BIO Pre Lab 13 – DNA and RNA

09 Jun BIO Pre Lab 13 – DNA and RNA

Question
Pre-Lab Questions

Arrange the following molecules from least to most specific with respect to the original nucleotide sequence: RNA, DNA, Amino Acid, Protein
Identify two structural differences between DNA and RNA.
Suppose you are performing an experiment in which you must use heat to denature a double helix and create two single stranded pieces. Based on what you know about nucleotide bonding, do you think the nucleotides will all denature at the same time? Use scientific reasoning to explain why.

Experiment 1: Coding

In this experiment, you will model the effects of mutations on the genetic code. Some mutations cause no structural or functional change to proteins while others can have devastating affects on an organism.

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Materials

Red Beads

Blue Beads

Yellow Beads

Green Beads

Procedure:

Using the red, blue, yellow and green beads, devise and lay out a three color code for each of the following letters (codon). For example Z = green : red : green.
In the spaces below the letter, record your “code”.

C:

E:

H:

I:

K:

L:

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

M:

O:

S:

T:

U:

_ _ _

_ _ _

_ _ _

_ _ _

_ _ _

Create codons for:

Start:

Stop:

Space:

_ _ _

_ _ _

_ _ _

Using this code, align the beads corresponding to the appropriate letter to write the following sentence (don’t forget start, space and stop): The mouse likes most cheese
How many beads did you use?
There are multiple ways your cells can read a sequence of DNA and build slightly different proteins from the same strand. We will not go through the process here, but as an illustration of this “alternate splicing”, remove codons (beads) 52 – 66 from your sentence above.

What does the sentence say now? (re-write the entire sentence)
Mutations are simply changes in the sequence of nucleotides. There are three ways this occurs:

Change a nucleotide(s)
Remove a nucleotide(s)
Add a nucleotide(s)
Using the sentence from exercise 1B:
Change the 24th bead to a different color. What does the sentence say now (re-read the entire sentence)? Does the sentence still make sense?
Replace the 24th bead and remove the 20th bead (remember what was there). What does the sentence say (re-read the entire sentence)? Does the sentence still make sense? If it doesn’t make sense as a sentence, are there any words that do? If so, what words still make sense?
Replace the 20th bead and add one between bead numbers 50 and 51. What does the sentence say now? Does the sentence still make sense?
In 3.a (above) you mutated one letter. What role do you think the redundancy of the genetic code plays in this type of change?
Based on your observations, why do you suppose the mutations we made in 3.b and 3.c are called frame shift mutations?
Which mutations do you suspect have the greatest consequence? Why?

Experiment 2: Transcription and Translation

DNA codes for all of the proteins manufactured by any organism (including you!). It is valuable, highly informative and securely protected in the nucleus of every cell. Consider the following analogy:

An architect spends months or years designing a building. Her original drawings are valuable and informative. She will not provide the original copy to everyone involved in constructing the building. Instead, she gives the electrician a copy with the information she needs to build the electrical system. She will do the same for the plumbers, the framers, the roofers and everyone else who needs to play a role to build the structure. These are subsets of the information contained in the original copy. Your cell does the same thing. The “original drawings” are contained in your DNA which is securely stored in the nucleus.

Nuclear DNA is “opened up” by an enzyme called helicase, and a subset of information is transcribed into RNA. RNA is a single strand version of DNA, where the nucleotide uracil, replaces thymine. The copies are sent from the nucleus to the cytoplasm in the form of messenger RNA (mRNA ). Once in the cytoplasm, transfer RNA (tRNA) links to the codons and aligns the proper amino acids, based on the mRNA sequence. Protein builders called ribosomes float around in the cytoplasm, latch onto the strand of mRNA and sequentially link the amino acids together that the tRNA has lined up for them. This construction of proteins from the mRNA is known as translation.

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Materials

Blue beads
Green beads
Red beads
Yellow beads
Pop-it® beads (8 different colors)
*Pen or pencil

*You Must Provide

In this experiment:

Regular beads are used as nucleotides.
Pop-it® beads are used as amino acids.

Procedure

Use a pen or pencil to write a five word sentence using no more than eight different letters in the space below.

Now, use the red, blue, green, and yellow beads to form “codons” (three beads) for each letter in your sentence. Then, create codons to represent the “start, “space” and stop” regions within your sentence. Write the sentence using the beads in the space below:

How many beads did you use?

Assign one Pop-It® bead to represent each codon. You do not need to assign a Pop-It® bead for the start, stop and space regions. These will be your amino acids.

Connect the Pop-It® beads to build the chain of amino acids that code for your sentence (leave out the start, stop, and space regions).

How many different amino acids did you use?

How many total amino acids did you use?