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Content Benchmark L.12.A.2
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Life Science
Heredity
  L.12.A.1
  L.12.A.2
  L.12.A.3
  L.12.A.4
  L.12.A.5
Structure of Life
Organisms and Their Environment
Diversity of Life
Content Areas
Nature of Science (NOS)
Life Science
Earth Science
Physical Science

Students know DNA molecules provide instructions for assembling protein molecules. E/S

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.

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.

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.

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.

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 sickle-cell 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 turn “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

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Content Benchmark L.12.A.2

Students know DNA molecules provide instructions for assembling protein molecules. E/S

Common misconceptions associated with this benchmark:

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 should 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 that 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

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Content Benchmark L.12.A.2

Students know DNA molecules provide instructions for assembling protein molecules. E/S

Common misconceptions associated with this benchmark:

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

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Content Benchmark L.12.A.2

Students know DNA molecules provide instructions for assembling protein molecules. E/S

Sample Test Questions

1st Item Specification: Recognize that the DNA code carries instructions for making protein molecules.

Depth of Knowledge Level 1

  1. What is the DNA sequence for the following mRNA sequence: CUCAAGUGCUUC?
    1. CUCAAGUGCUUC
    2. GAGUUCACGAAG
    3. GAGTTCACGAAG
    4. AGACCTGTAGGA
  1. If the base sequence in DNA is ATCG, the mRNA sequence is
    1. AUCG
    2. ATCG
    3. TAGC
    4. UAGC
  1. The sequence of nitrogenous bases in mRNA is
    1. identical to the template strand of DNA on which it forms.
    2. complementary to the template strand of DNA on which it forms.
    3. determined by the sequence of bases in tRNA
    4. complementary to the sequence of bases found in the ribosome.
  1. Which of the following is NOT a structural difference between RNA and DNA?
    1. A DNA molecule has two strands, while RNA has one strand.
    2. DNA contains the base thymine, while RNA contains the base uracil.
    3. The sugar in DNA is deoxyribose, while in RNA it is ribose.
    4. Due to their sizes DNA, can the leave the nucleus and RNA cannot.
  1. Amino acids are carried to the ribosome by the
    1. messenger RNA.
    2. ribosomal RNA.
    3. transfer RNA.
    4. coded RNA.

Depth of Knowledge Level 2

  1. If the base sequence in DNA is ATCG, the tRNA sequence is
    1. AUCG
    2. ATCG
    3. TAGC
    4. UAGC
  1. What tRNA molecules would be needed to carry amino acids for the following
    DNA sequence: AGTCCGTTA?
    1. TCAGGCAAT
    2. AGTCCGTTA
    3. AGUCCGUUA
    4. UCAGGCUUA
  1. Use the table showing mRNA codons to answer the question below.


(From http://www.safarikscience.org/biologyhome/7_dna/codon_question.png)

What is the amino acid sequence for the following mRNA sequence: CUCAAGUGCUUC?

  1. Val–Tyr–Arg–Gly
  2. Val–Asp–Pro–His
  3. Leu–Leu–Gly–Asp
  4. Leu–Lys–Cys–Phe
  1. Use the table showing mRNA codons to answer the question below.


(From a http://www.safarikscience.org/biologyhome/7_dna/codon_question.png)

What would be the DNA sequence for a segment of protein with an amino acid sequence of Val–Tyr–Arg–Gly?

  1. CTGTATGCGCCC
  2. CAGATAGCGCCC
  3. GTCTATCGCGGG
  4. GUCUAUCGCGGG
  1. Use the table showing mRNA codons to answer the question below.


(From http://www.safarikscience.org/biologyhome/7_dna/codon_question.png)

What would be the amino acid sequence for the following DNA sequence: AAACCTAGT?

  1. Ile – Pro – Ser
  2. Phe – Gly – Ser
  3. Ile – Gly – Ser
  4. Phe – Pro – Ser
  1. Use the table showing mRNA codons to answer the question below.


(From http://www.safarikscience.org/biologyhome/7_dna/codon_question.png)

During protein synthesis, tRNA molecules carried the following 3 amino acids to a
ribosome: Ala – Pro – His. What is the DNA sequence for these three amino acids?

  1. CGAGGCGTA
  2. GCUCCGCAU
  3. GCTCCGCAT
  4. CGTGGCGAA

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Content Benchmark L.12.A.2

Students know DNA molecules provide instructions for assembling protein molecules. E/S

Answers to Sample Test Questions

  1. C, DOK level 1
  2. D, DOK level 1
  3. B, DOK level 1
  4. D, DOK level 1
  5. C, DOK level 1
  6. A, DOK level 2
  7. C, DOK level 2
  8. D, DOK level 2
  9. B, DOK level 2
  10. B, DOK level 2
  11. A, DOK level 2

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Content Benchmark L.12.A.2

Students know DNA molecules provide instructions for assembling protein molecules. E/S

Intervention Strategies and Resources

The following is a list of intervention strategies and resources that will facilitate student understanding of this benchmark.

1. The Dolan DNA Learning Center provides a number of activities, animations and other resources for the teacher. The DNA Teacher Guide is of particular interest to teachers. At this site “The chromosome 11 Flyover” gives students a “tour” of the tip of chromosome 11 and 28 genes found in this region along with other types of DNA such as repeats and introns.

To review what is available at The Dolan DNA Learning Center go to
http://www.dnalc.org/home.html

2. DNA and RNA pairing excercise
To reinforce the pairing of bases in DNA and RNA the teacher can provide this paper and pencil exercises. Give students a “sample” DNA sequence such as TACCAGCTTCAA and have the student determine the complementary DNA strand. Next have them produce the mRNA code and use the Genetic Code table to determine the amino acid that this mRNA would produce. A coloring exercise similar to this can be found the website below.

To utilize a paper and pencil coding exercise go to
http://www.biologycorner.com/worksheets/DNAcoloring.html

3. The PBS series DNA
DNA series webpage are lesson plans for using this series in the classroom. Teacher will need a copy of this series, but if not available there are interactive audio visual activities that

To utilize an interactive base pairing exercise at the DNA Workshop found at PBS go to
http://www.pbs.org/wgbh/aso/tryit/dna/index.html
To learn more about this series go to
http://www.pbs.org/wnet/dna/

4. Photo 51 Activity
Another PBS show that can be used by teachers is the Nova program Secret of Photo 51.
This show traces the efforts by Rosalind Franklin to unlock the secrets of DNA’s structure. In particular an interactive activity explains the use of X-ray diffraction and how this famous photo 51 was used to determine the shape and dimensions of DNA

To use this activity at the Photo 51 site go to http://www.pbs.org/wgbh/nova/photo51/

5. The Genetics Learning Center also has an interactive computer activity that allows student to transcribe and translate a gene.

To use this activity go to http://learn.genetics.utah.edu/

6. Role playing activity on transcription
site below contains a role playing activity that involves the process of translation. In this activity produce a section of the hemoglobin protein. The first site contains the directions and second additional information for this activity.

To use this activity go to http://sciencespot.net/Media/protsynoutline.pdf and http://sciencespot.net/Media/protsyncodes.pdf

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Benchmark
Support Pages

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Sample Questions:
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Intervention Strategies & Resources:
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