Chapter 11: Transcription And Rna Processing

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Transcription

Back 1

- Process through which RNA is formed along a DNA template

- The enzyme RNA polymerase catalyzes the formation of RNA from ribonucleoside triphosphates

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Translation

Back 2

- Occurs on ribosomes

- Protein (polypeptide) synthesis directed by a specific messenger RNA

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Gene Transcript

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- The RNA molecule produced by transcription of a gene

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Genetic Code

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- The set of 64 nucleotide triplets that specify the 20 amino acids and polypeptide chain initiation and termination

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Codons

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- A set of three adjacent nucleotides n an mRNA molecule that specifies the incorporation of an amino acid into a polypeptide chain or that signals the end of polypeptide synthesis

- Codons with the latter function are called termination codons

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Ribosomes

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- Cytoplasmic organelle on which proteins are synthesized

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Messenger RNA (mRNA)

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- RNA that carries information necessary for protein synthesis from the DNA to the ribosomes

- Codes for proteins

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Primary Transcript

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- Called pre-mRNA in eukaryotes

- The RNA molecule produced by transcription prior to any postranscriptional modifications

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pre-mRNA

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- The primary transcript of a eukaryotic gene prior to processing to produce an mRNA

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Introns

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- Intervening sequences of DNA bases within eukaryotic genes that are not represented in the mature RNA transcript because they are spliced out of the primary RNA transcript

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Exons

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- The segments of a eukaryotic gene that correspond to the sequences in the final processed RNA transcript of that gene

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Splicing

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- The process that covalently joins exon sequences of RNA and eliminates the intervening intron sequences

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Spliceosomes

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- The RNA/protein complex that excises introns from primary transcripts of nuclear gens in eukaryotes

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Transfer RNA (tRNA)

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- RNAs that transport amino acids to the ribosomes, where the amino acids are assembled into proteins

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Ribosomal RNA (rRNA)

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- The RNA molecules that are structural and enzymatic components of ribosomes

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Small Nuclear RNA (snRNA)

Back 16

- Small RNA molecules that are located in the nuclei of eukaryotic cells

- Most snRNAs are components of the spliceosomes that excise introns from pre-mRNAs

- With proteins, it forms complexes used for RNA processing

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MicroRNA (miRNA)

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- Another name for short interfering RNA (siRNA)

- Double stranded RNA molecules 21-28 base pairs long that mediate the phenomenon of RNA interference

- Used to block the expression of mRNAs

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Central Dogma of Molecular Biology

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- Genetic information flows from DNA to DNA during chromosome replication

- Genetic information flows from DNA to RNA during transcription

- Genetic information flows from RNA to protein during translation

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Template Strand

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- Transcribed strand of a gene

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Nontemplate Strand

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- Contemplate strand of a gene

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Sense RNA (Sense Strands)

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- A primary transcript or mRNA that contains a coding region (contiguous sequence of condons) that is translated to produce a polypeptide

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Antisense RNA

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- RNA that is complementary to the pre-mRNA or mRNA produced from a gene

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RNA polymerase

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Promoter

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- A nucleotide sequence to which RNA polymerase binds and initiates transcription

- A chemical substance that enhances the transformation of benign cells into cancerous cells

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Transcription Bubble

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- A locally unwound segment of DNA in which an RNA transcript is being synthesized

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Where are Genes present?

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- In the nucleus

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Where are polypeptides synthesized?

Back 27

- In the cytoplasm

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Transcription Unit

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- A segment of DNA that contains transcription initiation and termination signals and is transcribed into one RNA molecule

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The Process of Transcription

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1. Initiation

2. Elongation

3. Termination

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Initiation (of DNA, RNA, or Protein Synthesis)

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- The incorporation of the first subunit (nucleotide or amino acid) during the synthesis of a macromolecule (DNA, RNA, or polypeptide)

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Elongation (of DNA, RNA, or Protein Synthesis)

Back 31

- The incorporation of the second and subsequent subunits (nucleotides or amino acids) during the synthesis of a macromolecule (DNA, RNA, or polypeptide)

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Termination (of DNA, RNA, or Protein Synthesis)

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- The release of a complete macromolecule (DNA, RNA, or polypeptide) after the incorporation of the final subunit (nucleotide or amino acid)

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Holoenzyme

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- The form of a multimeric enzyme in which all of the component polypeptides are present

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Tetrameric Core

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-

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Sigma Factor

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- The subunit of prokaryotic RNA polymerases that is responsible for the initiation of transcription at specific initiation sequences

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Upstream Sequences

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- A sequence in a unit of transcription that precedes the 5' transcription start site

- The nucleotide pair in DNA corresponding to the nucleotide at the 5' end of the transcript (RNA) is designated +1.

- The preceding nucleotide pair is designated -1.

- All preceding (-) nucleotide sequences are upstream sequences

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Downstream Sequences

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- A sequence in a unit of transcription that follows (is located 3' to) the transcription start site

- The nucleotide pair in DNA corresponding to the nucleotide at the 5' end of the transcript (RNA) is designated +1. The following nucleotide pair is designated +2

- All of the following (+) nucleotide sequences are downstream sequences

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-10 Sequence

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- TATAAT sequence

- An AT_RICH SEQUENCE IN PROKARYOTIC PROMOTERS THAT FACILITATES THE LOCALIZED UNWINDING OF DNA and the initiation of RNA synthesis.

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-35 Sequence

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- The recognition sequence

- TTGACA

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Consensus Sequences

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- The nucleotide sequence that is present in the majority of genetic signals or elements that perform a specific function

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Recognition Sequence

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- (-35 Sequence)

- TTGACA

- A nucleotide sequence in prokaryotic promoters to which the sigma factor of RNA polymerase binds during the initiation of transcription

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Termination Signal

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- In transcription, a nucleotide sequence that specifies RNA chain termination

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Rho-dependent Terminators

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Rho-independent Terminators

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RUT

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- rho utilization

- A rho protein binding site

- Rho protein binds to the rut sequence in the transcript and moves 5' to 3' following RNA polymerase

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In eukaryotes, the majority of the primary transcript of genes that encode polypeptides undergo what three major modifications prior to their transport to the cytoplasm for translation?

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1. 7-Methyl guanosine caps are added to the 5' ends of the primary transcripts

2. Poly(A) tails are added to the 3' ends of the transcripts, which are generated by cleavage rather than by termination of chain extension

3. When present, intron sequences are spliced out of transcripts

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5' cap on most eukaryotic mRNAs

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- 7-Methyl guanosine residue joined to the initial nucleoside of the transcript by a 5'-5' phosphate linkage

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3' Poly(A) tail on most eukaryotic mRNAs

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- A polyadenosine tract 20 to 200 nucleotides long

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Heterogeneous nuclear RNA (hnRNA)

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- Eukaryotes

- The population of primary transcripts in a nucleus

- Most hnRNAs are noncoding intron sequences

- Most hnRNAs actually consists of pre-mRNA molecules undergoing various processing events before leaving the nucleus

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RNA Polymerase I

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- Location = Nucleolus

- Products = Ribosomal RNAs, excluding 5S rRNA

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RNA Polymerase II

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- Location = Nucleus

- Products = Nuclear pre-mRNAs

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RNA Polymerase III

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Location = Nucleus

- Products = tRNAs, 5S rRNA, and other small nuclear RNAs

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Transcription factors

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- A protein that regulates the transcription of genes

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RNA Polymerase IV

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- Location = Nucleus (plants)

- Products = Small interfering RNAs (siRNAs)

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RNA Polymerase V

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- Location = Nucleus (plants)

- Products = Some siRNAs plus noncoding (antisense) transcripts of siRNA target genes

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Chromatin Remodeling

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- Must occur before transcription can begin

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Short Interfering RNAs (siRNAs)

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- Also known as microRNA molecules

- Double-stranded RNA molecules 21-28 base pairs long that mediate the phenomenon of RNA interference

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TATA Box

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- A conserved promoter sequence that determines transcription start site

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CAAT Box

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- A conserved nucleotide sequence in eukaryotic promoters involved in the initiation of transcription

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Basal Transcription Factors

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- Proteins required for the initiation of transcription in eukaryotes

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Transcription Factor X for RNA Polymerase II (TFIIX)

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- A protein required for the initiation of transcription by RNA polymerase II in eukaryotes

- X represents any one of several different factors designated A through F

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What is the function of the nucleus?

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- The function of the nucleus is to regulate the activity of the cell

- This is carried out by the production of proteins

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RNA

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- An intermediary molecule that is needed since DNA never leaves the nucleus and protein synthesis occurs in the cytoplasm

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Volkin and Astrachan

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- 1956

- Used 32P to show burst of RNA synthesis following bacteriophage infection

- The labeled RNA was quickly degraded

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Speigelman

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- 1961

- Demonstrated that the unstable RNAs synthesized after infection could hybridize to the viral genome and not E. coli DNA

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Polyadenylation

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- The addition of poly(A) tails to eukaryotic mRNAs

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Poly(A) Polymerase

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- An enzyme that adds poly(A) tails after cleavage

- Tracts of adenosine monophosphate residues about 200 nucleotides long, to the 3' ends of the transcripts

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RNA Editing

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- Posttranscriptional processes that alter the information encoded in gene transcripts (RNA)

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Guide RNAs

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- RNA molecules that contain sequences that function as templates during RNA editing

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R-loops

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- Single-standed DNA regions in RNA-DNA hybrids formed in vitro under conditions where RNA-DNA duplexes are more stable than DNA-DNA duplexes

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Splicing Endonuclease

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- Makes two cuts precisely at the ends of the intron

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Splicing Ligase

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- Occurs in stage II

- Joins the two halves of the tRNA to produce the mature form of the tRNA molecule

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A general theme in biology is what?

Back 73

- Metabolism occurs via sequences of enzyme catalyzed reactions

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Spliceosomes

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- The RNA/protein complex that excises introns from primary transcripts of nuclear genes in eukaryotes

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Small Nuclear Ribonucleoproteins (snRNPs)

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- RNA-protein complexes that are components of spliceosomes

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What makes RNA tough to study?

Back 76

- The fact that it degrades quickly

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Spiegelman Experiment

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1. Infect E. coli cells with bacteriophage T4

2. Add 3H-uridine to the medium at various times - 2, 4, 6, 8, and 10 minutes - after infection, and incubate infected cells for one minute

3. break open the bacteria and isolate the RNA

4. Determine what proportions of the radioactive RNA hybridize to E. coli DNA and to phage T4 DNA

5. Incubate at 65 degrees celsius overnight. Remove and wash filters extensively. Measure radioactivity on each filter

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Flow of Genetic Information

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DNA --> RNA --> Protein

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Reverse Transcription

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What does all transcription result in?

Back 80

- The production of an RNA molecule

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What is the end product for rRNA, tRNA, snRNA, and miRNA?

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- The RNA molecule itself

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What is used in translation to produce an amino acid sequence in a protein?

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- The mRNA

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mRNA is processed first in eukaryotes; initially called what?

Back 83

- Pre-mRNA

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What is the intermediate for making protein?

Back 84

- mRNA

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RNA synthesis occurs in which direction?

Back 85

- 5' to 3' direction

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What are the precursors for RNA synthesis?

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- Ribonucleoside Triphosphates

- GTP

- ATP

- CTP

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What is RNA is complementary to?

Back 87

- The DNA template strand

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What is RNA identical to?

Back 88

- To the DNA contemplate strand

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Do RNA chains need a primer? why?

Back 89

- No, because they can be synthesized de novo