Chapter 13: Synthesis and Processing of the Proteome

Question 1

aminoacylation

Answer 1

• process by which the correct amino acid is attached to each tRNA
• specificity of aminoacylation ensures that the tRNA carries the amino acid denoted by the codon that it pairs

Question 2

codon–anticodon recognition

Answer 2

• the interaction between tRNA and mRNA
• base pairing between the anticodon of the tRNA and a codon in the mRNA
• This specificity ensures that protein synthesis follows the rules of the genetic code

Question 3

isoaccepting tRNAs

Answer 3

• Bacteria contain 30–45 different tRNAs
• eukaryotes have up to 50 tRNAs
• there are only 20 amino acids
• this means that all organisms have different tRNAs that are specific for the same amino acid
• tRNAs are named by the amino acid specificity with a superscript suffix to distinguish different isoacceptors
  
  • tRNAGly¹ and tRNAGly²

Question 4

as well as the standard RNA nucleotides (A, C, G, and U), tRNAs contain a number of _____ _____, 5–10 in any particular tRNA, with over 50 different modifications known altogether

Answer 4

• modified nucleotides

Question 5

cloverleaf structure

Answer 5

• formed by virtually all tRNAs
  
  • main exceptions being the tRNAs used in vertebrate mitochondria which sometimes lack parts of the structure: human mitochondrial tRNA^Ser
• ^​acceptor arm
  
  • formed by seven base pairs between the 5’ and 3’ ends of the molecule, before the CCA terminal sequence
  • The amino acid is attached at the 3’ end of the adenosine of the invariant CCA terminal sequence
• D arm
  
  • named after the modified nucleoside dihydrouridine
  • always present in this structure
• anticodon arm
  
  • contains the triplet of nucleotides called the anticodon
  • anticodon base pairs with the mRNA during translation
• V loop
  
  • contains 3–5 nucleotides in Class 1 tRNAs or 13–21 nucleotides in Class 2 tRNAs
• TψC arm
  
  • named after the sequence thymidine–pseudouridine–cytidine
  • always present
• ^​has invariant nucleotides (A, C, G, T, U, ψ, where ψ = pseudouridine)
  
  • invariant nucleotide positions are important
  • nucleotides in the D and TψC arms form base pairs that fold the tRNA into a compact L-shaped
  • V loop might also form interactions with the D arm
  • Each arm is approximately 7 nm long and 2 nm in diameter
  • has amino acid binding site at the end of one arm and the anticodon at the end of the other
• has semi-invariant (abbreviations: R, purine; Y, pyrimidine)

Question 6

The adaptor role of tRNA in translation

Answer 6

• The top drawing shows the physical role of tRNA, forming an attachment between the polypeptide and the mRNA.
• The lower drawing shows the informational link, the tRNA carrying the amino acid specified by the codon to which it attaches.

Question 7

aminoacyl-tRNA synthetases

Answer 7

• group of enzymes that attachm amino acids to tRNAs—“charging”

Question 8

chemical reaction that results in aminoacylation occurs in two steps

Answer 8

• An activated amino acid intermediate is first formed by reaction between the amino acid and ATP
• then the amino acid is transferred to the 3’ end of the tRNA
• link is formed between the –COOH group of the amino acid and the –OH group attached to either the 2’ or 3’ carbon on the sugar of the last nucleotide

Question 9

• With a few exceptions, organisms have 20 aminoacyl-tRNA synthetases, this means groups of isoaccepting tRNAs are aminoacylated by a _____ _____.
• the 20 aminoacyl-tRNA synthetases fall into two distinct groups
• there are different important differences w/these groups, but there is one difference that stand out which is

Answer 9

• single enzyme
• Class I and Class II
• Class I enzymes attach the amino acid to the 2’–OH group, whereas Class II enzymes attach the amino acid to the 3’–OH group of the terminal nucleotide of the tRNA

Question 10

• Aminoacyl-tRNA synthetase has _____ _____ for its tRNA covering some 25 nm² of surface area and involving the acceptor arm and anticodon loop of the tRNA, as well as individual nucleotides in the D and TψC arms.
• The interaction between _____ and _____ _____ is, of necessity, less extensive
• Errors do occur, at a very low rate for most amino acids but possibly as frequently as ______ aminoacylation in 80
• Most errors are corrected by the _______ ______ itself, by an editing process that is distinct from aminoacylation, involving different contacts with the tRNA, called _______

Answer 10

• high fidelity
• enzyme, amino acid
• one
• aminoacyl-tRNA synthetase, transamidation

Question 11

Transamidation

Answer 11

• is a chemical reaction in which an amide reacts with an amine to generate a new amide
• when the aminoacyl-tRNA synthetase attaches the incorrect amino acid to a tRNA, this amino acid is transformed into the correct one by a second, separate chemical reaction
• the amino acid that is synthesized by the modification process is one of the 20 that are specified by the genetic code
• example
  
  • enzyme responsible for synthesis of glutamic acid–tRNA^Glu initially attaches glutamic acid to the tRNA^Gln
  • glutamic acid is then converted to glutamine by transamidation catalyzed by a second enzyme

Question 13

codon–anticodon interactions

Answer 13

• base-paired polynucleotides are always antiparallel
• mRNA is read in the 5’→3’ direction
• first nucleotide of the codon pairs with nucleotide 36 of the tRNA, the second with nucleotide 35, and the third with nucleotide 34

Question 14

wobble

Answer 14

• reduces the number of tRNAs needed in a cell by enabling one tRNA to read two or possibly three codons
• Because the anticodon is in a loop of RNA, the triplet of nucleotides is slightly curved and cannot make a uniform alignment with the codon
• a nonstandard base pair can form between the third nucleotide of the
  codon and the first nucleotide (number 34) of the anticodon (wobble)
• G–U base pairs are permitted
  
  • 3’–♦♦G–5’ anticodon can base-pair with 5’–♦♦C–3’ & 5’–♦♦U–3’
    
    • used all the time
  • 3’–♦♦U–5’ anticodon can base-pair with 5’–♦♦A–3’ & 5’–♦♦G–3’
    
    • not used in eukaryotes to prevent reading of methionine
    • could result in a tRNA^Ile with the anticodon 3’–UAU–5’ reading the methionine codon 5’–AUG–3’
• Inosine
  
  • is a modified purine that can only occur in the tRNA
  • can base-pair with A, C, and U
  • 3’–UAI–5’ anticodon is sometimes used in tRNA^Ile because it pairs with 5’–AUA–3’, 5’–AUC–3’, and 5’–AUU–3’ forming the three-codon family for this amino acid
    
    • only 3’–♦♦C–5’ and 3’–♦♦U–5’ are used
    • 3’–♦♦A–5’ not used because pairing between I and A is weak and inefficiently recognized
    • To avoid this inefficiency, the human tRNA set, the 5’–♦♦A–3’ codon is recognized by a separate tRNA
    • This does not stop pairing between I and A all together

Question 15

superwobble

Answer 15

• Other genetic systems use more extreme forms of wobble, like uman mitochondria
• the nucleotide in the wobble position of the anticodon is virtually redundant because it can base-pair with any nucleotide

Question 16

ribosomes are now considered to play two active roles in protein synthesis

Answer 16

• Ribosomes coordinate protein synthesis by placing the mRNA, aminoacyltRNAs, and associated protein factors in their correct positions relative to one another.
• Components of ribosomes, including the rRNAs, catalyze at least some of the chemical reactions occurring during translation.