1. Organic Compounds
AP Biology

2. The Chemistry of Carbon

3. The Uniqueness and Variety of Carbon

7. Don’t forget the structure and function relationship
Don’t forget the structure and function relationship. The shape of a molecule is important because structure often determines function (or, if you prefer, the shape probably evolved for a particular function).
See page 41 in text.

8. Chemical Groups

9. Functional Groups; take place in the chemical reactions.

10. Macromolecules
Smaller organic molecules join together to form larger molecules (macromolecules)
4 major classes of macromolecules:
Carbohydrates
Lipids
Proteins
Nucleic acids

11. Polymers
Long molecules built by linking a chain of repeating smaller units together
polymers
monomers = repeated small units
Held together by covalent bonds (shared pairs of electrons)
• great variety of polymers can be built from a small set of monomers
• monomers can be connected in many combinations like the 26 letters in the alphabet can be used to create a great diversity of words
• each cell has millions of different macromolecules

12. How to build a polymer Condensation reaction Dehydration synthesis
Joins monomers by “taking” H2O out
1 monomer provides OH
the other monomer provides H
together these form H2O
requires energy & enzymes

13. How to break down a polymer
Hydrolysis
Use H2O to break apart monomers
Reverse of condensation reaction
H2O is split into H and OH
H & OH group attach where the covalent bond used to be
ex: Hydrolysis is used in digestion to break down large macromolecules
Most macromolecules are polymers
• build:
condensation (dehydration) reaction
• breakdown:
hydrolysis
An immense variety of polymers can be built from a small set of monomers

14. Carbohydrates

15. Carbohydrates are composed of C, H, O
(CH2O)x C6H12O6
Function:
energy u energy storage
raw materials u structural materials
Monomer: simple sugars (monosaccharides)
ex: sugars & starches

16. What functional groups?
carbonyl
aldehyde
ketone
hydroxyl

17. Sugars Most names for sugars end in -ose
Classified by number of carbons
6C = hexose (glucose)
5C = pentose (fructose, ribose)
3C = triose (glyceraldehyde)

18. Sugar structure
5C & 6C sugars form rings in aqueous solutions (in cells).
Notice carbons are numbered

19. Numbered carbons C 6' C O 5' C C 4' 1' C C 3' 2'

20. Simple & complex sugars
Monosaccharides
simple 1 monomer sugars
glucose
Disaccharides
2 monomers
sucrose
Polysaccharides
large polymers
starch

21. Disaccharide formed by dehydration synthesis.
Two monosaccharides joined by a glycosidic linkage.

22. Building sugars Dehydration synthesis monosaccharides disaccharide |
maltose |
glucose |
glucose |
maltose
glycosidic linkage

23. Dehydration synthesis
monosaccharides
disaccharide
sucrose = table sugar |
glucose |
fructose |
sucrose
structural isomers
glycosidic linkage

24. Polysaccharides Polymers of sugars costs little energy to build
easily reversible = release energy
Function:
energy storage
starch (plants)
glycogen (animals)
building materials = structure
cellulose (plants)
chitin (arthropods & fungi)
Polysaccharides are polymers of hundreds to thousands of monosaccharides

25. Branched vs linear polysaccharides
Can you see the difference between starch & glycogen?
Which is easier to digest?
Glycogen = many branches = many ends
Enzyme can digest at multiple ends. Animals use glycogen for energy storage == want rapid release.
Form follows function.

26. Polysaccharide diversity
Molecular structure determines function
isomers of glucose
How does structure influence function???

27. Digesting starch vs. cellulose
Starch = all the glycosidic linkage are on same side = molecule lies flat
Cellulose = cross linking between OH (H bonds) = rigid structure

28. Cellulose Most abundant organic compound on Earth
Cross-linking between polysaccharide chains:
= rigid & hard to digest
The digestion of cellulose governs the life strategy of herbivores.
Either you do it really well and you’re a cow or an elephant (spend a long time digesting a lot of food with a little help from some microbes & have to walk around slowly for a long time carrying a lot of food in your stomach)
Or you do it inefficiently and have to supplement your diet with simple sugars, like fruit and nectar, and you’re a gorilla.

29. Glycemic index Which food will get into your blood more quickly? apple
rice cakes
corn flakes
bagel
peanut M&M

30. Glycemic index
Ranking of carbohydrates based on their immediate effect on blood glucose (blood sugar) levels
Carbohydrate foods that breakdown quickly during digestion have the highest glycemic indices. Their blood sugar response is fast & high.

31. Glycemic index Which food will get into your blood more quickly?
apple 36
rice cakes 82
corn flakes 84
bagel 72
peanut M&M 33
Why do we find sweet foods pleasurable to eat?
Why are we attracted to sweet food?

32. Lipids

33. Lipids are composed of C, H, O
long hydrocarbon chain
Diverse group
fats
phospholipids
steroids
Do not form polymers
big molecules made of subunit smaller molecules
not a continuing chain

34. dehydration synthesis
Fats
Structure:
glycerol (3C alcohol) + fatty acid
fatty acid = long HC “tail” with COOH group at “head”
Look at structure… What makes them hydrophobic?
Note functional group = carboxyl
dehydration synthesis

35. Fat Triacylglycerol 3 fatty acids linked to glycerol
ester linkage = between OH & COOH
BIG FAT molecule!!

36. Dehydration synthesis
Pulling the water out to free up the bond

37. Fats Long HC chain polar or non-polar? hydrophilic or hydrophobic?
Function:
energy storage
very rich
2x carbohydrates
cushion organs
insulates body
think whale blubber!
What happens when you add oil to water
Why is there a lot of energy stored in fats?
• big molecule
• lots of bonds of stored energy
So why are we attracted to eating fat?
Think about our ancestors on the Serengeti Plain & during the Ice Age. Was eating fat an advantage?

38. Saturated fats All C bonded to H No C=C double bonds
long, straight chain
most animal fats
solid at room temp.
contributes to cardiovascular disease (atherosclerosis) = plaque deposits
Mostly animal fats

39. Unsaturated fats C=C double bonds in the fatty acids plant & fish fats
vegetable oils
liquid at room temperature
the kinks made by double bonded C prevent the molecules from packing tightly together
Mostly plant lipids
Think about “natural” peanut butter:
Lots of unsaturated fats Oil separates out
Companies want to make their product easier to use:
Stop the oil from separating Keep oil solid at room temp.
Hydrogenate it = chemically alter to saturate it
Affect nutrition?

40. Phospholipids Structure: glycerol + 2 fatty acids + PO4
PO4 negatively charged
other small molecules may also be attached
adenine (ATP)

41. Phospholipids Hydrophobic or hydrophilic?
fatty acid tails = hydrophobic
PO4 = hydrophilic head
dual “personality”
Phospholipids
amphipathic = think
interaction with H2O is complex
& very important!

42. Phospholipids in water
Hydrophilic heads attracted to H2O
Hydrophobic tails “hide” from H2O
self-assemble into aggregates
micelle
liposome
early evolutionary stage of cell?

43. Why is this important? Phospholipids define outside vs. inside
Where do we find phospholipids in cells?
cell membranes

45. Phospholipids & cells Phospholipids of cell membrane
double layer = bilayer
hydrophilic heads on outside
in contact with aqueous solution
hydrophobic tails on inside
form core
forms barrier between cell & external environment
Phospholipid bilayer
Note other molecules in membrane…

46. Steroids ex: cholesterol, sex hormones 4 fused C rings
different steroids created by attaching different functional groups to rings
cholesterol

47. Diversity in steroids
Same C skeleton, different functional groups

48. From Cholesterol  Sex Hormones
What a big difference a little atom can make!

49. Cholesterol Important cell component animal cell membranes
precursor of all other steroids
including vertebrate sex hormones
high levels in blood may contribute to cardiovascular disease
Cholesterol

50. Cholesterol
helps keep cell membranes fluid & flexible

51. Proteins

52. Proteins Structure: monomer = amino acids 20 different amino acids
polymer = polypeptide
protein can be 1 or more polypeptide chains folded & bonded together
large & complex molecules
complex 3-D shape

53. Amino acids O H | || —C— C—OH —N— R Structure: central carbon
amino group
carboxyl group (acid)
R group (side chain)
variable group
confers unique chemical properties of the amino acid
—N— H |
—C—
C—OH || O R

54. Nonpolar amino acids (Side Chains)
nonpolar & hydrophobic
Why are these nonpolar & hydrophobic?

55. Polar amino acids (Side Chains)
polar or charged & hydrophilic
Why are these polar & hydrophillic?

58. Building proteins Peptide bonds: dehydration synthesis
linking NH2 of 1 amino acid to COOH of another
C–N bond
free COOH group on one end is ready to form another peptide bond so they “grow” in one direction from N-terminal to C-terminal
peptide bond

60. Building proteins Polypeptide chains N-terminal = NH2 end
C-terminal = COOH end
repeated sequence (N-C-C) is the polypeptide backbone
grow in one direction

61. Protein structure & function
function depends on structure
3-D structure
twisted, folded, coiled into unique shape
Hemoglobin
Hemoglobin is the protein that makes blood red. It is composed of four protein chains, two alpha chains and two beta chains, each with a ring-like heme group containing an iron atom. Oxygen binds reversibly to these iron atoms and is transported through blood.
Pepsin
Pepsin is the first in a series of enzymes in our digestive system that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins.
Collagen– Your Most Plentiful Protein
About one quarter of all of the protein in your body is collagen. Collagen is a major structural protein, forming molecular cables that strengthen the tendons and vast, resilient sheets that support the skin and internal organs. Bones and teeth are made by adding mineral crystals to collagen. Collagen provides structure to our bodies, protecting and supporting the softer tissues and connecting them with the skeleton. But, in spite of its critical function in the body, collagen is a relatively simple protein.
pepsin
hemoglobin
collagen

62. Protein structure & function
function depends on structure
all starts with the order of amino acids
what determines that order of amino acids?
Lysozyme
Lysozyme protects us from the ever-present danger of bacterial infection. It is a small enzyme that attacks the protective cell walls of bacteria. Bacteria build a tough skin of carbohydrate chains, interlocked by short peptide strands, that braces their delicate membrane against the cell's high osmotic pressure. Lysozyme breaks these carbohydrate chains, destroying the structural integrity of the cell wall. The bacteria burst under their own internal pressure.
Glycolytic enzymes
Glucose powers cells throughout your body. Glucose is a convenient fuel molecule because it is stable and soluble, so it is easy to transport through the blood from places where it is stored to places where it is needed. Glucose is packed with chemical energy, ready for the taking. In a test tube, you can burn glucose, forming carbon dioxide and water and a lot of light and heat. Our cells also burn glucose, but they do it in many small, well-controlled steps, so that they can capture the energy in more useable forms, such as ATP (adenosine triphosphate). These ten enzymes control those small steps in the process of extracting energy from glucose.
Glycolysis (sugar-breaking) is the first process in the cellular combustion of glucose. Glycolysis is endlessly fascinating. In these ten enzymes, you can find examples of many of the important molecular processes that animate our cells. They have been perfected by evolution to perform their diverse chemical tasks quickly and efficiently--adding, removing, and shifting atoms without making mistakes. The pathway is carefully regulated, so that glucose is only broken down when energy is needed
Point out the active sites on each glycolytic enzym
the 10 glycolytic enzymes used to breakdown glucose to make ATP
lysozyme: enzyme in tears & mucus that kills bacteria

63. Primary (1°) structure Order of amino acids in chain
amino acid sequence determined by DNA
slight change in amino acid sequence can affect protein’s structure & it’s function
even just one amino acid change can make all the difference!
Sickle cell anemia: 1 DNA letter changes 1 amino acid = serious disease
Hemoglobin mutation: bends red blood cells out of shape & they clog your veins.

64. Sickle cell anemia glutamic acid is acidic & polar
valine is non-polar = tries to “hide” from water of cell by sticking to another hemoglobin molecules.

65. Secondary (2°) structure
“Local folding”
Folding along short sections of polypeptide
interaction between adjacent amino acids
H bonds between R groups
-helix
-pleated sheet
It’s a helix or B sheet within a single region. Can have both in one protein but a specific region is one or another

66. Secondary (2°) structure

67. Tertiary (3°) structure
“Whole molecule folding”
determined by interactions between R groups
hydrophobic interactions
effect of water in cell
anchored by disulfide bridges (H & ionic bonds)
How the whole thing holds together

68. Quaternary (4°) structure
Joins together more than 1 polypeptide chain
only then is it a functional protein
collagen =
skin & tendons
hemoglobin
Structure equals function wonderfully illustrated by proteins
Collagen is just like rope -- enables your skin to be strong and flexible.

69. Protein structure (review)
R groups hydrophobic interactions,
disulfide bridges 3°
multiple polypeptides
hydrophobic interactions
sequence determines structure and…
structure determines function.
Change the sequence & that changes the structure which changes the function. 1°
aa sequence
peptide bonds 2°
determined by DNA
R groups
H bonds 4°

70. Chaperonin proteins Guide protein folding
provide shelter for folding polypeptides
keep the new protein segregated from cytoplasmic influences

71. Protein models Protein structure visualized by X-ray crystallography
extrapolating from amino acid sequence
computer modelling
lysozyme

72. Denature a protein Disrupt 3° structure pH  salt temperature
unravel or denature protein
disrupts H bonds, ionic bonds & disulfide bridges
Some proteins can return to their functional shape after denaturation, many cannot
Example:
Eggs:
Cooking an egg permanently denatures the proteins.

73. Nucleic Acids

74. Nucleic Acids Function: store & transmit hereditary information
Examples:
RNA (ribonucleic acid)
DNA (deoxyribonucleic acid)
Structure:
monomers = nucleotides

75. Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C)
ribose in RNA
deoxyribose in DNA
PO4 group

76. Types of nucleotides 2 types of nucleotides different Nitrogen bases
purines
double ring N base
adenine (A)
guanine (G)
pyrimidines
single ring N base
cytosine (C)
thymine (T)
uracil (U)

77. Building the polymer

78. Nucleic polymer Why is this important? Backbone sugar to PO4 bond
phosphodiester bond
new base added to sugar of previous base
polymer grows in one direction
N bases hang off the sugar-phosphate backbone
Why is this important?

79. RNA & DNA RNA single nucleotide chain DNA double nucleotide chain
N bases bond in pairs across chains
spiraled in a double helix
double helix 1st proposed as structure of DNA in 1953 by James Watson & Francis Crick (just celebrated 50th anniversary!)

80. Pairing of nucleotides
Nucleotides bond between DNA strands
H bonds
purine :: pyrimidine
A :: T
2 H bonds
G :: C
3 H bonds
The 2 strands are complementary.
One becomes the template of the other & each can be a template to recreate the whole molecule.
Why is this important?

81. Information polymer Function series of bases encodes information
like the letters of a book
stored information is passed from parent to offspring
need to copy accurately
stored information = genes
genetic information
All other biomolecules we spoke about served physical or chemical functions. DNA & RNA are information storage molecules.
DNA well-suited for an information storage molecule:
chemically stable
stores information in the varying sequence of nucleotides (the genetic code)
its coded sequence can be copied exactly by the synthesis of complementary strands; easily unzipped & re-zipped without damage (weak H bonds)
damage to one strand can be repaired by addition of bases that match the complementary strand

83. Why is it important that the strands are bonded by H bonds?
DNA molecule
Double helix
H bonds between bases join the 2 strands
A :: T
C :: G
Why is it important that the strands are bonded by H bonds?
H bonds = biology’s weak bond
• easy to unzip double helix for replication and then re-zip for storage
• easy to unzip to “read” gene and then re-zip for storage

84. Copying DNA Replication 2 strands of DNA helix are complementary
have one, can build other
have one, can rebuild the whole
why is this a good system?
when in the life of a cell does replication occur?
when cells divide, they must duplicate DNA exactly for the new “daughter” cells
Why is this a good system?
mitosis
meiosis

85. DNA replication
“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”
James Watson
Francis Crick
1953
The greatest understatement in biology!

86. Watson and Crick … and others…
1953 | 1962
Discovered & published in 1953
Nobel Prize in 1962:
Watson, Crick, Wilkins

87. Maurice Wilkins… and…
1953 | 1962

88. Rosalind Franklin ( )
A chemist by training, Franklin had made original and essential contributions to the understanding of the structure of graphite and other carbon compounds even before her appointment to King's College. Unfortunately, her reputation did not precede her. James Watson's unflattering portrayal of Franklin in his account of the discovery of DNA's structure, entitled "The Double Helix," depicts Franklin as an underling of Maurice Wilkins, when in fact Wilkins and Franklin were peers in the Randall laboratory. And it was Franklin alone whom Randall had given the task of elucidating DNA's structure. The technique with which Rosalind Franklin set out to do this is called X-ray crystallography. With this technique, the locations of atoms in any crystal can be precisely mapped by looking at the image of the crystal under an X-ray beam. By the early 1950s, scientists were just learning how to use this technique to study biological molecules. Rosalind Franklin applied her chemist's expertise to the unwieldy DNA molecule. After complicated analysis, she discovered (and was the first to state) that the sugar-phosphate backbone of DNA lies on the outside of the molecule. She also elucidated the basic helical structure of the molecule.
After Randall presented Franklin's data and her unpublished conclusions at a routine seminar, her work was provided - without Randall's knowledge - to her competitors at Cambridge University, Watson and Crick. The scientists used her data and that of other scientists to build their ultimately correct and detailed description of DNA's structure in Franklin was not bitter, but pleased, and set out to publish a corroborating report of the Watson-Crick model. Her career was eventually cut short by illness. It is a tremendous shame that Franklin did not receive due credit for her essential role in this discovery, either during her lifetime or after her untimely death at age 37 due to cancer.

89. Interesting note… Ratio of A-T::G-C affects stability of DNA molecule
2 H bonds vs. 3 H bonds
biotech procedures
more G-C = need higher T° to separate strands
high T° organisms
many G-C
parasites
many A-T (don’t know why)
At the foundation of biology is chemistry!!

90. Another interesting note…
ATP Adenosine triphosphate
modified nucleotide
adenine ribose + Pi + Pi + Pi + +

91. Macromolecule Review

92. Carbohydrates Structure / monomer monosaccharide Function energy
raw materials
energy storage
structural compounds
Examples
glucose, starch, cellulose, glycogen
glycosidic bond

93. Lipids Structure / building block
glycerol, fatty acid, cholesterol, H-C chains
Function
energy storage
membranes
hormones
Examples
fat, phospholipids, steroids
ester bond (in a fat)

94. Proteins Structure / monomer amino acids levels of structure Function
enzymes u defense
transport u structure
signals u receptors
Examples
digestive enzymes, membrane channels, insulin hormone, actin
peptide bond

95. Nucleic acids Structure / monomer nucleotide Function
information storage & transfer
Examples
DNA, RNA
phosphodiester bond