Bio-Chemistry Fundamentals

Biochemistry

If you had visited Biology4Kids you may recognize the topics of this section. We felt it was more appropriate to have the biochemistry section here on Chem4Kids. It is one of the crossover fields of chemistry. Biochemists have to understand both the living world and the chemical world to be the best at their jobs.

The key thing to remember is that biochemistry is the chemistry of the living world. Plants, animals, single-celled organisms... They 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 happen to create those compounds.

Those cycles that repeat over and over are the things that allow living creatures to survive on Earth. It could be the constant process of photosynthesis in plants that creates sugars or the building of complex proteins in the cells of your body. Every cycle has a place and they are just one building block that helps organisms live. In each of those cycles, molecules are needed and changed. It's one big network of activity where each piece relies on all of the others.

Start with the Basics

While we have been talking about all of these cycles, we think it's important that you understand the different types of molecules you will find in biochemistry. You should be thanking us. We aren't going to go into the citric acid cycle and its ten steps. We won't even look at the eleven steps involved in the breakdown of glucose (glycolysis). At your level of understanding, it's enough to understand the difference between a steroid, an amino acid, and a carbohydrate. There will be plenty of time for you to memorize the pathways and the movement of molecules during each step of a cycle.

METABOLISM

Metabolism is such a big word to explain a simple idea. We all need energy to survive. Plants, animals, or bacteria, we all need energy. Energy doesn't just float around in a form we can use to survive. We need to eat (mainly sugars) and digest food. That process of chemical digestion and its related reactions is called metabolism. Metabolism is the total of all of the chemical reactions an organism needs to survive.

Sounds a lot like biology. Why's it here in biochemistry? Two main chemical processes make our world go round. There are two simple chemical reactions. The first is called glycolysis. That's the breakdown of sugars. The second process is called photosynthesis. That is the reaction that builds sugars. You need to remember that the overall metabolism of an organism includes thousands of chemical reactions. Glycolysis and photosynthesis are the cornerstones to life.

BUILDING UP

First, you need to build up the molecules that store energy. We'll start with photosynthesis. It's no use explaining the breakdown of sugars without telling you how they were made.

LIGHT (Energy) + CO₂ + H₂O --> C₆H₁₂O₆ + O₂

This is the reaction that only plants can do (and some algae/bacteria). They take sunlight and combine carbon dioxide (CO₂) and water (H₂O). They create Glucose (C₆H₁₂O₆) and oxygen gas (O₂). Remember, plants put the energy in glucose.

BREAKING DOWN

It's metabolism and the process of glycolysis that takes that energy out of the sugar related molecules.

C₆H₁₂O₆ + O₂--> Usable Energy (ATP) + CO₂ + H₂O

Cells then use that extra energy to power the functions of the cell. The energy isn't still floating around; it's stored in an excitable compound called adenosine triphosphate (ATP). ATP is the power molecule used all over organisms and their cells to power the secondary reactions that keep us alive.

SWEET SWEET CARBS

Carbohydrate is a fancy way of saying "sugar." Scientists came up with the name because the compounds have many carbon atoms bonded to hydroxide groups. Carbohydrates can be very small or very large molecules, but they are still sugars. What are they used for?

WHAT'S IT USED FOR?

A carbohydrate is called an organic compound because it contains carbon. Sugars provide living things with energy and act as substances used for structure. Some examples of structures might be the shell of a crab or the stem of a plant.

SACCHARIDES

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. You get the idea.

SIMPLE SUGARS

What about the simplest of sugars? A sugar called glucose is the most important monosaccharide on Earth. Glucose is used in cellular respiration and created by photosynthesis. 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.

POLYSACCHARIDES

When several carbohydrates combine, it is called a POLYsaccharide ("poly" means many). Hundreds of sugars can be combined in a 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.

SUGARS IN STRUCTURES

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 cotton, that's cellulose, too!

Polysaccharides are also used in the shells of such crustaceans as crabs and lobsters (chitin). It 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 needs 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.

ACIDS IN PROTEINS?

The first thing you might be asking is, "What is an amino acid?" There are over twenty, and each one of them is a little different. Amino acids are used in every cell of your body and are used to build the proteins you need to survive. All organisms need some proteins, whether they are used in muscles or as simple structures in the cell membrane. Even though all organisms have differences, they still have one thing in common, the need for basic chemical building blocks.

Amino acids have a two-carbon bond. One of the carbons is part of a group called the carboxyl group. A carboxyl group is made up of one carbon (C), two oxygens (O), and one hydrogen atom (H). The carboxyl group is acidic. The second carbon is a part of the amino group. Amino means there is an NH₂ group bonded to the carbon atom. In the image you see a "+" and a "-." Those positive and negative signs are there because, in amino acids, one hydrogen atom moves to the other end of the molecule. An extra "H" gives you a positive charge.

MAKING CHAINS

Even though scientists have discovered over 50 amino acids, only 20 are used to make something called proteins in your body. Of those twenty, eight are defined as essential. The other twelve can be synthesized by an adult body. Thousands of combinations of those twenty are used to make all of the proteins in your body. Amino acids bond together to make long chains and those long chains of amino acids are also called proteins.

SOMETHING CALLED SIDE GROUPS

The side groups are what make each amino acid different from the others. Of the 20 used to make proteins, there are three groups. The three groups are ionic, polar and non-polar. These names refer to the way the side groups (sometimes called "R" groups) interact with the environment. Polar amino acids like to adjust themselves in a certain direction. Non-polar amino acids don't really care what's going on around them. You already know about ions and things that are ionic. The ionic amino acids should be easy to understand.

ENZYMES MAKE THE WORLD GO 'ROUND

On Chem4Kids, we often talk about reactions and the molecules that change in those reactions. Those changes don't happen on their own. If you leave a blob of protein in a Petri dish, will it just break down to the amino acids? No. What will do it? Enzymes! Enzymes are the biological substance (proteins) that act as catalysts and help complex reactions occur everywhere in life.

LOCKS AND KEYS

When you go home at night and the door is locked, can it open itself? Nope. You need a key that is just the right shape to fit in that lock. Otherwise, you're stuck in the cold. Enzymes work in a similar way (locks and keys). Enzymes complete very specific jobs and do nothing else. They are very specific locks and the compounds they work with are the special keys. In the same way there are door keys, car keys, and bike-lock keys, there are enzymes for neural cells, intestinal cells, and your saliva.

Here's the deal: there are four steps in the process of an enzyme working.
1. An enzyme and a substrate are in the same area. The substrate is the biological molecule that the enzyme will attack.
2. The enzyme grabs onto the substrate with a special area called the active site The active site is a specially shaped area of the enzyme that fits around the substrate. The active site is the keyhole of the lock.
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.
4. The enzyme lets go. Big idea. When the enzyme lets go, it returns to normal, ready to do another reaction. The substrate is no longer the same. The substrate is now called the product.

CAN YOU STOP THEM?

Good question! We know what you're thinking. What if enzymes just kept going and converted every molecule in the world? They would never stop... like a monster! There are many factors that can regulate enzyme activity, including temperature, activators, pH levels, and inhibitors.
Science loves units. But then again, they are a necessity. If you are going to measure something you will need a way to tell people how much you have. Here are only a few we use in chemistry...

PERCENTAGES

When you need to know how much of something you have compared to the whole amount. It is figured out by taking a decimal number and multiplying by 100.
"I have 20% of what I started with." That means you lost 80%. L-L-Loser!

GRAMS, KILOGRAMS, MILLIGRAMS

These are measures of mass.
"This candy bar has a mass of only a few grams."

LITERS, MILLILITERS

These are measures of volume.
"I just bought a 2 liter bottle of soda."

CELSIUS, FAHRENHEIT AND KELVIN

These are different measurements scientists use for temperatures.
"It's freezing outside." That could mean it is 0oC, 32oF, or 273K (just Kelvins, no degrees).

ATOMIC MASS UNITS

The way to measure the mass of different atoms.
"Carbon-12 weighs 12 AMU."

CALORIES

A unit of energy.
"A calorie is the amount of energy needed to raise the temperature of 1 gram of water 1 degree Celsius."

JOULES

It is a unit of energy.
"4.18 Joules is the same as 1 Calorie."

SECONDS, MINUTES AND HOURS

Measures of time.
"There are 60 seconds in a minute and 60 minutes in an hour."

CONSTANTS IN CHEMISTRY

First we have to tell you what a constant is. Simply put... A constant is a number or measurement that is always the same. No matter where, when, or what condition. When you have a formula which asks for a constant it is always the same number. Here are some examples...

	6.02 x 1023 NAME: Avogadro's Number WHAT: It tells you the number of atoms in a mole or the number of molecules in a mole of a substance.
	9.1x10-31kg NAME: Mass of an Electron WHAT: We talk about electrons spinning around the nucleus of an atom. Well the me is the mass of one of those electrons.
	1.675x10-24g NAME: Mass of a Neutron WHAT: In the nucleus of an atom there are neutrons and protons. A neutron has this much mass.
	1.673x10-24g NAME: Mass of a Proton WHAT: In the nucleus of an atom there are neutrons and protons. A proton a mass of this amount.
	6.63x10-34Js NAME: Planck's Constant WHAT: Max Planck figured out that energy can be gained and lost by an atom. He used this constant to figure out how much energy. The "J" stands for Joules.
	3x108m/s NAME: Speed of Light (in a vacuum) WHAT: Scientists figured out that light always travels at the same speed in a vacuum. The number is really 299,792,458 meters per second, but we abbreviate it.
	9.8 m/s2 NAME: Acceleration of Gravity of Earth WHAT: What if you drop a ball from a height? It speeds up as it falls. The amount it speeds up (acceleration) is because of gravity.
	1.66x10-27kg NAME: Atomic Mass Unit (also called a Dalton) WHAT: It is 1/12 the mass of a Carbon-12 atom. It is the basis for figuring out the mass all other atoms.
	1.6x10-19C NAME: Charge of an Electron WHAT: This is the charge of one electron flying around the nucleus.
	.082 Latm/molK 8.3 J/molK 1.987 cal/Kmol NAME: Universal Gas Constant WHAT: This constant is used in the Universal Gas Law "PV=nRT". It has the same value for all gases. You use a different value depending on what measurements your formula uses.

CAREERS THAT USE CHEMISTRY

Not only are there all of these specialties to the large field of chemistry, there are loads of career paths you could choose. Some are 100% chemistry while others use chemistry every day but focus on other work. Some examples...

DOCTOR

You all know what a doctor is. Doctors have to know loads about biochemistry and the chemical reactions going on in your body. Not only how they work normally but what happens when they go wrong. They also have to understand how drugs affect your body's systems.

PHARMACIST, PHARMACOLOGIST

There are the people at the drug store who fill your prescriptions. There are also the people who study pharmacology in school and learn how to create new drugs to cure diseases. Someone with a Pharmacology major might work in a lab all day studying and creating new compounds. There are then several years of testing to see how the compounds interact with the human body.

UNIVERSITY RESEARCHER

These are the folks who spend their whole careers working at a university focusing on one or two specific ideas in chemistry. They may also be teachers of chemistry classes. They can work in any part of chemistry, not just the world of chemistry in living things (like the above examples). They often spend many years in school getting their Ph.D. before they begin their own research.

FORENSICS EXPERT

These scientists work with law enforcement officials. They go to scenes of the crime, gather clues, bring them back to their labs and analyze them. An example might be a murder scene where someone tracked mud all over the carpet. The forensics expert could come and take a sample of the mud, analyze the elements and then compare it to a database of mud around the city. That might help the police figure out where the mud came from and lead them to the killer.

HAZARDOUS MATERIALS EXPERT

Here's another time where you might work with law enforcement. These folks have information on thousands of types of chemicals and how they react with people, fire and the air. When there is a spill or exposure somewhere they come and work with fire fighters to evacuate people, tell them it's okay or maybe help tell them how to contain the unidentified chemicals. They work with huge databases of chemical information.
Here are some nice examples of chemicals and chemical reactions all around you. This is only a small portion of the chemistry that you will find around the world.

A - Alstonite - Amethyst - Andradite - Antimony (Solid) - Artinite - Asbestos - Atacamite - Azurite B - Barite C - Calcite - Celestine - Chemical Wash (Face) - Colemanite - Copper - Corellite D - Danburite - Dioptase - Dolomite - Duftite E - Epidote F - Feldspar - Flame/Fire G - Galena - Graphite - Gypsum H - Hazardous Materials (Classes) - Helium (Liquid, Gas) - Hematite I - Inesite J

K L - Lamp, Mercury - Light, Fluorescent - Light, Halogen - Light, Incandescent (Argon) - Light, Neon M - Magnetite - Meteorite (Iron) - Molybdenite N O - Orpiment P - Paint, Peeling - Petrified Wood - Pyrite Q - Quartz, Rose R - Rust (Iron) - Rutile S - Smithsonite - Sphalerite - Sulfur - Sylvite T U - Ulexite V - Vanadinite W - Water Softener X Y Z - Zinkenite