1. Chapter reference: 6

2. The emergence of biological function starts at the chemical level
ATOMS AND MOLECULES
The emergence of biological function starts at the chemical level
Everything an organism is and does depends on chemistry
Chemistry is in turn dependent on the arrangement of atoms in molecules
Chemicals of Life video next slide 

4. Molecules and ecosystems are at opposite ends of the biological hierarchy
Each level of organization in the biological hierarchy builds on the one below it
At each level, new properties emerge

5. A biological hierarchy
D. Organ: Flight muscle of a moth
A biological hierarchy
Rattlebox moth
C. Cell and tissue: Muscle cell within muscle tissue
Myofibril (organelle)
B. Organelle: Myofibril (found only in muscle cells)
Actin
Myosin
Atom
A. Molecule: Actin

6. Life requires about 25 chemical elements
A chemical element is a substance that cannot be broken down to other substances by ordinary chemical means

7. Atomic Structure p+ n0 e-
Nucleus
Electron Cloud

8. C 6 Carbon 12.011 Atomic Structure Atomic Number = protons/electrons
Atomic Mass = protons + neutrons

9. Properties of Subatomic Particles
Atomic Structure
Properties of Subatomic Particles
Useful Equations:
protons = atomic #
electrons = atomic #
neutrons = atomic mass - atomic #

10. Atomic Structure
Nitrogen
Hydrogen
Oxygen
Helium

11. Elements
92 elements occur in nature
About 25 different chemical elements are essential to life
Only 6 elements, CHNOPS, make up 99% of living tissue

12. Carbon, hydrogen, oxygen, and nitrogen make up the bulk of living matter, but there are other elements necessary for life

13. Goiters are caused by iodine deficiency
A goiter is an abnormal enlargement of the thyroid gland.
Atoms & Elements
Video next 

15. Elements can combine to form compounds
Chemical elements combine in fixed ratios to form compounds
Example: sodium + chlorine  sodium chloride

16. Atoms consist of protons, neutrons, and electrons
The smallest particle of an element is an atom
Different elements have different types of atoms

17. The nucleus is surrounded by electrons
An atom is made up of protons and neutrons located in a central nucleus
The nucleus is surrounded by electrons 2
Protons
Nucleus 2
Neutrons 2
Electrons
A. Helium atom

18. Neutrons are electrically neutral
Each atom is held together by attractions between the positively charged protons and negatively charged electrons
Neutrons are electrically neutral 6
Protons
Nucleus 6
Neutrons 6
Electrons
B. Carbon atom

19. Atoms of each element are distinguished by a specific number of protons
The number of neutrons may vary
Variant forms of an element are called isotopes
Some isotopes are radioactive

20. Why should I care? Radioactive isotopes can help or harm us
Radioactive isotopes can be useful tracers for studying biological processes
PET scanners use radioactive isotopes to create anatomical images

21. Electron arrangement determines the chemical properties of an atom
Electrons are arranged in shells
The outermost shell determines the chemical properties of an atom
In most atoms, a full outer shell holds eight electrons

22. Atoms whose shells are not full tend to interact with other atoms and gain, lose, or share electrons
Outermost electron shell (can hold 8 electrons)
Electron
First electron shell (can hold 2 electrons)
HYDROGEN (H)
Atomic number = 1
CARBON (C)
Atomic number = 6
NITROGEN (N)
Atomic number = 7
OXYGEN (O)
Atomic number = 8

23. Ionic bonds are attractions between ions of opposite charge
When atoms gain or lose electrons, charged atoms called ions are created
An electrical attraction between ions with opposite charges results in an ionic bond – + Na Cl Na Cl Na
Sodium atom Cl
Chlorine atom
Na+
Sodium ion
Cl–
Chloride ion
Sodium chloride (NaCl)

24. Sodium and chloride ions bond to form sodium chloride, common table salt
Na+
Cl–

25. Covalent bonds, the sharing of electrons, join atoms into molecules
Some atoms share outer shell electrons with other atoms, forming covalent bonds
Atoms joined together by covalent bonds form molecules

26. Water, Water, Everywhere!`
Water, Water, Everywhere!

27. Water is a polar molecule
THE PROPERTIES OF WATER
Water is a polar molecule
Atoms in a covalently bonded molecule may share electrons equally, creating a nonpolar molecule
If electrons are shared unequally, a polar molecule is created

28. In a water molecule, oxygen exerts a stronger pull on the shared electrons than hydrogen
This makes the oxygen end of the molecule slightly negatively charged
The hydrogen end of the molecule is slightly positively charged
Water is therefore a polar molecule
(–)
(–) O H H
(+)
(+)

29. Overview: Water’s polarity leads to hydrogen bonding and other unusual properties
The charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules
This attraction forms weak bonds called hydrogen bonds
Hydrogen bond

30. Like no other common substance, water exists in nature in all three physical states:
as a solid
as a liquid
as a gas

31. Hydrogen bonds make liquid water cohesive
Capillary
action in plants
Due to hydrogen bonding, water molecules can move from a plant’s roots to its leaves
Insects can walk on water due to surface tension created by cohesive water molecules
Surface tension/Cohesion

32. It takes a lot of energy to disrupt hydrogen bonds
Water is one of the few substances that remain a liquid at such a large range of temperatures (O-100 °C).  A large amount of energy must be invested to overcome the hydrogen bonds in liquid water to change it to the gas phase.

34. The chemistry of life is sensitive to acidic and basic conditions
A compound that releases H+ ions in solution is an acid, and one that accepts H+ ions in solution is a base
Acidity is measured on the pH scale:
0-6 is acidic
7 is neutral
8-14 is basic
Pure water and solutions that are neither basic nor acidic are neutral, with a pH of 7

35. (Higher concentration of H+) (Lower concentration of H+)
pH scale H+
OH–
Lemon juice; gastric juice
The pH scale
(Higher concentration of H+)
Increasingly ACIDIC
Grapefruit juice
Acidic solution
Tomato juice
Urine
NEUTRAL
[H+] = [OH–]
PURE WATER
Human blood
Seawater
Neutral solution
(Lower concentration of H+)
Increasingly BASIC
Milk of magnesia
Household ammonia
Household bleach
Oven cleaner
Basic solution

36. Cells are kept close to pH 7 by buffers
Buffers are substances that resist pH change
They accept H+ ions when they are in excess and donate H+ ions when they are depleted
Buffers are not foolproof

37. Why should I care? Acid rain threatens the environment
Some ecosystems are threatened by acid precipitation
Acid precipitation is formed when air pollutants from burning fossil fuels combine with water vapor in the air to form sulfuric and nitric acids

38. These acids can kill fish, damage buildings, and injure trees
Regulations, new technology, and energy conservation may help us reduce acid precipitation

39. Chemical reactions rearrange matter
REARRANGEMENTS OF ATOMS
Chemical reactions rearrange matter
In a chemical reaction:
reactants interact
atoms rearrange
products result
2 H2 + O2 
2 H2O

41. INTRODUCTION TO ORGANIC COMPOUNDS AND THEIR POLYMERS
Life’s structural and functional diversity results from a great variety of molecules
A relatively small number of structural patterns underlies life’s molecular diversity

42. Life’s molecular diversity is based on the properties of carbon
A carbon atom forms four covalent bonds
It can join with other carbon atoms to make chains or rings
Structural formula
Ball-and-stick model
Space-filling model
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.

43. Functional groups help determine the properties of organic compounds
Functional groups are the groups of atoms that participate in chemical reactions
Hydroxyl groups are characteristic of alcohols
The carboxyl group acts as an acid

45. Biological Molecules
Biological molecules are typically large molecules constructed from smaller subunits.
Monomer: single subunit
(mono = 1; -mer = unit)
Polymer: many units
(poly = many)

46. Cells link monomers to form polymers by dehydration synthesis1 2 3
Short polymer
Unlinked monomer
Removal of water molecule 1 2 3 4
Longer polymer

47. Polymers are broken down to monomers by the reverse process, hydrolysis1 2 3 4
Addition of water molecule 1 2 3
Coating of capture strand

48. Carbohydrates are a class of molecules
They range from small sugars to large polysaccharides
Polysaccharides are long polymers of monomers

49. Examples: sugars, starch, glucose
Function: Carbohydrates are good energy storage molecules.

50. Monosaccharides are the simplest carbohydrates
Monosaccharides are single-unit sugars
These molecules typically have a formula that is a multiple of CH2O
Each molecule contains hydroxyl groups and a carbonyl group
Monosaccharides are the fuels for cellular work

51. The monosaccharides glucose and fructose are isomers
They contain the same atoms but in different arrangements
Glucose
Fructose

52. Abbreviated structure
Many monosaccharides form rings, as shown here for glucose
Abbreviated structure

53. Cells link single sugars to form disaccharides
Monosaccharides can join to form disaccharides, such as sucrose (table sugar) and maltose (brewing sugar)
Glucose
Glucose
Sucrose
Maltose

54. Polysaccharides are long chains of sugar units
These large molecules are polymers of hundreds or thousands of monosaccharides linked by dehydration synthesis

55. Starch and glycogen are polysaccharides that store sugar for later use
Cellulose is a polysaccharide in plant cell walls
Starch granules in potato tuber cells
Glucose monomer
STARCH
Glycogen granules in muscle tissue
GLYCOGEN
Cellulose fibrils in a plant cell wall
CELLULOSE
Cellulose molecules
Figure 3.7
Carb video next slide 

57. Lipids include fats, which are mostly energy-storage molecules
These compounds are composed largely of carbon and hydrogen
They are not true polymers
They are grouped together because they do not mix with water

58. Fats are lipids whose main function is energy storage
They are also called triglycerides

59. Phospholipids are a major component of cell membranes
Phospholipids, waxes, and steroids are lipids with a variety of functions
Phospholipids are a major component of cell membranes
Waxes form waterproof coatings
Steroids are often hormones
Lipid video next 

61. Proteins are essential to the structures and activities of life
Proteins are involved in
cellular structure
movement
defense
transport
communication
Mammalian hair is composed of structural proteins
Enzymes regulate chemical reactions
“All enzymes are proteins but not all proteins are enzymes!”

62. Proteins are made from just 20 kinds of amino acids
Proteins are the most structurally and functionally diverse of life’s molecules
Their diversity is based on different arrangements of amino acids

63. Each amino acid contains:
an amino group
a carboxyl group
an R group, which distinguishes each of the 20 different amino acids
Amino group
Carboxyl (acid) group
Figure 3.12A

64. Amino acids can be linked by peptide bonds
Cells link amino acids together by dehydration synthesis
The bonds between amino acid monomers are called peptide bonds
Carboxyl group
Amino group
PEPTIDE BOND
Dehydration synthesis
Amino acid
Amino acid
Dipeptide

65. Overview: A protein’s specific shape determines its function
A protein, such as lysozyme, consists of polypeptide chains folded into a unique shape
The shape determines the protein’s function
A protein loses its specific function when its polypeptides unravel

66. A protein’s primary structure is its amino acid sequence
Secondary structure is polypeptide coiling or folding produced by hydrogen bonding
Primary structure
Amino acid
Secondary structure
Hydrogen bond
Pleated sheet
Alpha helix

67. Tertiary structure is the overall shape of a polypeptide
Quaternary structure is the relationship among multiple polypeptides of a protein
Tertiary structure
Polypeptide (single subunit of transthyretin)
Quaternary structure
Transthyretin, with four identical polypeptide subunits

69. NUCLEIC ACIDS
Nucleic acids are information-rich polymers of nucleotides
Nucleic acids such and DNA and RNA serve as the blueprints for proteins
They ultimately control the life of a cell

70. The monomers of nucleic acids are nucleotides
Each nucleotide is composed of a sugar, phosphate, and nitrogenous base
Nitrogenous base (A)
Phosphate group
Sugar

71. The sugar and phosphate form the backbone for the nucleic acid
Nucleotide
Sugar-phosphate backbone

72. DNA consists of two polynucleotides twisted around each other in a double helix
The sequence of the four kinds of nitrogenous bases in DNA carries genetic information
Base pair
Nitrogenous base (A)

73. Stretches of a DNA molecule called genes program the amino acid sequences of proteins
DNA information is transcribed into RNA, a single-stranded nucleic acid
RNA is then translated into the primary structure of proteins
Nucleic Acid video next 

75. Summary: Example of a Macromolecule Monomer
polysaccharide (complex carbohydrate)
monosaccharide (simple sugar)
fat (a lipid)
glycerol, fatty acid
protein
amino acid
nucleic acid
nucleotide