bio151 - ch 3

Chapter 3

The Chemistry of Organic Molecules

1

2

3.1 Organic Molecules

•  Organic molecules §  carbon §  hydrogen atoms.

•  4 Classes (biomolecules) exist in living organisms:

§  Carbohydrates §  Lipids §  Proteins § Nucleic Acids

3

Inorganic versus Organic Molecules

Carbon Chemistry §  Carbon is a versatile atom. •  It has four electrons in an outer shell that holds eight

electrons. •  Carbon can share its electrons with other atoms to form

up to FOUR covalent bonds.

C

?

?

? ?

Figure 3.1a

Carbon skeletons vary in length

Figure 3.1b

Double bond

Carbon skeletons may have double bonds, which can vary in location

Figure 3.1c

Carbon skeletons may be:

unbranched branched

Figure 3.1d

Carbon skeletons may be arranged in rings

§  The simplest organic compounds are hydrocarbons, which contain only carbon and hydrogen atoms.

§  The simplest hydrocarbon is methane, a single carbon atom bonded to four hydrogen atoms.

10

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 of organic molecules

Table 3.2

12

Isomers

•  Isomers are organic molecules that have identical molecular formulas but a different arrangement of atoms.

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

glyceraldehyde dihydroxyacetone

OH OH

H H

H C C C H

O

OH OH

H O

H C C C H

H

13

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 (polymer)

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

Fig. 3.3

Biomolecules

Polymer Category Subunit(s)

Polysaccharide Carbohydrates* Monosaccharide

Lipids

Proteins*

Nucleic acids*

Glycerol and fatty acids Fat

Polypeptide Amino acids

Nucleotide DNA,RNA

*Polymers © The McGraw Hill Companies, Inc./John Thoeming, photographer

15

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 LOST 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 §  Example: digestion of starch into glucose monomers

monomer OH


Synthesis and Degradation of Biomolecules

monomer OH +


+ monomer H monomer OH


Synthesis and Degradation of Biomolecules

monomer monomer

H2O

OH H +


monomer monomer

monomer monomer

Dehydration reaction

H2O

OH H

a. Synthesis of a biomolecule


+

monomer monomer


H2O

monomer monomer


monomer monomer

Dehydration reaction

H2O


monomer monomer

Hydrolysis reaction

OH H

b. Degradation of a biomolecule

H2O

monomer monomer


monomer monomer

monomer monomer

dehydration reaction

monomer monomer

H 2 O

OH H

OH H

b. Degradation of a biomolecule

a. Synthesis of a biomolecule

H 2 O

monomer monomer

hydration reaction


26

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. •  Enzymes are not consumed in the reaction. •  Enzymes are not changed by the reaction.

CARBOHYDRATES & LIPIDS Properties of:

27

3.2 Carbohydrates

•  Functions: §  Energy source §  Provide building material (structural role)

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

•  Varieties: monosaccharides, disaccharides, and polysaccharides

29

•  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

Monosaccharides


Fig. 3.6

H

C

HO a.

H OH

OH

6

5

4

3

1

c. d.

O O

H O H

H H

OH OH

OH H

HO b.

C6H12O6

CH2OH CH2OH C

C

H O

C 2 C

OH H

H

© Steve Bloom/Taxi/Getty

Glucose

31

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 and fructose.

§ Maltose is composed of two glucose molecules.

O O

OH glucose C6H12O6

HO

H H +

CH2OH CH2OH

glucose C6H12O6


Synthesis and Degradation of Maltose

glucose C6H12O6

CH2OH O O

OH HO

H H

+ dehydration reaction

glucose C6H12O6

CH2OH


O O O O

OH water

HO

H H O + +

dehydration reaction H2O

maltose C12H22O11 glucose C6H12O6

CH2OH CH2OH CH2OH CH2OH

glucose C6H12O6


O O O O

OH water

monosaccharide disaccharide water

HO

H H O

monosaccharide

+

+ +

+ de h yd r ation reaction

H2O



glucose C6H12O6


O O

O

maltose C12H22O11

CH2OH CH2OH


O O

water

O + H2O

maltose C12H22O11

CH2OH CH2OH


maltose C12H22O11

CH2OH O O

water

O + hydrolysis reaction

H 2 O

CH2OH


O O O O

OH

water HO

H H O + +

hydrolysis reaction H2O



glucose C6H12O6


O O O O

OH water

monosaccharide disaccharide water

HO

H H O

glucose C6H12O6

monosaccharide

+

+ +

+ hydrolysis reaction H2O

maltose C12H22O11

CH2OH

glucose C6H12O6

CH2OH CH2OH CH2OH Copyright © The McGraw-‐Hill Companies, Inc. Permission required for reproduction or display.

glucose C6H12O6 water

monosaccharide disaccharide water monosaccharide + +

dehydration reaction hydrolysis reaction



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. §  Peptidoglycan is found in the cell walls of bacteria.

a. Starch

b . Glycogen

Amylose: nonbranched starch granule

glycogen granule

Amylopectin: branched

150 nm

250 m


a: © Jeremy Burgess/SPL/Photo Researchers, Inc.; b: © Don W. Fawcett/Photo Researchers, Inc.

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

•  Varieties: fats, oils, phospholipids, steroids, waxes

Triglycerides: Long-‐Term Energy Storage

§  Also called fats and oils §  Functions: long-‐term energy storage and insulation

§  Consist of ONE glycerol molecule linked to THREE fatty acids by dehydration synthesis


C H H

C H

C H H

OH

OH

OH

glycerol a. Formation of a fat


+

C H H

C H

C H H

C O

C O

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

OH

OH

OH C O H

H H H H

H C

C C C C

H H H

in

HO

HO

HO

3 fatty acids glycerol a. Formation of a fat


3 H2O

3 H2O

+

C H H

C H

C H H

C O C O

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

OH

OH

OH C O H

H H H H

H C

C C C C

H H H

in

HO

HO

HO

3 water molecules



in

3 H2O

3 H2O

+

C H H

C H C H H

C O C O 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

H

H

H

H

C

C

C O

H

O C O O C

H

O C

fat molecule 3 water molecules


51

•  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

Triglycerides: Long-Term Energy Storage


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


Types of fatty acids b. Types of fats c.

saturated fat saturated fatty acid with no double bonds

mil

•  Most animal fats •  have a high proportion of saturated fatty acids, •  can easily stack, tending to be solid at room

temperature, and •  contribute to atherosclerosis, in which lipid-containing

plaques build up along the inside walls of blood vessels.

§ Most plant and fish oils tend to be •  high in unsaturated fatty acids •  liquid at room temperature •  Good source of dietary fats

55

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 water. §  Nonpolar fatty acid tails are oriented away from water.

•  Nonpolar fatty acid tails form a hydrophobic core.


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 CH2 CH3

CH2

O

C CH2 CH2 CH2 CH2 CH2 CH2

insi

de c

ell

outs

ide

cel

l

CH

1 2

Phospholipids Form Membranes

57

•  Composed of four fused carbon rings §  Various functional groups attached to the carbon skeleton

•  Functions: component of animal cell membrane, regulation •  Cholesterol makes the bilayer stronger, more flexible but less fluid, and less permeable to water-‐soluble substances such as ions and monosaccharides.

•  Examples: cholesterol, testosterone, estrogen

•  Cholesterol is the precursor molecule for several other steroids.

Steroids: Four Fused Carbon Rings


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

HO a. Cholesterol

c. Estrogen

OH CH3

O

CH3

OH CH3

CH3

HC CH3

HC CH3

HO

(CH2)3

© Ernest A. Janes/Bruce Coleman/Photoshot

CH3

CH3

Steroid Diversity

59

•  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

Waxes

60

Waxes

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

a: © Das Fotoarchiv/Peter Arnold, Inc.; b: © Martha Cooper/Peter Arnold, Inc.

PROTEINS & NUCLEIC ACIDS Properties of:

61

62

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.

•  A protein is a polypeptide that has folded into a particular shape and has function.

63

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

§  Muscle proteins and microtubules


C

H

R

acidic group

amino group

COOH H2N

R = rest of molecule

Amino Acids: Protein Monomers •  There are 20 different common amino acids. •  Amino acids differ by their R groups.


H Sample Amino Acids with Nonpolar (Hydrophobic) R Groups

C C H O

O C H

C O O

C H

C O O

C C H O

O S

C C O O

C C H O

O C

O C C H O

O C C H O

O C

O

C C H O

O C

O O

C C H O

O

C

C C H O

O

C H

C O O

C H

C O O

C H

C O O

C C H O

O C C

O O

CH2

H3N+

H3C CH3

H3N+

(CH2)2

CH3

H3N+

CH2

H3N+

H3N+

CH2

SH OH

CH

H3N+ H3N+ H3N+

CH2 (CH2)2

H3N+

CH2

N+H3

OH

H3N+

CH3

NH2

H3N+

H3N+

CH2

CH2

COO-

H3N+ CH2

CH2

CH2

H3N+

(CH2)3

NH

N+H2

NH2

H3N+

CH2

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 CH3

CH2 CH

CH2 H2N+

H2C

glutamine (Gln)

cysteine (Cys) serine (Ser)

tyrosine (Tyr) OH

CH

Sample Amino Acids with Ionized R Groups

CH3

NH2

H

CH2

amino acid

amino group


Synthesis and Degradation of a Peptide

+

amino acid amino acid

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




acidic group amino group

water

peptide bond

dipeptide



acidic group amino group


water

peptide bond

dipeptide

dehydration reaction hydrolysis reaction

water

peptide bond

dipeptide amino acid amino acid

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

71

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 §  Quaternary

•  Several Roles for proteins:

•  Enzymes**

•  Structural

•  Storage

•  Contractile

•  Transport

•  Defensive

•  Signal

•  Receptor

73

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 interactions, hydrogen bonding, ionic bonding, and covalent bonding

§ Quaternary •  Consists of more than one polypeptide


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 H

H H H

H H

H H

C O O

O O

O O

O H H

H H

H

H

§  Proteins consisting of one polypeptide have three levels of structure.

§  Proteins consisting of more than one polypeptide chain have a fourth level, quaternary structure.

•  Primary •  Single chain

•  Secondary •  Pleated sheet •  Alpha Helix

•  Tertiary •  Quaternary

77

Examples of Fibrous Proteins

a. b. c.


a: © Gregory Pace/Corbis; b: © Ronald Siemoneit/Corbis Sygma; c: © Kjell Sandved/Visuals Unlimited

§  A protein’s three-‐dimensional shape •  typically recognizes and binds to another molecule and •  enables the protein to carry out its specific function in a

cell.

79

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.

§  Mad cow disease is one example of a TSE disease.

80

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) •  Perform a wide range of functions within cells which include protein synthesis and regulation of gene expression

81

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.

•  Nucleotides are joined together by a series of dehydration synthesis reactions to form a linear molecule called a strand.


S

C

O P nitrogen-

containing base

pentose sugar

5'

4' 1' 2' 3'

phosphate

Nucleotides


S

C O

–O P O O

O– P nitrogen-

containing base

phosphate

pentose sugar Nucleotide structure a.

5'

4' 1' 2' 3'


S

C

O –O P O

O

O–

H

O C C

C C H

H H

H

P nitrogen- containing base

phosphate

pentose sugar deoxyribose (in DNA)

Nucleotide structure a.

OH

OH CH2OH

5'

4' 1'

2' 3'

b. Deoxyribose versus ribose


S

C O

–O P O O

O–

H

O C C

C C H

H H

H

O C C

C C H

H H

H


phosphate

pentose sugar ribose (in RNA) deoxyribose (in DNA)


OH OH OH

OH OH

CH2OH CH2OH

5'

4' 1'

2' 3'



H O

N

N H O N

C C C

C

C C

C C

H O N H N

N N

N

H N N

N C C C

C T U G A

Purines Pyrimidines

HN CH

CH CH

CH

CH HC CH

HN CH

guanine adenine uracil in RNA

Pyrimidines versus purines c.

cytosine thymine in DNA

NH2

HN CH3

NH2

H2N

O O O


S

C O

–O P O O

O–

H

O C C

C C H

H H

H

O C C

C C H

H H

H O

N

N H O N

C C C

C

C C

C C

H O N H N

N N

N

H N N

N C C C

H

C T U G A


phosphate

pentose sugar ribose (in RNA) deoxyribose (in DNA)


Purines Pyrimidines

OH OH OH

OH OH

HN CH

CH CH

CH

CH HC CH

HN CH

guanine adenine uracil in RNA

Pyrimidines versus purines c.

cytosine thymine in DNA

CH2OH CH2OH

NH2

HN CH3

NH2

H2N

O O O

5'

4' 1'

2' 3'


88

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

•  The bonding between the nucleotides in DNA is referred to as complementary base pairing.

Chargaff’s Rule

89


Fig. 3.19 O

H S

S

S

S

P

P

P

P

N N N N

N N

N N

N N

N N

CH3

NH2

NH2

Backbone

NH2

Cytosine

Phosphate

Ribose Adenine Uracil

Guanine C G P

S A U

U

G

A

C O

Nitrogen-containing bases

O O

RNA Structure


A T

N N N H

O N H

H

N N N

H

H

O

N H O N N N

N C

N s u g a r

s u g a r O N H

N

A A

T G G

C

G C

C

c. Complementary base pairing

Sugar

Thymine Adenine

Phosphate Guanine Cytosine

cytosine (C) guanine (G)

sugar

sugar

thymine (T) adenine (A)

CH3

Double helix b. a. Space-filling model

C G P

S A T

― ― ―

―

H

T

© Photodisk Red/Getty RF

DNA Structure

Complementary Base Pairing in

DNA

93

A Special Nucleotide: ATP

•  ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates.

•  ATP is a high-‐energy molecule due to the presence of the last two unstable phosphate bonds.

•  Hydrolysis of the terminal phosphate bond yields:

§  The molecule ADP (adenosine diphosphate)

§  An inorganic phosphate §  Energy to do cellular work

•  ATP is called the energy currency of the cell.


ATP

N N N

N + + P P P P P P N N N

N ENERGY

phosphate diphosphate

ADP

triphosphate

ATP b.

NH2 NH2

H2O

adenosine triphosphate c. a.

adenosine adenosine

c: © Jennifer Loomis / Animals Animals / Earth Scenes

bio151 - ch 3

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