Bio Unit 2

Objective 2.1: Describe the parts of an atom and overall atomic structure.

Objective 2.2. Explain how elements differ from one another. (Review of the Periodic table)

oAll matter is made of atoms.
oAn atom is the smallest unit of matter that cannot be broken down by chemical means
oAtoms are made up of three subatomic particles
oAtoms are neutral because they have the same numbers of protons and electrons.

Subatomic particle


Location in atom



Positive (+)

In the nucleus

1 amu



Neutral (0)

In the nucleus

1 amu (large)


Negative (-)

Outside the nucleus. Electron cloud

1/2000 amu


oAn element is a pure substance made of only 1 kind of atom.
oThe periodic table of elements is an organized chart of all the elements on our planet.
nIt’s organized by group (column) and period (row)
oAn element is represented by a 1 or 2 letter symbol on the periodic table.
nEx. H for Hydrogen. Cl for chlorine.
oThe number of protons determines the identity of the element.
nEx. H is hydrogen because it only has 1 proton. Cl is chlorine because it has 17 protons.
oThe periodic table gives us a lot of important information. The two key pieces are the atomic number and mass number.
oThe Atomic Number tells you how many protons are in an atom. The periodic table is organized according to Atomic Number
oRemember, a neutral atom has the same number of protons and electrons, so the atomic number also tells you have many electrons there are.
oThe atomic number NEVER changes because that would change the identity of the atom.
oThe mass number tells us the mass of the atom measured in Atomic Mass Units (amu)
oMass number is the number of protons plus the number of neutrons
oElectrons aren’t included because they have such a small mass.
oEx. Fluorine has 9 protons and 10 neutrons so the mass number is 19.

*The number of protons = Atomic number

*The number of neutrons=

  The Mass number – the atomic number

*The number of electrons = the number of protons = atomic number

  (this is only true when the atom is neutral   and has no charge)


Objective 2.3 You will be able to describe the characteristics of ionic and covalent bonds.

Atoms can join with other atoms to form different substances. They do this by forming a bond.
A compound is made of two or more atoms of different elements joined together.
The properties of compounds are very different from those of the elements that it is made of.
Ex. Na is sodium. Cl is Chlorine. NaCl is sodium chloride aka salt.
We will be learning about three types of bonds:
Covalent bonds
Polar covalent bonds
Ionic bonds
Atoms or ions bond so that they will have eight electrons in their outermost shells. This is called the Octet Rule.
Remember 8 is great? Valence electrons?
Covalent bonds occur when two or more atoms meet that have almost full outer shells of electrons. They will share electrons. These electrons are shared EQUALLY.
Covalent bonds generally form between two or more nonmetals.
Many famous compounds are covalent. Some examples are:
DNA, Sugar, Water
Polarity is when a molecule has a positive pole and negative pole.
In covalent bonds, electrons are not always shared equally. It’s like the atoms are having a tug-of-war.
Nonpolar covalent bonds: Atoms share electrons equally: both teams are equally strong. (This is what we just discussed).
Polar covalent bonds: An unequal sharing of electrons. Both teams are pulling on sides of the rope, but one team may be stronger.
Water has polar covalent bonds. The oxygen is stronger than the hydrogen, so they attract the electrons more.
This causes an unequal distribution of charge.
The oxygen is the negative pole
The hydrogens are the positive pole
This is also called hydrogen bonding
What does sodium (Na) have that it wants to get rid of? One electron.
What does Chlorine (Cl) really, really want? One electron.
What will Chlorine do? Steal Sodium’s electron!
An ion is an atom that has gained or lost electrons and therefore has an electrical charge.
An ionic bond is when ions of opposite charge form a bond.
In general, ionic bonds are formed between metals and nonmetals.
Ionic bonds are stronger than covalent bonds.
 Objective 2.4: Explain how the structure of water relates to its properties

Objective 2.5: Analyze the contribution of water to Earth's habitability.

?Water surrounds us and is important in our day to day lives.
?Planet earth is made ¾ water
?Your body is made up of 70% water
?Since water is all around us, why is it so important?
?70% of your body is water.
?This is because water helps move nutrients and other substances into and out of your cells.
?These nutrients will help your cells grow, which will help keep you healthy.
?Water is really good at storing energy.
?It absorbs heat more slowly and retains heat for longer periods of time
?Have you ever boiled water and removed it from the stove?  How long did it take to cool?
?Remember what homeostasis is?
?Homeostasis is the ability to maintain a constant internal temperature of 98.6°F
?When our bodies get hot from the weather or working out, we need to release this excess heat
?We do this by sweating!
?Sweating carries heat away from our bodies by the evaporation of water
?Evaporation means to disappear
?Remember what hydrogen bonds are?
?Water is made up of hydrogen bonds
?These bonds cause cohesion of liquid water
?Cohesion is the attraction between substances of the same kind
?Forms films and droplets
?Molecules are linked by hydrogen bonds at the surface like a crowd holding hands
?Cohesion causes surface tension
?Molecules at top do not have like molecules on all sides so they bond more strongly to the sides that do have like molecules
?Surface Tension prevents the surface of water from stretching or breaking easily.
?This is how so many drops were able to fit on a single penny in our lab!
?Adhesion is the attraction between different substances
?This is why some things get wet and some things do not.
?What is an example of something that gets wet?
?What is an example of something that does not?
?This property powers capillary action.
?Capillary action is water’s ability to move upward and climb.
?Plants drink water from the soil.  Water must reach the top of the plant so the leaves at the top get food.  How does this happen?
?Water is attracted to the walls of the tube.
?This attraction sucks the water up more strongly than gravity pulls it down.
?Explain how we saw capillary action in our lab with the marker and the filter paper.
?Co-hesion ~ Co-pilot (the same)
?Ad-hesion ~ Ad-verse (different)
?Cohesion water binds to water
?Adhesion water binds to other things
?Water is polar.  The oxygen is stronger than the hydrogen. This is why the oxygen is slightly negative and the hydrogen is slightly positive
?Because water is polar, other polar or ionic compounds can dissolve in it.
?Molecules of these compounds are attracted to the ends of water with opposite charges
?In a saltwater solution, sodium is attracted to the oxygen because sodium has a positive charge and oxygen has a negative charge
?This allows salt to dissolve in water
?Nonpolar molecules DO NOT dissolve in water
?Do oil and water mix? (oil is nonpolar and water is polar!)
?Remember nonpolar molecules do not have a charge
?Water is more attracted to itself
?This property will become more important when we talk about cell structure
 Objective 2.6: You will be able to distinguish between carbohydrates, lipids, proteins, and nucleic acids
a.  Atoms are incredibly small.  When atoms come together, they make molecules.
b.  There are four main molecules in living things: carbohydrates, proteins, lipids, and nucleic acids.
c.  Three atoms that are found in all the molecules listed above are carbon, hydrogen, and oxygen (CHO).
i.  In some molecules, nitrogen, sulfur, and phosphate will also be found.

d.  Any molecule that has a carbon atom in it is called an organic molecule.

i.  Carbon is very important to life because it can bond to four other atoms.
ii.  Thus, carbohydrates, proteins, lipids, and nucleic acids are all organic molecules.
i.  The smallest organic molecule is called a monomer.
1.  Think of a monomer as a brick that will be used to make a building.
2.  Monomer= building block
ii.  Monomers come together to form larger organic molecules called polymers.
1.  Think of a polymer as a building, made out of many bricks (monomers).
Carbohydrates are sugars and are the key to metabolism.
Identify sugars by their ending in –ose.
Metabolism is the break down of food into sugar for energy.
The building blocks are monosaccharides.
Carbohydrates have carbon, hydrogen and oxygen in a 1:2:1 ratio.
Monosaccharides linked together to form polysaccharides and are found in starches and cellulose.
The function of carbohyrates is to provide food and energy.
Glucose is the preferred energy source for the brain. Brain function drops off sharply if glucose is in short supply.
The carbohydrate looks like this. It has a ring shape.
What happens to the carbohydrates not used as energy? They become FATS or lipids!
Structure: Mostly carbon and hydrogen, some oxygen molecules
Lipids include fats, waxes, and steroids.
Lipids are non-polar and do not dissolve in water.

Building Blocks: fatty acids

Saturated fats: contains only single bonds. It’s a straight chain.
Unsaturated fats: contain at least 1 double bond. It has a bent shape.
Ex. Vegetable oil. They are usually *liquid at room temperature*
Structure: Contain carbon, hydrogen, oxygen, and NITROGEN!
The building blocks of proteins are amino acids.
There are 20 different

kinds of amino acids.

Proteins have several functions:
1. Build and restore body tissues (ex. Bones and muscle)
2. Supports the immune system and fight diseases
3. Carries materials in the body (Ex. Hemoglobin in your blood carries oxygen to your limbs)
4. Control the speed of reactions (Ex. Enzymes: lactase, maltase, galactosidase, amylase)
5. Regulate HOMEOSTASIS! (Ex. Hormones: insulin tells you to eat sugar)
Structure: Contain carbon, hydrogen, oxygen, nitrogen and phosphorus.
The building block of nucleic acids are nucleotides.
Nucleotides are used to make Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA)
Each nucleic acid has:
A phosphate group
a sugar
a nitrogen containing base.


2.10 & 11 A:  Chemical Reactions & Enzymes



·      Energy is all around

·      Energy is the ability to move or change matter

·      When you kick a ball the energy of your kick makes the ball move – your energy is transferred to the ball

·      There are many different kinds of energy

·      Energy is needed to cook an egg.  You use energy in the form of heat.

·      A click beetle needs energy to produce light.  They use a chemical reaction.

·      Energy is stored and released by chemical reactions

·      A chemical reaction is when bonds are broken between atoms

·      Remember how salt water is formed?


Chemical Reactions

·      In a chemical reaction, you create something new!

·      You have reactants:

o   NaCl + H2O

·      And you have products:

o   Na+ + Cl-

·      Reactants are what you start with

·      Products are what you end with

·      This is how scientists write this reaction:

o   NaCl + H2O  à Na+ + Cl-


Physical Reactions

·      There are also physical reactions

·      Physical reactions are when matter stays the same but changes in size, shape, or appearance

o   For example: crushing ice, sawing wood, denting a car

·      You are NOT creating something new.




Chemical reactions – bonds break


Physical reactions – reactants only change physically (their bonds stay the same!)



4 Things affect reactions

1.     Concentration – the more reactants you have the faster the reaction can take place

2.     Surface area – if a reaction has more room to take place it will occur faster

3.     Catalyst – a helper t make the reaction go faster

4.     Temperature – some things need a certain temperature to react


2.10 & 2.11 B:  Chemical Reactions & Enzymes



·       Chemical reactions need energy in order to happen.

·       The energy needed to start a chemical reaction is called activation energy

·       hx4ne040.jpgEnzymes increase the speed of chemical reactions

·       Enzymes are catalysts

·       Catalysts reduce the activation energy



Enzymes and Homeostasis

·       Remember what homeostasis is?

·       If enzymes were not catalysts we would not survive

·       Without catalysts to help maintain homeostasis, chemical reactions would not happen fast enough

·       For example:  your blood carries CO2 to your lungs so you can get rid of it from your body by exhailing it.  In your lungs CO2 reacts with water to form carbonic acid.  A catalyst is required to make this reaction happen quickly.

·       Without a catalyst: 2,000 molecules of carbonic acid produced per hour

·       With a catalyst: 600,000 molecules of carbonic acid produced per second

Enzyme Activity

·       hx4ne041.jpgEnzymes are specific

·       They will only work on certain substrates

·       A substrate is a substance that an enzyme works on

·       The shape of enzymes determine what substance they can react with

·       Enzymes are proteins with folds on their surface

·       The folds form pockets which are called active sites

·       Active sites are where enzymes interact with their substrate

Enzyme Activity

·       Enzymes need certain conditions in order to work correctly

·       The temperature and pH can change the shape of an enzyme

·       If the enzyme’s shape changes than it can no longer bind with its substrate

·       Therefore, the reaction will not happen

Energy and Reactions

·       Some chemical reactions need energy

·       Some chemical reactions release energy

·       For example: when making ice, the water releases energy to form ice crystals

·       When ice melts, it absorbs heat from the environment

·       When you hold something cold your hand gets cold because it is absorbing the heat from your hand

Endothermic vs. Exothermic

·       There are two types of reactions: endothermic and exothermic

·       Endothermic reactions need energy

o   Endo= into                                    thermic = heat           Heat needs to go into the reaction!

§  Ex. Melting ice

·       Exothermic reactions give off energy

o   Exo= exit                                    thermic = heat              Heat needs to exit the reaction!

§  Ex. Freezing water

·       Energy can be in the form of heat, light, or sound

·       Exothermic reactions can occur spontaneously (It can happen on its own, you don’t need to put in energy)




Making ice cubes

Melting ice cubes

A candle flame

Baking bread

Rusting iron

Cooking an egg

Formation of snow in clouds

Conversion of frost to water vapor

Condensation of rain from water vapor

Evaporation of water

The graph on the left is exothermic. You end at a lower energy level than what you start with.  This is because energy exited!

                  Ex. Making ice cubes.


The graph on the right is endothermic. You end at a higher energy level than what you start with. This is because energy goes into the reaction!

                  Ex. Cooking eggs.

Exothermic: The products have a lower energy than the reactants.

Endothermic:  The products have a higher energy than the reactants