Monday -Design lab

Today we reviewed your pineapple enzyme design labs and chose 2 possible ideas.

1. Independent Variable - juice type (orange, peach, grape, lemon).


2. Independent Variable - temperature (85, 60, 37, 24)

Part of your homework again tonight is to write up the PROCEDURE. You must have it written out when you arrive tomorrow.

Remember to use your original lab as a guide. You need to have a list of all the materials you need and then the steps (i.e. how to make the jello, how much to add to each tube, how many tubes does each group need). AND then a list of the IV, DEP, etc.

example from your original lab

1.      Label test tubes as “pineapple – hot,” “pineapple – RT,” “apple juice – hot,” “apple juice – RT,” and “water.”  Apply the tape at the top of the test tube with a “tail” as shown at right, so steam from the water bath does not remove the labels.

2.      Prepare gelatin in an appropriate beaker.

a.    Dissolve the contents of a gelatin packet in ¼ cup cold water.

b.    Add ¾ cup boiling water to the mixture and stir until completely dissolved.

3.      Pipette 3ml of juice or water into each test tube according to the labels, using transfer pipettes.  Do not cross-contaminate juices by using a pipette in different types of juice.

4.      Place your “hot” tubes in a beaker of water.  Heat the beaker on the hotplate until a thermometer in the water of the beaker reads 85°C.  Carefully remove the tubes from the heat.  Allow contents to come to room temperature (RT).

5.      Add 10 ml ROOM TEMPERATURE gelatin mixture to each test tube.  Use the big pipette for this and do not let the gelatin drip into the green pipetter.  Shake tubes well to ensure mixing of contents

6.      Refrigerate test tubes overnight.

We also reviewed the sickle cell gel electrophoresis handout. If asked could you answer the following questions..
1. What is the phenotype if someone is Aa? Explain
2. What is a recessive allele?
3. How do we use restriction enzymes to determine genotype of sickle cell?

The last part of your homework is the handout below

7 text homework 5 from lvilleDrFox

Thursday - More on Enzymes

Thursday we worked on the lab involving how proteolytic enzymes and/or heat affect proteins such as collagen. Collagen is a structural protein involved in skin, connective tissue and bones of animals. Below are a couple of images of collagen and how it is organized.

Enzymes have specific 'substrates' or targets on which they work. Some enzymes 'digest' or 'break down' their substrate, while others put 2 targets together. Which type is our 'proteolytic' enzyme from fruit? What is the enzyme's substrate in our lab? Will that enzyme break down another substrate?

Proteins (which is what enzymes are!) can be denatured by heat and some chemicals. This is the process of denaturation.

In our lab, we are looking how 2 variables affect

More on Restriction Enzymes and Gel Electrophoresis

Today we reviewed Restriction Enzymes and Gel Electrophoresis.

Homework for tomorrow: handout from today and prelab questions

Here is a great site for more practice with gel prediction, plasmids, and restriction enzymes.
Practice Reading a Gel (you can do the entire game for more instruction).

Here is a video that also takes you through a tutorial of what we did today.

Homework for Monday

Please read the article below and watch the video(s) and answer the questions provided. Remember..."is biology destiny?"

15 a life without fear from lvilleDrFox

Here is the video

Friendly to the Extreme: Meet Kids and Adults With Williams Syndrome - ABC News

Mutations/Protein Folding and Homework for tomorrow.

Today we reviewed translation and then talked about the videos you watched on Mutations and Protein Folding

HOMEWORK for tomorrow: Finish your electrophoresis lab

Mutations:

A change in the DNA sequence (Nucleotides or larger changes).

Can you identify the Fact or Fiction and explain?

¨ All mutations are bad…………………….¨ Mutations are a source of evolution…¨ Mutation can be silent……………………¨ Mutations only happen when DNA is exposed to things like radiation………………………..


What are the major types of mutation?

Point Mutations
Substitution - single nucleotide change 
Insertion - a base pair is added in the sequence
Deletion - a base pair is removed from the sequence

Both insertion and deletion can also be large chunks put in or removed

Duplication - a large section of DNA on a chromosome is copied. Is this always bad? Can the new portion gain a new function (after a LARGE time frame)

Translocation - the transfer of a piece of one chromosome to a nonhomologous chromosome. Remember the two chromosomes involved typically exchange pieces.

Can you answer the questions below?
1. What is the difference between Substitution and Insertion? Duplication and Translocation?
2. What is a silent mutation?
3. How is mutation involved in evolution?
4. What disease did we discuss that is a change in only 1 nucleotide and is the mutation only bad or does it help?
5. When will a mutation be heritable?

Protein Folding:

Today we talked about how the order and type of the amino acid in a polypeptide determines the folding structure of the protein

What are the 4 levels of protein folding?

Primary - string of amino acids

Secondary - alpha helix or beta pleated sheet

Tertiary - final protein folding (+/- aa come together, hydrophobic aa go on the inside, hydrophillic go on the inside)

Quaternary - multiple proteins fold/come together to form complexes

Here is a good website to try more protein folding

Types of amino acids:
1. Charged (+/-)
2. Polar vs. Nonpolar
3. Special Cases

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)

Timid Mice

Today we discussed the timid mice article. You will get more practice reading portions of a scientific article. I've posted a powerpoint. Can you fill out the table on the second slide?

The article discusses how stathmin affected the fear response of mice.

Translation and Mutation ppt

Here is the translation and mutation part of your powerpoint slides from class. Please do read through/print them out.

Translation mutation ppt from lvilleDrFox

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

Tuesday - DNA extraction and Beginning Translation

Today we did the Strawberry DNA extraction. You should be able to answer the questions below!

1. What are the following used for?
             Strawberry (why can't we use another fruit?)
             Soap/Salt
             Ethanol

2. How is DNA organized in the Cell?

3. Why does the DNA tangle when we remove it from the nucleus?

Here is good video describing the experiment!



We also started discussing translation. In your groups you came up with a starting list of the process. Try to answer the questions below

1. What are the main molecules involved in translation?
2. What is mRNA translated into?
3. What are the building blocks of that molecule?
4. What are codons and anticodons?

If you did not like the crashcourse video here are a couple more!



 (start at 5:15)

Or the HHMI video

Don't forget your homework is to continue the gizmo and read the Timid Mice article (on Veracross)

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?

Homework for Monday

Please read the sports gene article I handed out on Saturday and answer the questions at the end.

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)