The Genetic Code and Translation Flashcards by Heba Albasha

What is translation?

the process through which genetic information is converted to protein products essential for cellular function

*a number of genetic diseases are associated with defects in the protein synthesis apparatus

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DNA –(transcription)–> mRNA –(translation)–>

protein

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The genetic code is degenerate (redundant); what does this mean?

more than one item performing a required function (more than one code for same function)

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How do the four bases in DNA code for the 20 amino acids?

the code is a triplet (combinations of 4 bases in a 3 position code allow all 20 amino acids to be specified - there are 64 possibilities mathematically)
the code is non-overlapping (every consecutive triplet encodes an amino acid, no overlaps) (any given sequence of RNA however, can be read in different reading frames, depends on the starting position)
the code is universal (all life on earth uses the same code to specify the same amino acids)
the code is degenerate (i.e. redundant); 61 codons are responsible for endcoding the 20 amino acids, the remaining 3 codons (out of the 64) have a termination function; it is clear, therefore, that some amino acids are encoded by more than one codon

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How many of the 64 codons encode for the 20 amino acids and how many have the termination function?

61 code for the 20 amino acids

3 codons have a termination function

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Mutations in which position of the codon don’t typically change amino acids?

mutations in the third position of the codon

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How does tRNA read the code/message?

tRNA interprets the mRNA sequence by base pairing with the codon

*tRNA functions as an adaptor between nucleotide and protein sequences

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What are some characteristics of tRNA?

all tRNAs are about 80 nucleotides long and contain unusual (modified) bases
all tRNAs have slightly different sequences (in addition to the anticodon) often in the D and T loops (D, T, pseudo, and Y are modified bases)

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Where is the amino acid attached to the tRNA molecule?

at the 3’ terminal A

- it is attached via the 3’ hydroxyl group on the A nucleotide

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An amino acid is attached specifically based off what?

the anticodon

*each tRNA carries precisely the correct amino acid, as specified by the anticodon

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The amino acid is attached to the _____ molecule at the ___ terminal A. it is attached via the _______ on the A nucleotide

tRNA
3’
3’ hydroxyl group

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What is the role of amino acyl-tRNA synthetase?

to attach exactly the right amino acid to exactly the right tRNA

the correct amino acid is attached to tRNA by the enzyme amino acyl-tRNA syntehtase
the reaction uses ATP, ad the amino acid is attached to the tRNA by a high-energy bond
amino acyl-tRNA synthetases is a class of synthetase proteins
there are 20 amino acyl-tRNA synthetases, one fore each amino acid; each enzyme must be perfectly specific for both the amino acid and the tRNA

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if an amino acyl-tRNA synthetase is not perfectly specific for both the amino acid and the tRNA, what happens?

mistakes will be introduced into the final protein sequence

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When do the modifications to the tRNA sequence occur?

What are these modifications essential for?

after the initial transcription of the tRNA (post-transcriptional)

the modifications are essential for precise recognition of the correct tRNA by the amino acyl tRNA transferase

Psy (pseudo-uridine) and D bases (along with usual A, C, G, or U)

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Often, several tRNAs for a single amino acid, and amino acyl-tRNA synthetase must recognize the different tRNAs. How is this achieved?

recognition of the anticodon sequence

- presence and location of specific modified nucleotides (pseudo-uridine, and D dihydro-uracil) within tRNAs

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What are the two steps necessary for reading the genetic code by amino acyl-tRNA synthetases?

amino acyl-tRNA synthetase must attach the correct amino acid to the tRNA
the tRNA must bind specifically to the correct codon

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What is the action of amino acyl-tRNA synthetase?

to absolutely, specifically bind the tRNA

*for amino acids with more than one codon,the synthetase must accurately recognize several different tRNAs

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This tRNA synthetase process of binding amino acid to proper tRNA is extremely accurate. However, when virus is introduced, what happens?

mistake rate increases dramatically

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In response to a viral infection, errors in addition of amino acids to the appropriate tRNA will lead to what?

incorrect viral protein synthesis
incorrectly folded proteins are recognized for degradation
degradation will provide the viral peptides for immune presentation on the cell surface and a triggering of the immune response

There are 61 codons, we might expect 61 tRNAs. However, human cells contain 48 tRNAs. Therefore, some tRNAs must recognize more than one codon. What happens to perform this?

non-standard base pairing occurs between the third base of the codon and the corresponding anticodon base in the tRNA
*this third position is traditionally called the “wobble” position

(possibly board exam question)

The most important modified nucleotide is Inosine (closely related to a G). Inosine is a purine. it can base pair with A, c, and U. in each case, just 2 H-bonds are formed. Why is A to I base pairing unusual?

because it represents a Purine/Purine pair

Why is it called “wobble”?

Because there are two purines bonding, this isn’t normally. It is typically purine bound to
fill in

Anticodon is GAA
(example)
how will it base pair?

opposite way:
UUC
C will be wobble position (third position of anticodon which base pairs with third position of 
...
?

I allows for lots of different base pairing

just remember this

What are different human diseases associated with mutations in tRNA and amino acyl-tRNA synthetase?

- MELAS | - Charcot-Marie-Tooth disease

MELAS (Mitochondrial myopathy, Encephalopathy, Lactic Acidosis, and Stroke-like episodes)

- frequency of about 1 in 5000 people - one of the primary causes is a mutation in the mitochondrial genes encoding leucine tRNA - the mutation prevents efficient recognition of the tRNA by the appropriate leucyl-tRNA synthetase and inhibits synthesis of mitochondrial proteins

Charcot-Marie-Tooth disease

- common genetic disease (1 in 3000) that results in peripheral neuropathy - symptoms include muscle weakness and impaired sensitivity of extremities (numbness) - one form of the disease is associated with mutations in the gene encoding glycyl-tRNA synthetase (not complete loss of function) that attaches glycine specifically to its tRNA - four different missense mutations have been identified in different families

The only modified nucleotide that is ever in the wobble position is Inosine. However, G-U and G-C base pairing is also allowed in the wobble pairing not important details just know there is a wobble position that allows you to have less tRNAs than you would think

just know this

The coding sequence must be reading the appropriate reading frame. Translation always commences at what initiation codon?

AUG (codon for methionine)

What carries out translation?

ribosome (composed of RNA and protein) *translation, protein synthesis

Since most mRNAs contain multiple AUG sequences, both in frame and out of frame, which one does ribosome translation start at?

In eukaryotes, translation starts at the first AUG (nearest the 5' end of mRNA) it looks for the first one, methionine goes in from here, and sequence is read from here on

What is needed to commence translation?

a specific initiating methionine-tRNA *there are two met tRNAs, one for initiation and one for chain elongation

An (translation-)initiation complex is formed with several factors.

- initiating methionine-tRNA - GTP - small subunit of the ribosome - initiation factors (eIF-2, eIF-4E) * don't need to know the factors * small ribosomal unit complexes with these

What is needed on the mRNA to stabilize the initiation complex at the 5' end of an mRNA?

the 7meG cap | *RNAs without a cap cannot be bound by eIF-4E

The initiation complex moves along the mRNA until it locates what?

the first AUG sequence the eIF-2 (an initiation factor) unwinds mRNA

The peptide bond is formed when what two groups are joined? What does this reaction release?

- COOH of one amino acid - NH2 group of the next amino acid * the reaction releases a molecule of water (peptide bond is the O=C-N-H)

When the first AUG is located, what happens?

- GTP is hydrolyzed and eIF-2 leaves the complex | - the large subunit of the ribosome joins the complex and translation can commence

On the ribosome, the peptide bond is formed between amino acids that are both attached to tRNAs. Formation of the bond severs what?

severs the linkage to the previous tRNA (I think severs the one attached to COO)

What is peptidyl transferase?

the enzyme whose activity catalyzes peptide bond formation *located on the large ribosomal subunit (it is located between the Polypeptide and Acceptor sites)

What are the three sites of the large ribosomal subunit?

A - Acceptor P - Polypeptide E - Exit

What is the process of translocation? What is used in the translocation process?

- the action of peptidyle transferase simultaneously forms the peptide linkage and moves the ribosome one triplet along the mrNA - this frees up the acceptor site to receive a new tRNA molecule *GTP is used

What does the poly-A tail do for translation?

- increases translation | - the poly-A binding protein stabilizes binding of eIF-4E and other components of the translation initiation complex

What is a polyribosome?

the overall structure of a single mRNA being translated by multiple ribosomes simultaneously * each ribosome will start at the AUG closest to the 5' end and make its way along the mRNA * also commonly called polysome

Translation continues until a termination codon appears, in frame, in the acceptor position. What are the three termination codons?

UAA (u are annoying) UGA (u go away) UAG (u are gone)

When a termination codon is exposed in the vacant A site, what protein binds to the site? What else happens?

- a release factor protein binds to the site - a water molecule is added to the end of the polypeptide chain, severing its attachment to the final tRNA, releasing the protein into the cytoplasm *the ribosomal subunits separate and recycle

What catalyzes the activity of peptidyl transferase?

catalyzed by RNA, NOT by protein | *the enzyme activity is contained in a highly conserved sequence and structure

What is ricin?

- plant toxin - an extremely potent poison that inactivates ribosomes - one molecule of ricin in a cell can inactivate all of the ribosomes in the entire cell - ricin removes a single critical A base from the ribosomal RNA in the large subunit and completely abolishes peptidyl transferase activity *the Markov case in Cold War - died 4 days later