Biochemistry is one of the crossover fields of chemistry. Biochemists have to understand
both the living world and the chemical world. Even if you don’t want to become a biochemist,
you'll still have to understand atoms and molecules as a biologist. The bulk of biochemical
investigation focuses on the properties of proteins, many of which are enzymes. For historical
reasons, the biochemistry of metabolism has been one of the most extensively described
aspects of the cell.
The key thing to remember is that biochemistry is the chemistry of the living world. Plants,
animals, and single-celled organisms all use the same basic chemical compounds to live their
lives. Biochemistry is not about the cells or the organisms. It's about the smallest parts of
those organisms, the molecules. It's also about the cycles that create those biological
compounds.
Repeating Biochemical Cycles
You can probably guess that biochemical cycles repeat over and over. Those cycles allow
living creatures to survive on Earth. It could be the constant process of photosynthesis that
creates sugars in plants or building complex proteins in the cells of your body. Also, cycles
rely on enzymes and other proteins to move the atoms and molecules. Understanding the
helper molecules is as important as learning about the cycles themselves.
Every cycle has a place, and each one is just a small piece that helps an organism survive. In
each cycle, molecules are used as reactants and then transformed into products. Life is one
big network of activity where each piece relies on all of the others. A compound, such as an
herbicide, may only break one part of one cycle in a plant. However, because everything
needs to work together, the whole plant eventually dies.
Organic macromolecules (also called biomolecules) are the molecules which exist in all living things.
They are life’s building blocks. All living things are formed from these organic molecules. There are
four categories of organic molecules: Carbohydrates, lipids, proteins and nucleic acids. They are also
known as macromolecules, which means “giant molecules”.
Organic molecules have four common characteristics. First, they are all carbon based, meaning they
all contain carbon. Second, they are formed from just a few elements which join together to form
small molecules which join together, or bond, to form large molecules.
The third characteristic of all organic molecules is that each is kind of organic molecule is built from a
single type of building block. For example, the building block of carbohydrates is sugar, the building
block of lipids is fatty acids, the building block of protein is amino acids and the building block of
nucleic acids is the nucleotide. When these building blocks (monomers) are joined together, they
form a large molecule (polymer), just as bricks joined together form a wall. For example, sugars join
together form a carbohydrate.
The last common characteristic of all organic molecules is that their form determines their function.
That means that their shape determines how they will behave and how they will react with other
molecules. For example, the order of amino acids in a protein will determine the shape and function
of the protein just as the order of words in a sentence shapes the meaning of the sentence.
Carbohydrate is a fancy way of saying "sugar." Scientists came up with the name because the molecule has
many carbon (C) atoms bonded to hydroxide (OH-) groups. Carbohydrates can be very small or very large
molecules, but they are still considered sugars. Plants can create long chains of these molecules for food
storage or structural reasons.
A carbohydrate is called an organic compound, because it is made up of a long chain of carbon atoms.
Sugars provide living things with energy and act as substances used for structure. When sugars are broken
down in the mitochondria, they can power cell machinery to create the energy-rich compound called ATP
(adenosine triphosphate).
Scientists also use the word saccharide to describe sugars. If there is only one sugar molecule, it is called a
monosaccharide. If there are two, it is a disaccharide. If there are three, it is a trisaccharide.
What about the simplest of sugars? A sugar called glucose is the most
important monosaccharide on Earth. Glucose (C6H12O6) is created by
photosynthesis and used in cellular respiration. When you think of table
sugar, like the kind in candy, it is actually a disaccharide. The sugar on
your dinner table is made of glucose and another monosaccharide called
fructose (C6H12O6). These sugars have the same numbers of atoms, but
they are different structures called isomers.
When several carbohydrates combine, it is called a polysaccharide ("poly" means many). Hundreds of sugars
can be combined in a branched chain. These chains are also known as starches. You can find starches in
foods such as pasta and potatoes. They are very good sources of energy for your body.
An important structural polysaccharide is cellulose. Cellulose is found in plants. It is one of those
carbohydrates used to support or protect an organism. Cellulose is in wood and the cell walls of plants. You
know that shirt you're wearing? If it is made of cotton, that's cellulose, too! There can be thousands of
glucose subunits in one large molecule of cellulose. If we were like some herbivores or insects, such as
termites, we could eat cellulose for food. Those animals don't actually digest the polysaccharides. They have
small microorganisms in their bellies that break down the molecules and release smaller sugars.
Polysaccharides are also used in the shells (chitin) of crustaceans, such as crabs and lobsters. Chitin is similar
in some ways to the structure of cellulose, but has a far different use. The shells are solid, protective
structures that need to be molted (left behind) when the crustacean begins to grow. It is very inflexible. On
the other hand, it is very resistant to damage. While a plant may burn, it takes very high temperatures to
hurt the shell of a crab. If you know the way crabs are cooked, you know that the crab meat cooks on the
inside of the shells when it is boiled. There is no damage to the shells at the temperature of boiling water
(H2O at 100oC).
Lipids are another type of organic molecule. When you think of fats & oils, you should know that
they are lipids. Lipids are also used to make steroids and waxes. Lipids are made mostly from carbon
and hydrogen, and are generally not soluble in water.
Waxes are used to coat and protect things in nature. Bees make wax. It can be used for structures,
such as the bees' honeycombs. Your ears make wax. It is used to protect the inside of your ear.
Plants use wax to stop evaporation of water from their leaves. There is a compound called cutin that
you can find in the plant cuticle covering the surface of leaves. It helps to seal and protect plant
structures. Don't worry about plants being able to breathe. There are still small holes that let gases
in and out of the leaves.
Steroids are found in animals within something called hormones. The basis of a steroid molecule is a
four-ring structure: one ring with five carbons and three rings with six carbons. You may have heard
of steroids in the news. Many bodybuilders and athletes have used anabolic steroids to build muscle
mass. The steroids make their bodies add more muscle than they would normally be able to. Those
anabolic steroids help bodybuilders wind up stronger and bulkier (but not faster). Steroids are also
used in necessary medicines. Some help people with acne, while others are used as muscle relaxers
for injuries.
Fat is also known as a triglyceride. It is made up of
a molecule known as glycerol that is connected to
one, two, or three fatty acids. Glycerol is the basis
of all fats and is made up of a three-carbon chain
that connects the fatty acids together. A fatty acid
is just a long chain of carbon atoms connected to
each other.
There are two kinds of fats, saturated and unsaturated. Unsaturated fats have at least one double
bond in one of the fatty acids. A double bond happens when four electrons are shared or exchanged
in a bond. They are much stronger than single bonds with only two electrons. Saturated fats have no
double bonds.
Fats have a lot of energy stored up in their molecular bonds. That's why the human body stores fat
as an energy source. When you have extra sugars in your system, your body converts them into fats.
When it needs extra fuel, your body breaks down the fat and uses the energy. Where one molecule
of sugar only gives a small amount of energy, a fat molecule gives off many times more.
Proteins are macromolecules that contain nitrogen as
well as carbon, hydrogen & oxygen. Proteins are made
of amino acids. Even though a protein can be very
complex, it is basically a long chain of amino acid
subunits all twisted around like a knot.
As proteins are being built, they begin as a straight chain
of amino acids. This chain structure is called the primary
structure. Sometimes chains can bond to each other
with two sulfur (S) atoms. Those bonds would be called a
disulfide bridge.
After the primary structure comes the secondary
structure. The original chain begins to twist. It's as if you
take a piece of string and twist one end. It slowly begins
to curl up. In the amino acid chain, each of the amino
acids interacts with the others and it twists like a
corkscrew (alpha helix) or it takes the shape of a folded
sheet (beta sheet). We talked about amino acids that are
hydrophobic and hydrophilic. Those desires to stay away
or be close to water (H2O) play a part in the twisting.
Let's move on to the tertiary structure of proteins. By now you're probably getting the idea that
proteins do a lot of folding and twisting. The third step in the creation of a protein is the tertiary
structure. The amino acid chains begin to fold even more and bond using more bridges (the disulfide
bridges).
We can finally cover the quaternary structure of proteins. Quaternary means four. This is the fourth
phase in the creation of a protein. In the quaternary structure, several amino acid chains from the
tertiary structures fold together in a blob. They wind, entwined, in and out of each other. Some of
the most famous protein blobs are hemoglobin in human red blood cells and the photosystems in
plant chloroplasts.
Some proteins control the rate of reaction and regulate cell processes. Some are used to form bone
and muscle. Others transport substances into or out of cells, or help fight disease.
Nucleic acids are the building blocks of living organisms. You may have heard of DNA described the
same way. Guess what? DNA is just one type of nucleic acid. Some other types are RNA, mRNA, and
tRNA. All of these "NAs" work together to help cells replicate and build proteins.
DNA stands for deoxyribonucleic acid.
RNA stands for ribonucleic acid. The
mRNA and tRNA are messenger RNA
and transfer RNA, respectively. You
may even hear about rRNA which
stands for ribosomal RNA. They are
called nucleic acids because scientists
first found them in the nucleus of cells.
Now that we have better equipment,
nucleic acids have been found in
mitochondria, chloroplasts (small
structures found in cells), and in cells
that have no nucleus, such as bacteria
and viruses.
Nucleic acids are actually made up of chains of base pairs of nucleic acids stretching from as few as
three to millions. When those pairs combine in super long chains (DNA), they make a shape called a
double helix. The double helix shape is like a twisty ladder. The base pairs are the rungs. We're very
close to talking about the biology of cells here. While it doesn't change your knowledge of the
chemistry involved, know that DNA holds your genetic information. Everything you are in your body
is encoded in the DNA found in your cells. Scientists still debate how much of your personality is
even controlled by DNA.
There are five easy parts of nucleic acids. All nucleic acids are made up of the same building blocks
(monomers). Chemists call the monomers "nucleotides." The five pieces are uracil, cytosine,
thymine, adenine, and guanine. No matter what science class you are in, you will always hear about
ATCG when looking at DNA. Uracil is only found in RNA. Just as there are twenty amino acids needed
by humans to survive, we also require five these five nucleotides.
These nucleotides are made of three parts:
1. A five-carbon sugar
2. A base that has nitrogen (N) atoms
3. An ion of phosphoric acid known as phosphate (PO43-)
Enzymes are proteins that act as biological catalysts. A catalyst is a
substance that speeds up the rate of a chemical reaction. Enzymes speed
up the chemical reactions that take place in cells.
How do enzymes do their jobs? Let’s say you ate a piece of meat.
Proteases would go to work and help break down the peptide bonds
between the amino acids. Will all enzymes break down all substances?
No.
Enzymes are very specific catalysts and usually work to complete one
task.
An enzyme that helps digest proteins will not be useful to break down carbohydrates. Also, you will not find all
enzymes everywhere in the body. That would be inefficient. There are unique enzymes in neural cells, intestinal cells,
and your saliva.
You know about cars and the assembly lines where they are
made. There are giant robots helping people do specific tasks.
Some lift the whole car, some lift doors, and some put bolts on
the frames. Enzymes are like those giant robots. They grab one or
two pieces, do something to them, and then release them. Once
their job is done, they move to the next piece and do the same
thing again. They are little protein robots inside your cells. The
robot that was
designed to move a car door can't put brakes on the car. The specialized robot arms just can't do the job. Enzymes
are the same. They can only work with specific molecules and only do specific tasks. Because they are so specific,
their structure is very important. If only one amino acid of the enzyme is messed up, the enzyme might not work. It
would be as if someone unplugged one of the cords in a robot.
Four Steps of Enzyme Action
1. The enzyme and the substrate are in the same area. Some situations have more than one substrate molecule that
the enzyme will change.
2. The enzyme grabs on to the substrate at a special area called the active site. The combination is called the
enzyme/substrate complex. Enzymes are very, very specific and don't just grab on to any molecule. The active site is a
specially shaped area of the enzyme that fits around the substrate. The active site is like the grasping claw of the
robot on the assembly line. It can only pick up one or two parts.
3. A process called catalysis happens. Catalysis is when the substrate is changed. It could be broken down or
combined with another molecule to make something new. It will break or build chemical bonds. When done, you will
have the enzyme/products complex.
4. The enzyme releases the product. When the enzyme lets go, it returns to its original shape. It is then ready to work
on another molecule of substrate.
“What if enzymes just kept going and converted every molecule in the world? They would never stop. They would
become monsters!" Don’t worry. There are many factors that can regulate enzyme activity, including temperature,
activators, pH levels, and inhibitors.
Energy in Reactions
Energy is released or absorbed whenever chemical bonds form or are broken. Chemical
reactions that release energy often occur spontaneously. Chemical reactions that
absorb energy will not occur without a source of energy.
Energy-Releasing Reaction
May occur spontaneously
Energy-Absorbing Reaction
Requires a source of energy
An example of an energy-releasing reaction is hydrogen gas burning, or reacting, with oxygen to
produce water vapor.
2H + O2→2H2O
The energy is released in the form of heat, and sometimes – when hydrogen explodes – light and
sound.
In order to stay alive, organisms need to carry out reactions that require energy. Plants get their
energy by trapping and storing energy from sunlight. Animals get their energy by consuming plants
or other animals. Humans release the energy needed to grow, to breath, to think, and even to dream
through chemical reactions that occur when we metabolize (break down) digested food.
Even chemical reactions that release energy do not always occur spontaneously. That’s a good thing
because if they did, things would just randomly burst into flames! Chemists call the energy that is
needed to get a reaction started the activation energy.
Biochemistry and Macromolecules
Name ________________________________
Biochemistry
1. Biochemistry is the chemistry of _____________________________________________________________.
2. The bulk of biochemical investigation focuses on the properties of ______________________, many of which are ____________________.
3. The biochemistry of ________________________________ has been one of the most extensively described aspects of the cell.
4. Biochemistry is about _________________________ that create biological compounds and molecules.
5. What are two examples of biochemical cycles?
6. Cycles rely on __________________________ and other proteins to move atoms and molecules.
7. In each cycle, molecules are used as ____________________________ and then transformed into ___________________________.
Organic Macromolecules
1. Macromolecules means __________________________________________.
2. What is the first characteristic common to all organic molecules?
3. What’s the second characteristic?
4. The third?
5. What are the building blocks for each of the four molecules?
Carbohydrates - ___________________________
Lipids - _____________________________
Proteins - ________________________________
Nucleic Acids - ________________________________
6. The building blocks are also known as _____________________________, which join together to form ____________________________.
7. The process is known as ___________________________________________.
8. What is the last common characteristic? Explain
Carbohydrates
1. Carbohydrates are also called “_____________________”.
2. What do plants use carbohydrates for?
3. Sugars provide ______________________ and ______________________________________________ for living things.
4. Where are sugars broken down to power cells? _______________________________ What is produced? _________________
5. One sugar molecule is a _______________________________, two molecules is a ___________________________________, and
three is a ____________________________________________.
6. What’s the simplest sugar? _________________________ What’s its chemical formula?
_____________________ How is it made? ______________________________
What’s it used for? ______________________________________________
7. Draw the structural formula diagram in the box to the right.
8. Table sugar is made up of __________________________ and
______________________________, which have the same number of atoms, but different
structures called _________________________.
9. Several carbohydrates combined are called a _________________________________________.
These long chains are also known as _________________________________, found in foods like __________________________________.
10. An important polysaccharide is ______________________________, found in ______________________________.
11. Who can eat cellulose?
How do they accomplish this?
12. Who else uses polysaccharides, and what do they use it for?
Lipids
1. What are four kinds of lipids?
2. Lipids are generally not water ___________________________.
3. What are waxes used for in nature?
4. Describe the structure of a steroid molecule.
5. Where are steroids found?
What, besides building muscle mass, are they used for?
6. Fat is made up of a molecule called _________________________, and is also known as a __________________________________.
7. What are the two kinds of fats?
8. What is the difference between the two?
9. Why do humans store fat?
Proteins
1. What four elements are proteins made of?
2. Describe the primary structure of protein.
3. Describe the secondary structure.
4. Describe the tertiary & quaternary structures.
5. What are two examples of proteins?
6. What are some of the things proteins are used for?
Nucleic Acids
1. What are four kinds of nucleic acids?
2. What do they do?
3. Nucleic acids are made up of ______________________________________________________.
4. Draw a diagram of the DNA double helix in the box to the right.
5. DNA holds your ______________________________________________________.
6. What are the four nucleotides that make up DNA?
7. What are the four nucleotides that make up RNA?
8. What are the three parts of a nucleotide?
1.
2.
3.
Enzymes
1. Enzymes are ___________________________ that act as _____________________________________________________.
2. What’s a catalyst?
3. Enzymes speed up the chemical reactions that take place in ___________________.
4. When you eat something, ________________________ go to work to break down the _____________________________
between the amino acids.
5. Enzymes have specific jobs such as …
6. Describe the four steps of enzyme action.
1.
2.
3.
4.
7. What are some factors that regulate enzyme activity?
Energy in Reactions
1. Energy is release or absorbed when chemical bonds are __________________________________________________.
2. Chemical reactions that release energy _______________________________________________________________.
3. Chemical reactions that absorb energy _______________________________________________________________.
4. Hydrogen gas reacts with oxygen to produce ________________________________________.
5. What are the reactants in this reaction?
What are the products?
6. What form does the energy take when it is released?
7. What is the energy needed to get a reaction started?
8. When we ____________________________ (break down) food we eat, we release energy to…
Read the directions below to complete the back of this sheet.
For each of the four biomolecules, choose one of these options:
a. Draw a cartoon version of the molecule performing its job or function.
b. Write a short poem or song that describes what the molecule does.
c. Write a short story of “a day in the life” of the molecule.
d. Draw a picture of the molecule in the role of a super hero, and explain its super powers.
Carbohydrates
Proteins
Lipids
Nucleic Acids