Chapter reference: 6

The emergence of biological function starts at the chemical level

• Everything an organism is and does depends on chemistry

• Chemistry is in turn dependent on the arrangement of atoms in molecules

ATOMS AND MOLECULES

Chemicals of Life video next slide

• Molecules and ecosystems are at opposite ends of the biological hierarchy

– Each level of organization in the biological hierarchy builds on the one below it

– At each level, new properties emerge

• A biological hierarchy

A. Molecule: Actin Atom

MyosinActin

B. Organelle: Myofibril (found only in muscle cells)

Myofibril (organelle)

C. Cell and tissue: Muscle cell within muscle tissue

Rattlebox moth

D. Organ: Flight muscle of a moth

• A chemical element is a substance that cannot be broken down to other substances by ordinary chemical means

Life requires about 25 chemical elements

Atomic Structure

p+

n0

e-Nucleus

Electron Cloud

Atomic Structure

6

CCarbon12.011

Atomic Number = protons/electrons

Atomic Mass = protons + neutrons

Atomic Structure

Subatomic Particle Symbol Location Charge Mass (amu)

Neutron n0 Nucleus 0 1.0087

Proton p+ Nucleus +1 1.0073

Electron e- Electron Cloud -1 0.00006

Properties of Subatomic Particles

Useful Equations:protons = atomic #electrons = atomic #neutrons = atomic mass - atomic #

Atomic Structure

Hydrogen

Helium

Nitrogen

Oxygen

Elements• 92 elements occur in nature

• About 25 different chemical elements are essential to life

• Only 6 elements, CHNOPS, make up 99% of living tissue

• Carbon, hydrogen, oxygen, and nitrogen make up the bulk of living matter, but there are other elements necessary for life

• Goiters are caused by iodine deficiency

Atoms & Elements

Video next

A goiter is an abnormal enlargement of the thyroid gland.

• Chemical elements combine in fixed ratios to form compounds

• Example: sodium + chlorine sodium chloride

Elements can combine to form compounds

• The smallest particle of an element is an atom

• Different elements have different types of atoms

Atoms consist of protons, neutrons, and electrons

• An atom is made up of protons and neutrons located in a central nucleus

A. Helium atom

2

2

2

Protons

Neutrons

Electrons

Nucleus

• The nucleus is surrounded by electrons

• Each atom is held together by attractions between the positively charged protons and negatively charged electrons

B. Carbon atom

6

6

6

Protons

Neutrons

Electrons

Nucleus

• Neutrons are electrically neutral

• Atoms of each element are distinguished by a specific number of protons

– The number of neutrons may vary

– Variant forms of an element are called isotopes

– Some isotopes are radioactive

• Radioactive isotopes can be useful tracers for studying biological processes

• PET scanners use radioactive isotopes to create anatomical images

Why should I care? Radioactive isotopes can help or harm us

• Electrons are arranged in shells

– The outermost shell determines the chemical properties of an atom

– In most atoms, a full outer shell holds eight electrons

Electron arrangement determines the chemical properties of an atom

• Atoms whose shells are not full tend to interact with other atoms and gain, lose, or share electrons

HYDROGEN (H)Atomic number = 1

CARBON (C)Atomic number = 6

NITROGEN (N)Atomic number = 7

OXYGEN (O)Atomic number = 8

Electron

Outermost electron shell (can hold 8 electrons)

First electron shell (can hold 2 electrons)

• When atoms gain or lose electrons, charged atoms called ions are created

– An electrical attraction between ions with opposite charges results in an ionic bond

Ionic bonds are attractions between ions of opposite charge

NaSodium atom

ClChlorine atom

Na+

Sodium ionCl–

Chloride ion

Sodium chloride (NaCl)

Na Cl Na Cl

+–

• Sodium and chloride ions bond to form sodium chloride, common table salt

Na+

Cl–

• Some atoms share outer shell electrons with other atoms, forming covalent bonds

– Atoms joined together by covalent bonds form molecules

Covalent bonds, the sharing of electrons, join atoms into molecules

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• Atoms in a covalently bonded molecule may share electrons equally, creating a nonpolar molecule

• If electrons are shared unequally, a polar molecule is created

Water is a polar molecule

THE PROPERTIES OF WATER

– This makes the oxygen end of the molecule slightly negatively charged

– The hydrogen end of the molecule is slightly positively charged

– Water is therefore a polar molecule

• In a water molecule, oxygen exerts a stronger pull on the shared electrons than hydrogen

(–)

O

(–)

(+)(+)

H H

• The charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules

– This attraction forms weak bonds called hydrogen bonds

Overview: Water’s polarity leads to hydrogen bonding and other unusual properties

Hydrogen bond

• Like no other common substance, water exists in nature in all three physical states:

– as a solid

– as a liquid

– as a gas

• Due to hydrogen bonding, water molecules can move from a plant’s roots to its leaves

• Insects can walk on water due to surface tension created by cohesive water molecules

Hydrogen bonds make liquid water cohesive

Surface tension/Cohesion

Capillaryaction in plants

– Water is one of the few substances that remain a liquid at such a large range of temperatures (O-100 °C).  A large amount of energy must be invested to overcome the hydrogen bonds in liquid water to change it to the gas phase.

It takes a lot of energy to disrupt hydrogen bonds

• A compound that releases H+ ions in solution is an acid, and one that accepts H+ ions in solution is a base

• Acidity is measured on the pH scale:

– 0-6 is acidic

– 7 is neutral

– 8-14 is basic

– Pure water and solutions that are neither basic nor acidic are neutral, with a pH of 7

The chemistry of life is sensitive to acidic and basic conditions

• The pH scale

pH scale

Acidic solution

Neutral solution

Basic solution

Incr

easi

ng

ly A

CID

IC(H

igh

er c

on

cen

trat

ion

of

H+)

Incr

easi

ng

ly B

AS

IC(L

ow

er

con

cen

trat

ion

of

H+)

NEUTRAL[H+] = [OH–]

Lemon juice; gastric juice

Grapefruit juice

Tomato juice

Urine

PURE WATER

Seawater

Milk of magnesia

Household ammonia

Household bleach

Oven cleaner

Human blood

H+

OH–

• Cells are kept close to pH 7 by buffers

• Buffers are substances that resist pH change

– They accept H+ ions when they are in excess and donate H+ ions when they are depleted

– Buffers are not foolproof

• Some ecosystems are threatened by acid precipitation

• Acid precipitation is formed when air pollutants from burning fossil fuels combine with water vapor in the air to form sulfuric and nitric acids

Why should I care? Acid rain threatens the environment

– These acids can kill fish, damage buildings, and injure trees

– Regulations, new technology, and energy conservation may help us reduce acid precipitation

• In a chemical reaction:

– reactants interact

– atoms rearrange

– products result

Chemical reactions rearrange matter

REARRANGEMENTS OF ATOMS

2 H2+ O2

2 H2O

• Life’s structural and functional diversity results from a great variety of molecules

• A relatively small number of structural patterns underlies life’s molecular diversity

INTRODUCTION TO ORGANIC COMPOUNDS AND THEIR POLYMERS

• A carbon atom forms four covalent bonds

– It can join with other carbon atoms to make chains or rings

Life’s molecular diversity is based on the properties of carbon

Structuralformula

Ball-and-stickmodel

Space-fillingmodel

Methane

The 4 single bonds of carbon point to the corners of a tetrahedron.

• Functional groups are the groups of atoms that participate in chemical reactions

– Hydroxyl groups are characteristic of alcohols

– The carboxyl group acts as an acid

Functional groups help determine the properties of organic compounds

Biological Molecules

Biological molecules are typically large molecules constructed from smaller subunits.

Monomer: single subunit

(mono = 1; -mer = unit)

Polymer: many units

(poly = many)

• Cells link monomers to form polymers by dehydration synthesis

1 2 3

Unlinked monomer

Removal ofwater molecule

1 2 3 4

Longer polymer

Short polymer

• Polymers are broken down to monomers by the reverse process, hydrolysis

Coating of capture strand

1 2 3

Addition ofwater molecule

1 2 3

4

• Carbohydrates are a class of molecules

– They range from small sugars to large polysaccharides

– Polysaccharides are long polymers of monomers

CARBOHYDRATES

Examples: sugars, starch, glucose

Function: Carbohydrates are good energy storage molecules.

• Monosaccharides are single-unit sugars

• These molecules typically have a formula that is a multiple of CH2O

• Each molecule contains hydroxyl groups and a carbonyl group

• Monosaccharides are the fuels for cellular work

Monosaccharides are the simplest carbohydrates

• The monosaccharides glucose and fructose are isomers

– They contain the same atoms but in different arrangements

Glucose Fructose

• Many monosaccharides form rings, as shown here for glucose

Abbreviatedstructure

• Monosaccharides can join to form disaccharides, such as sucrose (table sugar) and maltose (brewing sugar)

Cells link single sugars to form disaccharides

Glucose Glucose

Maltose

Sucrose

• These large molecules are polymers of hundreds or thousands of monosaccharides linked by dehydration synthesis

Polysaccharides are long chains of sugar units

• Starch and glycogen are polysaccharides that store sugar for later use

• Cellulose is a polysaccharide in plant cell walls

Figure 3.7

Starch granules in potato tuber cells

Glucosemonomer

STARCH

GLYCOGEN

CELLULOSE

Glycogen granules in muscle tissue

Cellulose fibrils ina plant cell wall

Cellulosemolecules

Carb video next slide

• These compounds are composed largely of carbon and hydrogen

– They are not true polymers

– They are grouped together because they do not mix with water

Lipids include fats, which are mostly energy-storage molecules

• Fats are lipids whose main function is energy storage

– They are also called triglycerides

• Phospholipids are a major component of cell membranes

• Waxes form waterproof coatings

• Steroids are often hormones

Phospholipids, waxes, and steroids are lipids with a variety of functions

Lipid video next

• Proteins are involved in – cellular structure

– movement

– defense

– transport

– communication• Mammalian hair is composed of structural

proteins

• Enzymes regulate chemical reactions

• “All enzymes are proteins but not all proteins are enzymes!”

PROTEINSProteins are essential to the structures and activities

of life

• Proteins are the most structurally and functionally diverse of life’s molecules

– Their diversity is based on different arrangements of amino acids

Proteins are made from just 20 kinds of amino acids

• Each amino acid contains:

– an amino group

– a carboxyl group

– an R group, which distinguishes each of the 20 different amino acids

Aminogroup

Carboxyl (acid)groupFigure 3.12A

• Cells link amino acids together by dehydration synthesis

• The bonds between amino acid monomers are called peptide bonds

Amino acids can be linked by peptide bonds

Amino acid Amino acid Dipeptide

Dehydrationsynthesis

Carboxylgroup

Aminogroup

PEPTIDEBOND

• A protein, such as lysozyme, consists of polypeptide chains folded into a unique shape

– The shape determines the protein’s function

– A protein loses its specific function when its polypeptides unravel

Overview: A protein’s specific shape determines its function

A protein’s primary structure is its amino acid sequence

Secondary structure is polypeptide coiling or folding produced by hydrogen bonding

Amino acid

Hydrogen bond

Alpha helix

Pleated sheet

Primarystructure

Secondarystructure

Tertiary structure is the overall shape of a polypeptide

Quaternary structure is the relationship among multiple polypeptides of a protein

Polypeptide(single subunitof transthyretin)

Transthyretin, with fouridentical polypeptide subunits

Tertiarystructure

Quaternarystructure

• Nucleic acids such and DNA and RNA serve as the blueprints for proteins

• They ultimately control the life of a cell

NUCLEIC ACIDSNucleic acids are information-rich polymers of

nucleotides

• The monomers of nucleic acids are nucleotides

Phosphategroup

Sugar

– Each nucleotide is composed of a sugar, phosphate, and nitrogenous base

Nitrogenousbase (A)

• The sugar and phosphate form the backbone for the nucleic acid

Sugar-phosphatebackbone

Nucleotide

• DNA consists of two polynucleotides twisted around each other in a double helix

– The sequence of the four kinds of nitrogenous bases in DNA carries genetic information Nitrogenous

base (A)

Basepair

• Stretches of a DNA molecule called genes program the amino acid sequences of proteins– DNA information is transcribed into RNA,

a single-stranded nucleic acid

– RNA is then translated into the primary structure of proteins

Nucleic Acid video next

Example of a Macromolecule

Monomer

polysaccharide (complex carbohydrate)

monosaccharide (simple sugar)

fat (a lipid) glycerol, fatty acid

protein amino acid

nucleic acid nucleotide

Summary: