Chemistry of Life

General Definitions

• Most of the Universe consists of matter and energy.

• Energy is the capacity to do work

• All matter is composed of basic elements that cannot be broken down to substances with different chemical or physical properties.

• Elements are substances consisting of one type of atom

• Atoms are the smallest particle into which an element can be divided.

• About 25 different chemical elements are essential to life

2.2 Life requires about 25 chemical elements

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

• Chemical elements combine in fixed ratios to form compounds

• Example: sodium + chlorine sodium chloride

2.3 Elements can combine to form compounds

General Definitions

• Subatomic particles• The proton is located in the center (or nucleus) of

an atom, each atom has at least one proton.

• Protons have a charge of +1

• The neutron also is located in the atomic nucleus (except in Hydrogen).

• The neutron has no charge

• The electron is a very small particle located outside the nucleus. It determines the chemical behavior of an atom.

• The charge on an electron is -1

• The number of protons in the atomic nucleus gives the atomic number.(H has 1, C has 6)

• 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

Figure 2.4B 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

Table 2.4

– The number of neutrons may vary – Variant forms of an element are called isotopes– Some isotopes are radioactive

Nuclear Decay• If a nucleus has too few or too many neutrons it may be

unstable, and will decay after some period of time. • For example, nitrogen-16 atoms (7 protons, 9 neutrons)

beta decay to oxygen-16 atoms (8 protons, 8 neutrons) within a few seconds of being created. – In this decay a neutron in the nitrogen nucleus is turned into

a proton and an electron by the weak nuclear force. The element of the atom changes because while it previously had seven protons (which makes it nitrogen) it now has eight (which makes it oxygen). Many elements have multiple isotopes which are stable for weeks, years, or even billions of years.

• Radioactive isotopes can be useful tracers for studying biological processes

• PET scanners use radioactive isotopes to create anatomical images

Radioactive isotopes can help or harm us

PET SCAN• Positron emission tomography, also called

PET imaging or a PET scan, is a diagnostic examination that involves the acquisition of physiologic images based on the detection of radiation from the emission of positrons.

• Positrons are tiny particles emitted from a radioactive substance administered to the patient.

The positron is the antiparticle or the antimatter counterpart of the electron. The positron has an electric charge of +1, a spin of 1/2, and the same mass as an electron.

Positron Emission• Positron emission is a type of beta decay,

sometimes referred to as "beta plus" (β+). In beta plus decay, a proton is converted, via the weak force, to a neutron, a beta plus particle (a positron) and a neutrino. Isotopes which emit positrons include Carbon-11, Nitrogen-13, Oxygen-15 and Fluorine-18;

• for example: these isotopes are used in positron emission tomography, a technique used for medical imaging.

http://en.wikipedia.org/wiki/Nuclear_decay

Electron-positron Collision

http://en.wikipedia.org/wiki/Electron-positron_annihilation

Image of the "annihilation" process known in elementary physics. It shows how a positron (e+) is emitted from the atomic nucleus together with a neutrino (v). The positron moves then randomly through the surrounding matter where it hits several different electrons (e-) until it finally loses enough energy that it interacts with a single electron. This process is called an "annihilation" and results in two diametrically emitted photons with a typical energy of 511 keV each.

How the procedure work?

• A radioactive substance is produced in a machine called a cyclotron and attached, or tagged, to a natural body compound, most commonly glucose, but sometimes water or ammonia.

• Once this substance is administered to the patient, the radioactivity localizes in the appropriate areas of the body and is detected by the PET scanner.

PET SCAN EQUIPMENT

• PET scanner has a hole in the middle and looks like a large doughnut.

• Within this machine are multiple rings of detectors that record the emission of energy from the radioactive substance in the body and permit an image to be obtained.

Inside the PET scanner

http://en.wikipedia.org/wiki/Annihilation

During the annihilation process two photons are emitted in diametrically opposing directions. These photons are registered by the PET as soon as they arrive at the detector ring. After the registration, the data is forwarded to a processing unit

How to separate healthy tissue from cancerous?

• Different colors or degrees of brightness on a PET image represent different levels of tissue or organ function.

• For example, because healthy tissue uses glucose for energy, it accumulates some of the tagged glucose, which will show up on the PET images. However, cancerous tissue, which uses more glucose than normal tissue, will accumulate more of the substance and appear brighter than normal tissue on the PET images.

Computed Tomography + PET

Image fusion readily localized tumor location in the spleen (arrow) in this patient with lymphoma(green arrowheads indicate normal physiologic activity in the bowel and kidney).

Unified Image

• 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

2.6 Electron arrangement determines the chemical properties of an

atom

Electrons and energy

From: Life: The Science of Biology, 4th

Edition, by Sinauer Associates

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

Figure 2.6

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)

Where does table salt come from?

• Supermarket?

• Please pass the NaCl…

• 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

Figure 2.7A

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 (cubic structure)

Figure 2.7B

Na+

Cl–

Halite (NaCl)

• Halite, sodium chloride, is found naturally in huge geologic deposits of salt minerals left over from the slow evaporation of ancient seawater.

http://www.science-education.org/classroom_activities/chlorine_compound/nacl.html

"Na" stands for "natrium," the Latin word for sodium.

Halophytes

• True halophytes are plants that thrive when given water having greater than 0.5% NaCl.

• They are salt-resistant!

Sabal palmetto shows remarkable tolerance of salt, even being able to grow where washed by sea water at high tide

• 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

Formation of covalent bonds

Methane CH4

From: Life: The Science of Biology, 4th

Edition, by Sinauer Associates

• Molecules can be represented in many ways

Table 2.8

Bonds

Molecules

• http://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.01a.pdf

• http://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.01b.pdf

• 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 moleculeTHE 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

Figure 2.9

(–)

O

(–)

(+)(+)

H H

Water

Water

• The charged regions on water molecules are attracted to the oppositely charged regions on nearby molecules– This attraction forms

weak bonds called hydrogen bonds

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

Hydrogen bond

• 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

• It takes a lot of energy to disrupt hydrogen bonds– Therefore water is able to absorb a great deal of heat

energy without a large increase in temperature– As water cools, a slight drop in temperature releases a

large amount of heat

Water’s hydrogen bonds moderate temperature

• Molecules in ice are farther apart than those in liquid water

Ice is less dense than liquid water

Hydrogen bond

ICEHydrogen bonds are stable

LIQUID WATERHydrogen bonds constantly

break and re-form

– Ice is therefore less dense than liquid water, which causes it to float

– If ice sank, it would seldom have a chance to thaw– Ponds, lakes, and oceans would eventually freeze

solid

• Solutes whose charges or polarity allow them to stick to water molecules dissolve in water– They form

aqueous solutions

Water is a versatile solvent

Figure 2.14

Ions in solution

Salt crystal

Cl–

Na+

Cl–

–

– –

–

–Na+

+

+

+

+

http://www.accessexcellence.org/RC/VL/GG/garland_PDFs/Panel_2.02b.pdf

• 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: – 0-7 is acidic – 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

Figure 2.15

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

Common Buffers Used in Biology

http://www.stolaf.edu/people/giannini/flashanimat/water/weakacid.swf

http://www.stolaf.edu/people/giannini/biological%20anamations.htmlhttp://www.chembio.uoguelph.ca/educmat/chm19104/chemtoons/chemtoons.htm

Cell’s composition

• Water• Inorganic ions• Organic ions

Inorganic ions

• Na• K• Mg• Ca• Cl• HPO4• HCO3

Organic ions

• formed by the actions of living things; and have a carbon backbone.

• carbon can make covalent bonds with another carbon atom, carbon chains and rings that serve as the backbones of organic molecules are possible.

Organic ions

• Chemical bonds store energy. The C-C covalent bond has 83.1 Kcal (kilocalories) per mole, while the C=C double covalent

bond has 147 Kcal/mole. • Each organic molecule group has small

molecules (monomers) that are linked to form a larger organic molecule (macromolecule). Monomers can be joined together to form polymers that are the large macromolecules made of three to millions of monomer subunits.

Macromolecules

• Carbohydrates (simple sugar)

• Lipids (fatty acids)

• Proteins (amino acids)

• Nucleic acids (nucleotides)