UNIT 1: BIOCHEMISTRY

AP Biology

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

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 Chemistry4.1-4.3

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

Diamond: perfect sp3

Graphite: sp2

Carbon Skeletons are highly variableLe

ngth

Bra

nch

ing

Hybri

d

Orb

itals

Which carbon are we looking at?

12

34

56

12

3

45

6

Naming Carbon Compounds

2-chlorohexane

2,3-dichlorohexane

1-fluoro 2,3-dichlorocyclohexane

12

34

56

12

34

56

12

3

45

6

Isomers

Different configurations with the same formula

Commonly found in organic molecules

Structural Isomers

Differ in covalent partners

propane 2-methyl propane

Molecular C4H10 C4H10

Structural CH3CH2CH2CH3 CH3CH(CH3)CH3

Alt Struc. CH3(CH2)2CH3

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

Enantiomers

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

LD

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

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 Breaking5.1

Making & Breaking Macromolecules

Making & Breaking Macromolecules

5.2 Carbohydrates

General information on carbohydrates

CnH2nOn (for monomers) n is usually between 3 and 8

-ose Frequently form rings

Glucose Isomers

Carbohydrates

α-D-Glucose

4

5

6

3

1

Starch (Amylose) α-1,4 linkage

Carbohydrates as energy/storage plants

2

α-D-Glucose

4

5

6

3

1

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

Cellulose and H-bonds

Carbohydrates as structure in plants

-D-Glucose

4

5

6

1

3 2

Hydrogen bonds

Carbohydrates as structure in animals

Chitin α-glucosamine 1,4 linkage

Sequence these from highest to lowest energy

Sequence these from highest to lowest energy

5.3 Lipids

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 acidaka oleic acid

Octadecanoic acidaka 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 http://www.wiley.com/legacy/college/boyer/0470003790/animations/catalysis_energy/catalysis_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

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. 3.16-1

Fig. 3.16-2

http://www.yellowtang.org/animations/dna_subunits_adv.swf

Nucleic acids for data storage

Nucleic acids for regulation