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2.1  Chemical Elements. Chemistry as it related to biology. QOD : (after quiz) Read the article and try to answer the question: Why does the doctor not recommend the use of external cooling (such as ice baths, cold water or even air conditioners) to reduce a fever.

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2 1 chemical elements

2.1  Chemical Elements

Chemistry as it related to biology


QOD: (after quiz)

Read the article and try to answer the question:

Why does the doctor not recommend the use of external cooling (such as ice baths, cold water or even air conditioners) to reduce a fever.

Are there any exceptions?

What is recommended to treat fever? Why?

Your should have thorough answers, including evidence you find in the article.

A. Matter

What is matter?



  • Compound
  • Protons
  • Neutrons
  • Electrons
  • Atomic number
  • Atomics Mass
  • Isotope
  • Orbital

Biochemistry Ch 2.1

Write a vocabulary list for yourself: try to define the ones you remember:

matter stuff has mass takes up space
Matter: “stuff” has mass, takes up space

Made up of elements: substance that cannot be broken down into other substances by a chemrxn

Compound: consist of 2 or more elements in a fixed ratio

Six elements:
  • C, H, N, O, P, S: make up 98% of living things.
  • C, H, O and N make up about 96%


B. Atomic Structure

a. Protons (p+):positively charged particles;

neutronshave no charge; both have about 1 atomic mass unit of weight. Both are found in the nucleusb. Electrons (e-) are negatively charged particles that orbit the nucleus


Periodic Table

Atomic number= number of protons

- can’t change or it changes the atomAtomic mass: about equal to the sum of its protons and neutrons

All atoms of an element have the same number of protons, the atom's atomic number



Isotopes are atoms with the same number of protons but differ in number of neutrons; e.g., a carbon atom has six protons but may have more or less than usual six neutrons.

carbon 14 break it down
Carbon 14  - Break it Down!

Carbon- 12 is the most common form of carbon, it has 6 protons, 6 electrons, and 6 neutrons

It is called Carbon 12 because that is its weight  (6 + 6 )

Carbon 14 has 2 extra neutrons, its weight is 14  (6 + 8 ); it is an isotope of carbon


Sample Question: A 200 g sample of muskopfonian is left in a container , the half life of muskopfonian is 1 hour. How much of the sample will be left after 4 hours?

A carbon with eight rather than six neutrons is unstable; it releases rays and subatomic particles and is a radioactive isotope.


200 x .5 =  100 (hour 1)

100 x .5  =  50  (hour 2)50 x .5 = 25 (hour 3)25 x .5 = 12.5 (hour 4)

or 200 x .54 = 12.5

Low levels of radiation such as radioactive iodine or glucose allow researchers to trace the location and activity of  the atom in living tissues; therefore these isotopes are called tracers which are used in CAT scans
 High levels of radiation can cause cancerous tissues and destroy cells; careful use of radiation in turn can sterilize products and kill cancer cells.

Pick your favorite element from the table.  Turn and tell your lab partner how many protons, electrons and neutrons it has, and what it's atomic weight is (if you can see it). Have your table partner then name the element.

E. Electrons and Energy1. Electrons occupy an orbital at some level near or distant from the nucleus of the atom.

S orbital: innermost, hold 2 elections

P orbital: after s, holds 8 elections

Outer elections have more energy and are less stable. So?

2. Electrons can be used to store and release energy!

3. When atoms absorb energy during photosynthesis, electrons are boosted to higher energy levels.

4. The innermost shell of an atom is complete with two electrons; all other shells are complete with eight electrons.

5. The outermost shell is the valance shell, and the number of valance e-in the outermost shell determine many of the atoms properties

draw it quick

1. Draw six protons in the nucleus of the atom. 

2. Draw six neutrons in the nucleus of the atom.

3. Draw two electrons in the first energy level and label them with their charge.

4. Draw four electrons in the second energy level and label them with their charge.

5. What element is it!? __________                           (the future of the human race depends on it!)

2.2 Elements and Compounds

Compounds:When two or more different elements react or bond together, they form a compound (e.g., H2O).

 Electrons possess energy and bonds that exist between atoms in molecules contain energy.



Ionic bonds:when electrons are transferred from one atom to another.

  • Attraction of oppositely charged ions holds the two atoms together in an ionic bond.
  • Losing or gaining elections gives ions a filled outer shell, so they are more stable
  • Ex: sodium (Na+) and Chlorine (Cl- ) make NaCl

B. Ionic Bonding



positively charged ion


negatively charged ion


Covalent bonds: when two atoms share electrons so each atom has octet of electrons in the outer shell.

C. Covalent Bonding

  • Hydrogen can give up an electron to become a hydrogen ion (H+) or share an electron with another atom to complete its outer shell of two electrons.
  • Strongest type of bond

Structural formulas represent shared atom as a line between two atoms; e.g., single covalent bond (H-H), double covalent bond (O=O)

Carbon has amazing bonding properties, as we will learn in the next chapter


Bonds can be represented using structural formation, where a line represent the sharing of 2 elections

D. Nonpolar and Polar Covalent Bonds

In nonpolar covalent bonds, sharing of electrons is equal= no charge

With polar covalent bonds, the sharing of electrons is unequal. = charge

Ex: water molecule (H2O), sharing of electrons by oxygen and hydrogen is not equal; the oxygen atom with more protons dominates the H2O association.              *The oxygen then assumes a small negative charge *

Hydrogen Bond:weak attractive force between slightly positive hydrogen atom of one molecule and slightly negative atom in another or the same molecule.
  • Weakest bond
  • mainly between O, N, F and an atom of hydrogen
  • Many hydrogen bonds taken together are relatively strong.
  • Hydrogen bonds between complex molecules of cells help maintain structure and function.

Hydrogen bonds create surface tension.


Notice the e- spend more time around the oxygen molecule: it’s has more protons to attract the elections

*the shape allows for one side to be more + and the other more -

van der waals interactions
Van der Waals Interactions

When you have a molecule which is electrically dipolar (equal but opposite in charge) you have attraction between the negative pole of one molecule and positive pole of the other molecule. They are usually weaker than hydrogen bounds but exist in all matter

title properties of water

Title: Properties of water

In your notebook, create a chart listing the properties of water, and why each property is important. Include example whenever possible

use pages 29-31



Examples of charts


Property 1

Property 2

Property 3

Property 4

Property 5


Pg 29-31



2.3. Chemistry of Water

A. Facts

1. All living things are 70.90% water.

2. Because water is a polar molecule, water molecules are hydrogen bonded to each other.3. With hydrogen bonding, water is liquid between 0 C and 100 C which is critical for life.


B. Properties of Water

High Specific Heat: The temperature of liquid water rises and falls more slowly than that of most other liquids.

- Most water stays a liquid

Because water holds more heat, its temperature falls more slowly than other liquids; this protects organisms from rapid temperature changes, living things don't freeze or boil easily

Calorie is amount of heat energy required to raise temperature of one gram of water 1o C.


2. Water has a high heat of vaporization.

a. Hydrogen bonds between water molecules require a large amount of heat to break.b. This property moderates earth's surface temperature; permits living systems to exist here.c. When animals sweat, evaporation of the sweat takes away body heat, thus cooling the animal.

3. Water is universal solvent, and facilitates chemical reactions both outside of and within living systems..

a. Water is a universal solvent because it dissolves a great number of solutes.b. Ionized or polar molecules attracted to water are hydrophilic.c. Nonionized and nonpolar molecules that cannot attract water are hydrophobic.

Solvents dissolve other substances (solutes) and do not lose their own properties.

If we use a simple and easy example, we can get a handle on the idea. Take a glass of warm water, put a teaspoon of table salt in it, and stir it. The salt will dissolve in the water and "disappear" from view. The water is the solvent here, the salt is the solute in this example, and the resulting salt water is a solution that we created. It's that simple.

4 liquid water is cohesive adhesive
4. Liquid water is cohesive & adhesive

Cohesion= H bonds between water molecules; H2O molecules tend to stick together.

Adhesive= ability of water to cling to other polar molecules

importance= Higher surface tension

Transport H2O against gravity in plants = capillary action

5 ice floats
5. Ice floats
  • Most (all?) substances are more dense when they are solid, but
  • notwater… Ice floats!
    • H bonds form a crystal
    • allowing life to survive the winter

Ice!I could use more ice!

And this hasmade all the difference!

create a venn diagram comparing acids and bases
Create a Venn Diagram Comparing Acids and Bases
  • Stomach acid
  • Citrus fruit: orange
  • Soap
  • Cleaning products
  • Baking soda
  • vinegar
  • Substances with hydrogen ions (H+)
  • Substances with hydroxide ions (OH–)
  • Taste sour
  • Taste bitter
  • Feel slippery
  • pH greater that 7
  • pH lower that 7

Neutral = pH of 7


Acidmolecules dissociate in water, releasing hydrogen ions (H+) ions: HCl ¨ H+ + Cl-.

Basesare molecules that take up hydrogen ions or release hydroxide ions. NaOH ¨ Na+ + OH-.

See also:  Acid & Base Coloring


Acids and Bases

Covalently bonded water molecules ionize; the atoms dissociate into ions.

  • When water ionizes or dissociates, it releases a small (107 moles/liter) but equal number of H+ and OH ions; thus, its pH is neutral.
  • Water dissociates into hydrogen and hydroxide ions: 

The pH scale indicates acidity and basicity (alkalinity) of a solution.

-Acid is a substance with pH less than 7; base is a substance with pH greater than 7.-As logarithmic scale, each lower unit has 10 times the amount of hydrogen ions as next higher pH unit;

* Buffers keep pH steady and within normal limits in living organisms..



Chemistry in Biology



  • Substances that dissociated into hydroxide ions (OH–)
  • Taste bitter
  • Feel slippery
  • pH greater than 7
  • Substances that dissociates into hydrogen ions (H+)
  • Taste sour
  • pH lower than 7
  • Examples
  • Stomach acid
  • Citrus fruit: orange
  • vinegar
  • Examples
  • Soap
  • Baking soda
  • Cleaning products
ph scale

H+ Ion


Examples of Solutions




Hydrochloric acid





Stomach acid, Lemon juice

Vinegar, cola, beer








Black coffee, Rainwater



Urine, Saliva


Pure water, Blood





Baking soda



Great Salt Lake




Household ammonia




Household bleach



Oven cleaner



Sodium hydroxide

pH Scale

tenfold changein H+ ions

pH1  pH2

10-1 10-2

10 times less H+

pH8  pH7

10-8 10-7

10 times more H+

pH10  pH8

10-10 10-8

100 times more H+

buffers cellular regulation




















Amount of base added

Buffers & cellular regulation
  • pH of cells must be kept ~7 to maintain homeostasis!

Buffers: solutions used to stabilize the pH of a solution

  • Control pH by using buffers
    • reservoir of H+
      • donate H+ when [H+] falls
      • absorb H+ when [H+] rises


H2O + CO2 H2CO3 HCO3 -+ H+

HCO3- = Bicarbonate (weak base)

H2CO3 = Carbonicacid (weakacid)

Major buffer system in blood

Maintainsblood pH between 7.38 and7.42


1. The only atom that has a nucleus with no neutrons is _________.

A) argon

B) carbon

C) oxygen

D) hydrogen

2. Which of the following elements is NOT one of the six that make up 98% of most organisms' body weight?

A) hydrogen

B) nitrogen

C) carbon

D) iron


Which of the following statements is true?

A) All isotopes give off subatomic particles.

B) All isotopes are radioactive.

C) All isotopes have the same number of protons.

D) All isotopes have the same number of neutrons.

What type of bond is formed when atoms share electrons?

A) ionic

B) covalent

C) hydrogen


If an atom has an atomic number of 17 and an atomic mass of 35, the number of neutrons in its nucleus equals _____.

A) 17

B) 18

C) 52

Which bond is most easily broken?

A) a hydrogen bond

B) a triple covalent bond

C) a single covalent bond


Hydrophobic molecules tend to be _________.

A) nonpolar

B) inorganic minerals

C) ionic

D) water soluble

The calcium ion (Ca2+) _____.

A) has accepted two protons

B) has given away two electrons

C) will form a covalent bond with the chlorine ion (Cl-)

D) All of these


The three isotopes of carbon 12C, 13C and 14C have different numbers of _______?

A) electrons

B) protons

C) neutrons

The combined number of ___________ will determine the number of electrons in orbital(s) around a neutral atom.

A) orbitals

B) neutrons

C) bonds

D) protons


Which of the following statements is true?

A) There are two polar covalent bonds in water.

B) There are two ionic bonds in water.

C) There is one ionic and one covalent bond in water.

D) Electrons are less attracted to oxygen than hydrogen.

The two parallel strands of DNA are held together by _______ bonds.

A) nonpolar

B) hydrogen

C) ionic

D) covalent


The calcium ion (Ca2+) _____.

A) has accepted two protons

B) has given away two electrons

C) will form a covalent bond with the chlorine ion (Cl-)

D) All of these

Hydrogen bonds form when ___________.

A) atoms share electrons

B) a slightly negative atom is attracted to a slightly positive atom

C) atoms gain electrons

D) atoms lose protons


Which of the following has a basic pH?

A) lemon juice

B) milk of magnesia

C) tomatoes

D) hydrochloric acid

Aquatic living things are able to survive the winter thanks to which property of water?

A) It is less dense as a solid than as a liquid.

B) It is cohesive and adhesive.

C) It is the universal solvent.

D) It resists changes of state (from liquid to ice or liquid to steam).



In a group of 4, each pick one paragraph of the article to read. (note: paragraph 2 is the hardest one, the back page will be more helpful)

When you are done reading, discuss as a group and try to answer the question:

Why does the doctor not recommend the use of external cooling (such as ice baths, cold water or even air conditioners) to reduce a fever.

Why do movie theaters put so much salt on popcorn?