1

Molecules of Life

Chapter 22

Great Idea:A cell’s major parts are constructed from a few simple molecular building

blocks

2

Chapter Outline

• Organic Molecules• Organic Chemistry• Proteins: The Workhorses of Life• Carbohydrates• Lipids• Minerals and Vitamins

3

Organic Molecules

4

Four Basic Characteristics

• Most molecules based on chemistry of carbon– Organic molecules

• Life’s molecules form from few elements– H, O, C, N 97.5% of body weight

• Molecules composed of simple building blocks– Arranged differently

• Shape determines behavior– Determines ability for bonding

5

Chemical Shorthand

• No H atoms or bonds to H are shown• C atoms are not shown explicitly

Shorthand

6

iClicker Question

• Most molecules in living systems are based on the chemistry of:

– A nitrogen– B carbon– C phosphorus– D sodium

7

iClicker Question

• Which four elements comprise 97.5% of our bodies’ weight?

– A P, S, Ca and Mg– B Fe, H, O, Na– C H, O, C, N

8

9

Remember Abundance of Elements in Solar System

Relative Abundance of Elements in the Sun

0

2

4

6

8

10

12

0 5 10 15 20 25 30 35 40 45

Atomic Number

Log

of R

elat

ive

Abu

ndan

ce

H

He

Li

Be B

C

C

N

O

Fe

Ne

Na

Mg

Al

Si

P

S

Cl

Ar

K

Ca

Fe

10

• C is a special case

• Valence electrons for C are four (one in each orbit of the 2nd shell)

• C – C: single covalent bond (one orbit; two atoms)

• C – C – C: two covalent bonds; two orbits; three atoms

Recall Covalent Bonds and Carbon

C - CC

C – C – C

C

11

12

Principles of Carbon Chemistry: Functional Groups

• Features of C macromolecules–Carbon skeleton (chains, branches, rings)–Groups of atoms attached to carbon

skeleton - functional groups• Hydroxyl (OH)• Amino (NH2)• Phosphate (P)

C

C – C – OH

C

13

Principle of Polymers

• Small molecules joined together to form large molecules up to 1,000’s of carbon atoms (macromolecules)

• Array of combinations, each with its own unique chemistry

• Principle of hierarchy theory and emergent properties

14

Simple to Complex Polymers of Carbon

Methane - 1 C atom Ethane – 2 C atoms

Fullerene – 60 + C atoms (Buckyballs)

15

Complex Carbon Polymers

aspirin

caffeinenicotene

Taxol – chemotherapy drug

16

Hierarchy Theory and Emergent Properties

Number of macromolecules, each with its own chemistry

Carbon Skeletons

(e.g., branch, chains, etc.

Functional Groups (e.g., OH, NH2, etc.)

Carbon Atoms

17

Principle of Polymers

• In living systems, polymers of carbon result in four major classes of macromolecules –Carbohydrates–Proteins–Nucleic acids–Lipids

• Potential diversity of carbon polymers

18

Hydrocarbons

• Carbon compounds with only two elements (carbon and hydrogen)

• Most simple compound: methane (CH4)

H|

H – C – H|H

19

Hydrocarbons: C to C Bonding

• C to C bond can be single bond (C-C)

Ethane

• C to C bond can be double bond (C = C)

Ethene or ethylene

• C to C bond can be triple bond (C = C)

Ethyne

• Saturated/unsaturated

20

Hydrocarbons• Alkanes (C – C bonds only)

– Methane (C1H4) Natural gas– Ethane (C2H6)– Propane (C3H8) Propane gas– Butane (C4H10)– Pentane (C5H12)– Octane (C8H18) Gasoline– Decane (C10H22)– Pattern: CnH2n + 2)

• Triple bond (C = C)• Double bond (C = C)• Aromatics (cyclic C atoms/aromatics)

– C6H6

21

Aromatic Hydrocarbons

22

Question

There are millions of organic compounds but only a few thousand inorganic compounds because ____?

A. Organic compounds are formed by living critters

B. There is more C on the Earth’s surface than most other elements

C. Atoms of elements other than C never combine with themselves

D. C atoms combine with up to four other atoms, including other C atoms

23

Functionality of Hydrocarbons

• Carbon skeleton

• Functional groups (e.g., OH)

24

Organic and Biochemistry

• Keys:– Structure of basic unit (monomer)– Polymer structure (macromolecule)– Functional group (e.g., OH, PO3 or NH2)

• Types of carbon polymers in living systems– Carbohydrates– Lipids– Proteins– Nucleic acids

25

Biochemistry

• Carbohydrates– Monomer: monosaccharide (glucose or C6H12O6)– Polymer: polysaccharide– Functional unit: hydroxyl or OH-

• Proteins– Monomer: amino acid (peptide)– Polymer: polypeptide and protein– Functional unit: amine or NH2

• Nucleic Acids– Monomer: nucleotide – Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA

(ribonucleic acid)– Functional units: organic N base, carbohydrate, and phosphate

• Lipids– Monomer: fatty acid + glycerol unit– Polymer: fats, phospholipids and steroids– Functional unit: glycerol (3 OH- groups)

26

iClicker Question

Fatty acids and glycerols are part of • A Carbohydrates• B Proteins• C Nucleic Acids• D Lipids

27

iClicker Question

• The monomer “monosaccharide” is what type of molecular polymer?

• A Carbohydrate• B Protein• C Nucleic Acid• D Lipid

28

iClicker Question

Amino acids are portions of• A Carbohydrates• B Proteins• C Nucleic Acids• D Lipids

29

iClicker Question

Nucleotides are portions of• A Carbohydrate• B Protein• C Nucleic Acid• D Lipid

30

Carbohydrates

31

Carbohydrates

• Structure– C, H, O

• Simplest– Sugars – CnH2nOn

• Monosaccharides• Polysaccharide• Starches• Cellulose

32

33

CarbohydratesKeysKeys

Monosaccharide or Glucose (CMonosaccharide or Glucose (C66HH1212OO66))Functional unit: hydroxyl or OHFunctional unit: hydroxyl or OH--

34

Monosaccharides

35

Polysaccharide: Glycogen

36

iClicker Question

• True or False: Starch and cellulose are both polymers of glucose.

– A True– B False

37

iClicker Question

• Individual sugar molecules are called:

– A glucoses– B starches– C monosaccharides

38

iClicker Question

• The general chemical formula for sugar is:

– A NaCl– B CnH2nOn

– C CnH2n+2

– D C20H38S2N4

39

Proteins: The Workhorses of Life

40

Amino Acids: The Building Blocks of Proteins

• Amino Acid–Carboxyl group–Amino group–Carbon atom–Side group

41

Amino Acids: The Building Blocks of Proteins

• Side Group–Makes amino acid unique

42

Amino Acids cont.

• Bonding– Two amino acids

• H bonds with OH • Forms H2O • Forms peptide bond

– Polypeptide• chain

• Protein– Large molecule– Chain of amino acids

• Only 20 amino acids in living organisms

43

The Structure of Proteins

44

Enzymes (protein catalysts)

• Enzymes–Specific shape & structure–Facilitates bonding

45

Enzymes

46

How Most Drugs Work

• Blocking enzymes–Block active site–Molecules cannot bond–Reaction does not take

place• Shape of molecules

–Block membrane transport

–Block neurotransmitters

47

Proteins

KeysAmino acid (monomer)Polypeptide (polymer)Functional unit: amine

or NH2

Polypeptide bond

serine – lysine – arginine – tryptophan – glutamic acid – etc.

48

Proteins: Linear Structure

49

Proteins: Linear Structure

50

Protein Conformation (1 and 2nd)

51

Protein Conformation (3rd & 4rd)

52

53

54

iClicker Question

• Proteins are made up of strings of basic building blocks called:

– A amino acids– B monosaccharides– C nucleotides

55

iClicker Question

• How many different amino acids appear in the proteins of living systems on Earth?

– A 10– B 20– C 50– D 200

56

iClicker Question

• The exact sequence of amino acids that go into a protein is called its:

– A primary structure– B secondary structure– C tertiary structure– D quaternary structure

57

iClicker Question

• In general, meat and dairy products supply low-quality proteins, while plant product supply high-quality proteins.

– A True– B False

58

iClicker Question

• Of the 20 amino acids, how many are “essential amino acids” for human adults?

– A 8– B 12– C 17– D 20

59

iClicker Question

• Shapes taken by the string of amino acids of a protein, such as a long helix or a sphere, are called its:

– A primary structure– B secondary structure– C tertiary structure– D quaternary structure

60

iClicker Question

• Silk, hair, and fingernails are made of:

– A proteins– B lipids– C carbohydrates

61

Nucleic AcidsKeys

Nucleotides Functional units: organic N base, carbohydrate, and

phosphate

62

Nucleic Acids as Polymers:DNA Double Helix

63

64

Lipids

65

Lipids

• Lipids– Insoluble in

water

• Role of lipids– Cell membranes– Store energy

• Phospholipids– Make up cell

membrane

66

Saturated and Unsaturated Fats

• Saturated–C is fully bonded–Basis of

cholesterol

• Unsaturated–Monounsaturated–Polyunsaturated

• hydrogenation

67

Cell Membranes

• Cell membrane–Hydrophilic–Hydrophobic

68

Biochemistry: Lipids

KeysFatty acids C16-18

Functional unit: glycerol (3 OH- groups)

69

Saturated Fats

70

Unsaturated Fats

71

iClicker Question

Fatty acids and glycerols are part of • A Carbohydrates• B Proteins• C Nucleic Acids• D Lipids

72

iClicker Question

• Saturated fats have no double bonds.

– A True– B False

73

iClicker Question

• The monomer “monosaccharide” is what type of molecular polymer?

• A Carbohydrate• B Protein• C Nucleic Acid• D Lipid

74

iClicker Question

Amino acids are portions of• A Carbohydrates• B Proteins• C Nucleic Acids• D Lipids

75

iClicker Question

Nucleotides are portions of• A Carbohydrate• B Protein• C Nucleic Acid• D Lipid

76

Biochemistry Summary

• Carbohydrates– Monomer: monosaccharide (glucose or C6H12O6)– Polymer: polysaccharide– Functional unit: hydroxyl or OH-

• Proteins– Monomer: amino acid (peptide)– Polymer: polypeptide and protein– Functional unit: amine or NH2

• Nucleic Acids– Monomer: nucleotide – Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA

(ribonucleic acid)– Functional units: organic N base, carbohydrate, and phosphate

• Lipids– Monomer: fatty acid + glycerol unit– Polymer: fats, phospholipids and steroids– Functional unit: glycerol (3 OH- groups)

77

Carbon Metabolism

Biosynthesis (Anabolism)

CO2 + H2O + Energy CH2O + O2(light) (C - C Bonds)

Catabolism

CH2O + O2 CO2 + H2O + Energy(C - C Bonds) (heat + chemical

energy – ATP)

Key is the C-C covalent bonding, which in turn is determined by electrons in the valence state, which in turn is underpinned by energy of electrons in their respective shells (storage and processing of energy via the making and breaking of C-C bonds)

78

79

Granola Bar and the Carbon Atom

The energy of a “granola bar” is a function of multiple excited electrons being kicked to a higher quantum level in a chlorophyll molecule; subsequently, that “potential energy” is snatched and stored chemically in acarbohydrate molecule. When you digest thecarbohydrate polymer and break the covalent bonds, the potential energy of the electron in an elevated state is released as heat/chemical energy in metabolism.

80

iClicker Question

The chemical reactivity of organic carbon compounds is a function of the reactivity of the ____.

A Carbon to carbon double bond (C = C)B Carbon to carbon triple bond (C = C)C Carbon to carbon single bond (C – C)D Functional groups bond to the carbon atomE Reactivity of the covalent bonds between

carbon atoms

81

Hierarchy in Biochemistry

Protein

Polypeptide

Amino Acid

Carbon Skeleton +Amine group (NH2)

82

Minerals and Vitamins

83

Minerals

• Minerals–All chemical elements except C, H, N, O

• Example–Calcium

• 2% of weight

84

Vitamins

• Vitamins– Organic molecules– Must be taken in with food

• Except vitamin D

• Water soluble– Vitamins B & C

• Fat soluble– Vitamins A, D, E, & K

• Function– Assist enzymes

85

SUMMARY

• Carbon is unique in its chemistry• Unusual behavior of carbon results in an

huge array of simple to complex molecules• Life as we know it is hard to imagine without

carbon behaving as a polymer• The chemistry of carbon is a case study of

the principle of hierarchy theory and emergent properties

• Carbon metabolism is the “currency” by which energy is processed, stored and used

• Weak chemical bonds (covalent carbon bonds) play a critical role in the chemistry of life

86

iClicker Question

• Which vitamins are water soluble?– A B and C– B A, D, E, and K– C F, G, and H

87

iClicker Question

• The information in this chapter influences me in terms of eating a healthier diet.

– A True– B False