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Molecular Biology > Protein Synthesis > Flashcards

Protein Synthesis Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

What are the similarities between DNA replication and transcription in prokaryotes

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2
Q

What are the differences between replication and transcription in prokaryotes

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Transcription not translation *

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3
Q

What are the characteristics of RNA polymerase in prokaryotes

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4
Q

What are the characteristics of E. coli RNA polymerase

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5
Q

How is transcription initiated in prokaryotes

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6
Q

What is the process of DNA footprinting

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7
Q

What is meant by the - 35 and -10 region and why is it called the consensus region

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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.

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8
Q

What is the role of a promoter

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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).

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9
Q

What is the role of the sigma subunit in RNA polymerase in initiation of transcription in prokaryotes

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10
Q

What are the roles of the different rna polymerase subunits in prokaryotes

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11
Q

What happens after RNA polymerase binds to the promoter in prokaryotes

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12
Q

What is meant by promoter clearance

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Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors

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13
Q

Outline the process of transcription in prokaryotes

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14
Q

What is the non template /coding strand

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15
Q

How can the expression of a gene be tested

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16
Q

Explain in simple terms elongation in transcription in prokaryotes

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17
Q

What happens in the transcription bubble in prokaryotes

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18
Q

What are the characteristics of elongation in transcription in prokaryotes

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19
Q

How is transcription terminated in E. Coli

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20
Q

How does Rho independent termination occur

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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

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21
Q

How does Rho dependent termination occur

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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

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22
Q

What are the characteristics of eukaryotic transcription

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23
Q

What are the differences between prokaryotic and eukaryotic transcription

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24
Q

how do eukaryotic promoters differ from prokaryotic promoters

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25
Q

What is a class II promoter

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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.

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26
Q

What does initiation of transcription in eukaryotes require

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27
Q

How is eukaryotic transcription initiated

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28
Q

How is RNA processed and modified after transcription in eukaryotes

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29
Q

What is the language that codes for amino acids in a polypept de

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30
Q

Recall the codons that code for the 20 amino acids

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31
Q

What is meant by the degeneracy of the triplet code

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32
Q

Why is degeneracy non random

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33
Q

What are open reading frames

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34
Q

What do reading frames do

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35
Q

What is the role of tRNA

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36
Q

What is the structure of tRNA

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37
Q

Explain the cloverleaf diagrams of tRNA

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38
Q

What are the modified versions of the base uridine

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39
Q

What are the modified versions of the base cytosine

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40
Q

What are the modified versions of the base adenosine

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41
Q

What are the modified versions of the base guanosine

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42
Q

Why are the normal RNA bases modified after transcription

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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)

43
Q

What are the common features of tRNA

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44
Q

What is tRNA charging ‘

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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

45
Q

How do amino acids join to tRNA

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46
Q

How do tRNA synthetases proofread

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47
Q

What is a ribosome

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48
Q

How are ribosomes isolated

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49
Q

Label this diagram of the 50S subunit of the ribosome

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50
Q

What is a ribozyme

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51
Q

What is needed for translation initiation in prokaryotes

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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

52
Q

What is the first step of the formation of the initiation complex for translation formed in bacteria

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53
Q

What is the shine - dalgarno sequence

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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

54
Q

What is the second step of the formation of the initiation complex for translation formed in bacteria

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55
Q

What is the third step of the formation of the initiation complex for translation formed in bacteria

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56
Q

What are the key facts about the initiation process of translation in bacteria

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57
Q

How is translation carried out accurately

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58
Q

What are the key characteristics of eukaryotic initiation of translation

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59
Q

How is the pre-initiation complex in eukaryotic translation formed

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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.

60
Q

Outline the process of initiation in eukaryotic translation

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61
Q

Outline the process of elongation in prokaryotic translation

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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

62
Q

How is a polypeptide formed in elongation phase of prokaryotic translation

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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.

63
Q

What are the key facts about elongation in prokaryotic translation

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64
Q

How does eukaryotic elongation in translation occur

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65
Q

How does termination occur in pro and eukaryotic translation

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66
Q

Name some antibiotics/ naturally occurring toxins and how they inhibit translation

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67
Q

Describe the process of translation in prokaryotes

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68
Q

Describe the process of eukaryotic transcription

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Molecular Biology (11 decks)

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