Lecture 11-12 - DNA to Protein

Question 1

What is an exosome (not the protein)?

Answer 1

A cell-derived vesicle found in eukaryotic fluids. They play a role in intercellular communication, the spread of various substance (proteins, lipids, mRNA, miRNA, and DNA), and can be vectors for drugs.

Question 2

How are mRNAs exported from the nucleus?

Answer 2

Certain proteins bind the 5’ cap and poly-A tail marking them for export and guiding them to the nuclear pore.

Question 3

What is nonsense mediated decay?

Answer 3

• final point of quality control
• scans mRNA as they leave the nucleus for premature stop codons
• stop codon is premature if exon binding proteins are still on the inside of the nucleus when a stop codon is detected

Question 4

Summarize the process of transcription to the final destination of the end product.

Answer 4

• transcription factors bind promotor DNA and attract RNA polymerase
• transcription bubble is formed separating the two DNA strands
• RNA polymerase adds RNA nucleotides complimentary to template strand
• RNA transcript is processed to include polyadenylation, 5’ capping, and intron splicing
• RNA stays in the nucleus or is exported

Question 5

What is miRNA?

Answer 5

• small, noncoding RNA

- used in RNA silencing and post-transcriptional regulation

Question 6

How is miRNA formed?

Answer 6

• miRNA gene is transcribed
• transcript forms a hairpin loop and is called pri-miRNA
• end is cleaved in the nucleus forming pre-miRNA
• pre-miRNA is exported from the nucleus
• hairpin loop is cleaved leaving miRNA duplex
• miRNA binds mRNA and targets for degradation or represses translation

Question 7

What is miRNAs role in gene expression?

Answer 7

• regulates expression of many protein coding genes
• a single miRNA can target several genes
• a single gene can be targeted by several miRNA
• this can be used to regulate various process and errors can result in disease

Question 8

Where is rRNA formed?

Answer 8

In the nucleolus

Question 9

What modifies rRNA and where does this occur?

Answer 9

• snRNP modify rRNA in the nucleolus

- most common modifications are psuedouridine and 2’-O-methylation

Question 10

When is the nucleolus present and absent? What is the reason for this?

Answer 10

• present in G1, S, and G2
• absent in mitosis

-nucleolus is site of production of ribosomes which are needed for protein production; greater demand for protein synthesis -> ribosome production

Question 11

What are cajal bodies? Where are they typically found and why?

Answer 11

• regions in the nucleus which are responsible for production of snoRNA and assembly of snRNPs
• typically found near the nucleolus as snRNPs are used in processing rRNA

Question 12

Describe the structure of tRNA.

Answer 12

• cloverleaf shape consisting of three loops
• one loop contains anticodon which hydrogen binds with mRNA
• 3’ end is connected to amino acid via an aminoacyl bond
• contains several modified nucleotides (pseudouridine and dihydrouridine) which are important for structure and function

Question 13

What is the wobble base pairing?

Answer 13

Variability in the the base pairing that occurs in the 3rd codon position.

Question 15

What is responsible for attaching amino acids to tRNAs?

Answer 15

Aminoacyl-tRNA synthetase

Question 16

How does aminoacyl-tRNA synthetase ensure that it attaches the correct amino acid to the tRNA?

Answer 16

• there are several synthetases each of which bind only a certain tRNA anticodon
• each tRNA has an editing site which allows in closely related AAs after attaching so they may be removed

Question 17

Which end of a growing amino acid chain is the next amino acid added to?

Answer 17

C terminus

Question 18

Even though the __________ of bacterial and eukaryotic ribosomal subunits differ, their __________ is similar.

Answer 18

Size; shape/structure

Question 19

What are the different functional sites found on ribosomes?

Answer 19

• A site: aminoacyl tRNA site
• P site: peptidyl tRNA site
• E site: exit

Question 21

What do elongation factors do?

Answer 21

• speed up peptide synthesis by hydrolyzing GTP

- EF-Tu/EF1 also increase accuracy

Question 22

What is the function of RNA found in the ribosome? Protein?

Answer 22

RNA acts as a ribozymes and is responsible for the function of the ribosome.
Protein provides structure and stability for the rRNA.

Question 23

What role do the 5’ cap and poly A tail have in initiation of translation?

Answer 23

Both are recognized by proteins which initiate translation. This means they must be near each other for translation to start and causes mRNA to form a loop.

Question 24

What is the start codon and what is required for the ribosome to recognize it?

Answer 24

AUG; flanking consensus sequence

Question 25

The binding of what causes termination of translation?

Answer 25

-binding of a release factor to the A site

Question 26

How do fungal antibiotics work?

Answer 26

They target binding sites of the ribosomal subunits.

Question 27

When do proteins fold and what makes them fold properly?

Answer 27

- start to fold while they are being synthesized | - correct structure is typically the most energetically favorable

Question 28

Which proteins correct misfolded proteins? How do they do so?

Answer 28

-chaperones (heat shock proteins) - misfolded protein is captured by hydrophobic interactions - protein is induced to unfold - ATP hydrolysis causes structural modifications which allow the protein to fold properly

Question 29

What protein is responsible for degradation of improperly folded proteins? How does it recognize these proteins?

Answer 29

- protease | - misfolded proteins are ubiquitinated and the protease cap has a ubiquitin receptor

Question 30

Why is it suspected that RNA was the original genetic material?

Answer 30

It is capable of storing information, forming complex structures, and having enzymatic activity.

Question 31

Describe the process of a ribosome moving down an mRNA transcript.

Answer 31

- new tRNA bind with codon in A site - carboxyl end of AA chain release from tRNA in P site and peptide bond forms to new AA - large ribosomal subunits moves down one codon, tRNAs are now in the E and P sites - small ribosomal subunit moves down one codon and ejects tRNA in E site