Molecules of Life

Chapter 3

阮雪芬Sep. 17, 2012

Impacts, Issues:Fear of Frying

• Trans fats in hydrogenated vegetable oil raise levels of cholesterol in our blood more than any other fat, and directly alter blood vessel function

Organic Molecules

• All molecules of life are built with carbon atoms

• We can use different models to highlight different aspects of the same molecule

3.1 Carbon – The Stuff of Life

• Organic molecules are complex molecules of life, built on a framework of carbon atoms ，以下四大物質皆含 C• Carbohydrates

• Lipids

• Proteins

• Nucleic acids

Carbon – The Stuff of Life

• Carbon atoms can be assembled and remodeled into many organic compounds• Can bond with one, two, three, or four atoms

• Can form polar or nonpolar bonds

• Can form chains or rings

Carbon Rings

Representing Structures of Organic Molecules

• Structural model of an organic molecule• Each line is a

covalent bond; two lines are double bonds; three lines are triple bonds

Representing Structures of Organic Molecules

• Carbon ring structures are represented as polygons; carbon atoms are implied

Representing Structures of Organic Molecules

• Ball-and-stick models show positions of atoms in three dimensions; elements are coded by color

Representing Structures of Organic Molecules

• Space-filling models show how atoms sharing electrons overlap

Three Models of a Hemoglobin Molecule

3.2 From Structure to Function

• The function of organic molecules in biological systems begins with their structure

• The building blocks of carbohydrates, lipids, proteins, and nucleic acids bond together in different arrangements to form different kinds of complex molecules

Functional Groups

• Hydrocarbon• An organic molecule that consists only of

hydrogen and carbon atoms

• Most biological molecules have at least one functional group• A cluster of atoms that imparts specific chemical

properties to a molecule (polarity, acidity)

Common Functional Groupsin Biological Molecules

Effects of Functional Groups: Sex Hormones

What Cells Do to Organic Compounds

• Metabolism• Activities by which cells acquire and use energy

to construct, rearrange, and split organic molecules

• Allows cells to live, grow, and reproduce

• Requires enzymes (proteins that increase the speed of reactions)

What Cells Do to Organic Compounds

• Condensation (脫水合成 )• Covalent bonding of two molecules to form a

larger molecule

• Water forms as a product

• Hydrolysis (加水分解 )• The reverse of condensation

• Cleavage reactions split larger molecules into smaller ones

• Water is split

What Cells Do to Organic Compounds

• Monomers• Molecules used as subunits to build larger

molecules (polymers)

• Polymers• Larger molecules that are chains of monomers

• May be split and used for energy

What Cells Do to Organic Compounds

Condensation and Hydrolysis

B) Hydrolysis. A molecule splits, then an —OH group and an H atom from a water molecule become attached to sites exposed by the reaction.

A) Condensation. An —OH group from one molecule combines with an H atom from another. Water forms as the two molecules bond covalently.

Animation: Condensation and hydrolysis

3.1-3.2 Key Concepts:Structure Dictates Function

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

• All of these organic compounds have functional groups attached to a backbone of carbon atoms

3.3 Carbohydrates

• Carbohydrates are the most plentiful biological molecules in the biosphere

• Cells use some carbohydrates as structural materials; others for stored or instant energy

Carbohydrates

• Carbohydrates• Organic molecules that consist of carbon,

hydrogen, and oxygen in a 1:2:1 ratio

• Three types of carbohydrates in living systems• Monosaccharides ( 單醣 )

• Oligosaccharides ( 寡糖 )

• Polysaccharides ( 多糖 )

Simple Sugars

• Monosaccharides (one sugar unit) are the simplest carbohydrates• Used as an energy

source or structural material

• Backbones of 5 or 6 carbons

• Example: glucose

Short-Chain Carbohydrates

• Oligosaccharides• Short chains of monosaccharides

• Example: sucrose, a disaccharide

sucroseglucose + fructose + water

Animation: Sucrose synthesis

Complex Carbohydrates

• Polysaccharides• Straight or branched chains of many sugar

monomers ( 種類有下列三大 )

• The most common polysaccharides are cellulose, starch, and glycogen• All consist of glucose monomers

• Each has a different pattern of covalent bonding, and different chemical properties

Cellulose, Starch, and Glycogen

Chitin

• Chitin • A nitrogen-containing polysaccharide that

strengthens hard parts of animals such as crabs, and cell walls of fungi

3.3 Key Concepts:Carbohydrates

• Carbohydrates are the most abundant biological molecules

• They function as energy reservoirs and structural materials

• Different types of complex carbohydrates are built from the same subunits of simple sugars, bonded in different patterns

3.4 Greasy, Oily – Must Be Lipids

• Lipids function as the body’s major energy reservoir, and as the structural foundation of cell membranes

• Lipids• Fatty, oily, or waxy organic compounds that are

insoluble in water

Fatty Acids

• Many lipids incorporate fatty acids• Simple organic compounds with a carboxyl group

joined to a backbone of 4 to 36 carbon atoms

• Essential fatty acids are not made by the body and must come from food• Omega-3 and omega-6 fatty acids

Fatty Acids

• Saturated, monounsaturated, polyunsaturated

Animation: Fatty acids

Fats

• Fats• Lipids with one, two, or three fatty acids “tails”

attached to glycerol ( 甘油 )

• Triglycerides (三酸甘油酯 )• Neutral fats with three fatty acids attached to

glycerol

• The most abundant energy source in vertebrates

• Concentrated in adipose tissues (for insulation and cushioning 絕緣和緩衝 )

Triglycerides

Animation: Triglyceride formation

Saturated and Unsaturated Fats

• Saturated fats (animal fats) 飽和脂肪酸• Fatty acids with only single covalent bonds

• Pack tightly; solid at room temperature

• Unsaturated fats (vegetable oils)• Fatty acids with one or more double bonds

• Kinked; liquid at room temperature

Trans Fats

• Trans fats• Partially hydrogenated vegetable oils formed by a

chemical hydrogenation process

• Double bond straightens the molecule

• Pack tightly; solid at room temperature

Cis and Trans Fatty Acids

Phospholipids

• Phospholipids• Molecules with a polar head containing a

phosphate and two nonpolar fatty acid tails

• Heads are hydrophilic, tails are hydrophobic

• The most abundant lipid in cell membranes

Phospholipids

Waxes

• Waxes• Complex mixtures with long fatty-acid tails

bonded to long-chain alcohols or carbon rings

• Protective, water-repellant covering

Cholesterol and Other Steroids

• Steroids (類固醇 )• Lipids with a rigid backbone of four carbon rings

and no fatty-acid tails

• 真核細胞模皆含有固醇：動物膽固醇，植物植物醇• Cholesterol (膽固醇 )

• Component of eukaryotic cell membranes

• Remodeled into bile salts, vitamin D, and steroid hormones (estrogens and testosterone) 固定細胞膜、分解成小分子、或者當激素用

Cholesterol

3.4 Key Concepts:Lipids

• Lipids function as energy reservoirs and waterproofing or lubricating substances

• Some are remodeled into other substances

• Lipids are the main structural components of cell membranes

3.5 Proteins – Diversity in Structure and Function

• Proteins are the most diverse biological molecule (structural, nutritious, enzyme, transport, communication, and defense proteins)

• Cells build thousands of different proteins by stringing together amino acids in different orders

Proteins and Amino Acids

• Protein• An organic compound composed of one or more

chains of amino acids

• Amino acid• A small organic compound with an amine group

(—NH3+), a carboxyl group (—COO-, the acid),

and one or more variable groups (R group)

Amino Acid Structure

Polypeptides

• Protein synthesis involves the formation of amino acid chains called polypeptides

• Polypeptide• A chain of amino acids bonded together by

peptide bonds in a condensation reaction between the amine group of one amino acid and the carboxyl group of another amino acid

Fig. 3-16a, p. 44

A DNA encodes the order of amino acids in a new polypeptide chain. Methionine (met) is typically the first amino acid.

B In a condensation reaction, a peptide bond forms between the methionine and the next amino acid, alanine (ala) in this example. Leucine (leu) will be next. Think about polarity, charge, and other properties of functional groups that become neighbors in the growing chain.

Peptide Bond Formation

Fig. 3-16b, p. 45

C A peptide bond forms between the alanine and leucine. Tryptophan (trp) will be next. The chain is starting to twist and fold as atoms swivel around some bonds and attract or repel their neighbors.

D The sequence of amino acid subunits in this newly forming peptide chain is now met–ala–leu–trp. The process may continue until there are hundreds or thousands of amino acids in the chain.

Peptide Bond Formation

3.6 Why Is Protein Structure So Important?

• When a protein’s structure goes awry, so does its function

Fig. 3-17a, p. 45

Levels of Protein Structure

Primary structureThe unique amino acid sequence of a protein

Fig. 3-17b, p. 45

Levels of Protein Structure• Secondary structure

• The polypeptide chain folds and forms hydrogen bonds between amino acids

Fig. 3-17c, p. 45

Levels of Protein Structure

• Tertiary structure• A secondary structure is compacted into

structurally stable units called domains• Forms a functional protein ( 三級結構以上開始有

功能 )

Fig. 3-17d, p. 45

Levels of Protein Structure

• Quaternary structure• Some proteins consist of two or more folded

polypeptide chains in close association• Example: hemoglobin

Just One Wrong Amino Acid…

• Hemoglobin contains four globin chains, each with an iron-containing heme group that binds oxygen and carries it to body cells

• In sickle cell anemia, a DNA mutation changes a single amino acid in a beta chain, which changes the shape of the hemoglobin molecule, causing it to clump and deform red blood cells

Globin Chains in Hemoglobin

Fig. 3-19a, p. 47

Molecular Basis of Sickle Cell Anemia

Fig. 3-19b, p. 47

Molecular Basis of Sickle Cell Anemia

Fig. 3-19c, p. 47

Molecular Basis of Sickle Cell Anemia

Proteins Undone – Denaturation

• Proteins function only as long as they maintain their correct three-dimensional shape

• Heat, changes in pH, salts, and detergents can disrupt the hydrogen bonds that maintain a protein’s shape

• When a protein loses its shape and no longer functions, it is denatured (蛋白質變性 )

3.5-3.6 Key Concepts:Proteins

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

• They include enzymes, structural materials, and transporters

• A protein’s function arises directly from its structure

3.7 Nucleic Acids

• Some nucleotides are subunits of nucleic acids such as DNA and RNA

• Some nucleotides have roles in metabolism

Nucleotides

• Nucleotide• A small organic molecule consisting of a sugar

with a five-carbon ring, a nitrogen-containing base, and one or more phosphate groups

• ATP• A nucleotide with three phosphate groups

• Important in phosphate-group (energy) transfer

ATP

Nucleic Acids

• Nucleic acids• Polymers of nucleotides in which the sugar of one

nucleotide is attached to the phosphate group of the next

• RNA and DNA are nucleic acids

RNA

• RNA (ribonucleic acid)• Contains four kinds of nucleotide monomers,

including ATP

• Important in protein synthesis

DNA

• DNA (deoxyribonucleic acid)• Two chains of nucleotides twisted together into a

double helix and held by hydrogen bonds

• Contains all inherited information necessary to build an organism, coded in the order of nucleotide bases

Fig. 3-21, p. 48

adenine (A) base with a double ring structure

thymine (T) base with a single ring structure

3 phosphate groups

sugar (deoxyribose)

guanine (G) base with a double ring structure

cytosine (C) base with a single ring structure

Four Nucleotides of DNA

The DNA Molecule

3.7 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

Summary: Organic Molecules in Living Things