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Molecules of Life

Chapter 22

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

blocks

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Chapter Outline

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

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Organic Molecules

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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

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Chemical Shorthand

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

Shorthand

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iClicker Question

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

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

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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

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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

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• 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

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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

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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

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Simple to Complex Polymers of Carbon

Methane - 1 C atom Ethane – 2 C atoms

Fullerene – 60 + C atoms (Buckyballs)

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Complex Carbon Polymers

aspirin

caffeinenicotene

Taxol – chemotherapy drug

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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

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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

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Hydrocarbons

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

• Most simple compound: methane (CH4)

H|

H – C – H|H

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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

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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

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Aromatic Hydrocarbons

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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

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Functionality of Hydrocarbons

• Carbon skeleton

• Functional groups (e.g., OH)

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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

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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)

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iClicker Question

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

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iClicker Question

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

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

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iClicker Question

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

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iClicker Question

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

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Carbohydrates

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Carbohydrates

• Structure– C, H, O

• Simplest– Sugars – CnH2nOn

• Monosaccharides• Polysaccharide• Starches• Cellulose

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CarbohydratesKeysKeys

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

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Monosaccharides

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Polysaccharide: Glycogen

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iClicker Question

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

– A True– B False

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iClicker Question

• Individual sugar molecules are called:

– A glucoses– B starches– C monosaccharides

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iClicker Question

• The general chemical formula for sugar is:

– A NaCl– B CnH2nOn

– C CnH2n+2

– D C20H38S2N4

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Proteins: The Workhorses of Life

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Amino Acids: The Building Blocks of Proteins

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

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Amino Acids: The Building Blocks of Proteins

• Side Group–Makes amino acid unique

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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

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The Structure of Proteins

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Enzymes (protein catalysts)

• Enzymes–Specific shape & structure–Facilitates bonding

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Enzymes

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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

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Proteins

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

or NH2

Polypeptide bond

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

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Proteins: Linear Structure

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Proteins: Linear Structure

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Protein Conformation (1 and 2nd)

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Protein Conformation (3rd & 4rd)

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iClicker Question

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

– A amino acids– B monosaccharides– C nucleotides

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iClicker Question

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

– A 10– B 20– C 50– D 200

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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

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iClicker Question

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

– A True– B False

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iClicker Question

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

– A 8– B 12– C 17– D 20

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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

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iClicker Question

• Silk, hair, and fingernails are made of:

– A proteins– B lipids– C carbohydrates

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Nucleic AcidsKeys

Nucleotides Functional units: organic N base, carbohydrate, and

phosphate

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Nucleic Acids as Polymers:DNA Double Helix

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Lipids

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Lipids

• Lipids– Insoluble in

water

• Role of lipids– Cell membranes– Store energy

• Phospholipids– Make up cell

membrane

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Saturated and Unsaturated Fats

• Saturated–C is fully bonded–Basis of

cholesterol

• Unsaturated–Monounsaturated–Polyunsaturated

• hydrogenation

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Cell Membranes

• Cell membrane–Hydrophilic–Hydrophobic

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Biochemistry: Lipids

KeysFatty acids C16-18

Functional unit: glycerol (3 OH- groups)

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Saturated Fats

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Unsaturated Fats

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iClicker Question

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

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iClicker Question

• Saturated fats have no double bonds.

– A True– B False

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iClicker Question

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

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

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iClicker Question

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

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iClicker Question

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

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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)

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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)

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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.

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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

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Hierarchy in Biochemistry

Protein

Polypeptide

Amino Acid

Carbon Skeleton +Amine group (NH2)

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Minerals and Vitamins

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Minerals

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

• Example–Calcium

• 2% of weight

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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

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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

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iClicker Question

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

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iClicker Question

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

– A True– B False