Term
What is the most powerful modulator of phosphofructokinase and how does it
originate and work? |
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Definition
| Fructose-2,6-bisphosphate – turns on PFK (positive modulator). Made from fructose-6-phosphate (PFK2 catalyzes this reaction and glucose-6-phosphate turns PFK2 on). |
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Term
| How are alanine and citrate important during glycolysis, even though they are not present in the formal pathway? |
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Definition
| Alanine – negative modulator of pyruvate kinase if there is a lot of alanine (a lot of amino acid) in the cell and not much sugar, cell will burn the alanine and save the sugar/glycolysis for later. Citrate – negative modulator of PFK if there is a lot of citrate, the Krebs cycle is active and the cell does not need to go through glycolysis to produce any more pyruvate |
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Term
| If 10 molecules of isocitrate are converted to succinate in the Krebs cycle, how many molecules of NADH will be produced? AcetylCoA? CO2? GTP? FADH2? Show the cycle. |
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Definition
| (I won’t show the cycle here, but it comes straight from your notes. Make sure you include sites of energy, NADH, and FADH2 production in your drawing). NADH – 20 AcetylCoA – 0 CO2 – 20 GTP – 10 FADH2 - 0 |
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Term
| Which three enzymes in the Krebs Cycle lead to the production of NADH? |
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Definition
| Isocitrate dehydrogenase, alpha-ketogutarate dehydrogenase, and malate dehydrogenase |
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Term
| If 12 molecules of glucose are catabolized to malate, how many FADH2 are produced? |
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Definition
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Term
| The Km of phosphofructokinase is 0.2. What happens to this value when citrate binds? Glucose-6-phosphate? ATP? Fructose-2,6-bisphosphate? Alanine? |
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Definition
| Citrate – increases Glucose-6-phosphate – decreases ATP – increases Fructose-2,6-bisphosphate – decreases Alanine – no change as alanine only modulates pyruvate kinase, not PFK |
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Term
| What reaction occurs in between glycolysis and the Krebs Cycle? How much NADH and CO2 are produced here for 6 molecules of glucose? What enzyme catalyzes this reaction? |
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Definition
| Pyruvate dehydrogenase reaction or the oxidative phosphorylation of pyruvate; For 6 glucose – 12 NADH, 12 CO2; pyruvate dehydrogenase catalyzes this reaction |
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Term
| Can acetylCoA enter the Krebs Cycle directly? What has to bind to it and what product is produced? What enzyme is used for this reaction? |
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Definition
| No, acetylCoA must be escorted by oxaloacetate. AcetylCoA + oxaloacetate = citrate. Citrate synthase catalyzes this reaction |
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Term
| Give two examples of regulation that occurs during the Krebs Cycle. |
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Definition
| Dr. Watts gave three examples: ATP is a positive modulator for isocitrate dehydrogenase. Succinate is a negative modulator for citrate synthase. Oxaloacetate is a negative modulator for succinate dehydrogenase |
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Term
Describe the electron transport system present in the mitochondria – both structure
and function. |
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Definition
| the electron transport system is present in the inner membrane of the mitochondria. It consists of four cytochrome complexes and the enzyme F1ATPase. Electrons are transferred from electron carriers to each of the four cytochrome complexes in turn. As electrons move through the complexes, protons bind briefly with the electrons and are released from the matrix to the intermembrane space. The electrons eventually end up on molecular oxygen to form metabolic water. The protons that were pumped into the IMS eventually move back to the matrix through F1ATPase and ATP is produced. |
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Term
| Why can’t electrons move backwards in the electron transport chain? |
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Definition
| As electrons move from complex to complex, the cytochromes undergo a conformational change that prevents the electrons from moving backwards. |
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Term
What elements can be used as the final electron acceptor in the electron transport
chain? What molecules can be formed and how? |
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Definition
| Oxygen or sulfur; water and hydrogen sulfide - accept electrons and protons attach after to form the molecule. |
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Term
Describe the fate of a typical proton in the matrix of the mitochondrion while the
electron transport system is active. |
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Definition
| A typical proton will be pumped from the matrix to the IMS and move back through F1ATPase to produce ATP. Some will end up on oxygen to form metabolic water. |
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Term
Every molecule of NADH gives up __ electron(s) to the cytochrome complex. As these electrons move through the complexes, __ proton(s) move from the ___ to the ___ space. For every ___ proton(s), ___ ATP molecule(s) are
produced. |
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Definition
Every molecule of NADH gives up 2 electron(s) to the cytochrome complex. As these electrons move through the complexes, 6 proton(s) move from the matrix to the intermembrane space. For every 6/2 proton(s), 3/1 ATP molecule(s) are
produced. |
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Term
| How many molecules of ATP are produced from one molecule of FADH2? Why? |
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Definition
| 2; There is no binding site for FADH2 until complex II of the cytochrome complexes. Therefore, only 4 protons are pumped from the matrix into the intermembrane space and only 2 molecules of ATP are produced. |
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Term
| List and describe the major RNA classes. |
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Definition
Ribosomal RNA (rRNA) – most abundant type in the cell
Messenger RNA (mRNA) – coder RNA that will be translated to protein; least abundant type in the cell and one of the most unstable (designed to be made fast, do its job, and be degraded
Transfer RNA (tRNA) – mechanistically involved in protein synthesis (specifically brings amino acids in to make a protein) Small nuclear RNA (snRNA) – produced and functions in the nucleus; 100 nucleotides in length; if it has a lot of uracil present it can be called uracil-rich small nuclear RNA (UsnRNA), which can act like an enzyme catalyst in the cell Heterogeneous nuclear RNA (hnRNA) – RNA that doesn’t fit into any other category Micro RNA (miRNA) or small cytoplasmic RNA (scRNA) – don’t know much about it but may be involved in triggers that induce metabolic traits and processes |
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Term
| How many types of RNA polymerases are present in prokaryotes? Eukaryotes? What are the types present and what classes of RNA do they transcribe? |
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Definition
| Prokaryotes – 1Eukaryotes – 3 Polymerase I: makes large rRNA (28, 18, and 5.8 S) Polymerase II: makes mRNA and UsnRNA Polymerase III: makes tRNA, small rRNA (5 S), and scRNA |
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Term
What genes are the three types of RNA polymerase responsible for
transcribing in eukaryotes? |
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Definition
| I – large rRNA (28, 18, 5.8 S) II – mRNA, UsnRNA III – tRNA, small rRNA, miRNA |
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Term
| What is a promoter and how is it useful during the process of transcription? |
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Definition
| Region on the coding strand of DNA that identifies the start of a gene tells polymerase where to start transcribing |
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Term
| List a couple functions of RNA polymerase during transcription. |
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Definition
Opens up the double helix to begin transcription Brings in nucleotides to create a new RNA strand
Unwraps and moves itself off the DNA when it reaches a termination sequence |
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Term
| The new strand of RNA produced during transcription is _______ to the template strand and __________________ ______ to the coding strand in the __ to __ direction. |
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Definition
The new strand of RNA produced during transcription is complementary to the template strand and identical (with the exception of ribose sugar and
uracil) to the coding strand in the 5’ to 3’ direction. |
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Term
| Describe the promotion of transcription that occurs in prokaryotes. |
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Definition
| Promoter region includes a TTGACA box and a TATATT box. The TATATT box is closest to the start of the gene, about 10 nucleotides upstream. There are about 17 nucleotides between the two boxes. The entire promoter region is approximately 35 nucleotides in length. This region tells RNA polymerase where and when to bind. |
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Term
| What is a hairpin loop? How does it form and what is its function? |
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Definition
| A hairpin loop is created when self-complementary sequences on the RNA transcript fold around and bond to each other to create a portion of the transcript that is double-stranded. It functions to increase stability and protection. It protects the 3’ end of the transcript from being degraded by exo-nucleases in the cell. |
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Term
| Only part of the mRNA transcript formed in eukaryotes codes for a protein. The __ __ _____ _____ _____ _____ region of the transcript is what the ribosome will recognize and bind to during translation. The other important region of this transcript is the __ _______ region. This transcript was produced by RNA polymerase __. These regions are NEVER _______. |
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Definition
| Only part of the mRNA transcript formed in eukaryotes codes for a protein. The 5’ non-coding (ribosomal binding site) region of the transcript is what the ribosome will recognize and bind to during translation. The other important region of this transcript is the 3’ noncoding region. This transcript was produced by RNA polymerase II. These regions are NEVER translated. |
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Term
| True or False: Post-transcriptional modifications are found in both prokaryotes and eukaryotes |
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Definition
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Term
| Why is an overtranscript created? How is it removed? |
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Definition
| An overtranscript is created because RNA polymerase II will not recognize the TTTT termination sequence and keep transcribing past the 3’ noncoding region for up to 1500 extra nucelotides. It is removed by a protein-RNA complex called UsnRNP (uracil rich small nuclear ribonuceloprotein). This complex will recognize a signal sequence – about 10 nucleotides upstream of the end of gene (AATAAA) – and cut the overtranscript off. |
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Term
Draw the addition of a G-cap to the 5’ end of the mRNA transcript. Why do we
add a G-cap? |
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Definition
|
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Term
| Why is an overtranscript created? How is it removed? |
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Definition
| An overtranscript is created because RNA polymerase II will not recognize the TTTT termination sequence and keep transcribing past the 3’ noncoding region for up to 1500 extra nucelotides. It is removed by a protein-RNA complex called UsnRNP (uracil rich small nuclear ribonuceloprotein). This complex will recognize a signal sequence – about 10 nucleotides upstream of the end of gene (AATAAA) – and cut the overtranscript off. |
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Term
| A ____ tail is attached to the __ end of the mRNA transcript by the enzyme _____ ____. It uses one molecule of ___ to add each extra ____ nucleotide. What percentage of mRNA transcripts will have this tail? |
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Definition
| A poly-A tail is attached to the 3’ end of the mRNA transcript by the enzymepoly-A synthetase. It uses one molecule of ATP to add each extra adeninenucleotide. What percentage of mRNA transcripts will have this tail? 85% |
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Term
| True or False: Exons are the intervening sequences that are removed during post-transcriptional modification |
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Definition
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Term
| What is a spliceosome and what is its function? |
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Definition
| A spliceosome is a complex of proteins and UsnRNA. It will cut introns out of the transcript and ligate the remaining exons back together to produce a single continuous coding region. |
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Term
| A strand of eukaryotic mRNA has a G-cap, a 40 nucleotide 5’ non-coding region, a 100 nucleotide 3’ non-coding region, a 110 nucleotide poly-A tail, 4 exons that are 40 nucelotides each in length, and 3 introns that are 20 nucelotides each in length. Answer the following questions. (1-7) |
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Definition
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Term
| 1) What is the maximum length of the immature mRNA transcript? |
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Definition
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Term
| 2) What is the length of the final mature mRNA that will be translated? |
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Definition
| Should read “What is the length of the final mature mRNA?” --> 411 |
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Term
3) What is the length of the mRNA transcript before post-transcriptional
modification? |
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Definition
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Term
| 4) What is the length of the gene? |
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Definition
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Term
| 5)What is the length of the protein that can be translated from the mature mRNA |
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Definition
| 160/3 = approximately 53 amino acids |
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Term
| 6) What is the length of the promoter region present inside of the gene? |
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Definition
| There is no promoter region inside of the gene and not enough information to decide its length. |
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Term
| 7) What is the length of the ribosome binding site (RBS)? |
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Definition
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Term
| What are the components of promoting transcription in eukaryotes and what are their functions? |
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Definition
Enhancer region – Very far upstream of the first nucleotide; serves to enhance the promoter region’s activity unravels heterochromatin a little bit so that it is easier for transcription factors to bind to the promoter, which in turn makes it easier for RNA polymerase to bind as well.
CAAT box – about 70-80 nucleotides upstream of the gene; where transcription factors will bind that serve to promote the binding of RNA polymerase; tells RNA polymerase WHEN to bind
TATA box – about 20-30 nucleotides upstream of the gene; tells polymerase where the first nucleotide is and WHERE to bind and start transcription |
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Term
Assume that 4 molecules of pyruvate enter the Krebs cycle and are
completely oxidized. Also allow oxidation of all electron carriers through the electron transport chain. How many protons are pumped from the matrix of the mitochondria to the inner membrane space? How many ATPs are created as a result of only the ETC? How many water molecules are formed? What enzyme allows for the production of ATP in the inner membrane of the mitochondria |
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Definition
| 88 protons; 44 ATP; 16 H2O; F1ATPase |
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Term
| he cytochrome complexes in the mitochondria have _____ ions in their core, normally present in the (oxidized or reduced) state. |
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Definition
| Metal ions in Oxidized state |
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Term
Which of the following proteins can be used to synthesize ribosomal RNA in eukaryotes? Circle all that apply.
a). RNA polymerase I
b). RNA polymerase II
c). RNA polymerase III
d). none of the above |
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Definition
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Term
| ________ RNA is usually about 100 nucleotides in length, and functions in the nucleus. It can act as an enzyme catalyst and has been found to have a lot of the _____ nucleotide present. |
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Definition
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Term
| raw a prokaryotic mRNA gene and promoter regions and mRNA transcript formed according to the following specifications: the gene should be 10 nucleotides downstream of the second conserved sequence and 10 nucleotides in length. Label the coding and template strands on the gene. |
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Definition
| see notes and mock exam key: Any sequence you want to write is fine as long as you include the promoter regions and the gene is 10 nt in length – make sure that you include the TTGACA and TATATT boxes (should be about 17 nt in between the two) and gene should be 10 nucleotides after TATATT on coding strand. Template strand should be complementary to the coding strand. Transcript should be identical to coding strand with the exception of uracil in the place of thymine. |
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Term
| Which RNA polymerase has the ability to transcribe all genes found in a eukaryotic cell? |
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Definition
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Term
| _______is the termination sequence present on a gene for prokaryotic mRNA. This is the (same or different) as the termination sequence present on a gene coding for eukaryotic mRNA. |
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Definition
Row of at least 4 T's (TTTT)
different |
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Term
| True or False: All RNA transcripts in eukaryotes undergo post-transcriptional modifications |
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Definition
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Term
| __________is the sequence of nucelotides present on the template strand of the gene for eukaryotic mRNA that signals UsnRNP to remove the over-transcript produced. This sequence is about __ nucelotides upstream of the end of the gene. |
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Definition
TTATTT (signal sequence)
10 |
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Term
| Give two functions of a spliceosome. |
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Definition
| Cuts introns out of the mRNA transcript and ligates the exons back together |
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Term
| True or False: All mature eukaryotic mRNA transcripts have a G-cap and a poly-A tail. |
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Definition
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Term
| List the two conserved sequences found in the promoter region of the gene for eukaryotic mRNA and describe their locations in relation to each other and the gene |
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Definition
| TATA and CAAT boxes – TATA box is 20-30 nt upstream of the gene, CAAT box is 70-80 nt upstream of the gene |
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Term
| Eukaryotes have __ S ribosomes, while prokaryotes have __ S ribosomes. The eukaryotic ribosome is made of a large subunit that is __ S and a small subunit that is __ S. (True or False): The large subunit is made exclusively of large ribosomal RNA. |
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Definition
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Term
| Draw and label a “Christmas tree.” What gene transcripts are being produced and in what ratio? What is the significance of the regions in between each Christmas tree |
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Definition
Drawing should be similar to what is given in the notes – straight line represents a strand of DNA, each section of tree represents the gene, each dot represents RNA polymerase I, each strand coming off dot represents the transcript, space in between genes is spacer region; email me if you would like to see a complete drawing
Large rRNA gene transcripts produced (18, 28, 5.8 S) in a 1:1:1 ratio
Spacer region contains the promoter and promoter-like sequences help promote and enhance transcription of the gene |
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Term
| Eukaryotic ribosomal subunits are assembled in the ______ region of the _____. Each subunit is made up of some combination of 4 ___ molecules and about __ proteins. ____ ribosomal RNA is synthesized in the ____ region of the nucleolus, while ___ ribosomal RNA is synthesized in the _____. The proteins that are incorporated into the structure of a ribosome are synthesized in the ____. Once these parts are all assembled into ribosomal subunits, they are exported to the _____. |
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Definition
granular
nucleolus
4 RNA
70 proteins
Large ribosomal
fibrillar region
small ribosomal
nucleoplasm
cytoplasm
cytoplasm |
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Term
| A eukaryotic mRNA transcript has a G-cap, a 40 nucelotide 5’ noncoding region, a 50 nucleotide 3’ noncoding region, a 100 nucelotide poly-A tail, 3 exons that are 20 nucelotides each in length, and 2 introns that are 10 nucleotides each in length. What is the length of the mature mRNA that is transported to the cytoplasm and the length of the mRNA that will be translated? |
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Definition
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