Sunday, February 17, 2008

Genetic Engineering: The Upside of Down (or Visa Versa.)

Genetic engineering is a wide and varied topic. To confine it to one small aspect of popular interest would be unfair to the whole prospect. There are certainly up sides and down sides to the entire field, though often a pro would be a particular area of interest, as would be a con. So let’s look at a few flash points of interest.
Recombinant DNA technology is a process of genetic introduction into an organism. This is often used on plasmids in bacteria because of the ease of independent reproduction. A good amount of DNA can be produced from this method. This is great for obtaining useful genes in deficient people. For example, insulin can be cloned in bacteria plasmids and may actually be used for treatment of Diabetes. I think this is great! We can use plasmids, which replicate independently of the host bacteria and can hold a fairly good amount of foreign DNA. Only studies will bring about treatments. Yet as in anything, I think it would take a long time and countless experiments before any such genes could be proven to be effective as well as safe.
Another hot issue is that of GMOs as food. GMOs, of genetically modified organisms, are already a part of most people’s diet. A significant amount of plants and animals consumed are GMOs. Because GMOs are fairly new to human consumption it is bothersome to think that they have not been tried and true before being sent to the public’s stomachs. They have made production efficient and have been able to produce bigger animals and plants. But what about the long term effects on: a. the human body b. the ecosystem? They have passed rodent testing, but rodents don’t live nearly as long as humans. This is a plus in one manner. The generations are shorter for longevity testing. The down side is that a mass amount of these products can’t really have an effect that we can be certain of. There is also the possibility that GMOs will overstep their physical bounds and affect the natural population. This is a dangerous game that we have begun to play on open land.
Lastly and expectedly, there is the highly controversial issue of stem-cell research. It is so controversial because of obtainment methods. They are extracted from human eggs five days after division has begun. This, of course, implies that the egg has been inseminated and life is generated. Some would say that life has not truly begun at this point. I would argue that cellular activity is a clear indication of life. We cannot be separated from it. We are, because of cellular activity. Cellular activity is because we are. Now there is the probability that this is all done with donor gametes that would be useless otherwise. This is true. However, I am with the older school that thinks it not wise to play God. This is not simply a conservative idea, but the idea of radicals the world over. Some who believe in a higher power or God think it not wise to mess with what that power has put in play. I agree. I also think that it is a highly un-Darwinian Evolutionistic to want to tamper with what natural selection has regulated. Who knows what would become of a world where all are strong, none are weak and all survive. There is a delicate balance of life and death, and though some may think this is divine and others think it chance, it is balanced because it works. It is delicate and who knows what unbalance may come of such alterations.

Friday, February 15, 2008

Compendium Review II: let's dig the duplication

I. Chromosomal Inheritance

A. Chromosomes and the cell cycle

B. Mitosis and meiosis
1. Mitosis
2. Meiosis
3. Comparison

C. Chromosome Inheritance

II. DNA

A. DNA/RNA: Structure and function?

B. Gene Expression

C. Genomics

D. DNA technology

III. Cancer

A. Cancer cells

B. Cancer causes

C. Diagnosis

D. Treatment


IV. Patterns of Inheritance

A. Genotype vs. phenotype

B. One and two-trait inheritance

C.When it's more than that

D. Sex-linked inheritance


I. Chromosomal Inheritance

A. Chromosomes and the Cell Cycle

Every human has 46 Chromosomes. They are paired into twenty three bonded pairs. Only the sex chromosome determines gender. In females there are two "homologous" (look a
likes)X chromosomes. Males have an Xchromosome and a Y chromosome. The two separate parts of a chromosome are called "sister chromatids." One is, basically, a duplicate of the other. They are held together by a weak hydrogen bond. This holding point is called the "centromere."
Interphase is the process in which a cell grows and prepares for division. This is also when a cell goes about its specific business. In humans about 90% of a cell's life is spent in int
erphase. There are three stage
A microscopic view of the
Male "X,Y" chromosomes.
B. Mitosis and meiosis

1. Mitosis
We briefly touched on Mitosis above. But what exactly is it and how does it work? Mitosis is simply division by duplication. The interpahse of a cell readied everything for duplication. Chromatin in the nucleus became dense as it was produced. This is when chromosomes become visible. The Chromosomes are duplicated which make the sister chromatids. When mitosis begins the centromeres divide (it is a weak bond.) The centrosome also duplicates. The centrosome is, naturally, at the center of the cell. It contains to centrioles. This centrosomes assembles fibers that attache to the chromatids and separates them. This happens during "anaphase", the third phase of cell division. The two that precede it are the prophase and metaphase. The final phase is telophase. In prophase The centrosomes duplicate as well as the chromosomes. The nuclear envelope disappears as the centrosomes begin to move to opposite sides. In metaphase the spindle fibers of the centrosomes attach to the centromeres of the chromatids and the centromeres become aligned in the middle. Anaphase is marked by the pulling apart of the chromatids to opposite sides of the cell. Equal numbers of chromosomes are taken to each side. Telophase shows the reappearance of nuclear envelopes as the daughter cells become visible. Chromosomes become chromatin again. All the while the organelles have moved and the middle of the cell has become pinched as it becomes two cells. This is the process of cytokinesis spoke of earlier.

2. Meiosis


We now that Mitosis is duplication division. Meiosis is reduction division. The parents cell has the diploid number of chromosomes. The chrmosomes duplicate. Then the first stage of meiosis takes place.This is the last time that paired chromosomes are together during meiosis. The cell splits in two and each cell takes one of each pair of chromosomes. This cell is now a "haploid" which means it has only half the number of chromosomes. THen the second stage of meiosis, or meiosisII, takes place. Here, the centromeres holding the chromatids together, separates. The new daughter cells of each original daughter cells, now have one chromatid each. So what started as one cell has now become four with only half the original number of chromosomes. The cells that reproduce through meiosis are gametes, or sex cells. The only way that the fulll number of chromosomes will be restored is through fertilization.

3. Comparison

Mitosis and meiosis are different in many different ways. Here are some of them:
1. Mitosis consists of one division. Meiosis has two.
2. There are four daughter cells as a result of meiosis. There are only two daughter cells in Mitosis.
3. Meiosis' daughter cells are haploids, with only half of the full number of chromosomes. Mitosis' cells are diploids with the full number of cells.
4. Mitosis' daughter cells are identical to the parent cell. Meiosis' daughter cells are not.
5. During the prophase of meiosis chromosomes cross over and exchange genetic information. This doesn't happen in mitosis.
6. Pairs of homologous chromosomes align at the "equator" of the cell during meiosis I. There is only one of each chromosome that aligns in mitosis.
7. Meiosis II and mitosis are very similar except the daughter cells of meiosis are haploids.
C. Chromosomal inheritance

Humans generally have 23 pairs of chromosomes. 22 of them are autosomes (not sex chromsomes) and 1 pair is sex chromosomes. Some people end up having irregular numbers f chromosomes because of nondisjunction (non separation of chromosomes) during meiosis. This can happen at either stage. It leaves one cell with too many chromosomes and the other with too little. When a cell with too many chromosomes is fertilized it is called trisonomy. When the opposite occurs it is called monosomy. The chances of survival for one with a trisonomy is greater than that of a monosomy. Also the chance is greater if nondisjunction has occured with the sex cells. Though the "disorders" are different the extra X or Y chromosomes have littler impact on survival. Down Syndrome is the result of having one too many chromosome 21s. Turner Syndrome is the result of having only the X sex chromosome, while Klinefelter Syndrome is the result of having an exta X chromosome. Sometimes a change in the structure of chromosomes will also cause mutations. If the broken ends don't reunite, reunite with a duplicate or reunite in the wrong place mutations occur. Williams syndrome is an example of deletion (the end of a chromosome is lost.)







Jeremy Vest, who has Williams Syndrome is a perfect
example of
its carriers natural draw to
music.

II. DNA

A. DNA/RNA: Structure and function

DNA, as previously discussed, is the material that contains genetic code. DNA must be able to do three things: 1. Replicate 2. Store genetic information 3. undergo mutations for diversity.DNA structure is a double helix. There are two backbone strands of polynucleotides
that contain the paired bases. These bases make rungs across the strands. The bases are Adenine and Thymine (complimentary and pair together) and Guanine and Cytosine (complimentary to each other.) When DNA replicates the strands split and a new strand joins each of the old strands. Then any breaks in the backbone strand are repaired and we have two DNA molecules. When errors occur in replication, they will usually be fixed by enzymes. Those that continue are called mutations.
RNA, instead of having the Thymine nucleotide, has Uracil as a complimentary bas
e to Adenine. RNA is single stranded.There are different RNA with different functions. mRNA (messenger RNA) carries the information from DNA templates to the cytoplasm for DNA synthesis. tRNA (transfer RNA) transfers amino acids to ribosomes for DNA synthesis. Each type of amino acid is carried by a different type of tRNA. rRNA (ribosomal RNA) make up the sub units of ribosomes for DNA sysnthesis.

B. Gene Expression


Proteins (which make up DNA and RNA) are made of amino acids. There are 20 amino acids that commonly make up proteins. Their number and position is what determines the type of protein one will be and the shape it will take. These are, naturally, integra
l to DNA synthesis and gene expression. The first step is called transcription. This is where mRNA transcribes the DNA template with genetic coding. It is then taken to the ribosome for translation. In translation, the nucleotides of the mRNA transcript are translated into amino acids for for gene expression.This genetic code, of four nucleotide bases, is a triplet code. The bases are read in units of three and each three base-section translates to a certain amino acid. These sections are known as codons. They are read by anticodons which are carried by tRNA that are attached to the correct amino acid for the protein being made.














Translation in progress, as anticodons
place amino acids in th
e right order.

C. Genomics


Genomics (the study of one's genome o
r collective heredity information) is, of course, a very important aspect of modern science. The Human Genome Project has been put together to better understand the human genome. They have succeeded in identifying most if not all of the genes of the human genome. The future goal is to understand a genes specific function and how it actually creates a human being. Comparative genomics is an attempt to determine the evolution of species, namely humans. They have, in doing so, made interesting insight to human disease and would hope to find more links to diseases.
Since proteins are often translated from genes. There is much to be studied in them IBM's "Blue Gene" supercomputer is one endeavor in proteomics, or the study of the proteome. It is also an advancement in Bioinformatics, the study of genomes with computer technology. There are many studies in these areas going on to help improve the human condition. Gene therapy is an applied region of genomics. This is where genetic material is put into the human cells for correction of genetic disorders. This is stil a very young science, but much progress is being made and treatment of many disorders are in the works.

D. DNA Technology

Cloning is a relatively young area of biology. It is the producing of copies of DNA. This is done asexually and technologically. Recombinant DNA is cloned DNA of more than one source. Plasmids in bacteria are a particularly common subject for this process. This way specific genes can be produced, then isolated for use. Polymerase chain reaction (PCR) is a process that takes a small section of DNA and copies the sequence. It has been used to determine DNA strands of mummified brains, identify unknown soldiers, determine fatherhood of posterity and determine perpetrators of crimes. Many products have come from cloning and biotechnology. Many plants have been engineered to be resistant to pests and herbicides. Animals have been given growth hormones to be larger and reproduce faster. The sky is really the limit with this technology.





The genetically modified tomato, on the
right is significantly larger than the
"organic" tomato.The
issue of Genetically Modified
Organis
ms (GMOs) is a highly
controversial topic.

III. Cancer

A. Cancer cells


Cancer is a name for many different types of diseases that can appear in almost any part of the body. The reason they are called cancer is that they all have certain things in common. Cancer is cellular. Cancer cells are conspicuous and abnormal. The nucleus of cancer
cells is irregularly large. They may have abnormal numbers of chromosomes. They fail to experience apoptosis, or irregular cell death. Cancer cells divide indefinitely with the potential to divide limitlessly. They form tumors. They do not respond to cellular growth obstructers. Mutations become more frequent making cancer cells increasingly irregular. Cancer metastasizes, that is invades lymph nodes or blood vessels to inhabit different areas.
Cancer cells have a mutation in one or both of the these genes: proto-oncogenes and tumor-suppressing genes. The proto-oncogenes promote the cell cycle and inhibit apoptosis. The genes are modified they are called oncogenes. This is a "better-working" version. The tumor-suppressing genes are, themselves, supressed or totally diffused.
Oncology is the study of cancer. Oncologists study cancer in all its forms. So
me different types of cancer are: lung, colon, pancreas, stomach, throat, lymphoma, leukemia, skin, breast and brain cancers.


Lung cancer cells
B. Cancer causes

Though understanding of of cancer's causes are not complete many things have come to be understood. First cancer can be hereditary. If one inherits certain mutated genes, cancer can occur. Another cause is environmental factors. Some of these are radiation, tobacco smoke, pollutants (asbestos, uranium, radon, benzidine, etc.) and viruses.


C. Diagnosis

Early detection of cancer is an important factor to success of treatment. Many ways are being developed and speculated for very early cancer detection. Those we have available now are physical warning signs, regular screening tests, tumor mark tests and genetic tests.
There are seven warning signs that one can determine the possibility of cancer. They were published by the American Cancer Society. The acronym of these signs spells "CAUTION." these are: 1. Change in bowel or bladder habits 2. A sore that does not heal 3. Unusual bleeding or discharge 4. Thickening or lump in the breast or elsewhere 5. Indigestion or difficulty swallowing 6. Obvious change in wart or mole

7. Nagging cough or hoarsness

D. Treatment

There are many types of treatment for cancer. Some have been used for a long time with nominal success. Others are simply being tested which will, hopefully, prove successful. The standard types of treatment are radiation, chemotherapy and surge
ry. Radiation therapy is when radiation (gamma rays, or X-rays) are applied to a specific, cancerous area. Radiation causes disruptions in chromosomes and more easily kill cancer cells, specifically. Surgery is used to remove cancer in situ (non-base penetrating cancer.) Chemotherapy is drug injection that kills cells. The idea is to kill as many cancer cells as possible while maintaining enough normal cells for the body to function.
Some more experimental therapies are immunotherapy (injection of ca
ncer-killing antibodies), p53 gene therapy (genetic expression that catalyzes aptosis in cancer cells) and antiangiogenic drug therapy.


Chemotherapy makes the body weak
and is often marked by body hair loss.


IV. Genetic Inheritance


A. Genotype vs. Phenotype

Genotypes are the genes of an organism. Alleles are specific types of traits in a gene. There are two alleles for each genotype and they affect the same trait. A familiar and basic way to look at this is is to chose a specific trait, such as that for freckles. The letter "f" is designated to this trait. Each allele would represent whether the trait would be freckles or no freckles. The allele for freckles is dominant, there fore it would be represented "F" whereas the recessive allele would be represented "f." If a person has freckles their genotype would, then, be "FF" or "Ff." The first form, "FF" is called homozygous dominant. This means that both alleles are the dominant. The second is called heterozygous, meaning both alleles are present. When a genotype is heterozygous the phenotype (ex
pressed trait) is always the dominant. If a person had no freckles, the genotype would "ff. " This genotype is called homozygous recessive.

B. One and two-trait inheritance

When an organism has only one trait, such as "FF" expressed above, the only allele the gamete would pass on is a dominant allele. The same is true if the organism were homozygous recessive. Now, if a heterozygous trait were present half of the gametes would carry the dominant allele, and half would carry the recessive allele, since the chromosomes split in half during meiosis. To figure out the possibility of a trait in offspring one would, simply, make a punn
ett square. This square is divided into four spaces with the alleles of one parent on the top and the alleles of another parent on the side. Combining each set of alleles in the corresponding square gives the possible outcomes of an offspring. When an offspring is heterozygous the individual is a monohybrid, because one trait is hybrid. When two traits are part of the two homologous chromosomes in meiosis1 there become four allele setups (i.e. widow's peak: W, or w, short fingers: S of s: possibilities WS, Ws, wS, ws.) These can be lined the same way on a punnett square, but instead of having four areas of possibility and probability, there are now sixteen!If an offspring is heterozygous in both traits they are a dihybrid.




A punnett square where "A" or "a" represents
an allele of a trait.
Most disorders are autosomal (not pertaining to sex chromosomes.) Disorder traits are passed on the same way as other genotypes. If a disorder is dominant any autosomal dominant of heterozygous carrier will be affected by it. If it is a recessive disorder than only those carrying autosomal recessive genotypes will be affected by it. If the disorder is recessive a child may carry a disorder that neither parent has. If the disorder is dominant than the child with it will virtually have to have a parent with it. However the child may not if the parent or parents do.There are many autosomal genetic disorders. Some recessive ones are Tay-Sachs disease, cystic fibrosis and sickle cell disease. Some dominant disorders are Marfan syndrome and Huntington disease.

C. When it's more than that

There are some traits that are controlled by multiple sets of alleles. These are called polygenic traits. Polygenes are often subject to the environment. Whenever large groups of people are surveyed for phenotypes of polygenes, the trend shows a belly type curve. Since dominant alleles will most likely be found in most of these people and because of environmental effects there will be a continual distribution.
Some phenotypes will have incomplete dominance or codominance. That means that neither trait takes dominance and a mixed phenotype shows up. Such as a wavy haired child coming from parents of which one has straight hair and the other curly. Some disorders act in this way.

D. Sex-Linked Inheritance

Most traits are autosomal, since 22 of the 23 chromosome pairs are autosomes. However, a few disorder are sex-linked, meaning they occur on the X or Y chromosome. Very few genes are on the Y chromosome (which, usually, only men have.) Most sex-linked traits, therefore, come from the X chromosome. Since this is true traits can be passed to either offspring from either parent.
The same is true for the sex-linked disorders. When int is an X-linked recessive disorder it is usually expressed more often in males than in females. That is because when an X-linked disorder is recessive the male only receives the recessive trait. The Y chromosome doesn't have an allele for it. Some of these are color blindness, muscular dystrophy and hemophilia.




Hemophilia, an X-linked recessive disorder
makes carriers susceptible to extensive
bleeding since they lake adequate
blood clotting proteins.





"IBM Research."http://domino.research.ibm.com/comm/research_projects.nsf/pages/bluegene.index.html

"tomatoes."http://www.american.edu/TED/images4/tomatoes.jpg

"Lung cancer."http://www.scienceclarified.com/scitech/images/lsbv_0001_0001_0_img0030.jpg

"Christi12"http://www.christithomas.com/images/MVC-003F15.jpg, used with permission.

Thursday, February 14, 2008

Lab Project 1: Cell Model



Here is a model of a functioning animal cell using simple household, office and construction supplies. Each product was handpicked for its resemblance to portrayal of organelles in in various cell illustrations and models. Here is a list of organelles. The numbers correspond to the numbers next to each item in the photo to the right. 1. Cell Membrane (wire and cloth basket) 2. cytoplasm (window sealer/packing straw) 3. Nucleus (tennis ball) nuclear pores (black spots on ball) 4. nucleolus, chromatin (orange cap, black space in ball) 5. mitochondria (the one represented here is different from the one I ended up using, which is a wooden carrot) 6. one of three chromosome pairs used in sub model (metal braces)7. ribosomes (hole-punched paper) 8. Golgi apparatus (taped rubber bands) 9. Endoplasmic reticulum (linked paper clips) 10. vesicles (red crayon. Lysosomes will later be shown as blue crayons with straw at center to represent digesting bacteria.) The flagellum will be represented as a cut hair tie.

Here is the nucleus inside the cell.Its function is the production of DNA The membrane is the wire and mesh basket and the straw and sealer(clear goo) is the cytoplasm. The yellow outer of the nucleus is the nuclear envelope. The shiny orange cap is the nucleolus and the black in represents the chromatin. The black spots on the outside of the tennis ball (or shall I say nucleus) are nuclear pores through which ribosomes and mRNA enter and exit the nucleus.

The paper clips, here, represent the ER (endoplasmic reticulum.) Its function is to put proteins to use. This is also where proteins fold. Glucose and other products are made there.The green dots are ribosomes. They are key to amino acid production. When found on the ER that ER is called rough ER. The ER lacking ribosomes is the smooth ER.


The orange ellipse in the photo below is the mitochondria. This is where ATP (fuel of cellular energy) is produced. The fused bands is the Golgi apparatus. These organelles receive vesicles with particles for construction of important molecules and sends vesicles out to secrete waste. The vesicles are the red cylinders. When they collect materials from outside the cell, it is called endocytosis. When they excrete materials it is called ectocytosis.










The blue cylinders are lysosomes. They digest bacteria (little straw in cylinder) to use particles or secrete them.












The "tail" here is the flagellum. Its function is cellular movement. Some cells have flagella. Others use cilia for movement and other functions.















Here is the complete, working cell. Now Let's take a look at what goes on in DNA production.














This is a paired chromosome ( the two metal braces) in the nucleus. Each human cell has 46 chromosomes. When a cell is ready to reproduce it copies each chromosome. They are then paired, like so. The colored wires represent the DNA that chromosomes are made up of. DNA is twisted in a "double helix" pattern. The rungs are genetic code. They are made up of four base units. When DNA is reproduced it, first, splits as shown above. Each side, then connects with a copy that has been made.


When The base units for DNA (adenine, guanine, cytosine and thymine) and other DNA products are needed mRNAs (messengers) take the information to ribosomes. There the information is read and tRNAs (transmitters) are put to use to make the necessary materials. The red spiral is an mRNA being read by the ribosome (green dot) the orange spirals are tRNA entering and leaving the ribosome.







It took hours to put together a model of the microscopic cell. It doesn't, of course, function as a live cell does. Cells are amazingly intricate. In the time it took me to make this model, millions of cells were born in my body. Millions of cells went about their usual business to keep me functioning normally. Millions of cells carried out tasks with such complicated instructions that it would make a city planner's head spin. There is, perhaps, much we can learn from the little cell. It functions smoothly. It works efficiently. It works together with other cells in great harmony. It identifies problems and takes care of them promptly. When a problem does arise, however, the results can be disastrous (cancer, disease.) If we might learn to take the efficiency and learn from the mistake of "bad cell multiplication" who knows what we might accomplish.


PS: for more information and photos on mitosis contact me at hexinduction@yahoo.com
Post
Post Script.: It turns out today (2/17) I was able to use my cell model to teach a friend's young children about cells. They were captivated by the colors. NOTE: teach kids with COLORS!!! haha.

Tuesday, February 12, 2008

Genetics and Flying Things: LAB

Genes are our unit of inheritance, well, physically so to speak. Offspring receive genes from the parent(s) which insures the parents' mark be carried on in posterity. But how does it all work? What are in genes? Which genes do offspring exhibit?
The genes of a particular trait in an organism are the genotype. Genotypes are the combination of traits appearing from the parents. One characteristic of each parent will appear in the genotype. The individual characteristics are called alleles. For example, the genotype for horns on our beloved dragon were to have double horns.A double horn trait is represented by H while a single horn trait is represented by h. But, just because the phenotype (or observable trait of the genotype) is double horns does not mean that the genotype of the dragon is HH. In actuality the genotype was Hh with double horns being the dominant trait (that which will appear when present) and single horn being the recessive trait (that which will only appear when two recessive traits are present). We call the genotype of our dragon heterozygous. A homozygous genotype will have the phenotype of whichever alleles are represented. If our dragon's phenotype had been a single horn that the genotype would have been hh. We call this homozygous recessive.
Our fruit flies are a perfect example of this. Both of the parent flies had the phenotype for long wings. However, both of them had a long-wing genotype that was heterozygous. The punnet square shows the possible outcomes of any offspring. Of course, there was only the possibility of two phenotypes: long wings and short wings. However, there were three possible genotypes. Since both parents parents were heterozygous there was 1/4 possibility the offspring would be either homozygous dominant(long-winged) or homozygous recessive(short-winged). The other half possibility, 1/2 chance was that the posterity would be heterozygous, and therefore long-winged.
Chromosomes are certainly vital to evolution and mutations are passed at the genetic level. It is interesting that we would study a punnett activity on fruit flies, since they have been the subject of practical evolutionary studies for 100 years now. Since fruit flies have a generational period of 11-12 days it would be easy to see how mutations could transform a species in a limited amount of time. For example, humans have been around for a little over one million years, according to general scientific thought. The experiments on fruit flies have well exceeded that one million years, translated. The results? The thousands of mutations imposed, if put into one single fly, would not resemble anything of a new species. Most of these mutated flies die out or, more often, revert back to the wild type, as if there was some type of genetic fail safe!!! Then again, I am sure they just evolved the fail safe, so they would never have to change species again.
This was, certainly, a very fun lab. Why I didn't do this in junior high and high school, I am not sure. Now I know who to blame for my small hands. DAD!!!





Sources:

"Elusive Icons of Evolution What do Darwin's finches and the four-winged fruit fly really tell us?"
Jonathan Wellshttp://www.actionbioscience.org/evolution/nhmag.html

Thursday, February 7, 2008

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, ultimatel
y, 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 [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 u
nit. 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 the
m 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 ha
s 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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