Restriction Enzymes

Today we discussed Restriction Enzymes and Gel Electrophoresis.

Watch the video from start to 9:28 and then using the notes from today and the video:
 Can you answer the following questions?
1. In what organism do you find restriction enzymes?
2. What are restriction enzymes used for in that organism?
3. What are the nucleotide sequences that a restriction enzyme looks for called?
4. Why does the organism's own DNA not get cut into pieces?
5. What are the small circular pieces of DNA called in the organism and what is usually found on these circles?


We also went over how to tell band size resulting from plasmids being cut by restriction enzymes.

Here is a video (watch till 4:50) on how to read a gel


 We also began talking about Gel Electrophoresis. (remember this is also in the above video)

Here is the virtual lab link
Can you answer the questions below?
1. What does GE do?
2. What type of charge does DNA have?
3. What do the black and red cords represent?
4. Which DNA 'runs' closer to the bottom (small or large)?

Here is the picture you will use from your lab to answer the postlab questions (the wells are on the left)

Thursday Translation continued

On Thursday you had a 5 minute quiz on the differences and similarities between transcription and translation. (make sure you can explain these)

Remember DNA (a gene)--->mRNA--->Protein--->Trait. Where does environment come into play?


You then drew the process of translation up on the board. Here are the steps of translation: Make sure you can explain the whole process!

1. mRNA exits the nucleus
2. mRNA goes to the ribosome (in the cytoplasm) and ribosome attaches to the mRNA
3. mRNA moves through the ribosome 1 codon at a time
4. tRNA comes in and reads codon, if the anticodon is the correct one (with the complementary bases) the amino acid gets added to the peptide chain (remember the first codon read will always be the start codon... what amino acid does this code for?)
5. The amino acids are covalently bound to each other (this is called a peptide bond)
6. Once the ribosome gets to the stop codon of the mRNA, this is the signal to stop translation.
7. The protein (peptide chain) is released from the ribosomes and tRNA
8. The protein is then folded in a 3 dimensional structure.

Think about the following questions:
Describe the process of translation
How does translation relate to making proteins?
Where does translation take place?
What is the result of translation?
What do proteins do?
How does this relate to "Is Biology Destiny?"

Also here is the correct video for the HHMI video of translation


Can you transcribe then translate the following sequence?
TAC CCG GTA TTA CAG TGG GAA TGA ATT

Today we reviewed "What is a gene"

Made of DNA
Codes for a protein
Has a promoter (start sign for RNA Polymerase)
Has a Terminator (stop sign for RNA Polymerase)
Has Exons (coding region)
Has Introns ('junk' DNA)

Link for "what is a gene"

Remember! Not All genes are expressed (made into proteins!) at the same time/same cell) - we will discuss this more in translation.

We began to talk about the transition from Transcription to Translation with the process of RNA editing (processing).
After transcription, the splicesome removes the unneeded introns and then ligates (glues) the remaining exons back together. After this a guanine 5' cap is placed on the 5' end of the new mRNA along with a poly A tail at the 3' end of the complete mRNA. The mRNA then leaves the nucleus and is ready to be translated into amino acids which are the building blocks of proteins!

We then discussed the sports gene article. Don't forget to review the 4 principles of natural selection!
Heredity
Variability
Selective Pressure
Differential survival and reproduction

This article plays into our question of the term! Is biology only destiny? Only environmental? or Both?

DNA Transcription

Today we reviewed replication and began discussing the central dogma and DNA Transcription.
Thought Questions:

1. What are the main differences between DNA replication and DNA transcription?
2. Why do cells do replication, why do they do transcription and how are the reasons different?
3. Why is the Central Dogma important?

Central Dogma: Gene--->mRNA---->Protein---->Trait  (Where does the environment come into play?)

The 2 main jobs of DNA are: 1. code for proteins (which result in traits). 2. Inheritance (pass along genetic information to offspring)

TRANSCRIPTION: (Basic Transcription video)
Jeopardy Game (Basics and Transcription are the only categories you need look at! the basic section still covers some things we've not discussed yet)

What is it?
Transcription is making a 'copy' of a gene to make a protein. (Many genes may be transcribed at one time, but not all of them).
What are the steps?
1. RNA polymerase unzips the DNA double helix at the beginning of a gene (where does it bind? -the promoter!).
2. Complementary Nucleotides (which have a sugar (ribose in RNA!), the phosphate group, and the nitrogenous bases) are brought in.
3. RNA polymerase connects the sugar-phosphate backbones of the nucleotides by covalent bonds.
4. Hydrogen bonds have formed between the nitrogenous base portions of the mRNA and DNA so these are broken
5. mRNA leaves the nucleus via pores to go to the ribosomes (where translation occurs!)

Here is the ppt on central dogma and transcription!

Central dogma transcription only from lvilleDrFox

Here is another document to help you review Transcription (don't worry about Translation yet!!). Don't forget Cells, Scope lab, and DNA replication!

03 transcribe and translate a gene (1) from lvilleDrFox

Finishing DNA replication and Homework For Thursday April 4th

Today we finished reviewing replication. You should be able to explain how and why it occurs. For thursday, please finish watching the video below and take notes. You should also read pgs 238-243 in your textbook and take notes.

Don't forget the Central Dogma

Gene---->Protein---->Trait

We will begin reviewing transcription and translation. Here is the Crashcourse video on both processes.

Here is a great video on the central dogma. It is a bit more detailed than we need but still a good one.

DNA replication

Today we talked about DNA replication and the enzymes involved. Can you answer the questions below?

1. Why do we need DNA replication?

2. What are the leading and lagging strands?

3. What is the name of the enzyme that unwinds the DNA for replication? What other molecule is involved in this process?

4. What does DNA Polymerase III do in replication?

5. What enzyme "glues" the Okazaki fragments together?

Below is the website you used to review these questions
DNA replication

Here is another great site to help you understand replication
More DNA replication

Here is a great video about Replication



Here is Mr. Anderson explaining replication. (You don't need to know about mitosis and binary fission)

DNA structure and Homework for Monday

On friday we began talking about the Structure of DNA (Deoxyribonucleic Acid)

The 3 main parts of a DNA molecule are:



1. The Sugar: Ribose







2. A Phosphate group:  (what do you think the X stands for?)







3. A Nitrogenous Base (Adenine, Guanine, Cytosine, Thymine and Uracil - this is a special one that is in RNA only)

One of each of these together makes up a Nucleotide:

As we begin to build a DNA molecule, how are the nucleotides connected to each other to build the rung of the ladder? 

Hydrogen Bonds! What are the numbers of the Carbons in the ribose sugar? What Carbon is the "1st" Phosphate group connected to? The 5' (five prime) Carbon. The phosphate of the next nucleotide is connected by the 3' Carbon. This is way when we discuss DNA we say it goes in the 5' to 3' direction. How are the nucleotides bonded to each other (i.e. the sides of the ladder)? Covalent bonds.

Why would you want the middle to be Hydrogen, and therefore weaker, but the sides be Covalent bonds (stronger)? 

Finally, your homework for Monday is to continue with the handout on DNA structure and replication. If you finish that one you should then begin the 2nd DNA handout (it has the website from BioTeach on the top).

Handouts for 3-28-13

Here are the 2 files from today on the 3 major experiments and DNA Structure/Replication

3 major experiments in confirming dna is the genetic material from lvilleDrFox

and

Griffiths and Hershey/Chase Experiments

Today you had a quiz on cell parts and atoms, molecules. We then started on your handout on the 3 major experiments that determined DNA is the genetic material. What other molecules were thought to be the material of heredity before DNA?

Here is the video we watched today. Make sure you are familiar with the 1st the experiments. Griffiths, Avery, and Hershey/Chase. We will likely use the video again when we move to DNA structure History.

Your homework for tomorrow is to complete the Microscope lab below is a video to remind yourself the proper use of a microscope.




Finally, Watch the crashcourse video on DNA structure and replication and begin working on your handout from class. I will create a new post with both handouts