Translation

Translation

Translation is among the most highly ______ across all organisms and among the most _______ costly for the cell. In rapidly growing bacterial cells, up to 80% of the cell's _____ and 50% of the cell's dry ____ are dedicated to protein synthesis

True or False: Transcription or DNA into RNA is a much more formidable challenge in information transfer than translation
True False

State an example illustrating the difficulty of translation as per the previous answer.

Francis H. Crick proposed that before their incorporation into ________, amino acids must attach to a special adaptor molecule that is capable of directly _______ with and _______ the three-nucleotide-long coding units of the mRNA.

Before their incorporation into _____, amino acids are attached to a class of RNA called _______ ____. Why are they called that?

The machinery responsible for translating the language of mRNAs into the language of proteins is composed of four primary components, name them:

Together, the four components, responsible for translating the language of mRNAs into the language of proteins, accomplish the extraordinary task of translating a code written in a _____ base alphabet into a second code written in the language of the ____ amino acids.

The mRNA provides the information that must be _______ by the translation machinery and is the _______ for translation. The protein-coding region of the mRNA consists of an ordered series of the three-nucleotide-long units called ______ that specify the order of the ____ ____.

The tRNAs provide the ______ ______ between the amino acids being added to the growing _______ chain and the _______ in the mRNA. Enzymes called _______ _______ couple amino acids to specific ______ that recognize the appropriate _______.

The ribosome, a multimegadalton machine, composed of both _____ and ______, coordinates the correct recognition of the _____ by each ______. The ribosome also catalyzes _____ bond formation between the growing polypeptide chain and the amino acid attached to the selected tRNA

The transaltion machinery decodes only a portion of each ______. The information for proteein synthessis is in the form of three-nucleotde codons, which each specifies ____ _____ _____

The protein coding regions of each mRNA is composed of a contiguous, non overlapping string of codons called an ____ ____ ____. Each one specifies a single _____ and starts and ends at _____ sites within the mRNA. Meaning?

Translation starts at the ___ end of the ORF and proceeds one ______ at a time to the __ end. The first and last codons of the ORF are known as the _____ and ____ codons.

Start codons for prok. (3) and euk. (1)

The start codons always code for the amino acid _______.

The start codon has two important functions

Two reasons why any stretch of mRNA could be translated in three different reading frames

Once ______ starts however, the reading frame is determined. Thus, by setting the location of the first codon, the _____ codon, it determines the _____ of all the following codons.

Three types of stop codons

Stop codons define the end of the _____ and signal _______ of the polypeptide synthesis.

mRNAs contain at least one ____. The number of _____ per mRNA is different between prokaryotes and eukaryotes. _______ mRNAs almost always contain a single ____. In contrast, ______ mRNAs frequently contain two or more ____

What is the result of prok. ORFs containing two or more ORFs

mRNAs containing multiple ORFs are known as _______ ______ and those encoding a single ORF are known as ______ _____.

The _______ mRNAs found in  bacteria often encode proteins that perform related functions, such as different steps in the biosynthesis of an _____ _____ or ______

For translation to occur, the ______ must be recruited to the mRNA. To facilitate binding by a _______, many prokaryotic ORFs contain a short sequence _______ (on the 5' side) of the start codon called the _______ ______ ______. This is also referred to as the ______-______ _______ after the scientists who discovered it

The RBS, typically located ____ to ____ bp on the __' side of the start codon, is complementary to a sequence located near the __' side of one of the ribosomomal RNA components. The complementary sequence is called the _____ ______ _____

The RBS base paris with the 16S ribosomal RNA (rRNA) thereby aligning the _______ with the beginning of the ____. The core of this region has the sequence 5'-CCUCCU-3' and prok RBS are most often subset the sequence 5'-AGGAGG-3'

The extent of complementarity and the spacing between the _____ and the _____ ______ has a strong influence on how actively a particular ORF is translated. Explain

Some prokaryotic ORFs lack a strong _____ but are nonetheless actively translated. These ORFs are not the first ORF in an ____ but instead are located just after another ORF in a _________ message. Keep in mind not all prokaryotes are _______.

In cases where the prok. is not polycistronic, the start codon on the downstream ORF often _______ the 3' end of the _________ ORF. Thus, a ribosome that has just completed translating the _______ ORF is positioned to begin translating from the start codon for the _______ ORF.

The arrangement in the previous card circumvents the need for an _____ to recruit the ribosome. This phenomenon of ______ translation between _______ ORFs is called _______ _______. **Here translation of the downstream ORF requires translation of the upstream ORF. So what happens in the case of a mutation that leads to a premature stop codon in the upstream?

Unlike their prokaryotic counterparts, eukaryotic mRNAs recruit ______ using a specific chemical modification called the ____ located where?

he 5'cap is a ______ _____ nucleotide that is joined to the 5' end of the mRNA via an unusual ___ to ___ linkage

Three steps of creating the 5' to 5' linkage

Two other features of eukaryotic mRNAs that stimulate translation

Many euk mRNAs lack kozak sequences, but their presence _______ the efficiency of translation. In contrast to proks., the bases are thought to interact with the ______ ___, not with an RNA component of the ribosome.

The poly-A tail is added enzymatically by which enzyme?

Despite its location at the 3' end of the mRNA, how does the poly-A tail enhance the level of translation of the mRNA

Importantly, in addition to their roles in translation, these 5' and 3' end modification protect euk mRNAs from rapid ________.

The heart of protein synthesis is the translation of nucleotide sequence info into _____ ____. This is accomplished by tRNA molecules, which act as _______ between codons and the amino acids they specify.

There are many types of tRNA molecules but each is attached to a specific _____ _____, and each recognizes a particular _______ or _______ in the mRNA. tRNA molecules are between 75 & 95 _______ long.

All tRNAs have certain features in common, name 2

The unusual bases in the primary structure of tRNAs is created ______________ (when) by enzymatic modification of normal bases in the polynucleotide. State two example and how they are derived

tRNAs share a common secondary structure that resembles a _______

RNA molecules typically contain regions of self complementarity that enable them to form limited stretches of _____ _____ that are held together by _____ ______. Other regions of RNA molecules have no complement and highly conserved pattern of single stranded and double stranded regions (_______ structure) that can be illustrated as a ________.

List the principal features of the tRNA cloverleaf (5)

The acceptor stem, so-named because it is the site of attachment of the ____ ____, is formed by pairing between the 5' and 3' ends of the _____ molecule. Where is the 5'-CCA-3'?

The ΨU loop is so-named because of the characteristic presence of the unusual base ________ in the loop. The modified base is often found within the sequence 5'-TΨUCG-3'. The variable loop sits between the ________ loop and the ______ loop and as its name implies, varies in size from ___ to _____ bases

The D loop takes its name from the characteristic presence of _________ in the loop. On the other hand, the anticodon loop, as its name implies, contains the ________. It is a _______ nucleotide long sequence that is responsible for recognizing the ______. It does so by _____ _____ with mRNA and is always bracketed on the 3' end by a ______ and on the 5' end by a ______

X-ray crystallography reveals an ______ tertiary structure in which the terminus of the _____ _____ is at one end of the molecule and the ______ _____ is ~70Α away at the other end

The acceptor stem and the stem of the ΨU loop form an ______ _____ in the final tRNA structure. Similarly, the anticodon stem and the stem of the D loop for a second _____ _____. Both of which align at a right angle to each other, with the ____ loop and the ___ loop coming together.

Three kinds of interactions that stabilize the L-shaped structure

tRNA molecules to which an amino acid is attached are said to be ______, and tRNAs that lack an amino acid are said to be ________.

Charging requires what type of linkage, and between which molecules?

This acyl linkage is a ____ ____ bond because its hydrolysis results in a _____ change in free energy. How is this significant in protein synthesis?

All aminoacyl-tRNA synthetases attach an amino acid to a tRNA in two enzymatic steps name them.

Adenylylation refers to transfer of _____ as opposed to adenylation, which would indicated the transfer of ______. The principal driving force for adenylylation reaction is the subsequent _______ of pyrophosphate by _______. What is the result?

What is the result of tRNA charging

Each of the 20 ____ ___ is attached to the appropriate tRNA by a single dedicated ____ _______. Because most ____ ____ are specified by more than one codon, it is not uncommon for ____ synthetase to recognize and charge or accept _____ tRNA(s).

The same tRNA synthetase is responsible for charging all tRNAs for a particular ____ ____. Thus, one and only one tRNA synthetase attaches each ____ ____ to all of the appropriate _____.

Most organisms have ____ different tRNA synthetases, but this is not always the case. For example, some bacteria lack a synthetase for charging the tRNA for ________ with its cognate amino acid. Instead, a single species of _________ ________ charges ______ as well as tRNA^Glu with ______. A second enzyme then converts the _______ moeity to a charged _______ (via _______)

Two important challenges faced by aminoacyl-tRNA synthetases

Why is the challenge faced by aminoacyl-tRNA synthetases in selecting the correct amino acid perhaps even more daunting than the challenge the enzyme facees in recognizing the appropriate tRNA

Despite the challenge in the previous card, the frequency of mischarging is very _____; typically 1 in _____ tRNAs is charged with the incorrect amino acid.

It is more challenging to understand the case of isoleucine and valine which differ by only a single _______ group. Valyl-tRNA synthetase can sterically exclude ______ from its catalytic pocket because ______ is larger than _____. In contrast, ______ should slip easily into the catalytic pocket of the isoleucyl-tRNA synthetase.

Although both valine and isoleucine will fit in the binding site, interactions with ________'s _______ group will provide an extra 2 to 3 kcal/mol of free energy

One common mechanism to increase the fidelity of an aminoacyl-tRNA synthetase is to proofread the products of the ______ reaction