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Chapter 2 Unit two nature of matter
STUDENT
Lecture Notes
All life depends on chemistry. Chemistry begins with the atom. 100 million atoms in a line would
equal1 cm. Atoms have protons, neutrons and electrons. Protons are_________________, neutrons
are neutral charged and electrons have a negative charge. Electrons are in constant motion and are
what allows for _________________ _________________. The loss of an electron makes the
molecule positive. An unequal number of protons and electrons will cause the molecule to be an
_______that has a positive (fewer electrons) or negative (more e- than p+) charge.
Isomers are important to biochemistry. An isomer has the same atomic mass, and has the same
number of molecules, but the arrangement is different. Glucose and Dextrose both have the same
chemical formula of C6H12O6. The carbon chains are aligned differently.
Draw and example:
Radioactive isotopes have larger number of _________________in the nucleus. They have a
different atomic mass. They decay (break down) into the same element or different element at a
constant rate. Carbon has an atomic mass of 12 (6P+ and 6N). Carbon 14 has 6P and 8N. As it
decays, it can be used to determine the age of organic matter.
Elements combine and form compounds. The bonding of elements can either be ionic (give or take
an electron) or covalent (share electrons). Most biological bonds are _________________. Water is a
covalent bond and has some unique properties. It expands when frozen, rather than sink. Ice is less
dense and water is polar (charged on different sides).
Draw a water molecule and label the polar parts.
The positive side (hydrogen) is attracted to negative molecules. The negative side (oxygen) is
attracted to positive molecules. This ability to bond with both positive and negative molecules makes
water a universal solvent. About 70% of our body is made of high quality H 2O.
Cohesion -attraction between molecules of the same type. This is why insects can walk on water and
water makes a bead when in a drop.
Adhesion- attraction between molecules of different types. Water will stick to the sides of glass
because of adhesion. It is the reason that we must read volume from the bottom of the meniscus.
Roots from plants use both adhesion and cohesion to bring water to the top of a plant.
Solution- mixture of two or more liquids or solids dissolved in liquids.
Solute- Solid being dissolved.
Solvent- liquid dissolving the solute.
Acid
pH _________________
Neutral
pH _________________
Base
pH _________________
The more H+ ions given off, the lower the pH. The more OH- ions given off (meaning very few H+
ions will be given off), the higher the pH.
Buffers can _________________ changes in pH.
Carbon Compounds.
Carbon has 4 bonding sites and can either be a negative 4 charge when combing with positives in
CH4. (Methane). Hydrogen is positive, so carbon is _________________.
In CO2 (carbon dioxide), Oxygen is negative, so carbon is _________________.
The diversity makes life possible. All protein fats and carbohydrates are carbon based. All life is
carbon based.
Since it has 4 bonding sites, it can create limitless shapes of covalent bonds. Large carbon chains are
called macro (large) molecules.
Carbohydrates
The smallest unit of a carbohydrate is _________________ C6H1206. When you combine several
simple sugars such as glucose, galactose and fructose, you form a carbohydrate chain. One glucose
unit is called a _________________. Several monomers combined are called a
_________________. Carbohydrates are called _________________ or polysaccharides. Poly =
many, Saccharide = sugar. 4 calories/gram.
Animals store excess sugars in their muscles as glycogen. Plants store it as starch. Cellulose is an
isotope of glucose. Humans cannot digest it. It is in the cell wall of plants wood is cellulose.
Lipids fatty fat fat not phat
Lipids are _________________ in water. They mostly have carbon and hydrogen atoms. One
saturated fat molecule has 98 hydrogen atoms, 54 carbon atoms and 6 oxygen atoms (pg46).
Lipids have 9 calories per gram.
1. They store energy
2. line cells membranes are also found in steroids
3. Aid in protection of organs.
. A saturated fat has all _________________bonds of hydrogen. Unsaturated fats have double
bonds.
As large as the fat molecules is, it is considered to be monomer. There are no polymer fats.
(PG 46) sub unit = glycerol+ 3 fatty acids
Saturated fats are worse for you because they are saturated with hydrogen. Saturated fats are solids
at room temperature. (Bacon grease, animal fat) unsaturated fats are liquids at room temperature.
NUCLIC ACIDS DNA & RNA
These macromolecules contain carbon, hydrogen, oxygen, nitrogen, and phosphorus. Each unit of
this large molecule is called a _________________. The nucleotide has 3 parts. Sugar- ribose,
Nitrogen Base ( A T G C ) and phosphorus. Several million nitrogen bases bonded together make
up ___________. The arrangement of the adenine, guanine, cytosine and thymine determine your
genetic makeup.
AATGCCTACCATGGC
CATGCGGTACCGTA
These are two examples different individuals DNA sequence.
PROTEIN – more variety than any other fat or carb.
They contain H, C, O and Nitrogen. The smallest unit of protein is an_________________ _______.
There are 20 different amino acids. This allows for the diversity of proteins. Hairs, nails and muscle
are proteins. Yet they are very different in shape ant texture. All _________________ are also
protein. Blood cells are protein. The proteins on the surface of cells are what cause organ transplants
to be rejected.
There are 4 buildings levels of proteins
1. Amino acid chain.
2. Twisting of that chain into a specific shape.
3. The chain is folded.
4. Combing two or more proteins.
Prions are specialized proteins that enter the ____________and cause holes in it along with other
tissue damage. Bovine Spongiform Encephalopathy is also called ________________________
Millions of chemical reactions takes place in your body every minute. These reactions are from
building new molecules or breaking down molecules.
List three examples of chemical reactions in your body.
CO2 + H2O  H2CO3 (carbonic acid) this is the way the blood carries CO2 to the lungs.
H2CO3  CO2 + H2O the lungs release.
When a chemical reaction takes place, either it requires energy or energy is _________________.
Movement of muscles requires energy. When we eat food, when food is broken down, energy is
released or stored as fat or glycogen.
Activation Energy - Energy needed to get a reaction started
Depending on the reaction, a certain amount of energy is required to begin the chemical reaction.
Enzymes- proteins
They are proteins that speed up chemical reactions, but are not absorbed or used up in the
reaction. These types of enzymes are called catalysts. They can also reduce the amount of
activation energy required for a reaction to take place
From the below chemical reaction with carbonic acid, an enzyme called carbonic anhydrase
speeds up that reaction by 10 million.
CO2 + carbonic anhydrase + H2O 
H2CO3 +
carbonic anhydrase
Why would this be so important?
Enzymes are like car keys, they only can fit into one ignition. Enzymes can only react with one
other molecule. This specific enzyme must fit into or attach to another molecule. (pg. 52)
The enzymes cellulase can only break down cellulose. Some people do not have the enzyme
lactase, which breaks down lactose sugar in diary products. Lactase only works on Lactose. It
will only break this molecule down. One enzyme, one molecule to bond to.
Enzyme Substrate complex (lock and key)
Each enzyme has a _________________shape that matches the molecule’s shape. This shape
where the reaction will take place is called the__________________ ___________.
The _________________is the molecule that will react with the enzyme. When the substrate
attaches to the activation site, anew product is formed. This new product can be a larger molecule or
two or more smaller molecules.
You eat an egg for protein. The egg protein combines with digestive enzymes to break it down into
the amino acids. These amino acids attach to enzymes that make human protein.
Draw an example below
THINGS THAT AFFECT ENZYMES
Enzymes activity can be altered or regulated due to:
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Biochemistry Vocabulary Study Guide
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Acid
Activation Energy
Adhesion
Affect Enzyme Activity
Amino Acid
Base
Carbohydrate
Catalyst
Cohesion
Common Element in Living
Things
Covalent Bond
Disaccharide
DNA
Electron
Element
Enzyme
Enzyme Inhibitor
Inorganic Molecule
Ion
Ionic Bond
Lipid
Lock and Key
Monosaccharide
Water
Neutron
Nucleotide
Organic Molecule
pH Scale
Polar Molecule
Polymer
Polypeptide
Polysaccharide
Protein
Proton
Substrate
32_______Large polymer made from many monosaccharide
34_______Found in the nucleus of an atom, positive charge
27_______2 or more carbons in a molecule
2_______Amount of energy needed to get a chemical reaction started
31_______Many amino acids connected, forming a protein chain
5_______Building block of proteins
10_______Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus
15_______Found on the periodic table
33_______Large polymer or polypeptide made from amino acids
18_______less than two or no carbon atoms in a molecule
21_______Large Macromolecule made of glycerin and 3 fatty acids
6_______pH 8 or more
7_______Many sugar molecules, forming starch
25_______Found in the nucleus of an atom, neutral charge
28_______Measurement of hydrogen ion concentration from 1-14
35_______Molecule that the enzyme will react with
26_______Monomer of DNA, containing A,T,G, or C
22_______One enzyme will fit with only one substrate
29_______One side of molecule is more positive or negatively charged
1_______pH 6 or less
4_______Temperature, pH, amount of substrate, amount of enzyme
30_______Term used for any large molecule formed from monomers
19_______The loss or gain of an electron in an atom
24_______pH neutral
13_______Polymer found in the nucleus of the cell, made from many nucleotides
17_______Prevents a enzyme substrate complex from forming
11_______Sharing of electrons by two atoms
3_______Attraction of different type of molecules
9_______Attraction of same type of molecules
20_______When one atom gives or takes electrons from another atom
23_______Single sugar molecule
16_______Specialized protein that aids in metabolism
8_______Speeds up chemical reactions
14_______Spinning around an atom, negative charge
12_______Two sugar molecules