Bis2A SS2 2020 Lecture Agenda

Lecture 1: Administrative Matters and Experimental Design

Welcome to Bis2A SS2 2020!

Read up on the characteristics of the three kingdoms of life: Archaea, Bacteria and Eukaryotes.

Have your sketch book/note paper ready today. We will be drawing and sharing pictures!

Learning Goals:

• A.1 Be able to describe (or at least look up) the structure and administrative details for this course from the syllabus.
• A.2 Be able to use the syllabus, Canvas, LibreText and Nota Bene as tools to gather information necessary to address questions you have been asked in class.
• A.3 Define and correctly use vocabulary terms used in the pre-lecture study guide, in assigned readings, and in lecture.
• A.4 Create a hypothesis or prediction based on given experimental data.
• A.5 Design an experiment with proper controls based on background material provided.
• A.6 Use the principles of the “design challenge” to dissect a complex problems into small manageable questions that can be addressed.
• A.7 Create a conceptual drawing of a cell that reflects your current mental model for how several requirements for life are manifest.
• A.8 Interpret information presented to you in graph form.

Lecture 2: Organelles, Characteristics of Atoms and Functional Groups

Chemistry review starts today! You will be expected to know Ionic, Covalent and Hydrogen bonding. Please check out all the learning goals associated with bonds and functional groups after lecture today. This is not a chemistry class but you would be surprised how much chemistry is in biology.

Cellular Infastructure LG:

• 3.1 Identify and illustrate the components of subcellular infrastructure that are important for distinguishing prokaryotic and eukaryotic cells and different types of eukaryotic cells.
• 3.2 Describe the functional roles of the cell membrane, the nucleus, the mitochondrion, the endoplasmic reticulum, the Golgi apparatus, the peroxisome, the lysosome, the vacuole, and the chloroplast and the interrelationships between them.

Biological Chemistry LG

• 1.1 Explain the nature of the different types of molecular bonds associated in biomolecules.
• 1.6 Explain how water is used for condensation and hydrolytic reactions.
• 1.8 Be able to use chemical principles to make predictions/hypothesis about familiar or unfamiliar functional groups.
• 1.24 Define electronegativity and explain how this concept is used to predict bonding patterns and how two atoms interact.

Lecture 3: Functional Groups and Macromolecules

We will discuss the 4 macromolecules today. Make sure you are comfortable identifying by name functional groups on the 4 macromolecules.

New Biological Chemistry LGs

• 1.1 Explain the nature of the different types of molecular bonds associated in biomolecules.
• 1.7 Be able to classify common biomolecules as a lipid, protein, carbohydrate, or nucleic acid. Be able to identify different classes within the same molecule, such as a lipoprotein or a lipopolysaccharide.
• 1.9 Diagram pentose and hexose sugars: be able to number their carbon atoms and identify the key functional groups on each molecule.
• 1.10 Diagram a nucleotide and identify their key functional groups.
• 1.11Describe the characteristics of the different types of lipids (saturated fatty acids, unsaturated fatty acids, steroids, etc.) and explain how their nonpolar nature contributes to their function.
• 1.12 Explain how the structural features of phospholipids enable the formation of lipid bilayers.
• 1.13 Compare/contrast the behavior of membranes with different lipid compositions, with respect to membrane fluidity.
• 1.14 Explain the role of water in the spontaneous formation of protein tertiary structure and cell membrane formation.
• 1.15 Explain how condensation reactions link monomers to form a polymer and produce water. Show your understanding by using a condensation reaction to form a dipeptide from two amino acid monomers (a peptide linkage) and to form a disaccharide from two glucose monomers (a glycosidic linkage.)
• 1.16 Understand the various features of an amino acid (carboxyl group, amino group, R group, alpha carbon) and how these features influence the properties of the amino acid.

Lecture 4: Proteins and Active Sites

Now is when we really dive into chemistry and proteins. You will be asked to connect what is happening on the enzyme catalytic scale to the single amino acid scale. How would changing one amino acid alter the whole enzyme? We will explore this concept at lecture today and next time.

New Biological Chemistry LG -->might not get to pH and pKA until lecture 5

• 1.4 Define pH, and understand the relationship between pH and water to predict the potential influence of changes of pH on biomolecules. Be able to use the
• 1.5 Predict the protonation state of an acid or base given the pKa and surrounding pH.

Lecture 5: Thermodynamics

We might also get to energy stories today as well. Energy stories are a concept generated by Bis2A instructors that is designed to help you go through a conceptual check list in your mind whenever you come across a new chemical reaction or process. We will practice making lots of energy stories in lecture over the next few weeks.

To continue developing our energy stories we need to take into account the transformation energy takes from the initial to the final state of a chemical reaction. Today we will focus on physically coupling endergonic and exergonic reactions together using enzymes.

New Energy Transformation LGs

• 2.1 Explain the first law of thermodynamics (conservation of energy): explain how energy can have different forms and how it can change form.
• 2.2 Explain the second law of thermodynamics (Entropy is increasing) and how it relates to biological reactions.
• 2.3 Apply the concept of the “conservation of mass” to metabolism and describe the different forms mass takes as it enters and leaves the cell
• 2.4 Apply the concept of the “conservation of energy” to metabolism and describe the different forms energy takes as it enters and leaves the cell.
• 2.5 Use a Gibbs enthalpy (energy) reaction coordinate diagram to interpret a biochemical transformation and to make predictions about whether the reaction is spontaneous or not.
• 2.6 Interpret reaction coordinate diagrams and associate changes in Gibbs enthalpy and activation energy with relative rates of reactions, equilibrium conditions, and whether a reaction is endergonic or exergonic.
• 2.7 Use tables of standard Gibbs enthalpy to predict whether two reactions can be theoretically productively coupled.
• 2.8 Be able to use the equation: $$\Delta H = \Delta G + T \Delta S$$, and explain what each term represents.
• 2.16 Identify the high energy bonds in ATP and how ATP hydrolysis can be coupled to endergonic reactions
• 2.17 Apply the “energy story” to any biochemical reaction or pathway: identify the key components, identify the energy source, and be able to determine how the energy is transformed by the reaction.

Lecture 6: Cell Membranes and Cytoskeleton

New Energy Transformation LGs

• 3.3 Solve the basic mathematical problems involving the surface-area-to-volume relationship and interpret the numerical solutions in terms of functional challenges faced by the cell.
• 3.5 Discuss some of the functional challenges the crowded interior of the cell poses, and construct a hypothesis for how these challenges might be overcome.
• 3.6 Explain how water and other molecules move in and out of cells. (DLG 1 pg51)
• 3.7 Discuss the various functional roles carried out by a biological membrane and distinguish between the various modes of transport across them. (DLG 4 pg51)
• 3.9 Compare and contrast microfilaments and microtubules and describe the important roles they play in the cell.
• 3.10 Differentiate among passive diffusion, facilitated diffusion and active transport and discuss the advantages and trade-offs associated with each of the processes.
• 3.11 Discuss the different strategies that cells use to move compounds against their concentration gradients.
• 3.12 Make predictions concerning t he properties of amino acid R-groups on amino acids located in different locations within membrane transport proteins.

Lecture 7: REDOX Chemistry and Coupled Reactions

I am going to introduce REDOX chemistry. You should be able to read a redox tower and use reduction and oxidation vocabulary terms.

We are jumping straight into metabolism now. We will be making connections between metabolism, redox chemistry, enzymes, bonds and functional groups.

What happens to food once it enters our cells? We will follow the electrons, the mass and the energy as we slowly breakdown glucose into smaller sugars through the process of glycolysis.

We will follow the mass (carbon) and the energy (electrons) we are harvesting from our food. Where will the carbon end up? What will the electrons power?

New Energy Transformation LGs

• 2.9 Define a redox reaction and explain the role of electrons in red/ox reactions.
• 2.10 Define “reduction potential” and explain how it is used to build an electron tower.
• 2.11 Given reduction half-reactions for two redox pairs and access to a redox tower (table of reduction potentials), predict which compound will act as an electron donor and which compound will act as an electron acceptor (Learning Goal, Discussion Manual, p. 15).
• 2.12 Explain how a coupled redox reaction works using the electron carrier NAD+/NADH and the simple reaction (A->B).
• 2.13 Use the concept of reduction potentials to predict the flow of electrons between electron carriers and between possible donors and acceptors.
• 2.14 Given a red/ox reaction, be able to calculate the $$\Delta E_0’$$ for the reaction using the equation: $$\Delta E_0’ = \Delta E_0’(oxidant) - \Delta E0’(reductant)$$
• 2.15 Be able to convert between DG0 and DE0 for a given red/ox reaction using the equation: DG0 = -nFDE0. Be able to define each variable and its role in the equation.
• 2.18 Create an “energy story” for glycolysis tracking energy sources, forms of energy, overall reactants and products, types of energy transformations, types of reactions involved in the energy transformation, and the mediators of the transformations.
• 2.19 Explain the process of substrate level phosphorylation, be able to identify the SLP reactions when given a collection of reactions, such as in a pathway.
• 2.20 Explain the process of fermentation and what the implications are for the cell.

Lecture 8: Coupled Reactions and Respiration and ETC

We will finish up central metabolism today with the ETC and ATP synthase.

New Energy Transformation LGs

• 2.21 Explain how an electron transport chain can generate usable “cellular energy” in the form of ATP and explain the roles of the electron, proton, electron/proton carriers used in an ETC.
• 2.22 Given a series of electron and electron/proton carriers and their associated reduction potentials, be able to generated a production (functional) ETC.
• 2.23 Describe the similarities and differences between fermentation, oxidative phosphorylation (respiration) and photophosphorylation.

Lecture 9: ATP Production and Photosynthesis

Photosynthesis is going to have its own set of organelles and vocabulary, HOWEVER, it really is not anything new! Everything we have been talking about in the last several lectures will be present in photosynthesis: redox chemistry, cyclic metabolic pathways, NADH, ATP and the Proton Motive Force.

This lecture we will make some connections between central metabolism and photosynthesis. After lecture ask yourself what components from central metabolism were also present in the process of photosynthesis?

New Energy Transformation LGs

• 2.23 Describe the similarities and differences between fermentation, oxidative phosphorylation (respiration) and photophosphorylation.
• 2.24 Explain the difference between cyclic and non-cyclic photophosphorylation. Be able to determine what products are made in each and where the electrons originate and terminate.
• 2.25 Describe the advantages to having two photosystems and the ability to use water (H2O) as an electron donor.
• 2.26 Describe the link between photophosphorylation and carbon fixation.
• 2.27 Compare and contest the three forms of ATP production (LG, Discussion Manual p. 27.)
• 2.28 Predict the consequences of metabolic cycles and explain how compounds within the cycle can be used a precursors for other pathways. Readings
• Light Energy and Pigments
• Photophosphorylation: Anoxygenic and Oxygenic
• Light Independent Reactions and Carbon Fixation

Lecture 10: Origin of Life and Global Metabolism

Review the protein structure and enzyme sections of the text.

Today we will be discussing metabolic pathway regulation, a key example of how cells can maintain homeostasis even with hundreds of thousands of competing metabolic reactions occurring all at once!

I recommend revisiting the interactive metabolic map from the ATP Production discussion. Find out how many reactions are using the same substrate or co-factor.

We will spend some class time reflecting on the power of cyclic metabolic pathways and metabolism on a global scale. We will also discuss, briefly, the theoretical origins of life on Planet Earth and what those early microbes may have been eating. We will discuss the question: If we found life on other planets, would we recognize it?

Lecture 11: DNA Structure and Replication

Cellular Infrastructure Learning Goals

Remember:

• 1.9 Diagram pentose and hexose sugars: be able to number their carbon atoms and identify the key functional groups on each molecule.
• 1.10 Diagram a nucleotide and identify their key functional groups.

New Information Storage and Information Flow Learning Goals

The lecture learning goals build on the learning goals from the Discussion Section:

• DLG 1. Explain what (and where) genetic information is.
• DLG 2. Identify key structures of nucleic acid monomers.
• DLG 3. Explain basic structures, processes, and steps involved DNA replication.
• DLG 4. Create complementary strands of DNA from a given sequence.
• DLG 5. Identify leading and lagging strands in a replication fork and bubble
• DLG 6. Know the enzymes involved in DNA replication and predict the results of their malfunctioning.
• 4.1 Diagram the process of DNA replication for the leading strand, include reactants, products, enzymes and the depiction of energy requirements for each step.
• 4.2 Repeat LG 4.1 for the lagging strand and include the design challenge associated with replicating the lagging strand template and the solutions afforded by Okasaki fragments and DNA ligase.
• 4.3 Describe the challenges of replicating the ends of linear chromosomes and how nature has solved this problem with telomerase.
• 4.4 Explain DNA replication as a source of genetic variation, the mechanisms that can change the frequency of mutation and the trade-offs associated with fixing error.

Lecture 12 and 13: Central Dogma: Transcription and Translation

New Information Storage and Information Flow Learning Goals

• 4.5 Describe the key components of the central dogma and how they relate to each other.
• 4.6 Dissect the chemical reaction responsible for RNA synthesis and tell its energy story.
• 4.7 Diagram the process of transcription, include reactants, products, enzymes and the sites on the DNA required for transcription to take place.
• 4.8 Explain the key differences between bacterial and eukaryotic gene expression.
• 4.9 Describe how eukaryotic gene transcripts are processed before translation and the significance of this for generating functional diversity.
• 4.10 Dissect the chemical reaction responsible for protein synthesis and tell its energy story. Compare and contrast this story with DNA synthesis and RNA synthesis.
• 4.11 Diagram the process of translation. The diagram should include the reactants, products, enzymes and the sites on the mRNA template required for translation to take place.
• 4.12 Create illustrations that serve as models of your understanding of how proteins are targeted to the correct compartment in a eukaryotic cell.
• 4.26 Explain the concept of a strong vs weak promoter. Predict consequences of strong and weak promoters on gene expression.

Lecture 14: Diversity and Mutations

New Information Storage and Information Flow Learning Goals

• 4.13 Explain what is meant by the genetic code being degenerate and include this in describing the effect of mutations on protein integrity.
• 4.14 Predict the consequences of a mutation in the DNA, RNA or in the protein using the terms gene, allele and mutation to describe a perturbation in the central dogma.
• 4.15 Relate these consequences from 4.14 to phenotype and overall organism fitness.
• 4.16 Define and explain the different vocabulary terms used to describe mutations (point, deletion, insertion, nonsense, frameshift, null, loss of function and gain of function) and be able to predict their impact on protein function.
• 4.19 Describe how genotype and phenotype are linked. If given a genotype, be able to predict the phenotype and vice versa.

Lecture 15: Gene Regulation and Epigenetics

New Information Storage and Information Flow Learning Goals

• 4.20 Be able to create, use, analyze a Punnett Square to determine the genotype or phenotype of an organism.
• 4.21 Explain and describe situations when single celled organisms will need to control gene expression and compare and contrast that with multicellular organisms.
• 4.22 Be able to rank the different levels of regulation discussed in class by energy efficiency for the cell.
• 4.23 Using a regulatory network, accurately interpret relationships between genes/proteins in the network and predict the location of regulation by various products in the pathway.
• 4.24 Examine and interpret genetic organization of a regulatory circuit and given some specific constraints make sensible predictions about the behavior of the circuit including the possible influence of environmental or genetic perturbations.
• 4.25 Describe how environmental information can shape transcriptional and translational output in ways that lead to different phenotypes and cellular specialization.

Lecture 16: Cell Cycle

Cell Division Learning Goals

• 5.1 Describe the design challenge associated with cell division and key subprolems associated with each phase of the cell cycle.
• 5.2 Create and discuss a picture of the different levels of organization in DNA and put each organizational level in the context of challenges faced during the cell cycle.
• 5.3 Explain the sequence of events that need to occur during mitosis and why they are necessary including the roles of microtubules, motor proteins, centrosomes, and the level of DNA condensation.
• 5.4 Create and discuss a picture that illustrates the importance of crossing over and chromatid exchange during meiosis I and explain what happens if these cross over events do not occur.
• 5.5 Explain the sequence of events that need to occur during meiosis and why they are necessary, including the roles of microtubules, motor proteins, centrosomes, and the level of DNA condensation.
• 5.6 Describe how allelic segregation and independent assortment result in inheritance of characteristics through the process of meiosis and sexual reproduction.