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MBIO2020 > 1.4 - Translation > Flashcards

1.4 - Translation Flashcards

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1
Q

what are the characteristics of tRNA?

A

-transcripted into large precursor molecules with regions of complementary binding
-single stranded and relatively short sequences (70-90 nucleotides)
-do not get translated (near final form after transcription is complete)
-processes by special exonucleases and endonucleases to produce their secondary structures (cloverleaf structures) that result from base-paired regions
-contain unusual bases

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2
Q

what are the unusual bases found in tRNA?

A

-some purine and pyrimidine bases get further modified in the maturation process (post-transcriptional modifications)
-dihydrouridine (D)
-pseudouridine (cactus symbol)
-ribothymidine (T)
-methylguanosine (mG)
-modified purine (Y)

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3
Q

what makes dihydrouridine?

A

-fully saturated pyrimidine ring (no double bonds)
-only single bonds

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4
Q

what makes pseudouridine?

A

-ribose joined to C#5 instead of N#1

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5
Q

what makes ribothymidine?

A

-methyl group added to the C#5 of uridine

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6
Q

where are tRNA genes found along the chromosome?

A

-scattered throughout
-may be present in an rRNA operon
-may form an operon with 2-7 different tRNA genes
-may be alone (monocistronic)

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7
Q

what is the role of tRNA?

A

carries amino acids to the translation machinery (ribosome)

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8
Q

what is contained on a tRNA?

A

-a specific 3 nucleotide sequences called an anti-codon

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9
Q

what is an anti-codon?

A

-a group of 3 bases that recognize a codon on the mRNA moelcule (codes for an amino acid)

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10
Q

how many amino acids are there?

A

-20 amino acids within the genetic code
-2 unusual amino acids

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11
Q

what is an amino acid composed of to give it its specialty?

A

-a unique side chain (R group) that vary in complexity
-chemical properties of the amino acid are determined by this

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12
Q

how is mRNA transcript read by the translation machinary?

A
  • 5’ - 3’ in sets of 3 (codons)
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13
Q

what can be said about the genetic code?

A

-it is degenerate (1 amino acid can have multiple codons)
-approximately 64 codons (61 for AA and 3 are stop codons)
-the redundancy in this will decrease the effects of error
-this means that a codon can determine an amino acid, but the amino acid cannot determine the specific codon sequence since there could be multiple

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14
Q

what is the start codon?

A

-AUG
-codes for methionine which has been chemically modified and is actually called N-formylmethionine (formyl group added)
-transformylase enzyme is what modifies the methionine

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15
Q

what are the stop codons?

A

-UAA
-UAG
-UGA
-do not code for any amino acids

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16
Q

how is the anti-codon read?

A
  • 3’ - 5’
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17
Q

how many tRNA molecules are there?

A

-if strict like replication and transcription, there would be 1 for each codon (64)
-there is actually only 1 tRNA molecule for each amino acid (at least 20 + special tRNAs for stop codons)
-designate by a suffix for the amino acid
-can be different subtypes for each amino acid

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18
Q

how do the anti-codons match with the different codons for each amino acid if there is not 64 anti-codons?

A

-wobble concept
-there is flexible base pairing between the 3rd position codon and the 1st position anti-codon (typically due to modified bases)
-1st and 2nd positions of the codon and 2nd and 3rd positions of the anti-codon are strict in following base pairing

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19
Q

how do we predict the rules of the wobble concept?

A

-hard to predict, but it is typically because of modifications in the tRNA bases
-ex: inosine which is a modified purine base can pair with any nucleotide

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20
Q

what are the 2 important components in the tRNA structure?

A

-acceptor domain
-anti-codon loop (central loop that determines amino acid placement)

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21
Q

what is the acceptor domain in the tRNA structure?

A

-where the amino acid is carried (3’OH at the end of the tRNA)
-3’ end has an unpaired CCA (A is the 3’ end)
-this end is generally not transcripted into the tRNA gene (added after)
-gets added sequencially by the CCA-adding enzyme using CTP and ATP as substrates
-the amino acid gets covalently attached to “A”

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22
Q

how is the correct amino acid linked to the tRNA?

A

-done as per the anti-codon
-facilitated by aminoacyl-tRNA synthetase which requires specific contacts to be made between the tRNA and synthetase (D loop, anticodon, and parts of the acceptor stem)
-done in 2 steps

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23
Q

what are the 2 steps that allow for the correct amino acid to be linked to a tRNA molecule?

A

-1st = activation of the amino acid by reaction with ATP (amino acid + ATP <-> aminoacyl-AMP + pyrophosphate PPi)
-the aminoacyl-AMP is an intermediate that gets formed and remains bound to the tRNA synthetase until collision with the tRNA molecule
-2nd = activated amino acid is bonded to the CCA stem and a charged tRNA is formed (aminoacyl-AMP + tRNA <-> aminoacyl-tRNA + AMP)
-there is a total of 2 energy rich phosphate bonds used to charge the tRNA molecule (from 1st step) so it can be costly energy wise

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24
Q

what happens after the aminoacyl-AMP is bonded to the CCA of its tRNA?

A

-exits the synthetase and the AMP is removed as well

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25
what are the 3 main sections of an mRNA?
-leader sequence -coding sequence -trailer sequence
26
what are the characteristics of a leader sequence on a mRNA molecule?
-at the 5' end of the mRNA transcript -contains a specific ribosome binding site which is also called the shine-dalgarno sequence) -does not get translated
27
what are the characteristics of a coding sequence on a mRNA molecule?
-has its information organized in codons (sets of 3 nucleotides) -begins with the AUG start codon (Fmet) -ends with a stop codon (does not code for an amino acid)
28
what are the characteristics of a trailer sequence on a mRNA molecule?
-transcribed to make the 3' end of the mRNA -determines the stability of the mRNA (degradation impeded by the secondary structure, modulated by RNA binding proteins in response to environmental stress signals)
29
what does it mean to read an mRNA transcript "in frame"?
-when starting from the start codon, there are reading frames set in the mRNA transcript (each frame = 1 codon) and there is no interruption between frames
30
how does a coding seqeunce become "out of frame"?
-deletion or addition of a nucleotide in the DNA sequence can cause the transcribed mRNA to be out of frame -creates a frame shift mutation which will affect the amino acid sequence and therefore affect the shape and function of the protein -stop codon could also appear too early or too late, both affecting the folding of the protein
31
what are the 3 types of protein functions?
-catalytic proteins -structural proteins -regulatory proteins
32
what are catalytic proteins?
-enzymes -catalysts for chemical reactions that occur in the cell
33
what are structural proteins?
-integral parts of the major structures within the cell (membranes, walls, ribosomes. etc)
34
what are regulatory proteins?
-control cell processes by a variety of mechanisms including binding to DNA and affecting transcription/gene expression (ex: DnaA binds to its own promotor on DNA to regulate its expression)
35
what is the composition of a protein?
-polymer of amino acids with varying size (polypeptide) -proteins can consist of one or more polypeptides -amino acid contains an amino group (NH2) and a carboxylic acid group (COOH) that are both attached to the alpha (central) carbon -bonds between amino acids are peptide bonds
36
how are peptide bonds formed?
-linkage between the carboxylic acid group (COOH) of one amino acid with the amino nitrogen of a second amino acid -results in the loss of one water molecule
37
what could result from a mRNA sequence in terms of a proteins final product?
-mRNA transcript could result in a polypeptide sequence that is the final protein product OR may be a part (subunit) of a final protein product -ex: RNA polymerase has multiple subunits
38
what is primary structure within a protein?
-linear sequence of amino acids in a chain that will determine the folding pattern which determines its biological activity -even one amino acid can change the function of a protein
39
what is secondary structure within a protein?
-created by hydrogen bonding between oxygen and nitrogen atoms of two peptide bonds -either will form an alpha helix or beta sheet -a polypeptide can contain regions of alpha-helix and regions of beta-sheet structures
40
who discovered the alpha helix?
-linus pauling
41
what is the tertiary structure within a protein?
-created by interactions between the R groups of the amino acids -a 3D form (folding) will depend on hydrophobic interactions instead of hydrogen bonding, ionic bonding, and disulfide bonding
42
what is the quaternary structure within a protein?
-seen in proteins that consist of two or more polypeptides -stabilized by various interactions and by disulfide bonds between cysteine nucleotides in 2 different subunits -ex: RNA polymerase
43
what are the basics of translation?
-biological polymerization of amino acids into polypeptide chains -achieved using charged tRNAs and the 70S ribosome -3 stages (initiation, elongation, termination)
44
what are the 2 subunits of the 70S ribosome?
-50S subunit (5S rRNA + 23S rRNA(majority) and 31 proteins form it) -30S subunit (16S rRNA and 21 proteins form it)
45
what is the overview of the initiation stage of translation?
-30S subunit binds to the shine dalgarno sequence in the transcript (30S subunit will help in selecting the correct tRNA for each codon) -translation begins with the special initiator aminoacyl-tRNA (formylmethionyl-tRNA) binding to the start codon AUG -50S subunit is added to complete the ribosome (will help in peptide bond formation and translocation of tRNAs from one site to another in the ribosome)
46
what happens to the formyl group on the starting methionine in the polypeptide?
-after completion of the polypeptide the formyl group will be removed and the N-terminal amino acid will be methionine
47
what does the initiation complex require?
-mRNA transcript -30S and 50S subunits of the ribosome -initiation factors (IF-1, IF-2, and IF-3) -special initiator tRNA with N-formylmethionine (fMet-tRNA) -GTP for energy (guanosine triphosphate)
48
what are the characteristics of the shine dalgarno sequence?
-within 3-9 nucleotides of the start codon -conserved consensus sequence of UAAGGAGGU which is complementary to a short sequence in the 16S rRNA to promote hydrogen bonding of the mRNA to the 30S subunit -it will position the ribosome with the start codon in the P-site -this is useful in bioinformatic analysis for structural genes
49
what are the 3 sites within the ribosome for translation?
-A (acceptor) site (entry for subsequent charged tRNAs) -P (peptide) site (peptide bond formation -E (exit) site (release of used tRNAs)
50
what are the steps to the process of binding the 30S subunit to the mRNA?
-IF-3 binds to the 30S subunit to prevent premature binding of the 50S subunit -IF-1 prevents loading of fMet into the A site (blocks the A site) - 3' end of the 16S rRNA will complementary bind to the shine dalgarno sequence at the 5' end of the mRNA to align the start codon with the P-site of the 30S subunti -IF-2 binds GTP and then binds fMet-tRNA to help guide it to the P site
51
what are the steps to the process of binding the 50S subunit?
-IF-1 and IF-3 get released -IF-2 cleaves GTP to finalize the positioning of fMet-tRNA in the P site -50S subunit then binds to complete the ribosome complex
52
what is the process of elongation?
-all subsequent aminoacyl-tRNAs will bind to the A site -requires 2 translation elongation factors and GTP -the charged tRNA is complexed with EF-Tu-GTP -anti-codon base pairs with the codon in the A site -correct pairing promotes the hydrolysis of GTP which releases EF-Tu-GDP -transpeptidation occurs to form the peptide bond between the amino acid in the A site and the amino acid in the P site -ribosome transocation then occurs to move the polypeptide containing tRNA and mRNA from the A site to the P site (done by EF-G-GTP aka bulldozer) -deacylated tRNA moves to the E site where it gets removed after a new charged tRNA has been brought to the A site
53
what are the 2 required translation elongation factors?
- EF-Tu and EF-Ts
54
how does EF-Tu-GDP get recycled back to EF-Tu-GTP?
-EF-Ts-GTP
55
what is the process of transpeptidation?
-peptidyltransferase catalyzes peptide bond formation between the carboxyl end (COOH) of the growing polypeptide in the P-site tRNA and the amino end (NH2) of the amino acid in the A-site tRNA -growing polypeptide gets transferred onto the amino acid in the A site -energy gets supplied by breaking the high energy bond between the polypeptide and the tRNA in the P site -ribozyme (from the 23S rRNA in the 50S subunit) functions as the peptidyltransferase
56
what is the process of ribosome translocation?
-once a peptide bond is formed, EF-G-GTP enters the ribosome and moves the polypeptide containing tRNA and the associated mRNA from the A site to the P site -requires hydrolysis of GTP bound to the EF-G (releases EF-G from the ribosome) -the deacylated tRNA which is now in the E site later exits the ribosome in conjunction with the incoming charged tRNA in the A site
57
what does each elongation cycle include?
-binding of a charged amino acid-tRNA, transpeptidation, and ribosome translocation -addition of 1 amino acid to the growing polypeptide -ending when a stop signal is encountered
58
how does translation get terminated?
-release factors recognized specific stop codons (RF1 for UAA or UAG, RF2 for UAA or UGA) -peptidyltransferase will try to pass the polypeptide chain to the release factor instead of an amino acid which triggers events to release the polypeptide -translocation by EF-G will cause dissociation of the ribosome from the mRNA (aided by ribosome release factor RRF)
59
how is transcription and translation coupled?
-several ribosomes can translate a single mRNA molecules simultaneously which forms a complex called a polysome -this increases speed and efficiency of translation as each ribosome will make a complete polypeptide -first ribosome can bind to the 5' end of mRNA before transcription is completed -useful because mRNA have a short lifespan which is specific to each mRNA, so coupling is very advantageous
60
how does a ribosome become stalled? how do you free a stalled ribosome?
-a defective mRNA that lacks a stop codon (from mutation, defective mRNA synthesis, or partial degradation) -ribosome becomes trapped because release factor cannot bind without a stop codon -trans-translation will free the ribosome
61
what is the process of trans-translation?
-there is production of a small RNA molecule called tmRNA (mimics tRNA as it carries an amino acid (alanine) and mimics mRNA as it is a short sequence and has a stop codon) -collides with the stalled ribosome and binds alongside the defective mRNA -protein synthesis will proceed by adding alanine and then continuing on to the short mRNA portion -adding these amino acids signals protease to degrade the protein and the ribosome dissociates as normal
62
what does the process of protein folding involve?
-chaperones (DnaK, DnaJ, GroEL, GroES) -DnaK and DnaJ are ATP dependent enzymes that bind to newly formed proteins to prevent them from folding too quickly -if proteins are folded improperly they are transferred to multi-subunit complexes such as GroEL and GroES to complete folding using ATP
63
what are the 2 unusual amino acids?
-selenocysteine -pyrrolysine
64
where can selenocysteine be found?
-in all domains of live -prevalence in methanogens
65
how is selenocysteine formed?
-converted from serine in a single step that is catalyzed by selenocysteine synthase (SelA) after tRNA-sec gets aminoacylated by seryl-tRNA synthetase (SerRS) -so a serine is added onto the tRNA and then by the use of SelA, it converts to selenocysteine
66
what encodes selenocysteine?
-a stop codon (UGA) that is followed by a selnocysteine insertion sequence element (SECIS)
67
what are the characteristics of pyrrolysine?
-prevalent in methanogens -encoded by the UAG stop codon with a similar mechanism of insertion as selenocysteine

MBIO2020 (12 decks)

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