Compendium 1: The Story, So Far.

I. From the beginning

A. Biotic checklist
1. The organization of systems
2.Reproduction
3. Growth
4. Homeostasis
5. Stimulus

B. Where do we fit in?
1. Ancestry: biological and cultural
3. Threatening Alterations

C. Why science?
1. Concepts: Theory's role
2. Modus Operandi
3. Modus Operandi II: The controlled Study
4. But, I heard it on the internet!

D. Evaluation

E. What does this mean to us?



II. The nitty gritty

A. Elementary and so forth
1. Elements
2. Atoms
3. What's the difference?
4.Molecules: They really bonded

B. Water; You made it all possible
1. Hydrogen bond
2. What water is like
3. The pH scale

C. Organic Molecules
1. Carbs
2. Lipids
3. Proteins
4. Nucleic Acids

III. It Ain't What you're buying, It's What You're Cell-ing.

A. The cell
1.Cell theory
2. The size of a cell
3. Cell structure

B. Cell organization

C. Open the gates: cell membranes

D. Protein Factory
1. Nucleus
2. Endomembrane System

E. Shape and Movement

F. Mitochondria
1. Cellular respiration
. Fermentation

IV. The Body

A. Types of Tissue

B. Cell Junctions

C. The Skin and Much More

D. Organ Systems

E. Homeostasis

I. From The Beginning

A. The Biotic Checklist

Life is all around us. There is no escaping that. Well, there is. It is called death. But, for a living creature there is no way to escape this world that is teeming with life. There are many different types of life forms, millions. Though, there are many different types of life and they vary greatly, there are a few things that all living have in common. For example: all living things use external energy, React to stimuli, whether internal or external, Develop through different stages as they grow, Maintain a relatively standard internal set of conditions and reproduce offspring of their own kind. 1 With unifying factors one can see that all life, no matter how different, has come from one origin and share very common factors.

1. The organization of systems

There is a system of structures that make up the organic world we live in. The smallest of these is the atom. It is the building block of all elements. Made up of electrons, protons and neutrons, the grouping of of two or atoms makes a molecule. Molecules, when grouped together form cells. Cells are the most basic unit of an organism. Some organisms may only be made of a single cell. Humans are made up of trillions of them. Cells group with other cells of the same kind to form tissue. They will, naturally, perform a common function. An organ is made up of tissue which functions in a concise manner. When different organs work together this is called an organ system. An organism often contains these complex systems, though simpler organism do not need these systems. The Co-inhabitance of many organisms of the same kind is called a population. When populations of different kinds live together they live in a community. The community in conjunction with the elements of the environment make up an ecosystem. All the ecosystems of the earth combined are the biosphere.

2. Reproduction

Cells that are, came from cells that were before them. Genes, or the "work plans" so to speak of the organism to be, are copied to be passed on to the posterity. DNA is the name of this code. We will learn more about DNA later on. A male of the species will contribute his DNA in sperm. Sperm fertilizes the egg of the female, which contains the female genes needed to be passed on to the offspring.

This image shows chromosomes, DNA and
genes, all integral to reproduction.

3. Growth

All living things grow and go through a series of changes. They are ever evolving from conception until death. Plants go from being seeds to being full grown grasses, shrubs, or trees. Animals begin as fertilized eggs and develop through various stages and the former resembles nothing of the adult species. This is true of every organism.

4. Homeostasis

The American Heritage Science Dictionary describes homeostasis as "The tendency of an organism or cell to regulate its internal conditions, such as the chemical composition of its body fluids, so as to maintain health and functioning, regardless of outside conditions. The organism or cell maintains homeostasis by monitoring its internal conditions and responding appropriately when these conditions deviate from their optimal state. The maintenance of a steady body temperature in warm-blooded animals is an example of homeostasis. In human beings, the homeostatic regulation of body temperature involves such mechanisms as sweating when the internal temperature becomes excessive and shivering to produce heat, as well as the generation of heat through metabolic processes when the internal temperature falls too low. "
Homeostasis is certainly true of higher animals and other organisms as well. It is a unique and wonderful governing phenomena.

5. Stimulus

Dictionary.com defines stimulus as, "something that excites an organism or part to functional activity." As organisms, we react to stimuli constantly. This is critical to the maintaining of homeostasis. Whether it is running from a potentially frightening situation, shivering when it is cold or retreating a finger after a paper cut, organisms, and higher animals, especially will always respond to the stimuli of the environment.



B. Where Do We Fit In?

All living creatures are biotic. You and I are as biotic as a bacteria or a ficus. However, there are classifications for organisms. The three major biotic domains are Archaea, Eubacteria and Eukarya, according to Columbia Electronic Encyclopedia. Within the domain Eukarya are four kingdoms, of which The animal kingdom is where humans are found. They are vertebrates who are the most highly developed of the mammals.

1. Ancestry: biological and cultural

Humans have a biological ancestry that makes them part of the living world. As such humans are active members of not only a community but of many ecosystems and, ultimately, the biosphere. We get timber from forested ecosystems. Fresh water ecosystems provide us with drinking water. The plains and other areas are ideal for farming. We exist in and live from the biosphere that we are found in.

However, humans have more than just a biological ancestry. They also have a history of culture. Culture is an advanced notion, unique only to humans. Culture is the idea that governs the behavior, art, language and expressed communications of a specific locale of people. The mere fact that we read this review as a matter of science is the product of cultural.


2. Threatening Alterations

There is no doubt that human activity alters our ecosystems. The more "developed" we become, the more organisms are lost in the destruction of ecosystems. Humans, therefore, as the most advanced of organisms have a responsibility to balance our activity to preserve the earth we live on, before we are responsible for the greatest extinction in earth's history.



C. Why Science?

"sci·ence /ˈsaɪəns/ Pronunciation Key - Show Spelled Pronunciation[sahy-uhns] –noun

1.	a branch of knowledge or study dealing with a body of facts or truths systematically arranged and showing the operation of general laws: the mathematical sciences.

2.	systematic knowledge of the physical or material world gained through observation and experimentation.

3.	any of the branches of natural or physical science.

4.	systematized knowledge in general.

5.	knowledge, as of facts or principles; knowledge gained by systematic study."

1. Concet: Theory's Role

Science is quite interesting. It is basically of study of examinations in order to understand the world in which we live. Scientists put together theories based on observation. Some theories become laws. Some become principles: generally, well accepted theories. Some theories will have to, realistically, stay theories as they cannot be disproved, but cannot be well proved.

2. Modus Operandi

Scientific information comes from scientific testing. To ensure quality and accuracy, certain procedures must followed and steps must be taken. These steps are referred to as the Scientific Method. First a scientist will make an observation. From that observation the scientist will formulate a hypothesis, or educated guess, as to the outcome of an experiment. Then the scietist will perform tests, or experiments to determine the outcome, or conclusion. The conclusion will either affirm or disprove the hypothesis. This information will, then, go to support a certain theory.


3. But, I Heard It On the Internet!

There are very good places to get scientific information. Scientific journals would, naturally, be the most obvious choice. The information is gathered under well-tested circumstances. Many government or institutional websites offer very accurate information. However, there are many websites that cannot be trusted for scientific, or any other, information. It is very important to find substantial proof for scientific claims made on non-institutional websites.


D. Evaluation
There is a lot of information given in a study to support the findings. However, some of the information be error values and other such swaying information. It is very important, therefore to read an entire study and not just the abstract and conclusion of a study. The methods, the studies and the statistics will give the complete picture of a study.

E. What Does This Mean for Us?

Science is the one observationally affirming way to know the world around us. As we apply science to technology we are able to improve our world. However, we also have the ability to do irreversible harm to our environments. If we, as humans believe there is a reason to preserve our biosphere, it is the only way to drive us to take responsibility for the knowledge and technology we possess. It is the only way we can assume responsibility to preserve those endangered elements of our earth.

II. The Nitty Gritty

A. Elementary and So Forth

there are millions, trillions and much more atoms in our bodies, much more, the world around us. The building blocks of everything are small. Yet smaller still is matter as a partial unit. It can be described as being much larger, too. This can be simple parts of atoms or can be described as you are matter, or the Pacific Ocean is matter. Matter is anything that has mass and takes up space.

1. Elements

Dictionary.com defines an element as, "Chemistry. one of a class of substances that cannot be separated into simpler substances by chemical means." There are only 92 elements that make up our natural universe, that we know of. Elements are charted on the periodic table. This shows the atomic weight, atomic number and symbol of each element.

2. Atoms

According to "Human Biology" "An atom is the smallest unit of an element that still retains the chemical and physical properties of the element." A hydrogen atom is the smallest unit of the element hydrogen. Atoms have a nucleus that contains the protons and neutrons. Circling this nucleus are the electrons. Atoms tend to have a balanced number of electrons, protons and neutrons.

3. What's the difference?

Isotopes are atoms with differing numbers of neutrons. So one elemental atom can actually have differing types within the same element.

4. Molecules: They really bonded

Molecules are the result of the bonding of atoms to one another. If nitrogen atoms bond together they will for nitrogen gas. When two different types of atoms bond together they form compounds. Water is a compound. It is made up of Hydrogen and Oxygen atoms. When oppositely charged atoms are attracted to each other this is called an ionic bond. When Atoms share electrons it forms a covalent bond.

B. Water, you made it all possible

Without water, we would not have life, at least not as we know it. Water is crucial to all living things on earth. It makes up approximately 70% of all living organisms.

1. Hydrogen bond

A hydrogen bond is very much like an ionic bond. Hydrogen, which is somewhat positively charged, due to the proximity of electrons to the oxygen is attracted to other oxygen molecules, which are lightly negative. The resulting effect is a weak bond, consequently called a hydrogen bond.

2. What water is like

Water has different properties in different environments that are unique. Most light-molecule compounds are gases at room temperature. Water is unique in that it is a liquid. This is important to our survival. It takes a temperature of Fahrenheit 212 or 100 Celsius to make water into vapor, or gas. Water, when frozen, is actually less dense than liquid water. This helps in organism flotation in water as well as insulating frozen bodies of water in the winter. Some compounds dissolve in water, because of the ionic attraction. Hydrophilic molecules are those that share this attraction making water solutions possible.

When below F 32 water becomes the solid, ice.

3. The pH scale

When water molecules break up it hydrogen breaking from the hydroxide (one hydrogen and one oxygen.) When liquids contain more of the hydrogen in the solution than hydroxide this solution is acidic. When the solution has more hydroxide that hydrogen it is a base. The pH scale shows The balance of these solutions in relation to pure water (H2O.) Bleach, ammonia and saltwater are all basic solutions. While coffee, beer and citrus juices are all acidic.

C. Organic Molecules


There are four different types of organic molecules. Organic molecules are those that consist of some carbon and hydrogen. The four different types are carbohydrates, lipids, proteins and nucleic acids.

1. Carbs

Carbohydrates are very important molecules. They are specifically good for energy. All Carbohydrates are made of hydrogen, hydroxide and carbon. Simple carbohydrates are those that contain less than seven carbon atoms. These are often referred to as simple sugars, or monosaccharides. Common simple sugars are glucose and fructose. These are both hexoses, which means they contain six (hex) carbon atoms.
Complex carbohydrates are called polysaccharides (poly=many, saccharide=sugar.) These are carbohydrates made up of multiple linked glucoses. Starch is a particular polysaccharide. It is found quite frequently in plants, especially those that we eat. Potatoes, corn and wheat are all foods high in starch. Glycogen is another complex carb found in these foods. There are some carbohydrates found in plants that are not readily digestible by animals. Carbohydrates, such as cellulose, are beneficial in that while the body cannot break them down they pass through the system as fiber. Fibers help keep cholesterol from being absorbed and can also help to keep one regular.

2. Lipids

Lipids are high in carbon and hydrogen levels, but contain very little oxygen. This makes them practically indissoluble in water. They carry more energy than other organic molecules. The first major type of lipids are the oils and fats. Fats are lipids found in animals and oils are found in plats. They both are excellent energy storage units. Fats and oils are made from the combination of fatty acids and glycerol. These are often referred to as triglycerides. Fatty acids always with a grouping of COOH. There are saturated and unsaturated fatty acids. Saturated fats play there part in cardiovascular problems because it causes solid lipids to clog blood vessels. Trans fatty acids are unsaturated fats that have been partially hydrogenated to make them slightly solid.
Phospholipids are those lipids that contain a polar phosphate chain. These tend to make up cell membranes as their polarized structure makes a good separation from water.
Steroids are lipids that have a carbon base with four carbon rings attached. Cholesterol makes these. Sex hormones are steroids.

3. Proteins


Proteins are very important to organisms from single cells to human beings. They are versatile and serve many different functions. They are used in transporting oxygen. These proteins are hemoglobin. They are elemental in muscle building which is important to motion and agility. Most hormones are proteins. These are metabolic messengers. Proteins are used to aid the bodies defense against harmful antigens. They are structural. Keratin is a protein that makes collagen, a fibrous substance that forms ligaments and skin.
The subunit of protein molecules is the amino acid. Amino acid contain the COOH branch, but also contain nitrogen. The nitrogen ends up somewhat positively charged as the electrons circle the oxygen molecules. This makes an attraction between amino acids called a peptide bond. Different proteins differ in structure and there are at least three levels of structures of proteins. Proteins, in order to be useful must "fold" themselves in certain ways to be used properly. How the do this is still quite unknown at this time, but they do, remarkably. When folds itself incorrectly, many things can go wrong. Misfolded proteins are linked to many diseases and cancer.

IBM's "Blue Gene" supercomputer
will test protein folding to find out
how it's done.

4. Nucleic Acids

There are two kinds of nucleic acids, both absolutely fundamental to the perpetuation of life. These are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA's main function is to keep strict gene patterns for reproduction. RNA is the messenger that convey's the code of the DNA. The bases for the genetic code which are found in DNA are adenine, thymine, guanine and cytosine. RNA's bases are the same except that uracil fits in the place where thymine would in DNA. Nucleotides(made up of phosphate, pentose and nitrogen) create the strands from which the bases connect. RNA is single stranded and DNA has a double helix structure. Hydrogen bonds between the bases hold the strands together.



III. It Ain't What You're Buying, It's What You're Cell-ing

A. Cells

Cells are the building block of life. Every organism is made up of cells. Some may only be a single cell. Other organisms, such as humans, are made up of trillions of cells. In fact human have about 5 million red blood cells in just one ml of blood!

1. Cell theory

The cell theory states much of the above statements. It states that, "A cell is the basic unit of life. All living things are made up of cells." and, "New cells arise only from preexisting cells."

2. Cell size

Cells tend to be about 100 micrometers in diameter. Some are smaller. Some are much larger, such as certain eggs, which are visible to the human eye. The smallness of a cell is important because a large cell would take much more energy to gain nutrients and expels waste. That is why, even in larger cells, division occurs without growth, so that cells become smaller and smaller, until they are quite manageable.
B. Cell organization

There are two different types of cells. The simplest is the prokaryotic cell. These are cells with no nucleus. Prokaryotic organisms are single-celled and the two types of them are bacteria and archaea. Eukaryotic cells do have a nucleus which is a membraned center where DNA is produced. Both types of cells have cell membranes, which is regulatory gate of what come in and leaves the cell. They both also have cytoplasm and organelles.
That is where similarities end between the two different types of cells. Within the Eukaryotic placement is the division of the cells of different kingdoms. The two largest are the animal cell and the plant cell. They differ in as few ways. For example, plant cells contain chloroplast, an organelle that makes photosynthesis possible.
Cells are fascinating and incredibly complex.

A cutaway model of a eukaryotic cell

C. Open the gates: cell membrane

All cells are surrounded by a plasma membrane. This membrane is made of phospholipids which, as we learned, have hydrophilic heads and hydrophobic tails. This membrane is what holds a cell together. It also determines what ions and molecules can enter the cell and which ones will leave the cell. Diffusion is one of the methods of entrance for molecules. Diffusion is the the movement of molecules from more populated to less populated areas. When When a molecule moves across the membrane it will go to where those molecules are less concentrated. Osmosis is diffusion of water molecules. In facilitated transport molecules that would not otherwise diffuse across the membrane are brought by protein carriers. Active transport is the facilitated transport of a molecule from lowest concentration to highest. This requires cellular energy which comes from the breakdown of ATP. The protein carriers are referred to as pumps, because they pump the molecule against their designated "flow."
The membrane is also crucial in the processes of endocytosis and exocytosis. During endocytosis forms a pouch that takes in materials from the outside of the cell. The three major types of endocytosis are phagocytosis, pinocytosis and receptor-mediated endocytosis. Whe materials are to be secreted in the same fashion. The process is called exocytosis.

D. Protein Factory

The nucleus of the cell is really the central "protein factory." Though there are other organelles involved

1. Nucleus

DNA is found in the nucleus of the cell. It is the most prominently noticeable feature of the cell. It is sealed with a membrane called the nuclear envelope. It is filled with a substance called nucleoplasm which is different than cytoplasm. Just outside the nuclear envelope are the endoplasmic reticulum. On the nuclear envelope are pores that let ribomal subunits and proteins in and out. Attached to the rough Endoplasmic reticulum are some of the ribosomes.

2. Endomembrane system

The endomembrance system is the name given to the system including the Golgi apparatus, lysosomes, the nuclear envelope, endoplasmic reticulum and vesicles. The Golgi apparatus is the series of saccules that takes in vesicles. These vesicles contain protein or lipids that will be changed. The vesicles then carry out waste particles or take their contents to the endoplasmic reticulum. On the rough endoplasmic reticulum are ribosomes that make proteins. Then the proteins enter the ER where they are modified. The smooth ER's job is to manufacture lipids. Lysosomes are one of the products of the Golgi apparatus. Their job is to digest particles, whether internal or external.

E. Shape and movement

Cytoplasm has a fibrous "skeleton" called the cytoskeleton. It is made up of the proteins of microtubules, Actin filaments and Intermediate filaments. Different. Cells have different types of movement. Some, such as sperm cells, use a flagellum. Others, such as egg cells, use cilia to move.

F. Mitochondria

Mitochondria are where the cell converts glucose energy into the chemical energy, ATP. Mitochondria have a maze-like shape inside containing enzymes to breakdown glucose.

1. Cellular Respiration

Cellular respiration is a series of reactions, using different enzymes. It is so called be cause the mitochaondria uses oxygen in the process and gives off carbon monoxide. A specific enzyme must perform its reaction on a specific substrate, otherwise the process will not be complete. Coenzymes are molecules that assist the enzyme. They may give or take atoms to make the reaction complete.

2. Fermentation

Fermentation, unlike cellular respiration, needs no oxygen. However it does use lactate and pyruvate is converted to lactate for the fermentation process. Fermentation should not occur as often as cellular respiration, because the amount of lactate produced is unhealthy. It can even be fatal when extended.

IV. The Body

The body is full of many different systems. There are different tissues. These different tissues, of course, form different organs.

A. Types of Tissues

Tissue is made of cells of the same type that will perform the same tasks. There are four major types of tissue. These are the: connective tissue, muscular tissue, nervous tissue and epithelial tissue. Connective tissue are made up of one of three types of protein fibers. Collagen fibers make a flexible tissue. Reticular fibers are flexible, but finer than collagen. Elastic fiber has a greater elasticity than collagen, but is weaker. The different connective tissues are cartilage, bone, blood and lymph. Muscular Tissue is made of muscle fiber tissue. It's main function is movement. The different types of muscle are skeletal muscle, smooth muscle and cardiac muscle. Nerve tissue is made of neurons and their nutrient supplier, neuroglia. The three parts of a neuron are the dendrites, the cell body and an axon.The main function of nervous tissue is communication. It is important to sensory understanding, processing that sensory data and providing the proper physical response. Epithelia tissue is protective and covers organs and surfaces (i.e. epidermis.)There are simple epithelia, which consist of only one layer of cells. Stratified epithelia, as the name implies, consist of layers of cells piled on top of each other with only the bottom layer touching the basement membrane. Some epithelia, such as sweat glands, have the function of secretion. These are called glandular epithelia.

B. Cell Junctions

Many cells in a tissue, especially epithelial, are held together by cell junctions. These junctions consist of joining of plasma membranes in three different ways:Tight junctions, adhesion junctions and gap junctions.

C. The skin and much more

In order to have an organ different types of tissue must work together. To have an organ system, different types of organs must work together. The skin has many organs and, thusly, tissue working together. It is referred to as the integumentary system. Skin has many jobs. It is protective, regulatory, productive and sensory. The skin has two layers: the epidermis/dermis and the subcutaneous layer. Epidermis is made up of many stratified tissue. The outermost layer is dead and keratinized. This makes the outer layer of skin waterproof. Dermis is below the epidermis. It contains most of the sensory receptors, which recognize pressure, hot, cold, pain and touch of a sexual nature. The subcutaneous layer is made, in part, of adipose tissue, which stores fat. This insulates the body. The many other organs found in the skin are: nails, hair follicles, oil glands and sweat glands.

A section of the integumentary system.

D. Organ systems

The integumentary system is just one of many in the body. The cardiovascular system is the blood circulation system. Lymphatic and immune systems control fluids, absorb fat and defend the body against infectious sicknesses. The digestive system absorbs nutrients in food and dispels the waste. The respiratory system maintains and regulates breathing. The urinary system dispels waste and controls pH balance in the body. The skeletal system supports and protects the body. The muscular sytem is responsible for movement. The nervous system receives, processes and reacts to sensory input. Endocrine systems produce hormones and regulate metabolism. The reproductive system produces sex hormones and produces and facilitates everything necessary to reproduction.

E. Homeostasis

We discussed, in the first chapter, that homeostasis is the maintenance of the body to keep internal conditions constant and stable. The endocrine and nervous systems are most important to maintaining homeostasis in the body. The nervous system perceives and responds to changes in the body. The endocrine system produces hormones that are integral to homeostasis, especially when internal changes occur. The two types of feedback are negative and positive. Negative feedback says something is not going right and needs to change. It is the most common function and helps maintain healthy glucose levels. Positive feedback tells the body to continue with a particular function or to aid a particular function.












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