Translation Chapter 13

Briefly describe the 3 stages of translation (a couple of sentences for each stage) mentioning the functional roles of the A, P and E sites.

-Initiation: initiation factors bind to the 5' mRNA cap and facilitate binding of the mRNA to the 40S ribosomal subunit. The subunit then scans the mRNA for the start codon. After finding the start codon, the first tRNA carrying Met binds to the P site and the 60S ribosomal subunit associates with the small subunit. -Elongation: a tRNA with an anticodon complementary to the codon in the A site binds to the A site. A peptide bond forms between the amino acid in the A site and the amino acid at the end of the polypeptide chain held by the tRNA in the P site. The growing polypeptide chain is then transferred to the tRNA in the A site and the ribosome translocates one codon in the 3' direction. The tRNA in the E site exits the ribosome and a new tRNA comes into the A site for the cycle to start again. - Termination: translation ends when there is a stop codon in the A site. The stop codon is recognized by a release factor which promotes release of the completed polypeptide and dissociation of the mRNA and ribosome subunits.

proteins have 3 or 4 levels of structure depending on whether the protein is composed on one or more than one polypeptide. Describe each of the 4 levels of protein structure (one or two sentences for each level will do.)

-Primary structure: Sequence of amino acids. - Secondary structure: Folding of local regions of the polypeptide chain. Common secondary structures are the alpha helix and beta sheet. - Tertiary structure: Overall 3D folded shape of a polypeptide. This is the final level of structure for a protein composed of a single polypeptide. Quaternary structure: The association of two or more polypeptides to form a multi-subunit protein.

wobble is at the __ end

3'

If a tRNA molecule carries glutamic acid, what are the two possible anticodon sequences that it could contain? Be specific about the 5' and 3' ends

3' - CCU - 5' or 3' - CUC - 5' (however, 3' - CUU - 5' could take care of both codons due to wobble.

___ scans the DNA for the first codon (Met)

40S subunit

A tRNA has the anticodon 5'-CCG-3'. Which tRNA anticodon will bind to this codon, and which amino acid does the tRNA carry?

5' - CGG - 3' (same as 3' -GGC- 5') The tRNA carries arginine (Arg) as specified by the codon.

An mRNA codon has the sequence 5'- ACG - 3'. Which tRNA anticodon will bind to this codon, and which amino acid does the tRNA carry?

5' - CGU-3' (same as 3'- UGC - 5') or 5' - UGU - 3' (same as 3' -UGU - 5') The tRNAs carry threonine (Thr) as specified by the codon.

If a tRNA has the anticodon sequence 3' - CCI - 5' what codon(s) can it recognize?

5' - GGU - 3', 5' - GGC - 3' , and 5' - GGA - 3' ; which all encode alanine

mRNA sequence is read __ as a series of __

5' -- 3'; triplet codons

Codons are always read __

5' to 3'

What is the amino acid sequence encoded by the following mRNA? 5'- GCC UAC AUG GGC AGU UUA AUU UCA UUU GUA UGA CCA -3'

5'- GCC UAC AUG GGC AGU UUA AUU UCA UUU GUA UGA CCA- 3' Met-Gly-Ser-Leu-Ile-Ser-Phe-Val

An mRNA encodes a polypeptide that is 312 amino acids in length. The 53rd codon in this polypeptide is a tryptophan codon. A mutation in the gene that encodes this polypeptide changes this tryptophan codon into a stop codon. How many amino aids would be in the resulting polypeptide: 52, 53, 259, or 260?

52

A polypeptide contains 200 amino acids. How many nucleotides are expected in the coding sequence of the gene?

600

__ binds to form the initiation complex

60S subunit

binds incoming tRNA with complementary anticodon

A (aminoacyl) site

What is a codon? How many nucleotides make up a codon?

A codon is a sequence of 3 nucleotides that specify an amino acid.

Is a codon specified by DNA, mRNA, or tRNA? Are codons read from 5' - 3' or 3' - 5'?

A codon is specified by mRNA. mRNA codons are read from 5' - 3'

In which of the following ribosomal sites, the A site, P site, and/or E site, could the following be found? A. A tRNA without an amino acid attached. B. A tRNA with a polypeptide attached. C. A tRNA with a single amino acid attached.

A. The E site and P site. (Note: A tRNA without an amino acid attached is only briefly found in the P site, just before translocation occurs.) B. The P site and A site. (Note: A tRNA with a polypeptide chain attached is only briefly found in the A site, just before translocation occurs.) C. Usually the A site, except for the initiator tRNA, which can be found in the P site.

If we assume that the tRNAs do not contain modified bases, what is the minimum number of tRNAs needed to recognize the codons fro the following types of amino acids? A. Leucine B. Methionine C. Serine

A. The answer is three. There are six leucine codons: UUA, UUG, CUU, CUC, CUA, and CUG. The anticodon AAU would recognize UUA and UUG. You would need two other tRNAs to efficiently recognize the other four leucine codons. These could be GAG and GAU or GAA and GAU. B. The answer is one. There is only one codon, AUG, so you need only one tRNA with the anticodon UAC. C. The answer is three. There are six serine codons: AGU, AGC, UCU, UCC, UCA, and UCG. You would need only one tRNA to recognize AGU and AGC, This tRNA could have the anticodon UCG or UCA. you would need two tRNAs to efficiently recognize the other four tRNAs. These could be AGG and AGU or AGA and AGU.

___ adds amino acid to tRNA

Aminoacyl tRNA synthase

uncharged tRNAs leave the ribosome

E (exit) site

What does it mean when we say that the genetic code is degenerate?

It means that the same amino acids can be specified by more than one codon. There are only 20 standard amino acids, but there are 61 different codons that specify amino acids.

What is the amino acid sequence encoded by the following mRNA? 3'- ACC AGU AUG UUU ACU UUA AUU UGA CGG GUA CAU CCG -5'

Met-Gly-Ser-Leu-Ile-Ser-Phe-Val

Amino acid sequence is always given __ to __

N-terminus to C-terminus

contains the tRNA with the growing polypeptide chain

P (peptidyl) site

Sequence of amino acids

Primary structure

Association of two or more polypeptides

Quaternary structure

Briefly describe the composition of eukaryotic ribosomes (how many subunits does a ribosome have, and which two types of macromolecule are ribosomes composed of)?

Ribosomes have a small 40S subunit and a large 60S subunit. The subunits are composed of ribosomal RNA (rRNA) and proteins.

Folding of local regions of the polypeptide chain

Secondary structure

What is the start and stop codon of mRNA?

Start- AUG Stop- UGA

Which codons are synonymous with CUU (synonymous codons specify the same amino acid)?

Synonymous codons are those that specify the same amino acid. Non-synonymous codons specify different amino acids. UUA, UUG, CUC, CUA, CUG are all synonymous with CUU.

Overall 3D folded structure of a polypeptide

Tertiary structure

What are the 5' and 3' untranslated regions?

The 5' untranslated region (UTR) is a region upstream from the translation start site, and it does not get translated to amino acid. The 3' UTR is a region downstream from the stop codon, and it does not get translated to amino acid.

Describe the components of eukaryotic ribosomal subunits and the location where the assembly of the subunits occurs within living cells.

The assembly process for the ribosomal subunits is very complex at the molecular level. In eukaryotes, 33 proteins and one rRNA assemble to form a 40S subunit, and 49 proteins and three rRNAs assemble to form a 60S subunit. This assembly occurs within the nucleolus.

If the DNA template strand is 5' - TCA ACG TAG CCA GGT CAT - 3' what is the amino acid sequence of the polypeptide it encodes? Which amino acid is at the N-terminus of the polypeptide, and which amino acid is at the C-terminus?

The mRNA is: 5' - AUG ACC UGG CUA CGU UGA - 3' The resulting polypeptide is therefore: Met-Thr-Trp-Leu-Arg Met is at the N-terminus and Arg is at the C-terminus

If the DNA coding strand is 5' - ATG ACG TCG CCA GGT TGA - 3' what is the amino acid sequence of the polypeptide it encodes? Which amino acid is at the N-terminus of the polypeptide, and which amino acid is at the C-terminus?

The mRNA is: 5' - AUG ACG UCG CCA GGU UGA - 3' The resulting polypeptide is therefore: Met-Thr-Ser-Pro-Gly Met is at the N-terminus and Gly is at the C-terminus

What is the role of aminoacyl-tRNA synthetase? The ability of aminoacyl-tRNA synthetases to recognize tRNAs has sometimes been called the "second genetic code". Why has the function of this type of enzyme been described this way?

The role of aminoacyl tRNA synthetase is to specifically recognize tRNA molecules and attach the correct amino acid to them. This ability is sometimes referred to as the "second genetic code" because the specificity of the attachment is a critical step in deciphering the genetic code. For example, if a tRNA has a 3' - GGG - 5' anticodon, it will recognize a 5' - CCC - 3' codon, which should specify proline. It is essential that aminoacyl-tRNA synthetase known as prolyl-tRNA synthetase recognizes this tRNA and attaches proline to the 3' end. The other aminoacyl tRNA synthetases should not recognize this tRNA.

What is translation?

The sequence of nucleotides in mRNA directs the linking together of amino acids in a precise order to form a polypeptide.

The diagram below depicts a gene and shows the positions that encode translational start and stop codons. Which strand (top or bottom) is the template strand for this gene? 3' --------TAC-------ATT----5' 5' --------ATG-------TAA---3'

The top strand is the template strand because, when transcribed, it will give an mRNA with the start codon at the 5' end and the stop codon at the 3' end.

How many standard amino acids are there? What distinguishes the different amino acids?

There are 20 standard amino acids distinguished by the side group. The side group gives each amino acid its distinct properties.

What is the function of aminoacyl tRNA synthase enzymes?

They add the correct amino acid to the correct tRNA molecule. A different aminoacyl tRNA synthase enzyme is required for each amino acid.

According to the original wobble rules, what is the minimum number of tRNAs needed to recognize all of the codons for Leucine (Leu)?

Three 3'- AAU- 5' could recognize UUA and UUG 3'- GAI - 5' could recognize CUU, CUC and CUA 3' - GAC - 5' or 3' - GAU - 5' could recognize CUG

__ carries the amino acids that is specified by the codon

Transfer RNA

Where does translation start and stop? Do the start and stop codons specify an amino acid?

Translation starts at a methionine (Met) codon, which specified the amino acid methionine (Met). Translation stops at a stop codon, which does not specify an amino acid.

What does it mean when we say that the genetic code is degenerate? Discuss the universality of the genetic code.

When we say the genetic code is degenerate, it means that more than one codon can specify the same amino acid. For example, GGG ,GGC, GGA, and GGU all specify glycine. In general, the genetic code is nearly universal, because it is used in the same way by viruses, prokaryotes, fungi, plants, and animals. There are few exceptions, which occur primarily in protists and yeast and mammalian mitochondria.

What is wobble between the codon and anticodon? In which position of the codon and anticodon is the wobble base located?

Wobble means that the nucleotides located in the 3' position of the codon and the 5' position of the anticodon do not always base pair according to the complementary AU/GC base pairing rules. For example, G at the 5' end of the anticodon can pair with either C or U at the 3' end of the codon.

The enzymes have an __ and an __

active site and an editing site

The quaternary structure is the association of __ and __

alpha helices and beta sheets mixed together

Two major secondary structures:

alpha helix and beta sheets

tRNA anticodons are associated with the specific ___ specified by the codon

amino acid

Polypeptides have an ___ and a ___

amino terminus (N terminus) and a carboxyl terminus (C terminus)

tRNA that has its amino acid binded

aminoacyl tRNA

A different ___ is used for each amino acid

aminoacyl tRNA synthase

A tRNA carrying its amino acid is referred to a a __ or an __

charged tRNA or an aminoacyl tRNA

Each codon is recognized by a __

complementary tRNA anticodon

The amino acid code is __

degenerate

After the stop codon there is another series that __

do not get translated to proteins

Alpha helices and beta sheets come about through __

hydrogen bonding

Initiation requires various __

initiation factors

Ribosomes have a __ and a __

large subunit and a small subunit

DNA sequence transcribed into an __

mRNA sequence

The same amino acid is specified by ___

more than one codon

Local regions of the polypeptide fold into the __

overall 3D tertiary structure

Amino acids are linked together by __ to form __

peptide bonds; polypeptides

Termination promotes the release of the __ and dissociation of the __

polypeptide; complex

The side chain determines the __

properties of an amino acid

Ribosomal subunit are composed of __ and __

rRNAs and proteins

Stop codon is recognized by a __

release factor

Termination occurs when __

ribosome reaches a stop codon

Translation takes place on __

ribosomes

The genetic code is degenerate meaning that the __

same amino acid can be specified by more than one protein

Wobble rules allow for the __

same tRNA to interact with more than 1 codon

Initiation factor facilitates binding of __ to __

small subunit to 5' mRNA cap

Stop codons do not __

specify proteins

Initiation factor recruits ___ to the ___

tRNA˄met; P site

There are not 61 different tRNA molecules; one tRNA can recognize more than one codon due to __

wobble