Chemistry for Bio 11

Chemistry is relevant to Biological Concepts

• All Living things are made of matter• The interactions of matter are described by

chemical principles• Biolgists are interested in:

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

Biochemical reactions

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

• Even the simplest living things contain impossibly complex pathways

Complex biological molecules

• All living things are made of complex macromolecules

• Chemical principles rule their assembly

Chemical energy

Photosynthesis creates molecules rich in energy:• 6CO2(g)+ 6H2O(l) + hν C6H12O6(s) + 6O2(g)

The Chemical Environment

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

• pH, salinity and other chemical factors influence

Basic principles of chemistry

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–

Elements are defined by the number of their protons

• There are 92 naturally occurring elements

• Many others have been synthesized

Atomic number: # protonsAtomic mass: protonsIsotopes- different atoms of

same element, with different # neutrons

Atomic weight: Naturally occurring average of isotopes of a substance

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

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 number of neutrons in atoms is variable

• Isotopes• Some isotopes are

stable, others are radioactive

Isotopes of carbon have important applications in biology and archaeology

Other radioactive isotopes are also important

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

Molecules, compounds, chemical reactions, and bonding

Elements combine in chemical reactions to form compounds

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

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

Covalent (incl. polar and nonpolar) and Ionic

Atoms are stable when their outer shells are filled with electrons

• Shell 1: Holds 2 electrons• Shell 2: Holds 8• Shell 3: Holds 8• Hydrogen- 1p, 1e, seeks a

second electron in its outermost shell

• Carbon seeks 4• The electrons in the

outermost shell are called valence electrons

Noble gases have a stable electron structure

• Their outer orbitals have a full complement of electrons

• Noble gases are very unreactive

In ionic bonding, an atom takes an electron from another atom, forming 2

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

In covalent bonding, pairs of valence electrons are shared, and molecules are formed

LE 2-17a

2 H2 O2 2 H2O

LE 2-6b

Nitrogen (N)Atomic number = 7

Oxygen (O)Atomic number = 8

In neutral molecules, carbon always forms 4 bonds

Structuralformula

Ball-and-stickmodel

Space-fillingmodel

Methane

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

LE 3-1b

Ethane Propane

Carbon skeletons vary in length.

LE 3-1c

Butane Isobutane

Skeletons may be unbranched or branched.

LE 3-1d

1-Butene 2-Butene

Skeletons may have double bonds, which can vary in location.

LE 3-1e

Skeletons may be arranged in rings.

Cyclohexane Benzene

Organic Chemistry

• The chemistry of carbon• Hydrocarbons are the

most basic example– Combustible– Can form rings

The variety of carbon compounds is limitless

All terrestrial life is based on carbon

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

Electronegativity determines properties of covalently bonded

molecules

Electronegativity = “electron greediness”

• Atoms in covalently bonded molecules do not always share electrons equally

• This creates polar molecules• Polar regions of water

molecules interact to form hydrogen bonds

• Hydrogen bonds: weak/temporary intermolecular forces

Hydrogen bonding in water determine many of water’s unique properties

• H-bonds can form a lattice (ice)

• H-bonds require much energy to break

• H-bonds give water surface tension

Hydrogen bond

Water dissolves many ionic compounds (“like dissolves like”)

Figure 2.11

Figure 2.12

LE 2-13

Hydrogen bond

Ice

Hydrogen bonds are stable

Liquid water

Hydrogen bondsconstantly break and re-form

pH is a measure of acidity/basicity

• pH = -log [H+] (logarithmic scale)• pH 1 6.9: acid• pH 7.114: base• pH 7 neutral• Acids donate [H+] to water• Bases remove [H+] from water (or donate [OH-]

to water)• Proteins are very 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 )

Figure 2.16a

Figure 2.16b