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; water soluble. An aldehyde if at end of a carbon backbone; a ketone if attached to an interior carbon of backbone In amino acids, fatty acids, carbohydrates; water soluble. Highly polar; acts as an acid (releases H+) carboxyl methyl hydroxyl carbonyl (ionized)(non-ionized) (ketone)(aldehyde)

Fig. 3.3, p. 36 In amino acids and certain nucleotide bases; water soluble, acts as a weak base (accepts H+) In nucleotides (e.g., ATP), also in DNA, RNA, many proteins, phospholipids; water soluble, 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 CLICK HERE TO PLAY

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 CondensationHydrolysis

Animation: Condensation and hydrolysis CLICK HERE TO PLAY

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

glucosefructose sucrose Fig. 3.6, p. 38 c Formation of a sucrose molecule

Complex Carbohydrates: Bonding Patterns

Complex Carbohydrates: Starch, Cellulose, and Glycogen

Fig. 3.8, p. 39 c Glycogen. In animals, this polysaccharide 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 CLICK HERE TO PLAY

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 CLICK HERE TO PLAY

Trans and Cis Fatty Acids

Triglyceride Formation

glycerol three fatty acid tails Triglyceride, a neutral fat Fig. 3.11, p. 40

Animation: Triglyceride formation CLICK HERE TO PLAY

Phospholipids  Main component of cell membranes Hydrophilic head, hydrophobic tails

hydrophilic head two hydrophilic tails Fig. 3.13, p. 41 b

c Cell membrane section

Animation: Phospholipid structure CLICK HERE TO PLAY

Waxes  Firm, pliable, water repelling, lubricating

Sterols: Cholesterol  Membrane components; precursors of other molecules (steroid hormones)

Animation: Cholesterol CLICK HERE TO PLAY

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

carboxyl group amino group

Fig. 3.15, p. 42

valine

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 primary structure: Amino acids bonded in a polypeptide chain.

Levels of Protein Structure

Fig. 3.17, p. 43 b Protein secondary structure: A coiled (helical) or sheetlike array, held in place by hydrogen bonds ( dotted lines) between different parts of the polypeptide chain. helical coilsheet

Levels of Protein Structure

Fig. 3.17, p. 43 c Protein tertiary structure: A chain’s coiled parts, sheetlike arrays, or both have folded and twisted into stable, functional domains, including clusters, pockets, and barrels. barrel

Levels of Protein Structure

Fig. 3.17, p. 43 d Protein quaternary structure: Many weak interactions hold two or more polypeptide chains together as a single molecule.

Animation: Structure of an amino acid CLICK HERE TO PLAY

Animation: Peptide bond formation CLICK HERE TO PLAY

Animation: Secondary and tertiary structure CLICK HERE TO PLAY

Animation: Globin and hemoglobin structure CLICK HERE TO PLAY

3.5 Why is Protein Structure So 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 secondary structure of this polypeptide includes several helixes. The coils fold up to form a pocket that cradles heme, a functional group with an iron atom at its center. The kind of molecular representation shown here is called a ribbon model, after its appearance. Appendix V has more details about such models.

Normal Hemoglobin Structure

alpha globin beta globin Fig. 3.18, p. 44 alpha globin b Hemoglobin is one of the proteins with quaternary structure. It consists of four globin molecules held together by hydrogen bonds. To help you distinguish among them, the two alpha globin chains are shown here in green, and the two beta globins are in brown.

Sickle-Cell Mutation

Fig. 3.19, p. 45 THREONINE VALINEHISTIDINELEUCINE GLUTAMATEPROLINEGLUTAMATE a Normal amino acid sequence at the start of a beta chain for hemoglobin.

Sickle-Cell Mutation

Fig. 3.19, p. 45 VALINEHISTIDINELEUCINEGLUTAMATEVALINETHREONINEPROLINE sickle cell normal cell b One amino acid substitution results in the abnormal beta chain in HbS molecules. Instead of glutamate, valine was added at the sixth position 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 together because 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 CLICK HERE TO PLAY

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 CLICK HERE TO PLAY

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 covalent bonding in carbon backbone hydrogen bonding between 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 CLICK HERE TO PLAY

Animation: Structure of ATP CLICK HERE TO PLAY