Welcome to Biology!

1. Welcome to Biology!

2. Unit 1: Biochemistry Chapter 1: The Molecules of Life Chapter 2: The Cell and its Components

3. Chapter 1: The Molecules of Life • Molecules • Interactions between and within molecules • Structure and shape of molecules • Macromolecules • The 4 major types • Roles in biological organisms • Biochemical reactions • The 4 major types • The role of enzymes in reactions

4. Section 1.1: Chemistry in Living Systems • All matter is composed of elements • Cannot be broken down into simpler substances by ordinary chemical methods • Approximately 92 naturally occurring elements • Only 6 elements serve as the chemical foundation for life • Carbon • Hydrogen • Nitrogen • Oxygen • Phosphorous • Sulfur

6. Atoms • An atom is the smallest particle of an element that retains the element’s properties • Atomic mass = sum of protons and neutrons • All atoms of an element have the same number of protons, but the number of neutrons can vary

7. Isotopes • Isotopes are atoms of the same element that have different numbers of neutrons • Radioisotopes are unstable and their nucleus decays over time • They are valuable diagnostic tools in medicine

8. Studying the Interactions of Molecules • A molecule is composed of two or more atoms and is the smallest unit of a substance that retains the chemical and physical properties of the substance • Organic molecules are carbon-based • Carbon atoms often bind to each other or hydrogen • May also include nitrogen, oxygen, phosphorous, and/or sulfur

9. Biochemistry • Biochemists study the properties and interactions of biologically important organic molecules • Biochemistry forms a bridge between chemistry (the study of the properties and interactions of atoms and molecules) and biology (the study of properties and interactions of cells and organisms). • Understanding the physical and chemical principles that determine the properties of these molecules is essential to understanding their functions in the cell and in other living systems

10. Interactions within Molecules • Intramolecular forces (“intra” = within) hold the atoms within a molecule together • These forces are generally thought of as the chemical bonds within a molecule • Chemical bonds within a molecule are called covalent bonds. • A covalent bond forms when the electrons of two atoms overlap so that the electrons of each atom are shared between both atoms

12. Interactions within Molecules • Some atoms attract electrons much more strongly than other atoms • This property is referred to as an atom’s electronegativity • Oxygen, nitrogen, and chlorine have high electronegativity • Hydrogen, carbon, and phosphorus have low electronegativity • When two atoms share electrons, the electrons are more attracted to the atom with the higher electronegativity • Electrons have a negative charge, so that atom would assume a slightly negative charge (∂-) • The atom with lower electronegativity assumes a partial positive charge (∂+)

13. Interactions within Molecules • This unequal sharing of electrons in a covalent bond creates a polar covalent bond • Ex: A water molecule contains two polar covalent O-H bonds, where the electrons in each bond are more strongly attracted to the oxygen atom • Molecules that have regions of partial negative and partial positive charge are called polar molecules

14. Interactions within Molecules • When covalent bonds are formed between atoms with similar electronegativities, the electrons are shared equally between the atoms • These bonds are considered non-polar • If these bonds predominate a molecule, the molecule is considered a non-polar molecule • Ex: Carbon and hydrogen • The polarity of biological molecules greatly affects their behaviour and functions in a cell

15. Interactions between Molecules • Intermolecular forces (“inter” = between) are forces between molecules • They form between different molecules or between different parts of the same molecule (if it is very large) • They are much weaker than intramolecular forces • They determine how molecules interact with each other and with different molecules • They play a vital role in biological systems

16. Interactions between Molecules • Intermolecular forces are usually attractive and make molecules associate together • They can be broken fairly easily if enough energy is applied • Intermolecular forces are responsible for many of the physical properties of substances • Two types of intermolecular interactions are particularly important for biological systems: • Hydrogen bonding • Hydrophobic interactions

17. Hydrogen Bonding • A water molecule has two polar O-H bonds and is a polar molecule • The slightly positive hydrogen atoms of one molecule are attracted to the slightly negative oxygen atoms of other water molecules • This type of intermolecular attraction is called a hydrogen bond. • Hydrogen bonds are weaker than ionic and covalent bonds and are represented by a dotted line • Many biological molecules have polar covalent bonds involving a hydrogen atom and an oxygen or nitrogen atom.

19. Hydrogen Bonding • A hydrogen bond is more easily broken than a covalent bond, but many hydrogen bonds added together can be very strong • The cell is an aqueous environment so hydrogen bonding between biological molecules and water is very important • They help maintain the proper structure and function of the molecules

20. Hydrogen Bonding • Ex: The 3-D shape of DNA, which stores an organism’s genetic information, is maintained by numerous hydrogen bonds • The breaking and reforming of these bonds plays an important role in how DNA functions in the cell

21. Hydrophobic Interactions • Non-polar molecules do not form hydrogen bonds • When non-polar molecules interact with polar molecules, they clump together • Non-polar molecules are hydrophobic, literally meaning “water-fearing” • Polar molecules have a natural tendency to form hydrogen bonds with water molecules and are hydrophilic, literally meaning “water-loving”

22. Hydrophobic Interactions • The natural clumping together of non-polar molecules is called the hydrophobic effect • This effect plays a central role in how cell membranes form and helps to determine the 3-D shape of biological molecules as proteins

23. Ions in Biological Systems • When an atom or group of atoms gains or loses electrons, it acquires an electric charge and becomes an ion • When it loses electrons, the resulting ion is positive and is called a canion. • When it gains electrons, the resulting ion is negative and is called an anion. • Ions can be composed of only one element, such as a sodium ion, Na+, or of several elements, such as a bicarbonate ion HCO3-

24. Ions in Biological Systems • Ions are an important part of living systems • Hydrogen ions, H+, are critical to many biological processes, including cellular respiration (the process by which cells break down nutrients into energy) • Sodium ions, Na+, are part of transport mechanisms that enable specific molecules to enter cells. • Since the cell is an aqueous environment, almost all ions are considered free or disassociated ions (Na+(aq)) since they dissolve in water, rather than as ionic compounds such as sodium chloride (NaCl(s)).

25. Functional Groups • Organic molecules that are made up of only carbon and hydrogen atoms are called hydrocarbons • Hydrocarbons share similar properties including: • Non-polar • Do not dissolve in water • Relatively low boiling points (depending on size) • Flammable • The covalent bonds between carbon and carbon and between carbon and hydrogen are “energy-rich” • Breaking them releases a great deal of energy • Most of the hydrocarbons you encounter in everyday life, such as acetylene, propane, butane, and octane, are fuels

26. Functional Groups • Though hydrocarbons share similar properties, other organic molecules have a wide variety of properties • Most organic molecules have other atoms or groups of other atoms attached to their central carbon-based structure. • A cluster of atoms that always behaves in a certain way is called a functional group • Functional groups contain atoms such as oxygen (O), nitrogen (N), phosphorus (P), or sulfur (S). • Certain chemical properties are always associated with certain functional groups

27. Table 1.1

28. Structures and Shapes of Molecules • A molecular formula shows the number of each type of atom in an element or compound • Ex: H2O, C3H7NO2, and C6H12O6 • Structural formulas show how the different atoms of a molecule are bonded together • When representing molecules using a structural formula, a line is drawn between atoms to indicate a covalent bond • A single line indicates a single covalent bond, double lines indicate a double bond, and triple lines indicate a triple bond

29. Structural Formulas

30. Structural Formulas • Structural formulas can also be presented in a simplified form, particularly for biological molecules • Carbon atoms are indicated by a bend in the line • Their symbol, C, is omitted • Hydrogen atoms attached to these carbon atoms are omitted but are assumed to be present

31. Shapes of Molecules • Structural formulas are 2-D representations, but molecules take up space in 3 dimensions • In fact, the 3-D shape of a molecule influences its behaviour Ball-and-stick Model Space-filling Model

32. Section 1.2: Biologically Important Molecules • Many of the molecules of living organisms are composed of thousands of atoms • These are called macromolecules, which are large molecules that often have complex structures • Many macromolecules are polymers • Long chain-like substances composed of many smaller molecules linked together by covalent bonds • These smaller molecules are called monomers, which can exist individually or as units of a polymer • The monomers in a polymer determine the properties of that polymer.

33. Protein Nucleic Acid Carbohydrate Lipid

34. Carbohydrates • Carbohydrates contain carbon, hydrogen, and oxygen in the ratio of 2 hydrogen and 1 oxygen for every carbon • The general formula for carbohydrates is (CH2O)n where “n” is the number of carbon atoms • Sugar and starches are examples of carbohydrates • They store energy in a way that is easily accessible by the body • Most carbohydrates are polar and dissolve in water • Due to high proportion of hydroxyl functional groups, and often carbonyl groups

35. Monosaccharides and Disaccharides • Monosaccharides are simple sugars that consist of 3 to 7 carbon atoms • “Mono” = one and “saccharide” = sugar • Common examples include: • Glucose is the sugar the cells in the body use first for energy (i.e. blood sugar) • Fructose is a principal sugar in fruits • Galactose is a sugar found in milk Glucose Fructose Galactose

36. Monosaccharides and Disaccharides • These 3 simple sugars have the same molecular formula (C6H12O6) but the 3-D shapes of their structures and the relative arrangement of their hydrogen atoms and hydroxyl groups differ • Molecules that have the same molecular formula but have different structures are called isomers • Due to their different 3-D shapes, they’re treated very differently by your body and in the cell • Ex: Your taste buds detect fructose as being much sweeter than glucose

37. Monosaccharides and Disaccharides • Two monosaccharides can join to form a disaccharide. • The covalent bond between them is called a glycosidic linkage • It forms between specific hydroxyl groups on each monosaccharide. • Common table sugar is the disaccharide sucrose (glucose and fructose) • Lactose (galactose and glucose) is found in dairy products Sucrose Glycosidic linkage

38. Polysaccharides • Many monosaccharides can join together by glycosidic linkages to form a polysaccharide (“poly” = many) • Three common polysaccharides are starch, glycogen, and cellulose • All three are composed of monomers of glucose, but they differ in the ways the glucose units are linked together • This results in them having different 3-D shapes

40. Starch and Glycogen • The differences in their 3-D shapes also leads to them having different functions • Plants store glucose in the form of starch and animals store glucose in the form of glycogen • They provide short-term energy storage, whereby glucose can be easily accessed from their breakdown within the cell • Starch and glycogen differ in their number and type of branching side chains • Glycogen has more branches so it can be broken down much more rapidly than starch

41. Cellulose • Cellulose carries out a completely different function. It provides structural support in plant cell walls. • The type of glycosidic linkage between monomers of cellulose is different from the type in starch and glycogen • The hydroxyl group on carbon-1 of glucose can exist in 2 different positions • These positions are referred to as alpha and beta • The alpha form results in starch and glycogen, while the beta form results in cellulose.

42. Lipids • Like carbohydrates, lipids are composed of carbon, hydrogen, and oxygen atoms • However, lipids have fewer oxygen atoms and a significantly greater proportion of carbon and hydrogen bonds • As a result, lipids are non-polar and hydrophobic (they do not dissolve in water) • Since the cell is an aqueous environment, the hydrophobic nature of some lipids plays a key role in determining their function

43. Lipids • The presence of many energy-rich C-H bonds makes lipids efficient energy-storage molecules • Lipids yield more than double the energy per gram that carbohydrates do • However, they store their energy in hydrocarbon chains so their energy is less accessible to cells than energy from carbohydrates • Lipids provide longer-term energy and are processed by the body after carbohydrate stores are used up

44. Lipids • Lipids are crucial to life in many ways: • Lipids insulate against heat loss • Lipids form a protective cushion around major organs • Lipids are a major component of cell membranes • Lipids provide water-repelling coatings for fur, feathers, and leaves

45. Triglycerides • Triglycerides are composed of 1 glycerol molecule and 3 fatty acid molecules • The bond between the hydroxyl group on a glycerol molecule and the carboxyl group on a fatty acid is called an ester linkage because it results in the formation of an ester functional group Ester Linkages 1 Glycerol 3 Fatty Acids

46. Triglycerides: Fatty Acids • A fatty acid is a hydrocarbon chain that ends with an acidic carboxyl group (-COOH) • A saturated fatty acid has no double bonds between carbon atoms • An unsaturated fatty acid has one or more double bonds between carbon atoms • One double bond = monounsaturated • Two or more double bonds = polyunsaturated • Humans can’t synthesize polyunsaturated fats and must consume them in their diet

47. Triglycerides: Saturated and Unsaturated Fats • The double bonds in a triglyceride affects its 3-D shape, which alters its behaviour in the body • Triglycerides containing saturated fatty acids are generally solid fats at room temperature • Ex: lard and butter • Triglycerides containing unsaturated fatty acids are generally liquid oils at room temperature • Ex: olive oil and canola oil

48. Triglycerides: Health • Saturated fat is linked with heart disease, while some unsaturated fats, particular polyunsaturated fatty acids, are known to reduce the risk of heart disease • A food preservation process called hydrogenation involves chemical addition of hydrogen to unsaturated fatty acids of triglycerides to produce saturated fats • A by-product of this reaction is the conversion of cis fats to trans fats, whereby remaining double bonds are converted to a trans conformation • Consumption of trans fats is associated with increased risk of heart disease

49. Phospholipids • Phospholipids are the main components of cell membranes • They are similar in structure to triglycerides, but a phosphate group replaces the third fatty acid • Attached to the phosphate group is an R group whichdefines the type of phospholipid • The “head” portion is polar and hydrophilic • The lower “tail” portion is non-polar and hydrophobic