Q2 – Week 9 – 20-21
week 9
Week of 1/19 – 1/22
*Please REFRESH this Page every time you view!!!
The 4 day – A, B, C, D cycle looks like this:
Day Period
7 8
Monday In class: A Academic Study AP BIOLOGY
Remote: Academic Study AP BIOLOGY
In class: B AP BIOLOGY AP BIOLOGY
Remote: AP BIOLOGY AP BIOLOGY
In class: C AP BIOLOGY AP BIOLOGY
Remote: AP BIOLOGY AP BIOLOGY
In class: D Academic Study AP BIOLOGY
Remote: Academic Study Academic Study
This week’s 4 day Schedule: I = In person, R = Remote
1/19 – Tuesday – “B” Day –period 7B, 8B– I 7(B) 8(B,D) AP BIOLOGY – (double period Lab)
-period 7B, 8B -R 7(B) 8(B,D) AP BIOLOGY – REMOTE INSTR
1/20 – Wednesday – “C” Day – period 7C, 8C -I 7(C) 8(A,C) AP BIOLOGY – (double period Lab)
– period 7C, 8C –R 7(C) 8(A,C) AP BIOLOGY – REMOTE INSTR
1/21 – Thursday – “D” Day – period 7D,8D – I 7(D) AP BIO ACADEMIC STUDY / 7(B) 8(B,D) AP BIOLOGY
– period 7D,8D – R 7(D) REMOTE INS / 7(B) 8(B,D) AP BIOLOGY REMOTE INSTR
1/22 – Friday – “A” Day – period 7A, 8A – I 7(A) AP BIO ACADEMIC STUDY(ASH) / 7(C) 8(A,C) AP BIOLOGY
–period 7A, 8A -R 7 (A) REMOTE INSTR – ASH / 7(C) 8(A,C) 20-21 REMOTE INSTR
1/19 – Tuesday – “B” Day –period 7B, 8B– I 7(B) 8(B,D) AP BIOLOGY – (double period Lab)
-period 7B, 8B -R 7(B) 8(B,D) AP BIOLOGY – REMOTE INSTR
The Blue Team is remote today. Please move to the Remote Instruction Page.
Period 7,8 –
1. DNA fingerprinting Lab complete together –
a) Measure the bands from the electrogel phoresis to obtain nucleotide numbers
b) Graph the Molecular ladder with linear and semi log paper
c) Choose the graph that is the most similar
d) Use the graph of your choosing to estimate the size (# of base pairs of your fragment)
2. Work on post lab questions.
Page 18 and Page 24 of the packet.
Crime Scene Lab Gels:
Wells:
ML , CS, Suspect #1 (Sintia), Suspect #2 (Will), Suspect #3 (Jess), Suspect #4 (Sophia), Suspect #5 (Mr.G)
|
Sophia  |
Will:  |
Jess |
Sintia:  |
Jess, I think its time to get an attorney…
Jessica’s and Sintia’s gel are the most conclusive!
Crime Scene Lab Gels:
Wells:
ML , CS, Suspect #1 (Connor), Suspect #2 (Grace), Suspect #3 (Sarah), Suspect #4 (Charlie), Suspect #5 (Mr.G)
|
Sarah:  |
Grace:
 |
|
Charlie:
 |
Conner:
 |
Sarah I would think its time to get an attorney!!
Connor, I would think of getting another forensics lab.
Finished gel reveal: Charlie!
1/19 – Tuesday – “B” Day Homework:
1. Complete PRC Form by using the Presentation posted below:
PCR Lab Form: Due Wednesday morning. You have 2 submissions.
Christie and Morgan’s Tranformation Lab test plates: |
|
End of Tuesday!
1/20 – Wednesday – “C” Day – period 7C, 8C -I 7(C) 8(A,C) AP BIOLOGY – (double period Lab)
– period 7C, 8C –R 7(C) 8(A,C) AP BIOLOGY – REMOTE INSTR
The Red team is remote today. Please move to the remote instruction page.
Period 7, Period 8:
1. PCR Lab – Tasters –
A: DNA extraction
Collected cheek cells, dissolved cell membranes, and digested proteins
1. Add 200ul of solution A to your microcentrifuge tube.
2. Lightly chew or scrape your teeth against the inside of your cheek to loosen cells.
3. Thoroughly roll provided cotton swab inside your cheek for no less than 10 seconds to collect cheek cells.
4. Place swab into marked centrifuge tube with Solution A.
5. Cut swab above the tube to a length that will fit inside the tube. Make certain the cap will shut tightly.
6. Press the tube against the vortex machine to thoroughly mix the sample, for at least 10 seconds.
Solution A contains components which chemically disrupt cell membranes and begins to unravel proteins.
Under these conditions, the cheek cells will begin to lyse or break open, spilling cell contents into the solution
in the tube.
7. Place sample in heat block or hot bath to incubate at 95 degrees Celsius for 10 minutes. Immediately place
tube in ice until ready for the next step.
This process continues to destroy proteins, particularly, those that damage DNA.
8. Load sample into microcentrifuge, taking care to balance the the centrifuge wit another sample directly
across from your sample to keep the centrifuge in balance as it spins. Close the internal and external lids.
9. Spin briefly (about 10 seconds) to pool condensation that has collected on the cap.
10. Remove the swab with tweezers (Tweezers should be rinsed with ethanol between samples to prevent
contamination).
B: 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
11. Add 20 ul of Solution B to the sample tube.
Solution B neutralizes the harsh conditions needed for lysis, preparing the solution for DNA isolation and
PCR to follow.
12. Close the tube lid tightly and vortex to mix for at least 10 seconds.
13. Load sample into microcentrifuge with the tube hinge pointing out, balancing out your sample tube, and
closing the lids.
14. Spin the sample for 1 minute at 12,000 rpm.
15. Look for a small clear round pellet near the bottom of the tube under the hinge. This pellet contains
cellular debris. The aqueous solution (supernatant) that has not precipitated into the pellet contains
cellular DNA.
C. 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
Celsius.
1. Prepare and label a small PCR tube with your name. Label both the top and the side of the PCR tube to ensure clarity.
2. Ensure that the 2x PCR MASTER MIX is on ice and has been spun at 6,000 RPM’s or greater in a
microcentrifuge for 10 seconds, vortexed for 10 seconds, then spun again for 10 seconds before opening
the Master Mix Tube.
3. Add 10 ul of 2x PCR MASTER MIX, 8ul water, and 2ul of supernatant from step 14 above (avoid pellet) to
the labeled PCR Tube for a total of 20 ul. The supernatant contains your genomic DNA for PCR. (It is
preferred that the PCR reaction mix is done on ice.)
4. Mix the 20 ul PCR reaction mixture by pipetting in and out with the pipette, and close the lid tightly.
5. Store the sample on ice until it is ready to be loaded in the thermal cycler.
6. Label and prepare PCR tubes for controls. At least one of the each POSIVE control WT (wild type) nad
MT (mutant) should be experimented, and one negative test tested.
4. Fly’s…
1/20 – Wednesday – “C” Day – Homework –
RED TEAM ONLY if you did not finish in class: The Blue Team will do this in class tomorrow:
1. Complete the DNA Fingerprinting Lab
Pages: 1,3,4 (Skip page 8 questions. Put a Y through page 8) 12, 18, 21, 22, 23, and 24.
Red Team and Blue Team:
2. Complete the practice AP questions below:
3. Complete the Form below with answers to the questions from the Genetics Review questions 2.pdf.
You have 2 submissions!
FORM for the Genetics Review questions 2.pdf:
End of Wednesday !
1/21 – Thursday – “D” Day – period 7D,8D – I 7(D) AP BIO ACADEMIC STUDY / 7(B) 8(B,D) AP BIOLOGY
– period 7D,8D – R 7(D) REMOTE INS / 7(B) 8(B,D) AP BIOLOGY REMOTE INSTR
The Blue Team is Remote. Please move to the Remote Instruction Page.
Period 7, 8 –
1. Review the PCR and Taster Form –
2. 1. PCR Lab – Tasters –
A: DNA extraction
Collected cheek cells, dissolved cell membranes, and digested proteins
1. Add 200ul of solution A to your microcentrifuge tube.
2. Lightly chew or scrape your teeth against the inside of your cheek to loosen cells.
3. Thoroughly roll provided cotton swab inside your cheek for no less than 10 seconds to collect cheek cells.
4. Place swab into marked centrifuge tube with Solution A.
5. Cut swab above the tube to a length that will fit inside the tube. Make certain the cap will shut tightly.
6. Press the tube against the vortex machine to thoroughly mix the sample, for at least 10 seconds.
Solution A contains components which chemically disrupt cell membranes and begins to unravel proteins.
Under these conditions, the cheek cells will begin to lyse or break open, spilling cell contents into the
solution in the tube.
7. Place sample in heat block or hot bath to incubate at 95 degrees Celsius for 10 minutes. Immediately place
tube in ice until ready for the next step.
This process continues to destroy proteins, particularly, those that damage DNA.
8. Load sample into microcentrifuge, taking care to balance the the centrifuge wit another sample directly
across from your sample to keep the centrifuge in balance as it spins. Close the internal and external lids.
9. Spin briefly (about 10 seconds) to pool condensation that has collected on the cap.
10. Remove the swab with tweezers (Tweezers should be rinsed with ethanol between samples to prevent
contamination).
B: 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
11. Add 20 ul of Solution B to the sample tube.
Solution B neutralizes the harsh conditions needed for lysis, preparing the solution for DNA isolation and
PCR to follow.
12. Close the tube lid tightly and vortex to mix for at least 10 seconds.
13. Load sample into microcentrifuge with the tube hinge pointing out, balancing out your sample tube, and
closing the lids.
14. Spin the sample for 1 minute at 12,000 rpm.
15. Look for a small clear round pellet near the bottom of the tube under the hinge. This pellet contains
cellular debris. The aqueous solution (supernatant) that has not precipitated into the pellet contains
cellular DNA.
C. 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
Celsius.
1. Prepare and label a small PCR tube with your name. Label both the top and the side of the PCR tube to ensure clarity.
2. Ensure that the 2x PCR MASTER MIX is on ice and has been spun at 6,000 RPM’s or greater in a
microcentrifuge for 10 seconds, vortexed for 10 seconds, then spun again for 10 seconds before opening
the Master Mix Tube.
3. Add 10 ul of 2x PCR MASTER MIX, 8ul water, and 2ul of supernatant from step 14 above (avoid pellet) to
the labeled PCR Tube for a total of 20 ul. The supernatant contains your genomic DNA for PCR. (It is
preferred that the PCR reaction mix is done on ice.)
4. Mix the 20 ul PCR reaction mixture by pipetting in and out with the pipette, and close the lid tightly.
5. Store the sample on ice until it is ready to be loaded in the thermal cycler.
6. Label and prepare PCR tubes for controls. At least one of the each POSIVE control WT (wild type) nad
MT (mutant) should be experimented, and one negative test tested.
1/21 – Thursday – “D” Day Homework:
Blue Team ONLY if you did not finish in class:
1. Complete the DNA Fingerprinting Lab
Pages: 1,3,4 (Skip page 8 questions. Put a Y through page 8) 12, 18, 21, 22, 23, and 24.
Red Team and Blue Team:
2: Please watch the first 7 minutes of the C-span video of the author who wrote a book on
Henrietta Lacks
3: Please watch the entire CBS news report on Henrietta Lacks:
4: Write your immediate response to the CBS video. What ever comes to mind in the form below:
Henrietta Lack’s video response:
5. Start the Genetics Test – (Take home portion – Multiple Choice – A
Please give yourself a 45 minutes time interval WITHOUT interruptions AS THIS FORM IS TIMED. Once You Click This link Below and enter your email you will get another link. Once you click that link the timer starts! Good Luck!
https://extendedforms.io/form/928afeca-4e1b-4bb4-961b-f7d8d6ed382a/login
End of Thursday.
1/22 – Friday – “A” Day – period 7A, 8A – I 7(A) AP BIO ACADEMIC STUDY(ASH) / 7(C) 8(A,C) AP BIOLOGY
–period 7A, 8A -R 7 (A) REMOTE INSTR – ASH / 7(C) 8(A,C) 20-21 REMOTE INSTR
Period 7,8:
1. Finish incubating digest.
2. Pour Gels.
3. Add loading Dye to samples
4. Load Gels with ML, WT, M, Student PCR’ed DNA
5. Run Gels.
6. Fly Lab
1/22 – Friday – “A” Day – Homework:
1. Study your vocab words. The next day your class is in person you will take the vocab section of the test.
2. Take another Multiple Choice section of the test.
Please use the following link to complete the Last Multiple section of test:
https://extendedforms.io/form/928d283e-31c2-4637-8547-b43d4b8f3aa5/login
3. The pGlo lab and Crime Scene Lab ARE DUE. They are both due on the next day you in person!
4) 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 (C3H8) reacts 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 9!