Chemistry for Bio 9

Spring 2011

Which of the following is/are properties of life?

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1. a complex organization 2. the ability to take in energy and use it 3. the ability to respond to stimuli from the

environment 4. the ability to reproduce 5. All of the choices are correct.

Lecture outline

• Chemistry- definition, scope, and relevance to biology

• Classification of matter• The atom and subatomic particles• Chemical bonding & reactions• Chemistry of water• Acids, Bases, and the pH scale

Chemistry is relevant to Biological Concepts

• Chemistry is the study of matter and its interactions

• All Living things are made of matter• Biolgists are interested in:

– Complex biological molecules– Chemical energy– Biochemical reactions– The chemical environment

Complex biological molecules

• All living things are made of complex macromolecules

• Chemical principles rule their assembly

Chemical energyPhotosynthesis creates molecules rich in energy:• 6CO2(g)+ 6H2O(l) + hν C6H12O6(s) + 6O2(g) • Earth has been transformed by chemical

reactions peformed by living things

Biochemical reactions

• All living things are collections of a vast number of chemical reactions

• Even the simplest living things contain impossibly complex pathways

The Chemical Environment

• The physical properties of water determine the fate of life on earth

• pH, salinity and other chemical factors influence

• Living things are profoundly influenced by their chemical environment

Chemical reactions performed by living things have transformed earth over billions

of years of its history

Classification of matter

Classification of matter

Mixtures can be homogeneous or heterogeneousMixtures can vary in composition of their ingredientsCompounds are defined substances with proportional amounts of ingredients: water, carbon dioxide, etc.Elements cannot be broken down into ingredients by chemical processes

Basic principles of chemistry

The periodic table is an organized display of all the elements in the universe

The Structure of the Atom

Subatomic particles- protons, neutrons electrons

Orbitals and the nucleus

All matter is comprised of atoms

• Atoms themselves are made of 3 kinds of subatomic particles– Protons– Neutrons– Electrons

• Protons and neutrons reside in the nucleus

All matter is ultimately comprised of atoms

• Atoms are the smallest individual unit of matter

• Atoms are comprised of protons, neutrons and electrons

Proton: Charge= +1, Mass= 1

Neutron: Chg= 0, mass= 1Electron: Chg = -1, mass= ~0Mass= p + nCharge = p - e

LE 2-4a

2

2

2

Protons

Neutrons

Electrons

Helium atom

Massnumber = 4

6

6

6

Protons

Neutrons

Electrons

Carbon atom

Massnumber = 12

Electroncloud

Nucleus

2e–

6e–

Reading the Periodic Table

Elements are defined by the number of their protons

• There are 92 naturally occurring elements

• Many others have been synthesized

Atomic number = # protonsAtomic mass (mass number) =

protons + neutrons of an individual atom

Atomic weight= Naturally occurring average of isotopes of a substance

The number of neutrons in atoms of a single element is variable

• Isotopes are variants of an element, differentiated by numbers of neutrons

• Some isotopes are stable, others are radioactive (radioisotopes)

Some isotopes are common, others rare

Many Isotopes for an element can exist; radioisotopes are radioactive

Radioisotopes can be used as tracers in medical diagnosis- Radioisotopes of

iodine target the thyroid gland

How is atomic weight different from atomic mass?

How is atomic weight different from atomic mass?

All carbon atoms have 6 protonsMost, but not all, carbon atoms have 6 neutrons, and weigh 12 AMU (atomic mass units)Carbon atoms with 7 neutrons weigh 13 AMUCarbon atoms with 8 neutrons weigh 14 AMU (and are radioactive)

The sodium atom contains 11 electrons, 11 protons, and 12 neutrons. What is the

mass number (atomic mass) of sodium?

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10%

62%

24%

1. 0 2. 11 3. 22 4. 23 5. 34

96% of human tissue is comprised of 6 elements

• Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous, Sulfur (CHNOPS)

• 25 elements serve known functions in the body, incl. Ca, K, Na, Cl, Mg, Fe

• Trace elements are essential, but in small quantities

A compound

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17%

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83%1. A) is a pure element. 2. B) is less common than a pure element. 3. C) contains two or more elements in a fixed

ratio. 4. D) is exemplified by sodium. 5. E) is a solution.

Atomic structure• Protons and electrons in

the nucleus• Electrons orbit around• Bohr atom- classic

model featuring electrons in “planetary” orbitals

• Each orbit holds a determined number of electrons (first holds two, 2nd and 3rd hold eight)

The second electron shell can hold a maximum of_____ electrons.

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1. 1 electron2. 2 electrons3. 4 electrons4. 8 electrons5. 16 electrons

Electrons in the outermost shell of an atom are called valence electrons

Atoms are stable when their outer valence shells are filled with electrons

The first valence shell holds 2 electronsThe 2nd and 3rd shells hold 8 electrons each

Intramolecular Chemical Bonds: Ionic bonds,

Covalent bonds, formation of molecules

Noble gases have a stable electron structure

• Their outer orbitals have a full complement of electrons

• Noble gases are very unreactive

Atoms are stable when their valence shells are filled with electrons

• What atoms are these?

• How could they satisfy their valence shells?

Elements combine in chemical reactions to form compounds

• Molecules- 2 or more atoms combined in specific ways• Compounds- different elements in a molecule, in exact,

whole-number ratios, joined by a chemical bond• 2 major kinds of intramolecular chemical bonds:

Covalent (incl. polar and nonpolar) and Ionic

In ionic bonding, an atom takes an electron from another atom

LE 2-7

Transfer ofelectron

NaSodium atom

ClChlorine atom

Na

Sodium ionCl

Chloride ion

Sodium chloride (NaCl)

Ions are charged atoms

• Ionic compounds are held together by the attraction of opposite charges

• Positive ion- cation (sodium)• Negative ion- anion (chloride)• Neutral ionic compounds are

called “salts” (NaCl is one kind of salt)

• Ionic comounds often form crystals

LE 2-7b

Na

Cl

The nucleus of an atom contains

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1. protons and neutrons. 2. protons and electrons. 3. only neutrons. 4. only protons. 5. only electrons.

What about two hydrogen atoms?

In covalent bonding, electrons are shared

• Atoms form as many bonds as they have vacancies in their outermost electron orbitals

• Atoms are bound together by the sharing of electrons

• Chemical reactions often involve the exchange of covalent bonds

LE 2-6b

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

Single, double and even triple bonds

can be formed• Bonds can be formed

between two of the same atoms, or two different atoms

• Covalent bonds fix two atoms together to form a molecular compound

In this way, a few elements can form all the molecules of the world

Covalent bonds hold together the macromolecules of life

• DNA, proteins, carbohydrates, etc- All held together by covalent bonds

Many chemical reactions solely involve exchange of covalent bonding partners

• Living things create macromolecular products for structure:

• 6CO2(g)+ 6H2O(l) + hν C6H12O6(s) + 6O2(g)

• Macromolecules as reactants are broken down for energy:

C6H12O6(s) + 6O2(g) 6CO2(g)+ 6H2O(l)

All the reactions of a living thing are called its metabolism

Electronegativity and its effect on chemical bonds

Polar and nonpolar moleculesHydrogen bonds

Electronegativity values can predict how atoms will bond

In covalent bonds, electrons do not always share time between bond partners equally

Comparisions of electronegativity• Na: 0.9• H: 2.1• C: 2.5• N: 3.0• Cl: 3.0• O: 3.5

Electronegativity = “electron greediness”

• Large differences in polarity of atoms in a bond creates polar molecules

• Relative electronegativity of Hydrogen and oxygen makes water a very polar molecule

• Polar- regions of positivity and negativity

• By Oxygen, water is (slightly) negative

• By Hydrogens, water is (slightly) positive

Intermolecular forces and the chemistry of water

Polarity and hydrophilicity,Nonpolarity and hydrophobicity,

hydrogen bonding, and the chemistry of water

The polarity of water allows hydrogen bonding

• Polar regions of water molecules interact to form hydrogen bonds

• Hydrogen bonds: weak/temporary intermolecular forces between positive and negative regions

• Inter- “between”• Intra- “within”

Water is a “universal solvent” and dissolves many polar and ionic compounds (“like

dissolves like”)

Other molecules can engage in H-bonding, w/ water or other substances

Hydrogen bonds hold together the two strands of a DNA double helix

Hydrogen bonding in water is the cause of many of water’s critical properties

Hydrogen Bonds help to make water cohesive, allowing water surface tension- water sticks to itself, holding droplets together and surfaces taut

When water H-bonds with other substances (like glass), adhesion results, causing capillary action

Capillary action allows redwoods to grow to heights over 300 feet

Just as heat breaks H-bonds, as water cools, more H-bonds form

Hydrogen bond

Ice

Hydrogen bonds are stable

Liquid water

Hydrogen bondsconstantly break and re-form

Because H-bonds have a fixed distance, the crystal lattice of water makes ice less dense

Hydrogen bonds require energy to break- water has a high specific heat

Water’s high specific heat allows evaporative cooling-and makes sweating an effective cooling mechanism

Due to water’s high specific heat, proximity to water has

a stabilizing effect on regional temperature

Water and hydrogen bonding

• Polar molecules are dissolved easily in water

• High specific heat allows evaporative cooling

• Crystal lattice of H-bonds causes ice to be less dense than liquid water, not more

• Hydrogen bonds give water surface tension

• Hydrogen bonds with other substances allow adhesion

Since ions do not share electrons, they may separate in solution

Water is a universal solvent, allowing many polar compounds to dissolve

Nonpolar molecules are mostly neutral

• C: 2.5, H: 2.1• Very few positive or negative

regions, if any• Hydrocarbons- compounds

solely made of hydrogen and carbon, e.g. fats, oils, & gas

• Nonpolar substances are hydrophobic and do not mix well with water

Acids, bases, and the pH scale

Ionic compounds dissolve in water, forming ions

• Many ionize completely• Salt: NaCl Na+ + Cl-

• Hydrochloric acid: HCl H+ + Cl-

• Sodium Hydroxide:NaOH Na+ + OH-

• Some (not all) substances which ionize affect the pH of a water solution

Like ionic compounds, water also forms ions sometimes

H2O ↔ H+ + OH-

• Spontaneously happens to water molecules

• 1/ 107 water molecules are ionized in distilled water

• In dH2O, [H+ ]= [OH-]

Hydrogen [H+] and Hydroxide [OH-] do not stay ionized for long, and quickly re-form into water

[H+] ions in solution is the cause of acidity[OH-] ions are the cause of basicity

Because pure H2O always forms [H+] ions and [OH-] in equal amounts, water is a neutral compound, neither acidic or basic

pH is a measure of acidity/basicity

• pH = -log [H+] (logarithmic scale)• pH 1 6.9: acid• pH 7.114: base• Acids donate [H+] to water• Bases remove [H+] from water –

often have a slimy feel• Strong acids & bases are ~equally

nasty• Proteins are sensitive to small

changes in pH

pH is a measure of acidity/basicity

• Acids donate [H+] to water• Bases remove [H+] from water

• Sodium Hydroxide:

– NaOH Na+ + OH-

• Hydrogen chloride: – HCl H+ + Cl-

• Which is acidic? Which is basic?

LE 2-15

Acidic solution

OH

H

HH

HOH

H H

H

OH

OH

OH

OH

OH

H

H

H

H

HH

I ncr

ea

sin

gl y

AC

IDI C

(Hi g

he

r c

on

c en

tra

t io

n o

f H

)Neutral solution

OH

OH

OH

OH

OH

OH

H

H

Basic solution

NEUTRALH

pH scale

Lemon juice, gastric juice

Grapefruit juice, soft drink

Tomato juice

Human urine

Pure water

Human blood

Seawater

Milk of magnesia

Household ammonia

Household bleach

Oven cleaner

Incr

ea

sin

gl y

BA

SIC

(Lo

we

r c

on

cen

tra t

i on

of

H )

Acid rain pollution can cause tremendous ecological damage

SO2 (g)+ H2O SO2·H2O SO2·H2O H++HSO3

- HSO3

- H++SO32-

Mechanism of acid rain

More effects of acid rain

Buffers can help control changes in pH

Water's surface tension and heat storage capacity is accounted for by its

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100%1. orbitals. 2. weight. 3. hydrogen bonds. 4. mass. 5. size.