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Q2 – Week 8 – 19-20

week 8

Week of 1/6 – 1/10


Plant Coleus this week!

1/6 Monday – Period 7 – Academic Study Hall
                           Period 8
1. Article
2. PCR Lab –   Notes in Marbles- Taster Lab Introduction – 
PTC Papers revisted – We did this with Hardy Weinberg
PRC basics
1: DNA extraction
    Collected cheek cells, dissolved cell membranes, and digested proteins
2: Prepared PCR tube Reaction 
    Added a solution neutralizer to remove harsh conditions that were needed for step 1.
    Added PCR Master Mix – primers, dNTP’s and Taq Polymerase    
3. Loaded Thermal Cycler (PRC Machine) and ran the protocol (40 cycles).

    Amplified the DNA small segment (around bp 785) of the TAS2R38 gene that the primers selected for.

    Once the PCR machine completed the 40 cycles I placed your amplified DNA in the freezer at -20 degrees     
Hardy Weinberg Tasters Activity Key p.pdf
View Download
Genosensor Corp Instructional manual USE.pdf
View Download
Recent Newsday (AP) Article:

PCR and the Tasters

1/6 – Monday –Homework:  
1:  Study for Genetics Test – 
Link to study Guide and vocab words  (it is posted as a separate page in quarter 2)
2. Complete PRC Form by using the Presentation posted above.
PCR Lab FormDue Tuesday morning.
 End of Monday!     

1/7 – Tuesday – period 6/7 – Lab day
1: PCR Taster Lab:
Yesterday we completed:
1: DNA extraction
    Collected cheek cells, dissolved cell membranes, and digested proteins
2: Prepared PCR tube Reaction 
    Added a solution neutralizer to remove harsh conditions that were needed for step 1.
    Added PCR Master Mix – primers, dNTP’s and Taq Polymerase    
3. Loaded Thermal Cycler (PRC Machine) and ran the protocol (40 cycles).

    Amplified the DNA small segment (around bp 785) of the TAS2R38 gene that the primers selected for.

    Once the PCR machine completed the 40 cycles I placed your amplified DNA in the freezer at -20 degrees     
This morning I prepared the agarose solution and poured the gels and 
4.  Completed a restriction enzyme digest
    I took each students PCR tube and transferred 10 microliters from each student’s PCR tube into a new     
    NUMBERED Clear microcentrifuge tube. Please use the photos above to determine which numbered  
    microcentrifuge tube is yours. 
    Remember that this “Restriction Digest” will cut our amplified DNA segments IF THERE IS A MUTATION in 
    the palindrome that the restriction enzyme is specific for.
Today in class:
5.  Perform Gel Electrophoresis 
     We will load our gels that I poured this morning and run the gels so that we can determine the number of bands      each student has based on YOUR DNA Code!
    We will also load Controls and DNA molecular ladder to identify the approximate length of our DNA segments.
    I will post a picture of the gels and we will identify if the genotype matches the phenotype for Tasting PTC!

PCR and the Tasters

1/7 – Tuesday Homework: 
1. Complete your notes in your marbles regarding the PCR / PTC Lab
2: Study for the Test – Do not use Google for the definitions!
3: Please watch the first 7 minutes of the C-span video of the author who wrote a book on 
     Henrietta Lacks
4: Please watch the entire CBS news report on Henrietta Lacks:
5:  Write your immediate response to the CBS video.  What ever comes to mind in the form below:

Henrietta Lack’s video response 1819

  End of Tuesday..             

1/8 – Wednesday – Period 7 – Academic Study Hall
1. Study for Tomorrow’s Genetic Test/ Vocab portion will be Friday.
    Study guide is in the Genetics Test Review Section in 2nd Quarter.
                                    Period 8 – 
1. PCR lab Wrap- Up
Photos of Gels –


 Gel #1:  Gel #2
 Gel #3: Gel #4:
 Gel #5:
 Molecular Ladder:



2. Fly lab – discussion of how to complete tomorrow.
DROSOPHILIA LAB packet p.pdf
View Download
1/8 – Wednesday Homework:
1.  Complete the pages 10,11,16, and 17 (Take home portion 1 of Genetics Test)
1. Study for the Genetics test.
End of Wednesday..

1/9 – Thursday – period 7.8
1.  Drosophila Sex Linked Lab – 
            a) Identify the phenotypes as a group
            b) combine with Class
            c) Complete Chi-squared and questions
                                Class Data:
                                                            Females                                 Males 
                                                        Wild/Mutant                  Wild/Mutant
Theresa and Emma –                                    15/3                                       7/11
K + K + G + J                                          2/ 8                                              8/7
Max & Dan                                              9/2                                             5/10
E & E                                                        13/1                                              1/15
Morgan square C .                               8/0                                               6/2
TOTAL                                                    47 / 14                                        27 / 45
Expected Ratios:                         1 : 0                   :                   0 : 1                                   
I have provide the math below to demonstrate how to complete the statistic without running into ZERO categories that will produce undefined values.
Null:  There is no significant difference between the number of F1 offspring 
             that is wild type females and mutant type males.
133 total fly’s —> 133/2 = 66.6 expected in each category
                                    0     –      e             (0 –  e)2     (0 – e)2 /e
                                    47   –    66.5   =     (- 19.5 ) = 380.25 /66.5 =   5.71
                                    45   –    66.5   =     (-21.5)2    = 462.25 /66.5 =   6.95
                                                                                                                      12.66 = Chi – squared value
                                        2 categories – 1 = 1 degree of freedom
Based on our Critical Values table 12.66 is larger than 3.84 for one degree of freedom (p value <.05) and thus we reject the Null and there must something other than chance or sampling errors for why our outcome is different than expected.  The alternative hypothesis is that the gender and eye color alleles are not x – Linked.
We know that this is not the case because Morgan’s experiments have proved that there is X linkage . The most probable reason is that our fly’s probably had multiple generations occurring because of our long holiday break.
2.  Genetics Test
1/9 – Thursday homework –
1. Complete the pages 12,13,14, 19 (skip question 70 tonight!),20 (Take home portion 2 of Genetics Test)
I may not have told you to take page 12 home so I am posting it here:
2. Study for the Genetics test – vocab!

1/10 – Friday – Period 7 – Academic Study Hall – Not today! 🙁

                             Period 8 – 
Genetics Test – Including Vocab section.
1/10 – Friday -Homework:
A) Complete the Drosophila lab packet – HAND IN Monday.
B) Begin Metabolism and Energy – Thermodynamics and Spontaneity 
A)Instructions to the Drosophila Packet Lab –
1.  Place the Class Data in on page 4 (once all of it has been posted)
2.  On page 5, circle which type of inheritance pattern you observe based on the data.
              Circle either recessive or dominant.
(White eyes are the mutant or mutation that is not the wild type) – Remember that our cross was with True breeders which you should know are homozygous (White eyed females and Red eyed Males).  One is homozygous dominant and one is homozygous recessive.
              Circle either autosomal or X-linked.
Look at your inheritance pattern or data.  Is the sex the fly linked with an eye color or allele?
3.  On Page 5, question 2, please write a punnet square that reflects your inheritance patterns that you identified above.
4.  On page 5, question 3, compare your punnet square with the actual data?  Are you expected results and observed results similar or dissimilar?   I gave you an example of my work under Thursday above.
5.  On page 6, Write a Null Hypothesis, calculate the Chi-Squared and determine the p-value.
6.  Explain the results of the Chi-squared results = Statistical Significance.
      Example:  We reject or accept the Null because….
7.  Explain the results in terms of genetics.
     Example:  The inheritance pattern (that I circled) is not/is supported and this means …. 
B) Begin Metabolism and Energy – Thermodynamics and Spontaneity 

*Connections –
 We are beginning are Energy Unit but we are really just picking up where we left off in genetics.  We left off in genetics where we observed anabolic (Trp Operon) and catabolic  (Lac Operon) pathways in E. Coli regulated by repressor allosteric proteins from upstream “switches” or regulatory genes.  Gene regulation that controls the transcription and thus the expression of the genes is often regulated by Inducers or Repressors that are tied to the concentration of compounds that obtained from our environment.  That is our genes interact with our environment!!!  Through Natural Selection we have adapted to become very efficient in our use of energy and resources available.  All life requires a constant supply of energy and it is absolutely advantageous for all organisms from simple prokaryotes like bacteria (E. Coli) or eukaryotes (US!) to use available energy efficiently.  In the case of the Lac Operon in the E. Coli it would not be efficient use of energy and resources to transcribe and translate enzymes that breakdown lactose if there is no lactose in our cells.  That energy and resources are available for other life sustaining processes if there is no lactose present and thus there is a clear selective pressure for organisms to maximize efficient use of Energy.  Without our adaption to harness Energy and use it efficiently there can not be DNA duplication in the S phase of Interphase of meiosis or mitosis which we started talking about this summer.
1:  Please read the Text 142 – 149. Concept 8.1 – 8.2
2: Read my passage ABOVE AND BELOW when directed to in the form.
*For question 3 – Please read The Second Law of Thermodynamics section and the first paragraph of the Biological Order and Disorder section on page 144 – 145 in the text. Then read my contribution below:
OK You should understand the Second Law of Thermodynamics describes that processes that occur without an input of energy are spontaneous and spontaneous processes are those that are “favored” on the universe because they increase the entropy (∆S) of the entire universe. Entropy is a measure of randomness but it can also be considered the dispersion or energy from concentrated sources to less concentrated sources. The dispersion of  energy from concentrated (ordered ) sources to less concentrated (more random) sources is the best way to explain entropy.  
For example, heat flows from Hot to Cold because of the 2nd Law of Thermodynamics. When Heat is released the surrounding gas molecules in the air move away faster with this energy (And Disperse the Energy).  COLD does not flow!!!  The universe favors the processes that disperse energy or increase randomness (of energy).  When the universe favors a certain pathway or process it is said to be spontaneous.  Do not confuse this with something that occurs without any input of energy (AS THE BOOK STATES INCORRECTLY!!) All chemical reactions require an input of energy (which is called activation energy) to start the reaction.  Even the most volatile explosives require a detonator or gasoline needs a match. Spontaneous processes or chemical reactions are favored because they are self-sustainable. When you light propane for your stove or BBQ do you need to have a continuous supply of energy to keep the propane lit?  When you start the BBQ don’t you just spark it once?  Does a rock the rolls down a hill need to be pushed down the hill continuously?   Both of these are spontaneous processes because they are sustainable on their own AND increase the entropy of the universe (disperse the energy).  
                                                                                                                REACTANTS                                PRODUCTS
In terms of the chemical reaction of propane:  C3H8  +  5 O2   –>   3 CO2  +  4 H2O  +  HEAT
1 Propane molecule (C3H8reacts with 5 oxygen molecules (O2)  
                                                                            to make 3 carbon dioxide molecules (CO2) and 4 water molecules (H2O)
                                                                    Thus 6 molecules        ——->      become 7 molecules
This reaction gives off HEAT (which makes surrounding gas molecules in the atmosphere move faster) AND creates more degrees of freedom of movement by increasing the total number of individual molecules that can move!  This disperses energy OR increases randomness. 
Thus there are 2 ways entropy (randomness or energy dispersion) can change:
1. Heat flowing into a system or out of a system (In the case of the combustion of propane above, Heat produced from the chemical reaction and moved toward surrounding gas molecules that causes them to move faster and thus disperse the energy from the concentrated source (propane tank) outward to the rest of the universe.
2. The change of the number of free particles (molecules) that can move independently.  Large molecules like propane have many atoms (like Carbon and Hydrogen) that are bonded to each other and although they do wiggle and vibrate when bonded together they are not as “free” to move as much as smaller molecules who have less atoms bonded to them. These smaller molecules with less atoms have more degrees of freedom and thus can disperse the movement energy outward into the universe if the products of reaction have more molecules than the reactants.  Also having more products in the gas or liquid phase in the products side of a reaction also contributes to an increase in Entropy, randomness, or dispersion of energy. 
This is a spontaneous process or direction that follows the second law of the thermodynamics!!!  Which means the reverse process must be non-spontaneous!!  Do you ever see propane reforming from carbon dioxide and water?  
If the forward is spontaneous then that means the pathway is favored by the universe and thus the reverse is NOT FAVORED and must be spontaneous.
Now in terms of cells, they must be able to make complex molecules from simper ones (anabolic). 
Life creates amazing amount or order!
Examples:  Translation of polypeptides from amino acids, Replication of DNA by combining nucleotides into double helix, and plants creating starch (many glucose molecule bonded together) from individual glucose molecules.  How is this possible if we are LOWERING the degrees of freedom so that the less molecules can disperse energy?  Remember that there are 2 factors, Heat Flow and the number of free particles!  So if the chemical reaction is creating less dispersed molecules which is not favored by the Second Law of Thermodynamics then, THEN there must BE A LARGE AMOUNT OF HEAT RELEASED to compensate for the Lack of “free molecules”.  THUS the Entropy of the universe (∆S) still increases and these anabolic processes are spontaneous!!  If heat was not released in these processes then processes would not occur.  Why are we warm?
Not all chemical reactions that build the order that life requires release energy so there must be another mechanism that increases entropy even though we are not compensating by releasing heat!  This is explained by COUPLING!  We are heterotrophs that require ENERGY to live.  This is why we must eat to live.  We ingest and 
break down food (break bigger molecules into smaller ones!) to gain energy (energy is released) and this process is clearly spontaneous because we are releasing heat and increasing the degrees of freedom of molecules. THIS ENERGY that we get from eating and digesting food (breaking down glucose) from a spontaneous process DRIVES the non-spontaneous process of building more complex molecules from simpler one.  So the order that life creates requires a continuos supply of energy to move in pathways that GO AGAINST THE 2nd LAW OF THERMODYNAMICS!!  Eventually the Universe wins!! 🙁
We say that spontaneous processes ( that increase the entropy ∆S of the universe because they disperse energy either by the heat released or by increasing the degrees of freedom by producing smaller molecules from larger ones) are self sustainable because they do not need a constant supply of energy to keep them going forward.  Non-spontaneous processes need a constant supply of energy to move them forward.  Because spontaneous processes are self-sustainable THEY PRODUCE FREE ENERGY ∆G) for use to use to accomplish non-spontaneous processes.  We obtain FREE ENERGY ∆G from our food! We obtain electricity on Long Island mostly by burning fuel oil (diesel) to boil water that creates steam and pressure to turn turbines (generators).  This process utilizes the spontaneous burning or combustion of diesel fuel to provide FREE ENERGY ∆G  to create electricity.  The electricity we do have to pay for….
Is a riding a pony spontaneous?  Is Entropy increasing in the universe?  Is it energetically favorable?  Does it create Free Energy?   Yes because I use the free energy of the pony to move me.  Because I am using the Free energy we say that ∆G (free energy is decreasing!!) or negative for spontaneous processes.  ∆S of the universe is positive and increasing for spontaneous processes.
End of Week 8!