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Quiz me . . .

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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Quiz me . . .

Postby jayson » Sun Nov 27, 2005 6:15 am

Hi I have been preparaing for my biology test on tuesday. Its on Molecular Genetics, the topis are


-DNA Structure
-DNA Replication
-Transcription
-Translation
-Control Mechanisms ( lac , trp operons)
-Mutation
-BioTechnology
- restiction enzymes
- plasmids
- recombinant DNA


Am in High School, grade 12.

I would really appreciate it if you can ask me few questions that would further help me prepare for the test. Like quiz sort of. Thanks in advance.
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Postby Bio-Hazard » Sun Nov 27, 2005 6:41 am

How was DNA discovered?
Who discovered it?
Why was the double helix form instead of the inside studied more?
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Postby sdekivit » Sun Nov 27, 2005 11:18 am

Transcription:

1: what different proteins are involved in eukaryotic transcription and discuss their function.

2: discuss the differences between transcription in prokaryotes and eukaryotes.

3: what post transcriptional processes are their after RNA has been synthesized in eukaryotes ?

Generegulation:

1: The three enzymes of the lac operon aren't synthesized in euimolar concentration. There's more B-galactosidase then permease and more permease then transacetylase. How can explain this ?

Translation:

1: Discuss the differences between translation in eukaryotes and prokaryotes.

Recombinant DNA:

We have discovered a new bacterial plasmid DNA of 12 kb long. We want to map this plasmid and therefore we use restriction enzymes. We only have 1 restriction enzyme in the lab.
We treat the DNA with very little of the restriction enzyme and analyse the fragments with an agarose gel. With a very low incubation time, partial digestion occurs. After 120 minutes no changes occur in the pattern on the agarose gel even after adding excess of enzyme.

The pattern we find is:

5 minutes incubation: band at 12 kb
10 minutes ,, : band at 9 kb and 3 kb
20 minutes ,, : band at 9 kb; 5,4 kb; 3,6 kb and 3 kb
60 minutes ,, : band at 9 kb; 5,4 kb, 3,6 kb, 3 kb, 2,5 kb and 0,5
................................kb
120 minutes ,, : band at 5,4 kb; 3,6 kb, 2,5 kb and 0,5 kb

1: after 5 minutes all plasmid molecules are cleaved one time. Explain this (how many forms of plasmid DNA are there?)

2: the various cleaving sites aren't cleaved at the same rate. How can you conclude this?

3: we isolate the first cleavingproduct of the 12 kb plasmid and we replace the phosphate group at the 5'-end with radioactive P. Then we incubate the radioactive labelled DNA with excess of enzyme. What will be the result of the analysis ?
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Postby jayson » Sun Nov 27, 2005 11:26 am

Bio-Hazard wrote:How was DNA discovered?
Who discovered it?
Why was the double helix form instead of the inside studied more?


DBA first discovered in 1869. Not as dna, but FriedRich Miescher found a phosohorus-rich matter inside the nuclei.

I don't understand the 3rd question.

Thanks though.

I was looking for more of a connection tye of question, rather then defenitions and facts.

Eg (it was posted here): How can a 53 codon gene translate into a 51 AA polypeptide.

That was a really good question, and my teacher like to give out connection question like that.
Last edited by jayson on Sun Nov 27, 2005 12:20 pm, edited 1 time in total.
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Postby jayson » Sun Nov 27, 2005 11:58 am

sdekivit wrote:1: what different proteins are involved in eukaryotic transcription and discuss their function.


Eukaryotic transcription: RNA polymerase – unwinds, and breaks hydrogen bonds
- uses the template strand to code mRNA (therefore the mRNA is same as the coding strand, except Uracil replaces Thymine
- activates at the start codon (AUG), stops at stop codon
(then again RNA polymerase is not a protein, but an enzyme)
Poly a polymerase – binds poly a tail to the 3’ end of the mRNA (post transcriptional modification) (again an enzyme)
Splicesomes – remove introns, and connect the exons. This creates a continues chain of exons, which carry the code for the protein. (post transcriptional modification)

sdekivit wrote:2: discuss the differences between transcription in prokaryotes and eukaryotes.

Prokaryotes : transcription does not need to finish to start translation
- DNA does not contain any introns
Eukaryotes – occurs in the nucleus
- introns have to removed by the splicesomes

sdekivit wrote:3: what post transcriptional processes are their after RNA has been synthesized in eukaryotes ?

- removal of the introns, done by splicesomes
- binding of the 5’ guanine cap at the 5’ end of the mRNA
- binding of the poly A tail at the 3’end of the mRNA by the poly-a-polymerase
sdekivit wrote:Generegulation:

1: The three enzymes of the lac operon aren't synthesized in euimolar concentration. There's more B-galactosidase then permease and more permease then transacetylase. How can explain this ?

- can you answer this please. You beat me at it.

sdekivit wrote:Translation:

1: Discuss the differences between translation in eukaryotes and prokaryotes.

Prokaryotes: Ribosome recognize the Shine-Delgano cap at 5’ end of the mRNA
- ribosomes are much smaller

Eukaryotes: Ribosome recognize the guanine cap at 5’ end of the mRNA
-bigger ribsomes than of prokaryotes
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Postby jayson » Sun Nov 27, 2005 12:05 pm

Recombinant DNA:

We have discovered a new bacterial plasmid DNA of 12 kb long. We want to map this plasmid and therefore we use restriction enzymes. We only have 1 restriction enzyme in the lab.
We treat the DNA with very little of the restriction enzyme and analyse the fragments with an agarose gel. With a very low incubation time, partial digestion occurs. After 120 minutes no changes occur in the pattern on the agarose gel even after adding excess of enzyme.

The pattern we find is:

5 minutes incubation: band at 12 kb
10 minutes ,, : band at 9 kb and 3 kb
20 minutes ,, : band at 9 kb; 5,4 kb; 3,6 kb and 3 kb
60 minutes ,, : band at 9 kb; 5,4 kb, 3,6 kb, 3 kb, 2,5 kb and 0,5
................................kb
120 minutes ,, : band at 5,4 kb; 3,6 kb, 2,5 kb and 0,5 kb

1: after 5 minutes all plasmid molecules are cleaved one time. Explain this (how many forms of plasmid DNA are there?)

- bases are smaller than 12kb, therefore they all cleaved once.

2: the various cleaving sites aren't cleaved at the same rate. How can you conclude this?

- please answer this

3: we isolate the first cleaving product of the 12 kb plasmid and we replace the phosphate group at the 5'-end with radioactive P. Then we incubate the radioactive labelled DNA with excess of enzyme. What will be the result of the analysis ?

- please answer this
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Postby jnkdna » Sun Nov 27, 2005 12:12 pm

jayson wrote:
I was look for more of a connection tye of question, rather then defenitions and facts.

Eg (it was posted here): How can a 53 codon gene translate into a 51 AA polypeptide.

That was a really good question, and my teacher like to give out connection question like that.


i gave that question. it was asked in the AS final exam on june'04.
i dont think i have any hard question 2 ask u. im still in grade 11..... :roll:
d nyt is darkest just before the dawn
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Postby jayson » Sun Nov 27, 2005 12:23 pm

my bad, i wrote "I WAS LOOK FOR", instead of "I was looking for". Sometimes I tend to skip words, am a very slow typer and my brain thinks ahead of my typing (thank god for that).

Regardless, jnkdna that was a good question, I didn't know methionine can be removed. Anyone know the name of the enzyme that does that ?
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Postby jnkdna » Sun Nov 27, 2005 12:40 pm

jnkdna... weird nickname isnt it? my classmates gave me that name when my bio teacher was explaining about introns. she said in lame mans language, introns r also known as junk dna. from dat moment onwards i was called junkdna(they also called me thet cuz my real name is dana)!
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Postby MrMistery » Sun Nov 27, 2005 4:59 pm

I never understood why they came up with the name of "junk dna". This name would suggest that intorns have no real purpose, and a high-school student learning his lessons for school would think evolution was stupid to put them there in eukaryotes. Even if we don't know the role of introns yet, many people came up with theories. While none have been fully proven(none that i know of) introns have a role for sure. we just need to find them.

Anyone know the name of the enzyme that does that ?

I asked myself the very same thing and couldn't find the answer in any book. It is a peptidase...
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Postby sdekivit » Sun Nov 27, 2005 10:03 pm

another difference between prokaryotic and eukaryotic transcription is de looping of DNA

--> prokaryotes have a transcription bubble, while eukaryotes need to form an proteincomplex to proceed in transcription. Also repressors and enhancerproteins are available in eukaryotes.

in prokaryotes, ribosomes recognize the Shine-Dalgarno-sequence and it's not a cap ! --> its a smaal piece of ribosomal RNA.

Why does the lac operon produce equimolar amounts of enzymes: the falling of of RNA-polymerase is a chance process. The further away the code for an enzyme is, the less it will be transcribed, because more polymerases fall of the chain.

how can we conclude the DNA-fragments aren't cleaved at the same rate? Well here's the answer:

after 5 minutes we see a band occuring at 9 kb. It is completely absent after 120 minutes. While the 3 kb piece begins to be cleaved after 20 minutes and ifs fully fragementated after 120 minutes --> faster then the 9 kb fragment.

Also we see that the 12 kb fragment is completely digested after 20 minutes. --> this cleaving site is cleaved the fastest.
--> a plausible explanation for this is that the 3 kb fragment isn't accesible when it is in the complete plasmid molecule.

you need to draw for yourself what happens when we label the 5'-side.

--> we label the 5' end of the 9 kb fragment and the 3 kb fragment. Therefore we can look whcih fragemtn will also be labelled: the 6,4 or 3,6 kb fragment or the 2,5/0,5 kb fragment

--> now we know the exact place of every cleavingsite in the plasmid molecule ;)
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Postby jayson » Mon Nov 28, 2005 12:11 am

thanks man, the equimolar amounts of enzymes... was a really good question.
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