DCollaboration Teams - Members share responsibility for posting refined answers to the guided readings - succinct, relevant, clear, and with pictures or a video to compliment.
When contributing to the reading guide, follow these steps:
1) First complete the reading guide on your own from the DNA unit page.
2) Write your response to a question in word and then copy it. Be sure to upload pictures and/or video for each question.
3) Click on the edit button and then go to the appropriate question and paste your answer below it. Sign your contribution with your first name and last initial and TEAM COLOR
4) Save the page by selecting "Save with comment" from the Save dropdown. Enter a comment (e.g. "I answered chp 26 question 3" - Tom S.) then click Save.
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1-3, 21-22

Alecia
Fernanda
Taihlor
4-6, 23-24

Ashley
Kelly
SamB
7-9, 25-26

Mr. V Jr.
Brett
10-12, 27-29

Ryan
Mike
Amy
13-15, 30-31

Katie
Alina
Dahlia
16-18, 32-33

Tyler
Chris
19-20, 34

Josh
Megan
Nikki

1. What did Garrod mean by “inborn errors of metabolism?”
  • He was the first to suggest that genes dictate phenotypes through enzymes that catalyze specific chemical reactions in a cell.
  • He says that the symptoms of an inherited disease reflect a person's inability to make a particular enzyme.
external image archibaldgarrod.gif external image DNA-RNA%5B1%5D.jpeg
  • For example, alkaptonuria, in which the unine is black from the chemical alkapton. Garrod reasoned that people have an enzyme that breaks down alkapton, whereas people with alkaptonuria have inherited an inability to make the enzyme that metabolizes alkapton.
~Fernanda R.


2. Describe the Beadle and Tatum experiment with mold in detail – use the diagram below to help. The logic behind both the experiment and the results are critical.
Mold.png
Mold.png





3. What was Beadle and Tatum’s final hypothesis?

their final hypothesis was the one gene one enzyme hypothesis. it states that the function of a gene is to dictate the production of a specific enzyme. researchers also show how a combination of genetics and biochemisrty could be used to work out the steps in a metabolic pathway.

Alecia Seliga

4. Use the diagram below to note the flow of genetic information in a eukaryotic cell – next to each label in the square – write the definition of the term.
ap_bio_1.png
Sam B.

5. Why does the “code” have to be in triplets and not singles or doubles?
The code has to be in triplets because there are only 4 bases of DNA which must code for the 20 amino acids. Triplets are the smallest unit of uniform length that can code for all amino acids. Genetic instructions for the polypeptide chain is written in DNA as a series of nonoverlapping, 3 nucleotide words.


This video describes the function of the triple band in coding.

Sam B.

6. What is the template strand?
The template strand of DNA is the one strand out of the two that is actually transcribed, where the gene determines the sequence length of bases of an mRNA molecule. It provides the template for ordering sequence of nucleotides in the mRNA transcript.



Sam B.

7. Compare and contrast the codon and anticodon?

A codon is an mRNA triplet. An anticodon is a section of three nucleotides at the bottom of the "clover-form" tRNA. At the ribosome, a matching anticodon of tRNA
attaches to the codon (i.e. UAC-AUG). Since the tRNA carries an amino acid, we can say that specific codons of mRNA can code for specific amino acids. Both use uracil in place of thymine in their bases.

external image anticodon.jpg

-Sam V.

8. How did Nirenberg “figure out” which amino acids went with which codes?

Nirenberg synthesized mRNA with identical letters to determine the codons for four amino acids. He placed these in a mixture of ribosomes and all amino acids. The first was a pure uracil chain. For every UUU, only the amino acid phenylalanine was attached, eventually creating a long polyphenylalanine chain. He created similar scenarios using the AAA, CCC, and GGG codons.

(you can skip ahead to 11:30)


-Sam V.

9. What is the reading frame?

A reading frame is the correct sequence of codons on the mRNA chain. They must be put in the exact order specified to produce the desired protein. Although split into codons, the frame is continuous.

You can imagine that a computer is a ribosome and the code is the mRNA in this simulation:


-Sam V.

10. What conclusions can be drawn from the similarities of the genetic code among living organisms?

Exceptions to the universality of the genetic code include translation systems where a few codons differ from the standard ones. Despite some exceptions, the evolutionary significance of the code’s must have been operating very early in the history of life-early enough to be present in the common ancestors of all modern organisms.

external image circulargenetictable.jpgexternal image homology.gifthese two photos show the similarities with organisms
- Mike G


11. upload a video of transcription and describe the steps.

Can't upload video but here is the link: http://www.youtube.com/watch?v=WsofH466lqk

The video already explains the video well but here are some key parts and what happens:


Eukaryotic promoters- commonly include a TATA box, a nucleotide sequence containing TATA, about 25 nucleotides upstream from the transcriptional start point. (By convention, nucleotide sequences are given as they occur of the non-template strand)


Several transcription factors- one recognizing the TATA box, must bind to the DNA before RNA polymerase II can do so.
Additional transcription factor-
(purple) bind to the DNA along with RNA polymerase II, forming the transcription initiation complex. The DNA double helix then unwinds, and RNA synthesis begins at the start point on the template strand.

transcription.jpgThis picture shows translation and what is happening




12. What is a transcription unit?

It is the stretch of DNA that is transcribed into an RNA molecule.



external image 0175.jpg this picture shows the transcription part of DNA

-Mike G

13. Describe the prokaryotic promoter and terminator.
The prokaryotic promoter initiates the the transcription of a particular gene (towards the 5' region of the strand), while the terminator is a nucleotide sequence in DNA that causes the RNA polymerase to cease transcription.

external image proini.gif

-Dahlia M.



14. upload a picture of a a eukaryotic promoter and explain the significance of different components

external image images?q=tbn:ANd9GcTkqMIUisB6mfNdG-Xub00-yjDwt6ObaNIqE7zRpU42u-XLzGMTNg
Eukaryotic promoters are difficult to characterize but are extremely diverse and lie upstream of the gene. The transcripitonal complex in the Eukaryotic promoter causes the DNA to bend back on itself. The Eukaryotic promoters contain something called a TATA box it is a DNA sequence found in the promoter region of genes in archaea and eukaryotes.
- Katie Halbruner


15. Contrast termination of transcription for prokaryotic and eukaryotic organisms.






16. Why is important that the promoter be upstream of the transcription unit?

It is where polymerase must bind to start transcription. It would transcribe something other than the transcription unit if it was somewhere else.

promoter.jpg
Ty H.

17. Why is RNA necessary?

In eukaryotes it is necessary because otherwise the mRNA would get degraded and would have excess DNA in it that is not needed to code the protein. This is because the mRNA must travel outside the nucleus into the rough ER before being translated.

MRNA.JPG

Ty H.

18. What does adding a 5’ cap and poly A tail mean and why is it important?
The 5’ cap is many Guanines added to the 5’ side of the mRNA and the poly A tail is many Adenines added to the 3’ end of the mRNA. It keeps it from degrading.

5'_cap_and_Poly-A_Tail.png

Ty H.

19. Define the following terms:
a. RNA splicing: The removal of large or noncoding portions (introns) of the RNA molecule after initial synthesis.


b. Introns: Noncoding segments of nucleic acid that lie between coding regions. Areas that are cut out of the sequence.


c. Exons: The other regions besides the Introns. They are a coding region of a eukaryotic gene. When expressed, they are separated from each other by Introns.


d. Spliceosome: snRNP's join with additional proteins to form an even larger assembly. A complex assembly that interacts with the ends of an RNA intron in splicing RNA, releasing the intron and joining of the two adjacent exons. Basically, they are enzymes that cut out the Introns.


e. snRNP’s: (Small nuclear ribonucleoproteins) they recognize certain splice sites; they are located in the cell’s nucleus and are composed of RNA and protein molecules. They assemble with other proteins to form the splicesome.


f. ribozymes:
The site of protein manufacturing containing two subunits. It is an enzyme-like RNA molecule that catalyzes reactions during RNA splicing.


g. UTR: UTR stands for Untranslated Region. It refers to one of the two sections on each side of a stand of mRNA. If it is found on the 5’ side, it is called a 5 UTR and if it is on the 3’ side, it is called a 3 UTR.


h. Alternative RNA splicing: A type of regulation at the RNA-processing level in which different mRNA molecules are produced from the same transcript, depending on which RA segments are treated as exons and which as introns.


i. domains: They are regions of a protein, or they are the taxonomic category above the kingdom level. The 3 domains are Archea, Bacteria, and Eukarya.



20. Describe the structure and function of transfer RNA.
The function of transfer RNA is to transfer amino acids from the cytoplasmic pool of amino acids into a Ribosome. The structure of transfer RNA consists of a single RA strand that is only about 80 nucleotides in length.




21. Why is the enzyme aminoacyl-tRNA synthetase important to translation and protein synthesis?
  • Each amino acid is joined to the correct tRNA by a specific enzyme (aminoacyl-tRNA syntheatse).
  • The active site of each enzyme fits only a specific combination of amino acids and tRNA.
  • There are 20 different synthetase one for each amino acid.
external image 2205.jpg
^^ shows how the enzyme makes the tRNA. It is too big in its original form. If you want to read the words zoom in.
~Fernanda R.~


22. What is “wobble”?

a wobbe explains why the synonmous codons for a given amino acid can differ in their 3rd base but usually not in their others. it is bascially a violation of the base pairing rules. the 3rd nucleotide (5 end) of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the 3rd position (3 end) of a codon.

MGA2-03-30.jpg
Alecia Seliga

23. upload a picture of ribosomal RNA and describe the structure and function of it's components.

rRNA has a structural function within the ribosomes, the ribosomes bind onto the mRNA and decode it to amino acids (provided by tRNAs)
image007.jpg.
the ribosomes then form the peptidyl bond between the amino acids to form a protein
Ashley A


24. Detail the steps of initiation of translation.
A ribosomal subunit binds to mRNA and also to a specific intitator of tRNA, which carries amino acid methionine. It moves downstream until it gets to the start codon, AUG.
This signals the start of translation. tRNA then hydrogen bonds with the start codon. Brett S.



Fig_1719_initiationA.jpgtranslation_initiation.jpg







25. Use the diagram below to detail elongation cycle of translation. Define terms.

trageting_proteins.png
trageting_proteins.png

The process of elongation begins in the cytosol with a free ribosomes. The brown item pictured above is a ribosomes with a red MRNA strand attached to it. Step2 synthesis of the polypeptide stops for a moment when the signal recognition particle(orange item) attaches to the peptide at the green and purple chain. Step 3 The signal recognition particle, now attached to the green end of the green and purple chain, attaches to a receptor protein in the membrane of the ER. The location of binding on the membrane is part of the translocation complex. Step 4 the signal recognition particle departs from the polypeptide, which continues to grow on to the other side of the membrane. Step 5 the signal peptide(green part of the green and purple chain) is now cut from the polypeptide by the signal cleaving enzyme. Step 6 The polypeptide departs from the ribosomes, folds into a shape that ends the process, leaving the protein inside the ER.
Brett S.


26. Use the diagram below to detail the termination of translation – define all terms.
termination.png
termination.png







27. What are polyribosomes?

polyribosomes are the sequence of ribosomes that attach to a mRNA and all translate it at the same time.

external image polyribosome.jpg
Ryan H


28. What is an example of a post translational modification of a protein?

Lipids, sugars, phosphate groups, or other molecules may be added to a protein which may activate it or tell it where to go in the cell. The polypeptide may also be cut at specific points which may also activate the protein.
external image image.axd?picture=2009%2F12%2Fgene+expression.jpg
Ryan H

29. What is a signal peptide?

A signal peptide is a sequence of amino acids that signal for the ribosome to be attached to the rough ER.
external image med-rib-e.gif
Ryan H

30. What is a signal recognition particle?
The signal recognition particle is a ribonucleoprotein that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes.
external image signalpep.gif
-Dahlia M.

31. Use the diagram below to highlight the signal mechanism for targeting proteins to the ER.
trageting_proteins.png
trageting_proteins.png




32. Define the following terms:
a. Mutations - changes in the genetic material of a cell.

b. Point mutations - chemical changes in just one base pair of a gene.

c. Base pair substitution - the replacement of one nucleotide and its partner with another pair of nucleotides.

d. Missense - when the altered codon still codes for an amino acid that thus makes sense, although not necessarily the RIGHT sense.

e. Nonsense - when the codon that is experiencing the mutation turns into a stop codon and causes the translation to be terminated prematurely.

f. Insertions - mutation involving the addition of one or more nucleotides.

g. Deletions - mutation in involving loss of one or more nucleotide.

h. Frameshift mutation - mutation occurring when the number of nucleotides inserted or deleted is not a multiple of three, resulting in the improper grouping of the following nucleotides into codons.

i. Mutagen - a chemical or physical agent that interacts with DNA and causes a mutation.



- CHRIS A.

34. How has a gene been “redefined” and why?
A gene is used to be a sequence of DNA that codes for enzymes. We already know that genes code for enzymes and other polypeptides. Some genes never code for polypeptides but stop at the RNA stage (rRNA or tRNA). Some genes are not fully coded becuase some parts of the gene are introns that are spliced out.