Term
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Definition
| The mechanism by which cells copy DNA into RNA (aka RNA synthesis). |
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Term
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Definition
| Genetic information flows from DNA to RNA to protein. |
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Term
| How does the mRNA intermediate allow for amplification that wouldn't be possible if DNA were directly read into protein? |
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Definition
| Many identical copies of RNA can be made from the same gene, and each RNA molecule can direct the synthesis of many proteins. |
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Term
| How does RNA differ from DNA? |
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Definition
1) Ribose rather than deoxyribose and
2) Uracil (U) rather than thymine (T).
*Since both U and T pair with A, rules for base-pairing complementarity are not altered. However, RNA exists in single-stranded form unlike DNA. |
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Term
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Definition
| The enzymes that carry out transcription. Like DNA polymerases, catalyze the formation of phosphodiester bonds that link the nucleotides together and form the sugar-phosphate backbone of the RNA chain. |
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Term
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Definition
| The strand of DNA that acts as a template for the synthesis of a complementary RNA strand. |
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Term
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Definition
| The RNA chain produced by transcription. |
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Term
| T or F: The transcript has a sequence identical to the template DNA strand, except it has U in place of T at the respective positions. |
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Definition
| False! It has a sequence identical to the non-template DNA strand, except it has U in place of T at the respective positions. |
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Term
| In what direction does transcription proceed? |
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Definition
| 5' to 3' direction (everything is added to the 3' OH). |
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Term
| In which direction is the template DNA strand read during transcription? |
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Definition
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Term
| What provides the energy needed for transcription? |
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Definition
| The ribonucleotides are covalently bonded together by phosphodiester bonds, the energy being supplied by the hydrolysis of two phosphate groups from the ribonucleotide triphosphate. |
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Term
| What unwinds the DNA strand prior to transcription? |
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Definition
| RNA polymerase. Note that there is no helicase-like enzyme. |
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Term
| What are some of the similarities between RNA and DNA polymerases? |
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Definition
1) All cellular RNAs are made by RNA polymerases, using NTPs as substrates, according to instructions given by the DNA template.
2) 5'—>3' synthesis, reading a template strand of a gene 3' --> 5'. |
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Term
| What are some of the differences between RNA and DNA polymerases? |
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Definition
1) Transcription involves de novo (“anew”) synthesis; no “primer” is required.
2) No proof-reading function (i.e., can’t back-up and correct mistakes).
3) No exonuclease activities.
4) DNA template is fully conserved (semi-conserved in DNA replication).
5) Only one of the two strands serves as a template for a given gene. |
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Term
| T or F: Promoters are transcribed. |
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Definition
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Term
| T or F: Terminators are transcribed. |
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Definition
| True. Unlike promoters, terminators are transcribed, although they are noncoding. |
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Term
| What are the three parts of transcription? |
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Definition
1) Initiation - where RNA polymerase binds to the promoter and begins RNA synthesis.
2) Elongation - where RNA synthesis proceeds down the gene uninterrupted.
3) Termination - where RNA polymerase recognizes the terminator sequence and falls off the template strand. |
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Term
| With regard to a gene, which direction is upstream? |
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Definition
| Upstream refers to the 5' direction. |
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Term
| What determines which DNA strand is to be transcribed? |
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Definition
| Since DNA is double-stranded, two different RNA molecules could in principle be transcribed from any gene, using each of the two DNA strands as template. The promoter, which is asymmetric, binds polymerase in only one orientation, and hence only one of the two strands is transcribed. However, the direction of transcription with respect to the chromosome as a whole will vary from gene to gene. |
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Term
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Definition
Covalent modification that occurs co-transcriptionally in maturing eukaryotic mRNA that includes:
1) RNA capping (5' end) - consists of a guanine nucleotide connected to the mRNA via an unusual 5' to 5' triphosphate linkage. This guanosine is methylated on the 7 position directly after capping in vivo by a methyl transferase. It is referred to as a 7-methylguanylate cap, abbreviated m7G.
2) Polyadenation - addition of a poly(A) tail to an RNA molecule. The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. |
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Term
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Definition
| Capping of the pre-mRNA involves the addition of 7-methylguanosine (m7G) to the 5' end. To achieve this, the terminal 5' phosphate requires removal, which is done with the aid of a phosphatase enzyme. The enzyme guanosyl transferase then catalyses the reaction, which produces the diphosphate 5' end. The diphosphate 5' prime end then attacks the α phosphorus atom of a GTP molecule in order to add the guanine residue in a 5'5' triphosphate link. The enzyme (guanine-N7-)-methyltransferase ("cap MTase") transfers a methyl group from S-adenosyl methionine to the guanine ring. This type of cap, with just the (m7G) in position is called a cap 0 structure. The ribose of the adjacent nucleotide may also be methylated to give a cap 1. Methylation of nucleotides downstream of the RNA molecule produce cap 2, cap 3 structures and so on. In these cases the methyl groups are added to the 2' OH groups of the ribose sugar. The cap protects the 5' end of the primary RNA transcript from attack by ribonucleases that have specificity to the 3'5' phosphodiester bonds. |
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Term
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Definition
| The pre-mRNA processing at the 3' end of the RNA molecule involves cleavage of its 3' end and then the addition of about 200 adenine residues to form a poly(A) tail. The cleavage and adenylation reactions occur if a polyadenylation signal sequence (5'- AAUAAA-3') is located near the 3' end of the pre-mRNA molecule, which is followed by another sequence, which is usually (5'-CA-3'). The second signal is the site of cleavage. A GU-rich sequence is also usually present further downstream on the pre-mRNA molecule. After the synthesis of the sequence elements, two multisubunit proteins called cleavage and polyadenylation specificity factor (CPSF) and cleavage stimulation factor (CStF) are transferred from RNA Polymerase II to the RNA molecule. The two factors bind to the sequence elements. A protein complex forms that contains additional cleavage factors and the enzyme Polyadenylate Polymerase (PAP). This complex cleaves the RNA between the polyadenylation sequence and the GU-rich sequence at the cleavage site marked by the (5'-CA-3') sequences. Poly(A) polymerase then adds about 200 adenine units to the new 3' end of the RNA molecule using ATP as a precursor. As the poly(A) tails is synthesised, it binds multiple copies of poly(A) binding protein, which protects the 3'end from ribonuclease digestion. |
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Term
| When does RNA capping and polyadenylation occur? |
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Definition
| RNA capping occurs just after the RNA polymerase has synthesized the 5’ end of the primary transcript and before it has completed transcribing the whole gene. Polyadenylation occurs following riboendonucleolytic cleavage of the primary transcript before it has completed transcription, and provides a 3’ end “tail” consisting of ~ 200 A residues. |
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Term
| What does modification of the ends of eukaryotic mRNAs facilitate? |
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Definition
1) Transport to the cytoplasm
2) Increased stability
3) Translational efficiency |
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Term
| T or F: Both eukaryotic and prokaryotic mRNA molecules are modified by capping and polyadenylation. |
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Definition
| False. The 5’ and 3’ ends of a bacterial mRNA are the unmodified ends of the chain synthesized by the RNA polymerase, which initiates and terminates transcription at those points, respectively. The corresponding ends of a eukaryotic mRNA are formed by adding a 5’ cap and the addition of a poly(A) tail, respectively. |
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Term
| T or F: Bacterial mRNAs can contain the instructions for several different proteins, whereas eukaryotic mRNAs nearly always contain the information for only a single protein. |
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Definition
| True. Prokaryotic mRNA is polycistronic while eukaryotic mRNA is monocistronic. |
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Term
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Definition
| Noncoding sequences interrupting eukaryotic transcripts. Introns must be removed to form the pre-mRNA. |
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Term
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Definition
| A modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation. For many eukaryotic introns, splicing is done in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs), but there are also self-splicing introns. |
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Term
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Definition
Coding sequences, plus 5’-UTR and 3’-UTR [UTR = UnTranslated Region]). Exons are
usually much shorter than introns, so the bulk of the RNA is removed from the primary transcript and degraded. |
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Term
| How do eukaryotic and bacterial genes differ? |
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Definition
| A bacterial gene consists of a single stretch of uninterrupted nucleotide sequence that encodes the amino acid sequence of a protein. In contrast, the coding sequences (exons) of most eukaryotic genes are interrupted by noncoding sequences (introns). |
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Term
| How do introns contribute to genetic diversity? |
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Definition
1) They expand the total repertoire of protein structures via alternative splicing (described below). Thus, even though humans have only five times as many genes as the single cell eukaryote baker’s yeast (~25,000 vs. ~6,000, respectively) they appear to have at least eighty times as many proteins (>500,000 vs. ~6,000).
2) Introns significantly expand the target size of genes within genomes, thereby increasing the potential of crossing over during meiosis, promoting hybrid vigor. |
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Term
| Are the sequences of introns conserved? |
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Definition
| The nucleotide sequences of different introns show little resemblance, except at key positions where they are conserved by a few short nucleotide sequences that act as cues for their removal. These sequences are present at or near the ends of the introns. |
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Term
| What recognizes special sequences that signal the beginning and end of an intron and covalently links the exons together? |
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Definition
| The special sequences are recognized by snRNPs, which cleave the RNA at the intron-exon borders and covalently link the exons together. |
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Term
| snRNP (small nuclear ribonucleoprotein particles) |
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Definition
| RNA-protein complex that recognizes special sequences that signal the beginning and end of an intron and covalently links the exons together. |
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Term
| The RNA splicing mechanism (diagram) |
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Definition
[image]
RNA splicing is catalyzed by an assembly of snRNPs (shown as colored circles) plus other proteins (not shown). One function of the complex of snRNPs is to bring the two ends of the intron together so that the reaction can take place. After the assembly of the snRNPs, a specific adenine nucleotide in the intron sequence (indicated in red) attacks the 5’ splice site and cuts the sugar- phosphate backbone of the RNA at this point. The cut 5’ end of the intron becomes covalently linked to the adenine nucleotide, forming a loop, or lariat, in the RNA molecule (see Fig. 7-16). The free 3’-OH end of the first exon sequence then reacts with the beginning of the second exon sequence, cutting the intron at its 3’ end and, at the same time, joining the two exons together. The outcome of these splicing reactions is that the two exon sequences become joined into a continuous (uninterrupted) coding sequence, and the lariat containing the intron sequence is released and eventually degraded. |
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Term
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Definition
| A set of proteins plus a uracil- rich RNA (U1 snRNA or U2 snRNA, etc.). Some of the proteins are conserved between different U-snRNPs. |
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Term
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Definition
| A complex of snRNA and protein subunits that removes introns from a transcribed pre-mRNA (hnRNA) segment. |
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Term
| How does alternative splicing produce different mRNAs? |
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Definition
| RNA splicing allows eukaryotes an additional advantage over prokaryotes in that the primary transcripts of many genes can be spliced in various ways to produce different mRNAs, depending on the cell type in which the gene is being expressed, or the stage of development of the organism. This allows different proteins to be produced from the same gene. Thus, rather than being wasteful, RNA splicing enables eukaryotes to increase the already enormous coding potential of their genomes. The final exon in the mRNA is distinguished by endonucleolytic cleavage of the primary transcript (prior to termination) and the attachment of a poly(A) tail co-transcriptionally by an enzyme known as a poly(A) polymerase. |
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Term
| What controls alternative splicing? |
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Definition
| Regulatory proteins that bind to specific sites in the respective pre-mRNA introns and/or exons that are under developmental- or tissue-specific control. |
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Term
| T or F: RNA splicing is a rare event. |
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Definition
| False. Roughly 90% of all human genes are alternatively-spliced. |
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Term
| Where does transcription take place? |
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Definition
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Term
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Definition
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Term
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Definition
| The process of turning on and off genes at a moment’s notice dictated by signals from the environment. |
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Term
| What accounts for cell/tissue differentiation? |
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Definition
| Differentiation arises from the accumulation of different sets of proteins due to altered states of gene regulation. The cells of an organism differ not because they contain different gene sequences, but because they express the same sets of genes differently. |
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Term
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Definition
| Many proteins are common to all the cells of a multicellular organism. These are called housekeeping proteins, derived from housekeeping genes, and include enzymes required for glycolysis as well as major structural proteins of the cytoskeleton. |
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Term
| Where are most genes regulated? |
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Definition
At the level of transcription. Transcriptional control dictates:
1) Which proteins are produced (majority are OFF at any given time).
2) Rate at which they are produced (high vs. low level). |
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Term
| Where can eukaryotic gene expression be regulated? |
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Definition
1) Transcription
2) RNA processing
3) RNA transport from the nucleus
4) Translation
5) Protein activity |
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Term
| How is transcription controlled? |
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Definition
| Transcription is usually controlled at the level of initiation, where RNA polymerase recognizes the promoter and forms the first phosphodiester linkage of an RNA chain. In addition to the promoter, nearly all genes, whether bacterial or eukaryotic, have regulatory DNA sequences that are needed in order to switch the gene on and off. Whether a gene is expressed or not depends on a lot of factors, including the type of cell and its surroundings. Some regulatory DNA sequences, such as those in bacteria, are as short as 10 nucleotide pairs. Others, particularly in eukaryotes, are very long (> 10,000 nucleotide pairs) and act as molecular microprocessors, responding to a variety of signals that they integrate into an instruction that determines the rate at which transcription is initiated. |
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Term
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Definition
| The process of turning on or off genes during embyro development, or in response to signals from the environment. |
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Term
| How does a gene regulatory protein bind to the major groove of DNA? |
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Definition
| Side groups of amino acids bond with specific base pairs in DNA, recognized at their edges, without the need to open the double helix. Typically, the protein-DNA interface would consist of 10 to 20 contacts, each involving a different amino acid and each contributing to the strength of the protein-DNA interaction, like velcro. |
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Term
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Definition
| An “activator protein” that activates transcription of the E. coli lac operon. The CAP- DNA complex forms a “genetic switch”, controlled by the presence or absence of cyclic AMP. CAP is one of many transcriptional regulatory proteins found in E. coli. Other organisms, including humans, have their own versions of activator proteins which act similarly. |
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Term
| What controls the CAP protein in E. coli? |
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Definition
| The presence or absence of cyclic AMP. |
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