Protein Synthesis Flashcards
What are the similarities between DNA replication and transcription in prokaryotes
What are the differences between replication and transcription in prokaryotes
Transcription not translation *
What are the characteristics of RNA polymerase in prokaryotes
What are the characteristics of E. coli RNA polymerase
How is transcription initiated in prokaryotes
What is the process of DNA footprinting
What is meant by the - 35 and -10 region and why is it called the consensus region
The -10 consensus sequence, called the -10 region, is TATAAT. The -35 sequence, TTGACA, is recognized and bound by σ. Once this interaction is made, the subunits of the core enzyme bind to the site. The A–T-rich -10 region facilitates unwinding of the DNA template, and several phosphodiester bonds are made.
The -10 and -35 regions of prokaryotic promoters are called consensus sequences because they are similar in all bacterial species.
What is the role of a promoter
A promoter, as related to genomics, is a region of DNA upstream of a gene where relevant proteins (such as RNA polymerase and transcription factors) bind to initiate transcription of that gene. The resulting transcription produces an RNA molecule (such as mRNA).
What is the role of the sigma subunit in RNA polymerase in initiation of transcription in prokaryotes
What are the roles of the different rna polymerase subunits in prokaryotes
What happens after RNA polymerase binds to the promoter in prokaryotes
What is meant by promoter clearance
Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors
Outline the process of transcription in prokaryotes
What is the non template /coding strand
How can the expression of a gene be tested
Explain in simple terms elongation in transcription in prokaryotes
What happens in the transcription bubble in prokaryotes
What are the characteristics of elongation in transcription in prokaryotes
How is transcription terminated in E. Coli
How does Rho independent termination occur
The rho-independent termination signals consist of stable hairpins followed by U-rich regions. The mechanism of intrinsic termination includes pausing of the transcription elongation complex (TEC) at the termination point and formation of the RNA terminator hairpin inside RNA polymerase
How does Rho dependent termination occur
Rho-dependent termination occurs by binding of Rho to ribosome-free mRNA, C-rich sites being good candidates for binding. Rho’s ATPase is activated by Rho-mRNA binding, and provides the energy for Rho translocation along the mRNA; translocation requires sliding of the message into the central hole of the rho protein which is a hexamer
What are the characteristics of eukaryotic transcription
What are the differences between prokaryotic and eukaryotic transcription
how do eukaryotic promoters differ from prokaryotic promoters
What is a class II promoter
Basal Transcription Machinery: Class II promoters contain core promoter elements recognized by the basal transcription machinery, including the TATA box (TATAAAA), which is located approximately 25-30 base pairs upstream of the transcription start site (TSS), and the transcription start site itself.
Initiation Factors Binding Sites: Class II promoters interact with general transcription factors (GTFs) and RNA polymerase II to initiate transcription. These factors include TFIID (which recognizes the TATA box), TFIIA, TFIIB, TFIIE, TFIIF, and TFIIH. Together, they assemble into the pre-initiation complex (PIC) at the promoter to initiate transcription.
What does initiation of transcription in eukaryotes require
How is eukaryotic transcription initiated
How is RNA processed and modified after transcription in eukaryotes
What is the language that codes for amino acids in a polypept de
Recall the codons that code for the 20 amino acids
What is meant by the degeneracy of the triplet code
Why is degeneracy non random
What are open reading frames
What do reading frames do
What is the role of tRNA
What is the structure of tRNA
Explain the cloverleaf diagrams of tRNA
What are the modified versions of the base uridine
What are the modified versions of the base cytosine
What are the modified versions of the base adenosine
What are the modified versions of the base guanosine
Why are the normal RNA bases modified after transcription
RNA modifications can (i) result in the formation of certain RNA structures and tune RNA biogenesis (as seen in rRNAs), (ii) refine molecular recognition (tRNAs) and (iii) encode dynamic regulatory signatures (mRNAs)
What are the common features of tRNA
What is tRNA charging ‘
The process of attaching an amino acid to its corresponding transfer RNA (tRNA) is called amino acid activation, also known as tRNA charging or aminoacylation
How do amino acids join to tRNA
How do tRNA synthetases proofread
What is a ribosome
How are ribosomes isolated
Label this diagram of the 50S subunit of the ribosome
What is a ribozyme
What is needed for translation initiation in prokaryotes
Formylmethionine, also known as fMet or fMet-Met, is a modified amino acid that serves as the initial amino acid in the polypeptide chain during protein synthesis in bacteria, mitochondria, and chloroplasts. It is structurally similar to methionine but with a formyl group (-CHO) attached to the amino group
What is the first step of the formation of the initiation complex for translation formed in bacteria
What is the shine - dalgarno sequence
The Shine–Dalgarno sequence is a ribosomal binding site in bacterial and archaeal messenger RNA, generally located around 8 bases upstream of the start codon AUG. The RNA sequence helps recruit the ribosome to the messenger RNA to initiate protein synthesis by aligning the ribosome with the start codon
What is the second step of the formation of the initiation complex for translation formed in bacteria
What is the third step of the formation of the initiation complex for translation formed in bacteria
What are the key facts about the initiation process of translation in bacteria
How is translation carried out accurately
What are the key characteristics of eukaryotic initiation of translation
How is the pre-initiation complex in eukaryotic translation formed
First, Met-tRNAiMet, eukaryotic initiation factor 2 (eIF2) and GTP form a ternary complex (TC). The TC, eIF3, eIF1 and eIF1A cooperatively bind to the 40S subunit yielding the 43S preinitiation complex, which is ready to attach to mRNA and start scanning to the initiation codon.
Outline the process of initiation in eukaryotic translation
Outline the process of elongation in prokaryotic translation
Elongation entails repetitive cycles of decoding, peptide bond formation, and translocation. Elongation begins as soon as the second codon of the ORF becomes accessible for reading by elongator aa-tRNAs and ends when the ribosome arrives at the stop codon.
ORF - open reading frame
How is a polypeptide formed in elongation phase of prokaryotic translation
1) The anticodon of an incoming tRNA pairs with the mRNA codon exposed in the A site. 2) A peptide bond is formed between the new amino acid (in the A site) and the previously-added amino acid (in the P site), transferring the polypeptide from the P site to the A site.
What are the key facts about elongation in prokaryotic translation
How does eukaryotic elongation in translation occur
How does termination occur in pro and eukaryotic translation
Name some antibiotics/ naturally occurring toxins and how they inhibit translation
Describe the process of translation in prokaryotes
Describe the process of eukaryotic transcription
