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80 Cards in this Set
- Front
- Back
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What is an advantage of RNA being single stranded? |
An RNA chain can fold up into a particular shape which can allow RNA molecules to have structural and catalytic functions |
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What are two ways DNA replication differs from RNA transcription? |
RNA does not remain H-bonded to the DNA complementary strand. It is instead released as a single strand. RNA molecules are much shorter than DNA because they are copied from limited regions of DNA |
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What is one advantage of releasing ssRNA immediately after transcription? |
Many RNA copies can be made from the same gene in a relatively short period of time |
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What are 2 differences between DNA and RNA Polymerase? |
RNA polymerase links ribonucleotides instead of deoxyribonucleotides RNA polymerases can start an RNA chain without a primer |
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What is one possible reason why RNA polymerase may not need to start a chain without a primer? |
Transcription does not have to be as accurate as DNA replication because errors in RNA transcription are much less significant |
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What provides the driving force for the polymerization reaction of the ribonucleotides? |
The nucleotides are in the form of ribonucleoside triphosphates (ATP,UTP,CTP,GTP) The energy stored in the phosphate-phosphate bonds are used for polymerization |
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What is located at the catalytic site of both DNA and RNA polymerase? |
Divalent metal ion such as Mg+2 |
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What are mRNA molecules? |
RNA molecules that are copied from genes which specify the amino acid sequence of proteins |
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What 2 components comprise the RNA polymerase holoenzyme? |
Sigma factor Core enzyme |
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What does the sigma factor do? |
Assists the core RNA polymerase enzyme in reading the signals in the DNA that tell it where to begin transcribing |
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What are the 5 steps in the transcription cycle of bacterial RNA polymerase? |
RNA holoenzyme binds to a promoter Polymerase unwinds the DNA Abortive synthesis (initial transcription) Elongation mode (actual transcription) Termination |
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Explain abortive synthesis (3 things) |
~10 RNA nucleotides are synthesized Interactions with promoter are broken Interactions with sigma factor are weakened |
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What are the 2 conformational changes to RNA polymerase after abortive synthesis |
Tighter binding to DNA Rudder shifts position |
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Describe the termination step of bacterial transcription |
A short DNA sequence, when transcribed into RNA, forms a hairpin loop which displaces the RNA transcript from the active site, which causes the RNA polymerase to be released Example of RNA folding into specific structures |
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What 2 promoters are required to initiate transcription in prokaryotes? |
TATA Box (-10) Consensus Sequence (-35) |
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What 3 promoters are required to initiate transcription in eukaryotes? |
TATA Box CAAT Box Enhancer Sequences (Upstream + Downstream) |
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What does TFIID do? |
Binds to the TATA Box promoter (-25) |
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What is TBP? |
TATA Binding Protein A subunit of TFIID which recognizes the TATA Box sequence |
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What happens after TFIID binds to the TATA Box? |
RNA Polymerase II and other transcription factors assemble at the promoter |
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In addition to the clamp and rudder domains, what distinct domain does the eukaryotic RNA Polymerase II have? |
C-terminal domain (CTD) |
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Describe the CTD (2 Things) |
A polypeptide tail consisting of 52 repeats of seven amino acids Contains serines which are phosphorylated by TFIIH |
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What are the 3 important functions of TFIIH? |
One of its subunits is a DNA helicase which unwinds the DNA double helix using ATP Phosphorylates CTD serine residues Releases RNA Polymerse II from the promoter |
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What 3 things do eukaryotic cells require for transcription initiation? |
Activator proteins Mediator protein complex Chromatin modifying enzymes |
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What do transcriptional activators do? (3 Things) |
Bind to specific sequences in DNA (enhancers) Attract RNA Polymerase II to the start point of transcription Help assemble RNA Polymerase II, Mediator and other proteins together |
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What is the mediator protein complex? |
A coactivator which serves as a bridge of communication between activator proteins, RNA Polymerase II and the transcription factors Main binding region is the CTD |
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What is the significance of requiring chromatin remodeling complexes for eukaryotic transcription initiation? |
DNA is packaged into nucleosomes, causing target DNA to sometimes be packed away into the structure |
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What are 2 major differences between the mRNA molecule resulting from eukaryotic transcription and an mRNA molecule resulting from prokaryotic transcription? |
Eukaryotic mRNA contains both introns and exons Eukaryotic mRNA almost always contains information for a single protein while prokaryotic mRNA has information for multiple |
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Not including transcription, what are 2 critical steps needed to produce an mRNA molecule in Eukaryotes? |
Covalent modification of the ends of the RNA Removal of intron sequences via RNA splicing |
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What are 2 types of covalent modification of Eukaryotic mRNA? |
5' capping 3' Polyadenylation |
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During elongation mode, what critical function does the CTD have? |
Allows new sets of processing proteins to associate with the CTD and then "hop" to the new RNA molecule as it emerges from the polymerase Examples: Capping factors + Splicing proteins |
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What 3 enzymes perform the 5' capping reaction? |
Phosphatase - removes phosphate from 5' end Guanyl Transferase - Adds GMP (5' to 5') Methyl Transferase - Adds methyl group to guanosine |
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Describe the 3 steps of pre-mRNA splicing |
A specific A-residue attacks the 5' splice site The cut 5' end becomes linked to the A (loop) Released 3' end reacts with the start of next exon sequence (this releases the intron loop) |
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What are snRNAs? (3 Things) |
Small Nuclear RNAs Recognize where splicing will take place Participate in chemistry of splicing |
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What is a snRNP? (3 Things) |
Small Nuclear Ribonucleoprotein A complex of 7 protein subunits + 1 snRNA snRNPs form the core of a spliceosome |
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What is exon definition? |
SR proteins (serine + arginine rich domains) assemble on exon sequences at the 3' and 5' end U1 is recruited at the upstream boundary U2AF is recruited at the downstream boundary |
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What are hnRNP complexes? (3 Things) |
Heterogeneous nuclear ribonucleoprotein complexes containing intron sequences Helps spliceosome differentiate between exons + introns Masks cryptic splice sites |
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What are CstF and CPSF? (4 Things) |
Cleavage stimulation factor Cleavage and polyadenylation specificity factor Travel with the RNA Polymerase tail and "hop" to the 3' end of the new RNA molecule Additional proteins are then attracted to the 3' end |
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Describe the 3 major steps in generating the 3' end of Eukaryotic mRNA |
RNA is cleaved Poly-A-polymerase (PAP) adds ~200 A nucleotides to the 3' end Poly-A binding proteins assemble onto the A's |
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What are Nuclear Pore Complexes? (2 Things) |
Aqueous channels in the nuclear membrane that directly connect the nucleoplasm and cytosol Macromolecules like mRNA require active transport to pass through |
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What is the Nuclear Export Receptor? (3 Things) |
A protein which is attached to the mRNA as the latter is spliced and polyadenylated Allows mRNA to pass through the pore complex Dissociates from the mRNA and is re-imported into the nucleus to be reused |
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What is rRNA? |
Ribosomal RNA which forms the core of the ribosome 4 types of rRNA in Eukaryotes |
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How are 3 of the 4 Eukaryotic rRNA made? |
By the chemical modification and cleaving of a single large precursor rRNA |
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What are the 2 common types of modifications of rRNA? |
2'-OH Methylation Uridine Isomerization |
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What are Guide RNAs? (2 Things) |
Modifications of rRNA are made at specific positions and are specified by Guide RNAs They base pair on the rRNA and bring an RNA modifying enzyme |
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What are snoRNAs? (3 Things) |
Small Nucleolar RNA Perform functions in the nucleolus Guide RNAs are snoRNAs |
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What are snoRNPs? |
Complexes which contain both the guide sequences (snoRNA) and the enzymes which modify the rRNA |
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What are the 2 basic functions of Transfer RNA (tRNA)? |
Bind to the codon of the mRNA Bind to the correct amino acid |
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What is wobble base pairing? |
Several codons can specify a single amino acid
tRNA can base pair with the first 2 nucleotides and mismatch with the third (wobble) |
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What do Aminoacyl-tRNA Synthetases do? |
Responsible for the recognition and correct attachment of an amino acid to a tRNA molecule |
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What are the 3 steps of activating an Amino Acid on a tRNA molecule? |
Amino acid is linked to an AMP molecule via ATP hydrolysis AMP group is transferred to a hydroxyl group on the tRNA molecule This transfer joins the amino acid to the tRNA |
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What are two mechanisms that ensure the tRNA synthetase will link the correct amino acid? |
Correct amino acid has the highest affinity for the active site of the tRNA synthetase An editing site rejects the CORRECT amino acid and removes incorrect ones via hydrolysis |
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What are the names of the 2 tRNAs involved in the growing of the polypeptide chain? |
Peptidyl tRNA which is attached to the C-end Aminoacyl tRNA which is carrying the next amino acid |
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What is the general function of the small subunit of a ribosome? |
To provide the framework on which the tRNAs can be accurately matched to the codons of the mRNA |
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What is the general function of the large subunit of a ribosome? |
To catalyze the formation of the peptide bonds that link the amino acids together into a polypeptide chain |
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What are the 4 binding sites of a ribosome? |
mRNA E-site (Exit) P-site (Peptidyl-tRNA) A-site (Aminoacyl-tRNA) |
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Name the 4 steps of Translation |
tRNA binding Peptide Bond Formation Large + Small Subunit Translocation |
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Describe step 1 of Translation (tRNA Binding) |
tRNA carrying the next amino acid in the chain binds to the ribosomal A-site by forming base pairs with the mRNA codon positioned there, so that the P-site and the A-site contain adjacent bound tRNAs |
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Describe step 2 of Translation (Peptide Bond Formation) |
The carboxyl end of the polypeptide chain is released from the tRNA at the P-site and is joined to the free amino group of the amino acid linked to the tRNA at the A-site, forming a new peptide bond Peptidyl Transferase is responsible for this step |
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Describe step 3 of Translation (Large Subunit Translocation) |
The large subunit moves relative to the mRNA held by the small subunit, thereby shifting the acceptor stems of the two tRNAs to the E- and P-sites of the large subunit |
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Describe step 4 of Translation (Small Subunit Translocation) |
The small subunit and its bound mRNA move exactly three nucleotides, resetting the ribosome so it is ready to receive the next aminoacyl-tRNA |
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How does EF-Tu help with the accuracy of translation? |
As it escorts an incoming aminoacyl-tRNA to the ribosome, EF-Tu checks whether the tRNA–amino acid match is corrrect Monitors the initial interaction between the anticodon of the aminoacyl-tRNA and the codon of the mRNA in the A-site |
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Explain EF-Tu and bent tRNAs |
Aminoacyl-tRNAs are “bent” when bound to the GTP-form of EF-Tu; this allows codon pairing but prevents incorporation of the amino acid into the growing polypeptide chain If the codon–anticodon match is correct, the ribosome rapidly triggers the hydrolysis of the GTP molecule, allowing tRNA to donate its AA |
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How is the “correctness” of the codon–anticodon match assessed? |
The rRNA folds around the codon–anticodon pair, and its final closure—which occurs only when the correct anticodon is in place—triggers GTP hydrolysis |
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What is EF-G responsible for? |
Catalyzes the translocation of the tRNA and mRNA down the ribosome at the end of each round of polypeptide elongation Hydrolysis of GTP moves it back |
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Describe the 4 steps of initiating protein synthesis in Eukaryotes |
The Met-tRNA is loaded into the small subunit along with eukaryotic initiation factors Small subunit binds to the 5' cap of the mRNA (recognizes eIF4E and eIF4G) Small subunit searches along mRNA for AUG Initiation factors dissociate and large subunit binds to complete the ribosome |
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What is the Shine-Dalgarno sequence? (2 Things) |
A specific ribosome binding site found in prokaryotic mRNA located upstream of the AUG Forms base pairs with the small subunit to position the AUG codon in the ribosome |
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How is translation terminated? (2 Things) |
Release factors bind to stop codons which are positioned on the A-site Forces peptidyl transferase to add a water molecule instead of an amino acid to the peptidyl-tRNA |
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What are polyribosomes? (2 Things) |
Large cytoplasmic assemblies made up of several ribosomes about 80 nucleotides apart along a single mRNA molecule Allows the cell to make many more protein molecules in a given time |
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What is nonsense-mediated mRNA decay? |
A mRNA surveillance system which eliminates defective mRNA before they can be efficiently translated into protein Triggered by Upf proteins which are bound on left over exon junction complexes |
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What is a molten globule? |
Proteins begin to fold while they are synthesized They contain most secondary structures, but are not in their final, highly ordered form |
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What are heat shock proteins? (3 Things) |
A type of molecular chaperone which aid other proteins in folding correctly Have affinity for exposed hydrophobic regions Hydrolyze ATP to carry out folding |
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What is a chaperonin? |
A type of molecular chaperone which forms an "isolation chamber" into which misfolded proteins are fed and provided with a favorable environment for folding Powered by ATP hydrolysis |
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What is a proteasome? |
An ATP dependent protease which destroys misfolded proteins "Barrel" full of proteases |
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What is ubiquitin? |
A recognition tag which marks proteins for destruction and is detected for by proteasome caps |
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Described the threading reaction of a proteasome |
ATP hydrolysis drives the unfolding of the target protein as it moves through the cap and exposes it to the proteases which line the inner core of the proteasome |
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What is E1? |
Ubiquiting activating enzyme which links to the C-end of ubiquitin Transfers activated ubiquitin to the E2-E3 complex |
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What is E2? |
Ubiquitin conjugating enzymes Act in conjunction with E3 accessory proteins to make an E2-E3 complex |
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What is the E2-E3 complex? |
Ubiquitin ligase E3 Component binds to degrons and helps form a polyubiquitin chain linked to lysine |
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What is the significance of the polyubiquitin chain? |
This chain linked at a specific lysine residue is recognized by a proteasome |
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What are 2 general ways to induce the degradation of a specific protein? |
Activation of a specific E3 molecule to create a new ubiquitin ligase Creation of an exposed degradation signal |
