Chapter 3 ppt

(1)

Biology

Sylvia S. Mader

Michael Windelspecht

Chapter 3 The Chemistry of

Organic Molecules

Lecture Outline

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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(2)

3.1 Organic Molecules

• Organic molecules

contain carbon and

hydrogen atoms.

• Four classes of organic molecules

(

biomolecules

) exist in living organisms

:



Carbohydrates



Lipids



Proteins

(3)

(4)

The Carbon Skeleton and Functional

Groups

• The carbon chain of an organic molecule is

called its skeleton or backbone.

• Functional groups

are clusters of specific

atoms bonded to the carbon skeleton with

characteristic structures and functions.



Determine the chemical reactivity and polarity

(5)

(6)

Isomers

• Isomers

are organic molecules that have

identical molecular formulas but a different

arrangement of atoms.

glyceraldehyde

dihydroxyacetone

OH

H

C

H

O

OH

H

O

(7)

7 Biomolecules

• Carbohydrates, lipids, proteins, and nucleic

acids are called

biomolecules

.



Usually consist of many repeating units

• Each repeating unit is called a

monomer

.

• A molecule composed of monomers is

called a

polymer

(many parts).

–Example: amino acids (monomer) are

joined together to form a protein

(8)

Fig. 3.3

Biomolecules

(9)

9 Synthesis and Degradation

• A

dehydration reaction

is a chemical reaction

in which subunits are joined together by the

formation of a covalent bond and water is

produced during the reaction.



Used to connect monomers together to make

polymers



Example: formation of starch (polymer) from glucose

subunits (monomer)

• A

hydrolysis

reaction is a chemical reaction in

which a water molecule is added to break a

covalent bond.



Used to breakdown polymers into monomers

(10)

monomer

OH

(11)

monomer

OH

+

(12)

+

H

monomer

OH

(13)

monomer

H

₂

O

OH

+

H

(14)

monomer

Dehydration

reaction

H

2 O

OH

H

(15)

monomer

(16)

H

₂

O

monomer

(17)

monomer

Dehydration

reaction

H

2 O

(18)

monomer

Hydrolysis

reaction

OH

H

₂

O

monomer

(19)

monomer

dehydration

reaction

monomer

H

₂

O

OH

H

OH

H

b. Degradation of a biomolecule

a. Synthesis of a biomolecule

H

₂

O

monomer

hydration

reaction

(20)

Synthesis and Degradation

• Enzymes are required for cells to carry out

dehydration synthesis and hydrolysis reactions.



An

enzyme

is a molecule that speeds up a

chemical reaction.

(21)

3.2 Carbohydrates

• Functions:



Energy source



Provide building material (structural role)

• Contain carbon, hydrogen and oxygen in a 1:2:1

ratio

(22)

• A

monosaccharide

is a single sugar molecule.

• Also called simple sugars

• Have a backbone of 3 to 7 carbon atoms

• Examples:



Glucose (blood), fructose (fruit) and galactose

• Hexoses

- six carbon atoms



Ribose and deoxyribose (in nucleotides)

• Pentoses

– five carbon atoms

(23)

Fig. 3.6

H

C

HO

a.

H

OH

6

5

4

3

1 c.

d.

O

H

O

H

OH

H

HO

b.

C

₆

H

₁₂

O

₆

CH

₂

OH

CH

₂

OH

C

H

O

C

2 C

OH

H

(24)

Disaccharides

• A

disaccharide

contains two

monosaccharides joined together by

dehydration synthesis.

• Examples:



Lactose (milk sugar) is composed of galactose

and glucose.



Sucrose

(table sugar) is composed of glucose

(25)

O

OH

glucose C

₆

H

₁₂

O

₆

HO

H

+

CH

₂

OH

CH

₂

OH

glucose C

₆

H

₁₂

O

₆

(26)

glucose C

₆

H

₁₂

O

₆

CH

₂

OH

O

OH

HO

H

+

dehydration reaction

glucose C

₆

H

₁₂

O

₆

CH

₂

OH

(27)

O

OH

water

HO

H

O

+

dehydration reaction

H

₂

O

maltose C

₁₂

H

₂₂

O

₁₁

glucose C

6

H

12

O

6

CH

₂

OH

CH

₂

OH

CH

₂

OH

CH

₂

OH

glucose C

6

H

12

O

6

(28)

O

OH

water

monosaccharide

disaccharide

water

HO

H

O

monosaccharide

+

de h yd r ation reaction

H

₂

O

maltose C

₁₂

H

₂₂

O

₁₁

glucose C

₆

H

₁₂

O

₆

CH

₂

OH

CH

₂

OH

CH

₂

OH

CH

₂

OH

glucose C

₆

H

₁₂

O

₆

(29)

O

maltose C

₁₂

H

₂₂

O

₁₁

CH

₂

OH

CH

₂

OH

(30)

O

water

O

+

H

₂

O

maltose C

₁₂

H

₂₂

O

₁₁

CH

₂

OH

CH

₂

OH

(31)

maltose C

₁₂

H

₂₂

O

₁₁

CH

₂

OH

O

water

O

+

hydrolysis reaction

H

2 O

CH

₂

OH

(32)

O

OH

water

HO

H

O

+

hydrolysis reaction

H

₂

O

maltose C

₁₂

H

₂₂

O

₁₁

glucose C

₆

H

₁₂

O

₆

CH

₂

OH

CH

₂

OH

CH

₂

OH

CH

₂

OH

glucose C

₆

H

₁₂

O

₆

(33)

O

OH

water

monosaccharide

disaccharide

water

HO

H

O

glucose C

₆

H

₁₂

O

₆

monosaccharide

+

hydrolysis

reaction

H

₂

O

maltose C

₁₂

H

₂₂

O

₁₁

CH

₂

OH

glucose C

₆

H

₁₂

O

₆

CH

₂

OH

CH

₂

OH

CH

₂

OH

(34)

glucose C

6

H

12

O

6

water

monosaccharide

+

monosaccharide

disaccharide

+

water

dehydration reaction

hydrolysis reaction

maltose C

12

H

22

O

11

glucose C

₆

H

₁₂

O

₆

(35)

Polysaccharides

• A

polysaccharide

is a

polymer of monosaccharides.

• Examples:



Starch

provides energy storage in plants.



Glycogen

provides energy storage in animals.



Cellulose is found in the cell walls of plants.



Chitin is found in the cell walls of fungi and

exoskeleton of some animals.

(36)

a. Starch

Amylose: nonbranched starch granule

glycogen granule

Amylopectin: branched

250 m

(37)

3.3 Lipids

• Lipids are varied in structure.

• Large nonpolar molecules that are insoluble in water

• Functions:



Long-term energy storage



Structural components



Cell communication and regulation



Protection

(38)

(39)

Triglycerides: Long-Term

Energy Storage



Also called

fats

and

oils



Functions: long-term energy storage and

insulation



Consist of one glycerol molecule linked to

(40)

C

H

C

H

C

H

OH

(41)

+

C

H

C

H

C

H

C

O

C

O

H

C

H

C

H

OH

C

O

H

C

H

in

HO

3 fatty acids

glycerol

(42)

3 H

₂

O

3 H

₂

O

+

C

H

C

H

C

H

C

O

C

O

H

C

H

C

H

OH

C

O

H

_H

H

C

H

in

HO

3 water

3 fatty acids

(43)

in

3 H

2

O

3 H

2

O

+

C

H

C

H

C

H

C

O

C

O

C

O

H

H H

C

H

C C

H

C

H

C

H

C

H

C

H

H H

in

OH

HO

H

C

C O

H

O

C

O

C

H

O

C

fat molecule

3 water

molecules

3 fatty acids

glycerol

(44)

• Fatty acids are either

unsaturated

or

saturated

.



Unsaturated

- one or more double bonds between

carbons

• Tend to be liquid at room temperature

– Example: plant oils



Saturated

- no double bonds between carbons

• Tend to be solid at room temperature

– Examples: butter, lard

(45)

Fig. 3.10

in 3 H2O

3 H2O

+

C H H C H C H H C O C O C H H H H

C H C H C H H C O C H H C H H C H H C H C H C H H C H C H C H H C H C H C H H C H H H C H H H C H H H H

C H C H C H H C O C H H C H H C H H C H H H H

C H C H C H H C H H C H H C H H C O H H

H H C C C C C H H H H H H H H H H H H H H H H H H C C

H H H H H H H H H H C C C C C C C C C C H H H H H H H H H H H C C C C C H H H H H H H H H H H H C C C C C C C H H H H H H H H H H H H C C C C C H H H

in OH

OH

OH HO HO HO

HO HO

unsaturated fat unsaturated fatty acid with double bonds (yellow)

corn corn oil

butter H H H H C C

C O H O C

O O C H O C fat molecule 3 water molecules 3 fatty acids

glycerol a. Formation of a fat

Types of fatty acids

b. c. Types of fats saturated fat saturated fatty acid with no double bonds

(46)

Phospholipids: Membrane Components

• Structure is similar to triglycerides



Consist of one glycerol molecule linked to two fatty

acids and a modified phosphate group

• The

fatty acids

are

nonpolar

and

hydrophobic

.

• The modified

phosphate group

is

polar

and

hydrophilic

.

• Function: form plasma membranes

• In water, phospholipids aggregate to form a lipid

bilayer.



Polar phosphate heads are oriented towards the

(47)

Fig. 3.11

.

O

R O P O 3 O

Polar

Head

glycerol

fatty acids

phosphate

Phospholipid structure

a.

Nonpolar Tails

b. Plasma membrane of a cell

CH₂ CH2

CH2

O O

C CH2 CH2

CH2 CH2

CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH₂ _CH 2 CH3

CH2

O

C _CH

2 CH₂ CH2 CH2 CH2 CH2

(48)

• Composed of four fused carbon rings



Various functional groups attached to the carbon

skeleton

• Functions: component of animal cell

membrane, regulation

• Examples: cholesterol, testosterone, estrogen

• Cholesterol is the precursor molecule for

several other steroids.

(49)

b . T e s t o s t e r o n e

HO

a. Cholesterol

c. Estrogen

OH

CH

₃

O

CH

3

OH

CH

3

CH

₃

HC

CH

₃

HC

CH

₃

HO

(CH

₂

)

₃

CH

₃

CH

₃

(50)

• Long-chain fatty acid bonded to a long-chain

alcohol

• Solid at room temperature

• Waterproof

• Resistant to degradation

• Function: protection

• Examples: earwax, plant cuticle, beeswax

(51)

51 Waxes

a.

b.

(52)

3.4 Proteins

• Proteins are polymers of

amino acids

linked

together by

peptide bonds

.



A peptide bond is a covalent bond between amino

acids.

• Two or more amino acids joined together are

called

peptides

.



Long chains of amino acids joined together are

called

polypeptides

.

(53)

53 Functions of Proteins

• Metabolism



Most enzymes are proteins that act as catalysts to accelerate

chemical reactions within cells.

• Support



Keratin and collagen

• Transport



Hemoglobin and membrane proteins

• Defense



Antibodies

• Regulation



Hormones are regulatory proteins that influence the metabolism of

cells.

• Motion

(54)

C

H

R

acidic

group

amino

group

COOH

H

₂

N

Amino Acids: Protein Monomers

• There are 20 different common amino acids.

(55)

H

Sample Amino Acids with Nonpolar (Hydrophobic) R Groups

C

H

_O

O

C

H

C

O

C

H

C

O

C C

H

_O

O

S

C C

O

C C

H

_O

O

C

O

C C

H

_O

O

C

H

_O

O

C

O

C C

H

_O

O

C

O

C C

H

_O

O

C

C C

H

_O

O

C

H

C

O

C

H

C

O

C

H

C

O

C C

H

O

C C

O

CH

2

H

₃

N

+

H

3

C

CH

3

H

3

N

+

(CH

2

)

2

CH

₃

H

3

N

+

CH

2

H

3

N

+

H

3

N

+

CH

2

SH

OH

CH

H

3

N

+

H

3

N

+

H

3

N

+

CH

2

(CH

2

)

2

H

3

N

+

CH

₂

N

+

_H

3

OH

H

3

N

+

CH

3

NH

2

H

3

N

+

H

₃

N

+

CH

2

CH

2

COO

-

H

3

N

+

CH

2

CH

2

CH

2

H

3

N

+

(CH

2

)

3

NH

N

+

_H

2

NH

₂

H

3

N

+

CH

2

NH

N

+

_H

histidine (His)

arginine (Arg)

aspartic acid (Asp)

lysine (Lys)

glutamicacid (Glu)

asparagine (Asn)

threonine (Thr)

Sample Amino Acids with Polar (Hydrophilic) R Groups

proline (Pro)

leucine (Leu)

phenylalanine (Phe)

methionine (Met)

valine (Val)

CH

3

CH

2

CH

2

H

2

N

+

H

₂

C

glutamine (Gln)

cysteine (Cys)

serine (Ser)

tyrosine (Tyr)

OH

CH

Sample Amino Acids with Ionized R Groups

CH

3

NH

2

H

(56)

amino acid

amino group

(57)

+

amino acid

_{amino acid}

acidic group

amino group

(58)

dehydration reaction

amino acid

_{amino acid}

acidic group

amino group

(59)

dehydration reaction

water peptide bond

dipeptide amino acid amino acid

acidic group amino group

(60)

dehydration reaction

hydrolysis reaction

water peptide bond

dipeptide amino acid amino acid

acidic group amino group

(61)

61 Levels of Protein Structure

• Proteins cannot function properly unless they

fold into their proper shape.



When a protein loses it proper shape, it said to be

denatured

.

• Exposure of proteins to certain chemicals, a

change in pH, or high temperature can disrupt

protein structure.

• Proteins can have up to four levels of structure:



Primary



Secondary



Tertiary

(62)

Four Levels of Protein Structure



Primary

• The sequence of amino acids



Secondary

• Characterized by the presence of alpha helices and

beta (pleated) sheets held in place with hydrogen

bonds



Tertiary

• Final overall three-dimensional shape of a

polypeptide

• Stabilized by the presence of hydrophobic

(63)

COO–

hydrogen bond Primary Structure

This level of structure is determined by the sequence of amino acids coded by a gene that joins to form a polypeptide.

Secondary Structure

Hydrogen bonding between amino acids causes the polypeptide to form an alpha helix or a pleated sheet.

Β (beta) sheet = pleated sheet α alpha) helix

C N

R

C R

C _N

C R C N C R N C R N R N C N R CH CH CH CH CH CH CH CH Tertiary Structure disulfide bond Quaternary Structure

This level of structure occurs when two or more folded polypeptides interact to perform a biological function. hydrogen bond

Interactions of amino acid side chains with water, covalent bonding between R groups, and other chemical interactions determine the folded three-dimensional shape of a protein.

peptide bond amino acid

H3N+

C C C C C C C C C C C C C C C C C C C C C C R R R R R R R R R O O O O O O O O O O O O N N N N N N N N N N N C

H H

(64)

Examples of Fibrous Proteins

a. b. c.

(65)

65 Protein-Folding Diseases

• Chaperone proteins

help proteins fold into their

normal shape.



Defects in chaperone proteins may play a role in

several human diseases such as Alzheimer disease

and cystic fibrosis.

• Prions

are misfolded proteins that have been

implicated in a group of fatal brain diseases

known as TSEs.

(66)

3.5 Nucleic Acids

• Nucleic acids are polymers of

nucleotides

.

• Two varieties of nucleic acids:



DNA (deoxyribonucleic acid)

• Genetic material that stores information for its own

replication and for the sequence of amino acids in

proteins.



RNA (ribonucleic acid)

(67)

67 Structure of a Nucleotide

• Each nucleotide is composed of three parts:



A phosphate group



A pentose sugar



A nitrogen-containing (nitrogenous) base

• There are five types of nucleotides found in nucleic

acids.



DNA

contains

adenine

,

guanine

,

cytosine

, and

thymine

.



RNA

contains

adenine

,

guanine

,

cytosine

, and

uracil

.

(68)

S

C

O

P

nitrogen-

containing

base

pentose sugar

5'

4'

_1'

2'

3'

phosphate

(69)

S

C

O

–

_O

_P

_O

O

–

P

nitrogen-

containing

base

phosphate

pentose sugar

Nucleotide structure

a.

5'

4'

1'

(70)

S

C

O

–

_O

P

O

–

H

O

C

H

P

nitrogen-

containing

base

phosphate

pentose sugar

deoxyribose (in DNA)

Nucleotide structure

a.

OH

CH

₂

OH

5'

4'

1'

2'

3'

(71)

S

C

O

–O

_P

O

–

H

O

C

H

O

C

H

P

nitrogen-

containing

base

phosphate

pentose sugar

deoxyribose (in DNA)

ribose (in RNA)

Nucleotide structure

a.

OH

_OH

CH

2

OH

CH

2

OH

5'

4'

1'

2'

3'

(72)

H

O

N

H

O

_N

C

_C

C

H

O

N

H

N

H

N

C

T

U

G

A

Purines

Pyrimidines

HN

CH

HC

CH

HN

CH

guanine

adenine

uracil in RNA

Pyrimidines versus purines

c.

cytosine

thymine in DNA

NH

2

HN

CH

₃

NH

2

H

2

N

O

(73)

S

C

O

–O

_P

O

–

H

O

C

H

O

C

H

O

N

H

O

N

C

_C

C

H

O

N

H

N

H

N

C

H

C

T

U

G

A

P

nitrogen-

containing

base

phosphate

pentose sugar

deoxyribose (in DNA)

ribose (in RNA)

Nucleotide structure

a.

Purines

Pyrimidines

OH

_OH

HN

CH

HC

CH

HN

CH

guanine

adenine

uracil in RNA

Pyrimidines versus purines

c.

cytosine

thymine in DNA

CH

₂

OH

CH

₂

OH

NH

₂

HN

CH

₃

NH

₂

H

₂

N

O

5'

4'

1'

2'

3'

(74)

Structure of DNA and RNA



The backbone of the nucleic acid strand is composed

of alternating sugar-phosphate molecules.



RNA is predominately a single-stranded molecule.



DNA is a double-stranded molecule.

• DNA is composed of two strands held together by

hydrogen bonds between the nitrogen-containing

bases. The two strands twist around each other to

form a double helix.

– Adenine hydrogen bonds with thymine

– Cytosine hydrogen bonds with guanine

(75)

(76)

N H

H N N N H H O O N A A T G G C G C C Sugar Thymine Adenine Phosphate Guanine Cytosine