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95 Cards in this Set
- Front
- Back
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What is the Central Dogma?
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DNA --> RNA --> protein (polypeptide)
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What are the four classes of RNA?
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1. mRNA
2. tRNA 3. rRNA 4. snRNA |
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What are the three Functional RNAs?
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1. tRNA
2. rRNA 3. snRNA |
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What does mRNA do?
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mRNA carries information specifying amino acid sequences of proteins from DNA to the ribosome
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What does tRNA do?
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tRNA serves as an adapter molecule in protein synthesis, translates mRNA codons into amino acids
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What does rRNA do?
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Plays catalytic roles and structural role in ribosomes
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What does snRNA do?
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snRNA, with proteins, forms complexes used in eukaryotic RNA processing
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What are the three major components of transcription?
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1. DNA template (1 of the 2 nucleotide strands)
2. rNTPs 3. Enzymes and proteins to catalyze the synthesis of RNA |
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What is the Transcription Unit?
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Region of the DNA that codes for an RNA and the sequences necessary for its transcription
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What are the three parts to the Transcription Unit?
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1. Promoter
2. RNA coding region 3. Terminator |
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What is the structural difference between thymine and uracil?
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Thymine has a methyl group at the 5 position of the pyrimidine ring while uracil does not.
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What is the second chemical difference between RNA and DNA?
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RNA has the sugar ribose (OH group connected to its 2' carbon) while DNA has deoxyribose (2 Hydrogens connected to 2' carbon)
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In DNA and RNA, the nucleotide bases attach to which carbon?
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1' carbon
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In DNA and RNA, the phosphate group is attached to which carbon?
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5' carbon which is attached to the 4' carbon in the sugar.
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What does RNA Polymerase do?
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Catalyzes the addition of each ribonucleotide to the 3' end of the strand.
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RNA Polymerase forms phosphodiester bonds between what?
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Between a triphosphate group at the 5' carbon of one nucleotide and the hydroxyl group at the 3' of another nucleotide
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All RNAs are transcribed from what type of genes?
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RNA-encoding genes!
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What is miRNA?
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Micro RNA is active in plant and animal cells that help in the post-transcriptional regulation of mRNA.
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What is siRNA?
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Small Interfering RNA helps protect plant and animal genomes from the production of viruses and from the spread of transposable genetic elements within the genome.
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What are Ribozymes?
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Catalytically active RNAs that can catalyze reactions including removal of introns (self-splicing)
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What is the Template Strand?
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Template strand is 1 strand of DNA that is used to assemble a complementary, antiparallel strand of ribonucleotides
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What is the Coding Strand?
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AKA nontemplate strand is complementary to the template strand
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Where is the promoter of the gene?
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Immediately UPSTREAM (5' to the start of transcription) called the +1 nucleotide
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What region is the portion of the gene that is transcribed into RNA?
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the Coding Region!
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What is the Termination Region?
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Portion of the gene that regulates the termination of transcription.
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Where is the termination region located?
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Immediately DOWNSTREAM (3' to the coding segment of the gene)
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What are the 4 ESSENTIAL stages of transcription?
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1. Promoter recognition
2. Transcription initiation 3. chain elongation 4. chain termination |
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Bacterial RNA polymerase is composed of what?
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A Pentameric (five-polypeptide) core enzyme connected to a sigma subunit when polymerase becomes active.
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In its active form, RNA polymerase is described as what?
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A holoenzyme!
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What is a holoenzyme?
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Intact complex with full enzymatic capacity.
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What enables RNA polymerase to bind specifically to particular promoter consensus sequences?
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The joining of the sigma subunit to the core enzyme to form a holoenzyme
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What is the purpose of Promoters?
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They regulate transcription cuz RNA can't initiate transcription without binding to a promoter sequence.
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What are Consensus Sequences?
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Short regions of highly similar DNA sequences located in the same position relative to the start of transcription in different gene promoters.
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Are promoters single or double stranded?
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Double stranded!
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Are promoter consensus sequences single or double stranded?
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Written in a single-stranded shorthand.
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The -10 position of the promoter is called what?
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Pribnow box sequence
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The -35 position of the promoter is called what?
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-35 consensus sequence
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TRUE OR FALSE: Prokaryotic cells DO NOT have INTRONS.
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TRUE!
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What is the purpose of sigma subunits?
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They identify the promoter so polymerase can bind!
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Holoenzyme binds to what?
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-35 and -10 consensus sequences!
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Which get removed in eukaryotic genes: introns or exons?
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INTRONS!
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What are the two steps of RNA polymerase holoenzyme initiates transcription?
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1. holoenzyme makes loose attachment to double-stranded promoter sequence
2. bound holoenzyme unwinds ~18 bp of DNA to form the Open Promoter Complex |
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What does RNA Pol I do?
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Transcribes three ribosomal RNA genes
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What does RNA Pol II do?
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Transcribes mRNAs that encode polypeptides as well as most snRNAs
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What does RNA Pol III do?
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Transcribes all tRNA genes, 1 snRNA, and 1 rRNA
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Where is a TATA box located?
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Located at a position -25 relative to the +1 transcription site.
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What is the most strongly conserved promoter element in eukaryotes?
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TATA Box!
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What is a TATA box?
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It is a promoter consensus sequence.
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What are the 3 main promoter consensus sequences?
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1. TATA box
2. CAAT box 3. GC-Rich Box |
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Where is the CAAT box located?
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Usually -80 when present in the promoter
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Where is the GC-Rich Box located?
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-90 or more upstream from transcription start (+1)
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What are Transcription Factors?
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TF proteins bind to promoter regulatory sequences and influence transcription initiation
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What is TFIID?
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Protein containing TATA-Binding Protein that binds to the TATA box and TBP-associated Factor.
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The assembled TFIID binding to the TATA box forms what complex?
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Initial Committed Complex
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After the initial committed complex is formed, what joins? What does this joining form?
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TFIIB and TFIIF and RNA Polymerase II joins the initial complex to form the Minimal Initiation Complex
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After the Minimal Initiation Complex is formed, what joins? What does this joining form?
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TFIIE and TFIIH which forms the Complete Initiation Complex
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Once TFIID, TFIIB, TFIIF, RNA Pol II, TFIIE, and TFIIH are assembled, the complete initiation complex does what?
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It directs the RNA pol II to the +1 nucleotide to begin assembly of mRNA.
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What are Enhancer Sequences?
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Sequences that bind to specific transcriptional proteins that can increase transcription of targeted genes.
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What are Silencer Sequences?
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Regulatory sequences that repress transcription of specific genes that may be located DISTANTLY from the sequence.
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What are the 3 modification steps done to mRNA before it leaves the nucleus?
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1. 5' capping
2. 3' polyadenylation 3. Intron-splicing |
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What is 3' Polyadenylation?
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Cleavage at the 3' end of mRNA and the addition of a tail of multiple adenines to form the Poly-A tail
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What is the Polyadenylation Signal Sequence?
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Sequence of 6 nucleotides that begins polyadenylation.
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What two ways can Introns be removed?
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1. Splicing
2. Self-Splicing |
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What is Splicing?
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Splicing is a way introns are removed by an snRNA protein complex called SPLICEOSOME.
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What is Spliceosome?
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SnRNA protein complex that removes introns by splicing them out of the mRNA.
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What is Self-Splicing?
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Self-splicing is the removal of introns once part of a mRNA through being catalyzed.
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5' capping of eukaryotic mRNA adds what shortly after transcription is initiated?
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Methylated guanine
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Consensus sequences at 5' splice site, 3' splice site and branch point serve as what?
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Guides during intron splicing
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How are ribosomal and transfer RNA molecules generated?
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Generated by cleavage of large precursor molecules transcribed in bacterial and eukaryotic genomes.
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What is RNA editing?
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Post-Transcriptional altering of nucleotide sequence causind it to differ from the template DNA sequence
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RNA Polymerase adds nucleotide in what direction?
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5' to 3'
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Holoenzyme in bacteria is made of how many polypeptides?
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4
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rNTPs are added in what direction?
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5' to 3'
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What is the rate of elongation?
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40 nucleotides per second
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What begins elongation?
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Change in conformation of RNA polymerase
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The terminator region is dependent on what?
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Rho protein
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What is Rho Protein?
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It is a protein that is involved in the termination of transcription in bacterial cells.
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What is the Rut Site?
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The site of attachment of rho protein that aids in rho-protein-driven bacterial transcription termination.
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Alteration of histone proteins allow for what?
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Access to DNA
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What are Introns?
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Non-coding regions!
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What are the three regions of mature mRNA?
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1. 5' untranslated region
2. protein coding region 3. 3' untranslated region |
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The transcript is processed with what 3 things?
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1. Capping
2. Poly A tail 3. Removal of Introns |
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The transcribed region is preceded by what? What is it controlled by?
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Transcribed region is preceded by promoter and is controlled by enhancers
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Which end of tRNA is the binding site end?
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3'!
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The anticodon loop on tRNA matches up with what on mRNA?
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Codon on mRNA and then determines the amino acid the tRNA carries
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What are Isoaccepting tRNA?
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31 tRNAs that specifically bind to single amino acid
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What structure does rRNA have?
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Tertiary structure (3D folding)
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Ribosomes have how many subunits?
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2
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Which mRNA processing event adds to the stability of the mRNA?
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Both the addition of the 5' cap and the poly A tail to the 3' end stabilizes mRNA.
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RNA Polymerase reads the template strand in what direction? Which direction does it produce the mRNA?
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Reads in 3' to 5' but produces mRNA in the 5' to 3' direction.
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What are the 5 steps to mRNA production in eukaryotes?
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1. Transcription,
2. 5' cap addition 3. addition of poly-A tail 4. exon splicing 5. passage through nuclear membrane |
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What is a characteristic of transcription in eukaryotes but not in prokaryotes?
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Exon splicing!
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What is the function of the 5' mRNA cap?
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It provides a site for ribosome binding in the cytoplasm.
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What are 3 properties shared by RNA and DNA polymerase?
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1. Dependent on DNA template sequence
2. Polymerizes nucleotides in 5' to 3' direction 3. Catalyzes phosphodiester bond formation |
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What does "coupling" mean?
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Coupling is a term that indicates how bacteria mRNA can be undergoing transcription at the same time its undergoing translation.
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