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53 Cards in this Set
- Front
- Back
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What is the coding strand of DNA? What's another name for it? What's the template strand? |
1. The strand that matches the RNAs sequence. Also called the non template strand 2. The strand with a sequence complimentary to the RNA. Acts as the RNA template. |
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True or false: A cell cannot express different genes at different rates. |
False. Cells are able to make different amounts of a gene protein based on cell needs. |
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What is different about RNA compared to DNA? |
1. Primarily single stranded 2. Ribose instead of deoxyribose 3. OH on 2' carbon instead of an H, so less stable 4. Uses urasil instead of thymine 5. Some can act as enzymes (called ribozyms) 6. Can fold into a variety of shapes 7. Is much shorter than DNA |
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How does uracil differ from thymine? |
It has a CH group instead of a CH3 group and is less stable. |
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In what direction does RNA polymerase transcribe DNA? |
Like DNA polymerase, it transcribes in a 3' to 5' direction. This means RNA is synthesized in a 5' to 3' direction. |
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How long is the short region of hybrid DNA/RNA double helix as DNA is transcribed? |
Approx. 9 nucleotides, forming only transiently as the polymerase moves. |
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How is RNA pol. Different from DNA pol.? |
1. It uses ribonucleotides for phosphates as substrates. Catalyzes linkage of ribonucleotides. 2. Can start an RNA chain without a primer. 3. Is not as accurate as DNA polymerase |
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What are some of the different types of RNA? |
1. mRNA: translated into proteins 2. rRNA: forms the core of ribosomes. Catalyzes protein synthesis (ribozymes) 3. microRNA: regulate gene expression 4. tRNA: bring amino acids to ribosome during translation. 5. Others include siRNA, snRNA, and lnRNA. |
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Describe transcription in bacteria. |
1. RNA polymerase contains a subunit called sigma factor that recognizes a DNA promoter 2. Sigma factor releases once transcription begins. 3. When polymerase hits a terminator sequence, it halts and releases the DNA template as well as the new RNA 4. Freed polymerase binds to a new sigma factor. |
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True or false: only one RNA polymerase can transcribe DNA a time. |
False. Many can do so at the same time. |
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What are the two promoter sequences in bacteria? Where are they located in relation to the start site? |
The -35 and -10 regions, and the sequences are highly conserved between organisms. They are upstream of the start site. RNA polymerase recognizes these sites. |
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What does the polarity (direction) of a promoter determine? |
It determines which DNA strand is transcribed since RNA polymerase can only move in a 3' to 5' direction. |
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Is the terminator nucleotide sequence transcribed into bacterial RNA? Is the promoter sequence? |
The terminator sequence is, but the promoter sequence is not. |
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What do the three eukaryotic RNA polymerases do? |
1. RNA pol. I: transcribes most rRNA genes 2. RNA pol. II: transcribes all protein-coding genes, miRNA genes, and genes for other non-coding RNAs (e.g. the spliceosome). 3. RNA pol. III: tRNA genes, 5S rRNA genes, and genes for many other small RNAs |
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What is different between eukaryotic transcription and bacterial transcription? |
1. Bacteria have one RNA polymerase. Eukaryotes have 3. 2. Eukaryotic polymerases need many accessory proteins, including general transcription factors. Bacteria polymerase only needs the sigma factor. 3. Bacteria don't have a nucleus, so transcripts can be translated while they're being made. 4. Bacterial genes are grouped in operons, so several genes can be on the same transcript. For eukaryotes, only one gene per transcript. 5. Bacterial DNA isn't packaged into nucleosomes. |
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Describe transcription initiation in eukaryotes. |
1. Eukaryotic promoters contain a TATA box 2. TFIID, a general transcription factor also know as the TATA-binding protein, recognizes the TATA box. 3. TFIIB binds once TFIID has bound to the promoter. 4. The rest of the GTFs and RNA pol. II assemble at the promoter. 5. TFIIH pries apart the double helix at the transcription start point using ATP hydrolysis energy. 6. TFIIH phosphorylates RNA pol. II, releasing most GTFs, so it can begin transcription. |
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What is the site if phosphorylation for TFIIH? |
The long polypeptide tail that extends from the RNA pol. II. |
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After eukaryotic transcription starts which GTF remains bound to RNA pol. II through multiple rounds of transcription initiation? |
TFIID |
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What does TFIID (the TATA-binding protein) do to the DNA when it binds to the TATA box? |
It bends the double helix. This helps attract the other GTFs. |
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What promoter locations attract what GTFs in eukaryotes? |
1. -35 location: TFIIB 2. -30 location: TBP (subunit of TFIID) 3. Transcription start site: TFIID 4. +30 location: TFIID |
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Where are rRNAs synthesized and combined with proteins to form ribosomes? |
The nucleolus. |
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What does phosphorylation of the RNA pol. II tail allow? |
RNA processing proteins to assemble there. (Allows 5' capping, splicing, and polyadenylation to add 3' poly-A tail). |
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What are the necessary modifications for pre-mRNA before it can be exported from the nucleus? |
Capping, polyadenylation, and splicing. |
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Where is the eukaryotic cap? What is it made of? How about the poly-A tail? |
1. The 5' end of RNA. It's a 7-methylguanosine 2. The 3' end. A series of Adenines.
Both help stabilize the mRNA. |
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What are the protein-coding sequences of eukaryotic genes? The non-coding sequences? |
Exons and introns respectively. |
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Mutations in what gene are responsible for the most prevalent form of hemophelia? |
Factor VIII, a 26-exon containing gene that functions in the blood clotting pathway. |
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How are introns removed from pre-mRNA? Describe the process. |
Splicing. 1. An adenine branch point in the middle of the intron attacks the 5' splice site and cuts the mRNA phosphodiester bonds. 2. The splice site becomes covalently linked to the 2' OH of the A's ribose, forming a lariat. 3. The 3' end of the revealed exon reacts with the 5' end of the next exon, joining them together and releasing the intron. |
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What recognizes the special splice site sequences in pre-mRNA, and what do they do in general? |
Small nuclear ribonucleoproteins (snRNPs). They direct the cleavage at the intron-exon boarders and catalyze the covalent linkage of the exon sequences. |
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What are the 5 snRNPs? What do they do? |
1. U1 and U2: Bind to the 5' splice site and lariat branch point respectively. 2. U4 (didn't say) 3. U5 (didn't say) 4. U6: Rechecks the 5' splice site by displacing U1 |
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What drives the formation of the spliceosome active site? |
Conformational changes in U2 and U6 snRNPs triggered by the hydrolysis of ATP by spliceosomal proteins. |
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What are exon junction complexes (EJCs)? |
A group of RNA-binding proteins the spliceosome deposits on the mRNA to mark the splice site as successfully completed. |
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What is alternative splicing? |
The process by which exons are skipped over. This allows one gene to make different proteins. |
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How does the nucleus know an mRNA is ready to be transported to the cytosol? |
It must have a 5' cap, a poly-A tail, and exon junction complexes. |
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What happens when an mRNA is deemed transport ready? |
A nuclear transport receptor associated with jt and guides it through the nuclear pore. |
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How are mRNAs eventually degraded? |
RNAses in the cytosol. |
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What determines how much protein is in a cell? |
Rates of transcription/translation and mRNA/protein degradation. |
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How many nucleotides make up a codon in the mRNA open reading frame? |
Three. This code is redundant, so some aa's have multiple codons. |
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What is the start codon and what does it code for? What are the stop codons? |
1. AUG. Codes for methionine in eukaryotes and formyl-methionine in bacteria 2. UAA, UAG and UGA |
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Describe the shape of a tRNA molecule. |
It is like a cloverleaf with four double stranded sections and three single stranded loops. The bottom loop is the anticodon loop, which helps in translation. Amino acids attach to the 3' end. Each tRNA code for a specific amino acid. |
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How do uncharged tRNAs bond with their amino acid? |
Aminoacyl synthetases bind to the tRNA. ATP is then hydrolyzed to provide energy to attach the aa to the 3' end of the tRNA. |
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Describe prokaryotic ribosomes. Eukaryotic ribosomes. |
1. 30S small subunit and 50S large subunit. 2. 40S small subunit and 60S large subunit. All ribosomes have an A (aminoacyl) site, P (peptidyl) site, and E (exit) site. |
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Where does the mRNA bind in the ribosome? |
The small subunit. |
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What are the four steps to translating an mRNA? |
After the ribosome is assembled: 1. A charged tRNA binds to the A site. It's anticodon must match the codon exposed here. 2. In the ribosome peptidyl transferase center of the large subunit, the C end of the aa in the P site is bound to the N end of the aa in the A site. 3. The large subunit translocates, moving the tRNA in the P site to the E site and the tRNA in the A site to the P site. 4. The small subunit moves three nucleotides along, exposing the next codon for translation to continue.
Rinse and repeat until a stop codon lines up with the A site. |
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What is a ribozyme? |
rRNA that can catalyze reactions such as the rRNA in the peptidyl transferase center of the ribosome. |
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Describe translation initiation in eukaryotes? |
The initiator tRNA, translation initiation factors, and the small ribosomal subunit recognize and bind to the 5' cap of an mRNA. Then, they scan along until they reach the start codon. The initiation factors dissociate and the large ribosomal subunit binds to the complex with the initiator tRNA in the P site, leaving the A site open to continue translation. |
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What is different about translation initiation in prokaryotes? |
There is no 5' cap on the mRNA. Instead, the small subunit binds to the Shine-Delgarno sequence, which triggers the rest of the complex to come together. |
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What is a release factor? |
It is the protein coded by a stop codon. When a stop codon is reached, a release factor binds in the A site. This causes the translation complex to dissociate. |
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What is a polyribosome/polysome? |
Multiple ribosomes translate an mRNA at the same time. The spiral structure formed is called the polyribosome/polysome. |
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How are antibiotics used to inhibit prokaryotic protein synthesis? Give some examples. |
Prokaryotic translation structures are slightly different from eukaryotic structures. Antibiotic inhibitors block protein or RNA synthesis in prokaryotes without harming eukaryotic cells. 1. Tetracycline: blocks binding of aminoacyl tRNA to A site 2. Streptomycin: prevents transition from initiation complex to chain elongation. 3. Chloramphenicol: blocks peptidyl transferase reaction 4. Cyclohexamide: blocks translocation step 5. Rifamycin: blocks initiation of transcription by binding to and inhibiting RNA polymerase |
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What are proteasomes, and how do they break down proteins? |
Large protein complexes with a cap on each end and four rings in between filled with proteases. The caps unfold targeted proteins, which are then degraded in the rings. |
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What are some of the post translation protein modifications? |
1. Protein folding 2. Phosphorylation 3. Glycosylation 4. Methylation There are more than 100 types of covalent modifications. |
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Why is it argued that RNA predates DNA? |
1. Life requires autocatalysis, which RNA can do but DNA can't. 2. RNA can store information as well as catalyze reactions DNA is better at maintaining genetic information, and proteins are better at catalyzing reactions, but RNA remains the link between the two. |
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What are some of the biochemical reactions ribozymes can catalyze? |
1. Peptide bond formation in protein synthesis (rRNA) 2. RNA splicing (small nuclear RNAs) 3. DNA ligation 4. RNA polymerization, phosphorylation, and aminocylation 5. RNA alkylation 6. C-C bond rotation (isomerization) |
