1. Chapter 2
Molecules of Life

2. Fundamental unit of matter Nucleus Protons: Positive charge; mass of 1
The Atom
Fundamental unit of matter
Nucleus
Protons: Positive charge; mass of 1
Neutrons: No charge; mass of 1
Electrons
Spin around the nucleus in orbitals (shells)
Negative charge; No mass
Electrically negative: # of protons = # electrons

4. Electrons Electrons carry energy. How??
Electrons are negatively charged as such, they are attracted to the positive charge in the nucleus. Meanwhile, electrons repel other electrons.
REMEMBER… OPPOSITES ATTRACT and SAME REPELS
Electrons spin around the nucleus at various levels. They are attracted to the nucleus but repel each other, therefore it takes work to keep them in orbit.
Example is an apple in your hand.

5. Volumes of space that surround the nucleus Electrons move in orbitals
Electron Orbitals
Volumes of space that surround the
nucleus
Electrons move in orbitals

6. Electron shells and electron orbitals
Constants:
The 1st shell in any atom can hold 2 electrons
The 2nd shell in any atom can hold 8 electrons
The 3rd shell in any atom can hold 8 electrons
Shell # of electrons each shell can hold
First shell
Second shell 8
Third shell
P + N

7. Electron Movement Electron shells = energy levels
Electron orbital = Volume of space around a nucleus where an electron is most likely to be found
Useful Analogy:
planets (electrons) ORBITING around the sun (nucleus)

8. Why is it necessary to understand how electron orbitals work
Why is it necessary to understand how electron orbitals work? This isn’t a Chemistry class, right??
Electrons and the energy they posses (their energy state) determine the chemical behavior of atoms thus, the losing, gaining or sharing of electrons is the BASIS FOR CHEMICAL REACTIONS IN WHICH CHEMICAL BONDS FORM (chemical bonds include hydrogen bonding, ionic bonding and covalent bonding).

9. If electrons couldn’t lose or gain other electrons, or share with other electrons, chemical bonds would NOT form!
Example, H2O

11. Element
a substance that cannot be reduced into a simpler component substance through a chemical process

12. http://cougar. slvhs. slv. k12. ca

13. How to Read the Periodic Table
Elements are arranged: LEFT to RIGHT and TOP to BOTTOM in order of increasing atomic mass.
Rows are arranged in periods Ex. H and He are in period C and O are in period 2
The period number of an element = highest energy level an electron in that element occupies in an unexcited state
Therefore,
H and He have 1 electron shell
C and O have 2 electron shells

14. C 12 Columns represent groups and families.
Each element symbol has 2 numbers listed: atomic number and atomic mass.
Atomic Number
Number of protons in the nucleus 6 C 12
Atomic Mass
Number of protons and neutrons in the nucleus

15. Fig. 3.3

16. Carbon Carbon Facts: 6 protons (Atomic # is 6)
6 neutrons (Atomic mass is 12…so, how do you get 6?)
N = Atomic Mass - P
6 electrons (Atomic # is 6)
Is the first electron shell full (inactive)?
Is the second electron shell full?
How many unpaired orbitals does C have?
Yes No 4

17. Can an element ever have a variable number of neutrons?
Carbon
Carbon Facts:
How many chemical bonds can Carbon form with other atoms? 4
Can an element ever have a variable number of neutrons?

18. Isotopes
Same atom but with a different # of neutrons, thus a different atomic mass
Atomic number = # protons in the nucleus
Atomic mass = # protons + # neutrons
Having a different number of neutrons in the nucleus DOES NOT change the chemical properties of an element BUT it DOES change the stability of the element!!

19. Isotope Atomic # # protons # protons # protons 6 6 6
Atomic Mass # P + # N #P + # N # P + # N
6 + 6 = 12
6 + 7 = 13
6 + 8 = 14

20. Medical Uses of Radioactive Isotopes
Short-lived isotopes are used clinically to diagnose pathological abnormalities/disease
Ex. Use of 99Tc for renal scan
99 Tc (tracer) is introduced through your bloodstream
Kidney cells take up the radioactive tracer (isotope of Tc = 99Tc)
A camera detects emissions from the tracer and records them.
What makes 99Tc specific for kidney cells?

21. The isotope is specific for a protein unique to kidney cells.
Remember, electrons are the basis for chemical reactions!!
So… if 99Tc has a different number of neutrons in its nucleus, the stability of the electrons in the other shell of that 99Tc atom are changed.
There are 43 isotopes of Technitium!
It just so happens that the particular stability of 99Tc seeks to form a chemical bond with this unique kidney protein.

22. Matter Any substance in the universe that has mass and occupies space
Matter is transformed through chemical bonding
Conservation of Matter = Matter cannot be created or destroyed but… it can be transformed
Use of an equation to show how matter is transformed:
Reactants Products
Sodium + Chloride Sodium chloride Na Cl NaCl

23. Important Bonds in Biological Membranes
Way in which atoms link to one another to form molecules
Links are formed through the exchange of electrons
Atoms are driven to react to become more stable
Atomic stability is achieved by filling an outer electron shell
Non-reactive elements have full outer shells = INACTIVE
Types of chemical bonding
Ionic bonding
Covalent bonding
Hydrogen bonding

24. Ionic Bonding
Creates ions (charged atoms): one atom loses electrons and becomes a (+) charged ion while another gains electrons and becomes (-) charged
Note: in charged atoms, the # of protons DOES NOT equal the # of electrons!!!! # Protons = # Electrons
Formed when atoms are attracted to each other by opposite electrical charges (i.e. magnet)
Two key properties of ionic bonding:
They are strong bond (although NOT the strongest)
They are non-directional

25. Ionic Bonding
Example: Table salt
Reactants:
Sodium atom has 1 lone electron in its outer orbital (Ax) +
Chloride atom has 7 electrons in its outer orbital (Ax)
Products:
Sodium ION that has given up an electron from its outer shell
Chloride ION that has accepted an electron from Sodium and has included it in its outer shell

26. Fig. 3.8

27. Both the sodium ion and the chloride ion are electrically attracted because of the opposite charges incurred by the altered electron orbitals.
This electrical attraction results in the formation of an elaborate matrix resulting in a crystal of table salt.

28. Covalent Bonds Electrons are shared between atoms
Two key properties of covalent bonding:
VERY STONG!!! (strongest type of bond)
Directional
Carbon ALWAYS forms a covalent bond!!!!!
2 types:
Non-polar Covalent: electrons are equally shared
Generates hydrophobic molecules (“water hating”)
Polar Covalent: electrons are unequally shared
Generated hydrophilic bonds (”water loving”)

29. Non-Polar Covalent Bond: Methane (CH4)

30. Non-Polar Covalent Bond: Methane (CH4)

31. Polar Covalent Bonding: H2O

32. Hydrogen Bonding
Links a polar covalent molecule to another polar covalent molecule
Results in VERY WEAK bonding BUT because so many are formed, the complex as a whole is VERY STONG

33. Hydrogen Bonding

34. Solutions A homogenous mixture of 2 or more substances
Solute = ingredient being dissolved
Solvent = substance that does the dissolving
Example. You make a solution of water and salt. Which is the solute and which is the solvent?
Solute = Salt
Solvent = Water
Components of solutions Acids Bases Salts pH

35. Components of Solutions, continued
Acids
A substance that puts hydrogen ions (H+ )into a solution
Example: Hydrochloric Acid placed in water
HCl + H2O Cl- + H+
Water HCl dissolved in water H H H H H H H H

36. Components of Solutions, continued
Bases
A substance that puts hydroxide ions (OH-) into solution
Example: Sodium Hydroxide dissolved in water
NaOH + H2O Na+ + OH-
Water NaOH dissolved in water OH OH OH OH OH OH OH OH

37. Components of Solutions, continued
Salts
A substance that puts other ions into solution (ions other than H+ and OH-)
Example: Sodium chloride dissolved in water
NaCl + H2O Na+ + Cl- + H2O Cl Na Na Na Cl Cl Cl Na Na Cl Na Na Cl Cl Na Cl

38. Salts are formed when acids and bases are added to each other; this results in neutralization of the acid and base.
HCl + NaOH NaCl + H2O
(Acid) (Base) (Salt) (Water)

39. Components of Solutions, continuedpH
A logarithmic scale that measures the acidity of alkalinity (basicity) of a solution
Note: the difference between 2 units on the pH scale is 10, therefore, the difference between 3 pH units is…
100
pH scale
Neutral : pH = 7
Acidic : pH < 7
Basic : pH > 7
Buffers keep pH within normal limits

40. pH scale Acidic Neutral Basic

41. The Importance of Water to Life
Three quarters of the Earth’s surface is water
Two thirds of the human body is composed of water
All organisms require water
Since water is an essential part of life, it’s surprising that the bond that 2 atoms of H make with 1 atom of O is so weak. Actually, the bond that forms a single H20 molecule (which is what type of bond??) lasts only 1 / 100,000,000,000 of a second!
However, water molecules form extensive lattices with other water molecules. This occurrence leads to the important physical properties of water!

42. Water
Water is a polar covalently bonded molecule that forms hydrogen bonds with other polar covalently bonded water molecules.
Universal solvent
Ice (solid water) is less dense than liquid ice.
Ex. Ice floats in liquid water
4. Water has a high capacity to store heat. Water stabilizes Earth’s temperature (Remember, water comprises ¾ Earth’s surface.
5. Adhesion and cohesion

43. Properties of Water
Bonds to hydrophilic substances and repels hydrophobic ones
Stabilizes temperature
Expands when it freezes
Cohesive
Dissolves substances

45. Cohesion Surface Tension
Since water is polar, it is attracted to other polar molecules. Cohesion occurs when the other polar molecule is water.
Surface Tension
Created by cohesion and due to the strong hydrogen bonding between the polar water molecules.

46. Chemistry: Macromolecules

47. Forming Macromolecules
Organic molecule
Formed by living organisms
Carbon-based core with functional groups attached
Functional group
Groups of atoms with special chemical properties
Confer specific chemical properties on the molecules that posses them
Ex.
Macromolecules
Potentially large molecules (Macro-) that are the building materials of cells. They are the material that makes up the body of cells and the machinery that runs within cells
Thousands of different types in an organism BUT the body is made of 4 types (protein, nucleic acid, carbohydrates, lipids)

48. Five Principle Functional Groups
Figure 3.17

49. More on Macromolecules
Polymer: a molecule made of MANY chains of a similar subunit
Monomer: a single molecule that is the BASIC building block of a macromolecule
Monomers can combine to form a polymer
View animation on Polymer formation

50. Dehydration Synthesis
The process of FORMING a macromolecule
Forms a COVALENT bond between two subunits:
A hydroxyl (OH) group is removed from one subunit
A hydrogen (H) is removed from the other subunit
Small molecule + small molecule large molecule + H20
View animation

51. Hydrolysis Reactions The BREAKING up of a polymer
Adds a water molecule (H20)
H20 comes in and…
A hydrogen becomes attached to one subunit
A hydroxyl (OH) becomes attached to the other subunit
Results in the BREAKING of the covalent bond that previously held the macromolecule (polymer) together
Large molecule + H small molecules
View animation

52. Carbohydrates Contain C, H, O atoms (1:2:1 ratio)
# Carbon atoms = # Oxygen atoms
Hydrophilic
Excellent for energy storage
Why?? The C-H bonds store energy. When an organism requires an energy source, C-H bonds are the ones most often broken. This results in the release of stored energy.
Comprise 1-2% of a cells mass
2 types: simple carbohydrates
complex carbohydrates

53. Simple Carbohydrates Monosaccharide Simple sugar
Consists of one subunit; smallest carbs
Ex. Glucose (C6H12O6)
Also, fructose, ribose, deoxyribose
See Figure 3.29
Disaccharide
Result of linkage of two monosaccharides
Ex. Sucrose, lactose, maltose
See Figure 3.30

54. Complex Carbohydrates
Polysaccharides
Long chain polymers of sugars
The body converts soluble sugars into insoluble forms (polysaccharides). These polysaccharides are then deposited throughout the body in specific storage areas.
Preferred form of energy storage
Plants: starch = glucose polysaccharide that plants use to store energy
Animals: glycogen = highly insoluble macromolecule formed of glucose and polysaccharides that serves as stored energy
Celluose = indigestible b/c we lack enzymes to break it down = fiber; synthesized by plants for cell wall construction
Utilized by plants and animals as structural polysaccharides (chitin and cellulose); linkage is unique such that the chains are not recognized by enzymes that normally break polysaccharide bonds.

55. Lipids
Contain C, H, and O
Hydrophobic (held together by non-polar covalent bonds)
Used as long term storage
Contains MORE energy-rich C-H bonds than carbs

56. Lipids I. Triglycerides (Fat)
Fats are synthesized from 2 components:
1. Fatty acid: long chain C and H atoms ending in a COOH group
2. Glycerol: a three C molecule; note, glycerol is an alcohol
Glycerol forms a backbone to which 3 fatty acids are attached via a dehydration reaction fat molecule
Provides long term energy storage, insulation

57. Lipids, continued Triglycerides
Saturated
Fatty acids with ALL internal carbon atoms forming covalent bonds with two hydrogen atoms
Animal source
Solid at room temperature and body temp (37C)
Unsaturated
Fats with fatty acids that have double bonds between 1 or more pairs of carbon atoms
Plant source
Kink imparts a 30° bend:
Liquid at room temperature Low melting point
When we eat fat, lipase digests the fat and breaks it down to the 3 individual fatty acids
The longer the fatty acid chain, the HIGHER the melting temp
I.E. Butter – is a saturated triglyceride (composed of different saturated triglycerides). That is why it melts slowly, not all at once! Different triglycerides melt at different temps.
Unsaturated fats melt at lower temps than saturated (> irregular the shape of unsat = lower melting point); as unsat increases, MP reduces
Solid at RT b/c they pack very well – they are straight like sticks, whereas unsaturated is liquid at RT b/c the kinks imparted by the double bonds make them pack less efficiently

58. Why are unsaturated fats good while saturated fats are bad for your health?
The C C bond in unsaturated fats creates a negative charge that causes the fat molecules to repel each other rather than stick together (as they do in long chain saturated fats).

59. Hydrogenation Example: Margarine
Margarine is formed from heating oil (unsaturated triglycerides) in the presence of a metal catalyst (aluminum) and hydrogen. That environment breaks the C C and replaces it with two hydrogen atoms producing very hard, saturated fats. Chemists vary the degree of time that hydrogenation occurs resulting in a product that is soft and spreadable (partially hydrogenated).
N.B. Margarine is 10-50% trans fatty acids = BAD
Margarine has been found to be contaminated with aluminum. Al is a causative agent in AD
Catalyst = something that facilitates a chemical reaction without itself being used up
AD = Alzheimer’s Disease

60. What is a trans-fatty acid?
Trans fatty acids have hydrogen atoms on opposite sides of the double bonded carbons
Cis fatty acids have hydrogen atoms that on the same side with each other
The enzymes that metabolize fat can only metabolize cis fatty acids

61. Butter is a saturated triglyceride
Butter is a saturated triglyceride. Why does butter soften as it melts, why doesn’t it instantly melt?
Because the fatty acid chains that come off the glycerol backbone differ. Each different fatty acid has a different melting point.

62. Common fats Saturated Unsaturated Palmitic acid Omega-3 Palmitic acod
Myristic acid = id’d from nutmeg; found in N-terminus of plasma mem associated cytoplasmic proteins

63. Types of Lipids II. Phospholipid III. Steroid
Glycerol + 2 fatty acids + phosphate group
Polar group at one end (glycerol and phosphate) and highly nonpolar group at other end (fatty acid tails)
Ex. Cell membrane
III. Steroid
4-interlocking rings
Found in cell membranes
Ex. Cholesterol, hormones
Per gram, Fat has twice the energy as carbs

64. Basic structure of a triglyceride
Basic structure of a phospholipid

65. Phospholipid Bilayer
Hydrophobic
Hydrophilic
Hydrophobic

66. Protein Comprises 10-30% cell mass
Functional roles (enzymes) and structural roles (collagen, keratin)
All proteins are a long polymer chain of amino acid subunits
small molecules, 20 total
all 20 have a basic structure of a central carbon atom to which the 4 following are attached: hydrogen atom
amino group (-NH2)
carboxyl group (-COOH)
an “R” group
Collagen = cartilage, bones, tendons
Keratin = feathers of birds

67. Amino Acids Nonpolar Hydrophobic Polar Uncharged Hydrophilic
Polar Ionizable (Acidic)
Hydrophilic
Polar Ionizable (Basic)
Hydrophilic

68. How to make a protein
Link specific amino acids together in a particular order
Peptide bond = covalent bond that links 2 amino acids together
Polypeptides = long chains of amino acids liked by peptide bonds

69. Protein Structure Structure determines function
What determines protein structure?
Amino acid sequence of the protein
Four levels of protein structure:
Primary
Secondary
Tertiary
Quaternary
All levels of protein structure are ultimately determined by amino acid sequence!!

70. Primary Structure of Protein
The sequence of amino acids of a polypeptide chain

71. Secondary Structure of a Protein
Initial folding of the polypeptide chain caused by formation of hydrogen bonds
Can result in sheets (Beta sheets) or coils (alpha helices) of polypeptides
Because some AAs are polar and some are nonpolar, a polypeptide folds in solution: nonpolar regions are forced together (forced by the polar groups and their attraction to water resulting in the polar groups repulsion of nonpolar amino acids)

72. Tertiary Structure of a Protein
A folded and twisted molecule
Repulsion by water forces nonpolar amino acids towards the interior leaving polar amino acids exposed to the exterior

73. Quaternary Structure of a Protein
Spatial arrangement of several component polypeptide chains

74. Denaturation What influences how a polypeptide folds in solution?
The polar nature of the environment
When the polar nature of the environment changes (↑ temp or ↓ pH), hydrogen bonding may be altered which may then cause unfolding of the protein, or denaturation.
Ex. Frying an egg

75. Nucleic Acids
Long polymers of nucleotides that serve as information storage devices of cells
Nucleotides have 3 components:
A five carbon sugar
A phosphate group (PO4)
An organic nitrogen-containing base
Polynucleotide chains
- Chain of nucleic acids in which sugars are linked in a line by the phosphate groups
…SUGAR – P – SUGAR – P - SUGAR – P …

76. Nucleic Acids DNA and RNA DNA (deoxyribonucleic acid)
Possible nucleotides: Adenine, Guanine, Cytosine, THYMINE
Structure: 2 nucleotide strands = double helix
RNA (ribonucleic acid)
Possible nucleotides: Adenine, Guanine, Cytosine, URACIL
Long, single strand
How do nucleic acids function as information storage devices?
Each nucleotide serves as a letter and each nucleic acid has different nucleotides (letters)

77. Nucleotides

78. Everyday Science
Lactose Intolerance – the inability to digest foods containing milk due to a lack of the lactase enzyme (enzyme, a protein that disrupts chemical bonds in other molecules allowing reactions to occur or preventing their occurrence).
Normally, milk sugar (lactose) is digested by the lactase enzyme. Lactase binds to lactose in milk and breaks the chemical bonds that are responsible for holding the sugar together. This allows the broken down sugars to pass through the bloodstream and be utilized by the body.
LI people lack the lactase enzyme, thus they cannot digest milk protein. This leads to a buildup of leading to nausea, cramps and bloaing.

79. Normal Lactose Metabolism
Milk Protein
Lactase
Lactose Glucose Galactose
Glucose _____Galactose
Bloodstream
GI tract
LI symptoms
Energy

80. Questions What is the strongest type of single bonded molecule?
Covalent bond (both polar and non-polar types)
2. Isotopes have a different measure of stability when compared to their ‘parent’ element on the periodic table. True or False
True
3. You can determine the number of neutrons present in an atom by subtracting the number of protons from the ____.
Atomic mass
4. When preparing a solution, you accidentally add too much of an acidic component. This creates an excess of _____. The desired pH is 8; the pH you measure is 6. You decide that it shouldn’t make too much of a difference, you’re only 2 units off. What is wrong with this logic?
H+, or Hydrogen ions

81. A difference of 2 units on the pH scale correlates to a 100 fold more acidic solution. Therefore, your solution has 100 times more Hydrogen ions then the desired solution concentration.

82. Websites for additional info from today’s lecture:
Interactive periodic table