UNIT 1: BIOCHEMISTRY AP Biology. AP Learning Objectives 2.8The student is able to justify the...

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UNIT 1: BIOCHEMISTRY AP Biology

Transcript of UNIT 1: BIOCHEMISTRY AP Biology. AP Learning Objectives 2.8The student is able to justify the...

Page 1: 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.

UNIT 1: BIOCHEMISTRY

AP Biology

Page 2: 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.

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

Page 3: 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.

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?

Page 4: 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.

Intro to Organic Chemistry4.1-4.3

Page 5: 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.

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

Page 6: 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.

Diamond: perfect sp3

Graphite: sp2

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Carbon Skeletons are highly variableLe

ngth

Bra

nch

ing

Hybri

d

Orb

itals

Page 8: 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.

Which carbon are we looking at?

12

34

56

12

3

45

6

Page 9: 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.

Naming Carbon Compounds

2-chlorohexane

2,3-dichlorohexane

1-fluoro 2,3-dichlorocyclohexane

12

34

56

12

34

56

12

3

45

6

Page 10: 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.

Isomers

Different configurations with the same formula

Commonly found in organic molecules

Page 11: 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.

Structural Isomers

Differ in covalent partners

propane 2-methyl propane

Molecular C4H10 C4H10

Structural CH3CH2CH2CH3 CH3CH(CH3)CH3

Alt Struc. CH3(CH2)2CH3

Page 12: 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.

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

Page 13: 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.

Enantiomers

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

LD

Page 14: 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.

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

Page 15: 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.

Macromolecules

Carbohydrates Lipids Proteins Nucleic acids

Page 16: 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.

What can they do?

• Energy• Storage• Structure

Carbohydrates

• Energy • Storage• Structure • Regulation

Lipids

• Structure • Catalysts• Energy • Regulation

Proteins

• Regulation• Storage

Nucleic Acids

Page 17: 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.

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

Page 25: 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.

Starch (Amylose) α-1,4 linkage

Carbohydrates as energy/storage plants

2

α-D-Glucose

4

5

6

3

1

Page 26: 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.
Page 27: 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.

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

Page 28: 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.
Page 29: 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.

Cellulose and H-bonds

Carbohydrates as structure in plants

-D-Glucose

4

5

6

1

3 2

Page 30: 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.

Hydrogen bonds

Page 31: 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.

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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Page 43: 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.
Page 44: 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.

Lipids as protection

Page 45: 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.

Lipids as hormones and vitamins

Page 46: 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.

Steroids as regulators

4-ring structure

Page 47: 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.
Page 48: 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.

Proteins 5.4

Page 49: 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.

Proteins

Page 50: 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.
Page 51: 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.

Proteins as structure

Collagen

Keratin

Histones

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Proteins for movement

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Proteins as energy

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Proteins for regulation

Page 56: 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.

Proteins for just about everything!

Page 57: 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.

Amino Acids

Different R groups give amino acids distinct properties

Page 58: 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.

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”

Page 59: 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.

Primary

Page 60: 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.

Primary continued

Page 61: 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.

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

Page 66: 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.

Denaturing

Page 67: 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.

Folding within a cell

Chaperonins (chaperone proteins) Protect the new polypeptide from

surroundings while it folds Do not control folding pattern

Page 68: 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.

Nucleic Acids 5.5

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Nucleic acids

Page 70: 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.
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Note 5’ and 3’ ends

Page 73: 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.

Fig. 3.16-1

Page 74: 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.

Fig. 3.16-2

Page 75: 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.

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

Nucleic acids for data storage

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Nucleic acids for regulation