BIOL275 master set

What are the 4 main phases of the cell cycle? What is the main goal of each? How much relative time is (typically) spent in each?

4 Phases in 24 Hours (if actively dividing) 1.) Gap1 (11 Hr): Cell carries out its normal differentiated functions 2.) Synthesis (8 Hr): DNA Synthesis - Replication of the genome 3.) Gap2 (4 Hr): Rapid protein production preparing for mitosis 4.) Mitosis (1 Hr): Division of genomes into two daughter cells

ETS complexes

Complexes I-IV of the ETS are each complicated blobs of multiple proteins working together.

Understand that microfilaments are made of actin monomers. What do we refer to as G-actin versus F-actin?

G-actin: Globular proteins that bind ATP F-actin: A polypeptide chain of G-actins forms an F-actin filament with barbed (+) and pointed (-) ends

What is G0? Would this be considered more likely a result of favorable or unfavorable conditions that the cell finds itself in?

G0: Indefinite break from cell cycle Occurs with lack of nutrients or proper signals from tissues

Considering the analogy of our tissues as a busy office place, can you see why for the proper productivity of the office most employees (cells) are busy in G1? And why addition of new employees (mitosis) is very important BUT represents a bit of down-time of the employee getting set up properly to begin/resume their assigned functions?

G1: When the cell is doing its cell type-specific job Tissues are a busy office where most workers (cells) are focused on tasks they were hired for Cells will stay in G1 until they get the signal to divide Addition of new employees (mitosis) takes time because it's like getting a new cubicle set up for them to be able to do their work.

In lecture slide 8, see how the cross-section of the β subunits reveals the enzymatic activity behind joining ADP + Pi to make ATP. Understand the significance of the gamma (γ) subunit turning and nudging (reshaping) the β subunits. What is powering the turning of the γ subunit?

Gamma (γ) subunit turning and nudging (reshaping) the β subunits allows ADP and P to come together to form ATP. H+ flow powers γ subunit

On the lecture slide discussing "Genetic variation from combining parental genomes" make sure you understand that even though the specific chromosome shown is the same one from Mom and from Dad (for example Chr 1), there are likely MANY subtle genetic variations in the specific DNA sequences (for example in the 3 highlighted genes). Where do these variations (polymorphisms) come from?

Genetic variation from combining parental genomes → From natural genetic variations (polymorphisms) and mutations → Some traits dominant/recessive, others are multi-gene in origin Polymorphisms come from slight genetic variations in each parents' genome

Understand the difference between a kinase and a phosphatase.

Kinase: Enzymes that transfer PO4- to targets (phosphorylation) Phosphatases: Enzymes that remove the PO4- group from target

How many ATP molecules get "spent" as part of glycolysis? How many ATP are made? Be careful it can be confusing depending whether you (or the text book) is referring to numbers of ATP at a given step or total overall net ATP produced.

Spent: 2 ATP Made: 2 ATP (net) (-2+2+2 = 2)

Understand that the huge number of fully differentiated cells in our body is replenished by a much smaller number of multipotent stem cells. Consider how these cells are either concerned with dividing or concerned with carrying out the cell-type specific roles they are designed for. Review: How does the process of cellular differentiation go hand-in-hand with changes in gene regulation?

The huge number of fully differentiated cells in our body is replenished by a much smaller number of multipotent stem cells → Either concerned with dividing or carrying out cell functions Cell Differentiation is the process of each cell "choosing" which genes it will express (though it contains all of your genome).

Understand what a Microtubule Organizing Center (MTOC) is. Can you give a couple examples of MTOCs in cells?

Tubulin dimers bind GTP to form MTs

What is the role of GTP in MT formation?

Tubulin dimers bind GTP to form MTs

Understand that NAD is basically two nucleotides joined at their phosphate group (but notice they are NOT connected in the same way as a nucleic acid backbone...can you spot the difference?)

Two nucleotides joined at their phosphate group connected by phosphate Os. Not phosphate to carbon.

Active site of a protein

the active site is where the substrate binding, activation, and catalysis occurs The active site of a protein may be highly specific for a particular substrate.

Understand that the simple definition of energy.

"energy = ability to cause matter to move and its resulting motion" holds true whether we are talking about a bowling ball or the atoms that make up the bowling ball. → Therefore "energy = ability to break and form atomic bonds in molecules" is really the same definition but framed in a way that makes better sense when thinking about cell biology.

Understand that the three main cytoskeletal fiber types work together (interconnected)

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Understand that organelles and other cytosolic components (such as protein complexes) aren't simply floating around inside the cell, they are suspended by a network of protein fibers

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Understand that the cell cycle is coordinated by cyclin proteins.

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Understand that the rising levels of cyclins are determined by signals that regulate expression of the cyclin gene that codes for them. For example, during G1 the cell may receive Epidermal Growth Factor (EGF) signals that up-regulate expression of G1-to-S cyclins.

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If it seems weird that the solution to running out of cellular glucose is to simply "make more glucose", consider that not all cells in our body do this...really only the liver and kidney cells do to support our body's tissues in times of need. They concentrate small leftover metabolites such as 3-carbon products (eg. lactate) from the glycolysis happening in other cells of our body and reassemble them back into the 6-carbon glucose. This newly made glucose (neogenesis) can then be released into the blood for distribution back to tissues that need it. Why bother putting it together as glucose again? → Because remember that the cells in our body expect glucose as the starting point to fuel the production of ATP, so the "recycled" fuel being handled by the liver has to be redelivered back to cells as glucose.

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Be comfortable drawing a picture of how the way sister chromatids line up during prophase of meiosis differently than in prophase of mitosis, and explain the purpose of this difference.

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For each stage of the Calvin Cycle, know: 1) what molecules are at the start and end of each stage 2) where CO2, water, NADPH and ATP are involved, 3) where products of the cycle can veer off to biosynthesis pathways (such as sugar), and 4) how the number of intermediate molecules involved in each stage change as they are combined/split/detoured away for other pathways.

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Glycolysis: Be mindful of the pathway splitting into two parallel paths (shown by 2X)

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Identify where the 5 steps of aerobic respiration are represented on lecture slide 9.

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Important concept: understand that checkpoints are the result of gradually building up levels of the critical proteins/enzymes/other biomolecules that are needed for the next phase that essentially "push" the cell to commit. So it's never a strict on/off switch, but rather signals within the cell reaching a point of no return. It's like you texting a couple friends to meet at Starbucks on a Saturday morning to decide what to do together (beach, movies, shopping?) and they start texting other friends to meet there, too. Pretty soon so many friends show up at Starbucks that you all HAVE to do something and can't just hang out there. Depending on who specifically showed up, this will influence what activities you decide to do (even if it means you get out-voted and you get stuck from peer-pressure doing something you hadn't planned to!).

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In lecture slide 8 be comfortable knowing how the (e-) move through the PSII and PSI photosystem chain that together represent the plant's version of an ETS. Know the names of the 7 molecules listed in green, and where they are as part of the ETS. Also, know at what points protons (H+) are being added to the thylakoid lumen side of the membrane. Understand that the two main outcomes of this ETS are 1) building up the H+ gradient that will power ATP synthase channels elsewhere on the membrane and 2) generation of filled NADPH "baskets" to carry the reducing power of (e-) elsewhere in the chloroplast.

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Since ATP is carrying around a small "packet" of the energy from glucose catabolism, often the analogy of ATP as money or currency is used. Just as with favorable or unfavorable exchange rates of international money, we can think that the ATP is "worth" some amount of energy, and therefore 1 ATP can be converted into many "lower value" currency (you can drive creation of lower-energy bonds) but 1 ATP cannot be exchanged for 1 "higher value" currency (you cannot drive creation of a higher-energy bond). Of course, just with money you could spend multiple ATP molecules to afford the higher-priced molecular bond. These money analogies get us thinking about how the thriving "business economy" of molecular pathways in our cells are designed to be powered by a standard energy unit ATP.

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On the simplified citric acid cycle overview, know the names of the 6 intermediate molecules in rectangles, and steps where CO2 and electrons (and reduced carriers) are coming out.

1.) Acetyl → Citric Acid (6C) 2.) Citric Acid → Ketoglutarate (5C) (-NADH/e-) 2.) Ketoglutarate → Succinyl-CoA (4C) (-NADH/e-) 3.) Succinyl-CoA → Succinate (4C) (ADP to ATP) 4.) Succinate → Fumarate (4C) (-FADH2/e-) 5.) Fumarate → Oxaloacetate (4C) (-NADH/e-) Each turn produces: 1 ATP 3 high-energy e- (NADH) 1 low-energy e- (FADH2)

Know the six different kinds of cellular work that require energy.

1.) Biosynthesis of new molecules 2.) Mechanical work 3.) Concentration molecules 4.) Electrical work 5.) Managing heat flow 6.) Bioluminescence

That are the 3 stages of the Calvin Cycle?

1.) Carbon added to a ribulose acceptor molecule 2.) Reduction by NADPH to Glyceraldehyde 3-phosphate (G3P) 3.) Regeneration of the original ribulose acceptor molecule (Ribose to Ribulose)

Name the 3 way common ways that enzymes activate the substrate.

1.) Distortion of substrate from tight contact with enzyme leads to easier breaking of bonds 2.) Enzyme may accept or donate protons 3.) Enzyme may accept or donate electrons, making a temporary covalent bond with substrate

What are the two main parts of photosynthesis in terms of what is being accomplished?

1.) Energy Transduction → Capture of solar energy and conversion into chemical energy (ATP) 2.) Carbon Assimilation → Using some ATP to rearrange CO2 to make carbohydrates

Be familiar with the main prosthetic groups used in ETS proteins. You don't need to draw them, BUT be able to describe what enables them to be good "baseball gloves"

1.) Flavoproteins → Have a partial FAD flavin mononucleotide (FMN) 2.) Iron-Sulfur Proteins → Have an Fe-S core attached to protein's cysteines 3.) Cytochromes → Contain a heme group with Fe at center → Or Fe with copper (Fe-Cu) at center 4.) Coenzyme Q → Non protein-bound (free floating) → Called ubiquinone

Review the big cartoon that breaks down the 5 stages of aerobic respiration starting from (1) anaerobic glycolysis through (5) ATP synthesis involving H+ membrane transporters. Be able to accurately describe what/how many of each type of molecule is entering/leaving each of the 5 stages.

1.) Glycolysis → Entering: 2 ATP → Leaving: 2 Pyruvate, 2 ATP, 2 NADH 2.) Pyruvate Oxidation → Entering: 2 Pyruvate → Leaving: 2 Acetyl CoA 3.) Citric Acid Cycle → Entering: Acetyl CoA → Leaving: 4 ATP (2 from glycolysis), 10 NADH (2 from glycolysis), 2 FADH2 4.) Electron Transport and Proton Pumping → Entering: 6 NADH, 2 FADH2 (powers proton pumps) → Leaving: Protons (H+) 5.) ATP Synthesis → Entering: Protons (H+) → Leaving: 36 ATP

Explain three reasons why cell division is so important in a multi-cellular organism like us.

1.) Growth of our bodies 2.) Replacement of lost or damaged cells 3.) Pass genetic material on to offspring

What are the three main types of cytoskeletal fibers that are in the cell? Look over Table 13-1 in the text. You don't need to memorize everything on it, but you should be able to identify structural differences among the fibers (type of protein, size of fiber, etc.)

1.) Microtubules 2.) Intermediate Filaments 3.) Actin Microfilaments Functions → Shape of cell (holding static or changing) → Positioning of cellular components → Intracellular transport and trafficking

Know the numbers of NADH and FADH2 generated in the first three steps of aerobic respiration. Where did these electron (e-) carrying "baskets" get loaded?

1.) NADH: 1+1 = 2 2.) NADH: 1+1 = 2 3.) NADH: 3+3 = 6, FADH2: 1+1 = 2 → 8 NADH: Accepts (e-) from glycolysis FADH2: Accepts (e-) from conversion of H-C-C-H bonds to C=C bonds

Be able to list the 5 stages of mitosis, for each one describing some of the hallmark events taking place.

1.) Prophase → Chromosomes condense into pairs 2.) Pro-metaphase → Chromosomes attach to spindles 3.) Metaphase → Chromosomes line up at the equator 4.) Anaphase → Sister Chromatids Separate 5.) Telophase (Cytokinesis) → Nuclear envelope reforms, Cell divides into two new daughter cells

Glycolysis: The number of carbon atoms in the molecules at the start and end of each phase ( you DON'T need to draw these)

1.) Start = 6 , End = 3 X 2 2.) (Start = 3 , End = 3 ) X 2 3.) (Start = 3 , End = 3 ) X 2

Understand the tally of ATP output from aerobic respiration presented in lecture slide 9. Realize that ATP are made either by substrate-level phosphorylation or H+ flow powering the F-type ATP synthases. Be able to explain how many NADH and FADH2 are involved at different stages, and how these represent the potential to make ATP. What's the total number of ATP made at the end of aerobic respiration? This number is the total including the products of glycolysis.

2 ATP Pathways: 1.) Substrate-level phosphorylation 2.) H+ flow powering the F-type ATP synthases Stage Outputs In Cytoplasm: → Glycolysis 1.) Substrate-level phosphorylation = 2 ATP 2.) 2 NADH → H Pump = 6 ATP 3.) 2 NADH → H Pump = 6 ATP In Mitochondria → Citric Acid Cycle 1.) Substrate-level phosphorylation = 2 ATP 2.) 6 NADH → H Pump = 18 ATP 3.) 2 FADH2 → H Pump = 4 ATP Net ATP Output: 38

What does the term tetrad/bivalent refer to when discussing meiosis?

A bivalent is one pair of chromosomes (sister chromatids) in a tetrad. A tetrad is the association of a pair of homologous chromosomes (4 sister chromatids) physically held together by at least one DNA crossover.

Be familiar with when/where the 5 cyclin types rise/fall during the cell cycle.

A: Peaks in G2 B: Peaks in between G2 and M (more M) D1: Peaks in G1 and has continuous peak through all stages D2: Peaks in S E: Peaks in G1

Remember that fully differentiated cells do their assigned job as determined by their particular program of gene regulation, whereas the job of a stem is IS to divide to replenish the differentiated cells as the latter get old, worn out, damaged or lost.

A typical differentiated (non-stem) cell in S, G2 and mitosis is like a new employee getting their cubicle set up - VERY important, but not the point of their job! (For stem cells, dividing *is* their job!)

Understand the example of alcohol metabolism in terms of the oxidation of ethanol being a tightly controlled process requiring multiple enzyme steps and intermediate metabolites. What role does the co-enzyme NAD+ play in this? Since the ADH and ALDH enzymes are proteins, consider how genetic variations in the coding amino acid sequence of these proteins could affect the ethanol catabolic pathway.

ADH converts ethanol to acetaldehyde, which is more toxic Aldehyde Dehydrogenase (ALDH) quickly converts CH3CHO to acetate Acetate is processed and becomes CO2 and H2O ADH facilitates reduction of NAD+ to NADH for supply to the body

ADH Enzyme Reaction Direction In bacteria and yeast, why would this favor one direction, and in humans when we drink wine the other direction would be favored? When our bodies use ADH to create acetaldehyde, does the fermentation pathway keep going in reverse all the way back to pyruvate, yes or no? (Hint: look back at the previous lecture when we discussed ADH).

ADH is an example of an enzyme that can catalyze a reaction in two directions, forwards or backwards between acetaldehyde and ethanol (because no energy input is required). → Direction will be driven by relative concentrations of the substrate and product Bacteria/Yeast: Sugars (acetaldehyde) → Alcohol Humans: Alcohol (ethanol) → Acetaldehyde to turn into CO2 and H2O No → Acetaldehyde is processed by ALDH to become CO2 and H2O wastes

Understand that the energy released by breaking of high-energy C-C glucose bonds allows for forming the terminal phosphoanhydride (3rd phosphate group) bond of ATP. Therefore ATP "carries around" that bit of energy from glucose until interactions with another molecule (such as an enzyme) breaks that bond to do work (synthetic, concentration gradient, electrical, mechanical, bioluminescent, etc.).

ATP makes energy portable around cell

Look at the molecular structure of ATP, and think about how this is really an adenosine ribo-nucleotide with extra phosphate groups. This is another wonderful example of how evolution found ways of using the same molecule for different functions (Nucleic acids = information storage, ATP = energy flow...using pretty much the same base+sugar+phosphate theme!)

ATP: Adenosine Ribo-Nucleotide with (2) extra phosphate groups Nature uses the same molecule but with a different number of phosphate groups/base groups for different functions

What is acetyl-coA? How is it made? What gets released during its synthesis? You do NOT need to draw coenzyme A, but be comfortable describing its overall structure (how it's made from separate functional units that we've seen in other biomolecules).

Acetyl-CoA: Acetyl Group attached to Coenzyme A → Entry point to citric acid cycle Synthesis: Pyruvate splits (CO2 + Acetyl) and acetyl group attaches to coenzyme A → CO2 and NADH are released → Other Metabolites: Proteins, Fats

Now look at the circular cartoon depicting the 1n/2n alternating life stages of moss. By evolving to allow two 1n cells to come together and become 2n, what evolutionary advantage is being shown here compared to the prokaryote example above? Notice at the end of the 2n life cycle it undergoes meiosis to enter the next 1n cycle. Are the four 1n cells shown emerging from meiosis in the cartoon identical?

Advantages: Genetic diversity → Better adaptation ability. Emerging cells are not identical because crossover occurs during meiosis

Look at the equation of glucose oxidation and all of the atoms represented by black, red, white balls. Can you see why 6 O2 is required to fully break down the glucose?

All of the atoms in the products were present in the reagents. → Mass is neither made nor destroyed, but simply rearranged into new bonds that are lower-energy than the starting ones, and the difference in energy can be harvested for work (stored as the 3rd bond of ATP) or lost as heat. → Need the 6 O2 to match the number of O2 in the products

Relative time spent in phases

Although we say a typical dividing human cell cycle is 24 hours, this is just a way to appreciate how much relative time each phase of the cycle takes. Most time is typically spent in G1 (convenient to say 11 hours), then S phase (8 hours), G2 (4 hours) and finally mitosis (1 hour).

Review the concept of cellular metabolism being the combination of anabolic and catabolic pathways. How do the terms endergonic and exergonic apply? When relating complex molecules to simpler molecules that compose them, how does the concept of ΔG fit in? What about highly reduced molecules versus highly oxidized ones?

Anabolism: Creation of complex molecules → Endergonic: +ΔG and energy has gone into the system Catabolism: Break down of molecules into simpler ones → Exergonic: -ΔG and energy has been released by the system Oxidized to Reduced: +ΔG → Endergonic Reduced to Oxidized: -ΔG → Exergonic

Apoptosis Triggers

Apoptosis may be triggered by... 1.) Immune cells detecting something wrong with a target cell 2.) Absence of survival factors such as nutrients or cell-to-cell signals 3.) Detection of gross genomic damage that cannot be repaired.

Understand why apoptosis is a very important process of cell death. Be familiar with the 3 main steps of 1) chromosome condensation, 2) nuclear fragmentation and DNA digestion accompanied by cytoplasmic "blebbing" and 3) cleaning up of remnants by phagocytic cells. Why is apoptosis important for both normal tissue development/maintenance as well as for dealing with potentially diseased cells?

Apoptosis: programmed cell death → Old/damaged cells need to be carefully recycled → Cannot simply burst, because release of potentially harmful signals → Apoptosis is a carefully managed series of events to turnover cells → A normal part of tissue development and maintenance 3 Main Steps 1.) Chromosome Condensation 2.) Nuclear Fragmentation and DNA digestion with cytoplasmic blebbing 3.) Cleaning up of remnants by phagocytic cells

Understand what the figure in lecture slide 8 is showing with the ETS complexes I-IV arranged like this. Note the electrical values on the Y axis and look back at the table in slide 6. Why are the large brown complexes with the (e-)-carrying prosthetic groups drawn like this?

Arranged energetically Each oval is a complex carrying a prosthetic group Based on the energy of where they fit on the table of holding on to electrons Able to see the flow of energy from high to low through the process

Recall that rearrangement of atomic bonds favors the formation of lower-energy bonds compared to higher-energy starting ones, and the "leftover" difference in energy is released (as heat or work to form other molecules). Look at the bonds involved in KMnO4 reacting with glycerol. Can you see why this reaction is so "ready to go" that mixing the two is enough to cause massive heat release?

Because it is at it most oxidized state and is spontaneous (doesn't require energy)

Why might the term "immortal" be appropriate for considering an organism that reproduces via binary fission?

Because it keeps replicating itself over and over with the same copies of DNA.

Look at the circular cartoon depicting the 1n life cycle of an early prokaryote 3.5 billion years ago. As the circle shows one 1n cell (the whole organism) dividing into two 1n cells, are those two different organisms genetically the same or different? What does that imply about the genetic variability of that species overall, and the ability of that species to adapt to selective pressures put on it?

Because the organism is haploid and reproduces through binary fission, only mitosis occurs so the "parent" and "child" are identical. There is limited genetic variability of the species overall and therefore less of an ability to adapt to pressures. So haploid life eventually evolved into diploids.

Enzymes

Biological Catalysts

Biological catalysts rate increase

Biological catalysts such as enzymes can increase reaction rates 100,000x faster.

Understand that the oxidation of biological molecules is exergonic, and involves the removal of 2 paired e- and H+ (the equivalent of 2 hydrogen atoms). However, also keep in mind these aren't simply 2H that go flying off somewhere, but rather are being simultaneously transferred to a recipient molecule (that is being reduced). That is why we write the [H2] in brackets.

Biological molecules are highly exergonic Dehydrogenation: pair of e- and pair of H+ removed

Why do biological reactions in our body actually run slowly compared to how quickly they could potentially run? (Hint: why is maintaining control so important for life?)

Biological reactions are not allowed to spontaneously run to equilibrium without control...life couldn't exist that way! → If bio reactions just ran on their own it would take way too long for the cascade of energy (w/o catalyst)

What are some functional similarities between chloroplasts and mitochondria?

Both generate energy for cells

What is the function of the Calvin Cycle? Understand how it is powered by products of the ETS.

Carbon fixation: Conversion of atmospheric carbon (CO2) into covalent bonds of organic molecules used by the cell Uses ATP created in ETS

What is the role of the mitochondria in mediating apoptosis?

Caspases: are enzymes that cleave other proteins Cytochrome C release from mitochondria is an apoptotic signal that activates caspases → May be stimulated by immune cell signals (T lymphocyte), Nutrient deficiency, DNA damage

What is achieved by having a catalyst influence the chemical reaction?

Catalysts make reaction rate increase dramatically

Describe how/why the polarity of the microfilament is associated with it having a "pointed" end and a "barbed" end. What is the functional significance of such a shape?

Caused by the structure/folding of the protein in 3D shape Barbed end is (+) positive Pointed end is (-) negative Monomers are added onto the positive barbed side. Barbing allows microfilaments to have a directionality. (Bag/Zip tie) Can only go one way or it will catch.

Understand that a cell will either be performing its normal differentiated functions or engaged in cell division but not both. Can you think of some specific reasons why mechanisms involved in either one would make the other processe(s) difficult, error-prone, or even dangerous?

Cell Cycle: Either normal work or division Not Both Because... → Mechanisms for DNA replication and gene expression get in the way of each other → Too many problems if both were happening simultaneously.

Important to understand that the cell cycles is NOT like pressing start on a stopwatch...

Cell cycles are a series of processes and decisions that are driven by increasing/decreasing activity of proteins within the cell - that's the closest you can get to the cell "thinking" about what it is doing.

What are centrioles? When assembled as centrosomes, how do these structures contribute to mitosis? (Hint: what does MTOC stand for?)

Centriole: Organelle pair in cell involved in the formation of spindles Centrosomes: protein structures that serve as microtubule-organizing centers (MTOCs) → Spreads to two sides of cells and forms spindle fibers that form mitotic spindle

Understand why the complex ringed structure of chlorophyll a and b enable them to "absorb" light and transduce that energy into alternating double-bonds within the molecule.

Chlorophyll a and b have a center Mg2+ ion and other groups (such as R) controlling alternating double bonds that move e- around → a and b have different light absorption frequencies → a and b are green because green is not absorbed and bounces back to our eyes The structure of the chlorophyll (double bonds) absorbs the photons of the light and begin flipping

Why would chlorophyll a have different wavelength sensitivity than chlorophyll b?

Chlorophyll a and b only excite at certain wavelengths → Molecular structure determines this sensitivity a and b have different double bond structures → different wavelength sensitivity

What is a chloroplast? Know the main structures.

Chloroplast: Photosynthetic factories → A leaf typically has 20-100 chloroplasts per cell Main Structures 1.) Stroma → Gel-like and filled with enzymes 2.) Thylakoids → Flat sac like structures 3.) Granum → Stack of thylakoids

CoQ and Cytochrome C Notice that CoQ is a free-floating molecule (not part of an ETS complex) and Cytochrome C between complex III and IV is part of a small protein (not big complex).

CoQ: Free-floating molecule (not part of an ETS complex) between complex I/II and III Cytochrome C: Free-floating molecule between complex III and IV → Part of a small protein (not big complex).

Explain what crossing over / homologous recombination is, and why this dramatically adds to the genetic variability generated in meiosis.

Crossing over occurs when chromosomal homologs exchange information during metaphase of Meiosis I. During this stage, homologous chromosomes line up on the metaphase plate and exchange genetic information. Allows for more than just "4 versions" of children

Why is cyanide so poisonous? How does it cause such profound harm to our cells?

Cyanide binds to heme group on Cytochrome C → Deactivates it because the heme group can no longer accept electrons → When disabled, Cytochrome C no longer transports electrons → Entire electron transport chain gets stuck → No ATP being made

Recognize there are 5 main cyclins

Cyclins are proteins, and thus their expression must be controlled (by growth factors) Cyclin A, B, D1 and D2, and E

How do cyclins actually coordinate the expression of all the appropriate proteins (how do they text the right group of friends to show up?) required to commit the cell into the next phase?

Cyclins work by guiding other proteins (have no enzymatic function themselves) → Cyclins bind to cyclin-dependent kinase (CDK) proteins, directing activity to different targets controlling gene expression → Determines WHICH potential other downstream proteins the CDK is able to bind to (and phosphorylate). Consider the complexity of all the resulting pathways of proteins talking to other proteins that ultimately control the expression of select genes, and how this is elegantly controlled by the presence of particular cyclins at the right time - and therefore how powerfully important it is that the levels of the different cyclins come and go in waves.

Understand the structure of FAD. You do NOT need to draw it. However, you should recognize the familiar component parts of it well enough that you can explain how this molecule's structure is different than NAD+.

Difference: FAD is a flavin adenine dinucleotide while NAD is a nicotinamide adenine dinucleotide. → FAD can accept two H (NAD only 1) → FAD is lower energy (only produces 2 ATP vs 3 in NAD)

Lactate Fermentation

Direct transfer of e- from NADH to pyruvate yields lactate → Benefit of this is recovering the NAD+ that is used in glycolysis Dairy Products, Muscles

Understand the mechanism behind why Mendel's purple pea flowers are a dominant trait against the recessive white flower trait. Conceptually understand how an allele may function as dominant or recessive trough a molecular mechanism such as this. Let's say the normal form of the pea plant's A1 gene with the "C" in its sequence is called the "P" allele and the version of the gene with "A" is called "p" allele. Why would plants that are PP or Pp make purple flowers, but plants that are pp make white ones?

Dominant alleles are functional enzymes → will show when present Recessive alleles are non-functional enzymes → will only show if no functional enzymes are present In flower ex. Dominant: Codes for pigment Recessive: Lack of functional code → no pigment (white)

What is the Energy of Activation of a biochemical reaction? What does the EA prevent from happening? Consider the analogy of the light switch and the "hump" of resistance it physically has when switching on/off. How is that resistance related to the EA?

EA: Energy requirement to break bonds so new ones can form → EA prevents reactions from happening spontaneously → Light switch with no resistance would be useless, constantly on or off with no control

Photosystem Process to Reaction Center

Each photosystem is made of many small groups of "antennae" which are proteins+chlorophyll. → When a photon hits a chlorophyll molecule in one of these areas, the absorbed energy excites an electron → Excitement (NOT the e- itself) is transferred via resonance transfer to neighboring antenna → Energy reaches Reaction Center

Why did first life on Earth evolve anaerobic (oxygen-free) pathways such as glycolysis for making ATP from glucose?

Earth is 4.6 billion years old → No atmospheric O2 for the first billion years → First life was likely photosynthetic bacteria making glucose from sunlight, CO2, H2O → Glucose catabolism to make ATP had to happen anaerobically (no O2 required)

Glycolysis: The end of glycolysis leaves you with what molecule(s)?

End Products: Pyruvate X 2, ATP X 2, NADH X2

What does the endosymbiosis theory have to do with chloroplasts and mitochondria and their relationship with eukaryotic cells?

Endosymbiosis Theory: Mitochondria and chloroplast in eukaryotic cells were once aerobic bacteria (prokaryote) that were ingested by a large anaerobic bacteria (prokaryote). Cell provides housing Organelles provide energy (rent)

In lecture slide 4, be comfortable relating what you see in the small boxed cartoons of the leaf at the left with the expanded details of the larger overall cartoon. We typically think of the net reaction of photosynthesis as Light +CO2 + H2O -> O2 + sugar...notice how the components of that net reaction are divided into the two main parts of energy transduction and carbon assimilation. Can you describe in words what the two parts are, and how one leads into the other?

Energy Transduction → Input of H2O and Sunlight → Output of ATP Carbon Assimilation → Input of CO2 → Output of Sugars ATP output from Energy Transduction provides energy for sugar creation in carbon assimilation.

Understand that glucose is the main fuel source for cells, but its energy potential (C-C) bonds must be converted into ATP to be distributed and widely used in cellular pathways (consider the analogy of burning coal to make electricity, and how being given a lump of coal to recharge your phone is pretty useless).

Energy from glucose must be converted into a more convenient molecular form (ATP) that energy-requiring processes in the cell are designed to use. Ex. Fuel source is coal and it goes into a coal factory → transformed into energy output (electricity) → changed into more convenient form to use

Consider that the oxidation of a molecule of glucose releases the same amount of energy by burning it or by cellular enzymes breaking it down. Does that surprise you? What advantage does that provide in terms of being able to harvest the released energy?

Energy is all in the molecule's bonds, and it doesn't matter how you break those bonds to release it. → But our cells cannot literally burn it with heat, we must use enzymes to carefully break the bonds one by one. → Advantage: Catalytic enzymes break bonds systematically which allows for the capture of some released energy as ATP

Look at where H2O and CO2 enter the reactions. Does this challenge your way of thinking about the net reaction Light + H2O + CO2 -> O2 + glucose? Look at the cartoon and think about what things are coming "in" from outside of the system, and what things are going "out".

Enter the reactions at different points 1.) H2O → Enters in thylakoid lumen Part 1 2.) CO2 → Enters in Stroma in Part 2 H2O and CO2 combined do not give the products. Rather H2O and CO2 each have their own reactions that give rise to components of the products 1.) H2O → O2 and ATP 2.) CO2 → Glucose (from ATP and calvin cycle) Moreover, H2O is always in the system, CO2 has to enter through the membranes. O2 stays inside while glucose exits

Understand how enzymes may be regulated by other factors that create allosteric changes or by phosphorylation

Enzyme control is achieved by binding other molecules or post-translational modification such as phosphorylation → Phosphorylation may activate or inhibit an enzyme Allosteric change: When a change in the shape of one region of a protein impacts a change in the shape of another region, allowing for regulation of activity.

Look at the structure of Vitamin B3. In the context of enzymatic pathways, do you now appreciate why vitamins are so important for proper health of our cells?

Every part of our body needs niacin to function

When FAD carries a pair of (H+) and (e-) in the form of two hydrogens, why is it we say that when it passes them on to another molecule the energy involved is lower than (e-) being passed on by NADH?

FADH2 carries its electrons in a lower potential energy state than the NADH molecule does. → Therefore when this energy is released in the transfer of electrons, FADH2 releases less energy than NADH

Understand that an important role of anaerobic fermentation is the recovery of electron (e-) carriers such as NAD+ that were reduced to NADH. In what step of glycolysis is NAD+ used, and why?

Fermentation converts NADH back to NAD+ → NAD+ used in phase 2

How does fermentation deal with processing pyruvate? What does it get out of pyruvate? Why might some of our tissues sometimes need to use fermentation?

Fermentation: Primitive organisms evolved extra anaerobic steps to utilize pyruvate → Replenishes supplies of e- acceptor NAD+ so glycolysis can continue → End Products: Lactate and ethanol (discarded by the cell as waste) Muscles perform fermentation when oxygen is used up too fast → Under these hypoxic conditions, lactate is converted into more glucose to compensate for inefficient ATP production

Can you list some reasons why an amoeba undergoing division is similar to one of our body's cells dividing? What are some important functional differences?

For amoeba, cell division is the reproduction of the complete organism Similar: → Divides when it has grown too big (organelles too far apart) → Passing on genetic material Differences: → cell division is the reproduction of the complete organism → Human cell division is just part of ourselves

Understand the concept of Gibbs Free Energy G of a system, and why the sign (+/-) of ΔG is important. Which one is thermodynamically spontaneous? What does that mean? When is work involved?

Gibbs Free Energy G is the energy in all molecules of a biological system → Change in Free Energy ΔG is either gained (+) by making more complex molecules or lost (-) by breaking into simpler molecules → ΔG = Gprod - Greactants → -ΔG is spontaneous

Look at the molecular model of glucose compared to ATP. Recall that glucose has potential energy of -686 kcal/mol when oxidized down to CO2 and H2O whereas the terminal (3rd) phosphate bond of ATP yields -7.3 kcal/mol when broken. ATP doesn't seem very impressive at first glance, does it? Then consider the amount of energy being released by a burning pile of coal, and how only a tiny bit of that energy actually flows through your USB phone charger. Likewise, ATP is a very controlled way to distribute the energy of glucose oxidization throughout the cell where needed (i.e. a large amount of energy spread around in small packets).

Glucose is a large, uncontrolled packet of energy → like coal when burned straight all the energy is released at once ATP comes in smaller, controlled packets of energy → like small amounts of electricity running through charger that charge your phone.

By the end of Phase 1 what has happened to the glucose molecule? Why did this require the "spending" of ATP?

Glucose molecule is split into halves → ATP molecules donate high energy phosphate groups during the two phosphorylation steps → ATP bond-breaking TP to DP also provides energy

Study the graph that shows the wavelength sensitivities of various photo-sensitive molecules. See the valley for chlorophyll a and b from 500-600nM...how does this explain why chlorophyll is green in color to our eyes?

Green wavelengths are not absorbed and bounce back to our eyes

In lecture slide 4, just as with the membranes of the mitochondria, understand what is happening regarding the use of a H+ gradient to power ATP synthesis. Identify areas on the cartoon that fall under the two main parts of photosynthesis.

H+ gradient/movement powers proton pumps in thylakoid membrane → produces ATP 1.) Energy Transduction → 1a-1c (Membrane, Thylakoid, Stroma) 2.) Carbon Assimilation → 2a-2c (Stroma, Outside)

How is energy related to the movement of molecules? When we add heat to an ice cube, why does it melt and become liquid? Why does it freeze again when cooled? Think in terms of how individual water molecules are involved.

Heat is going into the ice cube → When it is melting the energy breaks bonds between the molecules of the substance. → When it is cooled and frozen again, the energy decreases so it solidifies. Kinetic Theory → When heat is added to a substance, the molecules and atoms vibrate faster. As atoms vibrate faster, the space between atoms increases. The motion and spacing of the particles determines the state of matter of the substance

What is a heterokaryon cell? Why were these types of experiments important for understanding what drives the cell cycle phase?

Heterokaryon Cell: fused cell with two nuclei → Early experiments involved fusing cells at different cycles → Found that cells were forced into a later phase, even if not ready! → Helped prove levels of specific proteins determine cycle phase, not cell itself.

Review the example of the ball on the hill. What do we mean that the ball is meta-stable in this position? How is that like an atomic bond in a molecule?

High energy bonds are meta-stable like the ball on top of the hill (meta implies stable, but with potential to release energy) → All biological reactions require catalysts to make them happen

Humans certainly don't have life cycles involving alternating 1n/2n life stages because we have specialized body cells that are dedicated to making gametes directly (via meiosis in our ovaries and testes). Consider: how does this fit with the circular cartoon representing 2n-to-1n life cycles? Isn't this just the idea of shortening the 1n life stage to the shortest length possible, essentially eliminating it? Why was this an evolutionary trend? (Hint: again, think about mechanisms that drive genetic diversity)

Humans don't have 2 distinct life stages because it is not efficient/needed. The 1n life stage become so shortened that it basically seized to exist. We now directly make our gametes from 2n cells (no separation of stages) We are constantly in 2n life stage but we are also constantly directly making gametes (ovaries, testis, reproductive tissues) Shortening speeds genetic diversity because it forces gametes/sexes to develop distinctly

ETS Complexes I, III, and IV VS. Complex II

I, III, IV: Actively pump H+ as part of glucose catabolism II: Pumps H+ when succinate is used as an alternative starting molecule

Explain why reactions mediated by enzymes that don't require the input of energy are reversible, allowing the flow from substrate to products to go in either direction? (Hint: In lecture slide 1 think about the interaction between enzyme and substrate, and how this reaction is driven simply by specific molecular fit).

If the reaction doesn't require in input of energy (ATP molecules, NADH molecules, etc.) then the products and reactants have identical components.

In evolutionary advanced flowering plants (compared to more primitive ferns) note that the plant's life cycle still follows alternation of generations. But where is the separate gametophyte life stage? If a fern's two life stages have distinctly different appearances, does that mean a rose bush or tiger lily plant also has some "weird" alternate form? Explain why the flower represents another evolutionary step in shortening the 1n life stage...why is this beneficial?

In higher plants the gametophyte stages are physically reduced → The separate gametophyte life stage is the flower (no longer contained below) Flower plant as a whole → 2n Parts of flower (spores, bulbs, etc.) → 1n Significantly shrunk down 1n life stage → only creates flower when it is time to reproduce (not always present like in fern) → Useful because efficient?

If ATP production needs to be ramped up, why would the FNR enzyme redirect (e-) from being loaded onto NADP+ and instead send the (e-) back to Cytochrome b/f?

Increases H+ gradient which increases ATP synthesis

Increasing availability to organisms of what molecule drove evolution of additions to the glycolytic pathway? Why did levels of this molecule rise during prehistoric times?

Increasing availability of O2 Oxygen Rose because the evolution of early plants/algae began producing it faster from photosynthesis

Review how our chromosomes look (and function) during interphase versus mitosis. Consider how the jump-rope and pool noodle models we played with in class are the exact same molecule (the same chromosome) but in dramatically different packaged states - why are these changes necessary for our cells to successfully work with the DNA at these different times? (Keep in mind that for meiosis, the same comparison applies).

Interphase: Cell grows, replicates DNA, prepares for mitosis (Jump Rope) Mitosis: Replication of Cell → Division of DNA and Cell (Pool Noodle) Jump-Rope vs. Pool Noodle: The jump rope is the unraveled form of the DNA in the chromosome. DNA is only in this form when the cell is doing regular cell activities (DNA must be readable). It compacts into pool noodle form when replication occurs.

Isn't it odd that the fern gametophyte can fertilize itself resulting in a clone as it grows into the sporophyte (2n) stage? I mean, why bother making separate sperm and egg from the same individual if they just self-fertilize? (Hint: does it have to be sperm from the same individual that fertilizes the egg?)

It doesn't necessarily have to be self-fertilization If a sperm from another fern makes its way somehow to the plant (rain, animals, etc.) it can cross-fertilize

What are polar bodies? Why did evolution lead to their creation?

It is more evolutionary beneficial to give birth to one child at a time because of how helpless human babies are at birth. Much more work required for one baby than other animals. Polar bodies prevent 4 egg cells each pregnancy

Understand that it wouldn't make sense for enzymes working on oxidizing a target molecule to necessarily accept the e- themselves, since that would change their property, and they'd have to be "reset" (themselves oxidized) as the substrate of another enzyme. That would NOT be very inefficient. So small co-enzyme molecules such as NAD+ are used as electron acceptors (and are reduced to NADH). Thus, there only needs to be a system for resetting the NADH back to NAD+ which is far more efficient.

It's not efficient to have complex enzymes being reduced and then having to be reset to act again, so what's a better solution? → Enzymes often use another small molecule as the e- acceptor

How do kinesins work to transport / traffic cargo along MTs? (Kinesins are actually Chapter 14.1)

Kinesins move cell components along microtubules 1.) Leading heavy chain binds to ATP 2.) ATP binding causes conformational change; trailing heavy chain swings forward

What role do kinetochore proteins play in the spindle fibers attaching to chromosomes?

Kinetochores: proteins surrounding centromeres of sister chromatids → Act as attachment to spindle fibers

Cells evolved additional steps after glycolysis to "get more mileage" out of the pathway. What are the 3 main paths evolved to do this? What are the factors that determine which path can be expected?

Lactate Fermentation: Anaerobic Alcohol Fermentation: Anaerobic Gluconeogenesis: Arobic Factors: kind of organism, specific cell type, and availability of O2

Complex Connections

Large ETS complexes are actually NOT physically linked to each other in a row on the membrane, Float freely around on the membrane and as they bump into each other the (e-) transfer from one to another occurs.

Understand that the net reaction for photosynthesis makes it seem that H2O and CO2 enter the process together, but in reality this "what goes in and what comes out" simplified way of writing it out doesn't concern itself with the different steps involved. This is much the same when we look at the net reaction of glucose being fully oxidized down to CO2 and H2O...it doesn't give any hint of the many enzymatic steps behind it that we've learned about.

Light + 6H2O + 6CO2 → 6O2 + C6H12O6 → Notice that the H2O and CO2 are involved at different parts → Photosynthesis is the reverse of glucose oxidation: (C6H12O6 + 6O2 → 6CO2 + 6H2O) Both formulas are very simplified

What are the small cholorophyll+proteins groups called Light-Harvesting Complexes? Why is it important that they are freely floating within the membrane (in other words, they are transmembrane proteins that won't leave the membrane) and can associate with the PS photosystems? Why might their ability to relocate be useful in low versus high sunlight conditions?

Light-Harvesting Complexes: A pigment-protein complex that harvests light energy and converts it to exciton energy that can migrate to the photosynthetic reaction center where photosynthesis occurs. → Low Light: Packing together transfers energy more efficiently in low light → Bright light: mitigates the risk of overloading photosystem by grouping farther and have xanthophylls/other pigments in between to absorb extra energy Being free allows them to pack differently to respond to different conditions.

Why are some MTs considered "cytosolic" whereas others are "axonemal"?

MTs originate from Organizing Centers → Cells have special MT Organizing Centers (eg. centrosome, basal bodies) → Special tubulin proteins anchor the (-) end of the growing MT fiber → During mitosis, centrosome organizes the spindle fibers

How do α and β tubulin assemble to form a microtubule (MT)? What gives the MT polarity, and how is this functionally relevant to dynamic changes in the MT?

Made of a+b tubulin dimers that bind guanosine triphosphate (GTP) → Thirteen protofilaments of dimers form a hollow tube → Tube has a (+) end (b tubulin) and a (-) end (a tubulin) polarity MT grow from the (+) end and typically shorten from the (-) end

Understand how the development/maturation of human gametes (sperm and egg) fit the stages of meiosis. Importantly, why is it you end up with 4 haploid sperm but only 1 haploid oocyte?

Male → Meiosis 1: Diploid spermatocyte becomes 2 diploid mixed cells → Meiosis 2: 4 haploid cells (sperm) split from meiosis I Female (polar body produced each replication) → Meiosis 1: Diploid Oocyte gets rid of extra set of genome through polar body → Meiosis 2: Divides again to form a haploid egg. End with 3 polar bodies (1 from egg, +1 from oocyte division)

Glycolysis pathways sugar sources Does this mean the use of those other molecules is more efficient because the net ATP number made would be greater? Why or why not? (Hint: look carefully at lecture slide 9).

Many different sugars can feed into the glycolysis pathway and even non-sugars such as glycerol. → In several cases, this requires first converting the other type of sugar into glucose. → Some molecules can enter at different points of the glycolysis pathway, bypassing the first ATP-dependent steps of processing the glucose molecule. This does not make any pathways less or more efficient than others → they all have the same energy requirements and products

When it comes to sexual reproduction, what is the challenge posed by being a diploid organism?

Meiosis → Reproduction of complex organisms requires fusion of haploid cells (gametes)

Understand that meiosis involved 2 separate meiotic divisions (or part I and II). Why is one termed "reduction" division, and the other called "separation" division?

Meiosis I Reduction: Reduction from diploid to haploid cells Meiosis II Separation: The halving of the haploid meiosis I cells to form gametes (and swapping)

Is Meiosis I or Meiosis II more like mitosis?

Meiosis II

Understand the thought question about why meiosis isn't simply taking a diploid cell and dividing each parental genome into two different gametes (hint: since our gametes begin as diploid stem cells, it might be tempting to think meiosis just separates the two copies of the genome into two separate gametes.)

Meiosis also mixes the DNA of each gamete to give rise to genetic diversity. If not parents would only have "4 versions" of children.

State the main function of meiosis compared to mitosis - in other words, consider meiosis in the context of the previous question.

Meiosis: Cell divides twice to produce four cells containing half the original amount of genetic information. → Main function is to produce gametes for reproduction → Basis for genetic diversity Mitosis: Replicated chromosomes are separated into two new nuclei. Cell division gives rise to genetically identical cells. Divide twice and half/mix DNA vs. Divide once with identical DNA

Describe what the mitotic spindle is.

Microtubule-based bipolar structure that segregates the chromosomes in mitosis (pulls apart the chromosomes)

Can you identify three different opportunities during meiosis when parental alleles can be mixed up before being passed to offspring? (Hint: start from the genotypes of the parents and consider how the child's genotypes would be close but not identical to either of them)

Mixing (crossover) in both parents during meiosis (2) Mixing when gametes come together to form child (1)

How does the arrangement of microfilaments differ in different parts of the cell that are involved in motility versus withstanding physical stress? What are the roles of accessory proteins such as filamin and fimbrin?)

Motility (Spread): More filaments are parallel and arranged in one direction (Lamellipodium, Filopodium) Physical Stress: Roughly parallel in different directions or crisscrossed. (Stress fiber, Cell cortex) Proteins that hold microfilaments in place Filamin: Holds microfilaments together in crisscross Fimbrin: Holds microfilaments apart and parallel

Glycolysis: What role does the conversion of NAD+ to NADH perform?

NAD+ is an electron carrier that becomes NADH when it picks up an electron → Helps pass energy from glucose to other pathways in the cell.

In lecture slide 7, various (e-)-handling molecules of aerobic respiration are ordered by their affinity for staying reduced (holding onto the e- given to them). The more negative the ranking, the less likely they want to stay reduced (e.g. The NADH "basket" wants to get dumped out). The more positive the ranking, the more likely they are of staying reduced (e.g. O2 happy to become H2O). If you were to chain together a series of redox reactions with the intention of having (e-) transfer through the chain, can you see how this ordering makes sense with NAD+ at the top and O2 at the bottom? Can you also see by the position of NADH and FADH2 on this list why one transfers (e-) with greater ability to do work than the (e-) transferred by the other?

NAD+/NADH → Most Negative → Wants to be dumped out most O2/H20 → Least Negative → Wants to be dumped out least

Consider the lecture slide portraying the flow of energy and matter through the living things of our biosphere Earth. Appreciate the intimate connection between phototrophs (autotrophs like plants) and chemotrophs (heterotrophs like us). Does it surprise you that plants evolved before animals on our planet?

No, because animals needed oxygen to survive which is made by the plants who only use sun and carbon dioxide to make it Earth developed oxygen later but sun and CO2 before

Why are these checkpoints essentially "commitment" points? When a cell has passed through one, why can't it turn back? Why must the cell continue forward through DNA synthesis and/or mitosis rather than "bailing out" and returning to G1?

Once a cell passes a checkpoint it cannot go back. → Checkpoints are a build-up of critical proteins, enzymes, biomolecules needed for the next phase that push the cell to commit → Already has the materials for the next stage, cannot get rid of them etc.

Soup Analogy

Once the pink C-C bond has been broken in the lecture slide 8, that means all of the C-C bonds in the original glucose have been accounted for and oxidized. It's important to note that while the intermediate molecules all have several carbons that didn't come from the original glucose, these are essentially a way for the original C-C bond (s) of the starting glucose molecule to be passed along until they have basically been "absorbed" as part of the citric acid cycle. Think about the analogy I gave in class about a supermarket shelf with soup cans, and how even though cans from a particular shipment are removed and bought since the shelf is restocked every week it may appear that the cans don't go anywhere. That's like the C-C bonds from the original glucose molecule as they pass through the citric acid cycle (technically they've all been "sold" although it's hard to tell because the shelf still looks full). I don't know if this is really a good analogy, but I do like soup.

If an amoeba is a totally different organism than a human being, why is it that a human macrophage cell can look, move, and phagocytose bacteria and viruses the same way an amoeba can? Is it more than coincidence?

Ontogeny recapitulates phylogeny → Hypothesis that as we develop from fertilized egg (ontogeny) through embryonic stages, we pass through the forms of our evolutionary ancestors (phylogeny) → Our macrophages, immune cells that patrol and eat bacteria, use many of the same genes that amoebas use to control movement and phagocytosis → All life on Earth is connected by the thread of cellular evolution

What is an "open" versus "closed" system in terms of energy? Can life exist in closed systems? How are WE open systems? If we were closed up in a sealed chamber, do we die right away? What is the factor that limits this, and how does that make you think about the idea of energy flow in terms of molecules?

Open: There is an input of energy and an output of energy Closed: No energy going in so reaction is stopped and no products are formed Life can not exist in a closed system because we need the energy from the sunlight and co2 to sustain life We will not die right away but we will eventually without an input of energy (food, light, air, etc.) We have some stored as it goes through the flow steps but will eventually run out

Glycolysis: During which enzymatic steps is ATP spent? ATP made?

Phase 1: ATP investment phase (spent) Phase 2 and 3: ATP is produced

What are the 3 phases of glycolysis? Can you explain with a couple sentences each what is happening in the phases?

Phase 1: Prepare glucose molecule by splitting into two similar halves → 2 ATP Required (-2) Phase 2: Oxidize the half-molecules, using the released energy to make 2 ATPs and 2 NADH → Energy released from phase 1 used → Product: 2 ATP, 2 NADH (+2) Phase 3: Convert molecules into pyruvate → Product: 2 ATP (+2) Net Product: 2 ATP

When studying phase 2 of glycolysis, notice that 1,3-bisphosphate-glycerate is able to power the endothermic reaction of adding a 3rd phosphate onto the ADP. Look at the slide comparing this to money (currency).

Phosphate group from molecule is removed by enzyme Glucose-10 and added to ADP.

Photon Concept

Photon: light is a packet of wave energy that has a certain wavelength (even though this isn't a physics class, understanding what a photon is makes understanding photosynthesis easier).

Think about how the net reactions of photosynthesis and glucose oxidation really are opposites. Does this make sense to you? (Hint: consider the cyclic nature of energy and matter flow between life on our planet).

Photosynthesis: (Light + 6H2O + 6CO2 → 6O2 + C6H12O6) Glucose Oxidation: (C6H12O6 + 6O2 → 6CO2 + 6H2O) Makes sense, nature is a continuous flow of energy and balance so products all become reactants somewhere else.

Thylakoid Membrane Photosystems

Photosystems within the thylakoid membrane are complexes made of many proteins and photo-sensitive molecules (e.g. chlorophyll, beta-carotene, etc.).

Some of the most fragrant flowers are surprisingly plain in appearance both in terms of shape and colors. Can you explain why this is a "choice" being made by the plant?

Pigments and perfumes are expensive molecules that plants use sparingly, which is why flowers typically look colorful *or* smell nice but not both.

Under intense sunlight, the rate of (e-) transfer from the special P680 chlorophyll molecules of PSII (as well as the P700 in PSI) may exceed what the photosystem(s) can handle. As a result, unintended oxidized molecules will build up and potentially harm the cell. How do carotenoids counter-act this?

Pigments such as b-carotene / xanthophylls absorb light and extra e- to convert energy into heat that radiates away from plant.

Understand the different roles of chlorophylls a and b versus accessory pigments such as carotenoids (examples β-carotene and xanthophylls)

Pigments: Accessory pigments that help protect cells against intense light. → When seasons change (angle of sun changes) and enough photons aren't available, making chlorophylls is no longer worth it. → Protect plants from sunburn when chlorophylls aren't being made → Prevents chlorophyll from being overworked This is why plants change color in fall.

Be comfortable explaining how Prophase I of meiosis differs compared to Prophase of mitosis. You do NOT need to memorize the names of the various Prophase I events BUT you should be able to describe what is happening.

Prophase I Meiosis: Homologous chromosomes condense and become visible as the x shape we know, pair up to form a tetrad, and exchange genetic material by crossing over. Prophase I Mitosis: Chromosomes Condense

Describe some of the pros and cons of having a diploid genome (like ours) compared to a haploid genome?

Pros: → Greater flexibility in gene expression levels → Having backup "good" copy of a mutated gene → Variation in DNA sequences that may allow selection under changing pressures on species Cons: → More DNA = greater # of random mutations → Detrimental mutations may be passed on to next generation instead of selected against → Reproduction of complex organisms requires fusion of haploid cells (gametes) Regardless of our human-centric view, life on Earth exhibits genomes of varied ploidy (haploid, diploid, polyploid) that suits organisms best!

What kind of macromolecule is an enzyme?

Protein

What do we mean when we say the ETS proteins use prosthetic groups to shuttle electrons?

Prothetic Groups: Special (e-) carrying groups found in ETS proteins → (e-) temporarily part of Fe2+ ion or added to oxygen group Ex. Baseball Gloves

What is alcoholic fermentation? Compare and contrast that with lactate fermentation in terms of 1) what is achieved 2) what enzymes are involved and 3) how the end products differ in usefulness to the cell.

Pyruvate → Acetylhyde → Ethanol PDC Enzyme: Pyruvate → Acetylhyde ADH Enzyme: Acetylhyde → Ethanol End Product: Ethanol (Alcohol) → Waste Product (Not used like lactate is)

Explain what lactate fermentation accomplishes. What enzyme acts on pyruvate to do this? What is the resulting molecule?

Pyruvate → Lactate → Glucose → Compensate for lack of ATP in anaerobic conditions → Recovers NAD+ → Lactate Dehydrogenase Enzyme (Pyruvate → Lactate)

Why might these polymorphisms above exist in the population and not be eliminated through natural selection?

Recessive "unfavorable" alleles can be "hidden" by a favorable dominant allele and get continuously passed on. Also, because of how society has evolved, natural selection has less of an effect on human traits now.

What are redox reactions? What does it mean to be a reducing agent (and get oxidized) or an oxidizing agent (and get reduced?)

Redox Reactions: Transfer of electrons from a reducing agent to an oxidizing reagent → New bonds are lower-energy, and thus favorable → "Leftover" energy of the original bond is released (heat or work) Reducing Agent (gets oxidized): Loses Electrons Oxidizing Agent (gets reduced): Gains Electrons

What are some reasons why phosphate groups are so important for cellular functions involving energy and control of protein function?

Regulate protein function → Often transferred (such as from ATP) as a way to regulate substrate function

In the nice cartoon in lecture slide 4 (which I encourage you to spend time reviewing) it looks like from one glucose only 1 ATP is coming out of glycolysis and 1 ATP out of the citric acid cycle. I thought we get 2 ATP from glycolysis and 2 ATP from citric acid cycle. Is the cartoon wrong? (Remember I said it's easy to get confused with these numbers, so I'm encouraging you to keep this straight)

Remember, two cycles are occurring at once with both halves of the glucose molecule.

Where in the cell cycle are the 3 main checkpoints?

Restriction Point: G1 to S → Growth factors, nutrients, cell size, DNA damage G2 to M → Cell size, DNA damage, DNA replication Metaphase to Anaphase → Chromosome attachments to spindles

What is rubisco? What role does it play in the Calvin Cycle? I mentioned in class that because ALL photosynthetic life on Earth uses rubisco, it is considered the most abundant protein on the planet. Even though WE don't have rubisco on our bodies, it is estimated that for every person on the planet there is 15 lbs of rubisco surrounding us in the biosphere! (I wanted to clear that up in case students thought I was saying we have that much rubisco in our bodies, which would be very wrong).

Rubisco catalyzes CO2 assimilation into trioses Rubisco enzyme makes 3-phosphoglycerate (triose: three-carbon sugar) All phototrophs have it: the most abundant protein on Earth!

Why is ribulose 1,5-bisphosphate referred to as an acceptor molecule? Acceptor for what?

Rubisco → Catalyzes CO2 Accepts carbon from CO2

Enzyme protein side chains

Side chains involved in the active site may not be close together in the original linear polypeptide chain, yet when the protein folds up they end up forming the active site.

Glass Cup Anaology

Structure differences in chlorophyll a and b are like cup shapes influencing water rippling to sound frequency. Think about how the shape of the glass influences how the water will ripple in response to sound energy. → Depending on the shape/size/material of the container, the water will be more "sensitive" to specific frequencies of sound energy in the air. → Likewise, the specific shape of chlorophyll molecules influence the wavelength of light energy that they are sensitive to.

What are tetrads (or bivalents) referring to during meiosis? Why is this not present in mitosis?

Tetrads/Bivalents: Each pair of chromosomes—called a tetrad, or a bivalent—consists of four chromatids. At this point, the homologous chromosomes exchange genetic material by the process of crossing over Not present in mitosis because no crossover/swapping

Actual time spent in phases

The actual time spent in the phases depends on what the cell is being told to do (e.g. perform its normal tasks versus dividing), conditions the cells is experiencing (e.g. nutrient and oxygen supply) and any problems that need to be fixed (e.g. DNA replication errors, improper sister chromatid separation). Those are only a few examples of things that may speed up or slow down the cycle.

What is cytokinesis?

The cytoplasm of the dividing cell is divided forming two daughter cells → After Telophase

Why would enzymatic reactions that require the use of ATP not be so easy to reverse using the same enzyme?

The energy molecules are part of the reactants, therefore the products do not have identical components to the reactants anymore.

Understand the cartoon of the ball pushed down the hill. What does the man represent by his push? Why didn't the ball just roll by itself, but once shoved it easily heads downhill? Relate these points to the previous questions about bonds in two biological molecules that are reacting with each other.

The man represents the little energy being put into the reaction to start the process.

Consider the evolution of cellular respiration from Step (1): anaerobic glycolysis to the addition of steps such as (2): oxidation of pyruvate into acetyl-CoA, (3) the citric acid cycle and (4): the e- transport chain. Explain what are the purposes of (2),(3), and (4)?

The other steps evolved as a result of the availability of oxygen in the atmosphere. With O2 available can oxidize glucose all the way to CO2 and H2O → Glucose to Acetyl to CO2 and H2O → More ATP products 2.) Acetyl-CoA: PDH turns glucose in Acetyl → Entry point to citric acid cycle 3.) Citric Acid Cycle: Generation of many e- and the reduction of co-enzyme carriers (NAD+ → NADH) 4.) e- Transport Chain: Uses e- to generate lots of ATP and uses O2 to restore carriers (NADH → NAD+)

For the very scary Citric Acid cycle figure, you do NOT need to know how to draw out all the structures. Focus on understanding what is happening to the pink-shaded C-C bond that represents 2 of the original 6 carbons found in glucose that emerged from glycolysis as pyruvate.

The pink carbons themselves do not disappear but the functional group they were part of do. The carbons become part of a new group.

Explain why the generation of (e-) is so important? What will they be used for later?

The power parts of the respiration cycle. The electrons are used by the H+ pumps to generate ATP.

Understand that the oxidation of biological molecules takes place in our cells through carefully maintained steps. Eventually, it reaches the bottom, where there is nowhere else to roll (carbon dioxide). What do we then do with it?

The series of reactions going from most reduced state to most oxidized is NOT the ball rolling all the way down the hill at once → The ball rolling down one small slope, coming to a stop, and then needing another shove to roll down another small slope. → We breathe the end carbon dioxide out

When examining the multi-colored karyotype panel (ie. condensed chromosomes lined up to make them easier to count) be aware that there are two of each chromosome (why?), and that in the lecture slide image each one is an "X" shape. During what phase of the cell cycle is this cell? How is the term "sister chromatids" relevant to the "X" shape?

Their are two of each chromosomes → One from mom, One from dad When chromosomes are in the X shape the cell is in mitosis Sister Chromatids: Identical copies of chromosome pairs when DNA replicates

On lecture slide one, the (e-) going into the pool are tallied as "1+1" and "3+3". Why did I not simply write "2" and "6"? (Hint: what am I trying to remind you about)

There are two of the same processes with the two halves of glucose going on at the same time.

What do the (e-) that are carried around by NADH and FADH "baskets" have to do with 2 the H+ pumps of the electron transport system (ETS)?

These electrons power the H+ pumps of the ETS which produce ATP from ADP+P at the end respiration cycle. → Movement of (e-) through complex also moves H+ across the membrane

Understand that biological molecules in our cells are stable enough with their bonds such that they don't automatically react like KMnO4 reacting with glycerol. Why is this more compatible with life? What does that mean in terms of energy requirements to get biological molecules to react?

They require a little energy to be put in for the reaction to take place to make better bonds (lower energy) with another molecule This relates back to the cascade of energy for life molecules. The molecules must be in the right place at right time to receive released energy from previous molecule.

Once an evolutionary branch has led to organisms that make 1n gametes directly from 2n body cells (like us), what would need to happen to prevent an individual from self-fertilizing like what the fern's gametophyte stage can do? Think about it: how does this explain why the two sexes are different in appearance, physiology, behavior, etc.? We grow up taking it for granted that men and women are different, but have you ever asked WHY?

This forces the development of two distinct sexes that each carry one component of fertilization (men = sperm, women = eggs) so self-fertilization cannot occur. FORCES DIVERSITY FOR EVOLUTION

Understand the main function of the citric acid cycle What will the products be used for later?

To generate electrons (being carried away by co-enzymes such as NADH and FADH). Product (e-) used to power proton pump that powers ATP synethsis

Function of the PSI and II protein complexes

To move (e-) and in the process use that movement to... → Build up the H+ gradient across the thylakoid membrane → Generate reduced (e-) carrier "baskets" that can transfer (e-) to other metabolic pathways.

Why is the insoluble nature of intermediate filaments a major contribution to their role in maintaining cell structure?

Unlike MTs and microfilaments, IFs are highly insoluble: Provide Strength → Function as underlying shape and strength of cell → Several different proteins (e.g. vimentin, keratin, lamin) make IFs

Understand how the H+ gradient that is built up by the ETS pumps can now be used to power F-type ATP synthase transporters

Uses H+ gradient made from e- transport chain → H+ flow turns the g (gamma) subunit → Changes shape of the b (beta) subunits → Makes ADP and P come together → Can make 3 ATP per turn → H+ pumped due to one NAD+ makes 3 ATP → H+ pumped due to one FAD makes 2 ATP

Describe how the structure of vimentin and keratin is very different than that of actins or tubulin. What is meant by a protofilament?

Vimentin/Keratin: Actins/Tubulins: Protofilament:

What is meant by an interphase cell?

When the cell performs normal cell functions (not actively separating) → Replicating DNA → Obtaining Nutrients/Growing

Look at the light absorption plot in lecture slide 1 - what range of light wavelengths will no longer be absorbed by the plant cells once they stop making chlorophyll a and b, and only carotenoids are left?

Yellows, Reds, Oranges, are no longer absorbed and are then reflected back to our eyes.

Look at the micrograph of the cilia cross-sections. What are the little rings that you see inside?

a and b tubulin

Does it surprise you that many common life forms that we encounter in daily life aren't diploid like we are? For example, does it seem "weird" that a strawberry may be 10n? Or that different varieties of strawberries can actually have varied ploidy? (By the way, if the terms 1n, 2n, 10n, etc. confuse you, make sure you understand what these refer to)

xn: x amount of chromosome pairs Life on Earth exhibits genomes of varied ploidy (haploid, diploid, polyploid) that suits organisms best! Strawberries do not sexually reproduce → no need for separate gametes and human-like diversity

Understand that our muscle cells also perform lactate fermentation *if* they run out of oxygen (such as during strenuous exercise).

→ Because O2 is required for the aerobic respiration pathway that pyruvate is normally fed into to get more ATP In the absence of oxygen, the cell will make lactate instead. → That lactate will be removed from our muscles and sent to the liver where it can be made into more glucose via gluconeogenesis.

Understand what the amount of kcal means. What two molecules are the end result of how far we take glucose down this path? Why would this be different than burning glucose with a flame or decomposing glucose with acid in a beaker?

→ Ex. When we say 1 mol of glucose has 686 kcal of energy, we are saying that if glucose is broken down as far as our metabolism can take it, this is how much energy we get out. End Molecules: CO2 and Water

Understand that at the end of lactate fermentation the product can be used to build other molecules in the cell or potentially combined with other molecules to create glucose, whereas for ethanol fermentation the end product is mainly considered waste.

→ Lactate Product can be used to build other molecules or recreate glucose. → Ethanol is just waste

What is a (c)alorie? How is it different than a (C)alorie?

→ One calorie (cal) with lowercase "c" is energy needed to heat 1 gram of H2O one degree Celsius at 1 atm pressure. → Nutritional information (food labels) use Calories (Cal) with uppercase "C". One Cal = 1000 calories (or 1 kcal)

Understand that plants perform aerobic cellular respiration (using oxygen to fully catabolize glucose) just like we do. Why do plants need to do this if photosynthesis is so good at making ATP? Why do plants use up much of their ATP made from photosynthesis toward sugar production, if they have to break the sugar down to get the ATP back out of it anyhow?

→ Photosynthesis converts 26 photons of light into 9 ATP → However, many cells of a plant are not doing photosynthesis → Also consider at night there is no light for photosynthesis → Thus plant cells, just like ours, perform aerobic respiration to use the glucose they've saved to get ATP back → We depend on the glucose from plants, passed through the food chain, for our survival.

In true plants such as ferns, consider how the 1n and 2n life stages are distinctly different forms that look nothing alike. Note how the mature gametophyte (1n) stage just has to perform mitosis to result in gametes (why?). Are these gametes genetically identical to each other?

→ Self-fertilization of egg by self sperm serves to clone the plant → Cross-fertilization of egg by other fern sperm promotes evolution Can both clone and evolve Meiosis serves as a crossover for genes in gametes (not identical) for limited genetic diversity when cross-fertilization doesn't occur.