Chemistry of Life: Understanding Matter and Energy in Biology

1. Chapter 2 Chemistry of Life

2. Biology • Biology: The study of life • In order to understand life your must have a basic understanding of chemistry

3. Matter and Energy • Matter: anything that occupies spaces and has mass • Everything around us is matter • Element: a pure substance that cannot be broken down into other substances by chemical means • ex. gold, helium, mercury

4. MAtter • There are about 25 elements that are essential to life • Four elements make up 96% of living matter • Oxygen, Carbon, Hydrogen and Nitrogen • Trace Elements: elements that make up less than 0.01% of your body mass • Ex. Calcium Phosphorus, potassium and sulfur

5. MAtter

6. Matter • Compounds: a substance containing two or more elements that are chemically combined in a fixed ratio • Ex. H2O • A compounds properties may differ greatly from those of its component elements • Ex. NaCl

7. Atoms • Atom: the smallest possible particle of an elements • Atom of all elements are made of even smaller components called sub atomic particles • Proton: a subatomic particle with a single unit of positive charge (+) • Electron: a subatomic particle with a single unit of negative electrical charge (-) • Neutron: a subatomic particle that has a neutral charge ( Think of it like a proton and electron combined)

8. atoms • An atoms protons and neutrons are tightly packed together, forming a central core called the nucleus • Electrons have much less mass than neutrons and protons and continually move about the outside of the nucleus at high speeds • The attraction between the negatively charged electron and positively charged protons keeps the electrons close to the nucleus

9. atoms

10. ElemeNts • An important difference between elements is the number of protons in their nucleus • All atoms of a particular element have the same number of protons • The number of protons is known as the Atomic Number • Ex helium has two protons so it has an atomic number of 2

11. Elements • Left alone atoms generally tend to hold as many protons and electrons. • This creates an atom with an electrically neutral charge because the positive charge of the protons and the negative charge of the electrons cancel each other out • The number of electrons is not always equal to the number of protons, because some elements tend to lose or gain electrons (these atoms are called Ions)

12. Isotopes • Some elements have alternative forms called Isotopes • Isotopes have the same number of protons in their atom but a different number of neutrons

13. Radioactive isotopes • Radioactive Isotope: isotope in which the nucleus decays (breaks down) over time, giving off radiation in the form of matter and energy • Ex. carbon-14 • Radioactive isotopes have many uses in research and medicine because living cells use radioactive isotopes just as they would use the nonradioactive forms • They are like spies

14. Electron configuration • Electrons differ in the amount of energy they have and the how tightly they are held by the protons in the nucleus • Based in these properties electron are classified into different energy levels • The first and lowest energy level (nearest to the nucleus) can hold 2 electrons • The second level holds 8 • If the outermost energy level is not full the element is considered chemically reactive

15. Electron configuration

16. Ions • Ionic Bond: type of chemical bond that occurs when an atom transfers an electron to another atom • Ex. table salt NaCl • Ions: atoms or groups of atoms that have become electrically charged as a result of gaining or losing electrons

17. Covalent Bonds • Covalent Bond: forms when two atoms share electrons • Covalent bonds are represented using the element symbols and dots that represent the atoms outermost electrons

18. Bonding • Numbers of bonds • The number of bonds an atom can form usually equals the number of additional electrons that will fill its highest energy level. • Ex. a hydrogen atom can accept one additional electron so it can form only one bond • Ex. an oxygen atom can accept 2 additional electrons so its can form up to 2 bonds

19. Molecule • Molecule: two or more atoms held together by covalent bonds • Molecules can be modeled in three different ways • Chemical formula: tells you the number and types of atoms • Structural formula: indicates how atoms in a molecule are linked by bonds • Space filling model: shows three dimensional structure of the molecule

20. Chemical Reactions • Chemical reactions: breaking of old chemical bond and the formation of new chemical bonds that result in new substances • The starting materials in a chemical reaction are called the reactants • The ending materials in a chemical reaction are called products

21. Properties of Water • All living things are dependent on water • Structure of Water • Two hydrogen atoms attached to an oxygen atom by a covalent bond • What makes oxygen unique is that the oxygen atom hogs all of the electrons • This makes the oxygen more negatively charged than the hydrogen atoms • Polar molecule: a molecule in which opposite ends have electric charges

22. Properties of Water • Because the water molecule is polar the molecules are attracted to each other in a very specific way forming a hydrogen bond • The negative end attracts the positive end

23. Properties of Water • Hydrogen Bond: type of weak attraction between the hydrogen atom of one molecule and a slightly negative atom with in another molecule • Hydrogen bonds are very weak • These hydrogen bonds make water have some very unique properties

24. Properties of Water • The Unique Properties of Water • Cohesion: the tendency of molecules of the same kind to stick to one another • Water has a much stronger cohesion than other liquids • Adhesion: the type or attraction that occurs between unlike molecules • ex. water sticks to glass • Adhesion and cohesion are very important properties of water to life on Earth

25. Properties of Water • Temperature • Because of the hydrogen bonds water has a much greater resistance to temperature change • Ex. getting water to boil • Temperature: a measure of the average energy of random motion of the particles in a substance

26. Properties of Water • Low density of ice • Density is the amount of matter in a given volume • In most substances the solid state is more dense than the liquid state • But in water the solid form is much less dense than the liquid • This is why ice floats on water

27. Properties of Water • Water has the ability to dissolve other substances • Solution: a uniform mixture of two or more substances • Ex. when you dissolve salt into water • Solvent: the substance that dissolves the other substance and is present in the greater amount • Ex water • Solute: the substance that is dissolved and is present in the lesser amount • Ex. Salt

28. Carbon Based Molecules • Remember that an atoms bonding ability is related to the number of electrons in the outermost energy level • Carbon has four electrons in the outermost energy level which means that it has the ability the form up to four bonds with other atoms • Carbon atoms can form bonds with one or more other carbon atoms producing many different carbons skeletons • Organic Molecules: carbon based molecules • Inorganic Molecules: non-carbon based molecules • Hydrocarbons: organic molecules that are composed of only hydrogen and carbon • In addition to hydrogen atoms oxygen and nitrogen are also common

29. Carbon Based Molecules

30. Carbon Based Molecules • Functional Group: a group of atoms within a molecule that interacts in predictable ways with other molecules • Hydrophilic: attracts water • an example of a hydrophilic functional group is the hydroxyl group

31. Monomers and Polymers • Monomers and Polymers • Polymers: long chains or molecules that your cells link together • Monomers: the smaller units that make up polymers • Polymers can form long straight chains or the chains can fold over one other • A living organisms has thousands of different polymers that help the organisms perform different functions • These thousands of polymers are made up of only 50 different kinds of monomers

32. Monomers and Polymers • Building and Breaking Polymers • Organisms not only build polymers they also have to break them down • Ex. many of the molecules in your food are polymers. Your body must breaks down these molecules in order for it to use • Each time a monomer is added to a chain a water molecule is released • This is called a dehydration reaction because it involves removing a water molecule • De- (remove) Hydro- (water)

33. Building and breaking polymers Dehydration Reaction Hydrolysis Reaction Hydro-water Lysis- to break

34. Carbohydrates • Life’s large molecules are classified into four main categories: carbohydrates, lipids, proteins and nucleic acids • Carbohydrates: organic compound made up of sugar molecules. • Sugars contain the elements carbon, hydrogen and oxygen in the ratio of 1 carbon: 2 hydrogen: 1 Oxygen • Most sugars have a carbon skeleton with a ring shape

35. Carbohydrates • Monosaccharides • Monosaccharides contain just one sugar unit • Ex Glucose, fructose and Galactose • Sugar molecules are the main food supply for cellular work • Very similar to how a car uses gasoline

36. Carbohydrates • Disaccharides • Double sugars made from monosaccharides by using a dehydration reaction • Sucrose which consists of a glucose molecule linked to a fructose molecule

37. Carbohydrates • Polysaccharides (complex carbohydrates) • Long polymer chains made up of simple sugar monomers • Ex. Starch is a polysaccharide made entirely of glucose molecules • Starch is found in plant cells • Starch chains branch and coil up into loop • Animal cell do not contain starch they contain glycogen • Glycogen is a polysaccharide that helps animals store excess sugar

38. Carbohydrates • Some polysaccharides in plants serve as building materials • Ex. Cellulose- protects cells and stiffens the plant • Cellulose is also made of glucose molecules (like glycogen and starch) • Most animals, including people cannot digest cellulose because they lack the molecule necessary to break the bonds between the glucose molecules in cellulose • But some organisms like cows and termites can break down cellulose and use it for nutrients because they have microorganisms in their digestive tracts that are able to break down the cellulose

39. Carbohydrates

40. Carbohydrates • Almost all carbohydrates are hydrophilic because there are many hydroxyl found on them • This means that monosaccharides and disaccharides dissolve easily in water • On the other hand cellulose and some forms of starch are such large molecules that they do not dissolve in water

41. Lipids • Characteristics of lipids • Lipids are water avoiding • Hydrophobic: meaning water fearing • Uses of lipids • They can act as a boundary that surrounds and contains the watery contents in your cell • They can also store energy in your body

42. Lipids • Fats • Fat consists of a three-carbon backbone called glycerol attached to three fatty acids • Fatty acids contain long hydrocarbon chains • Some fats are solid at room temperature • Some fats are oil and liquids at room temperature Unsaturated Fat

43. Lipids • Saturated Fats • A fat in which all three fatty acid chains contain the maximum possible number of hydrogen atoms • All the carbon atoms in the fatty acid chains form single bonds with each other, and the rest of their bonds are with hydrogen atoms. • Saturated fats are solid at room temperature • Unsaturated Fats • Contains less than the maximum number of hydrogen atoms in one or more of its fatty acid chains, because some of its carbon atoms are double bonded to each other • Usually liquids at room temperature

44. Lipids • Steroids • A lipid molecule in which the carbon skeleton forms four fused rings • While all steroids have the core of four rings, they differ in the kinds of functional groups that are attached to the rings • Steroids can circulate in your body as chemical signals • Ex. estrogen and testosterone

45. Lipids • Maybe the best known steroid is cholesterol • It is an essential molecule found in the membranes that surround your cells • It is also the starting point from which your body produces other steroids

46. proteins • Function of Proteins • Protein is a polymer constructed from a set of just 20 monomers known as amino acids • Proteins are responsible for almost al of the day to day functioning of organisms • Proteins form the structures that make up fur, hair, muscles and provide long term nutrient storage • Proteins also have other functions including acting as signals and conveying messages from one cell to another

47. Proteins • Amino Acids • Each amino acid monomer consists of a central carbon atom bonded to four partners • Three of the central carbon partners are the same in all amino acids • One partner is a hydrogen atom • One partner is a carboxyl group • One partner is an amino group • What is different in each amino acid is the side group • The side group is responsible for the particular function of the amino acid

48. Proteins • Building a Protein • Cells create proteins by linking amino acids together into a chain called a Polypeptide • Each link is created by a dehydration reaction between the amino group of one amino acid and the carboxyl group of the next amino acid in the chain • There are an enormous variety of proteins that your body can create because there are many different orders the amino acids can go in • Think of amino acids as letters in an alphabet and the polypeptides are the words that you can make from the alphabet

49. Proteins

50. Proteins • Protein Shape • A protein in a simple form of an amino acid linked together cannot function properly • A functional protein consists of one or more polypeptides precisely twisted, folded and coiled into a unique shape • An unfavorable change in temperature, pH, or some other quality of the environment can cause the protein to unravel and lose it normal shape • This is called the denaturation of the protein