Differences in genomes differentiates banana cells from human cells, and the organization and structure of the DNA is crucial in how genes are activated and how a cell survives and functions.

Today we reviewed how DNA is organized in the cell, and the chemical structure of DNA. Using this knowledge, we conducted an experiment to extract DNA from 3 fruits - banana, kiwi and strawberry. We hypothesized which fruits have larger genomes and why - based on observations of the fruits, the plants themselves, and the native regions where the plants originate. Each step of the extraction was discussed based on the structure of the cells and the chemistry of DNA. Each student should finish the experiment by recording their final observations in their notebooks and recording the amount of DNA extracted for each fruit (using a graduated cylinder). We will finish our discussion on this experiment and genome organization next lesson.

Cellular respiration is the process in which cells generate the energy molecule ATP.

We started the lesson with an experiment demonstrating this process. Yeast and sugar were mixed together in a cup, and then some of this solution was added to a vial with a balloon attached. The students discussed their observations and how each step of cellular respiration was contributing to each observation. The students then learned about the electron transport chain through a video breaking down each step in the respiratory chain. We ended with a final experiment to visualize the ETC in action, and will finish this discussion next lesson.

As a note, please make sure to have all necessary ingredients (including the fruits) for our next lesson on 06/07.

Aired: 05/18/21 — Expires: 06/15/21 — Rating: TV-PG

In today’s session we reviewed the difference between kinetics and thermodynamics, and examined the impact Gibb’s Free Energy has behind biochemical reactions in more detail.

We learned how biochemical reactions utilize ATP hydrolysis for turning endergonic reactions exergonic. We then explored the 3D structure of an enzyme (phosphofructokinase 1) to see the structural means in which ATP hydrolysis is coupled to reactions. We will discuss how ATP is produced in the next session.

In addition, next week the students will need the following ingredients:

• Yeast

• Sugar

• Small balloon (fits well over the mouth of the vial that came in the Blue Light Experiment Kit)

• Plastic wrap

The following week (05/24) the students will need:

• Kiwi, strawberry, banana (one of each)

• Isopropyl alcohol

• Dish soap

• Salt

• Baggie

• Disposable cup

• Strainer and coffee filter

• Forceps or tweezers or chop sticks or fork

In today’s session the students explored enzyme activity in more mathematical depth, including specific activity and dissociation constants.

They then learned about types of inhibitors and drug design. Though the example of methotrexate (MTX) for use in inhibiting the enzyme dihydrofolate reductase in treating anthrax, we discussed how MTX functions as an inhibitor. We have also identified important differences between MTX and the substrate that allows for tighter binding in the active site. Using the program ChimeraX, the students then looked at the structure of DHFR from anthrax bound to MTX in order to propose changes to MTX to generate a more effective drug for treatment.

Over the past 3 lessons, the students have focused on how enzymes are able to catalyze reactions.

First, the students learned about chemiluminescence and conducted a glow-in-the-dark reaction as an analogous reaction to the firefly luciferase reaction. The students looked at the structure of firefly luciferase to better understand the 3 steps of enzyme catalysis. The students also discussed how protein motion and flexibility plays a role in catalysis through a molecular dynamics simulation of another enzyme – dihydrofolate reductase.

Continuing on our discussion of catalysis and enzymes, we summarized the catalase experiment we conducted last lesson.

We learned about the important biological purpose of catalase in prevention of accumulation of reactive oxygen species (ROS) and how ROS can impact the cell. Using the computer program ChimeraX, each of the Cogitanians looked at a catalase from different species, comparing these to that of yeast catalase.

In this discussion, the students exercised excellent scientific reasoning for the adaptation mechanisms presented in each structure.

In addition to the need for everyone to have their kits, safety eyewear and gloves, I would also like for them to each use a computer with ChimeraX installed (the program we use to visualize proteins). While the last 2 sessions were primarily focused on reactions, kinetics and enzymes in general; next (or two) will focus on active sites, inhibition and how enzymes are able to catalyze a reaction

ChimeraX Resources:

Download ChimeraX

UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI) at UC San Francisco.

Online Tutorials and User Guide

Enzymes, protein catalysts, are integral to the survival of the cell by speeding up biological reactions.

Today the students reviewed thermochemistry and the basics behind reactions, and then explored the concepts behind kinetics and why reactions occur. The students expanded upon this knowledge through the lens of biochemistry with a discussion of enzymes, substrates and cofactors. Through a hands-on experiment done together remotely, the students observed how addition of catalase (via yeast) sped up the decomposition of hydrogen peroxide into hydrogen and oxygen gas. We will continue to discuss the mechanism of yeast catalase and how this leads to a speedup in the reaction.

February 08/21

We finished up our review of much of the material we have covered thus far. We circled back to intermolecular forces, including introducing the new concept of Coulombic forces. We reviewed organic chemistry and then applied this to the reaction of dihydrofolate to tetrahydrofolate by the enzyme dihydrofolate reductase. We finished by reviewing expression and protein structure.

February 15/21

In today’s lesson, the students explored what happens after protein expression - protein folding. Here we discussed the basics of thermochemistry, and how entropic gains of water drive protein folding (through the hydrophobic effect). In order to reinforce the concepts learned on protein expression and folding, the students took part in an engaging hands-on activity. First, the students drew the cell and labeled important organelles involved in gene expression. Using pipe cleaners, the students walked through the location of DNA and genes in the nucleus, RNA polymerase transcribing the gene to mRNA, export of mRNA to the cytosol and eventually ribosome, and then translation to form the polypeptide chain. Using pipe cleaners and toothpicks to represent hydrogen bonds, the students then began folding their proteins, starting with various secondary structure elements. Next lesson we will continue folding our proteins, including tertiary and quaternary structure, glycosylation and discuss what happens when folding goes wrong.

From Protein Structure to Gene Expression

On January the 18th we finished our conversation about protein structure, and began discussing the specifics of gene expression. The students explored transcription through RNA polymerase, and filled in the complimentary sequences for the template and mRNA strands. We then discussed translation and the ribosome, tRNA and the specific binding pockets that enable translation. We finished on deciphering what amino acids various codons encode.

On January the 26th students focused on reviewing the important concept of gene expression, where we further discussed transcription and translation. They used ChimeraX, a free program developed by UCSF to explore the structure of the ribosome. Here the students identified binding of the small subunit to mRNA, as well as the largest subunit binding to tRNA and the binding pockets of the ribosome. We also discussed the mechanism of the ribosome in further detail.

Did you know the same battery we use today was invented in 1887? With only minor upgrade, the ‘dry cell’ battery was a scientific victory because they were liquid free and could be used in portable devices. Previously, batteries were large fragile glass containers with metal rods, which made them not the most household-friendly items. That said, old ‘wet cell’ batteries can still be found in modern day industries like automotive or telecommunication—you can even create your own battery at home using items around the house!

From turning on a lamp in your home to running solar panels, batteries play a large role in our everyday lives. The lowly battery is more than just a simple tool—the technology hasn’t changed much for centuries—and we depend on them more than you may think. In the U.S. alone, we throw away three billion batteries annually, which adds up to a lot of power.

Which got us to wondering, how do batteries work? Batteries consist of an anode (the negative end), a cathode (the positive end) and electrolytes. When a battery is plugged in, the electrolytes are provided a circuit to move between the two ends, which creates the power.

Seems simple, right? But can you name other important parts of the process, like oxidation or reduction? What about how a rechargeable battery works? We’ve outlined the entire process below in a helpful animation—so that the next time you’re turning on the television, you can visualize the entire cycle.

In today’s session on biochemistry, the students tested their knowledge of intermolecular interactions and nucleic acids.

We used the structure of DNA in order to differentiate intramolecular (covalent) bonding and intermolecular interactions, such as hydrogen bonding in base pairing. We then continued our discussion on organic structures. We discussed functional groups and identified which types of functional groups are able to participate in hydrogen bonding. The lesson concluded with a discussion on basic organic nomenclature. This will transition to a discussion on amino acids and proteins next time.

Today we finished reviewing intermolecular bonding,

then proceeded to discuss polymers, DNA and complimentary sequences. We reviewed gene expression and had a discussion about the current mRNA and vector vaccine platforms, tying in our new understanding of how DNA and RNA stability / methods of expression may play a role in the current challenges and advantages for each type of vaccine. Finally, we ended on an introduction to organic chemistry, which we will continue in our next lesson.

We’ve realized in 2020 that the way we’ve organized culture — from the economy to race to work — could be done radically differently. We’ve been modeling our life together on “survival of the fittest” long after science itself moved on from that. And we’re learning to see that in every sphere of life we inhabit ecosystems. Agustín Fuentes brings spacious insight into all of this as a biological and evolutionary anthropologist, exploring how humans behave, function, and change together. In this conversation, he is full of refreshingly creative and practical fodder for the necessary reinvention ahead.

Today we did a small review of previous concepts, including the mole, molar mass and intramolecular bonding. We then discussed intermolecular bonding in further detail. More time was spent expanding on the concept of dipoles and polar bonds, and how this polarity, which results from differences in electronegativity, leads to hydrogen bonding and / or dipole-dipole interactions. We also discussed van der Waals contacts, and finished the lesson on an exercise in which the students predicted all intermolecular forces that occur in homogenous mixtures of various compounds.

Should we teach our children scientific facts about the world, or should we teach them to do science? The answer, obviously, is both. Yet when physics, chemistry and biology struggle for independent spaces in the school timetable, it may be too much to hope that, along with the facts, children are being given any real idea of what science is like.

Explore stories of science discovery. Tumble is a science podcast created to be enjoyed by the entire family. Listen to stories about science discoveries, with the help of scientists! Join Lindsay Patterson (science journalist) and Marshall Escamilla (teacher) as they ask questions, share mysteries, and share what science is all about.

Common Polyatomic Ions;

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In our second session we reviewed the atomic structure of matter and further explored the periodic table through a game of “periodic spelling.”

We used the elements from the periodic table to spell our own names, and then determine the number of protons, electrons and charges (when ionized) of those elements. After this game and discussing the octet rule, we focused on the meaning of electronegativity and its importance in determining why C, H, N, O, P and S are the the 6 most commonly occurring elements in biomolecules. We then finished on a brief discussion about why life is based on carbon."

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CHNOPS

CHNOPS is an acronym that refers to the six most important elements that make up living things.

C. Carbon

H. Hydrogen

N. Nitrogen

O. Oxygen

P. Phosphorus

S. Sulfur