Chapter 3 The Chemistry of Organic Molecules AP Biology.

Chapter 3The Chemistry of Organic Molecules

AP Biology

Definitions

• Organic Molecules– Bonding of H, O, N, and other molecules to

carbon.– Characterize the structure and function of living

things

• Inorganic Molecules– Do not contain C and H together– Nonliving matter; however they play important

roles in living things

Functional Groups

• Functional groups are the parts of molecules involved in chemical reactions

• Give organic molecules distinctive chemical properties (ex. Polarity, hydophobic/philic, acidic, etc.)

• Six functional groups are important in the chemistry of life: (see Figure 3.2, pg 35)– Hydroxyl – Carbonyl – Carboxyl– Amino– Sulfhydryl– Phosphate

Isomers

• Isomers are molecules with the same molecular formula but different structures (different functional groups) and properties

Macromolecules

– Are large molecules composed of smaller molecules

– Are complex in their structures

Macromolecules

•Macromolecules are polymers, built from monomers• Four classes of life’s organic molecules are polymers– Carbohydrates– Proteins– Nucleic acids– Lipids

The Synthesis and Breakdown of Polymers

• Monomers form larger molecules by condensation reactions called dehydration synthesis

(a) Dehydration reaction in the synthesis of a polymer

HO H1 2 3 HO

HO H1 2 3 4

H

H2O

Short polymer Unlinked monomer

Longer polymer

Dehydration removes a watermolecule, forming a new bond

Figure 5.2A

The Synthesis and Breakdown of Polymers

• Polymers can disassemble by– Hydrolysis (addition of water molecules)

(b) Hydrolysis of a polymer

HO 1 2 3 H

HO H1 2 3 4

H2O

HHO

Hydrolysis adds a watermolecule, breaking a bond

Figure 5.2B

Carbohydrates• Monosaccharides

– Glucose– Fructose– Ribose/Deoxyribose

• Disaccharides– Lactose– Maltose– Sucrose

• Polysaccharides– Starch– Glycogen– Cellulose– Chitin

Lipids• Lipids are a diverse group of hydrophobic

molecules (nonpolar and insoluble)• Lipids– Are the one class of large biological

molecules that do not consist of polymers– Provide energy storage– Act as cell messengers

Fats– Are constructed from two types of smaller molecules, a

single glycerol and usually three fatty acids– Vary in the length and number and locations of double

bonds they contain

• Saturated fatty acids– Have the maximum number of hydrogen

atoms possible– Have no double bonds

(a) Saturated fat and fatty acid

Stearic acid

Figure 5.12

• Unsaturated fatty acids– Have one or more double bonds

(b) Unsaturated fat and fatty acidcis double bondcauses bending

Oleic acid

Figure 5.12

Waxes

• Chains of fatty acids bonded to an alcohol chain.

• Solid• Protective

• Phospholipids– Have only two fatty acids– Have a phosphate group instead of a third

fatty acid

• Phospholipid structure–Consists of a hydrophilic “head” and

hydrophobic “tails”CH2

O

PO O

O

CH2CHCH2

OO

C O C O

Phosphate

Glycerol

(a) Structural formula (b) Space-filling model

Fatty acids

(c) Phospholipid symbol

Hyd

rop

hob

i c t

ails

Hydrophilichead

Hydrophobictails

–

Hyd

rop

hi li c

head

CH2 Choline+

Figure 5.13

N(CH3)3

• The structure of phospholipids– Results in a bilayer arrangement found in cell

membranes

Hydrophilichead

WATER

WATER

Hydrophobictail

Figure 5.14

Steroids

• Steroids– Are lipids characterized by a carbon skeleton

consisting of four fused rings– Differ with functional groups

• One steroid, cholesterol– Is found in cell membranes– Is a precursor for some hormones

HO

CH3

CH3

H3C CH3

CH3

Figure 5.15

Proteins

• Support• Enzymes• Transport• Defense• Hormones• Motion

• Amino acids– Are organic molecules possessing both

carboxyl (acidic) and amino groups– Differ in their properties due to differing side

chains, called R groups

Amino Acid Polymers

• Amino acids– Are linked by peptide bonds (covalent)

Protein Structure

• A protein’s specific conformation (shape) determines how it functions

Four Levels of Protein Structure

• Primary structure– Is the unique sequence

of amino acids in a polypeptide

Figure 5.20–

Amino acid

subunits

+H3NAmino

end

oCarboxyl end

oc

GlyProThrGlyThr

Gly

GluSeuLysCysProLeu

MetVal

Lys

ValLeu

AspAlaValArgGly

SerPro

Ala

Gly

lle

SerProPheHisGluHis

Ala

GluValValPheThrAla

Asn

AspSer

GlyProArg

ArgTyrThr

lleAla

Ala

Leu

LeuSer

ProTyrSerTyrSerThr

Thr

Ala

ValVal

ThrAsnProLysGlu

ThrLys

SerTyrTrpLysAlaLeu

GluLleAsp

O C helix

pleated sheetAmino acid

subunitsNCH

C

O

C N

H

CO H

R

C NH

C

O H

C

R

N

HH

R C

O

R

C

H

NH

C

O H

NCO

R

C

H

NH

H

C

R

C

O

C

O

C

NH

H

R

C

C

ON

HH

C

R

C

O

NH

R

C

H C

ON

HH

C

R

C

O

NH

R

C

H C

ON

HH

C

R

C

O

N H

H C R

N HO

O C N

C

RC

H O

CHR

N HO C

RC

H

N H

O CH C R

N H

CC

N

R

H

O C

H C R

N H

O C

RC

H

H

C

RN

H

CO

C

NH

R

C

H C

O

N

H

C

• Secondary structure– Is the folding or coiling of the polypeptide into a

repeating configuration– Includes the helix and the pleated sheet

H H

Figure 5.20

• Tertiary structure– Is the overall three-dimensional shape of a

polypeptide– Results from interactions between amino acids

and R groups

CH2CH

OH

O

CHO

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3

CH3

H3C

H3C

Hydrophobic interactions and van der Waalsinteractions Polypeptid

ebackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge

• Quaternary structure– Results when two or more polypeptide chains

combine.

Polypeptidechain

Collagen

Chains

ChainsHemoglobin

IronHeme

Protein Structure

• http://www.stolaf.edu/people/giannini/

• http://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swf

•Denaturation is when a protein unravels and loses its native conformation(shape) Denaturation

Renaturation

Denatured protein

Normal protein

Figure 5.22

Nucleic Acids

• Made of nucleotide monomers

• Two Types: DNA & RNA– Differences in structure

ATP

• A nucleotide of ribose and adenine• 5-C sugar and 3 phosphates• High energy (bonds)