Molecules of Life

Chapter 3

3.1 Molecules of Life

Molecules of life are synthesized by living cells• Carbohydrates• Lipids • Proteins • Nucleic acids

Structure to Function

Molecules of life differ in three-dimensional structure and function• Carbon backbone• Attached functional groups

Structures give clues to how they function

Organic Compounds

Consist primarily of carbon and hydrogen atoms• Carbon atoms bond covalently with up to four

other atoms, often in long chains or rings

Functional groups attach to a carbon backbone • Influence organic compound’s properties

An Organic Compound: Glucose

Four models

Functional Groups

Fig. 3.3, p. 36

In alcohols (e.g.,sugars, amino acids);water soluble

In fatty acid chains;insoluble in water

In sugars, amino acids,nucleotides; watersoluble. An aldehydeif at end of a carbonbackbone; a ketone ifattached to an interiorcarbon of backbone

In amino acids, fattyacids, carbohydrates;water soluble. Highlypolar; acts as an acid(releases H+)

carboxyl

methyl

hydroxyl

carbonyl

(ionized)(non-ionized)

(ketone)(aldehyde)

Fig. 3.3, p. 36

In amino acids andcertain nucleotidebases; water soluble,acts as a weak base(accepts H+)

In nucleotides (e.g.,ATP), also in DNA,RNA, many proteins,phospholipids; watersoluble, acidic

amino

phosphate

icon

(ionized)(non-ionized)

Functional Groups: The Importance of Position

one of the estrogens

Fig. 3.4, p. 37

testosterone

Animation: Functional group

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Processes of Metabolism

Cells use energy to grow and maintain themselves

Enzyme-driven reactions build, rearrange, and split organic molecules

Building Organic Compounds

Cells form complex organic molecules• Simple sugars → carbohydrates• Fatty acids → lipids• Amino acids → proteins• Nucleotides → nucleic acids

Condensation combines monomers to form polymers

What Cells Do to Organic Compounds

Condensation and Hydrolysis

Fig. 3.5, p. 37

enzyme action at functional groups

enzyme action at functional groups

Condensation Hydrolysis

Animation: Condensation and hydrolysis

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Key Concepts: STRUCTURE DICTATES FUNCTION

We define cells partly by their capacity to build complex carbohydrates and lipids, proteins, and nucleic acids

The main building blocks are simple sugars, fatty acids, amino acids, and nucleotides

These organic compounds have a backbone of carbon atoms with functional groups attached

3.2 Carbohydrates – The Most Abundant Ones

Three main types of carbohydrates• Monosaccharides (simple sugars)• Oligosaccharides (short chains)• Polysaccharides (complex carbohydrates)

Carbohydrate functions• Instant energy sources • Transportable or storable forms of energy• Structural materials

Simple Sugars: Glucose and Fructose

Oligosaccharides: Sucrose

glucose fructose

sucrose

Fig. 3.6, p. 38

c Formation of a sucrose molecule

Complex Carbohydrates: Bonding Patterns

Complex Carbohydrates: Starch, Cellulose, and Glycogen

Complex Carbohydrates: Starch, Cellulose, and Glycogen

Fig. 3.8, p. 39

c Glycogen. In animals, thispolysaccharide is a storage form for excess glucose. It is especially abundant in the liver and muscles of highly active animals, including fishes and people.

Structure of cellulose

Animation: Structure of starch and cellulose

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Complex Carbohydrates: Chitin

Key Concepts:CARBOHYDRATES

Carbohydrates are the most abundant biological molecules

Simple sugars function as transportable forms of energy or as quick energy sources

Complex carbohydrates are structural materials or energy reservoirs

3.3 Greasy, Oily – Must Be Lipids

Lipids • Fats, phospholipids, waxes, and sterols• Don’t dissolve in water• Dissolve in nonpolar substances (other lipids)

Lipid functions• Major sources of energy• Structural materials• Used in cell membranes

Fats

Lipids with one, two, or three fatty acid tails• Saturated• Unsaturated (cis and trans)

Triglycerides (neutral fats )• Three fatty acid tails• Most abundant animal fat (body fat)• Major energy reserves

Fatty Acids

Animation: Fatty acids

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Trans and Cis Fatty Acids

Triglyceride Formation

glycerol

three fatty acid tails Triglyceride, a neutral fat

Fig. 3.11, p. 40

Animation: Triglyceride formation

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Phospholipids

Main component of cell membranes • Hydrophilic head,

hydrophobic tails

hydrophilic head

two hydrophilic tails

Fig. 3.13, p. 41

b

Fig. 3.13, p. 41

c Cell membrane section

Animation: Phospholipid structure

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Waxes

Firm, pliable, water repelling, lubricating

Sterols: Cholesterol

Membrane components; precursors of other molecules (steroid hormones)

Animation: Cholesterol

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Key Concepts:LIPIDS

Complex lipids function as energy reservoirs, structural materials of cell membranes, signaling molecules, and waterproofing or lubricating substances

3.4 Proteins – Diversity in Structure and Function

Proteins have many functions• Structures• Nutrition• Enzymes• Transportation• Communication• Defense

Protein Structure

Built from 20 kinds of amino acids

Fig. 3.15, p. 42

Fig. 3.15, p. 42

carboxylgroup

aminogroup

Fig. 3.15, p. 42

Fig. 3.15, p. 42

valine

Protein Synthesis

Protein Synthesis

Protein Synthesis

Four Levels of Protein Structure

1. Primary structure • Amino acids joined by peptide bonds form a

linear polypeptide chain

2. Secondary structure• Polypeptide chains form sheets and coils

3. Tertiary structure• Sheets and coils pack into functional domains

Four Levels of Protein Structure

4. Quaternary structure• Many proteins (e.g. enzymes) consist of two or

more chains

Other protein structures• Glycoproteins• Lipoproteins• Fibrous proteins

Levels of Protein Structure

Fig. 3.17, p. 43

a Protein primarystructure: Aminoacids bonded in apolypeptide chain.

Levels of Protein Structure

Fig. 3.17, p. 43

b Protein secondarystructure: A coiled(helical) or sheetlikearray, held in placeby hydrogen bonds( dotted lines) betweendifferent parts of thepolypeptide chain.

helical coil sheet

Levels of Protein Structure

Fig. 3.17, p. 43

c Protein tertiary structure: A chain’s coiled parts, sheetlikearrays, or both have folded and twisted into stable, functionaldomains, including clusters, pockets, and barrels.

barrel

Levels of Protein Structure

Fig. 3.17, p. 43

d Protein quaternarystructure: Many weakinteractions hold twoor more polypeptidechains together asa single molecule.

Animation: Structure of an amino acid

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Animation: Peptide bond formation

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Animation: Secondary and tertiary structure

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Animation: Globin and hemoglobin structure

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3.5 Why is Protein StructureSo Important?

Protein structure dictates function

Sometimes a mutation in DNA results in an amino acid substitution that alters a protein’s structure and compromises its function• Example: Hemoglobin and sickle-cell anemia

Normal Hemoglobin Structure

Fig. 3.18, p. 44

alpha globin

heme

a Globin. The secondarystructure of this polypeptideincludes several helixes. Thecoils fold up to form a pocketthat cradles heme, a functionalgroup with an iron atom at itscenter. The kind of molecularrepresentation shown here iscalled a ribbon model, after itsappearance. Appendix V hasmore details about such models.

Normal Hemoglobin Structure

alpha globin

beta globin beta globin

Fig. 3.18, p. 44

alpha globin

b Hemoglobin is one of the proteins with quaternary structure. Itconsists of four globin molecules held together by hydrogen bonds.To help you distinguish among them, the two alpha globin chainsare shown here in green, and the two beta globins are in brown.

Sickle-Cell Mutation

Fig. 3.19, p. 45

THREONINE VALINE HISTIDINE LEUCINE GLUTAMATEPROLINE GLUTAMATE

a Normal amino acid sequence at the start of a beta chain for hemoglobin.

Sickle-Cell Mutation

Fig. 3.19, p. 45

VALINE HISTIDINE LEUCINE GLUTAMATEVALINETHREONINE PROLINE

sickle cell

normal cell

b One amino acid substitution results in theabnormal beta chain in HbS molecules. Insteadof glutamate, valine was added at the sixthposition of the polypeptide chain.

c Glutamate has an overall negative charge; valine has no net charge. At low oxygen levels, this difference gives rise to a water-repellent, sticky patch on HbS molecules. They stick togetherbecause of that patch, forming rodshaped clumps that distort normally rounded red blood cells into sickle shapes. (A sickle is a farm tool that has a crescent-shaped blade.)

Sickle-Cell Mutation

Clumping of cells in bloodstream

Circulatory problems, damage to brain, lungs, heart, skeletal muscles, gut, and kidneys

Heart failure, paralysis, pneumonia, rheumatism, gut pain, kidney failure

Spleen concentrates sickle cells

Spleen enlargement

Immune system compromised

Rapid destruction of sickle cells

Anemia, causing weakness,fatigue, impaired development,heart chamber dilation

Impaired brain function, heart failure Fig. 3.19, p. 45

d Melba Moore, celebrity spokes-person for sickle-cell anemia organizations. Right, range of symptoms for a person with two mutated genes for hemoglobin’s beta chain.

Clumping of cells in bloodstream

Spleen concentrates sickle cells

Rapid destruction of sickle cells

Circulatory problems, damage to brain, lungs, heart, skeletal muscles, gut, and kidneys

Heart failure, paralysis, pneumonia, rheumatism, gut pain, kidney failure

Spleen enlargement

Immune system compromised

Anemia, causing weakness,fatigue, impaired development,heart chamber dilation

Impaired brain function, heart failure Fig. 3-19, p. 45

d Melba Moore, celebrity spokes-person for sickle-cell anemia organizations. Right, range of symptoms for a person with two mutated genes for hemoglobin’s beta chain.

Stepped Art

Animation: Sickle-cell anemia

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Denatured Proteins

If a protein unfolds and loses its three-dimensional shape (denatures), it also loses its function

Caused by shifts in pH or temperature, or exposure to detergent or salts • Disrupts hydrogen bonds and other molecular

interactions responsible for protein’s shape

Key Concepts:PROTEINS

Structurally and functionally, proteins are the most diverse molecules of life

They include enzymes, structural materials, signaling molecules, and transporters

Animation: Molecular models of the protein hemoglobin

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3.6 Nucleotides, DNA, and RNAs

Nucleotide structure, 3 parts:• Sugar• Phosphate group• Nitrogen-containing base

Fig. 3.20, p. 46

three phosphate groups

base (blue)

sugar (orange)

Nucleotide Functions: Reproduction, Metabolism, and Survival

DNA and RNAs are nucleic acids, each composed of four kinds of nucleotide subunits

ATP energizes many kinds of molecules by phosphate-group transfers

Other nucleotides function as coenzymes or as chemical messengers

Nucleotides of DNA

Fig. 3.21, p. 46

adenine(A)

base with a double-ring

structure

phosphate group

sugar (deoxyribose)

Fig. 3.21, p. 46

THYMINE(T)

base with a single-ring structure

Fig. 3.21, p. 46

GUANINE(C)

base with a double-ring

structure

Fig. 3.21, p. 46

CYTOSINE(C)

base with a single-ring structure

DNA, RNAs, and Protein Synthesis

DNA (double-stranded)• Encodes information about the primary structure

of all cell proteins in its nucleotide sequence

RNA molecules (usually single stranded)• Different kinds interact with DNA and one another

during protein synthesis

The DNA Double-Helix

Fig. 3.22, p. 47

covalentbonding incarbonbackbone

hydrogen bondingbetween bases

Key Concepts:NUCLEOTIDES AND NUCLEIC ACIDS

Nucleotides have major metabolic roles and are building blocks of nucleic acids

Two kinds of nucleic acids, DNA and RNA, interact as the cell’s system of storing, retrieving, and translating information about building proteins

Animation: Nucleotide subunits of DNA

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Animation: Structure of ATP

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