DNA+Review+Period+1

Under each concept term post or revise information to make a fantastic review guide.
 * [[image:dna_image.png width="153" height="46"]] || Why is it called the "Blueprint of Life?" || What is it a blueprint for? || What reads the blueprint? ||

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1. Explain why researchers originally thought protein was the genetic material. Researchers originally believed that protein was the genetic material because it made more sense that proteins were made out of many amino acids & DNA were made out of only 4 nucleotides. They also didn’t know about DNA transcription, translation or replication, so it was unknown how important DNA really was.
 * The Molecular Basis of Inheritance**
 * DNA as the Genetic Material**

Amanda M.

2. Summarize the experiments performed by the following scientists that provided evidence that DNA is the genetic material: a. Frederick Griffith-Was responsible for discovering that genetic substance is passed from organism to organism through a "Transforming Factor". Did this by mixing harmless bacteria with heat killed infectious bacteria. After being mixed, the once harmless bacteria caused disease in mice. b. Oswald Avery, Maclyn McCarty, and Colin MacLeod-Discovered that it was DNA not protein that was the aforementioned "Transforming Factor". This experiment was done by first purifying the DNA and proteins from a pneumonia bacteria. Then, both purified substances were injected into "healthy bacteria" to see which would transform into infectious bacteria. Only the bacteria injected with DNA were transformed into virulent bacteria. c. Alfred Hershey and Martha Chase- With their classic "Blender" experiment, Hershey and Chase confirmed that of Avery, McCarty and MacLeod. These scientists took viruses that inject bacteria and radioactively labeled either their proteins or their DNA. These two groups were then made to infect DNA. After this, both test groups were placed in blenders. The bacteria only displayed a radioactive glow in the viruses with radioactive DNA test group. The viruses remained glowing in the protein group. This was considered undenyable proof of DNA's status as the true genetic material. d. Erwin Chargaff-Was nice enough to discover the four bases ( Guanine, Adenine, Cytosine, and Thymine), and is attributed with "Chargaff's rule" which stated that in DNA, the amount of Guanine is always equal to the amount of Cytosine, and that the amount of Thymine is always equal to the amount of Adenine. This was discovered after Chargaff gauged the number of each base in different organisms' DNA.

I thought that this picture exemplified the DNA-Protein debate in both images and words. It is a Blair S. original, created in MS paint.

-Blair S.

3. Explain how Watson and Crick deduced the structure of DNA and describe the evidence they used. Explain the significance of the research of Rosalind Franklin.  During the 1950s, Crick was studying protein structure using X-ray crystallography. After visiting Crick at Cambridge University, Watson traveled to King's College and saw an x-ray diffraction image of DNA, which Rosalind Franklin produced. The image had spots and smudges which came from x-rays that were diffracted/deflected as they passed through "aligned factors of purified DNA." Using the image, Watson was able to deduce DNA's helix shape and width. He concluded that DNA was double stranded and had nitrogenous bases. Franklin's discovery helped Watson and Crick determine DNA's double-helix structure. -Carol S.

4. Describe the structure of DNA. Explain the base-pairing rule and describe its significance.

DNA’s structure is important because it allows for easy transcription. The DNA has a Phosphate group and a sugar molecule which makes up the "sides" of the DNA. The structure of the DNA is a double helix, or two strands tied together in a curl, this is important because it allows for an easier way to store, find, and copy information in something’s genetic code. To match each side of the DNA strand you have to have common base pairs (BPs), nucleotides, these BPs are adenine (A) which pairs with thymine (T), guanine (G) which pairs with cytosine (C), these BPs are connected by a Hydrogen Bond, a weak bond, so that they are easily split apart during translation and transcription. The BPs allow for more easy translation process by pairing three of the nucleotides into a codon and is used to make a protein. DNA’s structure allows for simple transcription when it is unfolded and begins translating the BPs into proteins, which become RNA, this process becomes easy and efficient during the DNA’s main process. media type="youtube" key="qy8dk5iS1f0?fs=1" height="385" width="480" -Pat E.



5. Describe the process of DNA replication, including the role of the origins of replication and replication forks. Explain the semiconservative replication model.
 * DNA Replication and Repair**

6. Explain the role of DNA polymerases in replication.

DNA polymerase I works on the Okazaki fragments by removing the RNA Primer that was placed there, and replacing it with the correct nucleotides. DNA Polymerase III pairs up base pairs, moving 5' to 3', after the DNA is split while it is being copied. media type="youtube" key="teV62zrm2P0?fs=1" height="385" width="480"An overview of DNA Replication that shows the importance of DNA Polymerase.

-Josh S.

7. Explain what energy source drives the polymerization of DNA.

The nucleotides that make up the DNA bring their own energy to the table. All nucleotides start out with 3 phosphates attached to the end (just like ATP, the energy source of life!) which make them hold enough energy to bind together when they are pairing up and creating DNA. When DNA Polymerase III attaches two nucleotides together, two phosphates are broken off and enough energy is released that a bond forms between the two nucleotides.

media type="youtube" key="jx-Q-i7FsRw?fs=1" height="385" width="480"Shows this process happening.

-Josh S.

8. Define antiparallel and explain why continuous synthesis of both DNA strands is not possible. Antiparallel- the opposite arrangement of the sugar-phosphate backbones in a DNA double helix. The continuous synthesis of both DNA strands is not possible because eventually, two nucleotides will not be able to bin dbecause the phosphate backbone cannot break off and attach to another.

9. Distinguish between the leading strand and the lagging strand. The leading strand is formed in the same direction as the movement of replication and can be synthesized continuously. The lagging strand is formed in the opposite direction and it is synthesized in short fragments that will ultimately bind together. Those short fragments are called okazaki fragments. -Nichole M.

This picture shows the leading strand moving in the same direction as replication. It also shows the lagging strand moving in the opposite direction and how it is fragmented together with okazaki fragments 

10. Explain how the lagging strand is synthesized even though DNA polymerase can add nucleotides only to the 3 prime end. Describe the significance of Okazaki fragments. The lagging strand of DNA synthesizes differently because the phosphates, which broke off during synthesis, break off in the wrong place. Therefore, DNA is synthesized 5'-3' in Okazaki fragments. Okazaki fragments are significant because they allow DNA to be replaced properly.

11. Explain the roles of DNA ligase, primer, primase, helicase and DNA polymerase. __Ligase:__ links essential enzymes for DNA replication. It also catalyses the bond of 3’ to 5’ at the end of a growing chain in the building of a new DNA fragment. __Primer:__ Has a free 3’ end and is bound to a complementary base which pairs with a template strand that is elongated during the process of DNA replication. __Primase:__ An enzyme that joins together the RNA nucleotides. This is the process of making the primer. <span style="font-family: Arial,Helvetica,sans-serif;">__Helicase:__ Important enzyme that unwinds the DNA strands before the replication process. <span style="font-family: Arial,Helvetica,sans-serif;">__Polymerase:__ An enzyme that catalyzes the elongation of DNA by adding nucleotides to the polypeptide chain. <span style="font-family: Arial,Helvetica,sans-serif;">Important types: <span style="font-family: Arial,Helvetica,sans-serif;">__P I:__ works on the Okazaki by removing RNA primer and replacing it with nucleotide base pairs. <span style="font-family: Arial,Helvetica,sans-serif;">__PIII:__ Pairs up the nucleotide base pairs (moving in the 5’ to 3’) direction, after DNA is split. <span style="font-family: Arial,Helvetica,sans-serif;"> <span style="font-family: Arial,Helvetica,sans-serif;">-Megan R

12. Describe the structure and function of telomeres.

Telomeres are the region at the end of a chromosome. It is repetitive DNA that protects the end of the chromosome, which protects it from deterioration. They compensate for incomplete DNA replication at the end of the chromosomes. Chromosomes are like shoelaces. Telomeres are like aglets (tips at the end of laces) they protect the shoelaces from fraying, just as the telomeres protect the chromosomes from decay.Chris G

13. Explain the possible significance of telomerase in germ cells and cancerous cells. Since telomerase is responsible for the upkeep of dna's length, as you get older and telomerase shuts off cells lifes' last about 50 division. This, however, is different for cancerous and germ cells for telomerase is active in both causing rapid divisions of cells that are mutated from the original copy which result in tumors.

media type="youtube" key="pQp0tklwG-Y?fs=1" height="385" width="480" Ryan E.

The Connection Between Genes and Proteins 1. Distinguish between the “one gene one enzyme” hypothesis and the “one gene one polypeptide” hypothesis and explain why the original hypothesis was changed. One gene- one enzyme hypothesis- the idea that genes act through the production of enzymes, with each gene responsible for producing a single enzyme that in turn effects a single step in a metabolic pathway. One gene- one polypeptide hypothesis- the premise that a gene is a segment of DNA that codes for one polypeptide. The original hypothesis was changed because scientists learned that not all proteins were nezymes. Then, they discovered that proteins were made from one or more polypeptides.
 * From Gene to Protein**

2. Explain how RNA differs from DNA. DNA stands for deoxyribonucleic acid, while RNA stands for ribonucleic acid. DNA, thus, carries a deoxyribose sugar and RNA contains a ribose sugar. DNA is composed of several types of nitrogenous bases: adenine, thymine, cytosine and guanine. RNA contains nitrogenous bases similar to DNA, but does not contain thymine. It contains uracil instead. Both DNA and RNA are sugars that are linked to a nitrogen compound at one end and a phosphorus group at the other. However, DNA generally consists of two strands wound together to form a double helix. RNA is typically single-stranded.

DNA is responsible for storing the genetic information and is found in the nucleus of the cell. When not in use, strands of DNA wind up tightly and form chromosomes. RNA is found in other parts of the cell (e.g., mitochondria) and are responsible for taking information present on DNA and turning it into something functional, by coding for various proteins through the process of transcription. For example, a strand of DNA may dictate an individual has blue-eyed genes. This information is taken from the DNA by the RNA, which is responsible for creating the blue pigment proteins necessary to express these genes.

-Amanda P.

3. Briefly explain how information flows from gene to protein. <span style="color: #0730e9; font-family: 'Comic Sans MS',cursive;">The flow of information from the genes determines the protein composition and thereby the functions of the cell. The process acts as though the information is a letter being sent through the two to tell the body the functions it should perform.

media type="youtube" key="pUYKxSvaHgg?fs=1" height="385" width="480" Ashley K.

4. Distinguish between transcription and translation. <span style="color: #aa1818; font-family: 'Lucida Console',Monaco,monospace;">Transcription- Synthesizing RNA onto a DNA sequence. Adenine (on the DNA) is now paired with Uracil (on the RNA). <span style="color: #aa1818; font-family: 'Lucida Console',Monaco,monospace;"> <span style="color: #aa1818; font-family: 'Lucida Console',Monaco,monospace;"> <span style="color: #aa1818; font-family: 'Lucida Console',Monaco,monospace;">Translation- Synthesizing polypeptides using the genetic information encoded in an mRNA molecule. When nucleotides change to amino acids, the "language" changes. <span style="color: #aa1818; font-family: 'Lucida Console',Monaco,monospace;">-Carol S.

5. Compare where transcription and translation occur in prokaryotes and in eukaryotes. <span style="color: #ff0000; font-family: 'Comic Sans MS',cursive;">

<span style="color: #ff0000; font-family: 'Comic Sans MS',cursive;">In eukaryotic cells, the transcription phase takes place inside of the nucleus. The pre mRNA is copied from the DNA and then spliced to make mRNA. Then, the mRNA strand leaves the nucleus and travels to the cytoplasm to be translated by the ribosome. In prokaryotic cells, there is no nucleus and so the mRNA is created in the cytoplasm and then it travels to a ribosome, also located in the cytoplasm to be translated. <span style="color: #ff0000; font-family: 'Comic Sans MS',cursive;">Peter Seliga

6. Define codon and explain the relationship between the linear sequence of codons on mRNA and the linear sequence of amino acids in a polypeptide.

<span style="color: #3c801c; font-size-adjust: none; font-stretch: normal; font: 14px Helvetica; margin: 0px;">**__ Codon __** __**:**__ a group of three nucleotides sequenced together that codes for one amino acid.

<span style="color: #3c801c; font-size-adjust: none; font-stretch: normal; font: 14px Helvetica; letter-spacing: 0px; margin: 0px;">When an mRNA is produces, codons line the edge and eventually code for each amino acid in a certain protein. The linear sequence codes for one single amino acid in the chain. Each triplet is assigned its own role as to what amino acid is brought forth. The sequence of codons relates directly to the sequence of amino acids in any polypeptide.



Shaun B

7. Explain why polypeptides begin with methionine when they are synthesized. <span style="color: #0730e9; font-family: Georgia,serif; font-size: 110%;">Methionine is the starting amino acid, codon AUG, for is symbolizes the start of protein translation from mRNA. Since it is also an essential amino acid all species require it, however people are not able to create methionine from sugars and amino acids, such as plants, so it much be ingested.

<span style="color: #0730e9; font-family: Georgia,serif; font-size: 110%;">Justin Gmedia type="youtube" key="t9PcwVOn3N4?fs=1" height="262" width="325"

8. Explain the significance of the reading frame during translation. (reference mutations) media type="youtube" key="kp0esidDr-c?fs=1" height="385" width="480" <span style="color: #ff0000; font-family: 'Comic Sans MS',cursive;">In translation, the ribosome reads the mRNA by codons, or sets of 3 nucleotides. This is called the reading frame. The appropriate tRNA anti-codon is matched up with the mRNA codon and the amino acid at the other end of the tRNA bonds to the other amino acids that have been laid out already and this creates a protein. If one of the nucleotides on the mRNA strand gets deleted, either because it never existed in the DNA copy or it was accidentally removed or damaged during the transcription process, then the sequence moves up one. For example, if you had a sequence of GATTACA and the first T was deleted, the sequence would now read GATACA. This is not the correct code, and so the incorrect protein is made. This is also called a mutation. <span style="color: #ff0000; font-family: 'Comic Sans MS',cursive;">Peter Seliga

9. Explain the evolutionary significance of a nearly universal genetic code. A nearly universal genetic code means that, from an evolutionary standpoint, every organism on this earth shares a common ancestor. It means that life arose only once on Earth, and that it was first RNA-based, and later evolved to be DNA-based. -Amanda P.

10. Explain how RNA polymerase recognizes where transcription should begin. Describe the promoter, the terminator, and the transcription unit. RNA polymerase knows where to begin transcription because it attaches to the promoter sequence, which is upstream from the terminator. It also knows where to end because of a terminator sequence. The DNA that is transcribed into RNA is called a transcription unit.
 * The Synthesis and Processing of RNA**

11. Explain the general process of transcription, including the three major steps of initiation, elongation, and termination. Initiation- After RNA polymerase binds to the promoter, the DNA strands unwind, and the polymerase initiates RNA synthesis at the starting point on the template strand. Elongation- The polymerase moves downstream, unwinding the DNA and elongating teh RNA transcript 5'-3'. In the wake of transcription, the DNA strands reform the double helix. Termination- eventually, the RNA transcript is released, and the polymerase detaches from the DNA.

12. Explain how RNA is modified after transcription in eukaryotic cells. (Splicing, Introns, and Exons)

13. Describe the structure and functions of tRNA.
 * The Synthesis of Protein**

A tRNA molecule consists of 70-80 nucleotides The structure of tRNA can be broken into its <span style="font-family: Tahoma,Geneva,sans-serif;">, its and its. 3' end always terminates with the sequence CCA, with the 3' hydroxyl of the ribose of the terminal A being the point of covalent attachment of the amino acid. TRNA’s have cloverleaf secondary structure due to four base-paired stems. The cloverleaf contains three non-base-paired loops: D, anticodon, and TpsiC loop. The tertiary structure of tRNA is best described as a compact "L" shape. The anticodon is a single-stranded loop at the bottom of the figure which later base-pairs with the triplet codon. The amino acid is attached to the terminal A on the upper right. The active sites (anticodon and amino acid) are maximally separated. As in proteins, the tertiary structure is dictated by the primary sequence. Transfer RNA’s main purpose is to transfer specific amino acids to growing polypeptide chain during the ribosomal site of protein synthesis during what you call translation. Another thing is that with each type of tRNA molecule it can only be attached by one amino acid, but because genetic code has various codons that show the same amino acid tRNA molecules hold different anticodons that may or may not hold the same amino acids. TYLER G.

14. Describe the structure and functions of ribosomes. <span style="color: #4e034e; font-family: 'Comic Sans MS',cursive; font-size: 120%;">Ribosome’s are the cells structure in which proteins are manufactured. Most cells contain thousands of ribosome which make proteins that will be used inside the cell. Ribosome’s resaves the mRNA which transfers information from DNA to the nucleus. They are made up of two parts or subunits called 60-s and 40-s <span style="color: #570d7d; font-family: 'Comic Sans MS',cursive; font-size: 90%;">(Katie W.)

<span style="color: black; font-family: 'Arial','sans-serif'; font-size: 11pt; line-height: 115%;">

15. Describe the process of translation (including initiation, elongation, and termination) and explain which enzymes, nucleotides, and energy sources are needed for each stage.

16. Describe two properties of RNA that allow it to perform so many different functions. RNA can perform different functions because it has a similar structure to DNA and because it has a similar structure to DNA and because it can produce proteins.

17. Compare protein synthesis in prokaryotes and in eukaryotes.

<span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">Prokaryotes:
 * <span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">Lack a nuclear membrane which makes process much faster.
 * <span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">Translation of mRNA into protein begins before transcription is complete.
 * <span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">Genes with related funstions are placed on same mRNA.

<span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">Eukaryotes:
 * <span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">The nuclear membrane present in eukaryotes makes process slower than in prokaryotes.
 * <span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">mRNA must be completely formed before passing through nucleus.
 * <span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">Introns are removed and exons are spliced together.
 * <span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">5' cap and 3' poly-A tail are added.
 * <span style="background-color: #000000; color: #ffffff; font-family: 'Arial Black',Gadget,sans-serif;">Translation occurs in the cytoplasm where usually mRNA only specifies a single protein.

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JOE PATRICK

18. Define point mutations. Distinguish between base-pair substitutions and base-pair insertions. Give examples of each and note the significance of such changes.

A point mutation is a mutation resulting from a change in a single base pair in the DNA molecule. Base-pair substitution is a mutation that causes the replacement of a single base nucleotide with another nucleotide of genetic material. A base substitution mutation may be a transition, in which a purine-pyrimidine pair is substituted by the other purine-pyrimidine pair, or a transversion in which a purine-pyrimidine pair is replaced by one of the two pyrimidine pairs. An example of a base pair substitution would be sickle cell disease, which converts a GAG codon to GTG. A base pair insertion mutation is a form of DNA mutation where one or more of the DNA bases of a DNA chain is added to another, changing the genetic coding of the chain dramatically and most usually having a detrimental effect. This would cause a change in all the amino acids after the insertion. The diagram below demonstrates the importance of the change of a single nucleotide. The change from GAG to GTG changed the amino acid from glutamic acid to valine, which causes sickle cell disease. Kim P

19. Describe several examples of mutagens and explain how they cause mutations.

1: Ultra Violet Radition present in sunlight- High energy UltraViolet rays like UVB and UVC are mutagens that directly cause damage in DNA. UVB in particular causes direct damage by exciting DNA molecules in skin cells, and damages cytosine bases. When DNA Polymerase comes to replicate it, it’s read as AA and not CC, thus causing a TT to be added, which in turn causes cancerous growths. UVA light indirectly causes damage in DNA by creating damaging intermediates, like hydroxl and oxygen radicals.


 * Note* UV rays, much like Diglett, may appear to be weak and underwhelming, but can whoop your butt.

media type="youtube" key="uN82GLQYAUQ?fs=1" height="385" width="640"

2: Gamma Radiation- Gamma rays and neutrons have the smallest wavelengths and the most energy of any wave in the electromagnetic spectrum. They suffeciently penetrate your body and cause widespread instances of radiation sickness and DNA damage.

media type="youtube" key="IjS0bTGCcJQ?fs=1" height="385" width="640"

3:X-Radiation- Damages DNA because it is a type of ionizing radiation that directly damages DNA by breaking chemical pairs and creating ions. It can also directly ionize DNA. X rays can attack water molecules, creating free radicals which then in turn damage and mutate DNA.

4: Benzene- a known carcinogen that used to be an additive in gasoline. Long term exposure to Benzene in the air is known to cause Leukemia. It damages the bone marrow, and can cause a decrease in red blood cells. Pure Benezne oxidizes in the body to produce Benzene oxide, which can’t be excreted quickly. This allows it to interact with the DNA further, causing damage.

Conclusion: Mutagens are chemical or physical agents that either directly or indirectly change the DNA of an organism to increase the occurance of mutations far beyond the norm. Chemical mutagens usually damage DNA by altering the structure and pairing properties of bases, while some like ultra violet radiation, can damage the Dna by producing free radicals.

<3 Anthony Q

1) Describe how DNA technology can have medical applications in such areas as the diagnosis of genetic disease, the development of gene therapy, vaccine production, and the development of pharmaceutical products.
 * General Biotechnology Concepts we’ve discussed**

2) Explain how DNA technology could be used in the forensic sciences. ====DNA technology can be used in forensic sciences in order to identify criminals by the means of testing small traces of evidence left behind by the perpetrator. This evidence can be such things as stray hairs, skin cells, blood, and finger prints. Finger prints tend to be the more used method to trace people. All evidence is collected and taken to a forensic lab to determine who the criminal is.====

Let this BioBytes gentleman handle the rest. Hopefully you remember him from that one video we watched in class...oh lordy...
media type="youtube" key="V2StM4-FWtc?fs=1" height="385" width="640"

Joe B xoxo
3) Describe how gene manipulation has practical applications for environmental and agricultural work. Explain how DNA technology can be used to improve the nutritional value of crops and to develop plants that can produce pharmaceutical products.

4) Discuss the safety and ethical questions related to recombinant DNA studies and the biotechnology industry. People are unsure whether to accept recombinant DNA studies and biotechnological industries. They are not educated about these issues and believe only the negative possibilities. People think that artificial is bad because it is not natural. They're against the idea of engineered products, but they do not realize how many products are actually modified.