1 3.1 Organic Molecules Organic molecules contain carbon and hydrogen atoms. Four classes of organic molecules (biomolecules) exist in living organisms:

1

3.1 Organic Molecules

• Organic molecules contain carbon and hydrogen atoms.

• Four classes of organic molecules (biomolecules) exist in living organisms: Carbohydrates Lipids Proteins Nucleic Acids

2

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

4

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

PolymerCategory Subunit(s)

PolysaccharideCarbohydrates* Monosaccharide

Lipids

Proteins*

Nucleic acids*

Glycerol and fatty acids Fat

PolypeptideAmino acids

Nucleotide DNA,RNA

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

6

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 Example: digestion of starch into glucose monomers

monomer monomer

monomer monomer

Dehydrationreaction

H2O

OH H

a. Synthesis of a biomolecule


+

monomer monomer

Hydrolysisreaction

OH H

b. Degradation of a biomolecule

H2O

monomer monomer


monomer monomer

monomer monomer

dehydrationreaction

monomer monomer

H2O

OH H

OH H

b. Degradation of a biomolecule

a. Synthesis of a biomolecule

H2O

monomer monomer

hydrationreaction


10

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.

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

12

• 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

13

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.

Figure 5.5 Examples of disaccharide synthesis

Polysaccharides

• Polysaccharides Storage:

Starch~ glucose monomers

Plants: plastids Animals: glycogen

• Polysaccharides Structural:

Cellulose~ most abundant organic compound; Chitin~exoskeletons; cell walls of fungi; surgical thread

Lipids 3.3• No polymers; glycerol and fatty acid

• Fats, phospholipids, steroids

• Hydrophobic; H bonds in water exclude fats

• Carboxyl group = fatty acid

• Non-polar C-H bonds in fatty acid ‘tails’

• Ester linkage: 3 fatty acids to 1 glycerol (dehydration formation)

• Triacyglycerol (triglyceride)

• Saturated vs. unsaturated fats; single vs. double bonds

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


in

3 H2O

3 H2O

+

CH

H

CH

CH

H

CO

CO

CO

H

H

H H

CCCCC

HHHHH

H

HH

HHH

HHHHHHH

C C

HH

H

HH

HHHHH

CCCCC

CCCCC

HHH

H

H

HHHHH

HCCCCC

HHHHH

HHHHHHH

CCCCCCC

HHHHHH

HHHHH

HC

CCCC

HH 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 molecule3 watermolecules

3 fatty acidsglycerol

a. Formation of a fat

20

• 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

21

• 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.

Steroids: Four Fused Carbon Rings

22

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.

23

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

acidicgroup

aminogroup

COOHH2N

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

OC

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

CO

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+

H3CCH3

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)

CHCH3

CH2CH

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

Synthesis and Degradation of a Peptide

dehydration reaction

hydrolysis reaction

water

peptide bond

dipeptideamino acid amino acid

acidic groupamino group


28

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

29

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 structureis determined by thesequence of aminoacids coded by agene that joins toform a polypeptide.

Secondary Structure

Hydrogen bondingbetween amino acidscauses the polypeptideto form an alpha helixor a pleated sheet.

Β (beta) sheet = pleated sheetα alpha) helix

C N

R

C

R

C N

C

R

C

N

C

R

N

C

R

NR

N

C

NR

CH

CH

CH

CH

CH

CH

CH

CH

Tertiary Structure

disulfide bond

Quaternary Structure

This level of structureoccurs when two or morefolded polypeptides interactto 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 bondamino acid

H3N+

C

C

C

CC

C

C

C

C

C

C

C

C

C

C

C

C

C

CC

C

C

R

R

R

R

R

R

R

R

R

O

O

O

O

O

O

O

O

O

O

O

ON

N

N

N

N

N

N

N

N

N

N

C

H H

H

H

H H

HH

H

H

C

O

O

O

O

O

O

O

H

H

H

H

H

H

31

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

32

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

Pnitrogen-containingbase

pentose sugar

5'

4' 1'

2'3'

phosphate

Nucleotides


S

C

O

–O P O

O

O–

H

O

CC

C C

H

H

H

H

O

CC

C C

H

H

H

HO

N

NH

O N

C CC

C

C

C

C C

HO N

HN

N

N

N

HN N

NCC

C

H

C T UGA

Pnitrogen-containingbase

phosphate

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

Nucleotide structurea.

PurinesPyrimidines

OHOHOH

OH OH

HNCH

CH CH

CH

CHHC

CHHN

CH

guanineadenineuracil in RNA

Pyrimidines versus purinesc.

cytosine thymine in DNA

CH2OH CH2OH

NH2

HN

CH3

NH2

H2N

O OO

5'

4' 1'

2'3'

b. Deoxyribose versus ribose

35

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.

36

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

NN

N + +PPP P P PN

NN

N ENERGY

phosphatediphosphate

ADP

triphosphate

ATPb.

NH2NH2

H2O

adenosine triphosphate c.a.

adenosineadenosine

c: © Jennifer Loomis / Animals Animals / Earth Scenes

Documents

1 3.1 Organic Molecules Organic molecules contain carbon and hydrogen atoms. Four classes of organic molecules (biomolecules) exist in living organisms: