Mr. Ramos
Water, Biochemistry, and Cell Morphology & Structure Study Guide
Students, here is a study guide for the Water, Biochemistry, and Cell Morphology & Structure Test. Read
it and study it carefully in conjunction with your class & book notes. Remember the test is worth 50% of
your total class grade. The test is curved. Take advantage of this generous study guide. I will NOT always
do these nice things for you all.
Water
Water is perhaps the most important molecule on Earth. Without water there could be no life.
Water is so important that about 60 – 75% of a person’s body weight is water, and about 71% of Earth is
covered in water. WOW!!
So what makes water so special? Well first of all the molecular formula for
water is H2O. This means that one oxygen atom is covalently bonded to two
hydrogen atoms.
A covalent bond is a chemical bond where atoms share their electrons. Two
hydrogen atoms share electrons with an oxygen atom, and these result in a
water molecule, H2O.
Finally, what makes water so unique is that the big fat oxygen atom does not like
to share its electrons equally with the two small hydrogen atoms. Oxygen is an
electron lover (aka an electronegative atom). Therefore, the electrons will spend
more time around the oxygen atom.
Because water does NOT share electrons equally, we refer to it as having a polar
covalent bond. So, in a regular covalent bond (aka non-polar covalent bond) the
electrons are shared equally, but in a polar covalent bond the electrons are shared
unequally.
Since the electrons spend more time around the oxygen atom, the oxygen atom will
become slightly negative relative to the hydrogen atoms that will become slightly
positive. This is a result of polarity.
Because water has a slightly negative charge and a slightly positive charge, it will act like a magnet and it
will stick to other water molecules. The attraction between one water molecule and another water
molecule is a result of hydrogen bonds (H2O ----- H2O)
*Please pay special attention to the difference between the covalent bond in H2O and the
hydrogen bond between H2O----H2O. Students get these two concepts wrong on tests. The polar
covalent bond is for the 2 hydrogen atoms and the 1 oxygen atom, while the hydrogen bond is for
several water molecules that attract each other like magnets.
The top part was actually the hardest part to understand…Now for the easier parts of water.
Water is the universal solvent. A solvent is a substance in greater quantity that will
dissolve another substance known as the solute. Water is the solvent and sugar is
the solute. If you put sugar in water, the water will dissolve it.
Water holds on to other water molecules as hard as they can (water buddies). This
property of water is called cohesion. Cohesion is when water sticks to water. The
water strider is able to walk on water because water will try to hold on to each
other to prevent the water strider from separating them.
Water can also stick to other substances other than itself. This is called adhesion. Isn’t water such a
friendly molecule? If you have a bathtub and a curtain, wet the curtain and cover the edge of the
bathtub to prevent water from spilling outside and wetting the floor. The wet curtain will stick to the
wall. This is adhesion.
or
When cohesion and adhesion work together, water can climb up the roots of plants and spread up and
out towards the leaves. The movement of water up the roots to the stem and leaves is called capillary
action.
Water has a high surface tension. This means that the water buddies will hold on to each other and
become tense. Moral of the story…Do not jump into a pool on a belly position, or the water will smack
you silly.
(this is going to hurt…)
(look how the tension holds the coin)
The next water property is density. Solid water (ice) is actually LESS DENSE than liquid water. This
allows ice to float. This is important because when the ocean freezes, the ice rises and the ocean
animals can still swim underwater. Water is actually densest at 4 degrees Celsius (this is cold water but
not frozen water).
The last water property is high heat capacity. Water can hold a lot of heat. This is
why our bodies carry so much water…So we do not burn or melt when we go out in
sunny Florida; moreover, the water will keep you from freezing if one day you
decide to go to New York during the holidays.
Water freezes at 0 degrees Celsius and boils at 100 degrees Celsius.
pH (literally stands for “power of hydrogen”)
The pH is a way to determine whether something is an acid, a base, or neutral.
The pH scale is logarithmic (that is a fancy way of saying you multiply by 10 for each increase or
decrease). For example: a pH of 2 is 100 times more acidic than a pH of 4 (10 x 10 = 100)
The pH scale ranges from 0 to 14, and 7 is neutral. Water has a neutral pH of 7.
A pH below 7 is considered acidic, while a pH above 7 is considered basic (aka alkaline).
The more hydrogen ions, H+, in a solution compared to hydroxide ions, OH-, the more acidic the
solution is.
The more hydroxide ions, OH-, in a solution compared to hydrogen ions, H+, the more basic the
solution is.
Every living thing has an optimal level of pH. This is level where the organisms can
actually live and survive. If the pH changes below or above the optimum range, the
organism may die. For example, blood has a pH range of 7.35 – 7.45. If blood pH
drops or rises, a person may die!
Your body needs to keep your blood at a pH between 7.35 – 7.45, or you may die if the
pH drops below 7.35 or rises above 7.45. How does your body keep the pH at this
range? Your body uses something called a buffer. A buffer is a compound used to
maintain the pH at a certain range.
When the pH becomes too acidic, the buffer will release basic ions to increase the pH back to its range.
When the pH becomes too basic, the buffer will release acidic ions to drop the pH back to its range.
Biochemistry
A macromolecule is a large molecule.
There are 4 macromolecules: carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates come from plants and are the body’s main source of energy.
Examples: rice, tomatoes, bread, pizza, beans, bananas, etc…
Carbohydrates contain the elements carbon, hydrogen, and oxygen in a 1:2:1 ratio.
Glucose is a simple sugar. It is a carbohydrate. Count the number of
carbon, hydrogen, and oxygen atoms in glucose. Glucose has 6
carbon atoms, 12 hydrogen atoms, and 6 oxygen atoms. Thus, the
molecular formula for glucose is C6H12O6. Notice that glucose has the
1:2:1 ratio because the number of carbon and oxygen atoms is the
same, while the number of hydrogen atoms is twice as much.
Sometimes simple carbohydrates like glucose are written as a ring (right), while other times it is written
in a linear manner (left).
Sugars typically end with the suffix –ose. This is how you know it is a sugar.
Examples of sugars: glucose, fructose, galactose, maltose, cellulose.
Glucose is a one sugar molecule. Glucose is a monosaccharide.
Lactose, the sugar in milk, is made up of two different sugars. Lactose is a disaccharide.
Cellulose is the sugar that makes the cell wall of plants. Cellulose is made up of many repeating sugars.
Cellulose is a polysaccharide.
Lipids are fats, sterols, waxes, etc…Keep it simple, lipids are fats.
Lipids contain the elements carbon, hydrogen, and oxygen. Lipids have the same exact elements are
carbohydrates. Oh, oh…How do we tell the difference? Lipids do NOT have the 1:2:1 ratio, and lipids
tend to have more carbon and hydrogen bonds while having very few oxygen atoms.
Lipids hate water. They are hydrophobic.
The functions for lipids include longer term energy, insulation, and water proof.
Lipids can be saturated with hydrogen atoms, or they can be unsaturated
by hydrogen atoms.
The saturated fat is a solid at room temperature and less healthy than the
unsaturated fat, which is a liquid at room temperature.
Proteins are made up of monomers called amino acids.
Amino acids, and thus proteins, contain the elements carbon, hydrogen, oxygen, and nitrogen. Notice
that proteins have one more element when compared to carbohydrates and lipids, and that extra
element is nitrogen.
All amino acids have 4 things in common
1. Amine group (NH2)
2. A central carbon atom
3. 1 hydrogen atom attached to the central carbon atom
4. A carboxylic acid group (COOH)
*The only thing that is different from one amino acid to the next is the side chain known as the R group.
Check out the R groups on the picture below. The R group for Alanine is CH3 while the R group of the
other amino acids is much more complicated.
If you want to connect two amino acids (or ANY other molecule), you need to
remove a water molecule. Removing water is called dehydration synthesis. If
you want to break a molecule, just add water. Adding water is called hydrolysis.
So, water tends to break things, and removing water tends to form things.
Examples of proteins include enzymes, antibodies, hormones, and food (meat).
Nucleic Acids are composed of monomers called nucleotides. Nucleic acids contain the genetic
information of an organism.
Nucleotides, and thus nucleic acids, contain the elements carbon, hydrogen, oxygen, nitrogen, and
phosphorus. If you see a phosphate group, or simply a phosphorus atom, you should select the
nucleotide/nucleic acid choice.
There are two kinds of nucleic acids: DNA and RNA.
The NA in DNA and RNA stands for nucleic acid…but I am sure you knew that since you are very smart.
DNA
Nitrogenous Bases: A, T, C, G
Double Stranded
Deoxyribose sugar
Deoxyribonucleic Acid
Phosphate group
RNA
Nitrogenous Bases: A, U, C, G
Single Stranded
Ribose sugar
Ribonucleic Acid
Phosphate group
Notice that DNA and RNA have the phosphate group in common and the bases A, C, and G. Everything
else is different.
Cell Morphology
The story of the cell begins with Robert Hooke and his invention of the microscope. Hooke placed a
piece of a cork (like from a wine bottle) under his microscope and noticed that the structure of the cork
under the microscope looked like jail cells. Hooke decided to use the word “cell” from there on.
After the microscope was invented, and we were able to study cells, the cell theory was born.
The cell theory states 3 things:
1. All living things are composed of cells (bacteria are cells, so they are ALIVE)
2. Cells are the basic unit of structure and function in living things
3. New cells are produced from existing cells (“Omnis Cellula e Cellula” – Rudolf Virchow)
*Viruses are not cells, nor do they contain cells; therefore, viruses are NONLIVING.
Cells are divided into two categories: Eukaryotic cells and Prokaryotic cells
-Eukaryotes = True Nucleus (these cells have a nucleus)
- Prokaryotes = Before Nucleus (these cells do not contain a nucleus)
There are 4 Eukaryotes: Animals, Plants, Fungi, & Protists
There are 2 Prokaryotes: Bacteria & Archaea
Nucleus
Organelles
Ribosome
Plasma Membrane
Size
Eukaryotic Cells
Yes
Yes
Yes
Yes
Bigger than Prokaryotes
Prokaryotic Cells
No
No
Yes
Yes
Smaller than Eukaryotes
Scientists use a compound light microscope to study cells.
Guess why they call it a compound light microscope…It
uses “light” to view the specimen, and it uses multiple
lenses (compound).
All you need to know about this type of microscope is to
multiply the lenses that you use to get your total
magnification, or power. The ocular lens found within the
eyepiece has a magnification of 10X. Then you will select
one of the three objective lenses: 4X, 10X, or 40X. Finally
multiply the ocular lens with the objective lens that you
decided to use.
Total Magnification: 10X x 40X = 400X
If a researcher at a university or private company is interested in looking inside the cell to investigate the
structure and function of each organelle, then he or she will need a more powerful microscope.
The electron microscope is more powerful than the light microscope. Instead of using light, the electron
microscope fires a beam of electrons.
Two types of electron microscopes:
1. Transmission Electron Microscope (TEM): lets you see inside a cell
2. Scanning Electron Microscope (SEM): lets you see the 3D outside of the cell
The downfall to the electron microscope:
1. Too expensive (you will not find one in High School)
2. You must use nonliving preserved cell specimens (no living cells
allowed)
Now we are ready to compare two special eukaryotic cells: the animal cell
and the plant cell.
Animal cells tend to be round (generally speaking) because they do not
have a cell wall.
Some animal cells have a tail called a
flagellum. Flagella allow cells to swim.
Sperm cells have flagella.
Plant cells, on the other hand, have a cell wall, chloroplast, and a large central vacuole.
Cytoskeleton of the Cell
Just as we have bones and muscles, the cell has its own skeleton, which is called the cytoskeleton.
The cytoskeleton is made up of microtubules, intermediate filaments, and microfilaments (aka actin
filaments)
Microtubules contain the protein tubulin & they participate in cell
division & cell movement
Examples: Centrioles, Cilia & Flagella.
Microfilaments contain the protein actin and are found in muscle cells. They also support cells & help
them move
Intermediate filaments are intermediate in size to the microtubules and microfilaments. You do not
need examples of intermediate filaments for the test, so don’t worry about these.
Animal Cell (a type of Eukaryotic Cell)
rRNA created & used
for protein assembly
Makes lipids &
detoxifies poisons
“Brain” of cell;
command center (DNA)
Cell membrane made
of phospholipid
bilayer regulates what
goes in or out of cell
Cellular
Respiration
(energy)
Releases spindles
that attach to
chromosomes
during cell
division
Finish making proteins
made on ribosome
Makes proteins
Protein sorting &
packaging (aka FEDEX
or UPS)
*Just because a cell has a cell wall does not mean it is a plant. Fungi and bacteria may have cell walls as
well.
In plants the cell wall is made of cellulose.
In fungi the cell wall is made of chitin.
In bacteria the cell wall is made of peptidoglycan.
Moral of the story… You need to look for more organelles to be 100% on the test that it is a plant. If you
notice that the organism has a cell wall, chloroplast, and central vacuole, then you can say that it is a
plant.
By the way, organelles are the organs of cells. The word organelle literally means “little organ.”
Plant Cell (a type of Eukaryotic Cell)
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Organelles:
Nucleus: cell’s command center (home of DNA)
Nucleolus: ribosomal RNA is assembled (rRNA)
Cytoplasm: area outside of the nucleus where the organelles are found
Plasma Membrane: the cell membrane regulates what goes in and out of the cell
Rough Endoplasmic Reticulum (RER): contains ribosomes & synthesizes proteins for cells to
export
Smooth Endoplasmic Reticulum (SER): does not contain ribosomes and is used to synthesize
fats and detoxification of drugs
Ribosome: factories for making proteins
Golgi Apparatus: modify, sort, and package proteins made in the rough endoplasmic reticulum.
Mitochondria: makes energy for the cell & contains its own DNA (cellular respiration)
Lysosomes: digest old organelles, macromolecules, and remove junk from the cell.
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Vacuoles: store materials, such as water, salts, proteins, and carbohydrates. They are like a
closet or kitchen cabinet. Plants have a large central vacuole, and animal cells have many small
vacuoles
Chloroplasts: converts sunlight into chemical energy & contains its own DNA (photosynthesis)
Cell Transport
The plasma membrane, or cell membrane, is found in every type of cell. It does not matter if the cell is
eukaryotic or prokaryotic. All cells must have a membrane. The plasma membrane regulates what goes
in or out of the cell.
The plasma membrane is made up of two layers of phospholipids, some proteins embedded in the
membrane, cholesterol, and some carbohydrates. This is referred to as the fluid mosaic model.
The two layers of phospholipids is called the phospholipid bilayer. Each phospholipid contains a water
loving phosphate head (hydrophilic) and two water hating lipid tails (hydrophobic).
The plasma membrane is selectively permeable (aka semi-permeable). This means that the membrane
allows some things to go through it and not others.
The following can pass through the plasma membrane phospholipid bilayer:
1. Small Non-polar molecules (e.g. oxygen molecule, carbon dioxide, methane)
2. Lipids (fats)
The following cannot pass through the plasma membrane phospholipid bilayer:
1. Large molecules (e.g. glucose)
2. Polar molecules (e.g. water)
3. Charged particles (e.g. Na+, Cl-, Ca2+)
Diffusion is the movement of particles from an area of higher concentration to an area of lower
concentration. There is simple diffusion and facilitated diffusion.
Diffusion does NOT require energy for it to occur. Diffusion is a form of passive transport.
No one likes to be crowded. Well, chemicals do not like to
be crowded either. Chemicals are a bit claustrophobic, so
they will spread out to less crowded areas. This sums up
what diffusion is.
If someone releases a bad odor in the front of the
classroom, eventually someone in the back of the room will
smell it. This is called simple diffusion. It is when molecules
spread to less concentrated areas.
Sometimes chemicals need help getting through the plasma
membrane from an area of higher concentration to an area
of lower concentration. This type of diffusion will occur if a
helper protein can make it happen. This is facilitated
diffusion.
Osmosis is the movement of water from an area of higher water concentration to an area of lower
water concentration through a selectively permeable membrane. Osmosis does not require energy; it is
another example of passive transport.
Look at the picture below. The U-shape apparatus is divided into the left and right side by a thin
selectively permeable membrane. There is water on the left and right side as well as salt (purple circles).
Question: Where is there more water in picture 1? Many students will say that there is the same
amount of water in picture 1; however, there is actually more concentration of pure water on the left
because there is less salt. Therefore, the water from the left will start to cross the membrane and go
over to the right side. You can see the water moving to the right in picture 2. This movement is osmosis.
Picture 1
Picture 2
Hypotonic solution: a water solution
with little amount of salt.
Hypertonic solution: a water solution
with a lot of salt.
Isotonic solution: a water solution
with equal concentrations of water
and salt.
You can see two real life examples of osmosis below:
1. When the red blood cell is placed in a hypertonic solution (a water solution with lots of salt), the
water from within the red blood cell will escape the cell & the cell will shrink.
2. When the red blood cell is placed in an isotonic solution (a water solution with equal water and salt),
the water will move in and out of the red blood cell at the same rate resulting in a normal cell.
3. When the red blood cell is placed in a hypotonic solution (a water solution with very little salt), the
water from the solution will enter the cell causing the cell to become huge and explode.
*Remember that diffusion and osmosis are examples of passive
transport (no energy required).
Active transport on the other hand, requires energy because the
particles are moving against their concentration gradient. In other
words, the particle is going from a less crowded area to a more crowded
area. The sodium-potassium pump is an example of active transport in
the body.
Sometimes cells need to bring in or out substances that are too large. When this happens, the cell finds
another way to get things in or out.
Endocytosis means to “bring in the cell.” Cells pinch and fold their entire plasma membrane to bring
something in. There are three different types of endocytosis.
1. Phagocytosis: “cell eating” – the cell brings in large food particles
2. Pinocytosis: “cell drinking” – the cell brings in liquids
3. Receptor-Mediated Endocytosis: the cell will bring in molecules that attach to cell receptors.
Exocytosis is when the cell takes large substances out of itself.