Intro to molecular biology 3

Question 1

List the 4 main differences between DNA and RNA?

Answer 1

1. dna has deoxyribose sugar (no OH group on c3) while rna has ribose ( implicaton : RNA less stable)
2. thymine used in DNA but uracil in RNA
3. DNA has stable double helix structure while RNA has more complex structures (can be stabilised by hydrogen bonds but sometiems can be single stranded, eg. pseudoknot structure)
4. DNA only has one function of storing info while RNA has many functions (catalyst, genetic message, adaptor, structural, guide RNA)

Question 2

What is transcription?

Answer 2

DNA is transcribed (copied) into mRNA, which then leaves the nucleus. In transcription :
DNA is used as a template
• Complementary to one strand
• RNA polymerase (5’to 3’)
• Not as accurate as DNA replication

Question 3

what is the difference between RNA polymerase and DNA polymerase?

Answer 3

1. DNA polymerase requires primer to initiate it, RNA does not (uses other factors)
2. DNA polymerase is faster (100 bases/sec) while RNA slower (40 bases/sec)

Question 4

Difference between DNA replication and translation?

Answer 4

1. Use of DNA/ RNA polymerase
2. DNA replication more accurate
3. Many copies can be made simultaneously in translation but only one copy can be made in replication

Question 5

How do RNA polymerases know

where to start and stop?

Answer 5

Right before the site where transcription begins, there is a sequence embedded in DNA called the promoter which facilitates attachment of RNA polymerase. The promoter stops right before the transcription start site and RNA polymerase goes downstream along the RNA coding region to produce RNA. At the end of the coding region (but still within it), there is a sequence called the terminator, which signals RNA polymerase to detach and fall off.

Question 6

What are the different RNA Polymerases and what do they generate?

Answer 6

RNA pol I- rRNA
• RNA pol II - protein coding RNA
• RNA pol III - tRNA

Question 7

What is the promoter for RNA pol II?

Answer 7

TATA box (repeat sequence of TATA found on DNA)
• starts around 25 bases upstream of start site
• TBP (tatabox binding proteins) distorts DNA once bound and Facilitates binding of RNA polymerase and transcription factors

Question 8

Explain how transcription factors work?

Answer 8

Transcription factors are trans-acting factors which bind to cis-acting promoter, thus aiding the RNA polymerase to bind and initiate transcription as RNA polymerase is unable to bind directly to promoter

Question 9

Housekeeping gene vs transcriptionally regulated gene?

Answer 9

housekeeping genes code for proteins that are needed quite often and need to be regularly produced, so it has certain motifs embedded to keep production going at a basal level. The expression of these genes do not fluctuate massively in response to signals

Transcriptionally regulated genes need to be able to be switched on and off. Have gene-specific transcription factors that might not always be bound on the DNA. So only transcripted when needed in response to signal.

Question 10

What happens in Frasier syndrome?

Answer 10

involves WT1 gene in which exon 9 (KTS) is included after splicing or not. In normal, it is important that the ratio between +KTS and -KTS is kept in balance when it is not it can affect function (ex glomerulus function - glomerulonephropathy)

Question 11

What is the gene number paradox?

Answer 11

it is how the relatively restricted amount of genes can code for a diverse variety of proteins

Question 12

Name 5 post-transcriptional modifications?

Answer 12

1. alternative promoter
2. alternative splicing
3. alternative 3’ ends
4. RNA editing
5. translational control

Question 13

the function of snRNA in splicing?

Answer 13

snRNA base pairs with sequences of pre-mRNA to recognize the position of intron-exon junctions (recognizes exon)
also has a catalytic binding function

Question 14

Pax6

Answer 14

absence of transcription factor PAX6 leads to a mutation affecting the eyes in humans, drosophila, mouse and even zebrafish. in humans, cornea opaque, retina degenerate, iris absent etc

Question 15

Other factors that help initiate transcription?

Answer 15

Relaxation of chromatin helps

1. Histone modifying enzyme
2. Chromatin remodeling complex

Question 16

How is mRNA processed

Answer 16

RNA capping (addition of 5’ cap after a few bases have been added) and polyadenylation (adding approx 250 adenine residues to the 3’ end known as poly-A tail)

Question 17

Why is mRNA processed

Answer 17

1. to protect it from being degraded by exonucleases
2. to identify it as mRNA
3. to aid its export

Question 18

What are enhancers?

Answer 18

• short sequences of DNA that is a positive regulative element for transcription
• its position and orientation are independent of transcription
• binds common (ubiquitous and cell type specific transciption factors)
• function to stabilise transcription machinery assembly by protein-protein interactions
• they work from long distance by two proposed models (scanning and looping)
• opposed by silencers

Question 19

process of transcription?

Answer 19

• binding of general transcription factors, mediators, histone acetylases, chromatin remodeling complexes, rna polymerase leads eventually to transcription beginning
• As polymerase moves along DNA, it unwinds and adds nucleotides to the 3’ ends of the growing RNA strand
• The mRNA is processed by adding an RNA cap and polyadenylation (poly-A tail)