Biology 121 – Concepts of BiologyDr. Fritzler

Chapter 2Chapter 2

Essential Chemistry for Biology

Start with Atoms• Atoms

– Fundamental building blocks of matter

– Composed of three smaller subatomic particles

– Positively charged _______________

– Uncharged (neutral) _______________

– Negatively charged _______________

– # _______________ = # _______________

– Protons and neutrons are part of the nucleus

– Electrons move around the nucleus

Nucleus

Protons

Neutrons

Electrons

Nucleus

Cloud of negativecharge 2 electrons

2

2

2

Proton• Positive charge• Determines element

Neutron• No charge• Determines isotope

Electron• Negative charge• Participates in chemical reactions• Outer-shell electrons determine chemical behavior

Nucleus• Consists of neutrons and protons

Atom

Elements• A pure substance consisting of atoms with the

same number of protons

• _______________ _______________ = quantity of protons (unique for each element)

– Ex: Carbon = 6

Mercury HgCopper Cu Lead Pb

H

Rb

K

Na

Li

Fr

Cs

Sr

Ca

Mg

Be

Ra

Ba

Y

Sc

Ac

La

Zr

Ti

Rf

Hf

Nb

V

Db

Ta

Mo

Cr

Sg

W

Tc

Mn

Bh

Re

Ru

Fe

Hs

Os

Rh

Co

Mt

Ir

Pd

Ni

Uun

Pt

Xe

Kr

Uuo

Rn

Ag

Cu

Uuu

Au

Cd

Zn

Uub

Hg

Ar

Ne

In

Ga

Tl

Al

B

Sn

Ge

Uuq

Pb

Si

C

Sb

As

Bi

P

N

Te

Se

Uuh

Po

S

O

I

Br

At

Cl

F

He

Th

Ce

Pa

Pr

U

Nd

Np

Pm

Pu

Sm

Am

Eu

Lr

Lu

Cm

Gd

Bk

Tb

Cf

Dy

Es

Ho

Fm

Er

Md

Tm

No

Yb

6

C12

Elements•There are 92 naturally occurring elements on

Earth.

• 25 elements are essential to life.

• Four elements make up about 96% of the weight of the human body:

– Oxygen

– Carbon

– Hydrogen

– Nitrogen

Carbon C: 18.5%

Hydrogen H:9.5%

Nitrogen N:3.3%

Calcium Ca: 1.5%

Trace elements: less than 0.01%

Boron B Manganese Mn

Oxygen O:65.0%

Magnesium Mg: 0.1%

Phosphorus P: 1.0%

Potassium K: 0.4%

Sulfur S: 0.3%

Sodium Na: 0.2%

Chlorine Cl: 0.2%

Cobalt CoChromium Cr

Iron FeIodine IFluorine FCopper Cu Silicon Si

Zinc ZnVanadium VTin Sn

Molybdenum MoSelenium Se

Trace Elements•Occur in smaller amounts and are essential

for life

•Deficiencies cause disease

– Example: An Iodine deficiency causes goiter

Isotopes• Atoms of the same element that differ in the

number of neutrons

• Example: 12C (6p and 6n), 13C (6p and 7n), 14C (6p and 8n)

• _______________ _______________ = protons plus neutrons

H

Rb

K

Na

Li

Fr

Cs

Sr

Ca

Mg

Be

Ra

Ba

Y

Sc

Ac

La

Zr

Ti

Rf

Hf

Nb

V

Db

Ta

Mo

Cr

Sg

W

Tc

Mn

Bh

Re

Ru

Fe

Hs

Os

Rh

Co

Mt

Ir

Pd

Ni

Uun

Pt

Xe

Kr

Uuo

Rn

Ag

Cu

Uuu

Au

Cd

Zn

Uub

Hg

Ar

Ne

In

Ga

Tl

Al

B

Sn

Ge

Uuq

Pb

Si

C

Sb

As

Bi

P

N

Te

Se

Uuh

Po

S

O

I

Br

At

Cl

F

He

Th

Ce

Pa

Pr

U

Nd

Np

Pm

Pu

Sm

Am

Eu

Lr

Lu

Cm

Gd

Bk

Tb

Cf

Dy

Es

Ho

Fm

Er

Md

Tm

No

Yb

6

C12

Radioactive Isotopes• _______________– atoms with the same #

protons, but different # neutrons

• Radioactive isotopes are not stable

– Nucleus (protons and neutrons) spontaneously decays into other elements and electrons are emitted

• Can be used as tracers and attached to molecules

– Example: Attach a tracer to glucose to monitor brain activity (PET scan)

Positron-Emission Tomography (PET) Scan

Electron Arrangement and the Chemical Properties of Atoms• Atoms acquire, share and donate electrons

• Some atoms do so easily, others do no

– The number and arrangement of electrons in atoms dictate acquisition, sharing and donation

Electrons and Energy Levels• Atoms have the same # electrons as protons

• Electrons orbit the nucleus of an atom in specific electron shells

• The farther an electron is from the nucleus, the greater its energy

• The number of electrons in the outermost shell determines the chemical properties of an atom

Shell Models

First electron shellcan hold 2 electrons

Outer electron shellcan hold 8 electrons

Hydrogen HAtomic number = 1

Carbon CAtomic number = 6

Nitrogen NAtomic number = 7

Oxygen OAtomic number = 8

Electron

Electron Interactions• Atoms whose outermost shell is not completely

full tends to interact with other atoms

– They donate, accept, or share electrons to eliminate vacancies

– Those with the outermost shell filled are chemically inactive and very stable

sodium11p+ , 11e-

chlorine17p+ , 17e-

argon18p+, 18e-

Electrical Charge• An atom with equal numbers of protons and

electrons has no net charge

• _______________ are atoms that carry a charge

– Have either gained (negatively charged) or lost (positively charged) electrons

Sodium atom11p+

11e-

no netCharge (weakly electro-negative)

Sodium ion11p+

10e-

net positivecharge

electronloss

Chlorine atom17p+

17e-

no netCharge (highly electronegative)

Chlorine ion17p+

18e-

net negativecharge

electrongain

Molecules and Mixtures• Molecule – forms when > 2 atoms join in

chemical bonds

• Chemical Bond – attractive force between atoms due to interactions of electrons

• Compounds – molecules consisting of > 2 elements (Ex: water is 2H bound to 1O)

• Mixture – elements intermingle but do not bind (Ex: Sugar into water – sugar dissolves, no bonds formed)

Chemical Bonding and Molecules• Chemical reactions enable atoms to donate,

acquire or share electrons to complete their outer shells.

• Chemical reactions usually result in atoms interacting through three types of bonds

– Ionic bond

– Covalent Bond

– Hydrogen Bond

Ionic Bonds• Strong association between a positive ion and a

negative ion (attraction of opposite charges)

A crystal of table salt isa cubic lattice of many sodiumions and chloride ions.

The mutual attraction ofopposite charges holds thetwo kinds of ions togetherclosely in the lattice.

a

b

A crystal of table salt isa cubic lattice of many sodiumions and chloride ions.

The mutual attraction ofopposite charges holds thetwo kinds of ions togetherclosely in the lattice.

a

b

Outer shellhas 1 electron

Outer shellhas 7 electrons

The outer electron is strippedfrom sodium and completesthe chlorine atom’s outer shell

NaSodium atom

ClChlorine atom

Completeouter shells

The attractionbetween theions—an ionicbond—holdsthem together

Na

Sodium ionCl

Chlorine ion

Sodium chloride (NaCl)

See Animation on Ionic Bonds(Posted to MyCourses)

Covalent Bonds• Form when two atoms share > 1 pairs of outer-

shell electrons

• _______________ covalent bond

– Atoms share electrons equally

• _______________ covalent bond

– Electrons are shared unequally

– Produces polar molecules – one end slightly negative, other slightly positive

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

Molecular hydrogen (H—H)

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

Molecular oxygen (O=O)

Two hydrogen atoms each share anelectron with an oxygen atom in twopolar covalent bonds. The oxygenexerts a greater pull on the sharedelectrons, so it has a slight negativecharge. Each hydrogen has a slightpositive charge.

Water molecule (H—O—H)

See Animation on Covalent Bonds(Posted to MyCourses)

Hydrogen Bonds•Attraction between a _______________ atom

and another atom

– Both have their own separate covalent bonds

•Are not chemical bonds

– Do not make atoms into molecules

– Weaker than ionic or covalent, and easily form or break

– Used to stabilize structures of large molecules

Hydrogen Bonds• Water is a compound in which the electrons in its

covalent bonds are shared unequally.

– This causes water to be a polar molecule, one with opposite charges on opposite ends.

2 H2 2 H2OO2

Hydrogen

gas

Oxygen

gas

Water

Hydrogen Bonds• The polarity of

water results in weak electrical attractions between neighboring water molecules.

– These interactions are called hydrogen bonds.

Hydrogen bond

Water – The Most Important Molecule

• Without water, there would be no life

• Life on Earth began in water and evolved there for 3 billion years

– Modern life remains tied to water

– Your cells are composed of 70%–95% water

• The abundance of water is a major reason Earth is habitable

Polarity of the Water Molecule• Water molecules are polar

– Form hydrogen bonds with each other and with other polar molecules

– Hydrophilic (water-loving) substances are polar– Hydrophobic (water-dreading) substances are

nonpolar (ex. Oils)

+ +

HH

O

-−slight negative charge on the

oxygen atomThe positive and negative charges balance each other; overall, the molecule carries no charge.

slight positive charge on the hydrogen

atoms

See Animation on Water Structure(Posted to MyCourses)

Water’s Life-Giving Properties• The polarity of water molecules and the

hydrogen bonding that results explain most of water’s life-supporting properties:

– Water molecules stick together.

– Water has a strong resistance to change in temperature.

– Frozen water floats.

– Water is a common solvent for life.

The Cohesion of Water• Hydrogen bonding provides _______________

(resistance of molecule separation)

Microscopic tubes

Cohesion due tohydrogen bondsbetween watermolecules

Evaporation from leaves drives the flow of water up and through the

plant

SE

M

Flow

of

wat

er

See Animation on Water Transport

(Posted to MyCourses)

Water Moderates Temperature• Because of hydrogen bonding, water has a strong

resistance to temperature change.

• Heat and temperature are related, but different.

– _______________ is the amount of energy associated with the movement of the atoms and molecules in a body of matter.

– _______________ measures the intensity of heat.

• Water can absorb and store large amounts of heat while only changing a few degrees in temperature.

•Earth’s giant water supply causes temperatures to stay within limits that permit life.

•Evaporative cooling removes heat from the Earth and from organisms.

The Biological Significance of Ice Floating

• When water molecules get cold enough, they move apart, forming ice.

• A chunk of ice has fewer molecules than an equal volume of liquid water.

• Ice floats because it is less dense than the liquid water around it. Hydrogen bond

Liquid water Ice

• If ice did not float, ponds, lakes, and even the oceans would freeze solid.

• Life in water could not survive if bodies of water froze solid.

The Biological Significance of Ice Floating

Water as the Solvent of Life• A _______________ is a liquid consisting of a

homogeneous mixture of two or more substances.

– The dissolving agent is the _______________.

– The dissolved substance is the _______________.

• When water is the solvent, the result is an aqueous solution.

Sodium ion in solution

Chloride ion in solution

Salt crystal

Na

Na

Cl–Cl–

Solvents form “spheres of hydration” around solutes

Acids, Bases, and pH• Ions are dissolved in fluids both inside and

outside each living cell

• _______________ ions are the most influential

– Chemically active

– Tons of them – they are everywhere

How do Acids and Bases Differ?• A chemical compound that releases H+ to

solution is an _______________.

• A compound that accepts H+ and removes it from solution is a _______________.

Basicsolution

Neutralsolution

Acidicsolution

Acids, Bases, and pH• pH scale

– Indicates hydrogen ion (H+) concentration of a solution

– Ranges from 0 (most acidic, most H+) to 14 (most basic or alkaline, least H+)

– At pH 7 (neutral) H+ and OH- concentrations are equal

Neutral

Basic

Acidic

pH scale

14

7

0

Lower H+

concentration

H+ = OH–

Greater H+

concentration

Buffers Against Shifts in pH• Enzymes and biological molecules function

properly only in a narrow range of pH

• Cells must quickly respond to pH shifts otherwise cellular processes halt

• Most cells and body fluids are buffered in order to maintain a constant pH

• A set of chemicals (an acid or base AND its salt) that keeps the pH of a solution stable

• A “salt” is any compound that dissolves easily in water, and releases ions other than H+ and OH-

– Form when an acid interacts with a base (Ex: NaCl)

HCl + NaOH NaCl + H20

Na+ + Cl- + H2O

Buffer System

• Buffers help maintain homeostasis

• Most biological processes proceed only within a narrow pH range, usually near neutrality (blood pH = 7.3 – 7.5)

– Acidosis: decline in blood pH

– Alkalosis: increase in blood pH

– Both are potentially lethal

Functions of Buffer Systems

Evolution Connection: The Search for Extraterrestrial Life• If life similar to ours has

evolved elsewhere in the universe, then it too would depend upon water.

• Recent NASA missions to Mars have detected evidence that liquid water flowed over the planet’s surface.