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MICR 221 > Lecture 8 > Flashcards

Lecture 8 Flashcards

1
Q

Q: What is streptomycin?

A

A: Streptomycin is one of the first antibiotics discovered, effective against Gram-negatives and tuberculosis. It is produced by the soil bacterium Streptomyces griseus and belongs to the class of aminoglycoside antibiotics, targeting the ribosome.

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2
Q

Q: Describe the role of ribosomes in translation.

A

A: Ribosomes translate mRNA by assembling at the ribosome binding site (RBS) and initiating translation at the start codon. Translation continues until reaching the stop codon. The Shine-Dalgarno sequence helps position the ribosome correctly on the mRNA.

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3
Q

Q: What enzyme catalyzes the attachment of amino acids to tRNA?

A

A: Aminoacyl-tRNA synthetase catalyzes the attachment of amino acids to tRNA.

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3
Q

Q: What is attached to the 3ʹ acceptor end of tRNA?

A

A: An amino acid is attached to the 3ʹ acceptor end of tRNA.

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4
Q

Q: How is the identity of the amino acid carried by tRNA related to its anticodon?

A

A: The identity of the amino acid is determined by the anticodon of tRNA.

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5
Q

Q: What is the role of the anticodon of tRNA during translation?

A

A: The anticodon of tRNA base pairs with the codon on mRNA during translation.

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6
Q

Q: What type of amino acid is carried by the initiator tRNA in bacteria, and what is its specific charge?

A

A: The initiator tRNA in bacteria is charged with N-formylmethionine (fMet).

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7
Q

Q: Which codon on mRNA does the anticodon (CAU) of the initiator tRNA (charged with fMet) bind to?

A

A: The anticodon (CAU) of the initiator tRNA binds to the start codon (AUG) on mRNA.

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8
Q

Q: What is the function of aminoacyl-tRNA synthetases?

A

A: Aminoacyl-tRNA synthetases charge tRNA molecules with the correct amino acids for protein synthesis.

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9
Q

Q: Describe the structure of aminoacyl-tRNA synthetases.

A

A: Aminoacyl-tRNA synthetases consist of two main domains:

Anticodon binding domain: Recognizes the anticodon of tRNA.
Catalytic domain: Attaches the correct amino acid to tRNA.

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10
Q

Q: What is the process by which aminoacyl-tRNA synthetases attach amino acids to tRNA?

A

A: Aminoacyl-tRNA synthetases activate the amino acid by linking it to adenosine triphosphate (ATP), forming a reactive ester bond. Then, the activated amino acid is transferred to the appropriate tRNA molecule.

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11
Q

Q: What is the composition of bacterial ribosomes?

A

A: Bacterial ribosomes are composed of ribosomal RNA (rRNA) and proteins.

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12
Q

Q: How do bacterial ribosomes compare to those found in eukaryotes?

A

A: Bacterial ribosomes (70S) are smaller than eukaryotic ribosomes (80S).

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13
Q

Q: Describe the structure of bacterial ribosomes.

A

A: Bacterial ribosomes consist of two major subunits: the small subunit (SSU; 30S) and the large subunit (LSU; 50S).

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14
Q

Q: How many bacterial ribosomes are typically found per cell?

A

A: There are typically more than 10,000 ribosomes per bacterial cell.

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15
Q

Q: What is the function of bacterial ribosomes?

A

A: Bacterial ribosomes catalyze the formation of peptide bonds between amino acids carried by tRNAs during protein synthesis.

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16
Q

Q: What is the role of tRNAs in protein synthesis?

A

A: tRNAs deliver amino acids to the ribosome during protein synthesis.

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17
Q

Q: How does the ribosome facilitate the interaction between tRNA anticodons and mRNA codons?

A

A: The ribosome helps align tRNA anticodons with mRNA codons during translation.

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18
Q

Q: What are the three tRNA binding sites on the ribosome?

A

The three tRNA binding sites are:

A site (aminoacyl site)
P site (peptidyl site)
E site (exit site)

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19
Q

Q: What is the role of nucleotides in 16S rRNA (30S subunit) during initiation of translation?

A

A: Nucleotides in 16S rRNA (30S subunit) bind to the mRNA Ribosome Binding Site (RBS) during translation initiation.

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19
Q

Q: What is the function of the P site during translation initiation?

A

A: The P site is the peptidyl site where the initiator tRNA binds during translation initiation.

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20
Q

Q: Where does the initiator tRNA bind during translation initiation?

A

A: The initiator tRNA binds to the start codon on the mRNA during translation initiation.

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21
Q

Q: What initiation factors are required during translation initiation?

A

A: Initiation factors IF-1, IF-2, and IF-3 are needed during translation initiation.

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22
Q

Q: What is formed when nucleotides in 16S rRNA bind to mRNA RBS, and the initiator tRNA binds to the start codon, along with the initiation factors?

A

A: The formation of the 30S initiation complex occurs during translation initiation.

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23
Q

Q: What kind of energy does the 50S subunit joining the 30S initiation complex during translation initiation need?

A

A: The 50S subunit joining the 30S initiation complex requires energy in the form of GTP.

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24
Q

Q: What complex is formed when the 50S subunit joins the 30S initiation complex?

A

A: The 70S initiation complex is formed when the 50S subunit joins the 30S initiation complex during translation initiation.

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25
Q

Q: What happens to the initiation factors (IFs) during the formation of the 70S initiation complex?

A

A: The initiation factors (IFs) are released from the ribosome during the formation of the 70S initiation complex.

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26
Q

Q: What is the state of the ribosome after the formation of the 70S initiation complex?

A

A: After the formation of the 70S initiation complex, the ribosome is ready for elongation, the next stage of protein synthesis.

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27
Q

Q: What is the role of elongation factor EF-Tu during translation elongation?

A

A: Elongation factor EF-Tu delivers the aminoacyl-tRNA complex to the A site of the ribosome.

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27
Q

Q: What energy molecule is required for the action of elongation factor EF-Tu?

A

A: The action of elongation factor EF-Tu requires GTP (guanosine triphosphate).

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28
Q

Q: Describe the interaction between tRNA and mRNA during translation elongation.

A

A: The anticodon of the tRNA in the A site base-pairs with the complementary codon on the mRNA.

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29
Q

Q: What process occurs between the amino acids in the A site and the P site during translation elongation?

A

A: A peptide bond is formed between the amino acids in the A site and the P site during translation elongation.

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30
Q

Q: What is the name of the enzymatic center responsible for forming peptide bonds during translation?

A

A: The Peptidyl Transferase Center (PTC) is responsible for forming peptide bonds during translation.

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31
Q

Q: Where is the resulting peptide located after peptide bond formation during translation elongation?

A

A: The resulting peptide is attached to the aminoacyl-tRNA in the A site of the ribosome.

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32
Q

Q: What process occurs as mRNA advances through the ribosome during translation elongation?

A

A: Translocation is the process by which mRNA advances through the ribosome during translation elongation.

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33
Q

Q: What elongation factor is responsible for translocation, and what energy molecule is required?

A

A: Elongation factor EF-G, along with GTP (guanosine triphosphate), is responsible for translocation during translation elongation.

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34
Q

Q: What happens to the uncharged tRNA in the E site during translocation?

A

A: The uncharged tRNA in the E site exits the ribosome during translocation.

35
Q

Q: What occurs to the tRNA with the growing peptide chain during translocation?

A

A: The tRNA with the growing peptide chain moves from the A site to the P site during translocation.

36
Q

Q: How are stop codons recognized during translation termination?

A

A: Stop codons are recognized by release factors.

36
Q

Q: Why is there no tRNA that corresponds to stop codons?

A

A: Stop codons do not have corresponding tRNA molecules.

37
Q

Q: What happens after translocation is completed?

A

A: Another tRNA is delivered to the A site, and elongation of the polypeptide chain continues.

37
Q

Q: What happens when the ribosome encounters a stop codon during translation termination?

A

A: The ribosome stalls at the stop codon, which can be UAA, UGA, or UAG.

38
Q

Q: What is the role of release factors during translation termination?

A

A: Release factors hydrolyze the polypeptide chain from the tRNA at the stop codon.

38
Q

Q: Why are bacterial ribosomes a major target for antibiotics?

A

A: Bacterial ribosomes are a major antibiotic target because translation is an essential process for bacterial survival.

38
Q

Q: What happens to the translation complex after termination?

A

A: After termination, the translation complex dissociates.

39
Q

Q: What occurs as a growing polypeptide extends through the ribosome exit tunnel?

A

A: The growing polypeptide extends through the ribosome exit tunnel during translation.

39
Q

Q: What is the significance of targeting bacterial ribosomes for antibiotic therapy?

A

A: Targeting bacterial ribosomes provides selectivity in antibiotic action because bacterial ribosomes differ from human ribosomes.

39
Q

Q: What is the consequence of macrolide binding to the ribosome exit tunnel?

A

A: Macrolide antibiotics prevent the elongation of the nascent polypeptide chain (NC) by blocking the exit tunnel of the ribosome.

40
Q

Q: Where is the ribosome located within the bacterial cell?

A

A: The ribosome is located in the cytoplasm of bacterial cells.

40
Q

Q: How can bacterial cells limit the amount of antibiotic in the cytoplasm?

A

A: Bacterial cells can limit the amount of antibiotic in the cytoplasm by decreasing influx (reducing the entry of the antibiotic into the cell) and increasing efflux (pumping the antibiotic out of the cell).

40
Q

What does it mean when an antibitotic is bacteriostatic?

A

inhibits growth, but does not kill. Growth results if removed.

40
Q

Q: How do macrolide antibiotics, such as erythromycin, exert their inhibitory effect on translation?

A

A: Macrolide antibiotics bind to the 50S subunit of bacterial ribosomes, blocking the exit tunnel.

41
Q

Where do lincosamides bind, and what is the consequence?

A

binds in the A site of the 50s subunit. disrupts positioning of A site tRNA in peptidyl-transferase center (PTC). This block peptide bond formation

41
Q

What type of bacteria is considered a bacteriostatic antibiotic?

A

tetracyclines

42
Q

What are post translational regulation mechanisms?

A

control protein activity. These include post translational modifications, and proteolysis

42
Q

How can antibiotics binding to the ribosome be prevented?

A

by modifying the ribosome or modifying the antibiotic

43
Q

What is translational regulation? What does it involve?

A

control of mRNA translation. Involves the use of translational riboswitches and small RNAs (snRNAs)

43
Q

Q: What is a riboswitch, and where is it located in mRNA?

A

A: A riboswitch is a secondary structure found in the leader region of mRNA.

44
Q

Q: How does the conformation of the riboswitch affect translation?

A

A: The conformation of the riboswitch impacts translation by determining the accessibility of the ribosome binding site (RBS) or Shine-Dalgarno sequence (SD).

45
Q

Q: What are the two possible conformations of a riboswitch, and what is the impact of each?

A

The two conformations are:

Sequestor: In this conformation, the RBS is unavailable, limiting translation.
Anti-sequestor: In this conformation, the RBS is available, promoting translation.

46
Q

Q: How is the conformation of the riboswitch controlled?

A

A: The conformation of the riboswitch is controlled by ligands, which bind to specific regions and induce conformational changes.

47
Q

Q: How are some riboswitches initially configured, and what is their default state?

A

A: Some riboswitches are configured as anti-sequestors by default, with the ribosome binding site (RBS) available for translation.

48
Q

Q: What triggers the turning off of riboswitches?

A

A: Riboswitches are turned off by ligands binding to specific regions within the mRNA.

49
Q

Q: What is the consequence of ligand binding to riboswitches?

A

A: Ligand binding causes the formation of sequestors and anti-antisequestors, rendering the RBS unavailable for translation.

50
Q

Q: How do translational riboswitches regulate gene expression?

A

A: Translational riboswitches regulate gene expression by controlling the accessibility of the ribosome binding site (RBS) based on the presence or absence of ligands.

51
Q

Q: What is the default state of some riboswitches?

A

A: Some riboswitches are off by default, configured as sequestors, with the ribosome binding site (RBS) unavailable for translation.

52
Q

Q: What triggers the activation of these riboswitches?

A

A: These riboswitches are turned on by ligands binding to specific regions within the mRNA.

53
Q

Q: What is the consequence of ligand binding to these riboswitches?

A

A: Ligand binding causes the formation of anti-sequestors, rendering the RBS available for translation.

54
Q

Q: How do translational riboswitches of this type regulate gene expression?

A

A: Translational riboswitches regulate gene expression by controlling the accessibility of the ribosome binding site (RBS) based on the presence or absence of ligands.

55
Q

Q: What are small RNAs (sRNAs) also known as, and what is their typical length range?

A

A: Small RNAs (sRNAs) are also known as noncoding RNAs and typically range in length from 25 to 500 nucleotides.

56
Q

Q: How do some sRNAs interact with mRNA?

A

Some sRNAs bind to mRNA in two main ways:

Cis-encoded sRNAs are produced from the same DNA strand as the mRNA, matching the template strand.
Trans-encoded sRNAs are produced from other DNA, not necessarily from the same gene locus.

57
Q

Q: How does the binding of small RNA (sRNA) to mRNA affect translation?

A

A: Binding of sRNA to mRNA can impact translation. Specifically:
Binding to the Ribosome Binding Site (RBS) can block initiation.
Binding to the gene can block elongation.

58
Q

Q: How does binding of small RNA (sRNA) to the leader region of mRNA affect translation?

A

A: Binding to the leader region can prevent the formation of the sequestor, making the Ribosome Binding Site (RBS) more accessible and leading to increased translation.

58
Q

Q: What is the consequence of binding sRNA to mRNA in terms of targeting mRNA for degradation?

A

A: Binding of sRNA to mRNA can target the mRNA for degradation by ribonucleases (RNases), resulting in decreased translation.

58
Q

Q: How does the availability of ferrous iron (Fe^2+) impact protein synthesis?

A

A: Ferrous iron (Fe^2+) is necessary for the function of many proteins. When Fe^2+ is limited, only essential Fe^2+-using proteins are made.

59
Q

Q: What is the role of RyhB (sRNA) when Fe^2+ is limited?

A

A: When Fe^2+ is limited, RyhB (sRNA) binds to mRNA for non-essential proteins, leading to the degradation of these mRNAs.

60
Q

Q: How is the transcription of RyhB controlled?

A

A: The Fur repressor controls the transcription of RyhB. When Fe^2+ is present, it acts as a co-repressor, inhibiting RyhB transcription.

61
Q

Q: What happens if Fe^2+ levels are high?

A

A: If Fe^2+ levels are high, the Fur repressor is active, leading to the inhibition of RyhB transcription.

62
Q

Q: What is post-translational modification (PTM) in the context of protein function?

A

A: Post-translational modification (PTM) refers to the chemical changes to an amino acid in a protein after it has been synthesized.

62
Q

Q: What happens when the concentration of ferrous iron (Fe^2+) is low?

A

When Fe^2+ is low:
The Fur repressor doesn’t bind, allowing the transcription of RyhB.
RyhB binds to mRNAs, targeting them for degradation.

63
Q

Q: How does PTM impact protein function?

A

A: PTM can significantly impact protein structure and its interactions with other proteins, influencing its function.

64
Q

Q: Provide an example of a common PTM and its effect on protein function.

A

A: One example of a common PTM is phosphorylation, which can either activate or inactivate enzymes by adding phosphate groups to specific amino acids.

65
Q

Q: In which biological processes are PTMs commonly involved?

A

A: PTMs are commonly involved in signaling pathways, where they play crucial roles in regulating protein activity and cellular responses.

66
Q

Q: How can protein function be controlled?

A

A: Protein function can be controlled by proteases, enzymes that cleave proteins.

67
Q

Q: What aspects of proteins can proteases impact?

A

A: Proteases can impact both the amount and the activity of proteins.

68
Q

What is protease activity controlled by?

A

internal and external stimuli

69
Q

Q: What is meant by multilevel regulation?

A

A: Multilevel regulation refers to the coordination of multiple regulatory mechanisms that work together to control gene expression.

70
Q

Q: Provide an example of multilevel regulation and explain its components.

A

A: An example of multilevel regulation is the interaction between RpoE and RseA:

RpoE (σ E) is a sigma factor that binds to RNA polymerase (RNAP) and controls the expression of damage repair genes.
RseA is an anti-sigma factor that prevents RpoE from binding to RNAP, thus regulating its activity.

71
Q

Q: How does membrane damage lead to the activation of the DegS protease?

A

A: Membrane damage activates the DegS protease.

72
Q

Q: What is the role of DegS protease upon activation?

A

A: DegS protease cleaves the periplasmic domain of RseA.

73
Q

Q: After the periplasmic domain of RseA is cleaved, what proteases cleave its cytoplasmic domain?

A

A: Proteases RseP and ClpXP cleave the cytoplasmic domain of RseA.

74
Q

Q: What is the consequence of the cleavage of RseA?

A

A: The cleavage of RseA releases RpoE (sigma factor), which increases the transcription of damage repair genes.

MICR 221 (12 decks)

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