cecie starr | beverly mcmillan chapter 2 chemistry of life

Cecie Starr | Beverly McMillan

Chapter 2

Chemistry of Life

Chemistry of Life

Key Concepts

•Atoms and Elements•Water and Body Fluids•Biological Molecules

2

2.1 Atoms and Elements

• Pure substances called elements are the basic raw material of living things.

• Each element consists of one type of atom.

• The parts of atoms determine how the elements of life are put together.

Atoms and Elements


• Matter takes up space and has mass.– Gas– Liquid– Solid

• Elements are pure substance that cannot be broken down to another substance.

• Atoms are the basic units of matter.


Oxygen 65Carbon 18Hydrogen 10Nitrogen 3Calcium 2Phosphorus 1.1Potassium 0.35Sulfur 0.25Sodium 0.15Chlorine 0.15Magnesium 0.05Iron 0.004Iodine 0.0004

Oxygen 46.6Silicon 27.7Aluminum 8.1Iron 5.0Calcium 3.6Sodium 2.8Potassium 2.6Magnesium 2.1Other elements 1.5

Human Earth’s crust

Figure 2-1 p16


• Subatomic particles– Protons: p+– Electrons: e-– Neutrons

• Atomic number• Mass number

proton

neutron

electron

Figure 2-2 p16


• Isotopes

• Radioisotopes– Unstable nucleus– Radioactive decay – Role in dating substances

Take home message

What are elements and atoms?

2.2 PET Scanning- Using Radioisotopes in Medicine

• Positron Emission Tomography (PET scanners)– Role in diagnosis of

diseases (tracers)– Treatment of cancers

Atoms and Elements tumors

SmokerNon-smoker

brain

lungs

heart

liver

kidneys

Figure 2-3 p17

2.3 Chemical Bonds: How Atoms Interact

• Atoms receive, donate, or share electrons.

• Whether an atom will interact with other atoms depends on how many electrons it has.

• Chemical bonds connect atoms into molecules.


Atoms interact through their electrons.• Electrons repel each other• Electron shells

– Contain a maximum of eight electrons – Equivalent to energy levels

• Electron orbitals


1 electronfirst shell

second shell

third shell sodium (Na) chlorine (Cl) argon (Ar)

neon (Ne)oxygen (O)

helium (He)

carbon (C)

hydrogen (H)

1 2

6 8 10

181711

1 proton

Figure 2-4 p18

6

B The second shell corresponds to the second energy level, and it can hold up to 8 electrons. Carbon has 6 protons, so its first shell is full. Its second shell has 4 electrons, and four vacancies. Oxygen has 8 protons and two vacancies. Neon has 10 protons and no vacancies.

neon (Ne)second shell carbon (C) oxygen (O)

8 10

C The third shell, which corresponds to the third energy level, can hold up to 8 electrons. A sodium atom has 11 protons, so its first two shells are full; the third shell has one electron. Thus, sodium has seven vacancies. Chlorine has 17 pro tons and one vacancy. Argon has 18 protons and no vacancies.

third shell argon (Ar)chlorine (Cl)sodium (Na)

181711

A The first shell corresponds to the first energy level, and it can hold up to 2 electrons. Hydrogen has one proton, so it has 1 electron and 1 vacancy. A helium atom has 2 protons, 2 electrons, and no vacancies. The number of protons in each model is shown.

first shell hydrogen (H) helium (He)

11 proton1 electron

2

Stepped Art

Figure 2-4 p18


Chemical bonds join atoms into molecules.• Chemical bonds• Outer shells and electron

vacancies

• Why is helium inert?

Table 2-1 p19


Molecules may contain atoms of a single element or of different elements.

• Molecule

• Compounds– Proportions of the

elements are always the same

• Mixture – Proportions may or

may not be the same

2H2

(hydrogen)2H2O

(water)

Reactants

4 hydrogen atoms+ 2 oxygen atoms

Products

4 hydrogen atoms+ 2 oxygen atoms

O2

(oxygen)

Figure 2-5 p19

2H2O(water)

Reactants

4 hydrogen atoms

+ 2 oxygen atoms

Products

4 hydrogen atoms

+ 2 oxygen atoms

2H2

(hydrogen)O2

(oxygen)+

Stepped Art

Figure 2-5 p19

Take home message

What is a chemical bond?

2.4 Important Bonds in Biological Molecules

In biological molecules the main kinds of chemical bonds are ionic, covalent, and hydrogen bonds.

Atoms and Elements

Table 2-2 p21


• Ions form ionic bonds.

• Positive ion, (cation) e.g., Na+- electron donor ( oxidized)

• Negative ion, ( anion ) e.g., Cl-- electron acceptor ( reduced )

• Ionic compound, e.g., NaCl or table salt

An ionic bond joins atoms that have opposite electrical charges.


electron loss

Chlorideion

17p+18e–

charge: –1

17

Chlorineatom

17p+17e–

charge: 0

17

Sodiumatom

11p+10e–

11p+11e–

charge: 0

charge: +1

Sodiumion

11

11

electron gain

Figure 2-6 p20


• Covalent bond: Share electrons– Single: H—H– Double: O=O– Triple: N≡N

• Nonpolar: Equal sharing of the electrons

• Polar: Unequal sharing of the electrons due to electronegativity difference

In a covalent bond, atoms share electrons.


Molecular oxygen (O=O)

Water molecule (H–O–H)

Molecular hydrogen (H–H)

8

1 1

1 1

8

8

Two hydrogen atoms, each withone proton, share two electrons ina single nonpolar covalent bond.

Two oxygen atoms, each with eightprotons, share four electrons in adouble covalent bond.

Two hydrogen atoms share electrons with an oxygen atom in two polar covalent bonds. The oxygen exerts a greater pull on the shared electrons, so it has a slight negative charge. Each hydrogen has a slight positive charge.Figure 2-7 p21


• Hydrogen bond– Weak attraction– Between water molecules– Between parallel strands of

DNA

A hydrogen bond is a weak bond between polar molecules.

hydrogen bond

water molecule water molecule

H

H

H

H

O O

Figure 2-8 p21

Take home message

What are the main types of chemical bonds that occur in biological molecules?

2.5 Water: Necessary for Life

• Water is required for many life processes.

• Other life processes occur only after substances have dissolved in water.

Water and Body Fluids


• Liquid between 32°F and 212°F

• No net charge; uneven distribution of charges

• Hydrophilic- means water-loving, or chemically attracted to water

• Hydrophobic- means water-fearing, or chemically repelled by water

Hydrogen bonding makes water liquid.


slight negative charge on the oxygen atom

Overall, the molecule carries no net charge

slight positive charge on each hydrogen atom

Figure 2-9 p22


• High heat capacity• Heat breaks the hydrogen bonds• Water as a coolant• Sweating and evaporative cooling

Water can absorb and hold heat.


• Solvent- easily dissolves ions and polar molecules.

• Solute- is the dissolved substance.

• Water forms spheres of hydration

Water is a solvent.


sphere of hydration

sodiumion

chlorideion

sphere of hydration

Figure 2-10 p23

Take home message

What are the chemical properties of water that help support life?

2.6 Focus on Health: How Antioxidants Protect Cells

• Oxidation in cells produces free radicals (unstable)– Threat to DNA

• Antioxidants– Neutralize free radicals– Examples

• Vitamins C and E• Alpha carotene

Water and Body Fluids

Figure 2-11 p23

2.7 Acids, Bases, and Buffers: Body Fluids in Flux

• Ions dissolved in the fluids inside and outside cells influence cell structure and functioning

• Hydrogen ions affect many body functions


• Hydrogen ions: H+

• Hydroxyl ions: OH-

• pH scale– pH 1–14– pH <7.0 = acid– pH 7.0: neutral, H+ and OH- are equal– pH >7.0 = base, – Tenfold change in concentration for

each pH unit of change

The pH scale indicates the concentration of hydrogen ions in fluids.

Figure 2-12 p24


Acids give up H+ and bases accept H+

• Importance of acids and bases in the human body

• Effect of strong acids and bases on the environment

Figure 2-13 p25


• Salt- releases ions other than H+ and OH-

• Key functions in cells

A salt releases other kinds of ions.


Buffers protect against shifts in pH.

• Buffer system

• Keep pH of a solution stable• Can bind or release H+ • Role of carbonic acid and the

bicarbonate ion in human blood

p25


Buffers protect against shifts in pH.

• Human blood: maintains pH range: 7.3–7.5

• Acidosis– blood pH below 7.0– leads to coma and death

• Alkalosis– blood pH increase to 7.8– leads to tetany and death

p25

Take home messageHow do acids, bases, salts, and buffers affect the makeup of body fluids?

2.8 Molecules of Life

• Molecules that make up living things are called biological molecules

• They are built on atoms of the element carbon

• The four classes of biological molecules are carbohydrates, lipids, proteins, and nucleic acids

• Organic compound- composed of carbon and at least one hydrogen atom

Biological Molecules


• Covalent bond- stable– Hydrocarbons– Straight chain– Branching– Ring structure

Carbon’s key feature is versatile bonding.single covalent bond

carbon atom

atoms branching from backbone

carbon backbone

or carbon rings

p26


Functional groups affect the chemical behavior of organic compounds.

• Functional groups give rise to specific properties – Hydroxyl– Methyl– Carbonyl– Carboxyl– Amine– Phosphate– Sulfhydryl

Figure 2-14 p26


Functional groups affect the chemical behavior of organic compounds.

AN ESTROGEN TESTOSTERONEFigure 2-15 p27


Cells have chemical tools to assemble and break apart biological molecules.

• Cell reactions use enzymes– Enzymes are proteins that help

to speed up chemical reactions.

Table 2-3 p27


Cells have chemical tools to assemble and break apart biological molecules.• Condensation reactions

– Polymers formed from monomers

• Hydrolysis reactions– Monomers formed from polymers

water

waterenzyme action at functional groupsenzyme action at functional groups

Figure 2-16 p27

Take home message

What are the main types of biological molecules?

2.9 Carbohydrates: Plentiful and Varied

• Carbohydrates are the most abundant biological molecules

• Cells use carbohydrates to help build cell parts or package them for energy



Simple sugars are the simplest carbohydrates.

• Monosaccharide, e.g., glucose

• Characteristics– At least two —OH groups joined

to a carbon backbone– Plus an aldehyde or ketone

group– Usually taste sweet and dissolve

in water– Five or six carbons are the most

common– Ratio of atoms is generally 1:2:1

(e.g. C6H12O6)

p28


Oligosaccharides are chains of two or more sugar monomers that are joined via dehydration synthesis.

Disaccharides are most common oligosaccharide.

glucose + fructose sucrose + water

Figure 2-17 p28


• Most common– Glycogen: storage form of glucose

in animals (in liver and muscles) – Starch: storage form of glucose in

plants (high amounts in potatoes, rice, wheat, and corn)

– Cellulose: indigestible fiber of plants (aids in human digestion)

Polysaccharides are sugar chains that store energy.

Figure 2-18 p29

2.10 Lipids: Fats and Their Chemical Relatives

• Cells use lipids to store energy, as structural materials, and as signaling molecules



• Lipids: nonpolar hydrocarbons

• Fats– Glycerol with one, two, or three fatty acids attached– Triglycerides

• Most common fat in human body• Richest source of energy

• Saturated vs. Unsaturated fats

• Cis vs. trans fatty acids

Fats are energy-storing lipids.


stearic acidA B oleic acid C linolenic acidFigure 2-19 p30

2.10 Lipids: Fats and Their Chemical Relativesglycerol

A triglyceride

+ 3H2O

Figure 2-20 p30


Figure 2-21 p31


Phospholipids are key building blocks of cell membranes.

• Phospholipids– Glycerol backbone– Two fatty acid tails– Hydrophilic phosphate head– Important component of all

cell membranes

hydrophilic head (orange)

twohydrophobic tails

hydrophobic tails

B Arrangements in a cell membrane

A A phospholipidFigure 2-22 p31


Cholesterol and steroid hormones are built from sterols.• Sterols

– Four fused-together carbon rings– Differ in the number, position, and

type of their functional groups

• Cholesterol: Vital component of animal membranes– Derivatives of cholesterol

include:• Vitamin D• Bile salts• Steroid hormones

B Cholesterol

A sterol backbone

Carbon rings

Figure 2-23 p31

2.11 Proteins: Biological Molecules with Many Roles

Proteins are the most diverse biological molecules with many roles.


Table 2-4 p32


Proteins are built from amino acids.

• Twenty amino acids– Small organic compounds– Chemical composition

• Amino group• Carboxyl group• Hydrogen• R group: determines the

chemical properties of the amino acid

Carboxyl Group

R Group (20 Kinds, EachWith Distinct Properties)

Amino Group

valine (val)

tryptophan (trp) methionine (met)Figure 2-24a p32


• Amino acids linked by peptide bonds

• Sequence determines primary structure

• Polypeptide chain – Backbone: —N—C—C—N—C—C—

The sequence of amino acids is a protein’s primary structure.


serine

methionine serinemethionine

Figure 2-25 p32

2.12 A Protein’s Shape and Function

• Once amino acids have been assembled into a protein, the protein folds into its final shape

• A protein's final shape determines its function



• Secondary structure due to hydrogen bonds– Helical coil– Sheetlike

• Tertiary structure – Continued folding– Twisted into functional

domains

• Quaternary structure– Globular

• Hemoglobin: four chains• Insulin: two chains• Many enzymes

– Fibrous• Collagen: most common

protein in humans• Keratin

Proteins fold into complex shapes that determine their function.


• Lipoproteins– Circulating proteins associated with cholesterol, triglycerides, and

phospholipids

• Glycoproteins– Oligosaccharides bonded to them– Surface of cells

Glycoproteins have sugars attached and lipoproteins have lipids.


• Effect of pH and temperature on protein’s structure• Disruption of hydrogen bonds leads to denaturation

Disrupting a proteins’ shape prevents it from functioning normally.

Figure 2-28 p35

Take home messageHow does a protein get its final shape?

2.13 Nucleotides and Nucleic Acids

• The fourth and final class of biological molecules- nucleic acids consisting of nucleotides



Nucleotides are energy carriers and have other roles.

• Nucleotide• Sugar• Phosphate• Nitrogenous base (cytosine, guanine, thymine, and adenine)

• ATP (adenosine tri-phosphate)• Three phosphate groups• Links chemical reactions that release energy when phosphate bonds

are broken

• Coenzyme• Move hydrogen atoms and electrons• Act as chemical messengers, such as cAMP


base (blue)

three phosphate groupssugar (red)

phosphorusoxygen

Figure 2-29 p36


• DNA – Contains sugar deoxyribose– Consists of two strands of nucleotides twisted in a double helix

• RNA– Contains sugar ribose– Consists of single strand of nucleotides

Nucleic acids include DNA and RNAs.

Take home message

What is a nucleic acid?

2.13 Nucleotides and Nucleic Acidsnucleotide

base

AFigure 2-30 p36

2.14 Food Production and a Chemical Arms Race

• Human and natural plant toxins• Effect of pesticides and

herbicides on humans

• Modern pesticides increase food supplies and profits for farmers


Figure 2-31 p37

Table 2-5 p39

cecie starr | beverly mcmillan chapter 2 chemistry of life

Documents

parts of atoms

elements oxygen

elements of life

elements matter

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p18 slide

elements water

p17 slide