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Dear Dr. Pat,
First of all, I want to congratulate you to composing such an excellent web site on genetics.  I loved reading it because it was written in such an amusing way and easy to understand.  I am an 18-year old Austrian student who is very interested in genetics (I even consider becoming a scientist working in the field of genetics).  I have read a little bit on this topic besides your web site. I have to write a 15 page paper on this topic for school and I really have to know exactly what I'm talking about because I'll have a very important oral exam on it.  That is why I'd like to ask you a few questions, if you don't mind :

1. Where are the amino acids produced ? I understand that the ribosomes just put them together if they get the order to do so from the t-RNA, but do they also produce the amino acids ?

2. How can you find out where a gene starts and where it ends if they are all sequences of nucleotides that are connected to each other without any space in between ?

3. What exactly are what you call "on" and "off- switches" ?

4. What is a genome ?

5. Could you explain to me how the building of a new human cell actually happens ?

As far as I know, the DNA is doubled and at the same time the m-RNA is produced and sends the message to the ribosomes which start to put the amino acids in the right sequence with the help of the t-RNA's.  The ribosomes then link the amino acids to form proteins. That's how the new cell is produced.  But what happens next ?  How does the DNA get into the new cell ?  How does the new cell which is still in the cytoplasm of the old cell get out of it ?  What about the "other form" of producing a new cell (Meiosis, Mitosis) - is that just for 2 reproduction cell (like egg and sperm) that have melted together to build new life ?  And is the other way of producing a new cell that I described before sort of natural cloning of a cell ?

6. Where are the nuclear bases and the sugar and the phosphate produced that later on make up the nucleotides needed for doubling the DNA and where are they stored so that the enzymes doubling the DNA can reach them ?

7. Do enzymes produce the m-RNA and the t-RNA inside the nucleus ? Where do they get the necessary "material" (nuclear bases, uracil, phosphate, sugar) from ?

I would be very grateful if you could answer my questions soon because I need to get done with my paper in time. Thank you so much for your help ! I really appreciate it !   Sincerely, Carmen

Dear Carmen,
Thank you so much for your kind words about our web site. We are happy that it is of help to you.

I will do the best I can in answering your questions.

Let me make one overall comment before getting to specific questions. That is, cells need to do continual maintenance and they need to adapt to changing conditions. This requires that protein synthesis go on almost non-stop. Some proteins made only to replace proteins that are getting old, and some being made to allow the cell to react to a changing situation.

1)Where are the amino acids produced?
Amino acids come from dietary protein that is broken down during the digestion process. All but about 8 amino acids can be changed from one to another in the body. These 8 are called 'essential' amino acids and must be brought into the body in the form of food. The others, as mentioned, can be taken apart and reformed into whatever assortment of the 20 amino acids that the cell needs. These reactions are catalyzed by specific enzymes in the cytoplasm. The t-RNA and ribosomes do not play a role in the synthesis of amino acid process, just the protein synthesis process (which is quite enough responsibility, thank you).

2) How do you know where a gene starts and ends?
Boy, these are all great questions. In biology, one can make a huge step forward in understanding if one thinks in 3-D. It takes a lot of imagination to think in 3-D about things that are so small they are invisible to our eyes, but it is worthwhile to try. The nucleotide sequence A-C-C-G has a much different 3-D shape than the sequence C-A-T-C. It also differs in the number and position of charged groups (+ and -). Specific enzymes can 'recognize' the 3-D shape and charge location of a special sequence of nucleotides, called a promoter. The promotor is located at the start of a gene sequence and a specific enzyme finds it and binds to it to start the mRNA off at the right place. The stop positions are similarly located by a special sequence at the end of the gene.

3) What exactly are what you call "on" and "off-switches"?
Well they can be many forms that accomplish the same thing. Some genes have their promoter covered up and need something to come along and uncover it so that mRNA can be made. The site on the DNA that allows the promoter to be uncovered would be called an on switch. Likewise, if you have a gene whose protein is needed almost all the time, you would want to let mRNA be made almost all the time. Therefore, only some time would you want to turn it off. The off-switch would cause the start position of the gene to be covered up. The exact ways these things are done are many and more complex than we would go into in our site.

4) What is a genome?
A genome is all the genes of an organism.

5) How does the building of a new human cell happen?
Mitosis (also known as: asexual reproduction or cell division) occurs something like this: The cell almost double in bulk. The chromosomes are reproduced exactly. The subcellular organelles (if any) are doubled in number. The nuclear membrane dissolves and the cell begins to pinch in the middle - forming a figure 8 type shape. The chromosomes are pulled into each half so that the identical chromosomes go into different halves. The middle eventually pinches closed and you have two new cells. The nuclear membrane reforms around the chromosomes. Each daughter cell has the exact same chromosomes as the parent cell had and would be considered 'clones' of the parent cell.

Meiosis (also known as: sexual reproduction) occurs in a very similar way, only the chromosomes are not reproduced. The chromosome pairs (one you got from your mother and one from your father) are separated into the daughter cells. In this way, one daughter cell may have a chromosome #1 from your mother and a chromosome #2 from your father. The other daughter cell would then have a chromosome #1 from your father and a chromosome #2 from your mother. The two daughter cells would therefore be different from each other. Meiosis is only done to produce sperm and egg cells (generally called gametes). If nature did not have a meiosis type of cell division for gamete production, each generation would have twice as many chromosomes as the previous generation. At some point, the cell would be too small to carry all those chromosomes.

6) Where are the nuclear bases and the sugar and the phosphate produced that later on make up the nucleotides needed for doubling the DNA and where are they stored so that the enzymes doubling the DNA can reach them?
If you go back far enough in the chain of events, it all comes from food. The body and the cells of the body digest the food into its most basic parts, such as bases, sugar and phosphate. The cells even break the bases down further and can reassemble them as needed. Other enzymes can take the bases and combine them with sugar and phosphate to make the DNA nucleotides. These reactions are carried out by enzymes in the cytoplasm. The nucleotides can be imported through the nuclear pores so that they are just hanging around inside the nucleus when DNA synthesis is going on.

7) Do enzymes produce the mRNA and the tRNA inside the nucleus? Where do they get the necessary 'material' from?
The mRNA and the tRNA are made in the nucleus by enzymes. But the building block nucleotides are made in the cytoplasm and are imported through the nuclear pores.

Here are a couple of web sites that may assist you in further information regarding these topics:

www.lif.icnet.uk/kids/cellsrus/cellsrus.html (for kids, but great presentation)

www.chem4kids.com/biology4kids

Let me know if you need any more information. Excellent questions. Be sure to try out some science classes in college; you very well might enjoy them a lot. Good luck on your paper,
Dr. Pat

Dear Dr. Pat,
Thank you so much for answering my questions immediately ! You gave me all the information I needed and you made it easy to understand.  Actually, I had once learnt where the amino acids come from but once you try to learn about and understand a new field as complex as genetic engineering you expect everything to be complicated and forget all the basic connections you have ever learnt.  Well, that's life.

Anyway, I was wondering if it would be possible for me to ask you just a few more questions. The problem is that I could not get a hold of a book about genetic engineering in English that was not too complicated for me to understand so I had to translate all the definitions of terms that I have to give in my paper from a German dictionary which was quite difficult. It would be great if you could check to see if my definition of genetic engineering sounds all right.

1. The method of the molecular biology to deliberately isolate and clone pieces of DNA from one organism and to integrate them into another one that does not have to be from the same species is known as genetic engineering. The goal of this science is the production of useful proteins that can either be used to fabricate medicine cheaper and changes in the genetic code that can improve the yield of domestic plants or the meat production of domestic animals. In order to work efficiently, genetic engineers need several "tools" such as restriction enzymes, reverse transcriptase and ligases.

2. I couldn't really find a good definition of enzymes (I know what they are but I'd need a one sentence definition).

3. What are "ligases" and what are they for ? How do they work ?

4. How do genetic engineers use reverse transcriptase (I know what it is and how it works) ?

5. How much is one molecule of DNA ?

6. Which diseases do retro - viruses cause ? HIV ?

7. I read this somewhere :
"There are three ways of integrating outside DNA into an organism:
a) through vectors (plasmids, bacterium something (I can't translate it) , retroviruses)
b) by injecting DNA into an embryo (???)
c) by using electric fields to open up the pores in the nuclear membrane to let outside DNA into the nucleus ".

Do you think you could explain to me how it works with plasmids and (in case you know) what the bacterium something could be and what they mean with "embryo" (a fertilized egg ?) in b ?

It would be great if you could answer these questions for me. But if it's too much trouble, just let me know, that's ok.

Thank you very much for your help !
Sincerely,  Carmen

Dear Carmen,
I will do my best to answer your questions.

Your definition of genetic engineering:
1. This definition is excellent. I might add that there are more and more goals for genetic engineering each day. For instance, many scientists and doctors would very much like to be able to cure genetic diseases this way.

2. Boy, that is some challenge; define an enzyme in one sentence. How about: An enzyme is a protein whose three-dimensional shape and charge allows it to catalyze specific chemical reactions.

3. Ligases are enzymes that splice DNA strands together. When DNA is synthesized it is made in very short pieces that need to be joined together; ligases do that job. They work by physically holding on to the ends of two DNA pieces and catalyzing the formation of a covalent bond between the pieces using the energy from ATP.

4. Sometimes scientists are able to isolate a specific RNA more easily than a specific gene the RNA is made from. Reverse transcriptase can make a strand of DNA by copying a strand of RNA (backwards from the normal DNA to RNA; thus 'reverse' transcriptase).

5. One strand of DNA makes up one chromosome. All 46 chromosomes in one of your cells stretched end to end would be about 5 feet long. All 46 chromosomes in one of your cells combined have about 6 billion bases. One molecule of DNA is a lot!

6. I confess to not knowing how many diseases are caused by retro-viruses, but HIV is one of them. I believe that the common cold is another, but I need to check that and get back to you.

7. The missing words may be bacteriophages or bacteria phages. Phages are viruses that infect bacteria instead of eukaryotic cells. The statement in b) is probably by injecting DNA into a nucleus of a large cell, like an egg or just fertilized egg cell (embryo). Plasmids are very interesting teeny tiny, circular pieces of DNA that exist inside bacteria. These pieces are replicated and pass between bacteria fairly frequently. Scientists can add the genes they want to a plasmid and add it back to bacteria. Then, by normal events, the bacterium will take up the plasmid and the scientist's added genes, too.

Hope is all helpful. Also, hope it is interesting.
Dr. Pat

 

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