DISCUSSION 1

1. If thermodynamics tells us that systems become more disordered over time, does life speed up or slow down this process? Does life disobey the second law of thermodynamics? Life creates order from disorder. This requires energy. Using energy to make order in one system tends to create disorder in another system. Usually, this process requires speeding up reactions that would normally take much longer otherwise. So, over the long term, life creates more entropy more quickly then would occur in its absence. This is inline with the 2nd law. 2. What are the absolute minimum criteria that distinguish living from nonliving things? Suggestions To believe something is alive, I would expect to see evidence of: Order/complexity/homeostasis in the form of repeated patterns, consistent shapes, maintenance of shape, temperature, and/or internal chemistry over time, etc. Energy -- Because creating order from disorder requires energy, Id expect anything alive to consume some type of fuel. Evolution -- since all life on earth came about and exists within the context of evolutionary change, Id expect to see some evidence of a (genetic) relationship between all living things. Information reproducing complex structures and maintaining homeostasis dont happen randomly. Id expect to see evidence of information that directs these processes (like genes in DNA). Reproduction life tends to make more of itself through various proceses of reproduction. Cells it appears that the smallest individual unit of life that can do all these processes independently is a cell. Anything smaller or less complex like a virus cannot do so without help from a host. 3. How is the idea of "vitalism" similar to "intelligent design creationism"? How is it different? Both suggest that life's origin, rules, mechanisms, etc are supernatural or outside of "regular" stuff. Creationism goes a step further by suggesting that these aspects of life are outside our ability to study them. We can never know or understand how life works or where it came from through normal observational methods -- because it is of a divine nature.

DISCUSSION 3
1. Where does the energy to break bonds come from?

The kinetic motion of surrounding molecules (measured collectively as temperature) supplies the energy necessary to break bonds. The faster molecules are moving (the hotter they are) the more likely a bond will be broken. 2. When a bond forms, where does the energy go? The energy required to create a bond is often stored in the form of conformational change of the host molecule (its shape / distribution of charges). You could think of it like winding a rubber band. When that bond is broken (i.e. the rubber band is released) the potential energy stored is transformed into kinetic energy that can drive change in some other molecule. 3. Is there some obvious advantage in storing energy in [H+] gradients? Gradients are systems which can be used by many proteins. They are easily rechargeable in part because the inputs and necessary structures (Protons (hydroniums) and membranes) are abundant in all cells. Gradients are also highly localized to the membrane, so that large changes in concentration dont (necessarily) affect the rest of the cell. 4. What would happen to a cell's ability to make ATP if it were exposed to a H+ carrier or channel? Assuming the cell cannot regulate the new channels, cells would lose the ability to establish a proton gradient. Because numerous life sustaining membrane based processes are driven directly by proton gradients, the cell would die pretty darn quickly, with or without OXPHOS and ATP. But you get the idea.

DISCUSSION 4
Suggested "Good" answers, written in Student-ese.

1. How (do you suppose) does an electron move through an electron transport chain? What happens to its energy as it moves through the chain? As excited electrons move through the electron transport chain - a series of big complex protein machines - some of their energy is used by those proteins to move H+s across the membrane to generate a H+ concentration gradient. As the electrons move from place to place, they have less and less energy. This probably means that each step "down" the electron transport chain is more + electronegative than the previous. The potential energy stored in the H gradient is used to bind an inorganic phosphate (Pi) to an ADP (a very endothermic - doesn't want to happen reaction) to generate the high energy molecule ATP, a kind of "universal" fuel that makes cells go. 2. Why are oxidation and reduction always coupled? A redox reaction actually describes ONE process, an electron moving from one molecule to another. We just give each step a name, so it can easily be mistaken for two independent processes. When an electron binds to a molecule, the molecule has been reduced, and its overall energy is increased (obviously). If an electron is taken from a molecule, is has been oxidized, and its overall energy is lower. Since reduction and oxidation (redox) is always a kind of "hand-off" from one molecule to another (because no electrons were hurt in the reaction process), we say the two are coupled. But really, it is a somewhat unnecessary distinction.

3. Why are carbohydrates good for storing energy? Lipids?

Bonds between atoms of equal or near equal electronegativity tend to have a lot of energy. Bonds between atoms that have different electronegativity tend to have low

energy. Carbohydrates and lipids are chock full of high energy C-C and C-H bonds (C and H have very similar electronegativity) and very few low energy C - O or H - O bonds (O is way more electronegative then C,H). At the same time, C-C and C-H reaction activation energy tends to be very high, which is why Big Macs do not often explode. This combination of high energy content, but low probability of spontaneous reaction makes carbs and lipids great molecules for long term storage of energy.

DISCUSSION 5
1. What factors can you imagine influenced the "universal" set of amino acids used in organisms? Though there are thousands of amino acids that occur in nature, only around 20 are employed by life, with no obvious reason why. It could be that the materials (precursors) necessary to build those amino acids were most available in the enviornment, so their synthesis was favored. It could also be that the processes that synthesize the universal set are favored - for example, they involve less complex pathways, or they are more stable in a wider range of conditions. Finally, it could be just random chance. The universal set might have been just the first of many possible to come together and be "good enough" to make life go, thus freezing further selection. The fact all organisms use this same set of amino acids indicate evolutionary relatedness among them 2. What does it mean that the two strands of a DNA molecule are anti-parallel? DNA strands are polymers that have polarity, meaning each monomer has a kind of "front-end" (5') and "back-end" (3'). Synthesis of each DNA strand can only happen in one direction (from the 3' end). The hydrogen bonding bases on separate strands are attracted to each other. But because of their orientation, the two DNA strands anneal together going in opposite directions (one goes 5' to 3', the other 3' to 5'). This is what is meant by anti-parallel. 3. Why is double stranded DNA better for storing information than either single-stranded RNA or DNA? Primarily stability. In general, single stranded DNA and RNA have numerous chemically active sites that can react with the environment, with other nucleic acids, or with enzymes. Such reactions would change the structure of the molecule, and thus change the information stored - which wouldn't be awesome. Double stranded DNA holds the critical information stored within the bases in a chemically unreactive shell of sugar and phosphates. Many viruses utilize RNA and single stranded DNA as their primary genetic storage molecule. After 2.5 billion years of evolution, every cell on earth has developed a kind of "immune system" that hunts down single stranded nucleic acid polymers, and destroys them. Double stranded DNA also enables the cell to repair damaged DNA more easily, using the undamaged strand as a template.

DISCUSSION 6
1. Why is it difficult for a large hydrophilic molecule to pass through a lipid bilayer membrane? What stops it? Explain. Large hydrophilic molecules are polar, they are constantly hydrogen bonding to the water they are dissolved in. This polarity gives the molecules a partial charge and allows it to hydrogen bond with water. Think of this as a crowded night club where everyone is pushing and pulling and jostling one another as they try to walk through the crowd. Hydrophobic molecules are non-polar; that is, there is no partial negative or positive charge in the molecule and therefore they repel water.

The phospholipid can be divided into two sections, a polar "head" group and a nonpolar tail group. The absence of water in the plasma membrane is also an absence of pulling on the polar or hydrophilic molecule. It is not so much as a repulsion between the hydrophilic and hydrophobic groups but an absence of attraction. 2. Why is the movement of materials through the membrane essential for life? Cells must be selectively permeable. The cell needs food, water, oxygen, signals etc. in order to function and reproduce. The cell also needs to remove waste and toxins. 3. Spiny carp are native to Northern Canada. They spend summers in the shallow waters of lakes feeding on insects. In winter, they hibernate at the lowest depths. Which cartoon (see worksheet PDF) best represents the lipid composition of the spiny carp cell membranes from summer to winter. Explain at least 2 criteria that informed your choice.

A is correct. During the warm months the membrane needs to be more solid or rigid. Likewise, during the cold months, to prevent freezing and damage (bursting of the cells) the membrane needs to change in order to maintain fluidity. This is accomplished by increasing the number of unsaturated bonds in the phospholipid chains.

DISCUSSION 7

1. What is the relationship between mutation and phenotype? Is the ploidy of a cell (e.g. whether it is diploid or haploid) relevant to this relationship? Explain. A mutation is a change in the genetic material (DNA) of a cell. A mutation can be null, beneficial, or deleterious. A phenotype can be seen or observed. The appearance of an organism is what is typically referred to as phenotype (brown hair, tall or short etc.), but other traits also fall under phenotype such as behavior and development. The DNA is the written code for all the proteins produced by an organism. These proteins are what create the appearance and traits for that organism. Therefore, a mutation in the DNA can cause a change in that organisms phenotype depending on the type of mutation. In a diploid organism, to affect the phenotype, the mutation will need to be a dominant mutation whereas in a haploid organism, the mutation will affect the phenotype directly. However, some changes (mutations) in DNA sequences do not result in a mutation such as the "wobble" bases that lead to the production of a correct amin acid sequence for a protein. 2. Describe (or draw) a scenario in which sexual reproduction leads to the loss of a deleterious allele from a population. Here the students should either draw or describe the steps in meiosis where independent assortment and recombination occur. They should show that during these processes deleterious mutations can be moved onto a single chromosome. Meiosis is sexual reproduction. It is meiotic recombination that can create chromosomes with greater amounts of deleterious mutations. This leads to the creation of a less fit organism , an organism less likely to reproduce, thus leading to a loss of those deleterious mutations from the POPULATION. 3. Do you think speciation requires mutation? Could a series of recombination events (without mutation) create a new species as well? Explain. Species: is a group of organisms capable of interbreeding and producing fertile offspring. A series of recombination events in combination with genetic drift CAN lead to new species without mutation. Genetic drift refers to the change in the frequency of an allele in a population over time from random sampling. See the following example: In population X there are multiple alleles per gene and on average these alleles are evenly distributed among the individuals of the population. During some dramatic environmental change a smaller population splits off of population X (we will call it population Y). Population Y is a small re productively isolated population where effects of sampling error (who mates with who) can alter the allele frequencies significantly. Overtime these changes in frequency will tend to fixate, which means that one allele will come to dominate the population whereas other alleles will be permanently removed from the population. Therefore, genetic drift is considered to be an important mechanism of evolutionary change (especially in small isolated populations). If in our example the alleles contributed to the periods of time that the population was fertile, after the populations diverge and Population Y and Population X both have a different 'fixed' allele they may have completely different times when the population can reproduce. Overtime, when population Y (which now becomes fertile for only the last month of summer) comes into contact with population x (which now becomes fertile for only the last month of spring), they may not be able to interbreed because they are no longer fertile at the same time.

DISCUSSION 8
1.Where is the information in a DNA molecule? Why must a double stranded DNA molecule be separated in order to be replicated? The information in a DNA molecule lies in the sequence of the four bases that make up DNA, Adenine, Guanine, Cytosine and Thymine. The sequence of these bases form the blueprint for the creation of mRNA and eventually proteins. But how then does the cell machinery distinguish Adenine from Guanine and etc? The cell relies on the unique structure of each base to distinguish the sequence of base pairs. Each base has differences in structure and electonegativity, and it is these differences that the cell uses to distinguish the bases. In order to access or 'read' the strands of DNA they first must be unwound from the double helix. This will allow the cell machinery to 'view' for 'feel' the structures of the bases and leaves the bases free to interact with the transcriptional machinery or the replication machinery in the cell. 2. Why is only a single RNA primer needed to synthesize the leading strands, but multiple primers are needed to synthesize the lagging strands? The lagging strand is synthesized in a discontinuous manner, meaning, there are multiple lagging strands and only one leading strand. An RNA primer is needed to supply the free 3'OH group required for DNA synthesis. The lagging strand contains multiple RNA primers because the enzymes that synthesize DNA can only work in one direction (they synthesize DNA from the 5' to 3' but read the DNA in a 3' to 5' direction) and the lagging strand is oriented in a 5' to 3' direction. As the leading strand lengthens from the RNA primer, the lagging strand will be extending in the opposite direction and must continually stop and restart as more of the DNA is unwound and accessible for DNA replication. 3.Would an "error-free" hereditary system be evolutionarily successful? An error-free system of heredity does not exist in nature. If populations did not have variation, or multiple types of alleles, and existed as a 'monoculture' they would be prone to large epidemics from disease, predators etc. In short, mutations are important for a population's survival in the long run. Populations must have the capacity for hereditary change, the driving force for evolution.

DISCUSSION 9
1. Aside from mRNA, which RNAs are involved in protein synthesis and what are their functions? There are three types of RNA that assist in protein synthesis: mRNA, tRNA and rRNA. tRNA, also called transfer RNA, are adapter molecules that contain a three nucleotide sequence, the anticodon, which will recognize its complementary codon on the mRNA strand. The tRNA also carries an amino acid specific to the anticodon sequence. Therefore, each codon on the mRNA will be "read" by the anticodon of a tRNA. When the anticodon and codon match, the amino acid carried by that tRNA will be transferred onto the growing amino acid chain. Ribosomal RNA (rRNA) associates with ribosomes to form the ribosomal complex. These complexes physically move along the mRNA and work alongside tRNA molecules to assemble the amino acid chain. 2. What would happen if an mRNA was created missing a base (a single base deletion) in the middle of the sequence? How would this affect the protein produced?

A single base deletion in the center of an mRNA strand will lead to a frameshift mutation. The reading frame after the deletion will be altered by one base pair for the rest of the length of the mRNA. When the reading frame is off by one base pair, during translation, each corresponding amino acid will be incorrect. This can lead to many types of products: A truncated protein: a frameshift mutation can often produce a truncated protein due to the creation of a premature stop codon. A non-truncated mutant protein: if the frameshift mutation does not result in a premature stop codon the sequence of the amino acids will be incorrect. The amino acid sequence determines the shape or structure of a protein. Changing the amino acid sequence will most likely produce a non-functional protein. 3. In discussion 9, what is the name of the bioinformatics tool you will be using that can compare primary biological sequences such as amino acid sequences and nucleotide sequences? BLAST: Basic Local Alignment Search Tool

DISCUSSION 10
1. How could a protein that acts as a transcriptional activator on one gene act as a transcriptional repressor on another? A transcription factor (TF) can act as both an activator and a repressor of transcription. For example, Gene A requires TF 1 to bind to the DNA near the promoter sequence in order to increase the affinity of RNA polymerase for the promoter, thus enhancing the transcription of Gene A. That same transcription factor may also act as a repressor for another gene, Gene B, by binding to a site of the DNA that blocks the ability of RNA polymerase to bind to the promoter. 2. Describe the possible effects of a mutation that alters the sequence normally recognized by a specific transcription factor. Transcription factors bind to specific binding sites in the DNA unique to that particular transcription factor. The transcription factor recognizes the pattern of available hydrogen bonding partners in the major and minor grooves of the DNA (a transcription factor does not open up the DNA base pairs). If a mutation were to occur in the binding site of a transcription factor there are several possible outcomes: The most likely outcome is that the transcription factor will no longer recognize this DNA sequence as its binding site and will not bind to the DNA. This will lead to reduced expression of the target gene if the transcription factor was an activator, or it will lead to increased expression of the target gene if the transcription factor was an inhibitor. The change in DNA sequences may cause the transcription factor to bind more tightly to the DNA, or permanently to the DNA.

3. From your discussion lab manual, what are the two ways that transcription levels of a gene can be altered? Gene transcription can be altered by positive or negative control. Positive control occurs when a transcriptional activator protein induces expression of a gene, possibly by enhancing the binding of RNA polymerase to the promoter region of that gene. Negative control occurs when a transcriptional repressor protein blocks expression of a gene by inhibiting the binding of RNA polymerase to the promoter region of that gene.