During the first half of the 20th century a debate among biologists centered around whether proteins or deoxyribonucleic acid (DNA) was the molecule of inheritance. In 1928,
Fredrick Griffith first proposed that the transfer of DNA between bacteria caused transformation, but could not provide convincing proof. In the 1940s Oswald Avery and others were able to devise experiments that provided the evidence that Griffith lacked. However it took an experiment by Alfred Hershey and Martha Chase in 1952 to finally demonstrate to the scientific community that DNA and not proteins was the molecule of inheritance.
Today we know that the coded message for our traits is based in the four nucleotides of DNA. These four bases adenine (A), thymine (T), guanine (G), and cytosine (C) are divided into two groups called purines (A & G) and pyrimidines (T & C). The Human Genome Project has confirmed that the DNA in a typical human cell contains over 3 billion base pairs (bp). In these 3 billion bp are 20,000 to 25,000 genes that code for proteins, which in turn code for our traits. Each gene is a specific sequence of nucleotides located on one of the DNA strands.
The DNA in the human body is spread over 24 distinct chromosomes which range in size from 50 million to 250 million bp.
To learn more about the findings of the Human Genome Project go to http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml
DNA is a nucleic acid that contains nucleotides running in two strands and twisted into a double helix. Each nucleotide contains three molecules (a base, a deoxyribose sugar and a phosphate group). The nucleotides pairings are shown in the illustration below. These pairings also referred as complementary base pairs.
Figure 1: The DNA molecule showing base pairing. http://student.ccbcmd.edu/~gkaiser/biotutorials/dna/images/u4fg8f.jpg
In the illustration above you will see that the base adenine is paired with the base thymine and the base guanine is paired with the base cytosine. The idea of these pairing was first discovered by Edwin Chargaff in the late 1940’s. In working with cells from different organisms Chargaff discovered that the percentages of adenine in a cell were equal to the percentages of thymine, and the percentages of guani ne were equal to the percentages of cytosine in the nucleus. These pairing have become known as “Chargaff’s Rule”.
However the meaning of this discovery was not clear until Watson and Crick developed their mode of DNA in 1953.
The genetic code in DNA is passed along via mitosis, meiosis or binary fission. Prior to these processes the molecules of DNA in the parent cell must be copied via DNA replication. In their 1953 paper Watson and Crick proposed that each strand of the DNA molecule makes a complementary copy of itself through DNA replication prior to cell division. In 1957, Meselson and Stahl devised an experiment that demonstrated this semi-conservation nature of DNA replication as first proposed by Watson and Crick. In this process each strand from the original DNA molecule gets a new complementary strand. Thus each new DNA molecule has 1 (one) st rand from the “old” molecule and one “new” strand that is an exact copy of the original.

Figure 2: The semi-conservative nature of DNA replication. http://fig.cox.miami.edu/~cmallery/150/gene/sf12x1.jpg
To learn more about the history of DNA’s discovery go to http://www.dnai.org/
Before the genetic code is passed from parents to offspring via meiosis or from one cell to another new cell via mitosis the DNA must be replicated. As illustrated in Figure 2 each strand of the DNA makes a complementary copy of itself.
In a simplified view the copying can be seen in Figure 3. The DNA “unzips” and complementary bases are brought to each strand and the new stands “rezip” forming two identical copies of the original DNA molecule.
Figure 3: A simplified view of DNA replication. http://library.thinkquest.org/18617/media/replicationsimple.gif
Biologists have discovered that the actual process is far more complicated. First a molecule called helicase unwinds the DNA double helix. Before DNA polymerase travels along each strand matching complementary bases, a short sequence of RNA nucleotides is matched with the separated strands by RNA primase. The copying of each strand, however, is different. One strand called the leading strand is copied in a continuous fashion, while the other called the lagging strand is copied in fragments called Okazaski fragments as seen in the illustration below. Later DNA ligase will join these fragments.

Figure 4: The replication of DNA along the leading and lagging strands. http://fig.cox.miami.edu/~cmallery/150/gene/c7.16.14.fork.jpg
The rate at which new nucleotides are added is about 50 per second and would take 53 days to replicate the largest human chromosome if replication began at one end and proceeded to the other end. As such the replication of any chromosome begins at many origins along the chromosome. In fruit fly chromosomes there are some 3500 origin sites where DNA replication begins simultaneously.
To learn more and to view an animation of DNA replication go to http://www.johnkyrk.com/DNAreplication.html
and, http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/dna-rna2.swf
and, http://www.emc.maricopa.edu/faculty/farabee/biobk/BioBookDNAMOLGEN.html
The later is a part of the online t extbook “Online Biology Book”. Numerous diagrams are included along with a description of DNA structure and replication. Links are also provided to other websites. back to top
Content Benchmark L.12.A.1
Students know genetic information passed from parents to offspring is coded in the DNA molecule. E/S
1. Students incorrectly assume that DNA is vastly different amongst members of the same species.
Despite the fact that humans contain over 3 billion bp in their DNA, researchers have found that most of DNA is quite similar. Based on sequencing to date it appears that on average two unrelated people have one different nucleotide per 1000 bases. Thus with 3 billion bp total bases this means there are 3 million differences between individuals or less than 0.01% difference between individuals. These differences are called single nucleotide polymorphisms or SNPs (pronoun ced “snips”)
Aside from the fact each human has a unique combination of genes; these genes are shared by all members of the human species. The goal of the Human Genome Project is to identify these genes and than determine what each gene codes for in humans.
To learn more about SNPs go to http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml
2. Students mistakenly assume that DNA coding for molecules is different between different species.

While a species has a unique gene pool that defines that species, many genes are shared by humans and other organisms. For example 45% of the genes found in fruit flies are also found in humans and we share approximately 96% of our genes with chimpanzees. This should not be surprising considering the number of biochemical pathways that are commonly found in organisms. For example most organisms obtain energy or ATP by cellular respiration and the enzymes (coded for by DNA) involved in this biochemical pathway are found in most organisms.
To learn more about the similarity of human and chimpanzee DNA go to http://news.nationalgeographic.com/news/2005/08/0831_050831_chimp_genes.html
3. Students incorrectly assume that mutations in DNA are always harmful.
Single base errors in DNA copying are called point mutations, however, these are rare. During DNA replication the error rate is 1 in 10,000 bases being copied. Most of these errors are corrected by DNA proof readers. Secondly if an error is not corrected, because of the redundancy of the genetic code the same amino acid may be coded for by the codon. This is called a silent mutation. Or an am ino acid with similar properties can be coded for by the “mutant” codon which is sometimes called a neutral mutation. Note the table below.
At the same time some point mutations can be harmful. In the table below the DNA triplet and mRNA codon are shown for the 6th amino acid for normal hemoglobin. In sicklecell anemia a mutation from T to A leads to the replacing of glutamic acid with valine. The result is an abnormally shaped hemoglobin molecule during low oxygen concentration in the blood. And if the first C is replace by A, the result is the termination of protein synthesis and no hemoglobin molecule is produced.
DNA Triplet mRNA codon Amino Acid Properties Mutation Type
CTC
CTT
CTA
CAC
ATC
GAG
GAA
GAU
GUG
UAG
Glutamic acid Hydrophobic Normal codon
Glutamic acid Hydrophobic Neutral
Aspartic acid Hydrophobic Silent
Valine
Stop
Hydrophilic Missense
Termination Nonsense
All humans with blood type O are also carrying a mutation. The genes for blood type code for proteins found on the red blood cell. Many inherit the genes for the A and B proteins. However due to a point mutation in our ancestral past the coding for these proteins was lost, thus those who inherit the alleles for O lack coding for either protein.
To learn more about DNA mutations go to http://www.genetichealth.com/G101_Changes_in_DNA.shtml#Anchor2 http://evolution.berkeley.edu/evolibrary/article/0_0_0/mutations_01
4. Students incorrectly assume that DNA and chromosomes are not the same.
Both of these are names for the same molecule. Humans have 46 chromosomes and each chromosome contains a specific sequence of DNA nucleotides which are codes for our genes. However, each chromosome contains a unique combinations of genes. Genes found in Chromosome #1 are not the same as those found in chromosome #2..
To learn more about what genes have been discovered on each human chromosome and to order a free poster showing human genome landmarks go to http://www.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/
5. Students inaccurately assume that the amount of genetic material is equal in males and females.
While each offspring, regardless of sex, receives 23 chromosomes from each parent, the amount of DNA and the genes they receive is not equal. Both males and female receive the same 22 pairs of autosomes (non-sex chromosomes) and therefore each receives equal number of genes for non-sexual characteristics found on these chromosomes. However the sex chromosomes (X and Y) do not contain equal number of genes or types of genes.
The X chromosome represents approximately 5% of the total DNA in cells and contains approximately 1300 genes. These 1300 genes not only include genes for femaleness, but genes for such traits as blood clotting and color vision. On the other hand the Y chromosome contains approximately 2% of the DNA in a cell or approximately 300 genes which will be inherited by males only, since females do not inherit a Y chromosome. Thus males inherit both the X and Y chromosomes, they will inherit all genes for the same traits as females, but females will lack any genes found on the Y chromosome.
To learn more about the X and Y chromosomes go to http://ghr.nlm.nih.gov/ghr/chromosomes
6.
Students incorrectly believe that the amount of DNA varies in organisms based upon their “complexity”
While is true that humans have approximately 1000 times more DNA than a typical bacterium, the Human Genome Project has reveled some interesting surprises. Humans have approximately 3.0 X 109 base pairs (bp) and 20,000 to 25,000 genes. But notice the figures for other organisms.

Organism DNA base pairs Approximate # of Genes Chromosome # Mutation Type
Rice
Maize
Mouse
3.9 X 109
2.5 X 109
2.5 X 109
Whisk fern 2.5 X 1011
Sea urchin 8.14 X108
37,000
Over 50,000
22,500
?
23,000
12
20
40
?
44
Normal codon
Neutral
Silent
Missense
Nonsense
To view more examples, go to http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GenomeSizes.html#Anopheles
In summarizing the findings of their 1938 experiment Beadle and Tatum made the statement “one gene, one enzyme”. In this experiment Beadle and Tatum concluded that the genes in the DNA molecule were responsible for the coding of enzymes, a type of protein. Today we also know that the genes in DNA also code other proteins such as melanin,
(a pigment found in our skin, hair and eyes) and insulin (a hormone involved in the regulation of blood sugar).
Each cell contains just one copy of the genetic information which codes for the hundreds of proteins needed by the cell at any given moment. Thus the process of coding for proteins needs many messengers to be delivered to the hundreds of ribosomes that are actively making these proteins. This process is a part of what Watson and Crick first proposed as the “Central Dogma.” In this process DNA makes a molecule called messenger RNA (mRNA) which delivers the genetic code to the ribosomes, which translates the code into proteins.
Figure 1: The Central Dogma of Molecular Genetics http://www.emc.maricopa.edu/faculty/farabee/ biobk/BioBookPROTSYn.html
To learn more about the Central Dogma of Molecular Biology, go to http://crystal.uah.edu/~carter/protein/dogma.htm
During the process of transcription one strand of DNA that contains the gene serves as a template to form mRNA. But unlike replication where thymine serves as the complementary base to adenine, uracil another pyrimidine base substitutes for thymine. Guanine and cytosine still pair. Once this complementary strand of mRNA is produced, the process is not finished as will be discussed later.

Figure 2. Transcription of RNA http://library.thinkquest.org/C0123260/basic%20knowledge/ images/basic%20knowledge/RNA/transcription.jpg
Biologists have learned that not all of the DNA present codes for proteins. In the case of humans it now appears that as little as 1.5% of bases in human DNA actually code for proteins. They have discovered that the DNA sequences that forms our genes and code for proteins are divided into exons (the meaningful or coded segments) and introns (the interrupting or noncoded segments). These introns will be cut out after the initial mRNA molecule is made. Afterwards the exons are joined forming the mRNA sequence that will code for the protein formation. This process is illustrated in Figure 3. Special enzymes called splicosomes help in the removal of the introns.
Figure 3. RNA splicing – removing the introns http://www.accessexcellence.org/RC/VL/GG/images/rna_synth.gif
To learn more about transcription go to http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html
To view animations of transcription go to http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/transcription.swf
or http://highered.mcgraw-hill.com/olc/dl/120077/bio30.swf

One of the major findings of the Human Genome Projects is that, at least in humans, these exons can be rearranged. Therefore one gene can actually be responsible for coding for two or three different, but related proteins. This also might explain why the number of genes in humans (approximately 20,000-25,000) is so small as compared to other organisms as C . elegans a “simple” roundworm that has about 19,000 genes.
Figure 4. The alternative arranging of exons. http://www.plantgdb.org/tutorial/annotatemodule
/images/alternativesplicing.jpg
In the formation of RNA the cell can actually make three types. As discussed above mRNA will carry the genetic code for a particular protein from the nucleus to the ribosomes where proteins are made in the cell. Two other types of RNA are also made from genetic code in the DNA. Ribosomal RNA (rRNA) is used along with other proteins to construct the ribosomes. A third called transfer RNA (tRNA) is formed and will carry amino acids from sources in the cytoplasm to the ribosomes during protein synthesis.
To learn more about the three types of RNA go to http://www.elmhurst.edu/~chm/vchembook/583rnatypes.html
In the process of translation or protein synthesis, ribosomes read the coded message in mRNA. As the message is read another form of RNA called transfer RNA (tRNA) delivers amino acids to the ribosomes. The ribosome themselves are formed from proteins and a third type of RNA called ribosomal RNA (rRNA). Note the illustration below.
The process can be divided into 4 stages:
1. Initiation – binding of mRNA, ribosomal subunit, and tRNA carrying methionine
2. Elongation/Translocation
– the ribosome moves along the mRNA reading the codons. The tRNAs with the appropriate complementary anticodon and amino acids joins the ribosome. For example if the mRNA codon is AUG, the tRNA anticodon would be UAC. As the ribosome moves along the mRNA, new tRNA molecule with complementary anticodons enter the ribosome. Amino acids are joined and the new protein continues to grow.

Figure 5: http://library.thinkquest.org/18617/media/anticodon.gif
3. Termination
– a stop codon enters the ribosome. There is no appropriate tRNA with an anticodon for stop codons. A releasing protein now enters the ribosome rather a tRNA.
Translation stops.
4. Disassembly
– the ribosome subunits break apart and “falls” from the mRNA. The new protein is released.
Figure 6: Translation or protein synthesis http://users.rcn.com/jkimball.ma.ultranet/
BiologyPages/T/Translation.html
To view animations of translation go to http://www.stolaf.edu/people/giannini/flashanimat/molgenetics/translation.swf
or http://highered.mcgraw-hill.com/olc/dl/120077/micro06.swf
The mRNA may continue to be read by other ribosomes. Biologists have discovered that often multiple ribosomes are “reading” the mRNA at any one time. These are sometimes termed polyribosomes. This will increase the rate of protein production as the cell can make multiple copies of the same protein at the same time.

Figure 7. Electron microgram of a polyribosome. http://bass.bio.uci.edu/~hudel/bs99a/ lecture23/polysome_only.gif
In the early 1960s the genetic code was worked out by a number of biologists. Using mRNA these biologists were able to determine that groups of 3-bases called a codon, code for one amino acid. The result of the work is illustrated in the table below. The first letter of the codon identifies the row; the second letter identifies the column; while the third letter identifies the amino acid at the intersection of the selected row and column. For example AUG codes for methionine. AUG is most often the codon used in coding for proteins. Notice that three codons do not code for any amino acids, but serve as stop signals.
Figure 8. The Genetic Code
– table version http://www.emc.maricopa.edu/faculty/farabee/biobk/code.gif
The genetic code shows redundancy, that is, there are multiple codons for many of the amino acids. One effect of this is to reduce the potential for harmful mutations.
Students might ask why the table starts with “U” rather than “A”. The answer is that the researcher started with mRNA consisting of uracil. The codon UUU was the first to be linked with an amino acid. The above table is the more tradition view of the genetic code, below is a more recent view. In this table the code reads from the inside out. Therefore the mRNA codon GAA codes for glutamic acid.
Figure 9. The Genetic Code
– circle version

http://www.biology.lsu.edu/heydrjay/1201/Chapter17/SCI_Amino_Acid_CIRCLE.jpg
To learn more about the genetic code go to http://users.rcn.com/jkimball.ma.ultranet/ BiologyPages/C/Codons.html
The redundancy of the genetic code as state earlier may help to reduce the effect of DNA base mutations. Single base errors in DNA copying are called point mutations, but are rare. During DNA replication the error rate is 1 in 10,000 bases being copied. Most of these errors are corrected by DNA proof readers. Secondly if an error is not corrected, the redundancy of the genetic code may end up coding for the same amino acid. (See the table below.) This is called a silent mutation. Or an amino acid with similar properties can be coded for by the “mutant” codon which is sometimes called a neutral mutation. (See the table below.)
At the same time some point mutations can be harmful. In the table below the DNA triplet and mRNA codon are shown for the 6th amino acid for normal hemoglobin. In sicklecell anemia a mutation from T to A leads to the replacing of glutamic acid with valine. This is called a missence mutation as the new protein does not function normally. This can be seen in sickle cell anemia. The effect of this mutation occurs when the oxygen levels in the blood drop, as during heavy exercise. When these low oxygen levels occur, the hemoglobin will become abnormally shaped, which in tu rn “stretches” the red blood cell. These abnormal red blood cells may cause blockage of blood vessels which can be fatal. Additionally if the first C is replaced by A, the result is the termination of protein synthesis and no hemoglobin molecule is produced. This is called a nonsense mutation.
To learn more about DNA mutations go to http://www.genetichealth.com/G101_Changes_in_DNA.shtml#Anchor2 http://evolution.berkeley.edu/evolibrary/article/0_0_0/mutations_01 back to top
Content Benchmark L.12.A.2
Students know DNA molecules provide instructions for assembling protein molecules. E/S
1. Students incorrectly believe that DNA is the same in all organisms.
Scientists have discovered that the four bases (adenine, guanine, thymine and cytosine) of DNA are common to living organisms on our planet, whether they are a bacterium causing a sore throat, to the rose we give on Valentine’s Day to the DNA found in our bodies. And while in most organisms the DNA triplet of TAC codes for methionine, not all the triplets code for the same amino acids in all organisms. Among the first differences discovered were in the DNA found in the mitochondria and certain microbes. In vertebrate mitochondria DNA the triplet ATA codes for methionine but in some other organisms they do not. As such teachers sh ould avoid calling the genetic code “universal”.
Variations to the genetic code can be found at: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG2
2. Students incorrectly assume that gene pairing in DNA and RNA are the same.
While true in the case of the paring of guanine and cytosine, this is not case for adenine and thymine. The A-T pairing occurs in DNA, but the base uracil replaces thymine in
RNA. In RNA the pairing is A-U. Thus if the DNA triplet is ATC the complementary RNA codon will be UAG.
A base pairing activity can be found at http://learn.genetics.utah.edu/units/basics/transcribe/
3. Students incorrectly think all the bases in DNA code for proteins.

Scientists have learned t hat approximately 1.5% of our DNA actually codes for proteins. The other 98.5% is sometimes referred as “DNA junk” or “DNA gibberish”. Over 50% of this non-coding DNA consists of repeating sequences sometimes 100s or 1000s of nucleotides long. Other sequences act as promoters (DNA sequences that attract the molecules that are necessary for replication and transcription) and genes for ribosomal RNA and transfer RNA.
To learn more about findings of the Human Genome Project go to http://biology.about.com/library/bldnamodels.htm
4. Students incorrectly think that one gene codes for only one protein.
This idea was believed to be true up until recently, but with discovers in the Humane Genome Project scientists have found otherwise. In humans it is now know that one gene may be responsible for the production of two or three different proteins. This occurs when the introns (non-coding regions of DNA) are removed from mRNA after transcription.
The remaining exons (coding regions of DNA) can be rearranged to produce different codon sequences and therefore different proteins.
To learn more about RNA processing go to http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/T/Transcription.html
5. Students incorrectly believe DNA is the genetic code for all organisms.
While true for all eukaryotes and prokaryotes, the exception includes viruses. While one can debate the status of viruses as an organism, but with retroviruses such as HIV
(human immunodeficiency virus) use RNA rather than DNA. Once the virus invades a host enzymes called reverse transcriptase converts the viral RNA to host DNA. Later this
DNA can be “switched on” and will produce new viruses.
To learn more about HIV and view an animation of the HIV life cycle go to http://www.hopkins-aids.edu/hiv_lifecycle/hivcycle_txt.html
6. Students incorrectly think mutations in DNA are always harmful.
All humans with blood type O are carrying a mutation. The genes for blood type code for proteins found on the red blood cell. Many inherit the genes for the A and B proteins.
However due to a point mutation in our ancestral past the coding for these proteins was lost, thus those who inherit the alleles for O lack coding for either protein.
At the same time mutations might be harmful to some, but prove a benefit to the majority of a population. As discussed above sickle cell anemia can prove to be fatal for those who have this disease. Yet, carriers of this disease (you only have 1 defective gene and not two) do not contract malaria which is the leading cause of death in the tropics.
While many DNA mutations may prove lethal, genetics mutations are also the ultimate source of news genes that might occur in species. These new gene can prove beneficial if the help a species to better adapt to its environment.
To learn more about the effects of mutations go to: http://www.talkorigins.org/faqs/mutations.html
back to top
Content Benchmark L.12.A.2
Students know DNA molecules provide instructions for assembling protein molecules. E/S
1. Students incorrectly think the Sun and other stars are burning and/or involve explosions
Simplistic definitions of stars such as “burning balls of gas” serve to perpetuate this misconception. For years, students hear that the Sun is far hotter than anything we know on
Earth; as a result, students often misapply analogies with lava, fire, and explosions, sometimes adding that the Sun or stars are hotter than these things on Earth. In fact, nothing like burning
– in particular, combustion, in which material is rapidly oxidized and releases heat and light – is taking place in stars. Rather, light is released in the process of nuclear fusion, in which lighter elements are combined into heavier elements.
To learn more about this and other student misconceptions, see http://aer.noao.edu/cgi-bin/article.pl?id=95
2. Students incorrectly think the Sun and other stars are powered by chemical reactions

Students also incorrectly identify the reactions in stars as chemical, rather than nuclear, or do not realize that there is a difference between the two. In chemical reactions, energy is released when electromagnetic bonds between the protons and electrons are broken or rearranged. Thus the atom retains its identity, although the electron structure is different from its state prior to the reaction. In nuclear reactions, however, it is the bonds of the strong nuclear force between protons and neutrons that are affected, changing the nuclear structure itself and resulting in new types of atoms.
To learn more about the different types of nuclear reactions, go to http://www.lbl.gov/abc/Basic.html
.
3. Students confuse nuclear fusion and nuclear fission
When students do know that nuclear reactions are present in stars, they can sometimes confusion nuclear fusion with nuclear fission (or simply not know the difference between the two). The processes are basically opposite of one another. In nuclear fusion, lighter elements are combined to create new, heavier elements (the most common example is hydrogen being converted into helium). In nuclear fission, heavier elements are broken apart into lighter elements (one example is the breaking down of uranium into barium and krypton). Both processes release energy. Nuclear fission is the primary source of energy used in today’s nuclear reactors, and in nuclear weapons. Sustained nuclear fusion is the primary source of energy in stars, and has not yet been replicated on Earth in any practical manner
– the conditions required are, as of now, too difficult to reproduce for productive use.
To learn more about the confusion of nuclear fission and nuclear fusion, go to http://www.lbl.gov/abc/wallchart/chapters/appendix/appendixg.html
One idea from the Cell Theory is that all cells must arise from pre-existing cells through a process of cellular division (mitosis or meiosis). In a one-celled organism, a mitotic cell division results in the creation of another individual of that species with identical DNA. In multicellular organisms, mitotic cell division results in new body cells for growth and repair. Some rare multicellular organisms reproduce asexually through mitosis to produce a complete, independent offspring with identical DNA. However, most multicellular organisms reproduce sexually which involves the production of cells with half the compliment of DNA (a haploid cell) that recombine with another haploid cell, usually from another organism, to produce a genetically unique cell with a full compliment of DNA that can now grow and develop into a new individual.
All cells progress through the cell cycle at some part of their lives. The cell cycle starts right after the successful division of two daughter cells. Cells that cease cell division, like nerve cells, are not considered to be in the cell cycle. The cell cycle consists of four distinct stages, G1, S, G2 and M (Figure 1). G1, S, G2 are collectively called Interphase.
Interphase is the period between cell division where the cell will grow, duplicate its DNA, and fulfill the role of the cell. The time that a cell remains in Interphase depends on the role of the cell. For example, human skin cells divide about once a day. Therefore, the cells will remain in Interphase approximately 22 hours. Conversely, a liver cell may go years without dividing.
Figure 1. The cell cycle. http://www.biology.arizona.edu/Cell_bio
/tutorials/cell_cycle/cells2.html
Figure 2. The cell in Interphase. http://staff.jccc.net/pdecell/celldivision
/mitosis1.html
The G1 (Gap 1) phase is the first part of Interphase. Most of the cell’s growth takes place in this phase. The cell will increase in size and synthesize new organelles. A cell may progress quickly to the S-phase or remain in the G1 phase near indefinitely.
The S (synthesis) phase follows the G1. Chromosomes are replicated in this phase. At the beginning of the S phase, each chromosome consists of a single double-helix strand of DNA, called a chromatid. At the end of the S phase, a chromosome consists of two sister chromatids.
Lastly, the cell enters the G2 (Gap 2) phase of Interphase. The cell will make final preparations for mitosis. This phase can be seen as a safety check point, where the DNA can be checked for errors.

After Interphase, the cell is ready to divide. Mitosis is divided into 4 major phases: Prophase, Metaphase, Anaphase, and Telophase.
1. Prophase
Prophase is the first phase of mitosis. Several processes take place during this phase. First, the chromatic material condenses into visible chromosomes and the sister chromatids are joined together at the centromere. The nuclear membrane disappears. In the cytoplasm, a pair of centrioles begins to separate and migrate to opposite poles of the cell. A network of microtubules begins to form between the centrioles called the spindle. The spindle fibers will be instrumental in guiding the chromatids to opposite ends of the cell.
Figure 3. This figure shows the relationship between
DNA, chromatin, chromatids, and chromosomes.
Figure 4. a.) The photograph shows two cells in Prophase.
( http://www.bio.txstate.edu/ ) b.)The diagram shows the important steps in Prophase. ( http://staff.jccc.net/pdecell/celldivision
/mitosis1.html
)
2. Metaphase
During Metaphase, the chromosomes line up along the middle of the cell and are attached to the spindle fibers by the centromeres.
Figure 5. a.) The diagram shows the important steps in Metaphase.
( http://staff.jccc.net/pdecell/celldivision/mitosis1.html
) b.) The photograph shows a cell in Metaphase.
( http://www.bio.txstate.edu/ )
3. Anaphase
Anaphase begins when the centromeres holding the sister chromatids together split and the spindle fibers shorten, pulling one chromatid toward each end of the cell.

Figure 6. a.) The photograph shows a cell in Anaphase.
( http://www.bio.txstate.edu/ ) b.)The diagram shows the important steps in Anaphase.
( http://staff.jccc.net/pdecell/celldivision/mitosis1.html
)
4. Telophase
Telophase is essentially the reverse of Prophase. The spindle fibers disappear, the chromosomes unravel back to chromatin, and two new nuclear membranes form.
Figure 7. a.)The diagram shows the important steps in Telophase. http://staff.jccc.net/pdecell/celldivision/mitosis1.html
) b.) The photograph shows a cell in
Telophase. ( http://www.bio.txstate.edu/ )
5. Cytokinesis
Occurring concurrently with Telophase is cytokinesis. Cytokinesis is the division of the cytoplasm. Cytokinesis is different in animal and plant cells. In plant cells, a cell plate forms a new cell wall divider between the two nuclei and grows outward until it fully separates the two daughter cells. In animal cells, the cell membrane is pulled inward by a ring of filaments. This make the cell appear to “pinch in” from the sides. This process continues until two new daughter cells result.
Figure 8. A comparison of cytokinesis in plant and animal cells.

From ( http://www.trentu.ca/biology/101/4.html
)
Figure 9. Cytokinesis in a plant cell. http://bio.txstate.edu
Figure 10. Cytokinesis in a animal cell. http://www.biologymad.com/
CellDivision/CellDivision.htm
Meiosis is a second type of cellular division. In meiosis, the result is 4 cells with half the complement of DNA instead of two identical cells. Therefore, the purpose of meiosis is to convert a diploid cell to a haploid gamete that would be involved in sexual reproduction to increase diversity in the offspring. The cells going through meiosis split twice, but the chromosome material is replicated only once. These two divisions are denoted as Meiosis I and Meiosis II.
1. Meiosis I
In Meiosis I, the number of chromosome sets is reduced by half (2n to n). The separation of each homologous chromosome pair is a random event which results in gametes containing a random combination of chromosomes. The phases of meiosis I are Prophase I, Metaphase I, and Anaphase I.
Prophase I
– The chromosomes enter Prophase I already replicated forming a pair of sister chromatids connected at their centromeres. The homologous chromosomes do not move independently as they did in mitosis. The homologous chromosomes pair up forming a tetrad (maternal and paternal homologous chromosomes each made up of two sister chromatids). Crossing over (or transfer) of genetic material may occur between homologous chromosomes, thereby increasing genetic variability. Other events of Prophas e I are very much like mitosis’
Prophase. The chromatin material coils up into chromosomes becoming visible, the nuclear membrane disappears, spindle fibers form, and centromeres separate.
Metaphase I – Just as in mitosis, the chromosomes line up on the middle of the cell. However, in meiosis the chromosomes line up with their homologous partner and attach themselves to the spindle fibers.
Figure 12. Anaphase I. http://www.biologycorner.com/worksheets/meiosis.html
Anaphase I
– Again Anaphase I looks very similar to Anaphase in mitosis. The chromosomes separate and travel toward the poles. The difference is that it is not the sister chromatids that are separating but the homologous chromosomes that separate resulting in half the number of chromosomes at each pole but each chromosome is double stranded. The separation of homologous chromosomes is called disjunction.

Telophase I
– Telophase I ends with the first meiotic division and cytokinesis. Some cells deconsolidate the chromosomes and form a simple nuclear membrane others do not and proceed directly into Prophase II. The result of Meiosis I is two haploid daughter cells.
Figure 13. An overview of Meiosis I ending with Telophase I. http://homepages.ius.edu/GKIRCHNE/Mitosis.htm
Telophase I
– Telophase I ends with the first meiotic division and cytokinesis. Some cells deconsolidate the chromosomes and form a simple nuclear membrane others do not and proceed directly into Prophase II. The result of Meiosis I is two haploid daughter cells.
2. Meiosis II
Meiosis II is simply the mitotic division of the two haploid cells resulting from meiosis I.
Prophase II – A new set of spindle fibers form.
Metaphase II
– The chromosomes line up on the middle of each cell and attach to the spindle fibers.
Anaphase II
– The sister chromatids separate and travel towards the pole.
Telophase II and cytokinesis
– the chromatids unravel into chromatin, nuclear membranes reform and the cell physically divided into two.

Figure 14. An overview of Meiosis http://www.nature.com/ng/journal/v37/n7/fig_tab/ng0705-662_F1.html
Content Benchmark L.12.A.3
Students know all body cells in an organism develop from a single cell and contain essentially identical genetic instructions. E/S
1. Students see the familiar X-shaped structure seen in a light microscope is a “basic” single (unreplicated) chromosome.
The X-shaped structures seen in a light microscope are condensed, replicated chromosomes containing two identical DNA double helices.
2. A chromosome is a chromosome - there is little differentiation between replicated and unreplicated states.
In late anaphase and G1 of interphase, a chromosome is unreplicated and consists of a single DNA double helix.
3. The X-shaped chromosomes are homologous chromosome pairs.
The X-shaped structures are unpaired, replicated chromosomes. Pairing of homologous chromosomes does not occur during mitosis.
4. Unreplicated chromosomes seen in anaphase are unpaired chromosomes.
These are simply unreplicated chromosomes, and this is the only time they are condensed and therefore visible.
5. The two non-identical homologous chromosomes in a parent cell go to separate daughter cells. back to top

In anaphase, the identical chromatids of a replicated chromosome go to separate daughter cells. Each daughter cell gets a complete copy of the chromosomes in the parent cell.
For more information on common misconceptions associated with this benchmark, go to http://www.biologylessons.sdsu.edu/classes/lab8/altern.html
Mutations are simply changes in the DNA code. The first thing that a student should understand when studying mutations is the difference between a somatic cell and a sex cell.
A somatic cell is a body cell that has a full complement of chromosomes while a sex cell (or germline cell) is a cell involved in sexual reproduction with half the number of chromosomes. Therefore, mutations can be separated into germline mutations, which can be passed on to offspring, or somatic mutations, which only affect the individual.
1. Point Mutation (or substitution)
This type of mutation is where only a single nucleotide in a gene has been changed. The effect can be quite dramatic. The result can be a nonsense triplet which will stop the protein’s construction. This will result in truncated proteins. A missense triplet may result coding for a different amino acid resulting in an incorrect protein. Lastly, silent mutations may occur coding for the same amino acid which results in no change to the protein.
Figure 1. An example of a point mutation. The DNA code is simply changed when an adenine is replaced with a cytosine. http://sps.k12.ar.us/massengale/chromosomes%20&%20human%20genetics.htm
Point mutations hay happen spontaneously when mistakes are made during DNA replication. The incidence of mutations can be increased by mutagens. A mutagen is a physical or chemical agent that can be harmful to DNA. Examples of mutagens are radiation (UV rays) or chemical (carcinogens).
Sickle Cell Anemia is an example of a point mutation. It is the most common inherited blood disorder affecting 72,000 Americans (www.ncbi.nlm.nih.gov). It is caused by the point mutation of a single amino acid, resulting in a valine being substituted for glutamine.
Normal Hemoglobin
Val His Leu Thr Pro Glu Glu Lys
Figure 2. Normal Red Blood Cells http://publications.nigms.nih.gov/moleculestomeds/pharmacology.html
Sickle Cell Anemia Hemoglobin

Val His Leu Thr Pro Val Glu Lys
Figure 3. Sickle Cell Red Blood Cells http://publications.nigms.nih.gov/moleculestomeds/pharmacology.html
2. Frameshift Mutations
A frameshift mutation results in the addition or deletion of nucleotides in the DNA sequence. Three nucleotides (a triplet) are translated into an amino acid through the process of translation. The addition or subtraction of nucleotides will shift the entire
Figure 4. This frameshift mutation shows that if the sequencing is shifted over only one nucleotide a completely different amino acid sequence results. http://ghr.nlm.nih.gov/handbook/illustrations/frameshift
Chromosomal mutations take place during cell division, either mitosis or meiosis. During cell division, the chromatin material shortens and thickens into chromosomes. A chromosome consists of two duplicate sister chromatids connected by a centromere. Each chromatid should separate and travel to opposite ends of the cell to create two identical daughter cells. Sometimes, mistakes happen in the separation of sister chromatids.
1. Reciprocal Translocation
Translocation is the transfer of a part of a chromosome with another nonhomologous chromosome during cell division. Chromosomes are actually fairly fragile and some break during cell division and the broken bits rejoin with neighboring chromosomes. If there is no loss of genetic information, the translocation is usually harmless. However, it can have reproductive results. A person who is a “carrier” of a translocation may have a higher incidence of miscarriage or have a higher probability of having a child with birth defects.

Figure 5. The translocation of a piece of chromosome 20 and chromosome 4. http://www.genome.gov//Pages/Hyperion/
DIR/VIP/Glossary/Illustration/translocation.cfm
2. Chromosomal Deletion/Duplication
A chromosomal deletion is just what it sounds like. A segment of DNA is lost in the cell during cell division. The lost piece broke off a chromosome and attached to the homologous chromosome. The result in cell division is one daughter cell has duplicate DNA and the other daughter cell is missing the same DNA sequence. The result can be detrimental. It can result in an unbalanced number of chromosomes. The resulting karyotype may be 45 or 47 (instead of 46) resulting a variety of birth defects. In somatic cells, an addition/deletion may also result in various types of cancers, especially leukemia.
Figure 6. Four types of genetic rearrangements. http://health.enotes.com/images/cancer/gec_01_img0056.jpg
3. Inversion mutation
In inversion mutation is where a piece of a chromosome breaks off and is reattached in reverse order. Inversions don’t appear to be harmful in the individual as long as there is no loss or gain of DNA. However, they are now a carrier and a resulting offspring has a small chance of inheriting an unbalanced chromosome arrangement with missing or extra components. (See Figure 6)
4. Nondisjunction/Polyploidy
The addition or loss of an entire chromosome is called nondisjunction. It results when two chromosomes remain connected instead of separating during meiosis. The result is extra or missing chromosomes. For example, an individual that inherits three copies of chromosome 21 (47 chromosomes) has a condition called Down’s syndrome. Most cases of nondisjunction results in nonviability of an offspring. Nondisjunction can also result in the development of cancers.

Figure 7. Nondisjunction during meiosis that results in two gametes missing a chromosome and two gametes with extra chromosomes. http://www.biology.iupui.edu/biocourses/N100/
2k2humancsomaldisorders.html
If an entire set of chromosomes fail to separate, a condition of polyploidy results. This is commonly found in plant cells.
Figure 8. Polyploidy that results in a viable offspring with twice the number of chromosomes as the parent. http://www.bio.miami.edu/dana/104/104F02_15.html
Somatic mutation vs. Gamete mutation
A somatic mutation is a mutation that takes place in any single cell of an organism except gametes and is not inheritable. Some current studies have suggested that a lifetime of accumulated mutations is why we age. Another result of harmful somatic mutations is cancer. The mutation starts in a single cell and as this cell divides uncontrollably, a tumor develops.
A mutation in sex cells results in an inheritable mutation. This mutation starts in a gamete (ie. egg, sperm, pollen, or ovule) and is passed into the resulting offspring. This genetic change, is therefore, present in every cell of the organism. Some genetic defects cannot result in a viable offspring. But if it does, a variety of genetic disorders can be expressed. back to top
Content Benchmark L.12.A.4
Students know several causes and effects of somatic versus sex cell mutations. E/S

1. Students often have difficulty conceptualizing gene expression (via protein synthesis) and that changes in the DNA code can be reflected in changes in gene expression.
Students have trouble seeing the big picture and following the pathway of DNA relationship through to gene expression. It is a very abstract complicated process that involves many steps and it’s easy for students to get lost in the details, so they give up. It is important that teachers break down each step and convey its relevance before moving onto the next step. Students need to have a good foundation in transcription, translations, and replication before mutations are introduced. Otherwise, the idea of mutations would only compound their confusion.
2. Students may understand how DNA is replicated, transcribed, and translated, but they still may not understand how a gene controls a trait.
Again, students have trouble seeing how one process plays into another. They may be able to draw the diagrams and flow charts but when asked to describe the purpose of each step students are often stumped. “So you may need to explain "up" or "down" how the parts relate to the whole -- up, how the item under discussion fits into something bigger, and down, how the item is made of smaller things. For example, if you are discussing genes, you should be prepared to go "up" to chromosomes, genomes, traits, etc., and "down" to DNA, cod ons, nucleotides, and bases.”
For more information about this misconception please visit this site: http://cirtl.wceruw.org/diversityresources/resources/resource- book/overcomingmisconceptions.htm
3. Students think that all mutations are inheritable and have trouble differentiating between somatic and germline mutations.
Students can tell you that all life forms are made up of cells and can even describe mitosis, but when pressed some still have misconceptions about how we start as a single cell. This single cell divides into two, then four, then eight, etc. The resulting ball of cells all have the identical set of instructions but begin to differentiate and take on specific roles. Students have a hard time understanding that a skin cell and a liver cell have the same identical set of instructions but use only portions of the code specific to the cell’s job. Students also misunderstand that cells continue to divide and grow even as adults and that mutations can occur in an adult skin cell that results in skin cancer. Students are also confused as to how a genetic mutation is passed on to offspring (L12A5).
For more information concerning misconceptions about genetic mutations please visit
( http://cirtl.wceruw.org/DiversityResources/resources/ resource-book/overcomingmisconceptions.htm)
A gene is the unit of heredity in living organisms. Genes are encoded in an organism's genome, composed of DNA or RNA, and direct the physical development and behavior of the organism. Multiple versions can exist for each gene. Different forms of a gene are called alleles. For example, a one allele can code for blue eyes and another brown. While some genes have only two alleles, many genes have three or more alleles. Diploid organisms contain two alleles for every gene.
The father of genetics is Gregor Mendel who conducted extensive studies on the heredity of pea plants. His research resulted in the Law of Segregation and the Law of
Independent Assortment. The Law of Segregation first states that each diploid organism inherits two genes for each trait, one from each parent. It also states that the two alleles are separated during gamete formation. The Law of Independent Assortment states that every trait is inherited independently of another, thus creating new combination of genes unique to that individual. We now know that some traits are linked because they are located on the same chromosome.
Mendel also concluded that some alleles will be expressed when present and others can be suppressed. The form of the gene that is always expressed when present is called dominant while the gene that is suppressed in the presence of the dominant form is called recessive . An identical pair of alleles for a trait is called homozygous (dominant or recessive) or and a mixed pair is called heterozygous . A heterozygous pair will always express the dominant trait. The pair of genes for each trait is called a genotype and the expression of that trait is a phenotype .
A Punnett square is a biological tool used to calculate the mathematical probability of inheriting a specific trait. It was named for an English geneticist, Reginald Punnett. A
Punnett square uses a system of letters to represent the alleles involved in the cross. A simple single trait problem is called a monohybrid cross. A capital letter represents the dominant trait and a lower case letter represents the recessive allele.
You would use the following procedure to set up a cross.
1. Determine the genotype of the parents.

2.
3.
4.
5.
Segregate the alleles to determine the gametes
Construct the Punnett square
Complete the Punnett square
Calculate the genotypic and phenotypic probabilities of each possible offspring.
For example: In squash, yellow ( Y ) fruit is dominant to green ( y ). A homozygous yellow plant is crossed with a green plant. Calculate the genotypic and phenotypic ratios of the offspring.
1. Parents’ genotypes: Homozygous yellow = YY Homozygous green yy
YY x yy
2. Segregate the alleles
3. Construct the Punnett Square
4. Complete the Punnett square
5. Calculate genotypic and phenotypic ratios.
Genotypic Ratio
Yy 4/4 100%
Phenotypic Ratio
Yellow 4/4 100%

1.
Dihybrid Cross
– A cross of two traits together. A Punnett square is used to determine the gametes that would be formed through independent assortment.
Problem: A homozygous round, homozygous yellow plant is crossed with a wrinkled, green seeded plant.
Figure 1: an example of a dihybird cross. (from http://fig.cox.miami.edu/~cmallery/150/mendel/heredity.htm
)
2. Codominance : Both alleles of a gene are expressed equally. A common example is blood types in humans. A person with blood type AB has the alleles for blood type A and
B. Two different capital letters are used to represent the codominent relationship.
Figure 2: Human blood groups are controlled by multiple alleles two of which are codominant
(A and B) (from http://duongchan.files.wordpress.com/2007/05/abobloodsystem.jpg
)
Problem: “Roan” coloring in cows also shows a codominent relationship. Red (R) hair is codominent to white (W). The heterozygous condition (RW) results in a roan color. A roan cow is crossed with a red bull. What is the probability of a roan offspring?

Figure 3: A Roan color pattern is expressed as a red coat with white splotches. (from http://www.ccs.k12.in.us/chsTeachers/BYost/Biology
%20Notes/CH11notescoincompletedom.htm
)
RR 2/4 50%
RW 2/4 50%
Red 2/4 red 50%
Roan 2/4 roan 50%
Answer: 50% chance of a roan offspring
3.
Incomplete Dominance
– This is sometimes called partial dominance. The heterozygous condition results in an intermediate (third) blended phenotype. A capital letter is used to represent one allele and the same capital letter prime represents the other allele
Figure 4: An example of incomplete dominance showing how red and white blends to form pink http://www.emc.maricopa.edu/faculty/farabee/biobk/BioBookgeninteract.html
Problem: Red (R) flower color in snap dragons shows an incomplete dominance relationship to white (R`). What is the probability of a pink flower from the cross of two pink flowered plants?
Parents: RR` x RR`

RR 1/4 25%
RR` 2/4 50%
R`R` 1/4 25%
Red 1/4 25%
Pink 2/4 50%
White 1/4 25%
Answer: 50% chance of producing a pink flowered plant. back to top
Content Benchmark L.12.A.5
Students know how to predict patterns of inheritance. E/S
1. Students do not understand both parents contribute genes for each characteristic. They believe that one parent contribute genes for some characteristics, while the other features come from the other parent.
Mendelian inheritance is the mode of inheritance for nearly all multicellular organisms. Inheritance is controlled by genes, which are passed on to the offspring in the same form as they were inherited from the previous generation. At each locus, the location on a chromosome of a particular gene, an individual has two genes one inherited from its father and the other from its mother. The two genes are represented in equal proportions in its gametes.
More details about gamete formation visit: http://www.biology.arizona.edu/CELL_BIO/tutorials/meiosis/main.html
).
2. Students believe that inherited traits are blended.
Blending inheritance is the erroneous idea that organisms contain a blend of their parent hereditary factors and pass that blend onto their offspring. Inheritance of certain traits like hair color, eye color, and skin tone are all controlled by multiple alleles therefore allowing for variation in color. Incomplete dominance results in an intermediate (third) phenotype. Although these traits appear to be a blend of inherited traits they are not. Each trait is still determined by the form of the gene (allele) inherited from parent to offspring.
3. Dominant alleles are generally the most frequently occurring alleles in a population.
Dominance refers to expression of an allele within an individual organism. Prevalence in the population is determined by fitness and natural selection. A good example to use to demonstrate this is polydactylism, an anatomic variation where an individual has more than the usual number of digits on the hand or feet. Polydactylism is a dominant trait yet it is not the most frequently occurring trait in the human population.

For more details about population genetics, visit: http://naturalsciences.sdsu.edu/ta/classes/lab2.4/altern.html
4. Dominant alleles are the most desirable ones.
Once again, dominance refers to expression of an allele within an individual organism. The word “dominant” in layman terms leads to this misconception. The expression, whether dominant or recessive, that is selective for by the environment is the most desirable. A good example to use to demonstrate this is polydactylism, an anatomic variation where an individual has more than the usual number of digits on the hand or feet. Polydactylism is a dominant trait yet it is not desirable.
The smallest thing that exhibits all of the characteristics of life is a single cell. Some organisms are made up of only one cell while complex organisms are made up of trillions.
The understanding of the Cell Theory, types of cells, and cellular organelle structure and function is essential to any biology student.
The Cell Theory is the summation of 150 years of research by many scientists, like Theodor Schwann and Matthias Schleiden. The research groups worked independently on topics of animal cells, plants cells, and cellular reproduction. These pieces contributed to what is now known as the Cell Theory. The Cell Theory has three main components:
1. All living things are composed of at least one cell.
2. Cells are the most basic unit of structure and function.
3. All cells come from preexisting cells.
Prokaryotic vs. Eukaryotic
Cells can be separated into two groups based on the presence or absence of membrane bound organelles. The first group lack organelles and are called Prokaryotic. Bacteria are prokaryotic.
Figure 1. A diagram of a prokaryotic cell. http://library.thinkquest.org/C004535/prokaryotic_cells.html
Eukaryotic cells contain many membrane bound organelles. Each organelle has very specific job to complete, like protein synthesis, trash clean up, or energy production. All organisms except bacteria are eukaryotic.

Figure 2. A diagram of a Eukaryotic cell. http://library.thinkquest.org/C004535/eukaryotic_cells.html
1. Cell membrane
The cell membrane separates the cell from the surrounding environment. It is composed of two layers of lipids with a variety of proteins and carbohydrates embedded in it. The membrane is often described with the Fluid Mosaic Model. It states that the embedded proteins and lipid layers actually move about, thus giving the membrane a fluidity to it.
Some proteins form channels to help move material through the cell membrane. Other proteins are chemical receptors that signal the cell to begin or stop some metabolic activities. The carbohydrates bound to the membrane allow the organism’s immune response system to differentiate between its own cells from foreign invaders.
Figure 3. A diagram of the two lipid layers of a cell membrane showing the variety of embedded proteins and carbohydrates. http://academic.brooklyn.cuny.edu/biology/bio4fv/page/pm_mos.htm
The membrane is semi permeable. Some things pass freely through the membrane while other substances must be transported across. Transport can be either a passive or active process. Passive transportation across the membrane does not require the expenditure of energy. Substances, like water and gases, can move freely across the membrane into and out of the cell. This process is called diffusion or the random movement of molecules from areas of high concentration to areas of low concentration until equilibrium is reached. A special type of diffusion is osmosis, the diffusion of water through a selectively permeable membrane. Water will also move into and out of a cell from areas of high concentration of water to low areas of concentration of water until an osmotic balance is reached.
Active transport allows a cell to move substances against the concentration gradient but it requires the expenditure of energy. One process uses the embedded membrane proteins to pump ions into or out of the cell. Another process, called endocytosis, actually has the cell membrane making pockets of materials by encircling a substance creating a vesicle. The vesicle then breaks off to the inside of the cell and releases the material to the cell. Endocytosis of a liquid is called pinocytosis and of a solid is called phagocytosis. The movement of materials out of the cell is called exocytosis.

Figure 4. Passive transport of lipid soluble molecules through a selectively permeable membrane http://www.emc.maricopa.edu/faculty/farabee/biobk/
BioBooktransp.html#Cells%20and%20Diffusion
Figure 5. An example of active transport. Protein channels are being used to move materials opposite the concentration gradient. http://www.rpi.edu/dept/chem-eng/
Biotech-Environ/Membranes/bauerp/mech.html
Figure 6. An example of active transport by endocytosis. http://www.sp.uconn.edu/~bi107vc/fa02/terry/membranes.html

2. Cell wall
The cells of plants, bacteria, and algae are enclosed by a rigid cell wall. The main purpose of the cell wall is to support and protect the cell. The cell wall lies outside of cell membrane and is usually composed of cellulose. The cell wall has large pores which allows all materials to pass (it is completely permeable). Sometimes, strands of membranes pass through the pores connecting neighboring cells. Animal cells do not contain cell walls.
3. Nucleus
This membrane bound organelle houses the control center of the cell. The nucleus protects and maintains the integrity of the DNA, the molecule that contains the coded instructions of the cell. An analogy would be the nucleus is a safe for the original blue prints (DNA) for a large project. Copies of the blue prints can be sent out of the nucleus but the original must stay safe.
Figure 7. The structure of a cell wall. http://genomics.energy.gov
Figure 9. Ribosomes located on rough endoplasmic reticulum.
http://web.mit.edu/esgbio/www/ cb/org/rough_er-em.gif
Figure 8. The nucleus.
The drawing above is from http://www.cdli.ca/~dpower/cell/nucleus.htm
4. Ribosomes
The site of protein synthesis is the ribosomes. The instructions from the DNA are delivered to the ribosomes by mRNA. Once the instructions are read, amino acids are

delivered to the ribosome by tRNA and put into proper order to construct the specific protein. Ribosomes located on the rough endoplasmic reticulum usually produce proteins to be exported from the cell and ribosomes floating in the cytoplasm usually produce proteins to be used by the cell.
5. Endoplasmic reticulum
The endoplasmic reticulum (ER) is a system of membrane channels throughout the cell. There are two types of ER, rough and smooth. The rough ER is studded with ribosomes giving it a rough appearance while the smooth ER lacks ribosomes. The ER’s primary purpose is to transport materials around the cell. The ER also provides a large membrane surface area on which many biochemical processes take place. It also divides the cell into compartments so more than one biochemical reaction can be completed concurrently.
6. Vacuoles
Vacuoles are fluid filled membrane organelles and primarily functions as long term storage. In plant cells, a single vacuole can occupy most of the cell space filled mostly with stored water. In animal cells, vacuoles are usually small (relative to the cell) and may contain proteins, fats, or carbohydrates.
7. Lysosomes
Lysosomes are membrane bound sacs that contain digestive enzymes that can collect, breakdown, and recycle worn out organelles.
http://bio.winona.edu/berg/IMAGES/elodea5.JPG
Lysosomes in immune defense cells, like white blood cells, engulf and destroy bacteria and viruses. In some organisms, lysosomes may also be used to digest macromolecules.
8. Chloroplasts
Chloroplasts are only found in plant and certain types of algae. Chloroplasts contain the pigment chlorophyll, giving plants their green color. The chloroplast is where photosynthesis takes place. The process of photosynthesis converts light energy from the sun into chemical energy in the form of glucose.
http://sun.menloschool.org/~cweaver/cells/e/lysosomes/
Figure 11. The chloroplast rendition below is from http://evogen.jgi.doe.gov/second_levels/chloroplasts/cpDNA_info.html
9. Mitochondria
Mitochondria are double membraned organelles. The outer membrane forms the boundary of the organelle, while the inner membrane is folded increasing the surface area necessary to produce energy (ATP and NADH) from the breakdown of sugars. The breakdown of macromolecules to release stored chemical energy is called cellular respiration. An average cell may contain 500 mitochondria. Cells that require large amounts of energy, like muscle cells, may contain thousands of mitochondria.
Figure 12. The mitochondria rendition above is from

http://www.nsf.gov/news/overviews/biology/interact08.jsp
10. Golgi apparatus
Golgi apparatus (or Golgi bodies) looks like stacks of flattened membrane sacs. The Golgi apparatus is responsible for processing, packaging, and storing products of the cell to be delivered to the cell membrane for release from the cell.
Figure 13. Golgi apparatus. The products of the cell are transferred from the ER to the Golgi and then, through a series of steps for packaging. The package is delivered to the cell membrane for release from the cell. http://publications.nigms.nih.gov/insidethecell/chapter1.html#4
11. Cytoplasm
Cytoplasm is the watery environment inside the cell and includes everything from the cell membrane to the nuclear membrane. It consists mostly of water with small quantities of salts and dissolved gases. The space outside the various organelles is more specifically called the cytosol. The cytosol also contains structural elements called the cytoskeleton which give the cell structure and may aid in the cellular movement of cilia and flagella.
12. Centrioles
Centrioles are a pair of organelles found in animal cells but not in plant cells.
During cell division, the centrioles move to opposite ends of the cells and form the spindle that pull the chromatids apart and move them to the opposite poles so two daughter cells can form.
Figure 14. This is late prophase showing the centrioles at each pole of the cell and the formation of a spindle between the centrioles. http://www.brooklyn.cuny.edu/bc/ahp/MBG/MBG3/M.Pro.late.html

Plant and animal cells have many key differences.
1. Plant cells have a cell wall.
2. Plant cells have chloroplasts and are photosynthetic.
3. Plant cells have a large central vacuole that can take up 95% of the cells volume.
4. Animal cells have centrioles
5. Lysosomes are common in animal cells and very rare in plant cells.
Figure 15. A typical animal cell. http://www.cod.edu/people/ faculty/fancher/ProkEuk.htm
Figure 15. A typical plant cell. http://www.lclark.edu/~seavey/genetics04/ lectures/lecturejan21.html
back to top
Content Benchmark L.12.B.1
Students know cell structures and their functions E/S
1. Cells are resting when they are not dividing
Cells are most metabolically active during interphase, the period between cell divisions. They are typically engaged in biosynthesis and growth during this time.
2. Respiration occurs in the lungs and is solely the process of gas exchange.
Respiration has two stages - gas exchange which occurs in lungs, gills, or stomata, and biochemical changes that occur in the cells (cellular respiration).
3. Cellular respiration is characteristic of animal cells but not plant cells. Plant cells photosynthesize instead.
All eukaryotic cells capture energy from the breakdown of sugars via cellular respiration in the mitochondria.
4. Plant and animal cells obtain their nutrients (food) from the environment.
Plant cells have the unique capacity to synthesize their own nutrient building blocks, 6-carbon sugar molecules, from inorganic substances such as CO2 and H2O. All other organisms and their cells must take in organic molecules derived directly or indirectly from plants.
5. Everything a cell needs gets into it by diffusion.

Only the smallest molecules such as H2O, CO2, and O2 can diffuse freely into and out of cells. Larger more charged molecules such as sugar and salt ions require active transport across the membrane.
The misconceptions listed in this section came from the website listed below. http://www.biologylessons.sdsu.edu/classes/lab7/altern.html
The human body begins to take shape during the earliest stages of embryonic development. Dividing cells begin forming the tissues and organs that compose the human body.
A tissue is a collection of cells that are similar in structure and that work together to perform a particular function. The human body has four main types of tissues. Muscle tissue is composed of cells that can contract. It can be further broken down into skeletal, smooth and cardiac muscle. Skeletal muscle moves bones in the trunk, limbs, and face, smooth muscle handles body functions that typically are not consciously controlled (example: moving food through your digestive system), and cardiac muscle found in heart functions to pump blood throughout body. Nervous tissue contains cells called neurons that receive and transmit messages in the form of electrical impulses. It is composed of the brain, spinal cord, and nerves. Epithelial tissue consists of layers of cells that line or cover all internal and external body surfaces. It provides a protective barrier. Connective tissue binds, supports, and protects structures in the body. It is the most abundant and diverse tissue that includes bone, cartilage, tendons, fat, blood, & lymph.
Figure 1 Figure 2
Figures 1 & 2 Illustrate tissue types found in two different organ systems.
Figure 1: http://www.emc.maricopa.edu/ faculty/farabee/biobk/stomTS.gif
Figure 2: http://www.lifespan.org/adam/graphics
/images/en/19917.jpg
An organ consists of various tissues that work together to carry out a specific function. Groups of organs interact to form an organ system. For each organism to survive the organ systems must work together. There are eleven organ systems that collaborate with each other in order for an organism to function. Those systems are the digestive, respiratory, muscular, circulatory, skeletal, nervous, integumentary, immune, excretory, endocrine and reproductive.
Mouth, throat, esophagus stomach, liver, pancreas small and large intestines
Digestive
Extracts and absorbs nutrients from food; removes wastes; maintains water and chemical balances
Respiratory
Muscular
Lungs, nose, mouth, trachea
Skeletal, smooth, and cardiac muscle tissues
Moves air into and out of lungs; controls gas exchange between blood and lungs
Moves limbs and trunk; moves substances through body; provides structure and support
Circulatory Heart, blood vessels, blood (cardiovascular)
Transports nutrients, wastes, hormones, and gases lymph nodes and vessels, lymph (lymphatic)
Skeletal Bones and joints
Protects and supports the body and organs; interacts with skeletal muscles, produces red blood cells, white blood cells, and platelets
Brain, spinal cord, and sense organs
Nervous
Regulates behavior; maintains homeostasis; regulates other organ systems; controls sensory and motor functions

Table 1: The structures and functions of the six major body systems ( http://www.sirinet.net/~jgjohnso/intro.html
)
Before your body can use the nutrients in the food you consume, the nutrients must be broken down physically and chemically. The process of breaking down food into molecules the body can use is called digestion. In humans, digestion begins in the oral cavity where food is chewed (mastication) with the teeth. The food enters the stomach upon passage through the esophageal sphincter. In the stomach, food is further broken apart through a process of churning and is thoroughly mixed with a digestive fluid, composed chiefly of hydrochloric acid. After being processed in the stomach, food is passed to the small intestine. This is where most of the digestive process occurs. After going through the small intestine, the food then goes to the large intestine. The food that cannot be broken down is called feces. Feces are stored in the rectum until they are expelled through the anus.
Figure 3 and 4 Illustrate the human digestive system
Figure 3: http://www.tuberose.com/
Graphics/Intestinal_Health.jpg
Figure 4: http://medicalimages.allrefer.com/ large/digestive-system-organs.jpg
It is the function of the respiratory system to transport gases to and from the circulatory system. The respiratory system involves both external respiration and internal respiration. External respiration is the exchange of gases between the atmosphere and the blood. Internal respiration is the exchange of gases between the blood and the cells of the body.
Figure 5: http://www.spiderspun.net/images/lungs.gif
Figure 6: http://www.umm.edu/ respiratory/images/respiratory_anatomy.jpg

If you are interested in the respiratory system and would like to know more about it go to http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookRESPSYS.html
Muscles make up the bulk of the body and account for about one-third of its weight. Their ability to contract not only enables the body to move, but also provides the force that pushes substances, such as blood and food, through the body. Without the muscular system, none of the other organ systems would be able to function.
Figure 7 and 8 Illustrate the muscle types and the parts of a muscle
Figure 7: http://www.medic101.com/EMP_Lessons/ cardiovascular/images/actin_myosin.gif
Figure 8: http://www.nides.bc.ca/Assig nments/Body/Bundles_files/musc.gif
To learn more about the muscular system go to http://webschoolsolutions.com/patts/systems/muscles.htm
Most of the cells in the human body are not in direct contact with the external environment. The circulatory system acts as a transport service for these cells. Two fluids move through the circulatory system: blood and lymph. The blood, heart, and blood vessels form the cardiovascular system. The lymph, lymph nodes, and lymph vessels form the lymphatic system. The cardiovascular system and lymphatic system collectively make up the circulatory system. Blood transports oxygen from the lungs to cells and carries carbon dioxide from the cells to the lungs.
To learn more about the heart, go to http://www.fi.edu/biosci/
To learn more in general about the circulatory system go to http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookcircSYS.html

Figure 9 and 10 Illustrate the circulatory system
Figure 9: http://www.3dscience.com/
3D_Images/Human_Anatomy/
Cardiovascular/Arteries_Full_Body.php
Figure 10: http://www.drugdevelopment- technology.com/projects/lipitor/images/
1_Labelled_Human_Heart.jpg
The adult human body consists of approximately 206 bones, which are organized into an internal framework called the skeleton. Because the human skeleton is an internal structure, biologists refer to it as an endoskeleton. The variation in size and shape among the bones that make up the skeleton reflects their different roles in the body.

Figure 11 Illustrate the human skeleton http://www.contmediausa.com/shop/app/products/
Human3D/Images/BS000A.jpg
Figure 12 Illustrate the human bone anatomy and structure http://www.sirinet.net/~jgjohnso/bonestruct4.jpg
To learn more about the skeletal system go to http://www.bio.psu.edu/people/faculty/strauss/anatomy/skel/skeletal.htm
and for additional information go to http://www.mnsu.edu/emuseum/biology/humananatomy/skeletal/skeletalsystem.html
Mental and physical activity and many aspects of homeostasis are controlled by the nervous system, a complex network of cells that communicate with one another. Within this communications network, a carefully organized division of labor exists so that each component of the nervous system operates effectively. As a result, a football player can weave through opposing tacklers, an architect can create an original design, and a student can understand this information.
To learn more about the organ systems go to http://biology.about.com/od/organsystems/a/aa031706a.htm
http://www.innerbody.com/htm/body.html http://www.sirinet.net/~jgjohnso/biologyII.html
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Content Benchmark L.12.B.2
Students know the human body has a specialized anatomy and physiology composed of a hierarchical arrangement of differentiated cells. E/S
1. Students incorrectly believe that the only gas humans breathe out during respiration is carbon dioxide.
External respiration is the exchange of gases between the atmosphere and the blood and involves more than just the exchange of oxygen in and carbon dioxide out. Actually when a person breathes the majority of gas that is exhaled is carbon dioxide, but it is not the only gas that escapes from the mouth or nose. In addition to carbon dioxide, a small amount of oxygen and water vapor is released back into the atmosphere. Although most students are aware that oxygen is the gas that we inhale and rely on to breath, they quickly forget about the water vapor that is exhaled with every breath. The water vapor is clearly seen in cold weather and it is at that very moment that people exclaim that they “can see their breath.” It can also be easily seen by exhaling onto a mirror or window.
For further information regarding the respiratory system visit http://www.42explore.com/respsyst.htm

2. Students incorrectly think the body systems operate in isolation from each other.
The levels of structural organization starts at the cellular level, then continues to the tissue level, organ level, organ systems, and ends at the organism. The principle organ systems of the human body in fact do not work alone at all. Each system carries out a specific function in the body, but in order for an organism to survive the systems must work together. This system collaboration is known as integration of organ systems. It is not until these systems working together do they constitu te the “total” organism and a completely living individual.
To learn more about why the body systems need to work together visit http://www.sirinet.net/~jgjohnso/intro.html
or http://www.kidinfo.com/Health/Human_Body.html
3.Students incorrectly think blood leaves the vessels and enters parts of the body.
Students that have developed an understanding about blood leaving the vessels in the human body are unknowingly confusing the concept with less complex organisms. Many invertebrates do not have a circulatory system at all. Their cells are close enough to their environment for oxygen, other gases, nutrients, and waste products to simply diffuse out of and into their cells. Open circulatory systems (evolved in crustaceans, insects, mollusks and other invertebrates) pump blood into a hemocoel with the blood diffusing back to the circulatory system between cells. Blood is pumped by a heart into the body cavities, where tissues are surrounded by the blood. In animals with multiple layers of cells, especially large land animals, this will not work, as their cells are too far from the external environment for simple osmosis and diffusion to function quickly enough in exchanging cellular wastes and needed material with the environment. In this case a closed circulatory system is utilized. Closed circulatory systems have the blood closed at all times within vessels of different size and wall thickness. In this type of system, blood is pumped by a heart through vessels, and does not normally fill body cavities.
For further information regarding the human circulatory system visit http://www.sirinet.net/~jgjohnso/circulation.html
or http://www.howstuffworks.com/heart.htm
4. Students incorrectly think blood vessels end in a dead end. They do not reconnect. Blood flows backward or travels through the body to another vessel going back.
The circulatory systems of all vertebrates are closed, meaning that the blood never leaves the system of blood vessels consisting of arteries, capillaries and veins. Arteries bring oxygenated blood to the tissues (except pulmonary arteries), and veins bring deoxygenated blood back to the heart (except pulmonary veins). Blood passes from arteries to capillaries then to veins where it returns to the heart. Capillaries are the thinnest and most numerous of blood vessels and are responsible for exchanging gasses and nutrients to the cells in exchange for their waste products. In the closed circulatory system of mammals, there are two subdivisions
—the systemic circulation and the pulmonary circulation. The pulmonary circulation involves circulation of deoxygenated blood from the heart to the lungs, so that it may be properly oxygenated. Systemic circulation takes care of sending blood to the rest of the body. Once the blood flows through the system of capillaries at the body’s tissues, it returns through the venous system. If all the vessels of this network in an adult human body were laid end-to-end, they would extend for about 60,000 miles (more than 96,500 kilometers); far enough to circle the Earth more than twice.
For further information on the closed circulatory system of humans refer to http://www.sirinet.net/~jgjohnso/circulation.html
or http://www.medtropolis.com/VBody.asp
5. Students mistakenly believe muscle cells can push and pull.
Skeletal muscle is voluntary, striated, and attached to the skeleton. Each skeletal muscle is an organ of 100’s or 1000’s of muscle fibers, as well as nerves and connective tissue. When muscle cells contract, they pull on the connective tissue (tendons), which transfers the force elsewhere. The connective tissue also gives the muscle elasticity.
Skeletal muscle, unlike other muscles, requires conscious effort that originates in the brain in order to contract. Because of the large amounts of energy used in contraction and the large quantity of wastes generated, a rich blood supply is needed by skeletal muscle. When muscles contract, they pull on the bones, which move bones at the joints. Joints are set up as lever systems: the fulcrum is where the two bones meet, one force is produced by the muscle, and the other by a load on the bone. Muscles can not push bones, they can only pull. Each bone is usually controlled by at least two muscles. One muscle pulls the bone one direction, the other pulls it back to its original position.
To learn more about the process by which muscles provide movement to the human body visit http://www.sirinet.net/~jgjohnso/muscle.html
or http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/M/Muscles.html
6. Students erroneously believe the small intestine is short; the large intestine is long.
The intestine is the portion of the digestive tract between the stomach and the anus. It is divided into two major sections: small intestine and large intestine.
The small intestine is about 6 meters (20 feet) long. The large intestine has a larger width but is only 1.5 meters (5 feet) long.
To learn more about the intestines function in the human body visit http://www.sirinet.net/~jgjohnso/nutrition.html
or http://kidshealth.org/kid/body/digest_noSW.html
Homeostasis, or the regulation of an organism’s internal environment is necessary to maintain conditions suitable for life. The internal equilibrium of the body is the ultimate gauge of its proper function. Homeostasis involves the maintenance of a consistent range in the concentration of certain molecules in the body. Disruption of homeostasis in the body systems can make an organism susceptible to disease and possibly lead to death. Body temperature and hormone levels are examples of mechanisms that are regulated

by the body to maintain homeostasis. Homeostasis encompasses many body processes. We probably think of maintaining a constant body temperature, but homeostasis also includes water balance, which is influenced by the amount of water in the external environment and whether it is fresh or salt water. Water balance is regulated through such things as thirst and urination. Other factors which are under regulation include internal salt concentration, pH (Despite the fact that cellular respiration creates CO2 which dissolves in our blood to make carbonic acid, the pH of our blood is buffered at 7.4 or we would die.), nutrients and various chemicals (regulated by factors like blood sugar level, feelings of hunger, or cravings for certain foods). Homeostasis is controlled by feedback loops (positive and negative), most of which are negative feedback loops. An example of a positive feedback loop (this particular one is not involved in homeostasis) is the process of giving birth to a baby. Labor contractions push the baby against the cervix causing the cervix to dilate. This, in turn, triggers the production of oxytocin, a hormone which triggers stronger contractions. A negative feedback loop works in the opposite direction from what it is trying to accomplish. An example of a negative feedback loop involved in homeostasis is maintenance of body temperature.
As a person’s body gets too hot, he begins to sweat in an attempt to lower the temperature. If someone’s body is too cool, he will begin to shiver in an attempt to increase the temperature.
The systems of the body cooperate in maintaining homeostasis, that is, the relative constancy of the internal environment despite external environmental changes. The circulatory system is critical to the internal environment in that tissue fluid is nourished and purified by the movement of small molecules across capillary walls. The digestive system contributes nutrients to the blood, while the excretory system removes wastes. The respiratory system takes in oxygen and excretes carbon dioxide. Oxygen is used during cellular respiration and carbon dioxide is a waste product of cellular respiration. The nervous and endocrine systems exert the ultimate control over homeostasis because they coordinate the functions of the body's systems. Main examples of homeostasis in mammals are as follows:
• The regulation of the amounts of water and minerals in the body. This is known as osmoregulation. This happens primarily in the kidneys.
• The removal of metabolic waste. This is known as excretion. This is done by the excretory organs such as the kidneys and lungs.
• The regulation of body temperature. This is mainly done by the skin.
• The regulation of blood glucose level. This is mainly done by the liver and the insulin and glucagon secreted by the pancreas in the body.
These hormones associated with the regulation of blood glucose are considered antagonistic because their actions have opposite effects; an increase in glucose concentration following glucagon secretion is counteracted by an insulin secretion.
To learn more about how the body maintains the internal environment in relation to its external environment go to http://www.mhhe.com/biosci/genbio/maderbiology/supp/homeo.html
http://www.biology-online.org/4/1_physiological_homeostasis.htm
http://www.biology-online.org/4/2_water_homeostasis.htm
http://www.biology-online.org/4/3_blood_sugar.htm
The overall effect of a disruption in the body’s internal environment is disease. Disease is a change that disrupts homeostasis in the body. Heart disease is the leading cause of death in the United States and is a major cause of disability. Almost 700,000 people die of heart disease in the United States annually. That is about 29% of all U.S. deaths.
Heart disease and strokes are common cardiovascular diseases. They are the third and first top cause of death for both genders. The most common heart disease in the United
States is coronary heart disease, which often appears as a heart attack. Cancer is the second leading cause of death in the United States. Cancer refers to any one of a large number of diseases characterized by the development of abnormal cells that divide uncontrollably and have the ability to infiltrate and destroy normal body tissue. Cancer can spread throughout your body. Cancer doesn't discriminate when it comes to race, sex or age
— anyone can get cancer. The American Cancer Society estimates that half the men and one-third of the women in the United States will develop cancer in their lifetimes. The American Cancer Society estimates that about 1.4 million new cases of cancer are expected in 2007, and about 560,000 people will die of the disease.
To learn more about the leading causes of death in the United States go to http://www.nutritionstreet.com/7deadlydiseases.shtml
Disease-producing agents such as bacteria, protozoans, fungi, viruses and other parasites are called pathogens. The main sources of pathogens are soil, contaminated water, and infected people or animals. Any disease caused by the presence of pathogens in the body is called an infectious disease. One-half of all human diseases are infectious. Not all diseases are caused by pathogens. Some diseases can be inherited, such as sickle cell anemia or be due to body aging (wear and tear) like osteoarthritis. Pathogens can be transmitted in four main ways. The first way is through direct contact, for example STD’s and influenza are easily spread through contact. The second way is through food or drink contamination which can result in poisoning, Salmonella, Botulism and E-coli are some common examples of food contamination. Some disease-causing germs travel through the air in particles considerably smaller than droplets. These tiny particles remain suspended in the air for extended periods of time and can be carried by air currents. If you breathe in an airborne virus, bacterium or other germ, you may become infected. Tuberculosis and SARS are two infectious diseases usually spread through the air, in both particle and droplet forms. The final way that someone is susceptible to disease is through intermediate organisms (vectors), for example, malaria which is spread by mosquitoes.
Diseases can be classified into two categories, endemic and epidemic. Endemic diseases are diseases that are constantly prese nt in a population like “the common cold”.
Epidemic disease occurs when many people in a given area are afflicted with the same disease in a short period of time. A very prominent epidemic occurred when people became infected with polio in the 1950’s. There are more common diseases that affect us in today’s world to which polio has fallen into the shadows of, and that is the common flu virus. Seasonal (or common) flu is a respiratory illness that can be transmitted person to person. Most people have some immunity, and a vaccine is available. Avian (or bird) flu (AI) is caused by influenza viruses that occur naturally among wild birds. Low pathogenic AI is common in birds and causes few problems. H5N1 is highly pathogenic, deadly to domestic fowl, and can be transmitted from birds to humans. There is no human immunity and no vaccine is available. At the time of this writing H5N1 does not seem to spread easily from person to person. Pandemic flu is virulent human flu that causes a global outbreak, or pandemic, of serious illness. Because there is little natural immunity to that “pandemic” strain of flu virus, the disease can spread easily from person to person. The influenza pandemic of 1918-1919 killed more people than the Great War, known today as World War I, at somewhere between 20 and 40 million people. It has been cited as the most devastating epidemic in recorded world history. More people died of

influenza in a single year than in four-years of the Black Death, or Bubonic Plague, from 1347 to 1351. Known as "Spanish Flu" or "La Grippe" the influenza of 1918-1919 was a global disaster.
To learn more about disease go to http://www.sirinet.net/~jgjohnso/immune.html
Carriers are people who harbor a disease without showing any signs, yet they can pass the disease on to others. Until 1876 it was quite difficult to determine the cause of a disease, in that year Robert Koch provided definitive proof of the germ theory by isolating the cause of anthrax and showing it to be a bacterium. From this came the development of Koch's Postulates, a set of rules for the assignment of a microbe as the cause of a disease.
1. The specific organism should be shown to be present in all cases of animals suffering from a specific disease, but should not be found in healthy animals.
2. The specific microorganism should be isolated from the diseased animal and grown in pure culture on artificial laboratory media.
3. This freshly isolated microorganism, when inoculated into a healthy non-immune laboratory animal, should cause the same disease seen in the original animal.
4. The microorganism should be re-isolated in pure culture from the experimental infection.
This is his most famous contribution to science and it is a testament to the utility of these postulates that they are stilled used today to discover the cause of new emerging diseases. Koch went on to apply these principles in the study of many other diseases including tuberculosis, cholera and sleeping sickness. It should be pointed out that Koc h’s postulates cannot be applied to all diseases. Also, it is not always possible to obtain a disease-causing microbe in pure culture. Koch developed the tools for obtaining pure cultures to attack the problem of disease. Advances in science often come from innovations in the available technology. Robert Koch was an important microbiologist because his pioneering work in the isolation and characterization of bacterial diseases helped to identify the causes of many of the maladies plaguing humanity. Further work by other scientists then began the long road to conquering them.
To learn more about a specific disease associated with humans go to http://www.cdc.gov/az.do
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Performance Benchmark L.12.B.3
Students know disease disrupts the equilibrium that exists in a healthy organism. E/S
1. Students incorrectly think cold weather and rain can cause a person to get a cold or flu.
This question has probably been asked since the first time the flu made someone sick. After all, cold and flu season occurs when the weather is cold. No matter how many times your mother and grandmother told you not to go out in the cold because you would catch a cold or the flu, it just doesn’t work that way.
The truth is that the flu and the common cold are caused by viruses. People get sick more often in the winter because they are exposed to each other more in the winter than in the summer. When it is cold outside, people tend to stay inside and are more likely to spread germs to one another. Also, because school is in session, kids are around each other all da y and are “not afraid” to share their germs. With so many people in such close contact, the likelihood of passing germs is much higher when it is cold outside than when it is warm and people are outdoors. The viruses that cause flu are found in the nose and throat and are sprayed into the air when an infected person sneezes, coughs or talks. It is the close proximity of people to one another that is the leading factor of the spread of the flu virus or common cold.
In tropical areas, where it does not get cold, the common cold and flu season generally occurs during the rainy season. But again, these illnesses are not caused by the rain.
They are just more prevalent because people come in closer contact with each other than they do during the dry season.
For further information regarding confusion about cold weather being linked to the common cold and flu visit http://health.howstuffworks.com/question38.htm
or http://www.alkaseltzer.com/asp/asp_coldflu_faq.html#q2
2. Students erroneously think that AIDS can be spread through casual contact with an HIV infected individual
Because the worldwide spread of HIV has had such a great effect on millions of people, a number of misconceptions have arisen surrounding the disease known as AIDS. You cannot become infected with HIV through day-to-day contact in social settings, schools or in the workplace. You cannot be infected by shaking someone's hand, by hugging or
"dry" kissing someone, by using the same toilet or drinking from the same glass as an HIV-infected person, or by being exposed to coughing or sneezing by an infected person.
HIV is transmitted through direct contact with the blood or body fluid of someone who is infected with the virus. That contact usually comes from sharing needles or by having unprotected sex with an infected person. A nursing infant could get HIV from a mother who is infected.
For further information regarding the HIV virus visit http://kidshealth.org/parent/infections/bacterial_viral/hiv.html

3. Students incorrectly believe viruses are made from or are the same as bacteria.
Viruses are tiny structures that can only reproduce inside a living cell. They range in size from 20 to 250 nanometers (one nanometer is one billionth of a meter). Outside of a living cell, a virus is dormant, but once inside, it takes over the resources of the host cell and begins the production of more virus particles. Viruses are more similar to robots, than to animal life.
Bacteria are one-celled living organisms. The average bacterium is 1,000 nanometers long. (If a bacterium were human size, a typical virus particle would be the size of a tiny mouse. If an average virus were the size of a human, a bacterium would be the size of a building over ten stories tall.) All bacteria are surrounded by a cell wall. They can reproduce independently, and inhabit virtually every environment on earth, including soil, water, hot springs, ice packs, and the bodies of plants and animals. Bacteria cause diseases such as pneumonia, meningitis, botulism, cholera, anthrax, and diphtheria.
For further information regarding the differences between viruses and bacteria visit http://www.mansfieldct.org/schools/mms/staff/hand/Immunebacteriavsviruses.htm
4. Students tend to inaccurately believe that all bacteria are harmful.
Most bacteria are harmless to humans. In fact, many are quite beneficial. The bacteria in the environment are essential for the breakdown of organic waste and the recycling of elements in the biosphere. Bacteria that normally live in humans can prevent infections and produce substances we need, such as vitamin K. Bacteria in the stomachs of cows and sheep are what enable them to digest grass. Bacteria are also essential to the production of yogurt, cheese, and pickles. However, some bacteria cause infections in humans. In fact, they are a devastating cause of human disease. E. coli, a type of bacteria found in our digestive tract, hel ps to turn our food into sugars and processed vitamins. Unfortunately, certain types (called strains) of E. coli can get from the intestines into the blood. This is a rare illness, but it can cause a very serious infection. One very bad strain of E. coli was found in fresh spinach in 2006 within the state of Nevada.
To learn more about types of bacteria that are harmful to humans visit http://www.cubanology.com/Articles/Virus_vs_Bacteria.htm
.
Ecology is the study of the interaction between organisms and their environment. Biotic factors are the living components of an ecosystem including interactions between organisms. Abiotic factors are the nonliving components that affect the living including water, oxygen, light, temperature, soil, and nutrient cycles. The abiotic factors collectively dictate where ecosystems exist.
Figure 1. Locations of world biomes. http://library.thinkquest.org/
11922/habitats/habitats.htm
Light: The energy that drives life on earth originates from the sun. The amount of sunlight dictates the growth of plants. Therefore, energy directly relates to where biomes are located. Both the intensity and duration of light varies with latitude. Radiant energy is greatest at the equator and decreases as you travel to the poles. Areas near the equator receive approximately 12 hours of daylight everyday. Areas near the poles receive 24 hours of weak intensity light in “summer” and 24 hours of darkness in “winter”. Figure 2 shows how one unit of energy from the sun at the equator covers a smaller area than the same unit of energy at the poles creating the weaker intensity of light at the poles. Day length varies with the seasons, lengthening as you approach the summer solstice and shortening as you move toward the winter solstice.

Figure 2. A unit of energy from the sun at the equator covers a smaller unit of area than the same unit of energy at the poles. From: http://wwwclass.unl.edu/geol101i/15a_climate.htm
Sunlight is also affected by depth of water. As light penetrates water, certain wavelengths are absorbed. The zone which is penetrated is called the photic zone and below that is the aphotic zone. Most of earth’s photosynthesis takes place in the photic zones of the oceans and the organisms that live in the aphotic zone are heterotrophic and feed off on the photic zone organisms that migrate to deeper depths.
Figure 3. Red and yellow light are absorbed in the first 15 meters
Figure 4. Red and yellow light are absorbed in the first 15 meters while blue light can penetrate 37.5 meters. while blue light can penetrate 37.5 meters. http://www.photo.net/learn/optics/ http://daac.gsfc.nasa.gov/oceancolor/ edscott/cf000030.htm
scifocus/oceanColor/oceanblue.shtml
Temperature: Temperature patterns are affected by both latitude and altitude. There is a direct relationship between the decreasing light energy received (as latitude increases) and the decrease in temperature. The hottest regions of earth are equatorial and the coldest regions are polar. As you travel away from the equator, these zones have decreasing average annual temperatures. Conversely, there is an inverse relationship between altitude and temperature. As altitude increases, average temperature decreases within the troposphere. As a result even the tops of equatorial mountains may have snow.
Water: Water is essential to life and is recycled through the water cycle (See Benchmark L.12.C.3). The amount of precipitation (including rain, snow, hail, and sleet) that an area receives dictates the type of vegetation. Precipitation is affected by latitude, altitude, topographic features, and proximity to large bodies of water.

Figure 5. Why are deserts at 300 degrees N/S of equator? http://www.earlham.edu/
~biol/desert/whatis.htm
The equatorial regions tend to be very wet while many deserts are located around 30 degrees north and south latitudes. Air over the equator is disproportionately heated because of the increased solar energy. This results in air masses that expand creating low pressure systems. As the air mass rises, it cools, and it loses its moisture. These air masses then move away from the poles, cool, condense, and sink creating a high pressure system. The increased air pressure and dryness causes the air mass to draw water out of the environment creating deserts.
Soil and Minerals: Soil is another non-living component important to the health of an ecosystem. Soil is defined as the unconsolidated mineral or organic material on the immediate surface of the earth that serves as a natural medium for the growth of land plants ( http://soils.usda.gov) . There are many types of soils and each one has unique characteristics, like color, texture, structure, and mineral content. The type of soil dictates the type of vegetation.
Figure 6: Soil profiles from various ecosystems. Notice how the differences in soils correlates to the type of vegetation supported.
From: http://jimswan.com/111/soil/soils.jpg
The process of soil formation in an ecological sense is called primary succession (see Benchmark L.12.C.2). In general, as soil forms, three distinct layers can be distinguished.
The uppermost layer is the topsoil or A Horizon. This includes organic matter and various living organisms. It is often dark in color from the high organic content (humus) which

is from the decay of dead plant and animal matter. The middle layer, or B Horizon is called the subsoil and consists of partially weathered rock particles and an accumulation of water soluble minerals leached from the topsoil. The bottom layer or C Horizon, consists of partially weathered parent rock with little organic matter.
Figure 7. A generic soil labeled profile http://www.mo15.nrcs.usda.gov/features/wissoil/sld005.htm
Climatograms: A climatogram is a graphical way to highlight the differences between biomes. The graph s hows a biome’s average monthly temperature and average monthly precipitation data on a single graph. The precipitation is presented as a bar graph using the left axis and the temperature data is plotted as a line graph using the right axis.
Figure 8: Two examples of climatograms. The data from Indonesia represents a tropical rainforest. The data from Arizona represents a desert. Indonesia: http://www2.kpr.edu.on.ca/cdciw/biomes/indonesia/abiotic_description.htm
Arizona: http://www2.kpr.edu.on.ca/cdciw/biomes/sonorandesert.htm
Ecological Hierarchy: Organisms in an ecosystem do not live in isolation. They interact with their environment and with other organisms. Therefore, an understanding of the organization of an ecosystem is necessary in the field of ecology. The hierarchy starts with the individual. The simplest grouping of organisms is a population. A population is defined as a group of organisms of the same species that have the potential to interact and interbreed with each other. For example, all of the mountain lions that live in the southern Sierra Nevada Mountains would be a population and the mountain lions in northern Nevada would be a separate populati on. A community consists of all the populations of different organisms in a given location. The community level of study looks at the inter-specific relationships, like predator prey relationships or competition. Food webs are another way to think about an ecological community. Food webs are covered in detail in Benchmark L.12.C.3. Lastly, the zone on Earth where life can exist is the
Biosphere. The Biosphere is about 20km thick extending from the floor of the ocean and reaching up to the limits of life in the atmosphere. An extended definition form
Wikipedia.org defines the biosphere as the outermost part of the planet's shell
— including air, land, surface rocks and water — within which life occurs, and which biotic processes in turn alter or transform.
Figure 9: An example of an ecological hierarchy from population to ecosystem.
Ecological relationships: Again, organisms do not live in isolation. They must interact with their environments and other organisms. Ecological relationships are relationships in which two different organisms interact regularly to the benefit of at least one of them. There are three basic types of ecological relationships: mutualism, commensalisms, and parasitism. The following table illustrates each type of relationship. A + sign represents a benefit, a 0 represents no effect, and a
– sign represents a harmful effect.

Mutualism
Commensalism
Parasitism
Organism #1
+
+
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An example of a mutualistic relationship is between termites and the bacteria that live in their digestive tract. Termites cannot digest cellulose and depend on the bacteria to release the nutrients in the wood while the termites give the bacteria nutrition and a place to live.
Barnacles have a commensalistic relationship with whales. The whales are not bothered by the barnacles but the barnacles rely in the water currents created b y the whale’s swimming to filter feed.
Tapeworms are parasitic and live inside the digestive tract of a host organism. The worm steals nutrients from the host to grow and reproduce. Consequently, the host loses nutrients, energy, and can suffer from tissue damage from the infestation.
Competition: Resources are limited in an ecosystem. Therefore, individuals must compete with individuals of their own species (intraspecific competition) and with other species (interspecific competition) to meet their survival needs. back to top
Content Benchmark L.12.C.1
Students know relationships of organisms and their physical environment. E/S
1. Species live independently of each other and there environment.
Organisms are constantly interacting with their environments abiotic factors, such as, water, light, soil, and air. Plants, for example, take the radiant energy from the sunlight, carbon dioxide and water to make their food through the process of photosynthesis. These are all abiotic factors. Animals must obtain their energy from other organisms like plants and other animals. These interactions are very specific and are important for stability in an ecosystem.
2. Symbiosis is limited to parasitism, where the parasite goal is to kill its host.
There are three types of symbiotic relationship, parasitism, commensalism, and mutualism. In a parasitic symbiotic relationship one organism benefits by getting food, shelter, and or protection at the expense of a secon d organism, it’s host. The parasite’s intention is not to kill the host because without the host the parasite will die as well. In a commensal symbiotic relationship, one organism is helped but the other is unaffected. In a mutualistic symbiotic relationship both organisms benefit from the relationship.
3. Biotic factors, like plants and animals, determine the biome.
Biomes are characterized by the predominant vegetation, but the two major determining factors of biomes are temperature and precipitation. Organisms must be adapted to live in the climate that is determined by temperature and precipitation. Many organism adaptations are driven by abiotic factors, for examples, some cactuses have spines that help to reduce water loss and to help shade from excessive sun. This adaptation is ideal for living in high temperatures with low precipitation.
A simple definition of biodiversity is the number and types of organisms in an environment. A desert has a much lower relative biodiversity than a tropical rainforest due to limited resources. Therefore, comparing biodiversity between biomes isn’t informative, but changes in an ecosystem’s biodiversity can be a red flag to detrimental environmental damage or of climatic shift. The number of species in an ecosystem can influence that system’s stability, productivity, and value to humans. Sometimes the loss of a single species in an ecosystem can completely shift the balance of the ecosystem.

Figure 1: An illustration of three levels of biodiversity. http://www.scq.ubc.ca/?p=528
There are several factors that affect biodiversity. These include but are not limited to succession and density independent and dependent limiting factors.
According to Dr. Mathew Williams at the University of Edinburgh, high biodiversity increases an ecosystem’s resilience and resistance. Resilience “describes the speed with which a community returns to its former state after perturbation.” In other words, high biodiversity reduces the amount of time it takes for secondary succession to proceed from disturbance until the climax community is reached. See below for a greater explanation of succession.
Resistance “describes the ability of a community to avoid displacement in the first place.” Species rich communities have high resistance to change from invasive species or environmental fluctuations like drought. Species-poor communities have empty niches which make them susceptible to invasion by an alien species.
Figure 2: Another theory, the rivet hypothesis, shown to the above figure claims that each species added to an ecosystem increases ecosystem functions. http://canadianbiodiversity.mcgill.ca/english/theory/ ecosystemfunction.htm
High biodiversity is like an insurance policy for the community. More diverse communities can respond to disruptions with little overall change in population make up. David
Tilman & John A. Downing conducted a study on grassland and biodiversity. They concluded that their study “implies that the preservation of biodiversity is essential for the maintenance of stable productivity in ecosystems.” More information can be found at: http://canadianbiodiversity.mcgill.ca/ english/theory/ecosystemfunction.htm
http://www.nature.com/nature/journal/

In the short term, ecosystems may appear to be stable but are in a constant state of flux. Minor changes occur as one species slowly replaces another in response to such factors as climate changes, human impact, or introduction of alien species. This process is called ecological succession. In land environments, succession is driven by the plants. If the plant species change, the herbivores respond, and the predators follow. The species that have the greatest impact on the overall shift in species are called the dominant species. The changes caused by the dominant species determine the type of other species that can survive in each successive community. Succession continues until the most mature, stable community evolves. This community is called the climax community. The climax community is the most stable and will remain unless upset by a catastrophic event like a flood, fire, clear cutting, volcanic eruption, etc.
There are two main types of succession, primary and secondary. Primary succession occurs when no soil is present. Therefore, the organisms that migrate into the area must contribute to soil formation before other, larger plants can move in. Weathering begins breaking down the bare rock into smaller particles, and then pioneer species can move in.
Lichens are a good example of a pioneer species. Lichens attach themselves to rocks with root like rhizoids. They secrete acids onto the rock surface, dissolving the rocks. This begins the formation of soil. Once there is a thin layer of soil, small herbaceous plants (like grasses) move in and further the formation of soil. This process continues until a mature soil profile is created and the climax community is established.
Figure 3: An example of primary succession. http://www.life.uiuc.edu/bio100/lectures/s06lects/03s06-succession.htm
Secondary succession is succession that takes place when soil is already present, usually following a catastrophic event that partially or completely removes the existing vegetation. Secondary succession occurs much faster than primary succession because soil already exists, a healthy seed bank in the soil may be present, or root stocks of previous plants may still be viable. Secondary succession usually begins with fast growing herbaceous ground cover that stabilizes the soil. Ultimately, the slower growing climax shrubs and trees re-grow and dominate the community again.

Figure 4: An example of secondary succession. http://www.life.uiuc.edu/bio100/lectures/s06lects/03s06-succession.html
For additional information on succession, go to http://www.nk2.psu.edu/naturetrail/succession.htm
http://www.countrysideinfo.co.uk/successn/index.htm
Limiting factors are resources in the environment that limit the maximum number of organisms that can survive in an ecosystem. Therefore, limiting factors define the carrying capacity of the ecosystem. Limiting factors can be divided into two categories, density dependent and density independent.
Density dependent factors are factors that affect large, dense populations more strongly that small, less dense populations. These include competition for food, water, and living space as well as disease and predation. Large, dense populations require that individuals compete for water, food, sunlight, space, pollinators, or other resources essential for life. There just isn’t enough to go around. Some individuals will obtain what they need to survive, others will obtain enough to stay alive but not enough to reproduce and/or raise offspring. Still others will not obtain enough to survive and will die.
Why is competition considered density dependent? The more individuals present, the faster resources will be exhausted. The fewer individuals present, the longer resources will last.
Figure 5. This graph shows that the number of eggs laid per female decreases as the density of females increases.

Predation is another density dependent limiting factor. The more prey animals are present the higher the predator count will be and conversely the lower the prey animals the lower the predator count. This is a classic predator/prey relationship. The predator population relies of the prey population for its very survival. So as the prey population increases, so does the predator. Eventually, the predator population will be so large that it will over hunt its prey, reducing the overall population, and drive its own population down.
(Click Image to Enlarge)
Figure 6. A graph showing the linked oscillation of a predator/prey relationship http://www.sfws.auburn.edu/ditchkoff/images/Lecture%
20Images/Carnivores/lynx-hare_cycle.gif
Lastly, disease and parasites can spread much faster through a dense population than through a spread out or less dense popul ation. The individuals in a dense population are more likely to come into contact with each other and transfer viruses, bacteria, and parasites.
Density independent limiting factors are things that will affect a population regardless of its size or density. Weather is usually the most dramatic density independent limiting factor. For example, a hurricane, flood, or extensive drought can destroy an entire population regardless of the raw number of individuals in the population. Fire, earthquakes, landslides and avalanche are other natural independent limiting factors. Human activities, like clear cutting, pollution, and pesticide/herbicide spraying, can also have a dramatic effect on any population.
A good exercise to work through with students to help them understand how changes in biodiversity affect other species is to construct a food web and then change one thing and see the cascading changes that could occur. The left side of the food web represents an open ocean ecosystem and the right side is a rocky shore/kelp forest ecosystem.
Even though these two ecosystems are miles apart they are still connected. Can you describe how overfishing of perch that cuts the population by 50% will affect both ecosystems?

Figure 7. A starting food ocean food web
Figure 8. This is only one scenario of what could happen in response to the fish population dropping by 50% . Blue arrows reflect whether the population increased or decreased in response to the perch population
(red arrow) dropped by one half.
The following is a possible explanation of the changes in this ecosystem due to a reduction in the number of perch. With the decrease in perch population first the seal then the
Orca population may decline due to the lack of prey. With the decrease in Orca the otter population may rise due to the lack of predators. As the otters increase in number, they prey more heavily on the sea urchins, causing a decline in their numbers. As the sea urchins decline in number the sea gulls numbers fall due to a reduction in their food source.
This is only one possibility of what could happen if the fish population dropped by 50%. It is open to class discussion to create other resulting food webs. back to top
Content Benchmark L.12.C.2
Students know how changes in an ecosystem can affect biodiversity and biodiversity contribution to an ecosystem. E/S

1. Students incorrectly believe populations will increase indefinitely because the resources are unlimited.
The carrying capacity of an environment is limited to the number of organisms it can sustain during the environments harshest season. For the desert this would most likely be the summer, and for the higher latitudes it would most likely be the winter. The factors that determine the number of organisms an environment can maintain are called the limiting factors. Limiting factors are resources, such as, water, oxygen, food, and space, as well as, environmental concerns such as temperature, rain/snow fall and the geographical arrangement or access to the needed resources. If a population’s size is greater than the carrying capacity then the organisms have exceeded the ability of the environment to support that population. The population will potentially suffer from starvation, dehydration, exposure, as well as, diseases, and fighting until the population is reduced in size to a level that the environment can support. This level will probably be well below the carrying capacity. The population is now set to rebound in number, and repeat this cycle, of fluctuating around the carrying capacity.
The activity “Oh! Deer,” found in the Project Wild guide or the slightly modified version found at the link below are an excellent interactive way for the students to simulate the changes in population due to limiting factors. This simple activity has the potential to promote an in-depth understanding of limiting factors and carrying capacity. To access the modified version: http://georgiawildlife.dnr.state.ga.us/assets/documents/Oh_Deer.pdf
2. Students incorrectly believe a size change in one population will not have an effect on other populations in the same food web because the chains are spread out.
Review the food web portion of this benchmark. In the example we see phytoplankton, perch, seals, and orca as representatives of an open water ecosystem food chain. We also see kelp, purple sea urchins, sea gulls, otters, and orca as representatives of a kelp forest ecosystem food chain. Together the two food chains represent a food web spread out over hundreds of miles. The over fishing of perch in the open ocean has a direct and significant affect on the kelp forest ecosystem. For additional information on food webs and chains, visit http://www.bigelow.org/edhab/fitting_algae.html
3. Students mistakenly believe that the relative population size of prey and predator populations have little or no affect on the overall size of the other population.
The figure illustrates the student’s misconception. Population A and B represent the predator or prey populations. It shows that one population is fluctuating but the other is stable. Predation is a density-dependent limiting factor. The predator population is dependent on the prey population for survival. If the number of prey decreases then the predator population will decrease as well. If the number of prey increases then the predator population will also increase. Refer to the figure 6; the graph depicts the classic predator prey relationship.
4. Students incorrectly believe that density-dependent factors are biotic, and density-independent factors are abiotic.
Density-dependent limiting factors are resources that individuals compete for in a population. The greater the size or density of the population the greater the competition for resources will be. These resources include but are not limited to food, space, water, and sunlight. The density-dependent limiting factors are both biotic (food) and abiotic (water, space, and sunlight). Density-independent limiting factors are factors that effect a population regardless of its size or density. Examples of density-independent limiting factors are floods, earthquakes, clear cutting, and drought. Density-independent limiting factors are usually catastrophic and include human impact such as cutting down forests. The following limiting factor activity may help students develop a better understanding of this concept.
Perch in Lake Winnipeg Limiting Factor activity http://www.gov.mb.ca/conservation/sustain/limfac.pdf

Students know how the amount of living matter an environment can support is limited by the availability of matter, energy, and the ability of the ecosystem to recycle materials.
E/S
All of life’s processes require energy to complete. The energy for these life processes is mostly derived from the sun. The radiant energy from the sun is captured by plants and converted to chemical energy (glucose) through photosynthesis. This chemical energy is now available to other organisms.
Figure 1.
( From http://www.eia.doe.gov/kids/energyfacts/sources/renewable/biomass.html)
Every organism in an ecosystem has a role as either a producer, a consumer or a decomposer. Primary producers (also called autotrophs) are responsible for converting energy from an unusable form (radiant energy) to a usable form (chemical energy). Green plants on land and algae in aquatic environments are the major types of primary producers. A small class of autotrophic organisms, called chemotrophs, obtains energy by the oxidization of molecules in the environment. Non-autotrophic organisms are consumers or heterotrophs. Consumers are organism that must obtain nutrients and energy from other living organisms. The often overlooked participants in an ecosystem are the decomposers. Decomposers obtain energy from the remains of dead plants and animals in the process they release the nutrients trapped in the dead tissues so that they can be then be reused by other members of the ecosystem.
The flow of energy from one organism to another can be modeled with a simple food chain. Figure 2 shows a simple terrestrial and aquatic food chain. A food chain always begins with the producer and follows the flow of energy through several levels of consumers. The first order consumers are herbivores who consume producers. The second order consumer feed on the first order consumers, etc. However, energy flow through an ecosystem is never as simple as represented by a food chain because consumers rarely have only one food source. A food web incorporates many interconnected food chains and provides a better picture of the true flow of energy in an ecosystem. A food web would also include decomposers as a link in energy transfer. Figure 3 is a good example of a complex food web. For more i nformation about food chains and webs see http://www.vtaide.com/png/foodchains.htm
.

http://www.geneseo.edu/
~saw3/food%20chain.html
(Click Image to Enlarge)

http://weedeco.msu.montana.edu/ class/LRES443/
Lectures/Lecture20/FoodWeb.JPG
Another model, of energy flow through an ecosystem is the trophic pyramid. The purpose of a trophic pyramid is to graphically represent the distribution of biomass or energy among the different trophic levels of the ecosystem. A trophic level is the position of an organism in an ecosystem (producer, first order consumer, etc). A pyramid is used as the model because it shows the decrease in energy available as you go through a food web. The availability of energy decreases as you travel up the pyramid because only 10% of energy absorbed becomes stored energy (available to transfer). The other 90% of energy is mostly lost as heat from metabolic processes and maintenance of daily life functions.
Figure 4. A typical trophic pyramid showing the decrease in energy available as move from one level to the next.
From: http://www.bio.miami.edu/ dana/106/106F05_8.html
Energy flows through an ecosystem and is ultimately lost to the environment. Matter, on the other hand, is recycled. Matter is finite. If matter was not cycled through the ecosystem, the supply would have been exhausted a long time ago. A simple matter cycle consists of an exchange of matter between living and non-living components of an ecosystem (Figure 5). Organisms incorporate various elements (compounds) from the environment into their bodies. When these organisms die, their bodies are broken down by decomposers and the compounds are released back into the environment.

Figure 5: A generic matter cycle
Energy flows through an ecosystem and is ultimately lost to the environment. Matter, on the other hand, is recycled. Matter is finite. If matter was not cycled through the ecosystem, the supply would have been exhausted a long time ago. A simple matter cycle consists of an exchange of matter between living and non-living components of an ecosystem (Figure 5). Organisms incorporate various elements (compounds) from the environment into their bodies. When these organisms die, their bodies are broken down by decomposers and the compounds are released back into the environment.

Figure 6: The Water Cycle
From: http://ga.water.usgs.gov/edu/watercycle.html
The water cycle, also called the hydrologic cycle, follows the continuous path of water. Water enters the vapor phase through evaporation and transpiration (the release of water vapor from plants and animals). The sun is the main source of energy that allows the water to under go a phase change. The water vapor rises, cools, and condenses forming clouds. The water droplets become heavier and eventually fall as precipitation. A small portion of the precipitation will be taken up by the plants and animals, more will infiltrate the soil, entering the water table, with the largest portion of the precipitation forming runoff on the surface of the land to drain into streams, rivers, lakes, and ultimately the ocean. The hydrologic cycle is a continuous process that recycles all the water on the planet.
Carbon dioxide makes up only 0.03% of the atmosphere but is the major source of carbon for additional biomass. Carbon dioxide is converted to organic carbon by photosynthesis in green plants. Organic carbon is then available to travel through the food web to eventually be released back to the atmosphere by cellular respiration and decomposition. Fossil Fuels are another link in the carbon cycle. Organic carbon has been trapped underground for millions of years in the form of coal, oil, and natural gas. This carbon, in the form of carbon dioxide, is released back to the atmosphere by the burning of fossil fuels. Carbon dioxide that is dissolved in the ocean can be absorb by animals and temporarily trapped in their skeletons and shells. It should be noted that humans are altering the carbon cycle with the increased use of fossil fuels.
Figure 7: The Carbon Cycle From: http://www.windows.ucar.edu/earth/Water/co2_cycle.html
Figure 8: The Nitrogen Cycle From: http://www.epa.gov/maia/html/nitrogen.html

Nitrogen comprises approximately 80% of the atmosphere but is not accessible to most life forms. It must be “fixed” before it can be absorbed. Nitrogen-fixing bacteria are responsible for converting atmospheric nitrogen into its ionic form, ammonium. Ammonium is converted to nitrites and nitrates. Plants can access this nitrate. However, animals must get their nitrogen from the food that they eat. Thus, nitrogen flows through the food web much like carbon. Nitrogen is returned back to the atmosphere through decomposers and then denitrifying bacteria.
Figure 9: Oxygen Cycle
From: http://telstar.ote.cmu.edu/environ/m3/s4/cycleOxygen.shtml
The oxygen cycle is very similar to the carbon cycle, but in reverse. Oxygen comprises approximately 20% of the atmosphere. Oxygen is removed from the atmosphere through cellular respiration and returned to the atmosphere by photosynthesis. Large amounts of oxygen are dissolved in large bodies of water. back to top
Content Benchmark L.12.C.3
Students know how the amount of living matter an environment can support is limited by the availability of matter, energy, and the ability of the ecosystem to recycle materials.
E/S
1. Students incorrectly think plants take in food from the outside environment, and/or plants get their food from the soil via roots.
Plants internally produce their food through the process of photosynthesis. Photosynthesis captures light energy, converts and stores that energy in the form of chemical bonds in glucose. This stored energy is used to carry out metabolic activity in the plant like the breaking down and the making of biomolecules.
2. Students incorrectly believe individuals higher in the food web have more energy because energy accumulates up the trophic level.
Trophic pyramids can represent biomass or energy among different trophic levels. Energy is used by organisms to live and grow. By the time you reach the top of the pyramid, most of the original energy has been used up by being converted into other forms of energy. Energy is also lost in the form of heat. Each trophic level only contributes approximately 10% of original energy obtained to the next trophic level. For more information access the following websites: http://www.wsu.edu/DrUniverse/plants.html

http://www.eduweb.com/portfolio/earthsystems/food/images/energy_pyramid.gif
3. Students incorrectly believe that there is a starting and ending point for food chains and webs.
Food chains and food webs should always include decomposers so that the model of energy and nutrient flow is cyclic rather than linear. In other words, energy and nutrients are not lock indefinitely in a food web being studied. When organisms die, defecate, or urinate the material is broken down by decomposers utilize the energy and return nutrients to the system.
When one views the biodiversity in Nevada it is surprising to note that only ten states are richer in their biodiversity. Nevada lists 3,872 species in the state, of which, plants are the most common with 2,875 species. In addition Nevada ranks sixth in terms of endemic species (native species not found elsewhere) with 309 species found only in Nevada.
The chart below shows the taxa where these endemic species are distributed.
Figure 1. Endemic species in Nevada by major taxa. http://dcnr.nv.gov/nrp01/figure3-1.gif

To learn more on Nevada’s biodiversity go to http://heritage.nv.gov/reports/scor2006.pdf and, http://www.natureserve.org/Reports/stateofunions.pdf
At the same time Nevada has 25 species that are on the Federal List of Endangered. Of these are 17 fish which include a number of pupfish in Ash Meadows.
To find the names of endangered species in Nevada go to http://heritage.nv.gov/endanged.htm
The names of additional threatened species in Nevada are found at http://www.fws.gov/nevada/protected_species/nevada_species_list.html
A map of threatened and endangered species is located at http://ecos.fws.gov/tess_public/StateListing.do?state=all
The question then becomes, why does Nevada have so much biodiversity relative to the other 50 states? Size alone is not the answer considering Texas the second largest state in area is second in biodiversity, while the largest state, Alaska ranks 49 in biodiversity. Of more importance is the geographical diversity in the state. Nevada lies in a geological region known as Basin and Range (see map below) which is vast system of valleys and mountain ranges. This area extends east-west from the Colorado Plateau to the Sierra Nevada, while stretching south from the borders of Nevada, Washington and Idaho to the northern parts of Mexico.
Figure 2. Extent of the Basin and Range topography in North America. http://en.wikipedia.org/wiki/Basin_and_Range
The Basin and Range topography has resulted from the extension or pulling apart of the earth’s crust in this area of North America. This stretching occurred as the North
American and Pacific Plates have moved apart over of the last 20 million years. As a result Nevada has hundreds of active extension faults which results in earthquake activity in most parts of Nevada. This stretching and pulling has also produced some of the thinnest crust on the earth.
This pulling continues today and the direction of this pulling can be seen in the map below.

Figure 3. Direction of tectonic plate separate between the Pacific and North American Plates. http://www.seismo.unr.edu/ftp/pub/louie
/class/100/plate-tectonics.html
To learn more about plate tectonics, go to http://www.ucmp.berkeley.edu/geology/tectonics.html
The formation of this geological feature has left Nevada with 314 named mountain ranges and 232 hydrographic basins. Twenty-five of these mountain ranges have peaks over
10,000 feet, while elevations of the larger valleys range from 500 to 6,800 ft above sea level. As can be seen in the map below these mountains and valleys tend to run in a north south direction. (Note in Spanish
“Nevada” means “snowcapped”.)
Figure 4. Topography of Nevada http://geology.com/state-map/nevada.shtml
The photo of the Kingston Range from Emigrant Pass illustrates this system of mountains and valleys.

Figure 5. Kingston Mountain Range. http://commons.wikimedia.org/wiki/Image:Kingston_Range_from_Emigrant_Pass.jpg
In addition, climate changes over the past 10,000 years have produced many freshwater lakes that have developed and disappeared along with other ecosystems such as mountain coniferous forests and riparian zones. These changes have provided the raw materials for evolution and natural selection. As ecosystems developed, disappeared or became isolated selective pressures were place upon organisms to adapt or become extinct. Nevada biodiversity can therefore be seen as a direct interaction between geological and biological evolution.
The geological action that created the basin and range topography also formed a number of mountain peaks which are isolated by broad valleys which surround them. An example of this “sky island” ecosystem can be seen in the Spring Mountains which is typically 20-30°F cooler than the valleys below. In this sky island biologists have identified nearly 40 endemic species of plants and animals including the Palmer chipmunk, the prairie falcon, spotted bat and blue mountain butterfly. This is the highest number of endemic species of any mountain range in the Great Basin. Ash Meadows (see below) is another example of this oasis of species in Armargosa Valley. Ash Meadows contained numerous artesian springs that sustained isolated populations of endemic fish. However, due to extensive ground water pumping many of the artesian springs have stopped flowing, resulting in the extinction or near extinction of their endemic populations.
The Basin and Range topography of Nevada is divided into four ecoregions. These include the Great Basin, Mojave Desert, Columbia Plateau and the Sierra Nevada.
Figure 6. Major Ecoregions of Nevada http://dcnr.nv.gov/nrp01/bio01.htm

A more detailed map of Nevada ecoregions can be found at: http://www.fws.gov/nevada/habitats/documents/na_eco.pdf
Figure 6. Central Basin Topography http://www.fws.gov/nevada/habitats/ecoregions_html.htm
The middle of the state is dominated by the Great Basin ecoregion. In fact over 68% of Nevada is covered by this ecoregion which also extents into Utah and parts of southern
California. This area is also part of the larger Great Basin Desert. Compared with other ecoregions in the U.S. the Great Basin ranks fifth in total species richness. In the higher valleys sagebrush (The Nevada State Flower) dominates, while creosote bush can be found in the lower valleys. Salt flats are scattered throughout this region. In the lower mountain elevations singleleaf pinyon (One of Nevada’s state trees) and juniper are common. In the widely dispersed higher mountainous elevations conifers and woodlands occur. Most of the yearly precipitation falls in the winter. As such the Great Basin is often termed a “cold desert”.
Figure 7a and 7b. Sagebrush http://www.netstate.com/states/symb/flowers/images/sagebrush2.jpg
The Great Basin makes up a landlocked drainage basin. The rivers in this ecoregion have no natural outlets to the ocean. It is bordered by the Rocky Mountains to the east and the Sierra Nevada to the west.

Figure 8. North American Basins http://en.wikipedia.org/wiki /Image:Basin_New.png
For a map showing the major rivers of Nevada go to: http://geology.com/state-map/nevada.shtml
The Mojave Desert (the smallest of the four major deserts found in the U.S.) is found in the southern part of the state.
Figure 9. Deserts of North America http://www.birdandhike.com/Veg/Veg_index.htm
In the Mojave Desert valleys are broader and mountain ranges are fewer as compared to the Great Basin. The area around Las Vegas illustrates the variety of life zones of the
Mojave Desert. These life zones can be seen in Figure 15 below. In the Lower Sonoran life zone (below 4000 ft) creosote bush and White Bursage are the dominant plants with
Mojave Yucca found at higher elevations. This area is also home to the endangered Desert Tortoise. The non-endemic red brome grass can be common, especially in high rainfall years. Temperatures range in excess of 110oF in the summer to 25oF in the winter.
As one moves up the slopes (from 4000 to 5000 ft) one enters the Upper Sonoran life zone. Here creosote bush, Joshua Tree (which is the indicator plant for this desert, as it is naturally found no place else in the world), various yucca and a mixture of shrub and cacti are found. One can find the Big Horned Sheep (The Nevada State Animal) in this zone.

Figure 10: Creosote bush http://www.americansouthwest.net/slot_canyons
/photographs700/creosotebush.jpg
To learn more about the creosote bush, go to http://www.birdandhike.com/Veg/Species/Shrubs/Creosote/Larr-trid.htm
Figure 11. Joshua Tree http://i1.trekearth.com/photos/8168/joshua_tree.jpg
To learn more about the Joshua Tree, go to http://www.birdandhike.com/Veg/Species/Yucca/Y_brev/Y_brev.htm
As one moves out of the Mojave Desert into lower mountainous elevations (5500-7500 ft) pinyon pine and juniper can be found. Pines and firs are limited to higher elevations sometimes with sages and bunchgrasses. At lower elevations one can find Blackbrush and Rabbit Brush. Throughout this region numerous cacti such as Prickly Pear,
Hedgehog Cactus and various varieties of cholla can be found. Generally less than 5 inches of precipitation falls during the summer monsoons and in winter. During the winter several feet of snow can sometimes occur at the highest elevations.

Figure 12. Pinyon Pine in the Sheep Range in southern Nevada http://www.birdandhike.com/Veg/Species/Conifers/Pine_Pinyon1/Pine_Pinyon1.htm
To learn more about pinyon pine trees, go to http://www.birdandhike.com/Veg/Species/Conifers/Pine_Pinyon1/Pine_Pinyon1.htm
In the higher mountainous (over 7000 ft) areas within the Mojave Desert ponderosa pine become the dominate vegetation type. Other plants found in this area include sagebrush, Manzanita, shrub Live Oak and Quaking Aspens.
Figure 13. Mary Jane trailhead, Kyle Canon, Mt. Charleston http://www.birdandhike.com/Veg/HabType/YellowPine/YellowPine.htm
As move up mountains beyond 8000 ft conifers continue to change until one reaches the alpine tundra. If you were to climb some of the higher elevation trails in Mt Charleston you would see white fir and Bristlecone Pine (Nevada’s second state tree). In the alpine tundra sedges and bunchgrasses would be seen.

Figure 14. Alpine Life Zone on Mt. Charleston http://www.birdandhike.com/Veg/Veg_index.htm
The idea of life zones was developed at the end of the 19th century by C. Hart Merriam, who was the first director of the U.S. Biological Survey. This scheme of life zones was developed in studies of the Grand Canyon and nearby San Francisco Mts. These life zones were developed to identify belts of vegetation and animals. They were expressed with increases in altitude. In addition annual totals in precipitation were considered.
To learn more about the concept of life zones, go to http://www.cpluhna.nau.edu/Biota/merriam.htm
and, http://www.runet.edu/~swoodwar/CLASSES/GEOG235/lifezone/merriam.html
Figure 15. Life Zones of Mt. Charleston and the Las Vegas Valley. http://www.birdandhike.com/Veg/Veg_index.htm

Figure 16. The Columbia Plateau Ecoregion, Jarbidge Mts. www.fws.gov/nevada/habitats/ecoregions_html.htm
In the northern part of Nevada the Great Basin Desert mixes in and joins the Columbia Plateau ecoregion. Geologically this region contains tablelands, intermountain basins, dissected lava plains and scattered mountains. With a cooler climate and volcanic soils a sagebrush steppe ecosystem prevails containing numerous perennial grasses. Near the Idaho border open prairie is evident with such large mammals as Mule Deer, Antelope and Elk being found here. Juniper woodlands and mountain mahogany tend to replace the salt desert scrub and pinyon woodlands of the Great Basin at lower elevations. At higher elevations Douglas-fir and aspen are common.
Figure 17. Jeffrey Pines
The Sierra Nevada ecoregion is found near Carson City and Reno. Lake Tahoe lies on the border between Nevada and California. Vegetation is mainly mixed conifer consisting of white fire and lodgepole pine on western slopes and Jeffery pine and lodgepole pine on eastern slopes. In higher elevations red fir, mountain hemlock and western white pine are seen.
These higher elevations receive more precipitation and are the source of rivers like the Truckee and Walker. These rivers provide water to lower elevations in the Great Basin.
There are many mountain lakes and meadow/riparian areas. At the highest elevations alpine conditions exist.
Within these four major ecoregions several other micro-regions can be identified including riparian zones and wetlands. In each case these add to the biodiversity of Nevada.
Riparian zones are quite diverse and include short or tall grasses, shrubs and trees including willow, cottonwood or aspen.

Figure 18. Riparian Habitat http://dcnr.nv.gov/nrp01/bio08.htm
One of the unique micro-regions in Nevada is its numerous wetlands. These include thousands of springs that are found throughout Nevada. A number of these springs are
“left-overs” from the last ice age. As the last North American Ice Age was in retreat 10,000 years ago, numerous isolated springs were created. Of particular interest is Ash
Meadows in the Armargosa Valley of southern Nye County. Today Ash Meadows supports 24 species of plants and animals (including the pupfish) that are found nowhere else in the world. This area represents the highest concentration of indigenous species in the United States and second greatest in North America.
Figure 19. Ash Meadows http://ndep.nv.gov/admin/ash.jpg

Figure 20. Desert Pupfish http://sciences.unlv.edu/desertsurvivors/Pages/episode4.htm
Figure 21. Pupfish Distribution in North America http://sciences.unlv.edu/desertsurvivors/images/episodepictures/e4/distribution.jpg
To learn more about Ash Meadows visit http://www.fws.gov/desertcomplex/ashmeadows/
To learn more about the desert pupfish, go to http://sciences.unlv.edu/desertsurvivors/Pages/episode4.htm

Figure 22. Precipitation Map of Nevada http://www.ocs.orst.edu/pub/maps/Precipitation/Total/States/NV/nv.gif

Figure 23. Relief Map of Nevada http://www.netstate.com/states/geography/mapcom/nv_mapscom.htm
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Content Benchmark L.12.C.4
Students know the unique geologic, hydrologic, climatic, and biological characteristics of Nevada’s bioregions. E/S
1. Students mistakenly believe that there is little biodiversity in Nevada.
Biological surveys of United States have shown that Nevada shows more biodiversity than most states. In fact only ten states show more biodiversity than Nevada and it ranks sixth in terms of endemic species. At present 309 species are located in Nevada and nowhere else. Of particular interest is the desert pupfish located in southern Nevada.
To learn more on Nevada’s biodiversity, go to http://heritage.nv.gov/reports/scor2006.pdf
and
( http://www.natureserve.org/Reports/stateofunions.pdf
)
For a checklist of wildlife in Nevada visit http://heritage.nv.gov/spelists.htm
Images of Nevada’s wildlife can be found at http://heritage.nv.gov/images.htm#vascplants
2. Students incorrectly believe that Nevada shows very little variation in plant life and is mostly desert.
While a large percentage of Nevada can be classified as desert the diversity of plant life ha s been greatly increased because of Nevada’s location in the Basin and Range geographical region. This geologically diverse region of mountains and valleys has produced many ecoregions within Nevada. As a result of isolation and time 3,872 species
(including 2,875 species of plants) are now found in Nevada.
The four major ecoregions are subdivided into smaller ecological regions as can be seen in the map below. Each of these major ecoregions should not be viewed as one region, but seen as “micro regions” which are often sub-divided from one another. This isolation is important in the evolution of species.
Refer to L.12.D.5 for a discussion on how isolation is important in the evolution of species.

Figure 24. Ecoregions of Nevada http://www.fws.gov/nevada/habitats/documents/na_eco.pdf
For a detailed discussion of vegetation in the Great Basin, go to http://www.fs.fed.us/ pnw/lagrande/sagebrush/docs/Gr%20 Basin%20PDF%20Sept03/Ch03_Vegetation_Sept03.pdf
3. Students confuse the Great Basin Desert with the Basin and Range geographical region.
The Basin and Range geographical region is a broad area in the western part of the United States (Refer to Figure 2) of valleys and mountains ranges. This area has resulted from tectonic actions of the Pacific and North America Plates. Within this geographical area are several large deserts including the Great Basin Desert (Refer to Figure 9), sometimes called the Great Basin. The Great Basin is an inland drainage basin located in the northern region of the Basin and Range geographical region and centered in
Nevada. This basin also extends into surrounding states of California, Oregon, Idaho and Utah.
When teaching all of the L.12.D benchmarks, it is imperative to help students understand the process of science. Most objections and misconceptions about evolution are directly related to the misunderstanding of how science works. When students understand the nature of science, they will understand how scientists have studied the process of evolution. As questions arise about a “supernatural” creation of Earth and the Universe, students who understand the nature of science will understand why supernatural forces cannot be studied as part of scientific processes.
Organisms can be classified into groups based on morphological, behavioral, and evolutionary relationships. Classifying organisms is important to scientists as it provides a framework and a common “language” which enables scientists everywhere to study and understand more about life on Earth. Biological classifications are based on how organisms are related. Taxonomy is the science of classification and includes the naming, describing, and classifying organisms into various groups.

The Linnean system of classification is a hierarchical classification system that has been used by scientists for nearly 200 years. This system, originally based on morphological and behavioral characteristics is still in use today, although with many modifications. The highest category in the hierarchy is “all living things” and the lowest category is a single species. A species is generally identified as a group of organisms which are capable of reproducing with the production of fertile offspring. The hierarchical divisions are as follows: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species. The following table shows the Linnean classification hierarchy of two organisms.
Category Domestic cat Common buttercup
Domain
Kingdom
Eukarya
Animalia (animals)
Eukarya
Planate (plants)
Phylum/Division Chordata (chordates) Anthophyta (flowering plants)
Class Mammalia (mammals) Dicotyledons (dicots)
Order
Family
Genus
Species
Carnivoria (carnivores) Ranunculales
Felidae (cats) Ranunculaceae (crowfoot family)
Felis silvestris
Ranunculus acris
Scientists currently recognize 3 Domains and 6 Kingdoms of living things:
Bacteria Archaea
Three Domains
Eukarya
The Six Kingdoms
Bacteria Archaea Protista Plantae Fungi Animalia
To learn more about Linneas and the Linnean system of classification see: http://huntbot.andrew.cmu.edu/HIBD/Exhibitions/OrderFromChaos/pages/intro.shtml
and http://anthro.palomar.edu/animal/animal_1.htm
Charles Darwin was a scientist/naturalist who gathered a significant amount of evidence indicating that populations change over time as the population amasses adaptations to environmental conditions. During voyages on the HMS Beagle, Darwin carefully observed, characterized and categorized different populations that seemed to have arisen from common ancestors. One of the classic examples is that of the Galapagos finches. Finches on different islands, geographically isolated from each other, had specific variations that seemed to aid in survival on the particular island. The finches were similar to each other and all had similarities to the finches on the mainland of South America, yet all had specific adaptations that enabled survival in their particular area. This type of evolutionary change is called adaptive radiation.
This diagram from http://www.pbs.org/wgbh/evolution/library/01/6/image_pop/l_016_02.html
illustrates the finches that Darwin observed. All of the finches are believed to have arisen from a common ancestor, but evolved different characteristics due to environmental conditions and available food sources on different islands.
These observations, as well as, other data collected on numerous organisms led Darwin to the theory of natural selection as the mechanism for evolution.

To learn more about Darwin’s studies and theory, see: http://www.geo.cornell.edu/geology/GalapagosWWW/Darwin.html
For a short video about Darwin and his studies, see http://www.pbs.org/wgbh/evolution/library/11/2/e_s_2.html
Linneas, Darwin, and other early scientists classified organisms by comparing physical characteristics. While physical characteristics are still useful in classification, it is now generally agreed by scientists that the evolutionary history can be more useful and accurate in the organization and classification of organisms. Organisms can be grouped according to their shared evolutionary history. Organisms that have a recent common ancestor are more closely related than those that have a more distant common ancestor.
Phylogeny is the classification of organisms based upon their evolutionary history. Evidence used to explain and determine phylogeny includes fossils (see L.12.D.3) , biochemistry (see L.12.D.2) , genetics (see L.12.A.1) , and structure. Phylogenetic trees are used to illustrate evolutionary relationships. The following phylogenetic tree illustrates the relationship of several animals. For example, the following diagram indicates that salamanders and frogs are more closely related than mammals and turtles.
Figure from: http://www.med.nyu.edu/rcr/rcr/course/tree.gif
To learn more about phylogeny and its usefulness in classification see: http://www.tolweb.org/tree/learn/concepts/whatisphylogeny.html
and http://evolution.berkeley.edu/evolibrary/article/phylogenetics_01
Homologous structures are anatomical features of different organisms that have a similar appearance or function that are inherited from a common ancestor. The wing of a bird, the forelimb of a cat, and the arm of a human are homologies because they are structurally and functionally similar and they are inherited from a shared ancestor. The more homologies different organisms have, the closer they probably are genetically.

This figure illustrates homologous structures in the forelimbs of several animals.
Source: http://virtuallaboratory.net/Biofundamentals/lectureNotes/Topic1-5_Evo.htm
Analogies are anatomical structures that have similar form or function in different species that have no known common ancestor. For example, the wings of a bat and the wings of a moth are similar in shape and function, but are very different internally and the wings did not evolve from a shared ancestor.
For additional information and examples of homolgies and analogies, see: http://evolution.berkeley.edu/evolibrary/article/0_0_0/similarity_hs_01
Biological evolution is the best scientific explanation for how life on Earth has changed and how it continues to change. We do not understand everything about evolutionary relationships among organisms. The evolutionary history of an organism is determined based on current knowledge, evidence, observations, and testing, and as new data becomes available, our understanding of relationships between organisms will continue to be revised. DNA analysis and other molecular technology available today provide data and information which can be used in classification system. (See L.12.D.2) back to top
Performance Benchmark L.12.D.1
Students know organisms can be classified based on evolutionary relationships. E/S
1. Appearance Misconceptions
Students incorrectly think that if organisms look alike, then they must have a common evolutionary history. When asked to classify organisms, students use obvious physical features, rather than processes or genetic relationships.
Convergent evolution is the development of similar traits or characteristics by taxonomically different groups of organisms. Convergent evolution often occurs when two groups of organisms occupy similar niches. Just because two organisms may have developed a similar characteristic trait, it does not necessarily mean that they are closely related.
For examples, birds and bats both have wings, an adaptation that allows them to fly. However, bats and birds evolved independently of each other.

For a discussion of convergent evolution, go to http://www.pbs.org/wgbh/evolution/library/01/4/l_014_01.html
2. Natural Selection Misconceptions
Students incorrectly believe that adaptations and hence, natural selection occurs as an organism changes due to some need, desired use of function, or an environmental condition, and that this change is then automatically passed to their offspring.
This misconception was held by Lamarck in the 1800’s, who concluded that parents can pass acquired characteristics on to their offspring.
Students have difficulty understanding basic concepts of evolution such as natural selection. They don’t conceptualize that mutations often occur randomly and that some of these random changes are selected for because they help in the survival and reproduction of the organism.
To read more about Lamarck, see: http://www.pbs.org/wgbh/evolution/library/02/3/l_023_01.html
Evolution through natural selection occurs instead through variations and changes in DNA that occur naturally and randomly. If a particular mutation is found in an organism which enables the organism to better survive in its environment, the organism is more likely to live, and to reproduce (survival of the fittest). Because the animal was born with that change and that it is in the DNA of the organism, that DNA, and therefore the trait, can be passed on to the offspring. Over time, when a significant number of changes have occurred, a new species may develop. Mechanisms of evolutionary change include: mutation —changes in the DNA of an organism migration
—a group of organisms from a particular species may migrate to a new, geographically isolated area and begin interbreeding among themselves but not with the parent population genetic drif t
—normal variations that occur in the genes of organisms, related to mutations natural selection —the organisms most likely to live and reproduce will be the ones that pass on their traits
More information about evolution through natural selection can be found at: http://www.pbs.org/wgbh/evolution/library/11/2/e_s_4.html
3. Scientific Theory Misconceptions
Students incorrectly think that evolution is “just a theory.” Students think that a scientific theory is similar to a theory as used in everyday discussions, that is, a theory is just a guess or a hunch, or what one person thinks.
The common-every-day use of the word theory means a guess or a hunch. A scientific theory does not have the same meaning as this common every-day theory. A scientific theory is well substantiated, supported by facts, laws, and tested hypotheses. A scientific theory is an explanation based on observation, experimentation, and reasoning. It is recognized in the scientific community as a general principal that helps explain natural phenomena. Theories can be tested, modified, and at times, rejected as new information and scientific knowledge is acquired. Scientific theories are valid and provide a basis for exploring new questions.
Additional definitions of scientific theory can be found at, http://www.ncsu.edu/labwrite/res/res-glossary.html
For NSTA’s position statement on scientific theories see: http://www.nsta.org/positionstatement&psid=10
(scroll down to the section entitled: The Nature of Science and Scientific Theories).
4. Human Evolution Misconceptions
Students incorrectly think that evolution of humans means the humans evolved from monkeys.
A comparison of human to chimpanzee DNA shows about a 98% similarity indicating that there is a genetic and evolutionary link. However, one species did not evolve from the other species. Rather, about 5 million years ago, modern apes and humans had a common ancestor which was not ape, nor human, nor monkey.
For a brief explanation of the Man from Monkey misconception see #6 at this link: http://www.bio.ilstu.edu/Armstrong/misconceptions.doc
When teaching all of the L.12.D benchmarks, it is imperative to help students understand the process of science. Most misconceptions about evolution are directly related to the misunderstanding of how science works. When students understand the nature of science, they will understand how scientists have studied the process of evolution. As questions arise about a “supernatural” creation of Earth and the Universe, students who understand the nature of science will understand why supernatural forces cannot be studied as part of scientific processes.

Cells of all organisms contain deoxyribonucleic acid, or DNA, which contains the information that determines, and controls cellular functions. The building blocks or monomers of
DNA are called nucleotides. Each nucleotide consists of a phosphate group, a sugar (deoxyribose) and one of 4 nitrogenous bases. The nitrogenous bases are adeni ne, guanine, cytosine, and thymine. The nucleotides of DNA are often referred to by a letter, which represents the base: A, T, G, or C.
To learn more about the structure of DNA, see http://www.rothamsted.ac.uk/notebook/courses/guide/dnast.htm
(Click Image to Enlarge)
Figure 1. This diagram demonstrates the basic structure of DNA.
(from http://www.accessexcellence.org/RC/VL/GG/dna_molecule.html
)
Particular segments of the DNA are called genes, and it is a gene that codes for the synthesis of a particular protein. Proteins determine the characteristics of a cell. The DNA nucleotide sequence and, more specifically the genes, give an organism its specific characteristics. For example, there are genes in human cells that code for the color of eyes, hair, and skin. There are also genes that code for the production of hormones, digestive enzymes, insulin, and all of the other proteins produced by cells. Large organized molecules of DNA in cells are called chromosomes. Chromosomes consist of the genes, regulatory and other intervening sequences of nucleotides, and proteins that help in the packaging of the DNA. Different organisms contain different types, sizes and number of chromosomes. Even though the chromosomes are different between organisms, the basic chemical structure of the DNA is the same in all organisms.
Figure 2. This diagram illustrates the relationship between DNA, genes, and chromosomes. (from http://www.bbc.co.uk/schools/gcsebitesize/biology/ variationandinheritance/0dnaandgenesrev4.shtml
)

To learn more about the relationship between DNA, genes, and chromosomes see http://www.ncc.gmu.edu/dna/dna.htm
Although organisms in different classification groups (genus, species, etc.) may be completely different, the fundamental chemical make-up of DNA is the same in all organisms.
The building blocks, called nucleotides, that make up the DNA in all organisms are the same: A, T, G, and C. It is the sequence of these nucleotides, and ultimately the number, type, and sequence of genes that makes one organism different from another. The nucleotides that make up DNA can be compared to our alphabet. All words in our language and many other world languages are made up of groupings of the same 26 letters. DNA has only 4 “letters”, but because DNA is a very long molecule, the number of variations in DNA is enormous.
Figure 3. This figure illustrates a piece of DNA replicating.
(from http://www.ornl.gov/sci/techresources/
Human_ Genome/publicat/primer/fig4.html
)
Before a cell divides, the DNA in the nucleus replicates itself. The mechanism for the replication process is controlled via the same processes in all three domains of life
(Archaea, Bacteria, and Eukarya). It is not understood exactly how this replication process has remained in place for approximately 3.5 billion years during which life has existed on Earth.
For discussion of research that provides evidence of nucleus replication, see http://www.lbl.gov/Science-Articles/Archive/LSD-molecular-DNA.html
Two general types of reproduction occur in organisms, both requiring cellular replication. In asexual reproduction, a cell will copy its DNA, then through complex processes called mitosis and cytokinesis, will split into tw o cells, each having a copy of the original cell’s DNA. In sexual reproduction, specialized sex cells will copy their DNA, then through complex process called meiosis and cytokinesis, will split into up to four cells, each containing half of the DNA of the original.

(Click Image to Enlarge)
Figure 4. This diagram illustrates what occurs with the DNA (chromosomes) during mitosis and meiosis.
Note that before either division, the DNA in the cells replicate. (from: http://www.accessexcellence.org/RC/VL/GG/comparison.html
)
Through many replications, changes in the DNA can occur. However these changes result only in different sequences of the nucleotides. The actual types of nucleotides do not change. As stated above, the DNA of all organisms is composed of the same chemical building blocks.
To learn more about mitosis and meiosis, see http://www.biology.arizona.edu/cell_bio/tutorials/cell_cycle/main.html
and http://www.biology.arizona.edu/cell_bio/tutorials/meiosis/main.html
.
With modern technology, scientists are able to determine the sequence of nucleotides in pieces of DNA. Using this technology, scientists have been able to study and compare
DNA of many organisms and the similarity between DNA samples is used to determine relationships between organisms. Because biological evolution involves genetic changes
(mutations) over time, the evolutionary relationship of organisms can be determined by comparing DNA. Different species with very similar DNA more recently descended from a common ancestor than did species with very different DNA. There is only about 0.1 percent difference in the DNA among different humans. The DNA of the species closest to humans, the chimpanzee is about 98 percent identical to that of humans.
To read about one example of how DNA and other scientific evidence has been used to determine the evolutionary relationship between different species of similar organisms
(birds), see http://www.stanford.edu/group/stanfordbirds/text/essays/Birds,_DNA.html
Because DNA codes for the production of proteins, comparison of proteins between species also provides evolutionary relationships between organisms. Cells of organisms that more recently shared a common ancestor will have a greater similarity in proteins produced than organisms that are more distantly related.
To read more about how molecular biology and DNA technology are used to determine relationships between organisms, see http://books.nap.edu/html/creationism/evidence.html
. This article from the National Academies of Science discusses various scientific studies and disciplines that support the theory of biological evolution.

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Performance Benchmark L.12.D.2
Students know similarity of DNA sequences gives evidence of relationships between organisms. E/S
1. Students do not understand that the chemical makeup of DNA is the same in all living organisms.
Molecules and basic life processes are common throughout all living organisms. If students successfully learn about basic biochemistry and cellular functions, it should be easy to help them understand the significance of DNA in identification and interrelationships of organisms. The chemical structure of DNA is the same in all organisms. Every molecule of DNA contains the same building blocks, or monomers, called nucleotides. The differences between organisms result from different numbers and orders of nucleotides. James Watson and Francis Crick were the first to describe the structure of DNA in 1953. Since then, the DNA of many organisms has been studied and the molecular basis for inheritance in all organisms has been confirmed.
To review the structure of DNA, see http://molvis.sdsc.edu/dna/index.htm
2. Students do not understand how a genetic change (change in DNA) can result in a phenotypic change.
DNA provides the directions, or the blueprint for protein production in cells. The order of nucleotides in specific segments of DNA directs the production of proteins. As students learn about protein synthesis, they will learn how the information in DNA gets translated into a series of amino acids which then eventually becomes protein. When teaching genetic change, mutations, and evolution it may be necessary to review the process of protein synthesis, emphasizing what happens when a change or a mutation in the DNA occurs.
For a good, easy to understand review of protein synthesis, see http://www.lewport.wnyric.org/JWANAMAKER/ animations/Protein%20Synthesis%20-%20long.html
.
A common example of the effects of a mutation is the production of hemoglobin, an oxygen carrying protein found in blood. “Defective” hemoglobin is produced when a different nucleotide is substituted for one specific correct nucleotide in the DNA segment coding for hemoglobin production. This one tiny change results in the substitution of one amino acid in a long chain of amino acids. This change causes a phenotypic change: producing hemoglobin that is not as effective at transporting oxygen. Mutations in DNA can occur due to normal cellular processes, environmental conditions, errors during DNA replication, or randomly by chance.
Just as a mutation in the DNA coding for hemoglobin can cause a phenotypic change, a mutation in any piece of DNA that codes for a protein can result in a phenotypic change in the cell and that organism. Of significance to evolution is when a mutation occurs in a gamete (sex cell) because that mutation will affect traits in future generations.
For an easy to follow discussion of mutations and evolution, see http://www.makingthemodernworld.org/learning_modules/biology/01.TU.03/?section=7
3. Students incorrectly think that if organisms look alike, then they must have common evolutionary decent.
When asked to classify organisms, students use obvious physical features, rather than processes or genetic relationships. Convergent evolution is the development of similar traits or characteristics by taxonomically different groups of organisms. Convergent evolution often occurs when two groups of organisms occupy similar niches. Just because two organisms may have developed a similar characteristic trait, it does not necessarily mean that they are closely related. For examples, birds and bats both have wings, an adaptation that allows them to fly. However, bats and birds evolved independently of each other.
For a discussion of convergent evolution, go to http://www.pbs.org/wgbh/evolution/library/01/4/l_014_01.html
When teaching all of the L.12.D benchmarks, it is imperative to help students understand the process of science. Most objections and misconceptions about evolution are directly related to the misunderstanding of how science works. When students understand the nature of science, they will understand how scientists have studied the process of evolution. As questions arise about a “supernatural” creation of Earth and the Universe, students who understand the nature of science will understand why supernatural forces cannot be studied as part of scientific processes.
The study of fossils is called paleontology. The study of rocks and land formations is called geology. By combining paleontology and geology, much can be learned about the history of Earth and the history of life on Earth. Fossils are the remains of once living organisms. Most fossils are remains of the hard parts of organisms that are no longer alive

(extinct species). The most common types of fossils form when shells, bones, or other parts of organisms are rapidly covered with layers of sediment. As additional sediment is deposited, the organism’s remains become compacted by the additional weight of the new sediment. Water in the soil seeps into the original bones and other solid remains, gradually replacing the original components of the once-living organism with minerals found in the water. Fossil formation occurs over a long periods of time, as the minerals in the organism are gradually dissolved and replaced to form a rock-like material, as spaces in the original organism are filled in with minerals.
To learn more about how different kinds of fossils form, see http://www.discoveringfossils.co.uk/Whatisafossil.htm
Fossils are found in sedimentary rocks. Sedimentary rock forms in layers. In most cases, the lowest layer is the oldest. Successive layers of sedimentary rock contain different groups of fossils. The different types of fossils in the different layers provide evidence that changes have occurred in living things through time. For additional information on the fossil record and how it contributes to our understanding of evolution, see “Evolution and the Fossil Record” found at http://www.agiweb.org/news/evolution.pdf
For additional information concerning strata, fossils, and geologic structure see Benchmark E.12.C.1
Geologists today are able to establish the relative age of the various layers of the earth’s crust based on their position and the fossils they contain. Both relative and absolute age of various rock layers can be determined using evidence provided in that layer, and the layers found immediately above and below. Fossils and geological formations can be used to provide relative ages of rock layers. For example, if the same type of fossil is found at two locations that are a great distance apart, the fossil provides evidence that the rock layers are probably of a similar age. Figure 1 (below) shows Index Fossils that are used to help establish the relative age of various rock formations.
Figure 1. Diagram of Index Fossils by Geologic Age. For more information as to how fossils are used to determine relative ages of rock layers see http://pubs.usgs.gov/gip/geotime/fossils.html
Using radioactive isotope half-life knowledge, absolute age of rocks can be determined (Figure 2)
Figure 2. Diagram of the relative amount of a radio isotope left in a sample after 3 half-lives.
(From: http://anthro.palomar.edu/time/time_5.htm
)

The relative concentration of a radio isotope to its daughter products can be used to help determine the absolute age of the strata, or fossil in question.
For further explanation of radiometric, or absolute dating, see the following sites: http://lilt.ics.hawaii.edu/belvedere/materials/Mass-Extinctions/Raddate.htm
, http://www.agiweb.org/news/evolution/datingfossilrecord.html
or http://pubs.usgs.gov/gip/fossils/numeric.html
It is estimated that our earth is approximately 4.5 billion years old. The first life (prokaryotes) probably appeared about 3500 million years ago (3.5 billion years ago). When the age of the rock layers are known, any fossils found in those layers can be considered the same age as the rock. Thus if a fossil is found in a rock layer that is known to be 100 million years old, then it is known that the fossilized organism lived (and died) about 100 million years ago.
Different types of fossils are found in different aged layers of rock. Therefore, the fossil record supports evolutionary theory by providing evidence that organisms that have lived in the past did change over time. If we examine fossils found in various layers of rock, and look at progressively older layers, we can see that there is a layer below which no human fossils are naturally found. As we progress backward in time, we will eventually see a layer below which no fossils of birds, no mammals, no reptiles, no fish, and eventually, no animal of any kind is found. This is evidence that the kinds of plants and animals, and other organisms have changed over time and is called the Law of Fossil
Succession (Figure 3 and 4).
Figure 3 Stratigraphic ranges and origins of some major groups of animals and plants
(from, http://pubs.usgs.gov/gip/fossils/succession.html
).
To learn more about the Law of Fossil Succession, go to http://pubs.usgs.gov/gip/fossils/succession.html
).
Figure 4. This diagram from the American Geological Institute illustrates how different fossils have been found in different aged layers of the earth.
The illustration is from http://www.agiweb.org/news/evolution/evolthrutime.html
Natural selection is considered a mechanism of evolution. Charles Darwin gathered evidence on many different organisms during voyages in the 18
00’s. Careful study and characterization of his data led Darwin to his theory of evolution through natural selection. His theory was based on four premises:

1. Variations exist among individuals within the same species.
2. All organisms produce more offspring that are able to survive.
3. Competition for space, food, other survival needs leads to the elimination of some organisms of each population.
4. The organisms that have variations which enable them to survive within their environment and through competition, are the ones most likely to survive and reproduce, thereby passing their characteristics on to their offspring (survival of the fittest, or natural selection).
For more information on Darwin’s theory, go to http://www.agiweb.org/news/evolution/darwinstheory.html
Fossils provide evidence that divergent and convergent evolution has occurred. Divergent evolution is when two or more related species become more and more dissimilar to each other. The species involved had a common ancestor, but due to natural selection and adaptations to different environments, the species became increasingly different from each other.
Convergent evolution occurs when two or more unrelated species develop similar characteristics as they adapt to similar environments.
Figure 5. Illustrates convergent evolution of some large vertebrate animals. The shark, ichthyosaur, and porpoise evolved separately, but have similar characteristics which enable them to live in the water and to be efficient predators (from: http://bio-ditrl.sunsite.ualberta.ca/detail/?P_MNO=1800 ).
To learn more about divergent and convergent evolution see http://bioweb.cs.earlham.edu/9-12/evolution/HTML/converge.html
To learn more about the link between paleontology, geology and evolution, see: http://www.agiweb.org/news/evolution/paleo_geo_evol.html
The information contained within this web site can be viewed as is, printed as a booklet, or ordered from the Website.
There are gaps in the branches of the fossil records of life. Gaps exist in the fossil record, partly because plants, microorganisms, and soft shelled organisms (majority of marine animals), are not likely to fossilize. Even hard bodied organisms do not frequently fossilize. In addition, changes in the land (erosion, metamorphosis, geological events) can destroy fossils if they were present. However the fossil record does provide significant evidence of evolution and of the history of life on earth. back to top
Performance Benchmark L.12.D.3
Students know the fossil record gives evidence for natural selection and its evolutionary consequences. E/S
1. Students incorrectly believe that individuals adapt to their environment.

Students incorrectly believe that adaptations occur in individuals in response to changes in their environment or the needs of the individual, rather than adaptation occurring on the species level and being changes in a population that accumulate over time. Students think that adaptations and hence, natural selection occurs as an organism changes due to some need, or changes in the environmental conditions, and that this change is then passed to their offspring.
Students have difficulty understanding basic concepts of evolution such as natural selection. They don’t conceptualize that mutations often occur randomly and that some of these random changes are selected for because they help in the survival and reproduction of the organism. Rather, students often believe that new variations occur due to some need, use of a function, or environmental condition, and that once an organism has acquired a characteristic, the change will be passed on to the offspring. This misconception was held by Lamarck in the 1800’s, who concluded that parents can pass acquired characteristics on to their offspring.
To read more about Lamarck, see: http://www.pbs.org/wgbh/evolution/library/02/3/l_023_01.html
2. Students incorrectly believe evolution through natural selection occurs through variations and changes in DNA that occur naturally and randomly.
If a particular mutation is found in an organism which enables the organism to better survive in its environment, the organism is more likely to live, and to reproduce (survival of the fittest). Because the change that occurred was in the DNA of the organism, that DNA, and therefore the trait, can be passed on to the offspring. Over time, when a significant number of changes have occurred, a new species may develop. Mechanisms of evolutionary change include: mutation
—changes in the DNA of an organism migration
—a group of organisms from a particular species may migrate to a new, geographically isolated area and begin interbreeding among themselves but not with the parent population. genetic drift
—normal variations that occur in the genes of organisms, related to mutations. natural selection
—the organisms most likely to live and reproduce will be the ones that pass on their traits.
More information about evolution through natural selection can be found at: http://www.pbs.org/wgbh/evolution/library/11/2/e_s_4.html
3. Students incorrectly believe that fossil evidence does NOT support evolution because there are too many “missing links” or missing transitional fossils.
A transitional fossil is one that links a more modern organism with a more primitive organism. A transitional fossil would have characteristics in common with both the primitive organism and the more modern organism. Transitional fossils are often called “missing links.” According to evolutionary theory, however, all organisms are in transition and therefore a specific “missing links” may not actually exist as organisms evolve. In addition there are many organisms that have existed in the past for which no fossils will ever be found, so there will always be gaps in the fossil record. This is because conditions required for fossilization to occur are not always present when on organism dies. Many examples of transitional fossils do exist, providing evidence that species do transition. Several examples are listed below, with links for additional information.
Reptiles to birds: http://www.agiweb.org/news/evolution/examplesofevolution.html
http://www.talkorigins.org/faqs/faq-transitional/part1b.html#bird http://www.fossilmuseum.net/paleo/paleonews/Archaeopteryx.htm
Terrestrial mammals to whales: http://www.agiweb.org/news/evolution/examplesofevolution.html
http://news.bbc.co.uk/1/hi/sci/tech/1553008.stm
http://www.talkorigins.org/features/whales/
Horse evolution http://chem.tufts.edu/science/evolution/HorseEvolution.htm
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1159167
When teaching all of the L.12.D benchmarks, it is imperative to help students understand the process of science. Most objections and misconceptions about evolution are directly related to the misunderstanding of how science works. When students understand the nature of science, they will understand how scientists have studied the process of evolution. As questions arise about a “supernatural” creation of Earth and the Universe, students who understand the nature of science will understand why supernatural forces cannot be studied as part of scientific processes.
Extinctions occur “often” in evolutionary history. Scientists estimate that more than 90% of the species that have lived on earth are probably extinct. Most extinctions occur due to selective nature of the species. That is, if an organism does not have or does not develop adaptations that allow it to flourish in an environment, that species will eventually die out. These are called background extinctions. The fossil record provides evidence that background extinctions regularly occur throughout time. However, the number of species which have become extinct at any one point in time is relatively low. Scientific studies show another type of extinction in which massive numbers of species become extinct in a short period of time. These are called mass extinctions. There are 5 recognizable periods of mass extinction in the earth’s history. There are several theories as to the cause of the mass extinctions, most of which hypothesize that major climatic and environmental changes occurred globally. These changes were most likely due to impact of extraterrestrial object or extreme geological activity such as many active volcanoes and crustal movements. Many species that were not adapted to the resulting changes, died out. The following sites provide more information about both mass and background extinctions: http://www.pbs.org/wgbh/evolution/library/03/2/l_032_01.html

http://www.earth.rochester.edu/ees207/Mass_Ext/higgins_mass2.html
http://sciencebulletins.amnh.org/biobulletin/biobulletin/story985.html
One of the largest mass extinctions was the Permo-Triassic (PT) extinction which occurred between the Permian Period and the Triassic Period about 248 million years ago.
Based upon fossil records and other evidence, it is estimated, that up to 90 percent of all existing species were lost during the P-T extinction. To learn more about the P-T extinction, see http://www.earth.rochester.edu/ees207/Mass_Ext/higgins_mass4.html
The most familiar mass extinction is associated with the demise of the dinosaurs. This Cretacious-Tertiary (KT) extinction occurred about 65 million years ago, between the
Cretaceous Period of the Mesozoic Era and the Tertiary Period of the Cenozoic Era. To learn more about the KT extinction, see http://www.earth.rochester.edu/ees207/Mass_Ext/higgins_mass3.html
Most scientists believe that the KT extinction was most likely caused by the impact of a large asteroid. Evidence of this asteroid includes deep sea core samples taken near the suspected impact area. The core samples provide evidence of ash and ejecta material as well as distinctive fossil variants above and below the ash layer.
Figure 1. This is a diagram of a deep sea core that supports the theory of an asteroid impact on earth at the KT time boundary. Diagram is from: http://www.nmnh.si.edu/paleo/blast/index.html
Other evidence of asteroid impacts near the K-T time boundary includes the presence of an unusually high concentration of Iridium in layers of clay at the K-T boundary.
Iridium’s sources are cosmic dust and the earth’s core. The high Iridium concentration therefore indicates that either an asteroid struck the earth or a massive volcanic eruption occurred at that time. The iridium layer was first discovered by Luis and Walter Alvarez in Italy in the 1970’s, but has also been observed in several other sites around the world.
The exact effects of an asteroid impact on life are debated by scientists. To learn more about the uncertainty of the cause of the KT extinction, see http://www.ucmp.berkeley.edu/diapsids/extinction.html
The following graph shows peaks of invertebrate extinctions over the last 600 million years. As the graph shows, there have been 5 major peaks indicating mass extinction episodes.

Figure 2. A graph of invertebrate extinctions over the last 600 million years.
The mass extinctions appear as periodic peaks rising above the background extinction levels. This data is from the work of D. M. Raup and J. J. Sepkoski.
From, ( http://www.enchantedlearning.com/subjects/dinosaurs/extinction/ )
This figure can be seen at http://www.enchantedlearning.com/subjects/dinosaurs/extinction/
Background extinctions can occur as a result of many things. The extinction of a species can occur through the process of evolution. Extinction by natural causes may be due either to actual death of a species or due to evolution of the species into one or more different species. Organisms become new species through modification over time. If the ancestral species disappears and is replaced by the new species, extinction has occurred. Evidence from the fossil records substantiates that many species have become extinct and new species have developed over time.
Many scientists believe that Earth may be in a 6th mass extinction phase, as many species are going extinct every day. Humans are not the sole cause of extinctions. However, since our appearance on earth, humans have had an impact on extinction of several species. This has occurred via hunting, habitat destruction, and other environmental impacts.
For more information on the human impact on extinctions, go to http://www.nmnh.si.edu/paleo/geotime/main/index.html back to top
Performance Benchmark L.12.D.4
Students know the extinction of species can be a natural process. E/S
1. Humans cause all extinction misconceptions
Students incorrectly believe that humans have caused all extinctions. Although humans do play a role in modern extinctions due to alteration and destruction of habitat, pollution, overexploitation, and disease there are other causes that contribute to the extinction of species. Some scientists believe that we may be in the midst of a sixth period of mass extinction. The rate of extinction is currently higher than the average background extinction rates, and some of this may be due to human influence. However humans are not the only factor affecting extinctions today. In fact, most extinctions that we know about today, occurred prior to the appearance of humans. As extinctions have occurred naturally throughout the history of life, they continue naturally today.
To learn how several esteemed scientists responded to questions about whether or not we are in the midst of mass extinction and how humans might be involved, see: http://www.pbs.org/wgbh/evolution/extinction/massext/index.html

2. Dinosaur extinction represents the failure of an entire branch of life
Although extinct now, dinosaurs represent one of the greatest successes of adaptation and survival. They existed on Earth for more than 150 million years, which is longer than any other land animal. Birds evolved from dinosaurs. To learn more about the success of dinosaurs, see http://www.nmnh.si.edu/paleo/dinosaurs/index.htm
Biodiversity refers to the variety of organisms and their genetic diversity on our planet. Today over 1.5 million living and 300,000 extinct species have been named and described. The actual number of species on our planet is not known, but some believe it may be at least 15 to as many as 30 million species. With this tremendous amount of diversity the question becomes “Why or how are there so many forms of life on our planet?” The answer to this question is evolution. In 1973, Theodosius Dobzhansky wrote that “Nothing in biology make sense except in the light of evolution.” Today biologists use the process of evolution to explain the diversity of life on our planet.
Evolution or descent with modification explains how the gene pools of species or populations change over time leading to the development of new species and therefore diversity of life. Biologists have described several mechanisms that lead to changes in gene pools over time. They include: a) Mutations b) Gene recombination c) Gene flow d) Genetic drift e) Natural Selection
Mutations refer to the genetic errors that accumulate in the genes within species and/or population s. Mutations that prove useful or allow organism to “better adapt” to their environment are rare and their accumulative effect is minor compared to the other factors, nevertheless mutations do allow for entirely new genes or DNA instructions to occur.
Recombination of genes in a sexually reproducing population is more important than mutations in producing variations that make adaptation possible. In sexual reproduction, individuals with a different array of genes are brought together. In this way some individuals in the population may be better adapted to the environment than others.
Gene flow results in the movement of genes between populations. Genes maybe introduced or removed from populations by immigration or emigration. The effect is to change the genetic composition by the addition or removal of genes. As compared to other factors, gene flow has a minor effect on gene pool composition.
Genetic drift results in the chance change in the gene pool. Genetic drift involves the random transfer of alleles from one generation to the next. This change can occur by what is known as a bottleneck or founder’s effect. In both cases alleles are passed on to the succeeding generations as a matter of chance rather than “fitness”.
A bottleneck occurs where a large population of organisms is reduced to a very few, which in turn grows back into a much larger population. The northern elephant seal is often used as an example of a bottleneck. Prior to 1890 there were tens of thousands of these seal along the Pacific Ocean coastline from Baja California to Alaska. However these animals were hunted to near extinction with less than 100 (some estimates being lower than 20) individuals remaining in 1890. Today upwards of 60,000 or more survive. Thus all northern seals today can trace their inheritance to those few surviving individuals of 1890. Examination by researchers of 24 gene loci in a representative sample of seals has shown no variations. Each of these genes has only one allele. When compared to the closely related southern seal no such similarity occurs. Other cited examples of bottleneck include the North American bison and the South African cheetah.
To learn more about genetic drift go to http://evolution.berkeley.edu/evosite/evo101/IIIDGeneticdrift.shtml
To observe a simulation of genetic drift go to http://www.biology.arizona.edu/evolution/act/drift/drift.html
Founder’s principle occurs where a statistically small population from an established population migrates and settles in a new area. The founder effect is likely responsible for near absence of blood group B in American Indians, whose ancestors arrived from Asia about 10,000 years ago. Northern Asian populations today have frequencies of blood type B ranging from 15 to 20%. More recent examples of founder’s principle are seen in religious isolates like the Dunkers and Old Order Amish of North America where their blood group gene frequencies are quite different from those in the surrounding populations, both in Europe and in North Ameri ca.
To learn more about blood type frequencies go to http://anthro.palomar.edu/vary/vary_3.htm
Next to genetic drift, natural selection has the greatest effect on the gene pool of a population or species. Nature produces variations within members of the same species or population which can resu lt in uneven advantages in their ability to survive. This is sometimes referred to as the “survival of the fittest”. Those individuals that have the greatest ability to survive also have a greater chance of reproductive success (will reproduce and leave of fspring) and therefore will pass their “better adapted” traits (or genes) to their offspring. Over time this can result in the change in the gene pool of a species. This process can lead to enough change that over time a new species appears. New species means increased biodiversity.

While natural selection accumulates and maintains favorable genotypes in a population it initially acts upon the phenotypes of the individuals rather than their genotypes. This can be illustrated in the three types of natural selection called directional, stabilizing and disruptive. In the 1970 Peter and Rosemary Grant were able to show a directional change in the beak size of the medium ground finch Geospiza fortis. Over a several year period the Grants were able to document an increase in beak size in response to drought and reduction of seeds these bird feed upon. While the size of the beak has been shown to be controlled by a gene, initially birds with larger beaks were favored by natural selection over birds with smaller beaks.
To learn more about the Grant’s work go to: http://www.pbs.org/wgbh/evolution/library/01/6/l_016_01.html
To learn more about the three types of natural selection go to: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Evolution.html
To learn more about natural selection go to http://evolution.berkeley.edu/evosite/evo101/IIIENaturalSelection.shtml
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Performance Benchmark L.12.D.5
Students know that biological evolution explains the diversity of life. E/S
1. Students incorrectly assume that evolution produces increasing complexity or more “perfect” organisms.
While natural selection tends to reduce the number of less fit organisms in a population, for evolution “good enough” is good enough. In nature, perfection is not necessary for survival. Some groups of organisms like sharks, fungi and mosses have changed little over the past 100 million years. On the other hand dinosaurs resided on earth for over
150 millions, but are no longer here. What is “better” at one time does not mean “better” at another time.
Vestigial structure can point to the imperfect nature of life on our planet. Defined as organs that have reduced or no apparent function, these structures can present problems for some organisms in which they are found. Take the human appendix as an example. In plant eating vertebrates, the much larger appendix serves to help in the digestion of plant material. While in humans seems to have no apparent function. And as a testament to it apparent loss of functions doctors in the United States performed approximately
300,000 appendectomies in 2000.
To learn more about this topic review the essay about the “less than perfect” eye at http://www.pbs.org/wgbh/evolution/change/grand/index.html
Also view the following webpage to see why it might be to a cheetah advantage to be a faster runner http://evolution.berkeley.edu/evosite/evo101/IIIE6aFitenough.shtml
In some cases “imperfection” is a better adaptation as in the case of malaria and sickle-cell anemia. For a discussion of this, go to http://evolution.berkeley.edu/evosite/evo101/IIIE6bBadgenes.shtml
2. Students mistakenl y assume that organisms can “will” themselves to change or they change because of an inner “need” to change and survive.
In the early 1800’s Jean-Baptiste Lamarck developed one of the earliest biological explanations for biological evolution. In his explanation, organisms could change because of the “need” to survive. Giraffes developed longer neck to satisfy the need to get leaves from trees. Among populations variations occur in gene pools. Either organisms have gene adaptations that are good enough to allow them to survive and reproduce or they do not. Whether genes are good enough for survival are determined by the requirement of the environment.

http://evolution.berkeley.edu/evosite/misconceps/IEneeds.shtml
To learn more about why Lamarck ideas are not valid explanations for evolutionary change go to http://necsi.org/projects/evolution/lamarck/webelieve/lamarck_webelieve.html
Although Larmark and Darwin both believed that the environment plays a role in shaping the evolution of organisms, their ideas on what other factors produced change over time differed.
To view a lesson that illustrates the difference between Lamarck and Darwin go to http://www.indiana.edu/~ensiweb/lessons/lam.darw.html
3. Students incorrectly assume organism can change by the use or under use of bodily structures or abilities.
At the time Lamarck developed his ideas, biologist lacked a basic understanding of how traits/genes were passed on. Changes that occur in somatic cells, such as those in the arms, legs or neck are not passed on. Despite all of his body building, Arnold Schwarzenegger will not pass his large muscles to his children. Only changes to genes in the gametes will be passed to his off-spring and such is the case with all living organisms.
Offspring inherit traits from parents, but the genes for these traits are found in the gametes. Any change in somatic or non-sex cells is not passed on to the offspring. A review of meiosis may be helpful at this point.
To learn more about Lamar ck’s ideas go to: http://evolution.berkeley.edu/evolibrary/article/_0/history_09
4. Students mistakenly assume that life changes by chance alone.
Chance does play a role in altering gene pool composition, random mutation and genetic drift can add or remove genes from a population. Yet, natural selection will ultimately determine which traits are “best adapted” for survival. Organisms that use camouflage as a protection from predators survive depending how “good” their camouflage is or is not. Those with the better camouflage survive in greater number and pass on their traits. Over time these “better adapted” individuals may increase in numbers.
In everyday language “chance” is often associated with fortune, luck or an usual event. In evolutionary biology a “chance” event is simply an event which is not caused by the organism itself. Nor is it an event which we could have predicted.
To learn more about evolution and chance go to http://www.talkorigins.org/faqs/chance/chance.html
5. Students incorrectly assume that evolution is “just” a theory and therefore is not a valid explanation for diversity of organisms on our planet.
This occurs because students have failed to understand the difference between the scientific meaning of theory and the everyday pedestrian use of the term. Scientific theories are explanations which are based on lines of observable evidence, enable valid predictions, and have been tested in many ways.

To review the nature and process of science go here http://evolution.berkeley.edu/evosite/nature/index.shtml
The idea of evolution (organisms change over time) was not a new theory even in Darwin’s time. What was lacking was an underlying mechanism for biological evolution. The idea of natural selection, first introduced by Darwin in the seminal work “On the Origin of Species” has grown and been modified overtime with the increase in understanding of biological concepts. Such discoveries include the discovery of DNA, increased understanding of genetics and the role DNA, RNA and proteins play in the expression of inherited traits.
Charles Darwin was a naturalist, meaning he was a trained observer of nature and natural history. From 1831 to 1836 he was employed as the naturalist aboard the H.M.S.
Beagle for a British science exploration voyage. During his time aboard, Darwin made and recorded many observations of the variations he saw within and between species. It was these observed differences that lead him to the idea that natural selection was the mechanism behind evolution.
Figure 1. Charles Darwin (from http://www.lucidcafe.com/library/96feb/darwin.html
)
The premise behind Darwin’s original work was the observed morphological similarities between some animals, and the obvious differences between others. This, aided with his understanding of selective breeding, gave him the idea that organisms could change over time without the influence of human i nterference.
Figure 2. Components of Natural Selection
(from http://evolution.berkeley.edu/evosite/evo101/IIIE6Nonrandom.shtml
)
The most well known example of natural selection is the malanism of the peppered moth during the industrial revolution in England. We will utilize this example throughout our discussion to describe the key factors in Darwin’s theory of natural selection.
Before the industrial revolution, the dominant form of the peppered moth was a lighter cream color with black s peckles. This coloration was an adaptation to the lighter colored trees they inhabited. There was an alternate form, the “carbonaria” form. This form is a darker color with a few white speckles. This alternate form was more susceptible to predation on the lighter colored trees. With the industrial revolution came large coal burning that caused the trees to turn to a darker color due to the build-up of soot on their trunks. When this happened the lighter colored moths were more exposed, and more susceptible to predation. With this increase in predation came a decline in the dominant cream colored form, but an increase in individuals with the darker coloring. Thus the lighter members of the population declined over time.
Natural selection has several tenets or underlying concepts that allow for it to be a mechanism for evolution.

Figure 3. Peppered Moths
(from http://www.bbc.co.uk/schools/gcsebitesize/science/images/bi06001.jpg
)
1. There is variability in a population.
In other words there are differences in phenotypes or appearances of the individuals within a population. In the peppered moth example the variation in the body color of the moths was variability in the population.
2. Not all individuals in the population reproduce. a. Not all individuals have the same fitness . Some groups die before they reproduce. Death can be from competition or unfavorable environmental conditions.
In our peppered moth example the moths with the light coloring originally were better suited for their environment and so therefore had greater fitness as they survived to reproduce and pass their genetic traits to their offspring. However, once the industrial revolution caused the tree color to change to black, the lighter colored moths no longer had greater fitness than the darker colored moths and so therefore fell to predation.
Figure 4. The Process of Natural Selection
(from: http://www.globalchange.umich.edu/globalchange1/ current/lectures/selection/selection.html
) b. Some traits (genotypes) confer an advantage of some sort to the individual, making better suited to their environment. (It is important to note that what may be better in one environment may not be in another environment, so the fitness of a genotype is dependent upon what environment the population lives in.)
3. Organisms produce more offspring than can survive to reproduce.
Take frogs for example. Frogs lay t housands of eggs. Not all of those eggs hatch as some are eaten, some dry out etc… Of the eggs that do hatch some survive to become

adult tadpoles (again predation and environmental factors can limit the number that live to reproductive age). The tadpoles undergo metamorphosis and form adults. Of the adults only some will survive to reproductive age (they have a higher fitness).
4. The variability in individuals is heritable. The traits of the surviving individuals in the population can be inherited by their offspring.
The traits that allow for survival become more numerous in the population, and eventually that characteristic will become the more prevalent form. Understand that Darwin lived long before the discovery of DNA (See L.12.A.1, & A.2) so had no genetic basis for his ideas of natural selection, they were derived from his observations of species throughout his travels and other life experiences. Although Mendel and Darwin lived at the same time, Darwin had no idea of the research Mendel was doing (See L.12.A.5). The ideas of mutation as a mechanism for introducing variation within a species is a relatively new idea, that has occurred in the past few decades.
Scientists now understand that random mutations within the genome (the genes that make up a species DNA) of an organism can be beneficial and are the source of new traits.
It is important to understand that the mutations are RANDOM, and can occur in different regions of the DNA sequence. If the mutation occurs in a non-coding portion of the
DNA, it will often not have a detrimental effect on the organism. If the mutation occurs in a coding region of the DNA, it can be lethal or detrimental mutation or it can introduce a new beneficial gene. In other words, not all genetic mutations are beneficial. In fact a majority of mutations do not allow for the survival of the individual to reproductive age.
A great modern example of natural selection is the apparent immunity of some individuals to HIV. Essentially individuals that had genetic mutations in a particular gene, called
CCR5-delta32, have immunity upon repeated exposure to HIV. It is now believed t hat these individuals with the mutant gene are survivors of a bottlenecking event… the bubonic plague.
Further detail about mutations can be found in the TIPS L12D5 performance benchmark .
For more information on immunity of some individuals to HIV, go to http://anthro.palomar.edu/synthetic/synth_4.htm
Remember that a bottlenecking event is an event that limits the number of individuals that reproduce (or are able to reproduce) and so therefore only the traits those individuals possess are found within the gene pool. These events can be caused by an isolation of some individuals from the original population, or the events can be caused by some catastrophe where the original gene pool is drastically reduced by massive death.
Figure 5. Genetic Drift
– Bottleneck Effect.
(from http://biology.unm.edu/ccouncil/Biology_203/
Summaries/PopGen.htm
)
In contrast to natural selection, artificial selection is driven by humans rather than nature. Artificial selection occurs when humans breed populations together to produce offspring with desired characteristics. The classic example of this is the differential breeding of wolves to produce a very large variety of canine subspecies. If you look at the over 400 different breeds of domestic dogs, it is obvious that they have similar ancestry. They are all obviously “dogs,” but each subspecies has characteristics that make it unique. These variations, rather than selected for naturally, were selected for by man. Humans have selected certain characteristics within one or a few individuals and bread them together in the hope that the offspring will possess the desired traits.
The problem with selective breeding is that it does not allow for other genes or traits to be introduced into the population. Thus the only genes within the gene pool are those that were within the original breeding population. If mutation occurs, they have the potential to be handed down to the next generation and all further generations. Thus problems like hip dysplasia can become common in certain subspecies of dogs. back to top
Performance Benchmark L.12.D.6

Students know the concepts of natural and artificial selection. E/S
Much of the following information is taken from an article that was published in the Journal of Research in Science Teaching in 1990. The authors discuss common misconception student have about natural selection and the role it plays in evolution.
Bishop, B.A. & Anderson, C.W. (1990). Student conceptions of natural selection and its role in evolution. Journal of Research in Science Teaching 27(5) 415-427.
1. Students mistakenly believe that nature
“needs” a change to occur.
One of the main misconceptions present in students is the idea that the environment creates a “need” for changes in the organism’s characteristics. Nature does not “need”.
While genetic mutation is random, the idea of natural selection is that those individuals with beneficial traits or a higher fitness for the given environment are the ones that survive. The organism does not develop a characteristic based on the need for a characteristic within the population; it is based on genetic variation and fitness over several generations.
Figure 6. Evolution Cartoon (from: http://evolution.berkeley.edu/evosite/evo101/IIIE6Nonrandom.shtml
)
2. Species Adaptations are Heritable: Students misunderstand the scientific concepts of adaptations and why something is heritable.
Another misconception that students hold is that an organism can adapt to their environment and hand that adaptation down to their offspring. It is important for students to understand that only variations that are herit able will be handed down from one generation to the next. If the organism develops a characteristic in it’s lifetime, it is not going to be heritable if it is not handed down in the gametes… it has to be part of the organisms genome to be passed on to the next generation.
For more information on this see: http://www.zi.biologie.uni-muenchen.de/evol/Evobio/Evo4-Summary.pdf
This is a very Lamarckian idea that orga nisms adapt to need rather than those that are more “fit” for their environment surviving because they have a selective advantage over other organisms that possess traits that are NOT fit for the environment. In other words only those organisms that survive can contribute to the gene pool of future generations.
Part of the reason for this misconception is the scientific understanding of the words adapt and adaptation, and the everyday usage of those terms. Often, they are not synonymous. The scientific definition of the word adaptation means either the process by which a population becomes more suited to its environment or the characteristics the population has inherited as a result of the process. Adapt, in contrast is a tenuous or temporary response to the environment. If I enter into an air conditioned room from a hot environment, it will take me time to adapt. This is not a heritable condition it is your body’s temporary response to the environmental conditions.
See also: http://evolution.berkeley.edu/evolibrary/article/0_0_0/misconcep_06
3. Use and Disuse of Organs: Students mistakenly assume that the disuse or use of a body part will determine its disappearance in future generations.

Students often incorrectly believe that use or disuse of an organ can lead to species changes (evolution). The driving force behind the loss of an organ is not due to a need it is due to the proportion of individuals wi th or without the trait surviving to the next generation. Because the trait may not be needed, it doesn’t confer an evolutionary advantage to have one so the disappearance of the trait is not detrimental to the species.