Unit 2: Chemistry IB Biology Higher Level Topic 3

Campbell Text References: Chapter 2: Chapter 3: Chapter 4: Chapter 5: Basic Chemistry Water Chemistry Carbon Chemistry Macromolecules

Chapter 2 Basic Chemistry

Vocabulary: Matter: Anything that takes up space and has mass. For our purposes , this means anything made up of atoms Elements Any substance that cannot be broken down into any other substance. This means all the atoms represented on the Periodic Table of Elements The most common elements in the human body are C,H,O and N which make up 96% of its total mass (SEE DIAGRAM BELOW) Compound- A substance consisting of two or more elements in a fixed ration. Ex. Table Salt (NaCl) is an ionic compound because it is joined by ionic bonds and water (H2O) is a molecular compound because it is joined by covalent bonds Atom - The smallest unit of matter that retains the properties (characteristics) of an elememt Neutrons An electrically neutral particle (no electrical charge) found in the nucleus of an atom. Protons- A particle in the nucleus of an atom with a positive electrical charge Electrons - A particle(s) which moves around the nucleus of an atom with a negative electrical charge Atomic Number The number of protons in the nucleus of an atom Potential Energy- The energy stored by matter as a result of its location or spatial arrangement. For our purposes, we say that the electrons in an atom have potential energy in proportion to their distance from the nucleus. Ie. the farther they are away from the nucleus (farthest shell) the more potential energy they have that could be released to do cellular

work (SEE DIAGRAM BELOW) (See the Electron Shell Diagram Below for more description of this concept) Valence Electrons- The electrons in the outermost electron shell of an atom Valence Shell The outermost electron shell of an atom Chemical Bond An attraction between two atoms resulting from the sharing of outer shell electrons (covalent) or the presence of opposite charges on the atoms. Either way, the two atoms gain complete outer shells in the process (SEE DIAGRAMS BELOW) a) Covalent Bond (non-polar and polar) A type of strong chemical bond in which two atoms share one or more pairs of valence electrons. b) Ionic Bond A chemical bond resulting from the attraction between oppositely charged ions. Molecule- Two or more atoms joined together by covalent bonds Ionic compound (salts) A compound resulting from the formation of an ionic bond also called a salt Electronegativity- The attraction of an atom for the electrons of a covalent bond. Some elements (like oxygen) have high a electronegativity. This means that when oxygen is in a molecule with Hydrogen (hydrogen has a lower electonegativity), the oxygen will exert more pull/attraction on the shared electrons than hydrogen will. This causes oxygen to take on a slight negative charge and hydrogen takes on a slight positive charge. (SEE DIAGRAM BELOW) Ion- An atom that has gained or lost electrons and therefore has acquired a charge. (this is because the number of protons no longer balance the number of electrons) a)Cation a positively charged ion (ex. Potassium ion is K+) b)Anion- a negatively charged ion (ex Chlorine ion is Cl-) Hydrogen bonds- A type of weak chemical bond formed when the slightly positive hydrogen atom of a polar covalent bond in one molecule is attracted to the slightly negative atom of a polar covalent bond in another molecule (SEE DIAGRAM BELOW) Chemical Reactons A process leading to chemical changes in matter-it involves the making or breaking of chemical bonds. a) Reactants A starting material in a chemical reaction b) Products An ending material in a chemical reaction

Concept Check 2.1 - What four chemical elements are most abundant in the food you ate yesterday?

Concept Check 2.2 - Look at the periodic table of elements (2 pages ahead) , and determine the atomic number of magnesium. How many protons and electrons does it have? How many electron shells? How many valence electrons are in the valence shell Concept Check 2.3 - Why does the following structure fail to make sense chemically? H-C=C-H

The Elements which make up Living Organisms

Atomic Structure

Electron Shell Diagram

Periodic Table of Elements

Polar Covalent Bonds in a Water Molecule and Electronegativity Concept

Ionic Bonds

Different Ways of representing Molecules You must know the difference between a Molecular Formula, An Electron Shell Diagram, a Structural Formula, and a Space-filling Model. The important thing to remember is that All of these formulas and models are simply different ways of writing or understanding the molecules

Hydrogen Bonds

Do Several of the CD Activities in Chapter 2 as necessary to Review

Review Test Basic Chemistry

1. Atoms are composed of a. protons. c. electrons. b. neutrons. d. All of the above The electrons of an atom a. are found in the nucleus along with the protons. b. occupy the space surrounding the nucleus.

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c. have a positive charge. d. are attached to the positive charge of neutrons. The smallest particle of matter that can retain the chemical properties of carbon is a(n) a. carbon molecule. c. carbon atom. b. carbon macromolecule. d. element. A substance that is composed of only one type of atom is called a(n) a. nucleus. c. element. b. cell. d. molecule. A molecule that has a partial positive charge on one side and a partial negative charge on the other side is called a a. nonpolar molecule. c. charged molecule. b. polar molecule. d. bipolar molecule. Sharing of electrons in the outer energy levels of two atoms a. results in ion formation. b. occurs in covalent bonds. c. only occurs if both are atoms of the same element. d. is found only among carbon atoms. Acidic solutions have a pH that is a. less than 7. c. a negative number. b. between 7 and 14. d. more than 7. Each individual element listed on the periodic table is composed of the same a. ions c. molecules b. atoms d. compounds

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.Using a periodic table, calculate how many electrons Nitrogen (N) must aquire (get) in order to have a filled outer or valence shell (to be happy!) a. 1 c. 3 b. 2 d. 4 10. Using the periodic table, choose which element would be stable all by itself and would not need to react with any other element to be happy. a. lithium c. boron b. neon d. oxygen 11. Based on your knowledge of bonding and using the periodic table, what kind of bond would you expect Lithum to make with other elements? a. ionic c. polar covalent b. covalent d. dipolar ionic 12. Using the periodic table, how many covalent bonds would you expect Sulpher (S) to make with another element a. 1 c. 3 b. 2 d. 4 13. Using the periodic table, how many protons does phosphorous have? a. 10 c. 20 b. 15 d. 25 If an element has 8 protons, it usually also has 8 a. electrons b. electrons and neutrons c. neutrons d. None of the above

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Using the periodic table, how many covalent bonds would you expect Nitrogen (N) to make with another element

a. 1 b. 2

c. 3 d. 4

16..

Which elements are the most common to living organisms? c. Oxygen d. Nitrogen e. All of the above

a. Carbon b. Hydrogen

Key 1)d 2)b 3)c 4)c 5)b 6)b 7)a 8)b 9)c 10)b 11)a 12)b 13)b 14)b 15)c 16)e

Chapter 3 and 4 Water and Carbon Chemistry

Vocabulary:
Polar molecule- a molecule (like water) with opposite charges on opposite sides Cohesion- the binding together/attraction of like-molecules (such as two water molecules) Adhesion- the attraction between different kinds of molecules Surface Tension- a measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension because of the hydrogen boding between surface molecules Kinetic Energy- the energy of motion- moving matter does work by imparting motion to other matter Specific Heat- the amount of heat that must be absorbed or lost for 1 gram of a substance to change its temperature by 1 degree Celsius. Since water has a high specific heat, it is able to hold onto its heat and maintain its temperature which helps living organisms that are living in water or who have water in their bodies. Solution- A liquid that is a mixture of two or more substances. a) Solvent- the liquid part of a solution it is the part that dissolves substances b) Solute the solid part of a solution which is dissolved in the solvent Hydrophilic- Having an attraction for water (water loving) Hydrophobic- Having an aversion for water (water fearing) Dissociation of water molecules- Water molecules (H2O) sometimes break apart into H+ and OHions. So any given sample of water has H2O molecules, H+ ions and OH- ions pH Scale - a measure of the H+ ion concentration in water. The scale ranges from 1-14 with the highest H+ ion concentrations at the low end of the scale (Ph of 1-6). We call these solutions Acidic. Neutral Ph is 7 and Basic (or alkaline Ph is 8-14). The important thing to remember is that most living organisms operate best under neutral Ph. If the Ph gets too acidic or alkaline, living organisms begin to have problems.

Organic- Molecules that do not contain carbon usually part of living organisms Inorganic- Molecules that do not contain carbon usually not part of living organisms Organic Chemistry- The study of carbon compounds like carbohydrates, proteins, lipids, and DNA

Functional Groups: A specific configuration of atoms, commonly attached to the carbon skeletons of organic molecules. These groups are the parts of a molecule that are invoved in chemical reactions with other molecules. ATP: This stands for Adenosine Triphosphate. This molecule stores energy that is used to drive chemical reactions in cells. The energy is released when the last covalent bond breaks, resulting in ADP + P.

Describe the most commonly occurring chemical elements in living organisms and their functions Functions of Carbon, Hydrogen, Oxygen, and Nitrogen Carbon Forms organic molecules / carbohydrates / fats / proteins / nucleic acids; Hydrogen Forms organic molecules / carbohydrates / fats / proteins / nucleic acids / Oxygen Aerobic respiration; Nitrogen Formation of amino acids / proteins / nucleotides / ATP / nucleic acids / DNA / RNA;

Describe other elements needed by living organisms that are need in smaller amounts, their location and their functions Molecule/Ion/Tissue Phosphorus ATP / ADP DNA / RNA / nucleotides; Phospholipids hemomoglobin; Function energy storage and release genetic material structure of cell membrane transports oxygen (in the blood);

Iron

Sulfur Calcium

Found in some proteins, vitamins, and hormones. Bone tissue and teeth

Varied Functions Bone structure Nerve Impulse

Sodium

Ions in Nerve Cells

Surface Tension of Liquid Water (picture on right) is produced by the attraction between adjacent water molecules

Do 3.1 Polarity of Water Do 3.2 Cohesion of Water

Explain the relationship between the properties of water and its uses in living organisms in maintaining constant internal temperatures, as a transport medium, and general habitat (6 marks) Water has a high heat capacity. This means it can hold a lot of heat and this helps many animals to maintain a constant internal temperature in cold climates Water is also an excellent coolant when it evaporates from skin and this quality helps them maintain a constant internal temperature in hot climates ; Water is a great solvent. This means it is capable of dissolving substances in it for transport within individual organisms; For example, blood is mostly water and enables dissolves substances such as glucose to be transported to cells for their source of energy. Also, plant sap is mostly water and enables minerals in the soil to be transported from the roots to the leaves through the plants vascular system. Water has cohesion This means that individual water molecules are slightly attracted to each other (forming hydrogen bonds). As a result, water and its dissolved minerals can be drawn up from roots to leaves in a continuous chain of water molecules. This is called capillary action Water is transparent allows plants to photosynthesize in water / allows aquatic animals to see; Water floats when it freezes lakes / oceans do not freeze, allowing life under the ice; Water provides aquatic habitat A place for aquatic organisms to live;

Be able to draw the Structure of a water molecule showing their polarity and hydrogen bond formation (similar to that shown below)

Do Concept Check 3.1 What is electronegativity and how does it affect interactions between water molecules? Do Concept Check 3.2 Describe how the properties of water contribute to the upward movement of water in a tree.

Basic Carbon Chemistry The term Organic means: compounds containing carbon (found in living organisms) The term Inorganic mean that the compounds do not contain carbon

2 basic arrangements of Carbon in organic Molecules 1. 2. Carbon Ring structur Carbon Chain structure

****(See Figure 4.5 below in Concept 4.1 for examples of carbon ring and carbon chain structures)

Functional Groups (functional groups are the parts of the carbon compounds/molecules that are involved in chemical reactions) ****See Figure 4.10 in Concept 4.3 for more information 1. 2. 3. 4. Hydroxyl - OH Carboxyl- COOH Amino- NH2 Phosphate- PO4 Do Activity 4.3 Functional Groups Do Concept Check 4.2 #1 and #3 Do Concept Check 4.3 #1 and #2

Chapter 5 Macromolecules
Vocabulary:
Macromolecule_ Term used to describe large molecules such as carbohydrates, lipids, proteins and nucleic acids Polymer- A long chainlike molecule consisting of repeating units of the same building blocks (monomers) linked by covalent bonds. These include 3 of the 4 organic macromolecules:

proteins, carbs, and nucleic acids (not lipids) Monomers: The repeating unit molecules of polymers. Examples of Monomers are monosaccharides, nucleotides and amino acids Condensation/Dehydration Reaction- A water of molecule is removed to form a bond (anabolic reaction) This reaction is used to link monomers together Hydrolysis- A water of molecule is added to bread a bond (catabolic reaction) . this reaction is used to break polymers down into monomers Carbohydrates: A sugar (mono, di, or polysaccharide) that has a 1:2:1 ratio of C:H:C ex. glucose is a monosaccaride with a molecular formula of C6H12O6 Lipids A family of compounds that includes fats, phosophlipids and steroids. All are insoluble in water (ie hydrophobic) Proteins: A three-dimensional polymer constructed from a set of 20 amino acid monomers Monosaccharides (simple sugars) like glucose, ribose and fructose join to form polysaccharides which are carbohydrates Disaccharides-a double sugar consisting of two monosaccarides joined by dehydration synthesis Polysaccharides- a polymer of up to over 1000 monosaccharides, formed by dehydration synthesis. The most common polysaccharide is starch which is a storage molecule used in plants that consists of long chains of glucose molecules Amino Acids (20 different kinds) join to form polypeptides which form proteins Nucleotides join to form DNA and RNA

Condensation/Dehydration and Hydrolysis Reactions are Shown Below

Outline the role of condensation and hydrolysis in the relationships between monomers and polymers. (2 marks) Condensation- A water of molecule is removed to form a bond (anabolic reaction) Hydrolysis: A water of molecule is added to bread a bond (catabolic reaction)

Which of the following reactions occurs when a dipeptide is formed between 2 amino acids? A. B. C. D. Hydrolysis Denaturation Condensation Oxidation

Answer : C

Be able to idenfity the structures of the Glucose, Ribose, Amino Acids and Fatty Acids Below Glucose Sugar molecule

Ribose Sugar Molecule

Fatty Acid Molecule

Amino Acid Molecule (This is only a typical diagrahm there are 20 specific types shown on Gohitr 5.17 in Concept 5.4

Please Note: The R group in the diagram shown above is what determines which of the 20 amino acids the molecule is. The other parts (NH3 and COOH groups) are the same for any amino acid

I. CH 3

The diagrams below show various molecular structures.

O (CH 2 ) n C OH II. HOH 2 C C H H C OH H C OH O H C OH

III. H C OH

CH 2 OH C H OH C H O H C OH H C OH

IV. H N H

R O C H C OH

(a)

Identify which of the diagrams represent (i) the structure of glucose. .................Answer is III................................................................................................. (ii) the structure of amino acids. ...................Answer is IV.............................................................................................. (iii) the structure of fatty acids. ....................Answer is I .............................................................................................

What molecule is molecule II?

(Answer is Ribose)

State Types of Bonds that join monomers Joining two adjacent monosaccharides - saccharide bond Joining two adjacent amino acids - peptide bonds

List three examples of each of monosaccharides, disaccharides, and polysaccharides Monosaccharides: glucose, galactose, fructose (fruit sugar) Dissaccharides: maltose, lactose (milk sugar) , and sucrose (table sugar) Polysaccharides: starch (plant energy storage) glycogen (animal energy storage) and cellulose (adds strength to plant cell walls)

State one function of each of the following carbohydrates Plants and Animals Glucose: Provides energy for cellular respiration Sucrose: Provides energy for cellular respiration Animals only Lactose (milk sugar) : Provides energy for cellular respiration Glycogen: Stores energy in the liver of animals for later use Plants only

Starch: Stores energy in roots of plants

Fructose (fruit sugar) : Provides energy for cellular respiration Cellulose; Adds strength to cell walls of plants

Do Activity 5.2 Carbohydrates

Compare the use of carbohydrates and lipids for energy storage in animals and plants Carbohydrates
(

stored as glycogen in animals(in liver) stored as starch in plants (in roots) more easily digested than lipids so energy can be released more quickly; Lipids: stored as fat in animals long-term energy storage more energy per gram than carbohydrates; **Sources of Lipids for Vegans (people who eat no animal products) include margarine / sunflower seeds / vegetable oil / peanuts / nuts

List 4 Functions of Lipids (know at least two of these) energy storage / energy supply; cushioning/protection; thermal insulation; constituent of cell membranes;

Do Activity 5.3

Lipids

Protein Structure and Function

Dont Forget: The Shape of a Protein is Key to Its Function!!!!

Describe the four levels of structure in a protein molecule (See pages 82 and 83 in Textbook) Primary Structure is the unique sequence of amino acids, each linked together by a peptide bonds Secondary Structure is the Beta pleated sheets and alpha helix Tertiary structure in globular proteins involves the folding of polypeptides. This folding pattern is stabilized by sereral types of bonds including hydrogen bonds and ionic bonds Quaternary structure of proteins is the linking together of two or more polypeptide subunits to form a single protein using the same bonding as for tertiary structure. An example of this is hemoglobin which has 4 subunits

Outline the difference between fibrous and globular proteins, with reference to two examples of each protein type

Fibrous proteins are in their secondary structure, which could be in the alpha helix or beta pleated forms. They are made of a repeated sequence of amino acids that can be coiled tightly around in a pattern that makes it a very strong structure. Two examples are keratin (in hair and skin) and collagen (in tendons, cartilage, and bones). Globular proteins are in their tertiary or quaternary structure, which is folded, creating a globular, three-dimensional shape. An example of globular proteins are all enzymes

(Know at least 4 functions of proteins including a specific example) . Hormones Insulin protein helps regulate blood sugar Enzymes Catalase protein catalyzes breakdown of hydrogen peroxide waste in blood Transport Proteins - In cell membrane (ion channels and proton pumps for active transport)

Structural proteins collagen (found in many animal cell tissue) / keratin / tubulin / fibroin Defence antibodies are proteins Receptors hormone receptor / neurotransmitter receptor on the cell surface

Do Activity 5.4 Protein Functions Do Activity 5.4 Protein Structure

Explain the significance of polar and non-polar amino acids. (4 marks)

Non-polar amino acids have non-polar (neutrally charged) R groups. \ Polar amino acids have R chains with polar groups (charged either positive or negative). Proteins with a lot of polar amino acids make the proteins hydrophyllic and therefore able to dissolve in water.

Proteins with many non-polar amino acids are more hydrophobic and are less soluble in water. With these abilities, proteins fold themselves so that the hydrophilic ones are on the inner side and allows hydrophilic molecules and ions to pass in and out of the cells through the channels they form. These channels are vital passages for many substances in and out of the cell.

DNA Structure (Be able to draw and label a DNA molecule showing the following features) The composition of the backbone of a DNA molecule is alternating sugar and photphate molecules Bases are toward the center AT and G---C A hydrogen bond connects adjacent base pairs between the two strands of DNA

Explain the structure of the DNA double helix, including its subunits and the way in which they are bonded together. subunits are nucleotides; one base, one deoxyribose and one phosphate in each nucleotide; four different bases adenine, cytosine, guanine and thymine; nucleotides linked up with sugar-phosphate bonds; two strands (of nucleotides) linked together; Complementary bases (A to T and G to C) hydrogen bonds between bases;

Do Activity 5.5 Nucleic Acid Structure

The parts of a deoxyribose molecule to which phosphates bind in DNA are Positions III and V
V CH2 OH O H I

IV H H H OH II OH III H

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