digestive system

 
Digestion - Eating and Elimination!
This is our favorite system. We love to eat and we love to poop. For the rest of the page we will refer to pooping as elimination. It's more technical that way. Anyway, your digestive system is all about getting food into your body, digesting the food, absorbing the nutrients you need, and elimination of the materials you don't need (feces). All animals have one sort of digestive system or another. Why? Anything that eats another creature (heterotrophs) must have a way of bringing nutrients in and getting rid of what they don't need.

What Does This System Do?
What does the system do? We're going to use you as the basis for our explanation of the digestive system. Let's start with eating. You get hungry and you eat. Once you put the food in your mouth, you start to chew and begin a process of mechanical digestion that grinds food down into a pulp.

Your body also starts to release enzymes that start the process of chemical digestion and the breakdown of biological molecules. Most chemical digestion happens in the stomach. The food moves through your digestive system and is eventually broken down into compounds and nutrients that your small intestine can absorb into the blood stream. The material you don't absorb continues into the large intestine where water is removed from the material and then whatever is left can be eliminated at your convenience. That's a decent overview of the process.

Interacting with Other Systems
The digestive system works very closely with the circulatory system to get the absorbed nutrients distributed through your body. The circulatory system also carries chemical signals from your endocrine system that control the speed of digestion.

The digestive system also works in parallel with your excretory system (kidneys and urination). While the digestive system collects and removes undigested solids, the excretory system filters compounds from the blood stream and collects them in urine. They are closely connected in controlling the amount of water in your body.

Malnutrition
Nutrition is one of the most important ideas you can learn about. You can get hundreds of diseases if you don't have a balanced diet. An extreme example of malnutrition is called Kwashiorkor that occurs when you don't get enough protein in your diet. There are many disease related to missing individual vitamins and minerals including scurvy (vitamin C), beri beri (vitamin B1), or a goiter (iodine). The resulting goiter shows how the lack of one specific element can change the way your endocrine system works.

You probably learn about getting enough calcium in your diet. Your bones, tissues, and nervous system all need that calcium. Did you know that some people who don't have enough calcium (Ca) in their diets replace the calcium in their bones with magnesium? It can happen because calcium and magnesium are so similar on an atomic level.
Digestive System

The digestive system is a group of organs working together to convert food into energy and basic nutrients to feed the entire body. Food passes through a long tube inside the body known as the alimentary canal or the gastrointestinal tract (GI tract). The alimentary canal is made up of the oral cavity, pharynx, esophagus, stomach, small intestines, and large intestines. In addition to the alimentary canal, there are several important accessory organs that help your body to digest food but do not have food pass through them. Accessory organs of the digestive system include the teeth, tongue, salivary glands, liver, gallbladder, and pancreas. To achieve the goal of providing energy and nutrients to the body, six major functions take place in the digestive system:
Ingestion
Secretion
Mixing and movement
Digestion
Absorption
Excretion
Digestive System Anatomy

Mouth
Food begins its journey through the digestive system in the mouth, also known as the oral cavity. Inside the mouth are many accessory organs that aid in the digestion of food—the tongue, teeth, and salivary glands. Teeth chop food into small pieces, which are moistened by saliva before the tongue and other muscles push the food into the pharynx.

Teeth. The teeth are 32 small, hard organs found along the anterior and lateral edges of the mouth. Each tooth is made of a bone-like substance called dentin and covered in a layer of enamel—the hardest substance in the body. Teeth are living organs and contain blood vessels and nerves under the dentin in a soft region known as the pulp. The teeth are designed for cutting and grinding food into smaller pieces.

Tongue. The tongue is located on the inferior portion of the mouth just posterior and medial to the teeth. It is a small organ made up of several pairs of muscles covered in a thin, bumpy, skin-like layer. The outside of the tongue contains many rough papillae for gripping food as it is moved by the tongue’s muscles. The taste buds on the surface of the tongue detect taste molecules in food and connect to nerves in the tongue to send taste information to the brain. The tongue also helps to push food toward the posterior part of the mouth for swallowing.

Salivary Glands. Surrounding the mouth are 3 sets of salivary glands. The salivary glands are accessory organs that produce a watery secretion known as saliva. Saliva helps to moisten food and begins the digestion of carbohydrates. The body also uses saliva to lubricate food as it passes through the mouth, pharynx, and esophagus.
Pharynx
The pharynx, or throat, is a funnel-shaped tube connected to the posterior end of the mouth. The pharynx is responsible for the passing of masses of chewed food from the mouth to the esophagus. The pharynx also plays an important role in the respiratory system, as air from the nasal cavity passes through the pharynx on its way to the larynx and eventually the lungs. Because the pharynx serves two different functions, it contains a flap of tissue known as the epiglottis that acts as a switch to route food to the esophagus and air to the larynx.

Esophagus

The esophagus is a muscular tube connecting the pharynx to the stomach that is part of the upper gastrointestinal tract. It carries swallowed masses of chewed food along its length. At the inferior end of the esophagus is a muscular ring called the lower esophageal sphincter or cardiac sphincter. The function of this sphincter is to close of the end of the esophagus and trap food in the stomach.

Stomach
The stomach is a muscular sac that is located on the left side of the abdominal cavity, just inferior to the diaphragm. In an average person, the stomach is about the size of their two fists placed next to each other. This major organ acts as a storage tank for food so that the body has time to digest large meals properly. The stomach also contains hydrochloric acid and digestive enzymes that continue the digestion of food that began in the mouth.

Small Intestine
The small intestine is a long, thin tube about 1 inch in diameter and about 10 feet long that is part of the lower gastrointestinal tract. It is located just inferior to the stomach and takes up most of the space in the abdominal cavity. The entire small intestine is coiled like a hose and the inside surface is full of many ridges and folds. These folds are used to maximize the digestion of food and absorption of nutrients. By the time food leaves the small intestine, around 90% of all nutrients have been extracted from the food that entered it.

Liver and Gallbladder
The liver is a roughly triangular accessory organ of the digestive system located to the right of the stomach, just inferior to the diaphragm and superior to the small intestine. The liver weighs about 3 pounds and is the second largest organ in the body. The liver has many different functions in the body, but the main function of the liver in digestion is the production of bile and its secretion into the small intestine. The gallbladder is a small, pear-shaped organ located just posterior to the liver. The gallbladder is used to store and recycle excess bile from the small intestine so that it can be reused for the digestion of subsequent meals.

Pancreas
The pancreas is a large gland located just inferior and posterior to the stomach. It is about 6 inches long and shaped like short, lumpy snake with its “head” connected to the duodenum and its “tail” pointing to the left wall of the abdominal cavity. The pancreas secretes digestive enzymes into the small intestine to complete the chemical digestion of foods.

Large Intestine

The large intestine is a long, thick tube about 2 ½ inches in diameter and about 5 feet long. It is located just inferior to the stomach and wraps around the superior and lateral border of the small intestine. The large intestine absorbs water and contains many symbiotic bacteria that aid in the breaking down of wastes to extract some small amounts of nutrients. Feces in the large intestine exit the body through the anal canal.

Digestive System Physiology

The digestive system is responsible for taking whole foods and turning them into energy and nutrients to allow the body to function, grow, and repair itself. The six primary processes of the digestive system include:

Ingestion of food
Secretion of fluids and digestive enzymes
Mixing and movement of food and wastes through the body
Digestion of food into smaller pieces
Absorption of nutrients
Excretion of wastes

Ingestion
The first function of the digestive system is ingestion, or the intake of food. The mouth is responsible for this function, as it is the orifice through which all food enters the body. The mouth and stomach are also responsible for the storage of food as it is waiting to be digested. This storage capacity allows the body to eat only a few times each day and to ingest more food than it can process at one time.

Secretion
In the course of a day, the digestive system secretes around 7 liters of fluids. These fluids include saliva, mucus, hydrochloric acid, enzymes, and bile. Saliva moistens dry food and contains salivary amylase, a digestive enzyme that begins the digestion of carbohydrates. Mucus serves as a protective barrier and lubricant inside of the GI tract. Hydrochloric acid helps to digest food chemically and protects the body by killing bacteria present in our food. Enzymes are like tiny biochemical machines that disassemble large macromolecules like proteins, carbohydrates, and lipids into their smaller components. Finally, bile is used to emulsify large masses of lipids into tiny globules for easy digestion.

Mixing and Movement
The digestive system uses 3 main processes to move and mix food:

Swallowing. Swallowing is the process of using smooth and skeletal muscles in the mouth, tongue, and pharynx to push food out of the mouth, through the pharynx, and into the esophagus.

Peristalsis. Peristalsis is a muscular wave that travels the length of the GI tract, moving partially digested food a short distance down the tract. It takes many waves of peristalsis for food to travel from the esophagus, through the stomach and intestines, and reach the end of the GI tract.

Segmentation. Segmentation occurs only in the small intestine as short segments of intestine contract like hands squeezing a toothpaste tube. Segmentation helps to increase the absorption of nutrients by mixing food and increasing its contact with the walls of the intestine.
Digestion
Digestion is the process of turning large pieces of food into its component chemicals. Mechanical digestion is the physical breakdown of large pieces of food into smaller pieces. This mode of digestion begins with the chewing of food by the teeth and is continued through the muscular mixing of food by the stomach and intestines. Bile produced by the liver is also used to mechanically break fats into smaller globules. While food is being mechanically digested it is also being chemically digested as larger and more complex molecules are being broken down into smaller molecules that are easier to absorb. Chemical digestion begins in the mouth with salivary amylase in saliva splitting complex carbohydrates into simple carbohydrates. The enzymes and acid in the stomach continue chemical digestion, but the bulk of chemical digestion takes place in the small intestine thanks to the action of the pancreas. The pancreas secretes an incredibly strong digestive cocktail known as pancreatic juice, which is capable of digesting lipids, carbohydrates, proteins and nucleic acids. By the time food has left the duodenum, it has been reduced to its chemical building blocks—fatty acids, amino acids, monosaccharides, and nucleotides.

Absorption
Once food has been reduced to its building blocks, it is ready for the body to absorb. Absorption begins in the stomach with simple molecules like water and alcohol being absorbed directly into the bloodstream. Most absorption takes place in the walls of the small intestine, which are densely folded to maximize the surface area in contact with digested food. Small blood and lymphatic vessels in the intestinal wall pick up the molecules and carry them to the rest of the body. The large intestine is also involved in the absorption of water and vitamins B and K before feces leave the body.

Excretion
The final function of the digestive system is the excretion of waste in a process known as defecation. Defecation removes indigestible substances from the body so that they do not accumulate inside the gut. The timing of defecation is controlled voluntarily by the conscious part of the brain, but must be accomplished on a regular basis to prevent a backup of indigestible materials.

Meiosis - It's for Sexual Reproduction
What are the big ideas here? There are two cell divisions. Mitosis has one division and meiosis has two divisions. You still have to remember PMATI, but now you do it twice. You also need to remember that four cells are created where there was originally one. That's four (4) cells with half of the amount of DNA needed by a cell. When a cell goes through meiosis, it's not concerned about creating another working cell.

Meiosis happens when it's time to reproduce an organism. The steps of meiosis are very simple. When you break it down it's just two PMATI's in a row. Scientists say Meiosis I and Meiosis II, but it's just two PMATIs. The interphase that happens between the two processes is very short and the DNA is not duplicated.

As we said, meiosis happens when it's time to reproduce. Meiosis is the great process that shuffles the cell's genes around. Plants do it, animals do it, and even fungi do it (sometimes). Instead of creating two new cells with equal numbers of chromosomes (like mitosis), the cell does a second division soon after the first.

That second division divides the number of chromosomes in half. When you have half the number of chromosomes, you are called a haploid cell. Haploid means half the regular number. Diploid is the opposite (two strands). Normal cells are considered to be diploid cells.

Step One
MEIOSIS I: This is basically like the PMATI of a regular mitosis. Pairs of chromosomes are lined up at the center of the cell and then pulled to each side. Meiosis is a bit different because there something called crossing-over happens with the DNA.

This crossing over is an exchange of genes. The genes are mixed up, not resulting in a perfect duplicate like mitosis. The cell divides, leaving two new cells with a pair of chromosomes each. Normally the cell would begin to go about its business of living and slowly duplicate the chromosomes for another mitotic division. Since this is meiosis, there is a very short interphase and division begins again.

Step Two
MEIOSIS II: In Prophase II the DNA that remains in the cell begins to condense and form short chromosomes. Each chromosome pair has a centromere. The centrioles also begin their journey to opposite sides of the cell. In Metaphase II all of the chromosomes line up along the center of the cell and the centrioles are in position for the duplication. Anaphase II shows the chromosomes split and move to opposite sides of the cell. Each one splits into two pieces. They don't divide up the DNA between the new cells; they split the DNA that exists. Each daughter cell will get one-half of the DNA needed to make a functioning cell.

Telophase II shows the DNA completely pulled to the sides and the cell membrane begins to pinch. When it's all over, you are left with four haploid cells that are called gametes. The eventual purpose of the gametes will be to find other gametes with which
they can combine. When they do, they will form a new organism.

 
Mitosis - When Cells Split Apart
Eventually cells need to duplicate. There are two main methods of replication, mitosis and meiosis. This tutorial will talk about mitosis.

The big idea to remember is that mitosis is the simple duplication of a cell and all of its parts. It duplicates its DNA and the two new cells (daughter cells) have the same pieces and genetic code. Two identical copies come from one original. Start with one; get two that are the same. You get the idea.

Beyond the idea that two identical cells are created, there are certain steps in the process. There are five (5) basic phases in the life-cycle of a cell. You should remember the term PMATI (pronounced PeeMahtEee). PMATI is the acronym for the phases of a cell's existence. It breaks down to.

PROPHASE - METAPHASE - ANAPHASE - TELOPHASE - INTERPHASE

We suppose it would be good to know what happens during those phases. Always remember - PMATI!

The Phases
Prophase: A cell gets the idea that it is time to divide. First, it has to get everything ready. You need to duplicate DNA, get certain pieces in the right position (centrioles), and generally prepare the cell for the process of mitotic division.

Metaphase: Now all of the pieces are aligning themselves for the big split. The DNA lines up along a central axis and the centrioles send out specialized tubules that connect to the DNA. The DNA (chromatin) has now condensed into chromosomes. Two strands of a chromosome are connected at the center with something called a centromere. The tubules actually connect to the centromere, not the DNA.

Anaphase: Here we go! The separation begins. Half of the chromosomes are pulled to one side of the cell; half go the other way. When the chromosomes get to the side of the cell, it's time to move on to telophase.

Telophase: Now the division is finishing up. This is the time when the cell membrane closes in and splits the cell into two pieces. You have two separate cells each with half of the original DNA.

Interphase: This is the normal state of a cell. We suppose that when it comes to cell division, you could call this the resting state. It's just going about its daily business of surviving and making sure it has all of the nutrients and energy it needs. It is also getting ready for another division that will happen one day. It is duplicating its nucleic acids, so when it's time for prophase again, all the pieces are there.

 
Peroxisomes - Another Enzyme Package
There are many ways that peroxisomes are similar to lysosomes. They are small vesicles found around the cell. They have a single membrane that contains digestive enzymes for breaking down toxic materials in the cell. They differ from lysosomes in the type of enzyme they hold. Peroxisomes hold on to enzymes that require oxygen (oxidative enzymes). Lysosomes have enzymes that work in oxygen-poor areas and lower pH.

Peroxisomes absorb nutrients that the cell has acquired. They are very well known for digesting fatty acids. They also play a part in the way organisms digest alcohol (ethanol). Because they do that job, you would expect liver cells to have more peroxisomes than most other cells in a human body. They also play a role in cholesterol synthesis and the digestion of amino acids.

Creating Hydrogen Peroxide
Peroxisomes work in a very specific way. Their enzymes attack complex molecules and break them down into smaller molecules. One of the byproducts of the digestion is hydrogen peroxide (H2O2). Peroxisomes have developed to a point where they are able to contain that hydrogen peroxide and break it down into water (H2O) and oxygen (O2). The water is harmless to the cell and the oxygen can be used in the next digestive reaction.

Mysteries of the Peroxisome
Peroxisomes have a single membrane that surrounds the digestive enzymes and dangerous byproducts of their work (hydrogen peroxide). The protein enzymes are usually created by lysosomes floating in the cell. They then insert the proteins into the peroxisome bubble. Peroxisomes continue to grow until they split in two. Where does the membrane come from? Scientists are still researching that answer. It may come from the endoplasmic reticulum, but it may be created in a way different from lysosomes. 

 
Lysosomes - Little Enzyme Packages
You will find organelles called lysosomes in nearly every animal-like eukaryotic cell. Lysosomes hold enzymes that were created by the cell. The purpose of the lysosome is to digest things. They might be used to digest food or break down the cell when it dies. What creates a lysosome? You'll have to visit the Golgi complex for that answer.

A lysosome is basically a specialized vesicle that holds a variety of enzymes. The enzyme proteins are first created in the rough endoplasmic reticulum. Those proteins are packaged in a vesicle and sent to the Golgi apparatus. The Golgi then does its final work to create the digestive enzymes and pinches off a small, very specific vesicle. That vesicle is a lysosome. From there the lysosomes float in the cytoplasm until they are needed. Lysosomes are single-membrane organelles.

Lysosome Action

Since lysosomes are little digestion machines, they go to work when the cell absorbs or eats some food. Once the material is inside the cell, the lysosomes attach and release their enzymes. The enzymes break down complex molecules that can include complex sugars and proteins. But what if food is scarce and the cell is starving? The lysosomes go to work even if there is no food for the cell. When the signal is sent out, lysosomes will actually digest the cell organelles for nutrients.

Why Don't They Digest the Cell?
Here's something scientists are still trying to figure out. If the lysosome holds many types of enzymes, how can the lysosome survive? Lysosomes are designed to break down complex molecules and pieces of the cell. Why don't the enzymes break down the membrane that surrounds the lysosome?

 
Microtubules - Thick Protein Tubes
Microtubules are usually discussed with microfilaments. Although they are both proteins that help define cell structure and movement, they are very different molecules. While microfilaments are thin, microtubules are thick, strong spirals of thousands of subunits. Those subunits are made of the protein called tubulin. And yes, they got their name because they look like a tube.

Elements of the Cytoskeleton
All of the microfilaments and microtubules combine to form the cytoskeleton of the cell. The cytoskeleton is different from cytoplasm (cytosol). The cytoskeleton provides structure. Cytoplasm is just a fluid. The cytoskeleton connects to every organelle and every part of the cell membrane. Think about an amoeba. All of the pieces work together so that the foot might reach out towards the food. Then lysosomes and peroxisomes are sent to begin digestion. The movement of the cell membrane, organelles, and cytoplasm is all related to the tubules and filaments.

Moving Chromosomes
Microtubules have many more uses than just cell structure. They are also very important in cell division. They connect to chromosomes, help them with their first split, and then move to each new daughter cell. They are a part of a small pair of organelles called centrioles that have the specific purpose to help a cell divide. Once the cell has finished dividing, the microtubules are put to work in other places.

Moving Organisms
Beyond the role they play in internal cell movement, microtubules also work together to form larger structures that work on the outside of the cells. They can combine in very specific arrangements to form cilia and flagella. Cilia are little hairs you might see on the outside of a paramecium or other protists. They flap back and forth to help the cell move. Flagella are long, thick tails. They whip around and sometimes twirl, pushing the cell along. 

 
Microfilaments - Stringy Proteins
You will find microfilaments in most cells. They are the partner of microtubules. They are long, thin, and stringy proteins (mainly actin) compared to the rounder, tube-shaped microtubules. We'd like to say you can find them here or there, but they are everywhere in a cell. They work with microtubules to form the structure that allows a cell to hold its shape, move itself, and move its organelles.

Making the Cytoskeleton
All of the microfilaments and microtubules combine to form the cytoskeleton of the cell. The cytoskeleton is different from cytoplasm (cytosol). The cytoskeleton provides structure. Cytoplasm is just a fluid. The cytoskeleton connects to every organelle and every part of the cell membrane. Think about an amoeba. All of the pieces work together so that the foot might reach out towards the food. Then lysosomes and peroxisomes are sent to begin digestion. The movement of the cell membrane, organelles, and cytoplasm is all related to the tubules and filaments.


You will also find many microfilaments in muscle tissue. They are called myofibrils when you find them in muscles. The two proteins myosin and actin work together to help the muscle cells relax and contract. The two proteins need each other and together they are called actomyosin. Combine those protein threads with some ions in the muscle cell and you get a huge contraction. The groups of actomyosin contracting are called sarcomeres. All of the muscle cells work together to make a muscle contract.

A Role in Cell Movement
Cells move in a variety of ways. We just talked about the contraction of a muscle cell. That is an extreme example. When you learn about single-celled organisms, you will understand that they need to move. They may need to glide from one area to another. The microfilaments are often found anchored to proteins in the cell membrane. Sometimes microfilaments are found floating free and connected to other filaments and tubules. Those binding proteins allow the microfilaments to push and pull on the cell membrane to help the cell move. 

 
Vacuoles - Storage Bins to the Cells
Vacuoles are storage bubbles found in cells. They are found in both animal and plant cells but are much larger in plant cells. Vacuoles might store food or any variety of nutrients a cell might need to survive. They can even store waste products so the rest of the cell is protected from contamination. Eventually, those waste products would be sent out of the cell.

The structure of vacuoles is fairly simple. There is a membrane that surrounds a mass of fluid. In that fluid are nutrients or waste products. Plants may also use vacuoles to store water. Those tiny water bags help to support the plant. They are closely related to objects called vesicles that are found throughout the cell.

In plant cells, the vacuoles are much larger than in animal cells. When a plant cell has stopped growing, there is usually one very large vacuole. Sometimes that vacuole can take up more than half of the cell's volume. The vacuole holds large amounts of water or food. Don't forge that vacuoles can also hold the plant waste products. Those waste products are slowly broken into small pieces that cannot hurt the cell. Vacuoles hold onto things that the cell might need, just like a backpack.

Helping with Support
Vacuoles also play an important role in plant structure. Plants use cell walls to provide support and surround cells. The size of that cell may still increase or decrease depending on how much water is present. Plant cells do not shrink because of changes in the amount of cytoplasm. Most of a plant cell's volume depends on the material in vacuoles.

Those vacuoles gain and lose water depending on how much water is available to the plant. A drooping plant has lost much of its water and the vacuoles are shrinking. It still maintains its basic structure because of the cell walls. When the plant finds a new source of water, the vacuoles are refilled and the plant regains its structure. 

 
Golgi Apparatus - Packing Things Up
The Golgi apparatus or Golgi complex is found in most cells. It is another packaging organelle like the endoplasmic reticulum (ER). It was named after Camillo Golgi, an Italian biologist. It is pronounced GOL-JI in the same way you would say squee-gie, as soft a "G" sound. While layers of membranes may look like the rough ER, they have a very different function.

Foundation of Vesicles
The Golgi apparatus gathers simple molecules and combines them to make molecules that are more complex. It then takes those big molecules, packages them in vesicles, and either stores them for later use or sends them out of the cell. It is also the organelle that builds lysosomes (cell digestion machines). Golgi complexes in the plant may also create complex sugars and send them off in secretory vesicles. The vesicles are created in the same way the ER does it. The vesicles are pinched off the membranes and float through the cell.

The Golgi apparatus is a series of membranes shaped like pancakes. The single membrane is similar to the cell membrane in that it has two layers. The membrane surrounds an area of fluid where the complex molecules (proteins, sugars, enzymes) are stored and changed. Because the Golgi complex absorbs vesicles from the rough ER, you will also find ribosomes in those pancake stacks.

Working with the Rough ER

The Golgi complex works closely with the rough ER. When a protein is made in the ER, something called a transition vesicle is made. This vesicle or sac floats through the cytoplasm to the Golgi apparatus and is absorbed. After the Golgi does its work on the molecules inside the sac, a secretory vesicle is created and released into the cytoplasm. From there, the vesicle moves to the cell membrane and the molecules are released out of the cell. 

 
Endoplasmic Reticulum - Wrapping it Up
Another organelle in the cell is the endoplasmic reticulum (ER). While the function of the nucleus is to act as the cell brain, the ER functions as a manufacturing and packaging system. It works closely with the Golgi apparatus, ribososmes, mRNA, and tRNA.

Structurally, the endoplasmic reticulum is a network of membranes found throughout the cell and connected to the nucleus. The membranes are slightly different from cell to cell and a cell’s function determines the size and structure of the ER. For example, some cells, such as prokaryotes or red blood cells, do not have an ER of any kind. Cells that synthesize and release a lot of proteins would need a large amount of ER. You might look at a cell from the pancreas or liver for good examples of cells with large ER structures.

Rough and Smooth
There are two basic types of ER. Both rough ER and smooth ER have the same types of membranes but they have different shapes. Rough ER looks like sheets or disks of bumpy membranes while smooth ER looks more like tubes. Rough ER is called rough because it has ribosomes attached to its surface.

The double membranes of smooth and rough ER form sacs called cisternae. Protein molecules are synthesized and collected in the cisternal space/lumen. When enough proteins have been synthesized, they collect and are pinched off in vesicles. The vesicles often move to the Golgi apparatus for additional protein packaging and distribution.

Smooth ER (SER) acts as a storage organelle. It is important in the creation and storage of lipids and steroids. Steroids are a type of ringed organic molecule used for many purposes in an organism. They are not always about building the muscle mass of a weight lifter. Cells in your body that release oils also have more SER than most cells.

The sarcoplasmic reticulum (SR) is a variation of the SER. It is able to store many ions in solution that the cell will need at a later time. When a cell needs to do something immediately, it doesn’t make sense to search the environment for extra ions that may or may not be floating around. It is easier to have them stored in a pack for easy use. For example, when you are running around and your muscle cells are active, they need calcium (Ca) ions. The SR can release those ions immediately. When you are resting, they are able to store them for later use.



Rough ER (RER) was also mentioned in the section on ribosomes and is very important in the synthesis and packaging of proteins. Ribosomes are attached to the membrane of the ER, making it “rough.” The RER is also attached to the nuclear envelope that surrounds the nucleus. This direct connection between the perinuclear space and the lumen of the ER allows for the movement of molecules through both membranes.

The process of protein synthesis starts when mRNA moves from the nucleus to a ribosome on the surface of the RER. As the ribosome builds the amino acid chain, the chain is pushed into the cisternal space of the RER. When the proteins are complete, they collect and the RER pinches off a vesicle. That vesicle, a small membrane bubble, can move to the cell membrane or the Golgi apparatus. Some of the proteins will be used in the cell and some will be sent out into intercellular space. 

 
Chloroplasts - Show Me the Green
Chloroplasts are the food producers of the cell. The organelles are only found in plant cells and some protists such as algae. Animal cells do not have chloroplasts. Chloroplasts work to convert light energy of the Sun into sugars that can be used by cells. The entire process is called photosynthesis and it all depends on the little green chlorophyll molecules in each chloroplast.

Plants are the basis of all life on Earth. They are classified as the producers of the world. In the process of photosynthesis, plants create sugars and release oxygen (O2). The oxygen released by the chloroplasts is the same oxygen you breathe every day. Mitochondria work in the opposite direction. They use oxygen in the process of releasing chemical energy from sugars.

Special Structures
We'll hit the high points for the structure of a chloroplast. Two membranes contain and protect the inner parts of the chloroplast. They are appropriately named the outer and inner membranes. The inner membrane surrounds the stroma and the grana (stacks of thylakoids). One thylakoid stack is called a granum.

Chlorophyll molecules sit on the surface of each thylakoid and capture light energy from the Sun. As energy rich molecules are created by the light-dependent reactions, they move to the stroma where carbon (C) can be fixed and sugars are synthesized.

The stacks of thylakoid sacs are connected by stroma lamellae. The lamellae act like the skeleton of the chloroplast, keeping all of the sacs a safe distance from each other and maximizing the efficiency of the organelle. If all of the thylakoids were overlapping and bunched together, there would not be an efficient way to capture the Sun’s energy.

Making Food
The purpose of the chloroplast is to make sugars that feed the cell’s machinery. Photosynthesis is the process of a plant taking energy from the Sun and creating sugars. When the energy from the Sun hits a chloroplast and the chlorophyll molecules, light energy is converted into the chemical energy found in compounds such as ATP and NADPH.

Those energy-rich compounds move into the stroma where enzymes fix the carbon atoms from carbon dioxide (CO2). The molecular reactions eventually create sugar and oxygen (O2). Plants and animals then use the sugars (glucose) for food and energy. Animals also breathe the oxygen gas that is released.

Different Chlorophyll Molecules
Not all chlorophyll is the same. Several types of chlorophyll can be involved in photosynthesis. You will hear about chlorophyll a and b most often. All chlorophylls are varieties of green and have a common chemical structure called a porphyrin ring.

There are other molecules that are also photosynthetic. One day you might hear about carotenoids in carrots, phycocyanin in bacteria, phycoerythrin in algae, or fucoxanthin in brown algae. While these compounds might be involved in photosynthesis, they are not all green or the same structure as chlorophyll. Accessory pigments such as carotenoids and fucoxanthin pass absorbed light energy to neighboring chlorophyll molecules instead of using it themselves. 

 
Mitochondria - Turning on the Powerhouse
Mitochondria are known as the powerhouses of the cell. They are organelles that act like a digestive system which takes in nutrients, breaks them down, and creates energy rich molecules for the cell. The biochemical processes of the cell are known as cellular respiration. Many of the reactions involved in cellular respiration happen in the mitochondria. Mitochondria are the working organelles that keep the cell full of energy.

Mitochondria are small organelles floating free throughout the cell. Some cells have several thousand mitochondria while others have none. Muscle cells need a lot of energy so they have loads of mitochondria. Neurons (cells that transmit nerve impulses) don’t need as many. If a cell feels it is not getting enough energy to survive, more mitochondria can be created. Sometimes a mitochondria can grow larger or combine with other mitochondria. It all depends on the needs of the cell.

Mitochondria Structure
Mitochondria are shaped perfectly to maximize their productivity. They are made of two membranes. The outer membrane covers the organelle and contains it like a skin. The inner membrane folds over many times and creates layered structures called cristae. The fluid contained in the mitochondria is called the matrix.

The folding of the inner membrane increases the surface area inside the organelle. Since many of the chemical reactions happen on the inner membrane, the increased surface area creates more space for reactions to occur. If you have more space to work, you can get more work done. Similar surface area strategies are used by microvilli in your intestines.

What’s in the matrix? It's not like the movies at all. Mitochondria are special because they have their own ribosomes and DNA floating in the matrix. There are also structures called granules which may control concentrations of ions. Cell biologists are still exploring the activity of granules.

Using Oxygen to Release Energy
How does cellular respiration occur in mitochondria? The matrix is filled with water and proteins (enzymes). Those proteins take organic molecules, such as pyruvate and acetyl CoA, and chemically digest them. Proteins embedded in the inner membrane and enzymes involved in the citric acid cycle ultimately release water (H2O) and carbon dioxide (CO2) molecules from the breakdown of oxygen (O2) and glucose (C6H12O6). The mitochondria are the only places in the cell where oxygen is reduced and eventually broken down into water.

Mitochondria are also involved in controlling the concentration of calcium (Ca2+) ions within the cell. They work very closely with the endoplasmic reticulum to limit the amount of calcium in the cytosol. 

 
Ribosomes - Protein Construction Teams
Cells need to make proteins. Enzymes made of proteins are used to help speed up biological processes. Other proteins support cell functions and are found embedded in membranes. Proteins even make up most of your hair. When a cell needs to make proteins, it looks for ribosomes. Ribosomes are the protein builders or the protein synthesizers of the cell. They are like construction guys who connect one amino acid at a time and build long chains.

Ribosomes are special because they are found in both prokaryotes and eukaryotes. While a structure such as a nucleus is only found in eukaryotes, every cell needs ribosomes to manufacture proteins. Since there are no membrane-bound organelles in prokaryotes, the ribosomes float free in the cytosol.

Ribosomes are found in many places around a eukaryotic cell. You might find them floating in the cytosol. Those floating ribosomes make proteins that will be used inside of the cell. Other ribosomes are found on the endoplasmic reticulum. Endoplasmic reticulum with attached ribosomes is called rough ER. It looks bumpy under a microscope. The attached ribosomes make proteins that will be used inside the cell and proteins made for export out of the cell. There are also ribosomes attached to the nuclear envelope. Those ribosomes synthesize proteins that are released into the perinuclear space.

Two Pieces Make the Whole
There are two pieces or subunits to every ribosome. In eukaryotes, scientists have identified the 60-S (large) and 40-S (small) subunits. Even though ribosomes have slightly different structures in different species, their functional areas are all very similar.

For example, prokaryotes have ribosomes that are slightly smaller than eukaryotes. The 60-S/ 40-S model works fine for eukaryotic cells while prokaryotic cells have ribosomes made of 50-S and 30-S subunits. It's a small difference, but one of many you will find in the two different types of cells. Scientists have used this difference in ribosome structure to develop drugs that can kill prokaryotic microorganisms which cause disease. There are even structural differences between ribosomes found in the mitochondria and free ribosomes.

Mixing and Matching Amino Acids


When are ribosomes used in the process of protein synthesis? When the cell needs to make a protein, mRNA is created in the nucleus. The mRNA is then sent out of the nucleus and to the ribosomes. When it is time to make the protein, the two subunits come together and combine with the mRNA. The subunits lock onto the mRNA and start the protein synthesis.

The process of making proteins is quite simple. First, you need an amino acid. Another nucleic acid that lives in the cell is transfer RNA. tRNA is bonded to the amino acids floating around the cell. With the mRNA offering instructions, the ribosome connects to a tRNA and pulls off one amino acid. The tRNA is then released back into the cell and attaches to another amino acid. The ribosome builds a long amino acid (polypeptide) chain that will eventually be part of a larger protein. 

 
Centrioles - Organizing Chromosomes
Every animal-like cell has two small organelles called centrioles. They are there to help the cell when it comes time to divide. They are put to work in both the process of mitosis and the process of meiosis. You will usually find them near the nucleus but they cannot be seen when the cell is not dividing. And what are centrioles made of? Microtubules.

Centriole Structure
A centriole is a small set of microtubules arranged in a specific way. There are nine groups of microtubules. When two centrioles are found next to each other, they are usually at right angles. The centrioles are found in pairs and move towards the poles (opposite ends) of the nucleus when it is time for cell division. During division, you may also see groups of threads attached to the centrioles. Those threads are called the mitotic spindle.

Relaxing When There's no Work
We already mentioned that you would find centrioles near the nucleus. You will not see well-defined centrioles when the cell is not dividing. You will see a condensed and darker area of the cytoplasm called the centrosome. When the time comes for cell division, the centrioles will appear and move to opposite ends of the nucleus. During division you will see four centrioles. One pair moves in each direction.

Interphase is the time when the cell is at rest. When it comes time for a cell to divide, the centrioles duplicate. During prophase, the centrioles move to opposite ends of the nucleus and a mitotic spindle of threads begins to appear. Those threads then connect to the now apparent chromosomes. During anaphase, the chromosomes are split and pulled towards each centriole. Once the entire cell begins to split in telophase, the chromosomes begin to unravel and new nuclear envelopes begin to appear. The centrioles have done their job. 

 
Chromosomes - Pull up Those Genes
Chromosomes are the things that make organisms what they are. They carry all of the information used to help a cell grow, thrive, and reproduce. Chromosomes are made up of DNA. Segments of DNA in specific patterns are called genes. Your genes make you who you are. You will find the chromosomes and genetic material in the nucleus of a cell. In prokaryotes, DNA floats in the cytoplasm in an area called the nucleoid.

Loose and Tight
Chromosomes are not always visible. They usually sit around uncoiled and as loose strands called chromatin. When it is time for the cell to reproduce, they condense and wrap up very tightly. The tightly wound DNA is the chromosome. Chromosomes look kind of like long, limp, white hot dogs. They are usually found in pairs.

Completing the Sets
Scientists count individual strands of chromosomes. They count individuals not every organism has pairs. You probably have 46 chromosomes (23 pairs). Peas only have 12. A dog has 78. The number of chromosomes is NOT related to the intelligence or complexity of the creature. There is a crayfish with 200 chromosomes. Does that make a crayfish five times smarter or more complex than you are? No. There are even organisms of the same species with different numbers of chromosomes. You will often find plants of the same species with multiple sets of chromosomes.

Chromosomes work with other nucleic acids in the cell to build proteins and help in cell division. You will most likely find mRNA in the nucleus with the DNA. tRNA is found outside of the nucleus in the cytosol. When the chromosomes are visible, cells with two complete sets of chromosomes are called diploids (46 in a human). Most cells are diploid. Cells with only one set (23 in a human) are called haploid cells. Haploids are most often found in cells involved in sexual reproduction such as a sperm or an egg. Haploid cells are created in cell division termed meiosis. 

 
Cell Nucleus - Commanding the Cell
The cell nucleus acts like the brain of the cell. It helps control eating, movement, and reproduction. If it happens in a cell, chances are the nucleus knows about it. The nucleus is not always in the center of the cell. It will be a big dark spot somewhere in the middle of all of the cytoplasm (cytosol). You probably won't find it near the edge of a cell because that might be a dangerous place for the nucleus to be. If you don't remember, the cytoplasm is the fluid that fills cells.

Life Before a Nucleus
Not all cells have a nucleus. Biology breaks cell types into eukaryotic (those with a defined nucleus) and prokaryotic (those with no defined nucleus). You may have heard of chromatin and DNA. You don't need a nucleus to have DNA. If you don't have a defined nucleus, your DNA is probably floating around the cell in a region called the nucleoid. A defined nucleus that holds the genetic code is an advanced feature in a cell.

Important Materials in the Envelope
The things that make a eukaryotic cell are a defined nucleus and other organelles. The nuclear envelope surrounds the nucleus and all of its contents. The nuclear envelope is a membrane similar to the cell membrane around the whole cell. There are pores and spaces for RNA and proteins to pass through while the nuclear envelope keeps all of the chromatin and nucleolus inside.

When the cell is in a resting state there is something called chromatin in the nucleus. Chromatin is made of DNA, RNA, and nuclear proteins. DNA and RNA are the nucleic acids inside of the cell. When the cell is going to divide, the chromatin becomes very compact. It condenses. When the chromatin comes together, you can see the chromosomes. You will also find the nucleolus inside of the nucleus. When you look through a microscope, it looks like a nucleus inside of the nucleus. It is made of RNA and protein. It does not have much DNA at all. 

 
Cytoplasm - Filling Fluid
Cytoplasm is the fluid that fills a cell. Scientists used to call the fluid protoplasm. Early on, they didn't know about the many different types of fluids in the cell. There is special fluid in the mitochondria, endoplasmic reticulum, Golgi apparatus, and nucleus. The only two 'plasms' left are cytoplasm (the fluid in the cell also called cytosol) and nucleoplasm (the fluid in the nucleus). Each of those fluids has a very different composition.

The cell organelles are suspended in the cytosol. You will learn that the microfilaments and microtubules set up a "skeleton" of the cell and the cytosol fills the spaces. The cytoplasm has many different molecules dissolved in solution. You'll find enzymes, fatty acids, sugars, and amino acids that are used to keep the cell working. Waste products are also dissolved before they are taken in by vacuoles or sent out of the cell.

Special Fluids in the Nucleus
Nucleoplasm has a little different composition. Nucleoplasm can only be found inside of the nucleus. It doesn't have big organelles in suspension. The nucleoplasm is the suspension fluid that holds the cell's chromatin and nucleolus. It is not always present in the nucleus. When the cell divides, the nuclear membrane dissolves and the nucleoplasm is released. After the cell nucleus has reformed, the nucleoplasm fills the space again.

More than Filling
The cytosol in a cell does more than just suspend the organelles. It uses its dissolved enzymes to break down all of those larger molecules. The products can then be used by the organelles of the cell. Glucose may exist in the cytosol but the mitochondria can't use it for fuel. The cytosol has enzymes that break glucose down into pyruvate molecules that are then sent to the mitochondria. 

 
Cell Connections and Communication
All living things communicate in one way or another. When you start looking at the world on a cellular level, you won't find communication in writing or words. Cellular communication is on a molecular level. This section talks about cells in a larger organism that are near each other. We don't cover the communication between single-celled organisms. They behave in different ways.

Gap Junctions
Gap junctions are one type of cell connection. When two cells are right next to each other, their cell membranes may actually be touching. A gap junction is an opening from one cell to another. It's not a big opening, but it is large enough for cytoplasm to move from one cell to another. The connections are called channels and they act like tunnels for the movement of molecules.

Desmosomes
Desmosomes are a second type of cell connection. They physically connect cells like the gap junction, but no opening is created. Proteins that bond the membrane of one cell to its neighbor create the desmosomes. You will find desmosomes in your skin cells. All of those proteins hold your skin together. The distance between the cells, however small, is about 10 times wider than the gap junction connections.

Tight Junction
The last type of connection we will introduce is the tight junction. Tight junctions happen when two membranes actually bond into one. It makes a very strong barrier between two cells. Cells have some distance with a desmosome. Gap junctions allow molecules to pass. Tight junctions form solid walls. These types of connections are often found where one area needs to be protected from the contents of other areas. 

 
Cell Wall - What's it for?
While cell membranes might be around every cell, cell walls made of cellulose are only found around plant cells. Cell walls are made of specialized sugars called cellulose. Cellulose provides a protected framework for a plant cell to survive. It's like taking a water balloon and putting it in a cardboard box. The balloon is protected from the outside world. Cellulose is called a structural carbohydrate (complex sugar) because it is used in protection and support.

Cell walls also help a plant keep its shape. While they do protect the cells, cell walls and cellulose also allow plants to grow to great heights. While you have a skeleton to hold you up, a 100-foot tall redwood tree does not. It uses the strong cell walls to maintain its shape. For smaller plants, cell walls are slightly elastic. Wind can push them over and then they bounce back. Big redwoods need strength in high winds and sway very little (except at the top).

Another Hole in the Wall
A cell wall is not a fortress around the delicate plant cell. There are small holes in the wall that let nutrients, waste, and ions pass through. Those holes are called plasmodesmata. These holes have a problem: water can also be lost. But even when the plant cell loses water, the basic shape is maintained by the cell walls. So if a plant is drooping because it needs water, it can recover when water is added. It will look just the same as when it started.

More Than Walls in Plants
You may hear about cell walls in other areas of biology. Bacteria also have a structure called a cell wall. Fungi and some ptotozoa also have cell walls. They are not the same. Only plant cell walls are made out of cellulose. The other walls might be made from proteins or a substance called chitin. They all serve the same purpose of protecting and maintaining structure, but they are very different molecules. 

 
Membrane Proteins - Bumpy Services
We spoke a little about the cell membrane and its structure. We also discussed the lipid bilayer. That lipid bilayer is not smooth around the entire cell. You will find thousands (millions?) of proteins throughout the cell membrane. Some are just on the inside of the cell and some on the outside. A special few cross the cell membrane. Each type of protein has a specific purpose. There are also embedded proteins in the other membranes for cell organelles.

A Tale of Two Types
There are two types of proteins in the cell membrane -- peripheral proteins and integral proteins. As you can guess from the name, integral membrane proteins are permanently connected to the cell membrane. They have large sections embedded in the hydrophobic (middle) layer of the membrane. Peripheral proteins are not bonded as strongly to the membrane. They may just sit on the surface of the membrane, anchored with a few hydrogen (H) bonds.

Integral proteins are the hard workers of the cell membrane. Some integral proteins cross the membrane and act as pathways for ions and molecules. Some of the ion movement may not require work (passive transport), but other processes require a lot of energy and pumping action (active transport). When you look at the whole membrane, there are very few integral proteins when compared to the number of peripheral ones.

Discovering Structures
This structure of the membrane with embedded proteins and a lipid bilayer was discovered in the early 1970's. Two scientists, Singer and Nicolson, first developed the theory of the "Fluid Mosaic Model." They used several different methods, such as the freeze-fracture technique and electron micrographs, to look closely at the cell membrane and its structure. They identified the proteins that sat on the surface, were sunk into the membrane, and the others that crossed the membrane.

 
Cell Membranes
According to cell theory, cells are the main unit of organization in biology. Whether you are a single cell or a blue whale with trillions of cells, you are still made of cells. All cells are contained by a cell membrane that keeps the pieces inside. When you think about a membrane, imagine it is like a big plastic bag with some tiny holes. That bag holds all of the cell pieces and fluids inside the cell and keeps any nasty things outside the cell. The holes are there to let some things move in and out of the cell.

Flexible Containers
The cell membrane is not a solid structure. It is made of millions of smaller molecules that create a flexible and porous container. Proteins and phospholipids make up most of the membrane structure. The phospholipids make the basic bag. The proteins are found around the holes and help move molecules in and out of the cell. There are also proteins attached to the inner and outer surfaces of the membrane.

Scientists use the fluid mosaic model to describe the organization of phospholipids and proteins. The model shows you that phospholipid molecules are shaped with a head and a tail region. The head section of the molecule likes water (hydrophilic) while the tail does not (hydrophobic). Because the tails want to avoid water, they tend to stick to each other and let the heads face the watery (aqueous) areas inside and outside of the cell. The two surfaces of molecules create the lipid bilayer.

Ingrained in the Membrane
What about the membrane proteins? Scientists have shown that many proteins float in the lipid bilayer. Some are permanently attached while others are only attached temporarily. Some are only attached to the inner or outer layer of the membrane while the transmembrane proteins pass through the entire structure. The transmembrane proteins that cross the bilayer are very important in the active transport of ions and small molecules.

Different Membranes of the Cell
As you learn more about cell organelles, you will find that they all have a membrane. Organelle membranes do not have the same chemical makeup as the cell membrane. They have different lipids and proteins that make them unique. The membrane that surrounds a lysosome is different from the membrane around the endoplasmic reticulum.

Some organelles have two membranes. A mitochondrion has an outer and inner membrane. The outer membrane contains the mitochondrion parts. The inner membrane holds digestive enzymes that break down food. While we talk about membranes all the time, you should remember they all use a basic phospholipid bilayer structure, but you will find many variations throughout the cell. 

cells are the starting point

Cells are the Starting Point

All living organisms on Earth are divided into cells. The main concept of cell theory is that cells are the basic structural unit for all organisms. Cells are small compartments that hold the biological equipment necessary to keep an organism alive and successful. Living things may be single-celled or they may be very complex such as a human being.

There are smaller pieces that make up cells such as macromolecules and organelles. A protein is an example of a macromolecule while a mitochondrion is an example of an organelle. Cells can also connect to form larger structures. They might group together to form the tissues of the stomach and eventually the entire digestive system. However, in the same way that atoms are the basic unit when you study matter, cells are the basic unit for biology and organisms.

In larger organisms, the main purpose of a cell is to organize. Cells hold a variety of pieces and each cell type has a different purpose. By dividing responsibilities among different groups of cells, it is easier for an organism to survive and grow.

If you were only made of one cell, you would be very limited. You don't find single cells that are as large as a cow. Cells have problems functioning when they get too big. Also, if you were only one cell you couldn't have a nervous system, no muscles for movement, and using the internet would be out of the question. The trillions of cells in your body make your way of life possible.

One Name, Many Types

There are many types of cells. In biology class, you will usually work with plant-like cells and animal-like cells. We say "animal-like" because an animal type of cell could be anything from a tiny microorganism to a nerve cell in your brain. Biology classes often take out a microscope and look at single-celled microbes from pond water. You might see hydra, amoebas, or euglena.

Plant cells are easier to identify because they have a protective structure called a cell wall made of cellulose. Plants have the wall; animals do not. Plants also have organelles such as the green chloroplast or large, water-filled vacuoles. Chloroplasts are the key structure in the process of photosynthesis.

Cells are unique to each type of organism. If you look at very simple organisms, you will discover cells that have no defined nucleus (prokaryotes) and other cells that have hundreds of nuclei (multinucleated).

Humans have hundreds of different cell types. You have red blood cells that are used to carry oxygen (O2) through the body and other cells specific to your heart muscle. Even though cells can be very different, they are basically compartments surrounded by some type of membrane.

Biology literally means the study of life. There are many different types of living organisms, environments, and combinations of genetic material. The science of biology includes all information related to studying living things, but a biologist does not and cannot study every facet of all living things. It would just take too much time. So, biologists specialize in certain areas of biology and focus their research.

With each specialist studying details of certain biological areas, the information can be pooled (usually at big conferences) and shared to make the knowledge base a bit wider. And that’s what science is: a continually growing knowledge base focused on things in nature, whether those natural things are banana trees, kangaroos, swordfish, dinosaurs, rocks, gases, or chemicals and cells that make up all of those things.