Chemistry for Bio 9

Which of the following is/are properties of life?

1. Cellular structure 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 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

Some isotopes are common, others rare

Many Isotopes for an element can exist; radioisotopes are radioactive

Radioisotopes can be used in medical diagnosis- Radioisotopes of iodine target

the thyroid gland

How is atomic weight different from atomic mass?

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

mass number (atomic mass) of sodium?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

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

Electron cloud model

• Currently accepted model of atomic structure

• 90% probability cloud• Mostly empty space• Unfilled orbitals found

in unstable, reactive elements

• Therefore, orbitals influence bonding

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

Intramolecular Chemical Bonds: Ionic, Covalent, and the formation of molecules

Atoms are stable when their valence shells are filled with electrons

• What atoms are these?

• How could they satisfy their valence shells?

Noble gases have a stable electron structure

• Their outer orbitals have a full complement of electrons

• Noble gases are very unreactive

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, forming

ions

LE 2-7

Transfer ofelectron

NaSodium atom

ClChlorine atom

Na

Sodium ionCl

Chloride ion

Sodium chloride (NaCl)

Ions

• Ions- Charged atoms or molecules

• Anion- negative ion• Cation- positive ion• Ionization- reaction

producing ions• Salt- a neutral

compound comprised of ions

LE 2-7a-2

Na

Sodium ionCl

Chloride ion

Sodium chloride (NaCl)

LE 2-7b

Na

Cl

The nucleus of an atom contains

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

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

Covalent bonds hold together the macromolecules of life

• 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

Many chemical reactions solely involve exchange of covalent bonding partners

Chemical reactions performed by your body create essential molecules your body needs

Beta-carotene Vitamin A(2 molecules)

Electronegativity and its effect on chemical bonds

Ionic bonds, covalent bonds, and intermolecular forces

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

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

dissolves like”)

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

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 determine many of water’s unique properties

• H-bonds can form a lattice (ice)

• H-bonds require much energy (usually heat) to break

• H-bonds give water surface tension

Hydrogen bond

Hydrogen Bonds help to make water cohesive, allowing water surface tension and 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

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

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

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-]

Because Oxygen is much more electronegative than Hydrogen,

water can occasionally Ionize

• H2O H+ + OH-

• Also called dissociation• Ions quickly reform into water:

– H+ + OH- H2O

• Approx 1 in 10,000,000 water molecules is dissociated at any given time (that is, 10-7)

Other substances ionize

• Usually ionic compounds• Many ionize completely• Salt: NaCl Na+ + Cl-

• Hydrochloric acid: HCl H+ + Cl-

• Sodium Hydroxide: NaOH Na+ + OH-

• Substances which ionize can affect the pH of a water solution

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- cause burns• Bases remove [H+] from water (or donate [OH-]

to water) – often have a slimy feel• Strong acids & bases are ~equally nasty• Proteins are sensitive to small changes in pH

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

The Relationships between Two Different Drinking Water Fluoride Levels, Dental Fluorosis and Bone

Mineral Density of Children• S.R. Grobler*, A.J. Louw, U.M.E. Chikte, R.J. Rossouw and T.J. van W. Kotze Oral and Dental Research Institute, Faculty of

Dentistry, University of the Western Cape, Republic of South Africa

Abstract: This field study included the whole population of children aged 10–15 years (77 from a 0.19 mg/L F area; 89 from a 3.00 mg/L F area), with similar nutritional, dietary habits and similar ethnic and socioeconomic status. The fluoride concentration in the drinking water, the bone mineral content, the bone density and the degree of dental fluorosis were determined. The left radius was measured for bone width, bone mineral content, and bone mineral density. The mean fluorosis score was 1.3 in the low fluoride area and 3.6 in high fluoride area. More than half the children in the low fluoride area had no fluorosis (scores 0 and 1) while only 5% in the high fluoride area had none. Severe fluorosis (30%) was only observed in the high fluoride area. The Wilcoxon Rank Sum Test indicated that fluorosis levels differed significantly (p < 0.05) between the two areas. No relationships were found between dental fluorosis and bone width or between fluorosis and bone mineral density in the two areas (Spearment Rank correlations). A significant positive correlation was found in the high fluoride area between bone mineral density over age. In the 12-13 and 13-14 year age groups in the high fluoride area, girls had higher bone mineral densities. However, a significant negative correlation (p<0.02) was found in low fluoride area (0.19 mg/L F) over age.

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

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