Protein Synthesis

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Can you name the Processes of Protein Synthesis?

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Alanine, Valine, Isoleucine, Leucine, Methionine, Phenylalanine, Tyrosine, and Tryptophan have _______ side chains.non-polar
Basic Amino Acids?3 amino acids
Acidic Amino Acids?2 amino acids (charged form)
Special Amino Acids?3 amino acids
Acetylation is the addition of what group to the N-Terminal residue? Most common form of amino acid chemical modification
Name for double ringed nitrogenous base?
Name for single ringed nitrogenous base?
3 components of a nucleotide?
Which Watson-Crick base pair is most stable?Three hydrogen bonds make it the more stable Watson-Crick base pair
What form is a right handed DNA helix?
Spaces between intertwined strands are described as what?
What form of DNA is wider and shorter due to removal of water? (Base pairs are tilted rather than perpendicular)
What form of DNA is a left handed helix? Due to alternating purine-pyrimidine nucleotides (G-C nucleotides)
What is the basis of hyperchromicity? Often in double stranded DNA because of shielding due to stacked bases
Function of Topoisomerase I?Breaks a phosphodiester bond
Function of Topoisomerase II?Also breaks phosphodiester bonds
Secondary structure of single stranded RNA? 2 forms
Tertiary structure of single stranded RNA?only 1 answer
Why does polymerization (3' attack of OH on alpha phosphate of rNTP) favored?For nascent RNA in transcription
What does Pyrophosphatase do?
Site on DNA at which RNA polymerase begins transcription?
DNA binding protein that functions to either activate or repress transcription depending on association with other proteins is called a ______?Can be kilobases away upstream or downstream from answer to Q23
DNA sequence that specifies where RNA polymerase binds and initiates transcription is called a _______?
What does CTD stand for?Must be phosphorylated in order for RNA polymerase II to move away from transcription start site. Only found on RNA polymerase II
TBP? (Give full name)First to bind to DNA helix in In Vitro assembly of RNA polymerase II pre-initiation complex. (Monomer which folds into a saddle-shaped structure --> dyad symmetry, however not identical. Interacts with minor groove in DNA, bending the helix considerably)
TFIIB? (Give full name)Monomeric protein, smaller than TBP in which its CTD contacts both TBP and DNA on either side of the TATA box while NTP extends toward transcription start site
Preformed complex that positions RNA Polymerase II over transcription start site?
Next two proteins that bind to complete pre-initiation complex?
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Helicase subunit of which transcription factor uses energy from ATP hydrolysis to unwind the DNA duplex?Same protein has a subunit that phosphorylates RNA Polymerase II CTD in order to move away from the promoter region.
Two key differences in In Vivo transcription initiation? One transcription factor forms a complex with TBP and TATA box DNA. Both of these will bind first to TATA box DNA, then other general transcription factors will bind as indicated afterwards
These encode enzymes involved in particular metabolic pathway or proteins that interact to form one multisubunit protein? (Prokaryotes)Coordinately regulated = all activated or repressed to the same extent
Most common sigma factor that binds to RNA polymerase in prokaryotes?Binds to six base pair sequence centered at -10 and seven base pair sequence centered at -35 from +1 site
Lac operon is controlled by which two elements or transcription?When lactose is not present, one of these binds to lac operator which overlaps the transcription start site therefore blocking the binding site of sigma factor 70 and hence transcription initiation. cAMP bind to other element which allows greater transcription rate
Conserved sequence TATA box is located approximately how many nucleotides upstream of start sequence?ex.answer in form: X-X
What is a CG rich stretch of 20-50 nucleotides with 100 base pairs of upstream of start site called?Found as an alternative promoter element
What are transcription control regions found lying within 100-200 nucleotides upstream of start site called?
What are transcription control regions found greater than 200 base pairs from start site?Can be found upstream, downstream, within introns, and after final exons of a gene
What are regulatory elements that function similar to answers of Q36 and Q37 in higher eukaryotes?
Unregulated, abnormally high expression of genes that results from inactivation of repressors that normally inhibit the transcription of these genes is termed what?
These contain DNA binding domains and repressor domainsDNA binding domain bind via non covalent interactions between atoms in the alpha helix of DNA binding domains and atoms on edges of major groove in DNA. Sometimes interactions with phosphate backbone and DNA in minor groove contribute to binding. This is deemed a helix-turn-helix motif
These contain DNA binding domains and activation domains
Identify the type of proteins with conserved 60 residue DNA binding motif similar to helix turn helix motif
Identify the type of proteins with regions folded around a Zn(2+) ion producing a compact domain.a) C2H2 = more common motif containing two cysteine (C) and two histidine (H) residues whose side chains bind to Zn(2+) ion. b) C4 = 4 conserved cysteine residues in contact with Zn(2+) is found in approximately 50 human transcription factors -> nuclear receptors
Identify the type of proteins with hydrophobic leucine at every 7th position in sequence and bind to DNA as dimers.
Identify the type of proteins with dimer transcription factor domain similar to Q44 motif except contain a non helical loop of the polypeptide chain that separates two alpha helicaN terminal helix with basic residues that interact with DNA, middle loop region, and C terminal region
Stimulatory transcription in nearly all types of eukaryotic cells that have an unstructured, random coil conformationStimulate transcription when they are bound to a protein co-activator
mRNAs are never free but associated with multiple proteins forming complexes considered to be called what?
What is added to the 5' end of a nascent RNA as it is being transcribed?Protects mRNA from 5'-exoribonucleases in the nucleus and cytoplasm.
Unusual bond that is formed from bonding answer to Q48 to 5' end of nascent mRNA
Release of this factor after 5' capping increases rate of elongation transcription
What are hnRNPs? (Give full name) Contain hnRNAs. Most have 1 or more RNA binding domain similar to transcription factors.
Most common RNA binding domains in hnRNPs.2 domains - only abbreviation required. Two other hnRNP domains include KH motif and RCG box
A residue in introns that forms an RNA branch in the lariat structure of introns is commonly called this nameThe 3' phosphate of intron and 3' O of exon ester bond is broken and a new 5' phosphate bond and 2' O of A residue ester bond is formed. the 5' phosphate of exon 2 and 3' O of exon 1 form ester bond and relieve intron form mRNA
Splicing requires presence of these RNAs and associated proteinsabbreviation only. U rich associated with 5-10 proteins
The splicing of answer to Q54 (previous question) bound to pre-mRNA form larg ribonucleoprotein complexes called what?Begin by base pairing U1 and U2 to pre-mRNA. U4 and U6 form a complex which allows U5 to bind. This U4/U5/U6 complex now binds to U1/U2/pre-mRNA complex. Rearrangement occurs and U1 and U4 dissociate. Both transesterfication reaction occur and the intron + answer to Q54 are released. Finally, the intron complex rapidly dissociates in which the intron is rapidly degraded by a debranching enzyme and other nuclear RNases. U1 associates closer to 5' end and U2 associates closer to the 3' end
Proteins that are associated with the answer to Q55 that help specify and bind to 3' end region of the intron.ex. U2AF promotes interaction of U2 snRNP with the branch point.
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Complex formed when hnRNPs bound to mRNAs after splicing (20 nucleotides to each exon-exon junction)RNA export factor (REF) is associated with this complex which functions in export of fully processed mRNPs to cytoplasm
Rule given to splicing because of first two and last two nucleotides or standard introns First two and last two nucleotides are conserved and are expressed 100% of the time in 'standard' introns
Proteins that interact with exons' exonic splicing elements to determine splicing sites.These proteins are a subset of hnRNP proteins. When bound to exonic splicing enhancers, these proteins mediate cooperative binding of U1 snRNPs to branch point through a network of protein-protein interactions
Conserved sequence 10-35 nucleotides upstream from poly(A) tail. (Give correct base sequence)Poly(A) tail is virtually eliminated with removal of this sequence. Also, a GU rich or U rich region approximately 50 nucleotide sequences downstream of cleavage site is another cleavage signal.
Protein that binds to answer to Q60 (previous question) region first.CstF (Cleavage stimulatory factor) binds to GU rich sequence which then binds Cleavage factor 1 (CFI) and Cleavage factor 2 (CFII). Finally Poly(A) polymerase (PAP) binds to complex before cleavage. This is called the cleavage/polyadenylation complex
Which protein causes the rapid addition of A residues after the first 12 or so A residues have been added?Deemed the rapid phase, this protein contains an RRM motif. This protein is essential for mRNA export into cytoplasm
This type of splicing produces different mRNAs that encode distinct proteins due to the the different splicing of intronsSexual determination in Drosophila through sxl protein which acts as a repressor between exon 2 and exon 3 of the sex lethal gene in female drosophila
A complex in the nuclear envelope that are large, 30 different proteins called nucleoporins 8 filaments extend into cytoplasm and 8 filaments extend into nucleoplasm. Filaments that extend into nucleoplasm have a terminal ring joined to form a nuclear basket.
These nucleoporins line the central channel of answer to Q64. Contain long stretches of hydrophillic amino acid sequences punctuated by hydrophobic repeatsForm a sieve like network, interacting with one another and constantly rearranging allowing small ions to pass through and blocking macro molecules
4 required proteins for nuclear import
3 nucleotide sequences in which each specifies a particular amino acidNot going to get any easier than this
Genetic code is said to be _______ meaning that a particular amino acid can be specified by multiple answer to Q67
Position in the tRNA, the third 3' base in an mRNA codon and corresponding first 5' base in its tRNA anticodonNonstandard base pairing can occur in this position, most common = G-U which fits almost as well as G-C. Adenine is rarely found in this position, Inosine which is a derivative of adenine can be found in this position instead, binding with C,A and U
eIF3 associates with which subunit of the ribosome?
eIF6 associates with which subunit of the ribosome?
Helicase subunit of this initiation factor bound to the 5' end of the eIF4 cap-binding complex unwinds RNA secondary structureScans entire mRNA, eliminating secondary structure. Scanning stops when tRNAi-Met anticodon recognizes start codon which is first AUG. Recognition of start codon leads to hydrolysis of GTP bound to eIF2
Which initiation factor positions the helicase subunit of answer to Q72 in the correct spot?
When correct base pairing between activated tRNA anticodon and mRNA codon occurs, the GTP of which factor is hydrolyzed? Binds to the A site domain of the ribosome.
Ribosome is translocated along mRNA a distance of one codon which is monitored by hydrolysis of GTP from which factor?In short, prevents ribosome from moving in wrong direction
This factor acts by binding to ribosomal A site and recognizing stop codon directlyStructurally similar to tRNA
This factor bound to GTP promotes cleavage of peptidyl-tRNA, releasing completed protein chainMonitors correct recognition of answer to Q76 to stop codon.
Binding of this protein to eIF4E on respective 3' poly(A) tail and 5' cap can form a bridge
miRNA associates with this complex which binds with target mRNPs by base pairing between multidomain argonaute protein bound miRNA and complementary region of 3' UTR or target mRNAinhibition by miRNAs requires two or more of these complexes + miRNA to bind to distinct complementary regions in 3' UTRs. The binding of these complexes to mRNA causes bound mRNP to associate with dense cytoplasmic domains many times the size of a ribosome called cytoplasmic RNA-processing bodies or P bodies.
These proteins in answer to Q79 (previous question) complexes with siRNA appear to be responsible for cleavage of target RNA 1 domain is homologous to RNase H enzyme that degrades RNA of RNA/DNA hybrid. When 5' end of siRNA and RISC complex base pair precisely with a target mRNA over a distance of one turn, this protein cleaves phosphodiester bond of target mRNA across nucleotide 10-11 of the siRNA and RNA.
Segments of DNA that can move around in the genome
 
 

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Created Oct 25, 2010ReportNominate
Tags:help, process, protein