steroids Another important variety of lipids is the steroids, all of which have a core of four carbon rings with various functional groups attached. Examples include cholesterol and such hormones as testosterone and estrogen.

66 Lipids phospholipids A third class of lipids is the phospholipids, each of which is composed of two fatty acids, glycerol, and a phosphate group. The phosphate end is polar and attracts water. The fatty acid end is nonpolar and repels water. The material forming the outer membrane of cells is largely composed of phospholipids.

67 Lipids waxes A fourth class of lipids is the waxes, each of which is composed of a single fatty acid linked to a long-chain alcohol. Waxes have an important sealing function in the living world. Almost all plant surfaces exposed to air, for example, have a protective covering made largely of wax.

68 Proteins Proteins are an extremely diverse group of biological molecules composed of the monomers called amino acids. Sequences of amino acids are strung together to produce polypeptide chains, which then fold up into working proteins. Important groups of proteins include enzymes, which hasten chemical reactions, and structural proteins, which make up such structures as hair.

69 Types of Proteins

70 Proteins Amino acids Amino acids: are the building blocks of proteins. contain a carboxylic acid group and an amino group on the alpha ( ) carbon. contain a side chain of atoms (R) are ionized in solution.

71 Proteins Amino acids There are 20 common amino acids found in human proteins. The 20 amino acids are classified into four categories based on their side chains (R- groups)

72 Proteins The 20 Amino acids

73 Proteins The Beginning of a Protein

74 Proteins Hierarchy of Protein Structure

75 Lipoproteins & Glycoproteins Lipoproteins Lipoproteins are biological molecules that are combinations of lipids and proteins. High-density and low-density lipoproteins (HDLs and LDLs, respectively), which transport cholesterol in human beings, are important determinants of human heart disease. Glycoproteins Glycoproteins are combinations of carbohydrates and proteins. The signal-receiving receptors found on cell surfaces often are glycoproteins.

76 Nucleic Acids Nucleic acids are polymers composed of nucleotides. The nucleic acids are composed of nucleotides that contain a sugar, a phosphate group, and one of five nitrogen-containing bases. There are two types of nucleic acids DNA, deoxyribonucleic acid DNA is the repository of genetic information The sequences of bases in DNA encodes the information necessary for production of proteins in living things. RNA, ribonucleic acid RNA transports the information in encoded in DNA to the sites of protein synthesis.

77 Nucleic Acids - Nucleotides Nucleotides consist of: A pentose sugar Deoxyribose for DNA Ribose for RNA A phosphate group A nitrogenous base either a pyrimidine or a purine The pyrimidines include: Cytosine (C) and Thymine (T) for DNA Cytosine (C) and Uracil (U) for RNA The purines include: Adenine (A) and Guanine (G) When Nucleic Acids hydrogen bond to each other they always pair up C to G, and A to T in DNA. For RNA, they pair up C to G and A to U.

78 Questions? Compiled by D. Leonard (Learning Specialist) The Academic Support Daytona State College