UNIT 1: BIOCHEMISTRY AP Biology

AP Learning Objectives 2.8The 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] 4.1The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. [SP 7.1] 4.2The 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] 4.3The 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] 4.17The student is able to analyze data to identify how molecular interactions affect structure and function. [SP 5.1] Text ,

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?

Intro to Organic Chemistry

Carbon Properties  Forms four equivalent bonds  Hybrid orbitals are common (sp 3, sp 2, sp)  Forms long chains with other carbons  Forms single, double, and triple bonds  Forms complex and varied molecules

 Diamond: perfect sp 3  Graphite: sp 2

Carbon Skeletons are highly variable Length Branching Hybrid Orbitals

Which carbon are we looking at?

Naming Carbon Compounds  2-chlorohexane  2,3-dichlorohexane  1-fluoro 2,3-dichlorocyclohexane

Isomers  Different configurations with the same formula  Commonly found in organic molecules

Structural Isomers  Differ in covalent partners propane2-methyl propane Molecular C 4 H 10 C 4 H 10 Structural CH 3 CH 2 CH 2 CH 3 CH 3 CH(CH 3 )CH 3 Alt Struc.CH 3 (CH 2 ) 2 CH 3

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 dichloroetheneCis-1,2 dichloroethene

Enantiomers  Differ in spatial arrangement around asymmetric carbon  Mirror images  L and D (or S and R)  cannot be superimposed LD

Functional Groups HydroxylCarbonylCarboxylAminoSulfhydrylPhosphateMethyl Structure Properties — — 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 — — OPO 3 2- Loses H to become ionized — — CH 3 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

Macromolecules  Carbohydrates  Lipids  Proteins  Nucleic acids

What can they do? Energy Storage Structure Carbohydrates Energy Storage Structure Regulation Lipids Structure Catalysts Energy Regulation Proteins Regulation Storage Nucleic Acids

Some Uses for Macromolecules Carbs Lipids Proteins Energy Carbs Lipids Nucleic acids Storage Carbs Lipids Proteins Structure Lipids Proteins Nucleic acids Regulation

Making and Breaking 5.1

Making & Breaking Macromolecules

5.2 Carbohydrates

General information on carbohydrates  C n H 2n O n (for monomers)  n is usually between 3 and 8  -ose  Frequently form rings

Glucose Isomers

Carbohydrates α-D-Glucose

 Starch (Amylose)  α-1,4 linkage Carbohydrates as energy/storage plants 2 α-D-Glucose

 Glycogen  α-1,4 linkage & α-1, 6 linkage  Branched spirals due to H-bonds Carbohydrates as storage in animals α-D-Glucose

 Cellulose and H-bonds Carbohydrates as structure in plants  -D-Glucose

Hydrogen bonds

Carbohydrates as structure in animals  Chitin  α -glucosamine 1,4 linkage

Sequence these from highest to lowest energy

5.3 Lipids

 Not water soluble  Polar carboxyl group  Non-polar hydrocarbon chain usual, but not steroids

Lipids

 Saturation determines room temperature state Lipids as Energy

Name that Molecule! Cis-9 octadecanoic acid aka oleic acid Octadecanoic acid aka stearic acid Cis-9, 12, 15 octadecanoic acid

Lipids as storage

Lipids as membranes

Lipids as protection

Lipids as hormones and vitamins

Steroids as regulators  4-ring structure

Proteins 5.4

Proteins

Proteins as structure Collagen Keratin Histones

Proteins for movement

Proteins as catalysts /animations/catalysis_energy/cata lysis_energy.htm

Proteins as energy

Proteins for regulation

Proteins for just about everything!

Amino Acids  Different R groups give amino acids distinct properties

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”

Primary

Primary continued

Secondary

Tertiary

Quaternary

When proteins break down  Δ pH  Δ temperature  Δ surroundings

Denaturing

Folding within a cell  Chaperonins (chaperone proteins)  Protect the new polypeptide from surroundings while it folds  Do not control folding pattern

Nucleic Acids 5.5

Nucleic acids

Note 5’ and 3’ ends

Fig

Fig

 ts_adv.swf ts_adv.swf Nucleic acids for data storage

Nucleic acids for regulation