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UNIT 1: BIOCHEMISTRY
AP Biology
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AP Learning Objectives
2.8 The student is able to justify the selection of data regarding the types of molecules that an animal, plant or bacterium will take up as necessary building blocks and excrete as waste products. [SP 4.1]
4.1 The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. [SP 7.1]
4.2 The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer. [SP 1.3]
4.3 The student is able to use models to predict and justify that changes in the subcomponents of a biological polymer affect the functionality of the molecule. [SP 6.1, 6.4]
4.17
The student is able to analyze data to identify how molecular interactions affect structure and function. [SP 5.1]
Text 4.1-4.2, 5.1-5.5
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Essential Questions
What types of molecules do organisms use for building blocks and excrete as wastes?
How do molecules and atoms from the environment build new molecules?
What interactions between molecules affect their structure and function?
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Intro to Organic Chemistry4.1-4.3
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Carbon Properties
Forms four equivalent bonds Hybrid orbitals are common (sp3, sp2, sp)
Forms long chains with other carbons Forms single, double, and triple bonds Forms complex and varied molecules
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Diamond: perfect sp3
Graphite: sp2
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Carbon Skeletons are highly variableLe
ngth
Bra
nch
ing
Hybri
d
Orb
itals
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Which carbon are we looking at?
12
34
56
12
3
45
6
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Naming Carbon Compounds
2-chlorohexane
2,3-dichlorohexane
1-fluoro 2,3-dichlorocyclohexane
12
34
56
12
34
56
12
3
45
6
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Isomers
Different configurations with the same formula
Commonly found in organic molecules
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Structural Isomers
Differ in covalent partners
propane 2-methyl propane
Molecular C4H10 C4H10
Structural CH3CH2CH2CH3 CH3CH(CH3)CH3
Alt Struc. CH3(CH2)2CH3
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Cis- and Trans- Isomers
Differ in arrangement around a double bond Due to the double bond, the atoms are not
free to rotate Trans-1,2 dichloroethene Cis-1,2 dichloroethene
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Enantiomers
Differ in spatial arrangement around asymmetric carbon Mirror images L and D (or S and R) cannot be superimposed
LD
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Functional Groups
Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Phosphate Methyl
Structur
e
Propertie
s
• —OH
• Forms hydrogen bonds
• Polar
O
• —C—
• Often aromatic
• —COOH
• Acid
• Loses H+ when ionized
• Ionized in cells
• —NH2
• Base- picks up H+ from surrounding
• —SH
• Cross links in proteins
• —OPO32-
• Loses H to become ionized
• —CH3
• Affects function of molecule
Used in
• Alcohols
• Sugars
• Almost everything
• Ketones if R’ is C-based
• Aldehydes if R’ is H
• Weak acids (acetic acid)
• Amino acids
• Proteins
• Hair perms
• G3P, ATP, DNA
• Abbreviated as P
• Hormones
• DNA
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Macromolecules
Carbohydrates Lipids Proteins Nucleic acids
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What can they do?
• Energy• Storage• Structure
Carbohydrates
• Energy • Storage• Structure • Regulation
Lipids
• Structure • Catalysts• Energy • Regulation
Proteins
• Regulation• Storage
Nucleic Acids
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Some Uses for Macromolecules
• Carbs• Lipids• Proteins
Energy
• Carbs• Lipids• Nucleic acids
Storage
• Carbs • Lipids• Proteins
Structure
• Lipids• Proteins• Nucleic acids Regulation
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Making and Breaking5.1
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Making & Breaking Macromolecules
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Making & Breaking Macromolecules
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5.2 Carbohydrates
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General information on carbohydrates
CnH2nOn (for monomers) n is usually between 3 and 8
-ose Frequently form rings
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Glucose Isomers
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Carbohydrates
α-D-Glucose
4
5
6
3
1
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Starch (Amylose) α-1,4 linkage
Carbohydrates as energy/storage plants
2
α-D-Glucose
4
5
6
3
1
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Glycogen α-1,4 linkage & α-1, 6 linkage Branched spirals due to H-bonds
Carbohydrates as storage in animals
α-D-Glucose
4
5
6
3
1
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Cellulose and H-bonds
Carbohydrates as structure in plants
-D-Glucose
4
5
6
1
3 2
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Hydrogen bonds
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Carbohydrates as structure in animals
Chitin α-glucosamine 1,4 linkage
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Sequence these from highest to lowest energy
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Sequence these from highest to lowest energy
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5.3 Lipids
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Lipids
Not water soluble Polar carboxyl group Non-polar hydrocarbon chain
usual, but not steroids
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Lipids
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Saturation determines room temperature state
Lipids as Energy
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Name that Molecule!
Cis-9 octadecanoic acidaka oleic acid
Octadecanoic acidaka stearic acid
Cis-9, 12, 15 octadecanoic acid
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Lipids as storage
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Lipids as membranes
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Lipids as protection
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Lipids as hormones and vitamins
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Steroids as regulators
4-ring structure
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Proteins 5.4
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Proteins
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Proteins as structure
Collagen
Keratin
Histones
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Proteins for movement
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Proteins as catalysts http://www.wiley.com/legacy/college/boyer/0470003790/animations/catalysis_energy/catalysis_energy.htm
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Proteins as energy
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Proteins for regulation
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Proteins for just about everything!
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Amino Acids
Different R groups give amino acids distinct properties
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Protein Folding
Primary- amino acid sequence Secondary- α-helix & β-pleated sheets Tertiary- intra-molecular
attraction/repulsion Quaternary- 2 or more polypeptides join
together and fold around one another “Fold.it”
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Primary
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Primary continued
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Secondary
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Tertiary
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Tertiary
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Quaternary
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When proteins break down
Δ pH Δ temperature Δ surroundings
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Denaturing
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Folding within a cell
Chaperonins (chaperone proteins) Protect the new polypeptide from
surroundings while it folds Do not control folding pattern
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Nucleic Acids 5.5
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Nucleic acids
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Note 5’ and 3’ ends
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Fig. 3.16-1
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Fig. 3.16-2
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http://www.yellowtang.org/animations/dna_subunits_adv.swf
Nucleic acids for data storage
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Nucleic acids for regulation