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CHAPTER 2. Life’s Chemical Basis. Atoms. Element- fundamental substance consisting of only one type of atom. C, N, H, O are the most commonly occurring elements in the human body.

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chapter 2


Life’s Chemical Basis


Element- fundamental substance consisting of only one type of atom. C, N, H, O are the most commonly occurring elements in the human body.

There are 110 different elements, but only 92 naturally occurring ones. Numbers 93-110 are very unstable and degrade quickly.

you try it name the elements




You try it - Name the elements
  • Sodium
  • Nickel
  • Cesium
  • mercury
  • Matter – anything that takes up space and has mass
  • Subatomic particles – electron, protons, neutrons
levels of chemical organization
Levels of Chemical Organization
  • Subatomic particles
  • Atom
  • Molecules
what are atoms
What Are Atoms?
  • Smallest particles that retain properties of an element
  • Made up of subatomic particles:
    • Protons (+)
    • Electrons (-)
    • Neutrons (no charge)
    • Note: protons and neutrons themselves are now known to consist of still smaller particles called quarks.
structure of an atom
Structure of an Atom
  • Nucleus
    • Contains protons and neutrons
    • Protons- subatomic particle with a small positive charge (+)
    • Neutrons- subatomic particle with no charge (0)
structure of atoms
Structure of Atoms






structure of an atom11
Structure of an Atom
  • Shells around the nucleus of an atom contain electrons.
    • Electron- subatomic particle with a small negative charge (-)
    • An atom usually

contains equal

numbers of protons

and electrons. When

it doesn’t it’s called

an ion.

how to read the periodic table
How to Read the Periodic Table

See Appendix IV in back of textbook for good periodic table.

Atomic Number- number of protons in a nucleus of an atom. This defines which element the atom is. Always the smaller number.

atomic number protons
Atomic Number = Protons
  • Symbol No

O 8

Ca 20

Na 11

Cl 17

K 19

Fe 26

N 7

how to read a periodic table
How to Read a Periodic Table

Mass Number- total number of protons and neutrons in the atomic nucleus. The larger number.

Mass Number =Number of protons + Number of neutrons

you try it
You Try It!

Symbol Protons Neutrons Mass

O 8 8 16

Ca 20 ? 40

Na ? 12 23

Cl 17 ? 35

K ? 20 39

Fe 26 30 ?

N 7 ? 14

putting radioisotopes to work
Putting Radioisotopes to work
  • Isotope- atoms with different numbers of neutrons.

Isotopes have different mass numbers


  • Carbon 12 has 6 protons, 6 neutrons
  • Carbon 14 has 6 protons, 8 neutrons
  • Radioisotopes – an isotope that spontaneously emits energy in the form of subatomic particles and x-rays when its nucleus disintegrates
  • Radioactive decay – isotopes that the nucleus is disintegrating and transforming one element into another spontaneously. (three types)
  • Half life – the amount of time for ½ of the mass of an radioactive isotope to break down
  • Two isotopes of carbon
    • Carbon 12 (12C)and Carbon 14 (14C)
    • Carbon 14
      • Half life -Decay time is 5700 yrs
      • If you have 100 grams of Carbon 14

after 5700 yrs you have 50 grams carbon 14 and 50 grams Nitrogen 13


Decay example- The nucleus captures an electron which basically turns a proton into a neutron. Here's a diagram of electron capture with beryllium-7

  • Have an unstable nucleus that emits energy and particles
  • Radioactive decay transforms radioisotope into a different element
  • Decay occurs at a fixed rate (half-life)
    • Carbon-14 becomes N-14 at a specific rate
radioisotopes can be used in medicine ecology botany and many other scientific fields
A “tracer” is a molecule in which a radioisotope has been substituted for a more stable isotope and can then be “traced” by the energy it releases as it decays.Radioisotopes can be used in medicine, ecology, botany and many other scientific fields.
popcorn chemistry
Popcorn Chemistry
  • When will each kernel pop?
  • After it pops, can it even go back to being a kernel?
  • What is released during the popping?
Like popcorn, there is no way to know which radioisotope will degrade first!
  • Also like popcorn, once radioisotopes change, they can never return to their previous state.
When radioisotopes degrade, energy is released.
  • Machines that can “see” this energy can be used to follow the path of the radioisotopes as they travel through a system, each one releasing energy as they degrade.
radioactive tracers can be used in
Radioactive tracers can be used in:
  • PET scans
  • Pharmaceutical research
  • Metabolic studies
  • X-rays

Concentrations of radioactive tracer bound to monoamine oxidase B (MAO B). Red shows the highest concentration. Clearly, lower concentrations are seen in the smoker. MAO B helps regulate nerve function and blood pressure.


When atoms combine with atoms

  • Atoms acquire, share, donate electrons.
  • Whether one atom will bond with others depends on the number and arrangement of its electrons.
  • The atoms of some elements do this quite easily and other do not.
  • When an atom has one or more vacancies in orbitals, it interacts with other atoms by donating, accepting, or sharing electrons (forming chemical bonds).
  • Electrons occupy orbital's, or defined volumes of space around an atom’s nucleus.
  • Successive orbital's correspond to levels of energy, which become higher with distance from the atomic nucleus.
  • One or at most two electrons can occupy an orbital.
  • The atoms with vacancies in orbitals at their highest level tend to interact and form bonds with one another.



No vacancy

electron organization
Electron organization
  • First shell-

Lowest energy

Holds up to 2


  • Second shell

holds up to 8



A model atomic structure is a diagram with successively larger circles, or shells, that keep track of all electrons in the orbital at a given energy level.

Max number of electrons in each shell

Shell Number electrons

1 2

2 8

3 18

4 32






17p+ , 17e-


11p+ , 11e-


6p+ , 6e-


8p+ , 8e-


10p+ , 10e-


1p+ , 1e-


2p+ , 2e-

electron vacancies
Electron Vacancies
  • Unfilled shells make atoms likely to react
  • Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells


7p+ , 7e-


6p+ , 6e-


1p+ , 1e-

you do it draw the shell configuration for each of these
You do it - Draw the shell configuration for each of these:
  • Na
  • Chlorine
  • K
  • Neon
  • Ca
  • 2, 8, 1
  • 2, 8, 7
  • 2, 8, 18, 1
  • 2, 8
  • 2, 8, 18, 2


  • What are these elements?
  • Hint: It’s protons equal it’s atomic number, and since it is an atom so do the number of electrons.

What are these elements?

A= oxygen

B= aluminum

C= Nitrogen

periodic table
Periodic Table
  • Each element in a family or group on the Periodic Table has common properties
  • Examples
    • Valence electrons
    • Ion formation
  • Lose electrons
    • Valence electrons 1-4
      • Na = 1 valence = +1 ion
      • Be = 2 valence = +2 ion
      • B = 3 valence = +3 ion
      • C = 4 valence = +4 ion
  • Gain electrons
    • Valence electrons 4-7
      • C = 4 valence = -4 ion
      • N = 5 valence = -3 ion
      • O = 6 valence = -2 ion
      • F = 7 valence= -1 ion
When an atom or molecule loses electrons, it becomes positively charged.
    • For example, when Na loses an electron it becomes Na+.
  • Positively charged ions are called cations.
When an atom or molecule gains electrons, it becomes negatively charged.
    • For example when Cl gains an electron it becomes Cl-.
  • Negatively charged ions are called anions.
  • An atom or molecule can gain or lose more than one electron.
valence electrons of 8a noble gases or inert gases
Valence Electrons of 8A- Noble Gases or Inert Gases

Element Valance electrons

He 2

Ne 8

Ar 8

Kr 8


new terms
New Terms

Chemical bond – joining one atom to another by electrons joining

Compound – are molecules that consist of two or more different elements in proportions combined by a chemical bond

Molecule – two or more atoms of the same element or different elements joined by a chemical bond


new terms46
New Terms

Formula- the proportional arrangement and short hand for a chemical

Chemical reaction- reacting two or more compounds and or molecules with one another

Reactants – the things that are mixed together in a chemical reaction

Products – the things that are produced in a chemical reaction


electron vacancies47
Electron Vacancies

Unfilled shells make atoms likely to react

Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells


chemical bonds molecules compounds
Chemical Bonds, Molecules, & Compounds

Bond is union between electron structures of atoms

Atoms bond to form molecules

Molecules may contain atoms of only one element - O2

Molecules of compounds contain more than one element - H2O


formulas chemical bookkeeping
Formulas & Chemical Bookkeeping

Use symbols for elements when writing formulas

*****(Need to remember!) Formula for glucose is C6H12O6

6 carbon

12 hydrogen

6 oxygen


chemical bookkeeping
Chemical Bookkeeping

Chemical equation shows reaction

Reactants ---> Products

Equation for photosynthesis:




















12 oxygens

12 hydrogens

6 oxygens

6 carbons

12 hydrogens

6 oxygens

24 hydrogens

12 oxygens

6 carbons

12 oxygens


major bonds in biological molecules
Major Bonds in Biological Molecules


The bonding behavior of biological molecules starts with the number and arrangement of electrons in each type of atom.

Ionic, covalent, and hydrogen bonds are the main categories of bonds between atoms in biological molecules.


new terms52
New Terms
  • Ionic Bonds – gain or lose control over e-
  • Covalent Bonds – share e-
  • Hydrogen Bonds – between H


ion formation
Ion Formation

Atom has equal number of electrons and protons - no net charge

Atom loses electron(s), becomes positively charged ion

Atom gains electron(s), becomes negatively charged ion

ionic bonding
Ionic Bonding

One atom loses electrons, becomes positively charged ion

Another atom gains these electrons, becomes negatively charged ion

Charge difference attracts the two ions to each other

formation of nacl
Formation of NaCl

Sodium atom (Na) (+1 ion)

Outer shell has one electron

Chlorine atom (Cl) ( -1 ion)

Outer shell has seven electrons

Na transfers electron to Cl, forming Na+and Cl-

Ions remain together as NaCl (no charge)


ionic bond
Ionic Bond

The electron from sodium atom is lost to the chlorine atom which gains the electron.


covalent bonding
Covalent Bonding

Atoms share a pair or pairs of electrons to fill outermost shell

Example below is a single bond

  • Single covalent bond
  • Double covalent bond
  • Triple covalent bond

Molecular hydrogen



Single bonds between H and carbon . Methane (lower right) has 4 single bonds formed with hydrogen.


triple bonds
Triple bonds

Share 6 electrons for three bonds (triple)


polar and non polar covalent bond
Polar and non-polar covalent bond

Non Polar – share electrons equally

Polar – do not equally share electrons

Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons.


water polar covalent molecule
Water – Polar Covalent molecule

Oxygen is much more electronegative than hydrogen

shared electrons spend more time with the oxygen part of the molecule than with the hydrogen part

Unequal sharing of electrons results in the oxygen having a partial negative charge and the hydrogen atoms having a partial positive charge.


water a polar covalent molecule
Water: A Polar Covalent Molecule

Molecule has no net charge

Oxygen end has a slight negative charge

Hydrogen end has a slight positive charge





covalent polar or nonpolar bonds
Covalent: Polar or Nonpolar Bonds

Non polar if atoms share electrons equally

Hydrogen gas (H - H)

Polar if electrons spend more time near nucleus with most protons


Electrons more attracted to O nucleus than to H nuclei


hydrogen bonding
Hydrogen Bonding

Atom in one polar covalent molecule is attracted to oppositely charged atom in another such molecule or in same molecule

Hydrogen bonds are weak.

Water molecule




hydrogen bonding68
Hydrogen Bonding

Important role in the structure and function of biological compounds.

Found in DNA

Gives DNA unique properties


properties of water
Properties of Water

Bonds to hydrophilic substances

Water loving

Repels hydrophobic ones

Water hating

Temperature stabilizing

Expands & floats when it freezes


water cont
Water cont.

Capacity to dissolve substances

Universal solvent

Evaporation – heat energy converts liquid water to a gaseous state

Form skin evaporation can help cool body

Water boils at sea level at 100C or 212F.

Water freezes at sea level at 0C or 32F.


water cont71
Water cont.

Cohesion – has the ability to resist rupturing when placed under tension

Cohesion causes high surface tension

Shows a capacity to resist rupturing when stretched

Helps to absorb nutrient laden water to grow

Water rise in tubes

Some evaporates in leaves

Pull other water molecules to fill in behind those evaporated




Liquid water

This slide shows hydrogen bonding (white dotted line)

Solids are more organized in shape.


why ice floats
Why Ice Floats

In ice, hydrogen bonds lock molecules in a lattice

Water molecules in lattice are spaced farther apart then those in liquid water

Ice is less dense than water

hydrophilic hydrophobic substances
Hydrophilic & HydrophobicSubstances

Hydrophilic substances


Hydrogen bond with water

Example: sugar

Hydrophobic substances


Repelled by water

Example: oil

temperature stabilizing effects
Temperature-Stabilizing Effects

Liquid water can absorb much heat before its temperature rises


Much of the added energy disrupts hydrogen bonding rather than increasing the movement of molecules

evaporation of water
Evaporation of Water

Large energy input can cause individual molecules of water to break free into air

As molecules break free, they carry away some energy (lower temperature)

Evaporative water loss is used by mammals to lower body temperature

water is a good solvent
Water Is a Good Solvent

Ions and polar molecules dissolve easily in water

When solute dissolves, water molecules cluster around its ions or molecules and keep them separated

water cohesion
Water Cohesion

Hydrogen bonding holds molecules in liquid water together

Creates surface tension

Allows water to move as continuous column upward through stems of plants

the ph scale
The pH Scale

Ions dissolved in fluids inside and outside the each living cell influence its structure and function.

Among the most influential are hydrogen ions.

They have far reaching effects largely because they are chemically active and because there are so many of them.


the ph scale82
The pH Scale

Measures H+ concentration of fluid

Change of 1 on scale means 10X change in H+ concentration

Highest H+ Lowest H+


Acidic Neutral Basic

ph scale
pH Scale
  • Water splits into ions
  • H+ is an acid
  • OH- is a base
  • The greater the number of H+ concentration the lower the pH.
  • The greater the number of OH- concentration the higher the pH.


acid base

Both can cause severe damage


Donate H+

Below 7


Accept OH-

Above 7

Also called alkaline


acid rain
Acid Rain

A coal-burning power plant emits sulfur dioxide, which dissolves in water vapor to form acid rain

salt water
Salt & Water

A salt is any substance that dissolves in water and releases ions (not H+)

Forms when and acid and a base are mixed.

HCL + NaOH H2O + NaCl

Hydrochloric acid reacting with sodium hydroxide produces water and sodium chloride (salt)

NaCl (solute) dissolves in water (solvent) forms Na+ and Cl- (ions)


buffers against shifts in ph
Buffers Against Shifts in pH
  • Cells must maintain homeostasis
  • Cells must respond to shifts in pH quickly
    • Respiratory acidosis – high carbon dioxide levels causing pH drop in blood , muscles tetany (continued muscle contraction)
    • Respiratory alkaosis – pH rises in blood
    • Blood pH drops can cause a coma if not corrected
  • Buffer systems reponds to readjust pH
    • Limited in ability


carbonic acid bicarbonate buffer system
Carbonic Acid-Bicarbonate Buffer System

When blood pH rises, carbonic acid dissociates to form bicarbonate and H+

H2C03 -----> HC03- + H+

When blood pH drops, bicarbonate binds H+ to form carbonic acid

HC03- + H+ -----> H2C03



Ions dissolved in fluids on the inside and outside of cells have key roles in cell function.

Acidic substances release hydrogen ions, and basic substances accept them.

Salts are compounds that release ions other than H+ and OH-.

Acid-base interactions help maintain pH, which is the H+ concentration in a fluid.

Buffer systems help maintain the body’s acid-base balance at levels suitable for life.