Lecture 14

Question 1

Translation

Answer 1

• the synthesis of proteins from mRNA
• translation takes information from the language of nucleic acid (ribonucleotides) and translates it into the language of proteins (amino acids)
• takes place in cytosol

Question 2

Genetic code:

Answer 2

• a set of triplet code codons of mRNA or DNA coding for amino acids
• mRNA is read in a non-overlapping, consecutive groups of three nucleotides known as codons

Question 3

How many codons are there:

Answer 3

• there are 64 codons that encode for 20 amino acids
• the code is redundant because several different codons encode for the same amino acid

Question 4

What is the initiation codon and what does it signal?

Answer 4

• it is AUG
• it signals the beginning of a polypeptide (and encodes for methionine)

Question 5

How many stop codons are there and what do they do?

Answer 5

• There are three: UAA, UAG, UGA
• They terminate translation

Question 6

How many possible reading frames are there in mRNA

Answer 6

• There are 3 possible nonoverlapping reading frames in mRNA going in one direction (5’ to 3’)

Question 7

What is an open reading frame and why are they important?

Answer 7

• ORF is a reading frame that has the potential to code for a protein or polypeptide
• The first base of the ORF is a start codon and it ends with a stop codon
• Usually greater than or equal to 50 codons

Question 8

Types of mutations:

Answer 8

Missense mutation is a mutation in which a single nucleotide changes that results in a codon that codes a different amino acid

Nonsense mutation is a mutation that results in a premature stop codon

Silent mutation is a mutation that takes place in the gene but has no negligible effect on the gene product

Frameshift mutation is a mutation that causes a shift in the reading frame. This can be caused by deletions or insertions of nucleotides

Question 9

What are transfer RNAs (tRNA)?

Answer 9

• tRNAs act as a bridge between RNA and protein
• tRNAs are composed of a single strand of RNA that forms a double helical structure
• tRNA contains a 3-nucleotide anticodon that recognizes the codons on the RNA. mRNA and tRNA are oriented antiparallel
• each tRNA can be linked to a specific amino acid

Question 10

What is the aminoacyl-tRNA synthetases

Answer 10

• the aminoacyl-tRNA synthetases couples the correct amino acid to the correct tRNA molecule using ATP
• when coupled to an amino acid, tRNA is said to be charged
• there is a different synthetases for every amino acid

Question 11

Ribosomes:

Answer 11

• translation is conducted by ribosomes in the cytoplasm
• ribosomes are very large complexes of ribosomal RNA (2/3) and protein (1/3)
• each ribosome has two subunits, one large and one small

Question 12

What is a ribozyme:

Answer 12

• RNA molecules with catalytic activity
• rRNA allows for the catalytic activity and determines overall structure of ribozyme

Question 13

What are the distinct sites on a ribosome

Answer 13

• A= aminoacyl-tRNA site
• P= peptidyl-tRNA site
• E= exit site

Question 14

How does mRNA interact with the ribosome?

Answer 14

• It binds to the small subunit
• The ribosome moves along the mRNA in a 5’ to 3’ direction

Question 15

Initiater tRNA is the only one that can bind directly to the P site of the small subunit. All other bind to the A site

Question 16

Initiation of translation (eukaryotes)

Answer 16

1. The initiator tRNA binds to the P site of the small subunit along with initiation factors
2. The mRNA binds to the small subunit, recognizing 5’ cap
3. This moves until it encounters the first AUG
4. Initiation factors dissociate and the large ribosomal subunit binds
5. A charges tRNA molecule binds to the A-site
6. The methionine in the P-site is linked to the amino acid in the A-site through a peptide bond

Question 17

Translation (continuation in eukaryotes)

Answer 17

• Step 1 : Aminoacyl-tRNA bind to the A site by base pairing with the codon
• Step 2 : The carboxyl end of the polypeptide chain is uncoupled from the tRNA at the P site and joined by a peptide bond to the free amino group of the amino-acid linked to the tRNA at the A site by a peptidyl transferase
• Step 3 : Translocation of the large subunit relative to the small subunit the two RNA are moved to E and P sites of the large subunit
• Step 4 : The small subunit translocate moving three nucleotides along mRNA bringing it back to the original position relative to the large subunit. It reset the ribosome on an empty A site allowing the binding of the next amino-acyl tRNA

Question 18

Termination: translation in eukaryotes

Answer 18

1. When a stop codon is encountered, a protein known as release factors bind
2. The peptide is transferred into a water molecule (instead of another amino acid) causing the peptide chain to be released
3. The ribosomes dissociate

Question 19

Translation in bacteria

Answer 19

• Very similar, but some differences
• The mRNA has no 5’ cap so instead the small subunit recognizes the Shine-Dalgarno sequence which lies upstream of the start codon

Question 20

Compare polycistronic and monocistronic mRNA

Answer 20

• Bacteria has polycistronic mRNA: several genes are encoded on the same mRNA transcript
• Each individual gene has its own Shine-Dalgarno sequence, so that each product can be individually translated
• Eukaryote mRNA is usually monocistronic

Question 21

What are a polyribosome:

Answer 21

• A single mRNA transcript can be translated by several ribosomes simultaneously
• This increases overall rate in protein synthesis
• Occurs both in prokaryotes and eukaryotes

Question 22

Differences between prokaryotic and eukaryotic translation have be used to create
- Antibiotics

What antibiotic blocks the binding aminoacyl-tRNA to A site of ribosome
- Tetracyline

What antibiotic blocks the peptidyl transferase reaction on ribosomes (step 2)
- Chloramphenicol

What antibiotic blocks the translocation reaction on ribosomes (step 3)
- Cycloheximide

Question 23

What are proteases?

Answer 23

• Proteases are enzymes that degrade proteins

Question 24

What are proteasome?

Answer 24

• Proteasome is a large protein machine that degrades proteins in eukaryotes. Unfolds proteins and degrades them in the interior of a chamber

Question 25

List a couple of post translational modifications

Answer 25

- Phosphorylation - Glycosylation - Proteolytic cleavage

Question 26

Autocatalysis:

Answer 26

the ability to catalyze reactions directly or indirectly to the production of molecules like itself (RNA can do this)

Question 27

RNA can…

Answer 27

- Store information and catalyze reactions - Formation of peptide bonds, splicing, RNA polymerization and DNA logation

Question 28

Provide evidence that supports the idea of an RNA world

Answer 28

- Ribose can be formed from formaldehyde under conditions that stiumulate primitive earth - Ribose is easier to form than deoxyribose - Spontaneous deamination of cytosine to form uracil