Unit 1 Ch.

2 Notes

Atoms – All matter consists of atoms.

Protons, Neutrons, Electrons – Subatomic particles that make up atoms.
Protons are positively charged.
Neutrons are uncharged.
Electrons are negatively charged. (-1 charge)

Elements that make up 95% of organisms (CHNOPS – pronounced Shnops)

Carbon
Hydrogen
Nitrogen
Oxygen
Phosphorus
Sulfur

Difference between weight and mass, is that mass does not change, weight changes based on the
gravitational pull.

Protons and Neutrons are found in the nucleus of an atom.

Protons are positively charged, while Neutrons are uncharged.
The number of protons is equal to the number of electrons.
Electrons are negatively charged and are found in the Electron shell which circulates the nucleus.
The first electron shell, houses ONLY 2 Electrons, every one outside of that can house up to
8 Electrons

Protons and Neutrons’ Atomic Mass Unit (AMU) is 1

Electrons’ AMU is 0

Radiation is an energy that comes from a source and travels through space at the speed of light.
Anything can radiate but we are mostly concerned with un-natural radiation such as that coming from
machinery, propulsion systems, auxiliaries, and electronics, etc.

Interpreting the Periodic Table.

Groups are Vertical columns.

So they’re described horizontally.
Periods are Horizontal rows.
So they’re described vertically.

HYDROGEN DOES NOT have a neutron in its nucleus.

Atomic Number is the number of protons in the nucleus.
Mass Number is the number of protons and number of neutrons.
The atomic number is both the number of protons and electrons.
So, how many electrons are in the valence shell of a Carbon atom?
We know that there are 6 protons (thus 6 electrons) we also know that the inner shell can only
house 2 electrons, so there has to be 4 in the valence shell of the Carbon atom. BUT we know that the
valence shell can accommodate up to 8, so the Carbon atom is unstable as it needs 4 more electrons.
The mass number is the protons and neutrons added up. So if you know that the mass number of Carbon
(for example) is 12, and you know that the amount of protons is 6 (the atomic number) then you know
that there are 6 neutrons.
And Isotope is when the same element, have a different (than standard) number of neutrons, so, if
carbon’s atomic number is 13 instead of 12, we know that the isotope is 13 because the original form has
12 as the mass number, so we know that there are 6 protons (atomic number) and then 7 neutrons.

Lets take Carbon for example. Carbon has an atomic mass of 12, and its atomic number is 6, so we know
it has 6 protons and 6 neutrons, and since the number of protons is equal to the number of electrons, there
are 6 electrons.
 1.) How many more electrons could the above pictured Carbon atom take? 4
Now, lets take Hydrogen; hydrogen is a little different as it’s so light, Hydrogen has an atomic mass of 1
yet it’s atomic number is 1, thus it only has 1 proton, but 0 neutrons.
Chemical Bonds
Hydrogen Bonds occur when partially positive hydrogen atoms attract partially negative atoms nearby. An
example includes the attraction between two molecules of water.
Ionic Bonds occur when atoms are held together by an attraction between negatively and positively
charged ions. Examples include NaCI and MgCI2 (Example below)

Covalent Bonds occur when two atoms share electrons in such a way that each atom has an octet of
electrons in the outer shell. An example includes H2, O2, CH4, notice how the Hydrogen shares its
electrons with a single bond, notice how the Oxygen does the same. In the methane notice how the carbon
atom bonds to four hydrogen atoms.
Single Covalent Bonds occur when one pair of electrons are shared between the outer shells of two atoms,
an example of this is the bond between two hydrogen atoms.
Double Covalent Bonds occur when two pairs of electrons are shared between the outer shells of two
atoms. Examples of this include the bond
between 2 oxygen atoms.
Triple Covalent Bonds occur when three
pairs of electrons are shared between the
outer shells of two atoms. Examples
include the bond between 2 nitrogen
atoms.
Example of a covalent bond (below)

Properties of Water
Water is a polar compound.
Polar – unequal sharing of electrons (delta positive/negative) (phillic)
Non-Polar – equal sharing of electrons (phobic)
Water has a high heat of vaporization.
Water can also be used as a solvent for polar molecules.
Hydrophilic – Water Attracting
Hydrophobic – Water Repelling
Because water has hydrogen bonding (cohesion) and can adhere to polar surfaces (adhesion) it is cohesive
and adhesive.
Water assists in transporting nutrients in your body.

The ability of water molecules clinging to each other is referred to as Cohesion.

This clinging ability is due to the fact that water molecules are held together by hydrogen bonds.

Fun Facts about water

1. Plants absorb water from roots and transport it to the rest of the plant, this is because water
molecules are cohesive and adhesive.
2. The liquid portion of our blood is 90% water and transports vital dissolved substances, this is
because water is a good solvent.
3. Most organisms, especially those that are warm blooded, are able to maintain a constant body
temperature, even in colder weather.
4. When we sweat, it cools our bodies because water has a high heat of vaporization.
5. Aquatic organisms are insulated by upper layers of ice during cold winters.
6. The ocean doesn’t freeze solid in the winter because the ice layers act to insulate the water below.
7. Blood fills the narrow tubular vessels within the cardiovascular system.
8. Large bodies of water absorb and store heat during the summer and release it slowly throughout
the winter because water has a high heat capacity.
9. Water is most dense at 4 degrees Celsius, thereby Frozen water is much less dense than liquid
water, this is why it floats on water too.
Acids and Bases
H+ is a hydrogen ion that has lost all its electrons.
OH- is a hydrogen is a hydrogen ion that has a oxygen and hydrogen molecule along with a negatively
charged electron.

Acids are found in foods like lemon juice, vinegar, and coffee.
HCI (Hydrogen Chloride) is an example of a strong one.
Acids have a pH value ranging from 0 to 6.
Acids increase hydrogen ions.
Hydrogen Ions are also called protons because there are no electrons in the nucleus.
pH is used to reflect the acidity or basicity (alkalinity of solutions)
Concentration of Ions are in brackets, not parenthesis.
pH below 7 is acidic [H-]=[OH-]
pH above 7 is basic [H+]=[OH+]
pH of 7 is neutral [H+]=[OH-]
Bases are commonly associated with milk of magnesia or bicarbonate soda which decreases stomach acid.
Bases have a pH value ranging from 8 to 14.
Sodium Hydroxide is an example of a strong one.
Bases take up hydrogen ions, and increase OH-
Buffers are what keep pH levels within normal limits.
Human buffers are Bicarbonate ions and carbonic acid found in blood buffers the pH to 7.4

Both of these can become caustic enough to eat through metal.

Buffers
A chemical solution that keeps pH within normal limits but absorbing excess hydrogen is a buffer.
In humans, our blood pH is about 7.4, if it drops, Acidosis can occur, if it rises, Alkalosis can occur.
Both of these conditions can be harmful to humans.
pH stability in blood is achieved through a built-in buffer.
When hydroxide ions are added to blood, this reaction produces bicarbonate ions.
When hydrogen ions are added to blood, this reaction produces carbonic acid.

Organic and Inorganic molecules

Organic molecules include lipids, proteins, carbs, and nucleic acids.

They always contain Hydrogen and Carbon (anything with.)
They always constitute living matter. (Hydro-Carbon chain.)
Carbon always needs 4 bonds with Hydrogen, because it needs 4 more valence electrons.

Functional Groups are a specific combination of chemical motifs, where there will be a remaining
molecule. Phosphate is very important in any nucleic acids. Etc.
Inorganic molecules include salts and water and constitute nonliving matter.

What is a Monomer? Any molecule that can bond to another identical monomer to form a polymer.
What is a Polymer? Macromolecules

The structure of a Carbohydrate

Monosaccharides – a single sugar molecule with a carbon backbone of three to seven carbons
Disaccharides - two monosaccharides that have been joined by a dehydration rection. (maltose)
Polysaccharides - long polymers that contain long chains of glucose subunits.
Starch – Storage form of glucose in plants. Starch is a polymer of glucose molecules with some
branching.
Glycogen – Multi branched polymer of glucose. Glycogen is a highly branched polymer of glucose
molecules.
---------------the chemical linkage is difference from starch to glycogen ------------------------------------

Cellulose – glucose units joined such that oxygen atoms are in alternating up/down positions.
Chitin – found in the exoskeleton of crabs, is another structural polysaccharide.
Formula for glucose is C6 H12 O6, Glucose is a Hexose, referring to its six-carbon sugar construction.
The structure of a Lipid (hydrophobic)
-Fats and Oils are comprised of glycerol and 3 fatty acids.
They also function as long-term energy storage.
-Phospholipids have a hydrophilic head and a hydrophobic tail and make up the plasma membrane.
These lipids are comprised of 2 fatty acid tails and a glycerol phosphate head.
-Steroids contain no fatty acids; they instead provide flexibility to the plasma membrane.
Cholesterol, Testosterone, and Estrogen are examples of steroids.

Steroids are composed of a carbon skeleton of four fused rings.

Fat molecules are aka a Triglyceride, which means it has one glycerol molecule and three fatty acids.

Saturated Fatty Acids have no double bonds between carbon atoms. (the more saturated the more solid)
Unsaturated fatty acids have one or more bonds between carbon atoms.
Trans Fatty Acids are hydrogenated which makes them more stable at room temperature. (not natural
therefore this fatty acid is not good for your body as it cannot break it down.)

The Polypeptide construction

Amino Acids contain an amino group, an acid group, and a variable R group.
These groups are arranged around a central carbon atom.
Amino acids are joined together by a dehydration reaction, during which a covalent bond is formed
between each individual amino acid.
When two or more amino acids are bonded together, a molecule called a peptide is formed.
When a chain of amino acids is bonded together, a poly peptide is formed.
The behavior and function of a polypeptide depends upon the sequence of the amino acid.

Protein Structure
A sequence of polymers that are composed of amino acids strung together in a strand forms a primary
structure.
Once amino acids begin to form bonds with one another to create helical or sheet-like formations, a
secondary structure is formed.
When amino acids bond further, creating a globular shape, it is referred to as its tertiary structure.
When two or more polypeptides bond together into a working protein, it represents a quaternary structure.
Amino Group (NH2)
Acidic Group (COOH)
Four of the 20 common amino aids are alanine (Ala,) valine (Val,) cysteine (Cys,) Phenylalanine (Phe.)
REMEMBER (below)

Proteins have up to 4 levels of organization

- Primary Structure (insulin)
- Secondary Structure
- Tertiary Structure
- Quaternary Structure (hemoglobin)

What is Emulsification? (Clothes Detergent)

- Fats and oils can disperse in water with the help of emulsifiers.
- Emulsifiers contain molecules with a polar and non-polar end.
- The nonpolar end of emulsifiers surrounds fat or oil droplets, and separates them.

Difference between DNA and RNA

DNA (Deoxyribonucleic Acid)
Contains a deoxyribose sugar.
Double Stranded
Stores genetic information.
Contains bases, guanine, cytosine, adenine, and thymine.
In DNA, sugar and phosphate alternate.
RNA (Ribonucleic Acid)
Single Stranded
Serves as a temporary intermediate between genes and polypeptides.
Contains ribose sugar.
 Contains bases guanine, cytosine, adenine, and uracil.
DNA and RNA are nucleotides, which are a molecular complex of
Phosphates
Pentose (ribose or deoxyribose
nitrogen-containing base.
- DNA contains adenine(A), thymine(T), guanine(G), and cytosine(C.)
- In RNA uracil replaces thymine.

Finally, ATP
ATP, or Adenosine Triphosphate provides energy for nerve impulse conduction, muscle contraction, and
many other chemical reactions necessary for life.
It is a nucleotide that is comprised of adenine, ribose, and three phosphate molecules.
The phosphates are held together by unstable bonds.
These bonds have a high energy associated with them, so when they break, energy is released, and
adenosine diphosphate is formed.