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Intro to Microbiology Biol 357 > Translation > Flashcards

Flashcards in Translation Deck (56):
1

What are the core components of a traditional bacterial mRNA?

Messenger RNA. It caries codes from the DNA in the nucleus to the sites of protein synthesis in the cytoplasm. 3-nitrogen containing bases, amino acids, and proteins.

2

What is the function of 23S in bacterial Translation?

It is a component of large subunit 50S. This ribosomal peptidyl transferase activity resides in domain V of this rRNA, and this domain is the most common binding site for antibiotics that inhibit translation.

3

What is the function of 16S in bacterial Translation?

It is a component of small subunit 30S that binds to the Shine-Dalgarno sequence. Used in reconstructing phylogenies due to the slow rates of evolution for this region of the gene.

4

What is the function of 5S in bacterial Translation?

Unclear function. 5S rRNA gene deletions reduce the protein synthesis rate and have a more profound detrimental effect on cell fitness than deletions of a comparable # of copies of other rRNA genes.

5

What is the function of tRNA in bacterial Translation?

Reads the message of nucleic acids, or nucleotides, and translates it into proteins or amino acids. The process of making a protein from a mRNA template is called translation.

6

What is the function of ribosomal proteins in bacterial Translation?

Proteins that constitute ribosomes. May be structurally important within the ribosome, for instance, in interacting with rRNA and may also function directly in translating mRNA into protein, which is the main function of ribosomes.

7

What is the function of IF1 in bacterial Translation?

Associates with the 30s ribosomal subunit in the A site and prevents an aminoacyl-tRNA from entering. It also modulates IF2 binding to the ribosome by increasing its affinity.

8

What is the function of IF2 in bacterial Translation?

An essential GTP/GDP-binding protein whose main recognized function is to interact specifically with initiator fMet-tRNA and to position it correctly around the ribosomal P site, thereby increasing the rate and fidelity of translation initiation.

9

What is the function of IF3 in bacterial Translation?

Required for 30S subunit to bind to the initiation site in mRNA. It also stabilizes free 30S subunits, enables 30S subunits to bind to mRNA, and checks for accuracy against the 1st aminoacyl tRNA. Plus it allows for rapid codon-anticodon pairing for the initiator tRNA to bind quickly to.

10

What is the function of tRNA synthestases in bacterial Translation?

Also called tRNA-ligase, is an enzyme that attaches the appropriate amino acid onto its tRNA, It does so by catalyzing the esterification of a specific cognate amino acid or its precurser to one of all its compatible cognate tRNA.

11

What is the function of EF-Tu in bacterial Translation?

Elongation Factor Thermo Unstable. Elongation factor responsible for catalyzing the binding of an aminoacyl-tRNA to the ribosome. It is a G protein.

12

What is the function of EF-G in bacterial Translation?

Translocase. Elongation factor involved in protein translation. As a GTPase, EF-G catalyzes the movement of transfer RNA (tRNA) and messenger RNA (mRNA) through the ribosome.

13

What is the function of RF1 in bacterial Translation?

Recognizes the termination codons UAA and UAG

14

What is the function of RF2 in bacterial Translation?

Recognizes UAA and UGA

15

What is the function of RF3 in bacterial Translation?

A GTP-binding protein that leads to the dissociation of RF1/RF2 after peptide release

16

What is the function of formyl-methionine in bacterial Translation?

When the codon is used for initiation, fMet is used instead of methionine, thereby forming the 1st amino acid as the peptide chain is synthesized.

17

What is the function of 30S subunit in bacterial Translation?

Complex of 16S ribosome and 19 proteins. Implicated in the binding of transfer RNA to messenger RNA. Responsible for the binding and reading of mRNA during translation.

18

What is the function of 50S subunit in bacterial Translation?

Contains rRNA and proteins. Functions to help catalyze peptide bond formation, prevents premature polypeptide hydrolysis, provides a binding site for the G-protein factors, and helps protein folding after synthesis.

19

What is the function of anticodons in bacterial Translation?

Found on molecules of tRNA. Their function is to base pair with the codon on a strand of mRNA during translation. This action ensures that the correct amino acid will be added to the growing polypeptide chain. A tRNA molecule will enter the ribosome bound to an amino acid.

20

What is the function of 5' cap in bacterial Translation?

Protects nascent mRNA from degradation and assists in ribosome binding during translation. A poly(A) tail is added to the 3' end of the pre-RNA once elongation is complete.

21

What is the function of Shine Dalgarno Sequence in bacterial Translation?

A ribosomal binding site in mRNA located around 8 bases upstream of start codon AUG. The RNA sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning the ribosome with the start codon.

22

What is the function of the Ribosome binding site in bacterial Translation?

A sequence of nucleotides upsteam of the start codon of mRNA transcript that is responsible for the recruitment of a ribosome during the initiation of protein translation.

23

What is the function of N-terminus in bacterial Translation?

The first part of the protein that exits the ribosome during protein biosynthesis. It often contains signal peptide sequences "intracellular postal codes" that direct delivery of the protein to the proper organelles.

24

What is the function of C-terminus in bacterial Translation?

The end of the amino acid cahin, terminated by a free carboxyl group.

25

What is the function of A site in bacterial Translation?

Point of entry for tRNA (except for 1st aminoacyl tRNA)

26

What is the function of P site in bacterial Translation?

Point of entry for the 1st aminoacyl tRNA and is where the peptidyl tRNA is formed in the ribosome.

27

What is the function of E site in bacterial Translation?

The exit site of the now uncharged tRNA after it gives its amino acid to the growing peptide chain.

28

What is the mRNA structure?

1) 5' triphosphate serves as a defacto "cap" to protect mRNA from degradation by cellular RNases
2) 5' - untranslated region (UTR) usually around 50 bp on average, may contain regulatory information
3) Ribosome binding site (RBS/Shine Dalgarno Sequence) located 6 bp upstream of ORF
4) Open reading frame with starting codon AUG
5) 3' UTR
6) Transcriptional stop site (poly U for intrinsic termination or not for Rho-dependent termination

29

What occurs during Translation initiation?

1) 30S binds to IF1, IF3 binds to an mRNA. IF3 blocks 50S binding. The 16S portion of the 30S binds to Shine-Delgarno sequence with help of IF3
2) IF2-GTP binds to fMet tRNA and this complex binds to the 30S+IF1+IF3
3) IF1 checks for AUG anticodon in the P site
4) fMet enters into the P site
5) GTP is hydrolyzed
6) Other IFs released
7) 50S binds to complex and GTP is hydrolyzed

30

What occurs during Translation elongation?

1) Meanwhile in the cytoplasm, the amino acids are charged by aminoacyl transferases in the following reaction:
amino acid + ATP -> amino acid-AMP + PPi
tRNAs are then charged with amino acid-AMP by tRNA synthetases in the following reaction:
amino acid-AMP + tRNA -> amino acid tRNA + AMP
2)EF-Tu (A small base GTPase) binds to charged aminoacylated amino acids and both enter through a pore. The tRNA are evaluated for its anticodon.
3) ED-Tu hydrolyzes GTP and is released from the ribosome
4) Peptide bond formation occurs through the 23S rRNA and the peptide chain transfers to the tRNA in the A site
5) The ribosome ratchets over one spot via EF-G to move the P (now deacylated) and A tRNAs to the E and P sites respectively. GTP is hydrolyzed during translocation.
6) Repeat until a stop codon is reached

31

What occurs during translation termination?

1) Termination codon enters A site. No tRNAs for stop codons.
2) Release factors 1 or 2 [RF1 (recognizing the UAA, UAG stop codons) or RF2 (recognizing the UAA and UGA stop codons)] bind to the ribosome
3) RF3 catalyzes the release of RF1 and RF2
4) The ribosome breaks open and translation stops

32

What removes the formyl group on the first methionine?

Peptide deformylase

33

What cleaves off N-terminal methionine?

Methionine aminopeptidase

34

In what organisms is the N-terminal methionine not formylated and there are more initiation factors?

Eukaryotes

35

What occurs to terminal tRNA during termination?

This is still unknown, but it is known that I may be facilitated by EF-G translocation and a protein called ribosome release factor.

36

What organisms have operons and the mRNA can be polycistronic?

Bacteria

37

Translation is?

The transfer of information from the mRNA to form the polypetide

38

What are the tRNA binding sites of Ribosome?

-Peptidyl (donor; P) site which binds initiator tRNA or tRNA attach to growing polypeptide (peptidyl - tRNA)
-Aminoacyl (acceptor; A) Site which binds incoming aminoacytl tRNA
-Exit (E) site which briefly binds empty tRNA before it leave the ribosome

39

What occurs during initiation?

The free 50S and 30S subunits are joined with mRNA, aided by small polypeptides called initiation factors (IFs)

40

What is the byproduct of GTP hydrolysis during initiation?

Addition of a large subunit

41

What is the byproduct of GTP hydrolysis during elongation?

Codon recognition and translocation

42

What is a polysome?

When several ribosomes are simultaneously translating a single mRNA molecule, the complex

43

What is the elongation cycle for translation?

There are three phases:
1) aminoacyl-tRNA binding
2) Transpeptidation reaction
3) Translocation

44

What occurs during the transpeptidation reaction?

Peptide chain is transferred from P site to A site

45

What occurs during translocation?

Three simultaneous events:
1) Peptidyl-tRNA moves from A site to P site
2) Ribosome moves down one codon
3) Emptry tRNA leaves P site

This requires GTP hydrolysis

46

How does termination of protein synthesis occur?

-It takes place at any one of three stop codons called nonsense codons: UAA, UAG, and UGA
-Release factors (RFs) help aid in recognition of stop codons. 3 RFs function in prokaryotes.

This requires GTP hydrolysis

47

What is the stringent response?

A cellular response to idle ribosomes that includes decrease in rRNA and tRNA production. It achieves balance within the cell between protein production and protein requirements. It is a global mechanism triggered by amino acid starvation.

48

Equilibrium between alternative RNA structures that differ in energy is temperature-dependent. True or false? Why?

True. Temperature shifts can differentially affect the accessibility of translation initiation regions (TIR) and thereby influence the fate of transcripts by increasing/decreasing their translation and stability.

49

What occurs with a riboswitch?

ITs interaction with an effector (red rhombs) such as amino acids, nucleotides, vitamins can either activate (upper panel) or inhibit (lower panel) translation of the downstream gene, which in turn can lead to stabilization or degradation of the corresponding mRNA(s).

50

How do prokaryotic ribosomes differ from eukaryotic ribosomes?

Bacteria: 30S+50S=70S
Eukaryotes: 40S+60S=80S

51

Which bacterial rRNAs are found in the 30S? The 50S?

16S in the 30S; 23S and 5S in the 50S

52

What are the steps in prokaryotic translation?

Initiation, elongation, and termination

53

At what steps in translation is energy required?

GTP - loading the tRNAs, ribosome ratcheting; ATP - aminoacylating tRNA

54

What are polysomes?

Multiple ribosomes on one mRNA

55

How is translation different in archaea?

Ribosomes are the same size, but different in composition. More complex.

56

How are proteins folded and localized?

Spontaneous or chaperone-assisting folding; localized by secretion systems.