SciHawks

Bio 3,6- we focused on the effect of pH (acidity- low pH or basicity-high pH) on a given enzyme's shape and thus on its rate of activity. We discussed the meaning of pH in terms of concentration of H+ ions in an aqueous solution (e.g. a water mixture like cytoplasm); the greater the concentration of H+, the LOWER the pH, and the more acidic (sour-tasting) the solution.
We saw that each specific enzyme has a particular and narrow "optimal"/best pH range in which it has its proper, natural shape with which it will temporarily bind and catalyze the reaction of its substrate molecule(s). Above or below this pH range, a catalyst will denature/unravel due to the action of too much H+ or too little H+ on the "side groups" of the amino acids that make up the enzyme/protein.

AP Chem- we finished our redox titration analysis problem and determined that commercial hydrogen peroxide is commonly a 3% by mass aqueous solution. We learned that potassium permanganate acts as its own indicator in a titration because it has a deep purple color and it gets reduced to colorless Mn 2+ ion.
We then did two other problem types: one involving "consecutive reaction" stoichiometry, which really proved/showed that coefficients in equations can ONLY and EVER be used to show reaction RATIOS and NEVER the actual quantities that are reacted or produced! In these problems, expect the coefficient to change for the same exact substance in the two different equations because each equation/reaction is independent of the other and the balanced stoichiometric mole ratios of the reactants are likely to be different for different reactions.
We then began a "mixture" problem in which we will use the "weighted average" method to determine the percent composition of each component in the mixture.

Bio 3/6- we discussed some of the factors that can affect the rate of enzyme activity.
We focused on the effect of temperature on an enzyme: at low temperatures, the enzyme retains its natural 3-D shape so that it can speed up the reaction of the substrate molecule(s) when it collides with and binds them; at low temperatures, though, this collision rate is low so the overall enzyme activity rate is low.
As temperature increases, both enzyme and substrate molecules move faster and collide more frequently so the rate of enzyme activity increases.
However, beyond a given enzyme's optimum/optimal temperature, the enzyme moves too fast and collides with even greater forces causing it to unravel/denature and lose its shape and its active site.

AP Chem- we discussed some of the top errors on the stoichiometry exam- these errors can and should be avoided by frequently practicing, especially within a few hours after class, the various problem types using the efficient and simpler methods used in class.
We then started a solution stoichiometry analysis problem using a redox titration setup.

Because we have no school on Monday, I will schedule extra help on Tuesday @ 8:15 AM in Room 308. AP Chem students may want to go over their stoichiometry tests. Bio students may have questions about the current Biochem unit or general scientific method or graphing questions.
See you there.

Interesting article on "synthetic biology" i.e. chemically synthesizing DNA with specific genes to make new life forms: http://www.newyorker.com/reporting/2009/09/28/090928fa_fact_specter?printable=true

excerpt: "...working with hair samples from two woolly mammoths—one of them sixty thousand years old and the other eighteen thousand—has tentatively figured out how to modify that DNA and place it inside an elephant’s egg. The mammoth could then be brought to term in an elephant mother. “There is little doubt that it would be fun to see a living, breathing woolly mammoth—a shaggy, elephantine creature with long curved tusks who reminds us more of a very large, cuddly stuffed animal than of a T. Rex.,” the Times editorialized soon after the discovery was announced. “We’re just not sure that it would be all that much fun for the mammoth.”
Bio 3/6 - we discussed the various functions of proteins: enzymes speed up the rate of reactions by positioning substrate molecules properly for bond breakage (hydrolysis) or formation (synthesis),
transport proteins carry needed molecules or even wastes to other parts of the body, hormones help signal "target cells" to regulate the various other life functions in the body, antibodies are the main proteins of the immune/defense response of the body; antibodies bind to foreign organisms' surface proteins and immobilize/mark for death the pathogen, motor proteins are capable of sliding over each other causing muscle contraction and other motions.
We then focused on enzymes, showing that they work to hydrolyze or synthesize particular substrates based on the specific complementary shape of the substrate and enzyme.
I posted a video showing an enzyme catalyzing (speeding up) the hydrolysis of a substrate molecule. I also posted a biochem practice quiz to which I'll post the answer key later.

AP Chem- we learned the "half-reaction" method for balancing redox reactions in either acidic or basic solution; the base solution process requires two more steps than the acid solution process.
I posted a few relevant worksheets on Blackboard.
We began our percent composition/empirical formula of a hydrate lab by showing the proper technique for manipulating a crucible. We will perform the rest of the procedure next week.
We will also apply solution stoichiometry to our half-reaction method balanced redox equations.

Welcome Jericho parents! I was glad to meet you tonight and I look forward to working with you to achieve success for your sons and daughters in Biology and AP Chemistry this year.

Bio 3/6- we reviewed the four major organic biological molecules: carbohydrates, lipids, proteins, and nucleic acids. We then focused on proteins, which have the greatest variety of structures and "jobs"/functions due to the fact that they are made up of up to 20 different amino acids in specific sequences that are between 50 to over 1000 amino acids long!
We saw the similarities and differences among the 20 amino acids and noted that the "side chains" of the amino acids cause the protein to "fold" or morph into a particular shape. A protein's specific shape gives it a specific function.
We then noted that proteins can only maintain their ideal shape in environments of a particular acidity; otherwise, the amino acid chain unravels/"denatures" and the protein loses its shape and can no longer function.
We then did a lab with acid/base indicators that have different colors in acidic and basic solutions.

AP Chem- we continued stoichiometry in our new unit that focuses on solutions. In order to calculate the number of moles of reactants or products in solutions, we typically will have to use the concentration and volume data about the solutions.
We saw how to properly prepare and/or dilute a solution in a "volumetric flask".
We will also be balancing equations by mass AND charge in this unit that contains many REDOX reactions that occur in solution.

Bio 3/6- The unit hw is posted on Blackboard (handed out in 6th period, will be handed out in 3rd period also) and is due on Friday, October 2nd because our next unit exam is on Tuesday, October 6th.
We discussed the various types of carbohydrates and showed how complex sugars could be made by chaining together simple sugars via enzyme assisted "dehydration synthesis"; water is formed from the H of one simple sugar and an OH of a second simple sugar causing two of the atoms from the two simple sugar rings to bond thus creating one larger, two-ring sugar (e.g. maltose or sucrose). We then saw the opposite process, "hydrolysis", which uses H2O to break apart the complex sugar as the H bonds to an O from one sugar ring and the OH bonds to the C from a second sugar ring. Hydro means "uses water", lysis means "to break apart".

We then discussed the structure of fats/lipids/triglycerides. These molecules usually contain three long hydrocarbon chain "tails" and are formed from the dehydration synthesis of ONE glycerol molecule and THREE fatty acid molecules, so the "building blocks" of fats are glycerol and fatty acids.
I will post a Blackboard link to an animation of dehyration synthesis and hydrolysis.

AP Chem- we took our unit exam on Stoichiometry. Anyone who misses any of these important test days is reminded to schedule, as soon as possible, a (different) makeup test AFTER school.

Bio 3/6- we reviewed our first unit exam. Review the class notes from each day and use them to answer the hw questions and you will automatically be preparing efficiently and optimally for each test. Pay special attention to when I alert you to "common errors" made by hundreds of past students. Learn from their mistakes so that you don't make the same mistakes. If you follow the methods as taught in class, you are much less likely to make errors, and you are much more likely to answer the questions accurately and with sufficient detail.

We reviewed the two types of compounds: salts and molecules, and then we started our focus on the major organic biological molecules, starting with carbohydrates.
After the break, we broke into groups to do a scientific investigation activity in which we will critique each step of each group's process.

AP Chem- we did a reverse engineered atomic mass problem in which we calculated the percent abundance of the two isotopes of chlorine based on the atomic mass of chlorine and the individual isotope masses of chlorine-35 and chlorine-37.
We then did another gravimetric analysis problem; we solved this one by simply applying the law of conservation of mass and the percent composition formula. These specific problems usually require solving a quadratic equation.
We then began another limiting reactant problem, the solution to which is posted on Blackboard.
The list of question types for tomorrow's exam was given in class so check the Blackboard notes if you missed it.

Bio 3/6 - we began our new Biochemistry unit by looking at the structure of atoms, the smallest unit of an element that has the properties of that element. We then looked at two types of compounds that can form from two or more elements: ionic compounds (salts), which are lattices/3-D geometric arrangements of cations and anions that are ionically bonded to each other in all directions, AND molecules, which are two or more NONmetal atoms that are COVALENTLY bonded together by SHARING valence electrons. Unlike ionic compounds, moleculare compounds are made up of individual and separate molecules that are not bonded to each other, e.g. each water molecule contains two H atoms covalently bonded to ONE O atom and no two water molecules are bonded together even in a solid ice cube.
We listed the six most important biological elements and the major bio-molecules that contain them.
We stated the definition of organic (CH) and inorganic compounds and went over some of the major biological organic compounds: proteins, nucleic acids, lipids, and carbohydrates.

AP Chem- we finished the limiting reactant stoichiometry problem, using the concept of "moles of reaction". The reactant with the smallest mole of reaction ratio (actual divided by theoretical) must be the limiting reactant and MUST be used to determine the quantities of products formed.
We then did the typical questions from these problem types: amount of excess reactant left over, quantity of each product formed, and (given an actual quantity of product made) the percent yield.

Bio 3/6: took our first unit exam and then finished our discussion of the microscopy lab.

AP Chem- We balanced the equation from our previous combustion analysis problem. Remember, always balance the "free" elements, if any, last.
We did a complex problem showing gravimetric analysis in order to determine the identity of an unknown element in a compound. Video tutorials of gravimetric analysis will be posted on Blackboard.

Bio 3/6 - we reviewed microscopy and did a couple of quantitative examples involving measurement of cell length, conversion of low power field of view to high power field of view, and conversion of millimeters to micrometers.
We discussed the test format so that you know the structure of the test as well as how to answer graphing and scientific investigation questions.
I'm about to upload to blackboard a couple of tutorial videos on graphing and the scientific method. I think that you will find them helpful.
I have also posted some tried and true test-taking skills advice. The file is on Blackboard. Be sure to consistently follow those rules and you will guarantee a higher score! Following these techniques requires effort but ultimately they make the tests easier and more manageable.

AP Chem- we finished our percent composition to empirical formula problem and then went on to the next logical step of determining the molecular formula, given the molar (gram formula) mass data. We calculated the "scaling factor", ALWAYS a whole number (otherwise you had made a previous error!) that multiplies the subscripts of the empirical formula.

We then did a percent composition to empirical formula problem involving a HYDRATED salt.

Finally, we discussed combustion analysis and did a problem involving analyzing the masses of the combustion products, CO2 and H2O, in order to determine the empirical formula of the combusted unknown organic compound.

Bio 3/6 - we discussed the major errors that people make when graphing data: inconsistent increments, mislabeled or misplaced axes, and incomplete use of the graph grid.
We then practiced a step-by-step method for properly graphing any data:
1. We identified the independent and dependent variables by reading the information and see which variable depended upon the other.
2. We got the "range" of data by subtracting the low value from the high value.
3. We determined the increments value (per box) by dividing the range by the number of boxes and rounding the answer to a convenient number.

Note that both axes need their own independent starting values/numbers and that you NEVER have to start at zero unless the data does so. There is never a need for a squiggly line if you follow the method that we used today.

AP Chem- okay, our Blackboard class webpage was dysfunctional for a while today but it seems to be working okay now.
we discussed the definition of "atomic mass" and did a sample calculation using the two natural isotopes of chlorine.
We discussed and applied the "AP Magic Triangle" in order to quickly inter-convert from moles to grams, particles, or (for ideally behaving gases) liters.
We did a few percent composition problems including the percentage of water in a hydrated salt.

Bio 3/6 - VERY IMPORTANT REMINDER/UPDATE: the Unit One exam has been rescheduled to be given this FRIDAY, September 18th (there was a temporary switch to Thursday but that change was almost immediately cancelled). Even so, tonight I will still post the homework answers and additional practice test files on Blackboard. You do not have to hand in the homework for this unit; just use the posted answers as a guideline for the level of detail and quality of homework expected for the upcoming units. Compare your homework answers to the ones posted.

We discussed "Peer Review", the final step in the process of an initial scientific investigation/paper/study. In this case, "peers" are scientists who will look critically at your scientific paper, examining your process for flaws, bias, and sources of random error. We defined random "error" as the unavoidable cause of some variation in any measurement/experiment due to factors that naturally fluctuate randomly. Random error will equally likely skew the results positively or negatively. Random error/variation can never be completely eliminated from any experiment BUT sources of random error can be MINIMIZED in a given experimental setup.
To deal with the problem of random error/variation, scientists perform multiple trials of an experiment and then AVERAGE the results so that the AVERAGE of the random error is closer to zero so that the results are more accurate.

We then discussed the difference between a scientific Law and a scientific Theory. We learned that Theories are much more powerful in that they can explain the how and why of natural phenomena whereas Laws, while very useful, can only describe the "what" of natural phenomena. Laws are often written as mathematical equations.

AP Chem- we finished examples of the Law of Multiple Proportions and then we discussed the influence of Avogadro's Law on the early models of matter, showing that atoms must combine in specific, whole number ratios.
We also got an initiation into the correct method for drawing Lewis dot structures.
Tomorrow, we will begin moles, stoichiometry, and the more advanced problems that can be solved with these tools.

Bio 3/6- we discussed the part of the scientific method involving proper experimental design: the importance of controlled variables except for the independent variable, the necessity of a control/comparison group, the requirements of large sample size, repeated trials, random selection of members of each group, etc.
We discussed the proper way to think about measuring, collecting, and organizing data that will support or contradict the hypothesis/prediction.
We briefly discussed the final part of the sci. method involving submission of the experimental findings for peer review.

AP Chem- had our first exam of the year. This first exam will give you an idea of the strength of your chemistry background coming into this course. You are encouraged to review your test at extra help and/or by appointment.

Bio 3/6 - we discussed the difference between aerobic (uses oxygen) and anaerobic respiration (no oxygen used) to extract energy from nutrient molecules such as glucose. Aerobic respiration releases much more energy per molecule of glucose respired.

We discussed the scientific method from the initial step of making observations to formulating a scientific question to making a prediction/hypothesis that shows the cause and effect relationship between two factors to properly testing that prediction with a controlled experiment.
We will discuss experimental data collection and organization of data, making conclusions, and the "peer review" process tomorrow.

We began a microscope lab by showing how to prepare a wet mount slide and seeing an easier way to get a specimen into focus. Learn this way correctly now so that you can save a lot of time and effort for the rest of the year.

AP Chem- we discussed the Laws of Constant Composition and Multiple Proportions, which showed that atoms of elements must combine in simple, whole number ratios.
We applied these laws to several examples.
We reviewed a bit for tomorrow's exam, which will cover the summer assignment in its entirety as well as material from this past week of class.
The test and all tests this year will take the whole two periods so be prepared.
May you have a very good initial start to this quarter- no exams are easy in this course but prepared students have, in the past, done very well on these tests.

Bio 3/6 - we wrapped our discussion of the life processes focus on some general characteristics of all organisms. We then began a discussion about scientific thinking, the types of problems that can be addressed by science, and the methods that are used to support or to disprove a claim.
Tomorrow, we will do a couple of examples of the scientific method involving proper experimental design.

AP Chem- we discussed the neutralization of bases by the weak acid, ethanoic acid. We wrote out the formula and net ionic equations for this reaction.
We then drew out and discussed the cause for each of the solubility rules, showing that Coulomb's Law dictates the relationship between ionic bond strength and the solubility of the salt. Ions that are small and highly charged form strong ionic bonds (high charge and small distance between ions) so that even multiple ion-dipole attractions to water molecules are insufficient to break the ionic bonds among the ions in the lattice; thus salts of those ions tend to be insoluble.
Ions that are large and have a low charge form weaker ionic bonds (low charge and larger distance between ions) so that sufficient multiple ion-dipole attractions to water molecules are will outweigh the ionic bonds among the ions in the lattice causing multiple water molecules to dissolve/break away each ion from the lattice; thus salts of those ions tend to be soluble.

Bio 3/6 - we expanded our discussion of living vs. dead vs. non-living by giving examples of non-living things that may have very complex collections of molecules but that are fundamentally not organized in cell units; non-living things cannot independently perform all of the various life functions though non-living things can use energy sources to "function" or "work" i.e. a computer performing a calculation. We discussed the minimum necessary requirements for organisms/living things and saw that it is not SUFFICIENT to have a collection of highly organized molecules to be alive.
We described, gave examples, and discussed the purpose of the various life functions and tried to develop a mnemonic to remember all of them.
We then began to discuss lab safety- please get your lab safety agreements signed by Thursday, thank you.

AP Chem- we mapped out the various forms of matter starting with single pure substances and then mixtures of two or more substances. We gave several examples of each type of matter and drew out their structure, in some cases.
I will post later tonight, on Blackboard, some practice questions for Friday's test and also the answers to the text part of your summer assignment..

Bio 3/4 , 6/7, and AP Chem- looking forward to working with you this year. I wish to foster in you an appreciation and greater understanding of science and scientific reasoning so that you may experience your environment in a more thoughtful and interesting way. In addition to describing physical and biological phenomena, we will explore and explain how and why these phenomena occur.