Chapter 2 The Chemical Basis of Life

Outline

2.1 Atoms and Atomic BondsMatter is anything that takes up space and has mass.Atomic Structure

2.2 Water's Importance to LifeThe Structure of WaterProperties of Water

2.3 Acids and BasespH and the pH Scale

2.1 The Nature of Matter

Matter ( 物質 )

• refers to anything that takes up space and has mass.

• can exist as a solid, liquid, or gas• composed of elements,

– elements --substances that cannot be broken down into another substance

– There are 92 natural elements.

– Four elements make up about 96% of the body weight of most living organisms—carbon, hydrogen, oxygen, and nitrogen.

Figure 2.1 Elements in living organisms.

Atomic Structure• The atomic theory states that elements

consist of atoms atoms.

• Atomic symbol—name of the atom or element

– Hydrogen = H

– Sodium = Na

– Chloride = Cl

• Subatomic elements

Neutrons ( 中子 ) —no electrical charge, found in nucleus

Protons ( 質子 ) —positive charge, found in nucleus

Electrons ( 電子 ) —negative charge, found outside of nucleus

• Mass number ( 質量數 ) is equal to sum of protons and neutrons—electrons have about zero mass

• Atomic weight changes with gravity

6

12CMass number

Atomic numberChemical symbol

+ –

–

–

= proton = neutron = electron

outside nucleusinside nucleus

nucleus

b.a.

++–

++

Figure 2.2 Two models of helium (He).

Arrangements of Electrons in an Atom

Electrons are constantly moving. Useful to construct models of atoms with energy levels or electron

shells Each shell contains a certain number of electrons. For atoms up through number 20

• 2 electrons fill first shell• 8 electrons fill each additional shell

Octet rule ( 八階法則 ) for valence ( 原子價 ) shell• Valence shell—outermost shell• If an atom has more than 2 shells, the outer shell is most stable

with 8 electrons• Atoms can give up, accept, or share electrons to have 8

Chemical properties of atoms are largely determined by the arrangement of their electrons

• Atomic number

All atoms of an element have this same number of protons

Also gives number of electrons if an atom is electrically neutral

• Periodic table

Elements’ chemical and physical characteristics recur in a predictable manner

Atoms are arranged in periods (rows) and groups (columns)

Figure 2.3 A portion of the periodic table.

Isotopes

• Atoms of the same element that differ in the number of neutrons

• Isotopes have the same number of protons but a different number of neutrons (different mass numbers)

• Unstable and may decay, emitting radiation

• Radioactive isotope behavior is essentially the same as a stable isotope of same element

• Can be used as tracer—PET scan

• Can cause damage to cells leading to cancer

• Can be used to sterilize medical equipment

C12

6C14

6 P31

15

P32

15

Figure 2.4 PET scan.

Figure 2.5 High levels of radiation.

Types of Chemical Bonds

Molecule ( 分子 ) —group of atoms bonded together

• O2, H2O, C6H12O6, N2

Compound ( 化合物 ) —molecule containing atoms of more than one element

• H2O, C6H12O6

2 types of bonds

• Ionic ( 離子鍵 ) —attraction between opposite charges

• Covalent ( 共價鍵 ) —sharing electrons to complete outer shell

Types of Chemical Bonds (cont.)

Covalent bonding

2 atoms share electrons

2 hydrogen atoms can share electrons to fill their outer shell—orbitals overlap.

Structural formula ( 結構式 ) —uses straight lines H-H

1 line indicates 1 pair of shared electrons.

Molecular formula ( 分子式 ) —simply shows number of atoms involved H2

• Double covalent bond—sharing 2 pairs of electrons

Oxygen gas O2 or O=O

• Triple covalent bond—sharing 3 pairs of electrons

Nitrogen gas N2 or N≡N

• Single atom may form bonds with more than one atom May be represented by ball-and-stick

models or space-filling models

• Chemical formulas and reactions Reactants—molecules that participate in reactions

•Shown to the left of the arrow

Products—molecules formed by reactions•Shown to the right of the arrow

Equation is balanced if the same number of each type of atom occurs on both sides of the arrow.

•An overall equation for photosynthesis

•Molecular formula for glucose

6 CO2

carbondioxide

6 H2Owater

C6H12O6

glucose+ 6 O2

oxygen+

C6H12O6

one molecule

indicates6 atomsof carbon

indicates6 atomsof oxygen

indicates12 atomsof hydrogen

2.2 Water’s Importance to Life

• Life began in water

• Single most important molecule on Earth

• All organisms are 70–90% water

• Water has unique properties that make it a life-supporting substance

• Properties stem from the structure of the molecule

The Structure of Water Polar covalent bond

• Atoms do not share electrons equally.• Oxygen is more electronegative than hydrogen.• Electrons spend more time around the oxygen nucleus than the

hydrogen nuclei.• Oxygen end becomes slightly negative/hydrogens become slightly

positive—NOT an ionic bond or ions Hydrogen bond—slightly positive hydrogen of one water molecule

attracted to the slightly negative oxygen in another water molecule

O

H H

Oxygen is slightly negative (–)

a.

Hydrogens are slightly positive (+)

b. hydrogen bond

Solvency Cohesion and adhesion High surface tension High heat capacity High heat of vaporization Varying density

Properties of Water

Properties of Water

• Water is a solvent

Due to polarity and H-bonding, water dissolves many substances

Hydrophilic—molecules attracted to water

Hydrophobic—molecules not attracted to water

Water causes NaCl to dissociate

•Cohesion ( 內聚 )Ability of water molecules to cling to each other due to hydrogen bonding

• Adhesion ( 黏附 )Ability of water molecules to cling to other polar surfaces

• Allows water to be excellent transport system both in and outside of living organisms

•Contributes to water transport in plants

Properties of Water (cont.)• Water also has a high surface tension ( 表面張

力 ).• Water molecules at the surface cling more tightly to

each other than to the air above.• Mainly due to hydrogen bonding

Water strider

•Water has a high heat capacity ( 容量 ).•The many hydrogen bonds linking water molecules allow water to absorb heat without greatly changing its temperature.•Temperature of water rises and falls slowly

•Water has a high heat of vaporization ( 蒸發 ).•Takes a great deal of energy to break H bonds for evaporation•Heat is dispelled as water evaporates.

•Ice is less dense than water.•Unlike other substances, water expands as it freezes.•Ice floats rather than sinks.•It makes life possible in water.•Ice acts as an insulator.

Figure 2.12 Properties of ice.

2.3 Acids and Bases• Water dissociates into an equal number of hydrogen ions (H+) and hydroxide ions (OH–)

Acidic Solutions (High H+ Concentration)• Lemon juice, vinegar, and coffee

• Acids release hydrogen ions

Basic Solutions (Low H+ Concentration)• Milk of magnesia and ammonia

• Either take up hydrogen ions or release hydroxide ions

pH and the pH scale

• Mathematical way to indicate the number of hydrogen ions in solution

• pH scale ranges from 0 to 14

• pH below 7 is acidic—more [H+] than [OH–]

• pH above 7 is basic—more [OH–] than [H+]

• pH of 7 is neutral—[H+] equal to [OH–]

Buffers ( 緩衝溶液 ) and pH

Figure 2.14 Acidosis.

Chemical or combination of chemicals that keeps pH within normal limits

Resists pH change by taking up excess H+ or OH–

pH of blood is about 7.4—maintained by buffer

Chapter 3 The Organic Molecules of Life

Outline

3.1 Organic MoleculesThe Carbon AtomThe Carbon Skeleton and Functional Groups

3.2 The Biological Molecules of the CellsCarbohydratesLipids Proteins Nucleic Acids

3.1 Organic Molecules• Organic chemistry

• Biological molecules

• Organic molecules contain carbon and hydrogen.

• Inorganic molecules do not (H2O and NaCl)

Figure 3.1 Organic molecules as structural materials.

The Carbon Atom Total of six electrons—4 in outer shell

Almost always shares electrons with elements such as hydrogen, nitrogen, and oxygen

Can bond with as many as 4 other elements

Most often shares electrons with other carbon atoms

Carbon chains can vary in length, and/or have double bonds, and/or be branched.

Carbon chains can form rings of different sizes and have double bonds.

Figure 3.2 Hydrocarbons are highly versatile.

Hydrocarbons—chains of carbon atoms bonded only to hydrogen atoms

Isomers—same number and kinds of atoms in a variety of arrangements

•May have different properties

The Carbon Skeleton and Functional Groups

1. Size and shape of carbon skeleton or backbone

2. Functional group—specific combination of bonded atoms that always has the same chemical properties and always reacts the same way

Reactivity of organic molecule largely dependent on attached functional groups

Often use R to stand for the rest of the molecule

3.2 The Organic Molecules of Cells• 4 categories—carbohydrates, lipids, proteins, and nucleic acids

• As your body digests food, these compounds are released and used to assemble the large macromolecules that make up your cells.

Corn

Pasta

Rice

Bread

Potato

Cheese

Lard

Ice cream Oil

Butter

Tofu

Meat

Milk

NutsBeans

Eggs

Protein foodsLipid foodsCarbohydrates.

3.2 The Organic Molecules of Cells (cont.)

•Monomers—subunits

• Polymer—monomers joined together

•Dehydration synthesis reaction Joins monomers to form polymersEquivalent of removing a water molecule

•Hydrolysis Breaks polymers apart Water is used to break the bond

Carbohydrates Almost universally used as immediate energy source in living things Play structural roles Polymers of monomers called saccharides or sugars Monosaccharide, disaccharide, polysaccharide

Monosaccharides: Ready Energy Single sugar molecule

Simple sugars

3–7 carbon backbone

Glucose C6H12O6

• 2 isomers—fructose ( 果糖 ) and galactose ( 半乳糖 ).

• Cells use glucose as the energy source of choice.

• Ribose ( 核醣 ) and deoxyribose are found in RNA and DNA.

Figure 3.8 Glucose.

Disaccharides: Varied Uses

2 monosaccharides bonded together

Maltose ( 麥芽糖 ) —yeast breaks down maltose in beer for energy and produces ethyl alcohol

•Fermentation

Sucrose ( 蔗糖 ) —table sugar

Polysaccharides as Energy Storage Molecules

Polymers of monosaccharides Some function as energy storage

molecules•Plants store glucose as starch ( 澱粉 ).

•Animals store glucose as glycogen ( 肝糖 ).

Some function as structural components•Cellulose—plant cell walls

Most abundant of all organic molecules

Digested only by some microbes•Chitin—crab, lobster, insect exoskeletons

Polysaccharides as Structural Molecules

• Cellulose ( 纖維素 ) is the most abundant polysaccharide on earth because it comprises the cell walls of plants.

• Chitin ( 幾丁質 ) is a polysaccharide that forms the exoskeleton of crabs, lobsters, and insects.

Lipids All are insoluble in water

Long nonpolar hydrocarbon chains

Relative lack of hydrophylic functional groups

Very diverse structures and functions

Fats and oils used for long-term energy storage

Oil may help waterproof skin, hair, and feathers.

Fats and Oils: Long-term Energy Storage

• Triglycerides are composed of 1 glycerol ( 甘油 ) and 3 fatty acids ( 脂肪酸 ) .

• A fat or oil is formed when a dehydration reaction adds fatty acids to the –OH groups of glycerol and broken down by hydrolysis reactions.

• Since three fatty acids are attached to a glycerol, fats and oils are often called triglycerides ( 三酸甘油酯 ).

Fatty Acids• Fatty acids are either . . .

Saturated—no double bonds between carbon atoms

•Butter is solid at room temperature.

Unsaturated—one or more double bonds between carbon atoms

•Oil is liquid at room temperature.

•Trans fatty acids have been artificially hydrogenated to make them more solid.

Fatty Acids (cont.)• The saturation of fats affects human health.

– Saturated fats such as trans fats contribute to heart disease.

– Unsaturated oils, such as monounsaturated and polyunsaturated oils, can have a protective effect against atherosclerosis.

Elaidic acid, a trans fatty acid (one double bond) found in many snack foods.

C18H34O2carboxyl groupdonut

characteristic of a trans fat

Fatty Acids (cont.)

菜籽油

紅花

椰子

Phospholipids ( 磷脂 ) : Membrane Components

Form the bulk of the plasma membrane

One end of the molecule is water-soluble.

•Polar phosphate head

Other end of the molecule is not water-soluble

•Nonpolar fatty acid tails

Steroids: Four Fused Rings

Figure 3.14 Steroid diversity.

Lipids made of 4 fused rings

No fatty acids but are insoluble in water

Derived from cholesterol ( 膽固醇 )

Differ only in functional groups

( 睪丸素 )

( 雌激素 )

Proteins• Many functions: support, metabolism, transport,

defense, regulation, and motion– Proteins such as keratin ( 角質 ) and collagen

( 膠原 ) have structural roles.– Proteins are also enzymes that speed up the

chemical reactions of metabolism.– Proteins such as hemoglobin ( 血紅素 ) are

responsible for the transport of substances within the body.

– Proteins form the antibodies ( 抗體 ) of the immune system that defend the body from disease.

– Proteins such as insulin ( 胰島素 ) are hormones that regulate cellular function.

– Contractile proteins such as actin ( 肌動蛋白 ) and myosin ( 肌凝蛋白 ) allow parts of cells to move and muscles to contract.

Amino Acids: Subunits of Proteins

• Proteins are composed of amino acid monomers

• Amino acids have three elements to their structure.– An amino (–NH2) group– A carboxyl (–COOH) group– The R (Residual) group

• 20 different amino acids• Differ according to R group

Peptides

• Peptide—two or more amino acids covalently linked

• Peptide bond ( 胜鍵 )—formed by dehydration reaction between two amino acid monomers

• Polypeptide—chain of many amino acids joined by peptide bonds

• Amino acid sequence determines the final three-dimensional shape of protein.

Shape of Proteins Function determined by three-dimensional shape

• Loss of structure and function—denature Usually due to pH or temperature

Primary structure—amino acid sequence

Shape of Proteins (cont.)

• Secondary structure—portions of chain form helices ( 螺旋 ) or pleated ( 起褶的 ) sheets ( 薄板 ,).

Shape of Proteins (cont.)

• Tertiary structure—overall three-dimensional shape of interacting secondary structures

• Quaternary structure—more than one polypeptide chain interacting

.

Quaternary structure: more than one polypeptide

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Nucleic Acids• Deoxyribonucleic acid (DNA)• Stores genetic information• Ribonucleic acid (RNA)• Helps to make proteins• Nucleic acids ( 核酸 ) are polymers of nucleotides

( 核甘酸 ).• Nucleotides have three parts.

– A phosphate group (–PO4-)

– A 5-carbon sugar– A nitrogen-containing base

• The 5-carbon sugar differs between DNA and RNA.

– Ribose is the sugar found in RNA.

– Deoxyribose is the sugar found in DNA.

• There are four possible nitrogen-containing bases in DNA or RNA.

– The bases in DNA are thymine ( 胸腺嘧啶 ), adenine ( 腺嘌呤 ), cytosine ( 胞嘧啶 ) and guanine ( 鳥糞嘌呤 ).

– The bases in RNA are uracil ( 尿嘧啶 ), adenine, cytosine, and guanine.

Nucleic Acids (cont.)

• The phosphate groups and sugars of nucleotides are linked to form the backbone of a DNA or RNA molecule.

• The nitrogen-containing bases show specific complementary ( 互補的 ) base pairing.– In DNA or RNA, guanine is

always paired with cytosine.– In DNA, thymine is always

paired with adenine.– In RNA, uracil is always paired

with adenine.

• DNA is a double helix formed from two spiral strands.

Relationship Between Proteins and Nucleic Acids Sequence of bases in DNA determines sequence of amino acids in a protein Sequence of amino acids determines a protein's structure and function Small changes in the DNA may cause large changes in a protein. Sickle cell disease

•Individual’s red blood cells are sickle-shaped

•One amino acid difference

•Inherited disease