Biology Quiz 2 Flash Cards
Why are cells unable to harvest energy from the combustion of organic compounds?
Most immediately, the heat of combustion would throw the cell dramatically out of homeostasis and probably destroy it. Another reason is that harvesting energy from combustion reactions is difficult and inefficient. Natural selection tends to favor the most efficient method in this case, by harvesting energy via the chemical potential energy of ATP.
How does an action spectrum meaure the efficiency of photosynthesis?
The action spectrum measures the efficiency of photosynthesis by comparing the oxygen output of chloroplasts when exposed to different wavelengths of visible light.
How is ATP synthesized?
ADP and Pi (inorganic phosphate) use energy from catabolism in order to synthesize ATP. Because ATP is unstable, it requires energy to create, yet does not require energy to release energy.
Utilizing the first law of thermodynamics, where can discrepancies in energy be accounted for in a collision of two masses?
Discrepancies in energy could be made up in the form of heat (friction in the case of a physical collision).
Why is it believed that autotrophs using photosynthesis develop before heterotrophs?
The early atmosphere lacked oxygen, which is required by heterotrophs. Therefore, the autotrophs had to develop first in order to produce the oxygen that would eventually develop heterotrophs.
Why are blunt ends in DNA not efficient for cloning?
Without the sticky ends, the plasmids will normally seal itself back together, making it impossible to insert a restriction fragment.
Is it possible for a plant to receive too much light?
Yes, If a plant is accustomed to receiving a certain amount of light and suddenly receives more, then the reaction centers can become overwhelmed with energy and the photosynthetic machinery may be damaged.
Why can't glucose be oxidized to produce CO2 and H2O in just one step in our body?
because the release energy of this reaction is very high and will incinerate the cell in if released at once.
Why do you think there aren't many animals that act as both autotrophs and heterotrophs?
This is most likely due to the fact that autotrophs developed first, so the development of autotrophs and heterotrophs occurred during different times, although there are many possible reasons for this.
Give an example of how ncRNA can affect gene expression.
miRNA, small ,single-stranded RNA molecules, bind to complementary strands of mRNA. This can silence expression of the mRNA the result of this being that no protein is produced.
What is one possible application of RNAi?
It is hypothesized that RNAi's purpose is to combat viruses. This behavior has been observed in plants and in certain animal cells.
What is a microarray and how might it be more harmful than helpful?
It is possible that non-pertinent data be considered as statistically significant, in which case gene identification could be heavily skewed.
How do exons and introns increase genetic diversity in eukaryotes?
The cell can vary which sequences are treated as exons and which as introns, allowing it to create different proteins from the same gene.
What could a build-up of lactic acid in your muscle cells have been caused by?
Most likely some form of activity that causes anaerobic respiration in the cells, such as sprinting, weight lifting, etc.
What is it about ATP that produces a good amount of energy?
ATP is a very unstable molecule consisting of adenine and 3 phosphate groups. Hydrolysis breaks ATP down to ADP which has a much lower energy state. This difference in energy states is the source of energy.
How could doctors use advanced forms of gel electrophoresis to diagnose patients?
Advanced gel electropheresis could sequence blood samples on the spot in order to look for any markers of specific diseases.
Explain why there is significantly more biomass at the bottom of the food chain than at the top.
All of the energy in organisms originates in autotrophs, which comprise the bottom of the food chain. Since energy is exponentially lost in each level of the food chain, only so much biomass can be sustained at each successive level in the food chain.
How are competitive and non-competitive enzyme inhibition differentiated?
An enzyme inhibitor is competitive if it binds to the enzyme's active site and blocks the substrate from binding. A non-competitive inhibitor binds to an allosteric site, not the active site, and changes the shape of the enzyme from there.
You conduct an experiment: you have several samples of a particular species of plant and you shine different colored light on each sample. After a few weeks, hypothesize what would happen to the plants and why.
Because the mix of chlorophyll and other pigments in the plants' cells determines what spectrum photosynthesis occurs best at, the growth of plants in different-colored light should correspond. Chlorophyll a is most efficient in purple and red light, so the samples exposed to purple or red light should have higher growth than plants exposed to light in the middle of the spectrum like green or yellow. In fact, since chloroplasts can't absorb green light, the plants exposed to only green light should die.
The Corpse Plant does not photosynthesize. Why is it mostly white?
Because the plant is not photosynthetic, it contains no photosynthetic pigments. Most plants are colored according to the colors corresponding to the wavelengths of light their pigments reflect. Since the corpse plant has no such pigments, it absorbs all wavelengths of visible light and is white.
How might a plant adapt to be able to grown in light of any color?
Different light-absorbing pigments absorb different parts of the electromagnetic spectrum. In theory, if the right pigment was present, plants could absorb energy from even non-visible parts of the spectrum even though less of this light makes it through Earth's atmosphere.
Explain how our cells use energy coupling.
Energy coupling is a process where an exergonic reaction is used to drive an endergonic reaction. A common exergonic reaction in our bodies is the hydrolysis of ATP. This reaction provides the activation energy for most endergonic reactions in the cell.
What is the difference between exergenic and endogonic reactions? How can you tell the type of a reaction?
Exergonic reactions release energy, while Endergenic reactions absord energy. Endergenic reactions can decrease entropy of the system and increase potential energy, thus to test for them you would expect to see products of lower entropy, i.e. gas > liquid, liquid > solid.
Under what circumstances will a chemical process occur spontaneously?
If the reaction in question increases total entropy, in line with 2nd law of thermodynamics. In addition, the reaction must have no activation energy.
What is the purpose of a marker lane in gel electrophoresis?
Interpreting gel electrophoresis is based on identifying proteins by length. The marker lane contains known proteins with known lengths, providing a metric for length. This allows us to determine the length of the proteins forming bands in the other lanes and identify the proteins from those lengths.
Using only the principles of cellular respiration, give a reason why a brain transplant would be more difficult than a kidney transplant.
Neural cells, unlike other muscle tissues in the body, require aerobic respiration. While a kidney may be able to survive longer periods without oxygen, a brain would very quickly become irreversibly damaged.
Genotype controlls phenotype. Is it true the other way around--would altering a phenotype change an organisms genotype? Why or why not?
No, altering an organisms phenotype would not alter it's genotype. It's the same as if I drew a happy face on my hand. My children would not be born with happy faces on their hands (but wouldn't that be rad?!).
Is it possible to just have the dark reaction and fix CO2 without having the light reaction?
No, because the light reaction produces ATP and NADPH that are used in the dark reaction.
Suppose that scientists are trying to create a closed ecosystem with a food chain. Is a fixed amount energy enough to substain this system?
No, because there is about 10-25% of the energy is passed on from one link in the food chain and a lot of the energy becomes heat loss and cannot be used again.
How can ncRNA affect cell activities even though it doesn't code for new proteins?
Noncoding RNA are not useless. miRNA and siRNA can regulate gene expression by binding to complementary mRNA strands and blocking translation, Other kinds of ncRNA have even been found to code for peptides. Little is yet known about the functions of most ncRNA strands, but they play a part in the cell's functionality.
Why are many obligate anerobes deep-sea dwellers?
Obligate anerobes cannot survive in the presence of oxygen, so the low-oxygen environment of the deep sea is a good location for them.
Sequencing DNA using a template is similar to DNA replication. What are the common macromolecules involved in both processes?
Other than the template, sequencing with PCR uses the same elements: primers, nucleotides and DNA polymerase.
Explain the role of electron acceptors in metabolic pathways.
Oxygen acceptors such as oxygen, sulfates, and nitrates are reduced in such metabolic pathways. Regardless of the type of organism, this allows for respiration to occur.
What does photosynthesis have to do with the metabolism of humans?
Plants fix CO2 in the air into organic compounds by photosynthesis. Humans get energy to fuel their metabolic processes by eating organic compounds from plants and animals.
Why do reptiles require significantly less food than humans and other mammals?
A major energy expendature in the human body is the effort to maintain a constant body temperature. Reptiles are cold-blooded, meaning they spend far less energy trying to regulate their body temperature, meaning they don't need as high of an energy intake as humans and other mammals.
What is a metabolic pathway and how do enzymes play a part in these pathways?
A metabolic pathway is one strand of a of metabolic process in the network along which a molecule is converted to another. Enzymes are the driving catalyzing elements in metabolic pathways.
Explain how a person's physical apperance can change substantially due to aging while their DNA remains the same.
A person's DNA is not the sole factor in determining their physical form. The central dogma of biology states that DNA makes RNA that makes proteins. Which strands of RNA are made (and subsequently, which proteins are made) is controlled by gene regulation, a cell's ability to selectively express or repress genes. As a person ages, their gene expression changes substantially, causing their cells to change the amounts of proteins manufactured, resulting in what we perceive as aging.
If chlorophyll a is the main method of photosynthesis, why are other pigments (such as chlorophyll b and carotenoids) so important?
Chlorophyll b allows for light of different wavelengths to be absorbed, thus allowing for photosynthesis to occur even when the respective light wavelength required by chlorophyll a doesn't exist.
If we can help catalyze chemical reactions by heating them, why can't we do the same with enzymes (biological catalysts) in cells?
It could kill the cell! More importantly, heating the cell could denature the proteins resulting in sadness and bad things.
Give two reasons why bacteria is used so commonly in gene cloning.
Firstly, they have plasmids that can be easily modified and second, they reproduce very fast. So the inserted genes can be produced more of the gene everytime they divide?
Why did oxygen-consuming organisms come to exist?
For years, plants emitted oxygen into the atmosphere. At the time, oxygen was toxic to most organims. Through random mutations and natural selection, organisms started to actually use oxygen in their metabolism. Now, all animals use oxygen to fuel their metabolisms.
What effect do gene-specific transcription factors have on the transcription rate?
Gene-specific transcription facotrs, activators or repressors, increase or decrease the transcription rate by binding to specific DNA sequences.
What is the difference betweeen a gene and an allele?
Genes are a group of DNA nucleotides which later produces proteins that exhibit the phenotype of that gene. Allele refers to the different types of genes of the same group that would produce different alleles.
Say you had a very small sample of DNA from an extinct species and you wanted to run tests on it but the sample was too small & rare. What method could you use to increase your sample and how is this done?
You could use PCR to increase your sample which involves 3 steps: 1. heating it to seperate the strands. 2. annealing primers to the sequence by cooling it. 3. use DNA polymerase to extend the strand. now repeat cycle several times
Why might prokaryotes want shorter tails on their mRNAs?
Shorter tails indicate shorter mRNA lifespan, which allows prokaryotes to reproduce mRNA to quickly adapt to their changing environments.
What is one enviromental factor that can cause incorrect protein production? How does it affect the production process?
UV light from the sun can cause base pair swaps. That slight change in the DNA causes a change in the polypeptide produced (or cause it not to be produced). The protein then does not fold correctly, so it is either useless or performs its function incorrectly.
How can a virus be used in gene therapy? What are the limits of such therapy?
Viruses can be used as a viral vector for applying gene therapy, as the virus carrying a particular gene sequence enters the cell, and the cell then uses the introduced gene to produce proteins. Such therapies are limited, as they only effect somatic cells, and thus need to alter large numbers of cells
Given what you know about energy, why must we intake more energy than we output as useful work (ie. movement, organ function, etc.)?
We must intake more than we output because of the second law of thermodynamics: entropy is always increasing. Therefore, we always lose some of the energy we intake to heat and other non-useful inefficiencies.
Describe the functions of three different types of RNA that may be present in a cell.
mRNA is the RNA that codes for proteins. mRNA is translated by ribosomes. tRNA helps with the translation process. It brings amino acids to the ribosome and pairs with the matching mRNA. miRNA and siRNA are RNAi agents. They silence gene expression by binding to mRNA before it can be translated.
What is the difference between miRNA and siRNA?
miRNA is created within the cell and operates to suppress when usually bind imperfectly to its host RNA. siRNA is similar, except it can come in the form of dsRNA and from external sources. For siRNA to function, it mainly has to bind perfectly to its RNA target.
Describe how anaerobic respiration differs from aerobic respiration.
Anaerobic respiration does not use oxygen as the final electron acceptor. It can use various other acceptors that are not as electronegative as oxygen. Anaerobic respiration does allow for the creation of as much ATP as aerobic respiration does.
Why can translation start while transcription is still in progress in bacteria?
Because bacteria lack a nucleus and other membrane-bound organalles and both processes happen in the cytoplasm.
How are riboswitches used in biomedical research?
Because riboswitches could repress transcription, they have the potential to kill bacteria. This has great potential for drug design such as antibacterials.
Understanding the energy pyramid, explain the benefits of vegetarianism.
By being a vegetarian, you are now a primary consumer instead of a secondary one. This means that you obtain energy from 10% of producers rather than 10% of 10% of producers, or 1%.
Explain the energy coupling process cells use when storing and releasing energy.
Cells store energy in ATP by adding a phosphate group to ADP, which is an exogonic process. This process is used to drive the energonic process of ATP hydrolosis, which is energonic because the process results in high potential energy.
What reaction produces oxygen for the atmosphere?
Photosynthesis splits a water molecule, freeing an oxygen atom.
Why is rubisco so abundant?
Rubisco is very abundant because it is necessary for carbon fixation, which provides all the carbon used in living organisms.
How is cyclic electron flow different from linear electron flow?
"In cyclic electron flow, photosystem II is bypassed. Electrons emerging from PS I re-enter PS I rather than reducing NADP+. As a result, no NADPH is produced, but ATP is. "
How could a heat map be beneficial for a scientist studying a disease?
A heat map allows the scientist to see the increase or decrease in gene expression. This may help them learn more about the cause or effects of the disease.
What is meant by the term "DNA fingerprint"? How do scientists create and differentiate DNA fingerprints?
A DNA fingerprint is a virtual fingerprint that is generated by analyzing a person's DNA. The basis of a DNA fingerprint are short tandem repeats (STRs), repeated series of base pairs that occur in different places along the DNA strand for each person. Where these STRs occur on a person's DNA is unique (except with twins), and is the basis of their DNA fingerprint.
What is the difference between catalysts and enyzmes?
Enzymes are catalysts, but catalysts can also be inorganic.
What would happen if enzymes did not exist?
Reactions would proceed too slowly to be able to sustain life.
If flourescent tagging of dideoxynucleotide molecules was not avaiable, what is another way that DNA sequencing could be done?
The DNA sequencing reaction could be performed in four different containers, each with one of the terminating molecules. Gel electrophoresis could be run in separate channels for the results of each of the reactions and the heights of the molecules in the different channels could be used to deduce the sequence of the DNA without flourescent tagging.
How do bacteria adapt to their enviornment so quickly?
The mRNA in bacteria have shorter lifespans, so they can reproduce mRNA more often that is adapted to their enviornment.
How would life on Earth be affected if the light and heat provided by the Sun suddently stopped?
Almost all life on Earth is dependent - directly or indirectly - on the energy provided by the Sun. If it were to cease, all animal and plant life would eventually die off due to a lack of food. As far as we know, the only life that would survive are bacteria that thrive on volcanic vents deep in the ocean, which obtain energy from various minerals produced by the vent.
Why are most anaerobes small?
Anaerobic processes are much less efficient at producing ATP than are aerobic processes, so the cells get less energy from the same amount of material. In order for this energy to be sufficient, the organisms are small.
Why would you expect that growing (green) plants in green light would result in less growth than in white light?
Chlorophyl reflects green light, thus growing plants under green light would not provide the plant with enough energy, as the green light would be reflected
Why do almost all plants contain chlorophyll a?
Chlorophyll a is the molecule in the reaction center of the photosystem. It is the molecule which can actually participate in the generation of ATP and NADPH. Because of this, even when auxiliiary pigments are present, chlorophyll a is still (generally) required.
"Oxygen tends to react with any atom less electronegative than itself. Because only one element, flourine, is more electronegative than oxygen, oxygen "reacts" with almost everything." If flourine is more electronegative, why don't we use flourine instead of oxygen in our bodies?
Flourine is not nearly as abundant as oxygen is in the earth's crust. Evolution favored oxygen because there was so much more oxygen. HF is hydroflouric acid, a very caustic substance that would be detrimental to our livelihood...
Evaluate the impact that a viable artificial photosynthesis system would have on some aspect of human life: for example, the fuel industry.
If humans could engineer an artificial photosynthesis system, they could produce fuel and energy from sunlight, the source of the vast majority of life on Earth's energy. If we could harness photosynthesis for energy, we would not have to rely in coal or fossil fuels or the planet's other scarce resources for fuel.
What would happen to animals if plants ceased to exist? What would happen to plants if animals ceased to exist?
If plants ceased to exist, animals would die without the oxygen and organic molecules plants create. If animals ceased to exist, it would have less effect on plants because plants produce their own CO2.
Why is ATP ideally suited to be the primary energy-carrying molecule for life on Earth?
It is made of elements that are abundant in organic systems, it is highly efficient, and it exists in chemical equilibrium such that it can be recycled repeatedly after use.
Explain the purpose of pigments in the light-harvesting center under excessively high lighting conditions.
Some pigments, specifically carotenoids, can continue to capture light energy. However, instead of passing it along to the site of photosynthetic reactions (which in this case could be catastrophic), it can dissipate the energy more safely as heat.
Jean Baptista van Helmont had a 5-pound tree in 200 pounds of dried earth, watered the tree over five years, and ended up with a 169 pound tree in 200 pounds of earth. He, then, concluded that the whole tree had grown from water alone. Obviously, we know this isn't true. Where did he go wrong?
The tree could have absorbed nutrients from the earth to help its growth, and some of the water may have seeped into the Earth to replace that lost mass.
What are some ways a plant can reflect that is being exposed to quality light?
Their pigments absorb more strongly so the plants should be brighter in color and produce more oxygen in good light.
Based on what we know about energy transfer across trophic levels, how do you think vegetarians are at an advantage?
Vegetarians consume foods that gain energy directly from the sun. Vegetarians can gain the same amount of energy from 1 buschel of corn as meat eaters can from a cow that had to eat 10 buschels of corn to produce that same amount of energy. Vegetarians have up to 10x more efficient energy consumption than meat eaters.
Why do warm-blooded animals have to eat much more often than cold-blooded animals?
Warm blooded animals use more energy to regular their body temperature so they have to feed more often to produce more ATP.
Why might oxygen's role be filled by sulfate, nirite, or sulfur?
These molecules are also electron acceptors, and can be used as oxidizers with lesser efficiency than oxygen.
Why are tertiary consumers typically the highest level of consumers in a food chain?
This is because about 90% of the energy is lost at each trophic level. Tertiary consumers are at the fourth trophic level away from when solar energy from the sun is convrted to chemical energy. This means tertiary consumers receive a tiny fraction of the energy originally given by the sun. It is not feasible for an ecosystem to sustain populations of consumers above the tertiary level.
What is the most common source of energy used in cellular respiration?
Though many compounds can be utilized for this process, the most commonly used is glucose.
Comparing the Earth currently and a couple hundred million years ago, we can see that the CO2 content in the atmosphere is much less than it was before. What could this suggest as a possible solution for global warming?
Well, a couple hundred million years ago, photosynthesis came about. If we plant billions of plants to eat the CO2, that could help rid the CO2 in the atmosphere.
What makes it difficult to sustain high intensity activity for a long period of time?
When muscles are being worked, they use up oxygen which is necessary for oxidative phosphorylation to form ATP. When oxygen is depleted, the mitochondria use fermentation which creates lactic acid. This lactic acid builds up and makes muscles sore.Fermentation is only about 7% as effective as aerobic respiration, however, so humans cannot sustain it for a long period of time.
Describe the potential positive results of cyclic electron flow and short circuiting of theelectron transport chain.
"Cyclic electron flow is probably a relic of evolution and it has merely remained as a result of the past. The potential positive coming out of the electron transport chain short circuiting is that plants could use it as a way to protect themselves when there is too much light. "
(1) Explain the process of polymerase chain reaction (PCR) and (2) its signifiance to modern biology.
(1) PCR is a process used to generate large numbers of copies of a certain desired gene sequence. To perform PCR, a solution containing a DNA sample, DNA primers, DNA polymerase, and the four base pairs (A, C, T, and G) is prepared. The solution is then placed in a thermocycler which alternatively warms and cools the solution. The first warming cycle denatures (unzips) the DNA double helix into two individual strands. The subsequent cooling cycle causes the primers to bind to their target sites on the two strands of DNA. The next warming cycle causes the DNA polymerase to complete the two DNA strands demarcated by the primers and generate twp complementary DNA strands. The DNA then denatures again, and the process repeats. (2) PCR is invaluable to the modern study of biology, as it allows biologists and scientists to study DNA and genes in ways that were impossible before its invention. Studying a single sample of DNA is very difficult, as the sample is very small and therefore prone to error in sampling. PCR makes the sample size arbitrarily large such that the sample can be studied with more greater ease and accuracy. It has numerous practical applications, such as in forensic DNA testing.
When might a human use anaerobic respiration to produce ATP?
A human might produce ATP largely from anareobic respiration when sprinting, i,e when the body does not have enough oxygen in the bloodstream
Why is ADP more stable than ATP?
ATP has three phosphate groups bonded to each other, and phosphate groups have negative charge. This results in significant electrostatic repulsion, which is lessened when one phosphate group is removed.
Many energy-storing molecules exist, including ones with higher energy than ATP. Explain one possible reason why ATP has evolved to be the primary energy transfer molecule of the cell.
ATP hydrolysis is an exergonic, energy releasing process, giving it the ability to power numerous reactions within cells. Evolution has selected ATP to be the primary energy storage molecule in life simply for the sake of efficiency - if only one molecule is needed, it isn't necessary to store a bunch of different types of energy. Furthermore, most of the processes in the cell have evolved to use exactly the amount of energy released by the ATP they consume and extra energy from a molecule with more stored energy would simply be wasted.
A biochemist explains that the reason ATP is an excellent molecule for transporting and storing chemical energy is due to its phosphate bonds. He claims that the bonds' instability makes the hydrolysis reaction proceed unaided in normal cellular conditions with extremely little activation energy this means that it is very easy for the cell to 'access' this stored energy. Is his logic correct? [Hint: No] Where is the flaw in his argument?
ATP is rather stable at normal cellular conditions (pH~7), the activation energy for the hydrolysis reaction is relatively high. It is only in the presence of an enzyme that the activation energy becomes low enough for the reaction to proceed. It is important that it works this way. If the hydrolysis reaction proceeded unaided in normal cellular conditions, energy could not be stored. It would be released uncontrollably in a manner that may or may not be particularly compatible with the continuation of life.
Why would harvesting too much light be detrimental to a plant? How would plants adjust to the increase of light?
Abrupt change in light can cause the reaction centers to be overwhelemed due to the great increase in energy, which can then damage the photosynthetic machinery. Plants can adapt by turning a relective white, or migrate their chloroplasts to locations of less light.
Describe how acetylation increases transcription frequency in eukaryotic cells.
Acetylation reduces the charge of the histones which the DNA is wrapped around, causing them to pull less strongly on the aforementioned DNA. This produces space around the DNA which allows the transcription enzymes to latch on and create mRNA.
Explain why are aerobic processes more widely in larger organisms than anaerobic processes.
Aerobic processes are more efficient. They generate more output (ATP) for the same amount of input (generally glucose). For example, an anaerobic process such as fermentation does not break down glucose as fully as aerobic respiration, leaving much of the stored energy from the input glucose in the end products.
Explain how fermentation is used in either the process of making wine or cheese?
Alcohol fermentation and lactic acid fermentation are both rpocesses of fermentation that break down sugars but create different byproducts. Alcohol fermentation is a two-step rpocess in which yeast break down the sugars of the grape juice into ethanol and carbon dioxide gas. Lactic acid fermentation breaks down the sugars in the milk.
How might alternative RNA splicing cause eukaryotes to be able to produce more types of proteins than eukaryotes?
Alternative RNA splicing allows eukaryotic cells to produce multiple proteins from the same mRNA transcript. Since certain segments can be either introns or exons, the expression of one gene can result in multiple proteins. Prokaryotes do not use alternative RNA splicing only one protein corresponds to each mRNA sequence. As a result, alternative RNA splicing allows eukaryotes to have a greater diversity of proteins.
Why is ATP used as our "energy currency" as opposed to other molecules which provide more energy?
Although other molecules provide more energy, they would only be able to drive half the reactions ATP drives. This is because the extra energy in reactions that don't need all of the energy provided by ATP or other molecules is dissipated as heat. Most reactions in our cells don't need more energy than ATP provides. It is more efficient to use ATP than a more energy rich molecule.
Describe the difference between anabolic and catabolic reactions.
Anabolic reactions consume energy to synthesize complicated molecules such as amino acids. Catabolic reactions are different because they are reactions that break things down and release energy. Anabolic reactions would not work without the catabolic reactions that power them.
Using the first law of thermodynamics, explain why anabolic reactions (polysaccharide synthesis, for example) require energy coupling.
Anabolic reactions result in an increase in potential energy. Energy must be expended to facilitate this reaction (as the total energy within a closed system must remain constant, according to the 1st law of thermodynamics). Energy-coupled reactions allow an exergonic reaction (such as the conversion of ATP to ADP) to drive an endergonic reaction. This would allow the anabolic reaction ot take place.
Why did the discovery of ncRNA change research of the human genome?
Before the discovery of ncRNA, scientists were primarily focused on the DNA which coded for proteins. After the discovery that ncRNA affects the transcription/translation process, the research project expanded to include studying all of the DNA.
Compare and contrast repressible operons and inducible operons.
Both repressible and inducible operons are methods for controlling gene expression. However, repressible operons prevent gene expression in the presence of an allosteric inhibitor, and inducible operons prevent gene expression in the absence of an allosteric inhibitor.
Why is cellular respiration better than just burning glucose in the presence of oxygen?
Burning glucose generates heat which is not particularly useful or easy for the cell to capture as energy. Furthermore, so much energy would be released so fast that the cell would burn up.
Why are there so many steps in the citric acid cycle of cellular respiration (in terms of energy production)?
By passing the stored energy of highly electronegative molecules to less electronegative molecules in a sequence of several steps, the cycle is able to have a controlled release of the energy stored. If it was all released at once, less of the energy would be stored in ATP and there would be a lot of waste in the form of heat and light.
With what we know about biological energy production, how do you think this might impact future technologies?
By studying the way bacteria and even humans create energy, we can harness that energy for our future technologies! http://www.scientificamerican.com/article.cfm?id=bacteria-eating-viruses-may-power-cell-phones
How do carotenoids protect plants from too much light?
Carotenoids absorb the energy from the light but then dissipate this energy as heat instead of passing the energy to the reaction center. This can occur through transformations of the carotenoids to slightly different molecules, and this response is quick.
What does the plant do if exposed to too much light?
Cartenoids absorb the excessive light but don't funnel it to chlorophyll and dissipate it instead as heat. This is called quenching. These also exist in our eyes and skin to protect us from overexposure to light.
Compare anabolic and catabolic processes and explain how they are related.
Catabolic processes break down molecules while anabolic processes build them. The energy and materials from catabolic processes can be used in anabolic processes.
Explain the difference between catabolic and exergonic reactions.
Catabolic reactions refer to wheter the reaction breaks down molecules, while exergonic reactions refer to whether the reaction relases energy.
What is the importance of cellular respiration?
Cellular respiration is pretty much the most important process in your body. While people tend to think that eating things and photosynthesis creastes all the energy we need, cellular respiration is the process by which we actually release the energy from these food sources, thereby transforming it to movement and kinetic energy.
Explain how and why cofactors assist enzymes.
Cofactors are chemicals such as zinc and iron ions that help enzymes catalyzing reactions by expediting electron transfer. They help transfer chemical groups between molecules to transform the subtrates. If the enzymes had to work without cofactors, catalysis would be slower.
Evaluate the advantages and disadvantages of storing an entire genome onto plasmids instead of creating a cDNA library from mRNA templates.
Copying the entire genome into a plasmid library is more complete than a cDNA library, which contains only copies of exons from the mRNA templates. Not all introns are non-coding, so if researchers wanted to study these functions they would need the entire genome. However, for common purposes of expressing eukaryotic genes, a cDNA library is more efficient.
Why do scientists go through the trouble of reverse transcriptase to make cDNA from mRNA?
DNA is a much more stable molecule than RNA. If someone wants to perform an experiment on a genetic sample, then they run the risk of the sample breaking down if they use RNA. With DNA, this is much less likely.
A researcher argues that, in the case of insulin production as mentioned in the text, checking for the expression of the lac-Z gene (blue vs. white colonies) is unnecessary. He says that because the target plasmid already contains the antibiotic gene, simply growing the bacteria in an antibiotic medium will differentiate between successful (insulin-producing) and unsuccessful (no added insulin gene) bacteria. Do you agree or disagree with his reasoning?
Disagree. The antibiotic medium differentiates only between cells which contain the target plasmid. Of those that survive, the lac-Z test is required to differentiate between bacteria in which the insulin gene has been successfully inserted into the target plasmid and bacteria which contain the target plasmid but for which the insulin gene insertion has failed.
Describe what the template strand is and its purpose during transcription.
During transcription, DNA is transcribed into RNA and the transcription unit is the unit of DNA that undergoes transcription. Within in this DNA unit, the template strand is the DNA strand that is actually transcribed.
How does the electron transport chain prevent releasing all of the energy from NADH and FADH2 at once?
Each carrier molecule of the electron transport chain is more electronegative than the one preceding it therefore, by the end of the chain, the electrons reach a more stable state, allowing a controlled and gradual release of energy.
Explain the importance of sequentially increasing electronegativities in the electron transport chain.
Each step in the process will attract electrons slightly more than the previous step. This allows the reaction to proceed while only releasing small amounts of energy each time.
How is the proton gradient used for chemiosmosis produced?
Electrons from electron carriers are passed down the electron transport chain. Each time the electron is passed down, it is passed to a more electronegative carrier, so there is a release of energy. This energy is used to pump a proton across the matrix membrane, creating a proton gradient.
How might the environment affect gene expression?
Environmental factors, such as light may activate specific transcription factors that differ under different light conditions. An example is a butterfly that developed dusky wings as opposed to intensely colored wings when placed under green light as a caterpillar.
What distinguishes enzymes from ribozymes?
Enzymes are composed of protein, whereas ribozymes are made of RNA.
How may enzymes lower activation energy?
Enzymes can bind to substrates so that they meet in the correct orientation. They can put stress onto a substrate so that chemical bonds are more likely to break.They can provide the proper environment for the reation, such as creating a different pH or hydrophicility. Also, they can remove parts of a substrate, such as electrons.
How do enzymes lower the activtion energy required for reactions?
Enzymes lower the activation energy of reactions by properly aligning and applying forces/torque to substrates, or by adding pieces directly to the substrate
How does epigenetic inheritance compare to genetic inheritance?
Epigenetic inheritance is inheriting phenotypic expression through means other than genes in DNA. This typically occurs through inheritance of epigenetic tags, such as methylation of DNA and methylation and acetylation of histones.
What is epigenetic inheritance and how could it cause inheritable health defects?
Epigenetic inheritance is when DNA methylation is used to transcriptionally inactivate DNA. The methylation pattern is preserved during DNA replication and can be passed through the gametes to the next generation. If by accident a gene was "turned off", this could be passed on to other cells and offspring, which could cause health defects.
Explain how epigenetcs work
Epigenetics is the study of heritable changes in phenotype that occur without affecting the underlying genotype. Often this happens as Histones and Methyl groups bind to DNA. Epigenetics is passed down to offspring for several generations.
Explain the difference between Heterochromatin and Euchromatin. What might change the state of chromatin
Euchromatin is lightly packed and is undergoing active gene transcription. Heterochromatin is more densely packed and contains dna that is being actively inhibited or suppressed. Chromatin state changes due to cellular signals or gene activity, enabling or suppressing dna in a region-specific manner
Explain the importance of electron transport chains in photosynthesis
Explain the importance of electron transport chains in photosynthesis
Given the differences between aerobic and anaerobic processes, why might facultative anaerobes prefer aerobic respiration?
Facultative anaerobes will prefer aerobic respiration (even though they have the ability to perform both aerobic and anaerobic processes) because aerobic respiration produces more ATP per molecule of glucose.
Why do you think farmers may prefer using cloning techniques rather than traditional growing techniques?
Farmers can make clones from the plants that did the best in a season and replicate the results since the cloned plants are exactly the same.
Why are fatty acids better sources of fuel than carbohydrates?
Fats provide more energy per gram than carbohydrates because of the the high potential energy in the bonds of their structures.
Are fevers good or bad? What different impacts can it have on enzymes?
Fever can help by increasing reaction rates of the body's defenses and could denature proteins in bacterial pathogens, but fever could also denature enzyems in our body if the temperature is increased over a long time.
How do fevers help combat illness?
Fevers serve two main rolls in fighting illness from pathogens. The first is that the increased environmental heat helps denature the proteins in the pathogen, killing it. The second is that it increases the enzymatic rate of your immune system from the increased kinetic energy, making your immune system more effective in fighting the pathogen.
Why is G3P considered the most useful product of photosynthesis?
G3P can be used to easily construct many carbo-macromolecules that plants need, such as cellulose, starch, or glucose.
What is the difference between genetic inheritance and epigenetic inheritance?
Genetic inheritance is the inheritance of genetic material from parents to offspring. Epigenetic inheritance is inheritance of factors other than genetic material. Epigenetic inheritance is less well understood than genetic inheritance.
The breakdown of glucose is a nontrivial cellular process. How can cells complete this reaction while still gaining energy?
Glucose breakdown is an exergonic reaction which means that there is more energy in the reactants than the products. Because of the first law of thermodynamics, energy must be given off during the reaction which fuels the cell.
During PCR, why is it necessary for each step to be carried out in different temperatures?
Heat provides the necessary energies to provide different processes. The processes require some kind of activation energy for the reactions to carry out.
How does histone methylation impact transcription?
Histone methylation increases the affinity of histones for DNA, so the histones bind tightly to the DNA, preventing transcription.
What is the effect of histones on transcription?
Histones are naturally attractive to DNA. Thus their charge determines if the DNA is tightly coiled (and thus not available for transcription) or loose, allowing it to be transcribed.
Explain how histones affect gene regulation.
Histones are proteins around which DNA can be wrapped. Without histones, DNA segments would be extremely long and unwieldy to duplicate.
What are the two major factors in epigenetic inheritance, and how do they affect genes?
Histones wrap up DNA, making it inaccessable. Methyl groups bond to CpG groups, inactivating promoters and turning off genes.
Despite the high rate of expression of housekeeping genes, why would it be a bad idea for a scientist to use one of their promoters as an expression vector?
Housekeeping genes produce proteins necessary for the cell to survive. A cell with a housekeeping gene interrupted by a replication fragment would probably die before yielding much protein.
Why is photosynthesis necessary for human life?
Humans need to get energy by eating organic compounds (plants and other animals). Even the animals that we eat first had to eat plants. If there were no plant matter, humans would not be able to get the organic compounds necessary to live. Plants are able to synthesize those compounds from inorganic compounds using photosynthesis.
In general, what is the energy transfer during ATP hydrolysis and ATP synthesis?
Hydrolysis of ATP provides energy to drive endergonic reactions in the cell and ATP synthesis relies on the energy provided by digestion. Hydrolysis releases energy and synthesis absorbs energy.
Do you agree with using DNA technology to modify our food? Why?
I think it can be dangerous to genetically modify our foods. My biggest concern is that we destroy genetic diversity in crops. Imagine we breed the perfect strain of corn and then continue to promote the growth of that type of corn (which actually happens). If an organism comes along that destorys that corn, we'll have no corn at all left. By destroying the diversity, we made it easy for the organism to kill all of the corn, instead of what would have been just a fraction of the corn population had we not artificially selected for it.
Do you think DNA cloning is an evolutionary step forward or backward? Why?
I think it would be a step backward. By specifically producing/cloning one DNA sequence, "nature" has gone astray. Natural selection isn't occuring because humans are interfering with the natural populations, so it would be a bad move for evolution.
How would you feel about doctors having access to every patient's genome sequence? Why might someone disagree with your point of view?
I think it would be very useful for doctors to know a patient's genome sequence, and I would allow my doctor to have access to mine. It would allow them to attack problems that would arise in the future and potentially save a lot more lives. Some people are against this, however. Some people don't want to know "what's in store" for them and would rather live unencumbered by the knowledge that they will, for example, have Huntington's disease. People also worry that if genome sequences become available, they will be discriminated against by insurance companies.
How would a base pair deletion affect the functionality of an enzyme?
If a base pair is deleted in a section of DNA that codes for an enzyme, every codon will be shifted one base pair over. That means that all of the following codons are wrong. If this happens at the wrong place in the DNA, the enzyme could fold differently enough that its overall structure or active site would be useless.
In the perspective of enzymes, why can certain cells only live within certain temperature ranges?
If the cells live in the wrong temperature, enyzmes may not work properly and metabolism cannot occur properly or fast enough.
In the production of recombiant DNA, why is it bad if the restriction enzyme leaves behind a blunt end?
If the restriction enzyme leaves blunt ends on either the target DNA sequence or the host plasmid, the two will not be able to easily attach together to form the recombiant DNA plasmid.
In terms of energy distribution, why is there not usually a consumer in the food chain higher than tertiary?
If the transfer of energy through the food chain is examined it becomes clear that the exponential loss of energy after each level in the food chain makes it unsustainable to have higher consumers than tertiary. In most cases there aren't higher consumers than tertiary consumers.
Why are restriction enzymes so important in gel electrophoresis? What might happen if the wrong enzymes were used?
If the wrong restriction enzymes are used, the DNA will be cut in the wrong places. As a result, the banding patterns will be off and the results may not be useful.
The product created by a mutated enzyme is causing a serious illness. What is one way the symptoms might be minimized?
If we could use or create a product that would bind to that enzyme's active site, it would be able to bind less of its normal substrate and therefore create less harmful product.
Explain how catalysts lower the energy necessary to start a reaction but do not change the net energy input of the reaction.
In many chemical reactions, the energy of the reactants moves up in energy before moving back down again. This is similar to how if you cross a mountain range, you will move up in elevation (and potential energy) before going down to the other side. If the other side is at a different elevation than your starting point, net energy was still put in to get there. Catalysts do not change the elevation of either the start or end points - instead they simply lower the height of the mountain in between. As such, the energy needed to start the reaction lowers while the net energy of the reaction does not change.
How can DNA technology help solve crimes?
Investigators can use small amounts of DNA found at crime scenes to identify criminals using short tandem repeats. Short tandem repeats are short base sequences that repeat a different number of times in each individual. PCR and gel electrophoresis are used to visualize the number of each specific STR an individual has. The DNA profiles of the suspects and evidence are compared to see if they were at the crime scene.
Why do organisms like reptiles have many isozymes while humans have fewer?
Isozymes are different enzymes that work at different temperature but catalyze the same reaction. Reptile body temperature changes more than human's so they need more isozymes.
Why is it less important for human bodies to contain isozymes than it is for reptile bodies?
Isozymes are seperate enzymes for catalyzing the same reaction, but at different temperatures. Human bodies stay at a relatively constant temperature, whereas reptile bodies fluctuate through wide ranges of temperature depending upon the environment. Therefore, human bodies will rarely encounter problems with enzyme functionality due to temperature change, but reptile bodies often will. Isozymes are therefore required as a defence against such temperature-induced problems.
What is the importance of differentiation for multicellular organisms?
It allows for complex organisms to happen. For example, babies start as unicellular zygotes. However, through differntiation, specialized cells form which become the nervous system or muscular systems. Differentiation is necessary in order to have cells which have specialized purposes.
What is the benefit of having a large numnber of different pigments in the light-harvesting complex?
It allows the photosynthetic process smooth and continuous and absorb as many wavelenghts as possible. If light suddenly gets shaded, the photosynthesis will have minimum disruption.
If a gene is successfully inserted into a plasmid but fails to be expressed, what might have happened? How would you tell if it's being expressed?
It is possible that the gene was not inserted in an expression vector and lacked a promoter to express it. Running tests such as GFP reporting, RT-PCR, or in situ hybridization can check if the gene is being expressed or not.
Provide real life application examples and their distinguishing features for both types of fermentation.
Lactic acid fermentation: for baking purposes. Alcoholic fermentation: for brewing purposes. The main difference is that the initial 2 pyruvates generated are converted into 2 lactic acid molecules for the former, and 2 ethanol molecules for the latter.
Describe how Mendel was able to infer changes in genotype through observing phenotype.
Mendel bred pea plants over several generations, carefully recording which combinations of plants produced certain results. Eventually, he observed a pattern of heredity that he attributed to certain biological factors. These factors are what we now know as genes.
Explain why muscles burn under intense exercise.
Muscles burn from generating lactic acid during lactic acid fermentation. This occurs when the body can't produce enough ATPs to generate power for the exercise i.e. not enough oxygen is inputted. The result is that the body generates lactic acid as its final product, which causes a burning sensation.
How would you determine what part of a protein production process was going wrong?
Often during the production process, there are intermediate proteins involved in making the final protein. If a final protein is necessary for survival, organisms with a mutation that affects an intermediate protein will die. You can determine which intermediate protein is mutated by adding and removing those proteins in the medium and seeing if the organism survives.
What are some of the dangers of gene therapy using retroviruses to introduce normal DNA in people with gene related disease?
One danger is that the insertion of a new gene may cause the expression of an old previously inactive gene, which can sometimes cause cancer and other disease.
Why is ATP used as our energy molecule instead of other molecules that can provide more?
One of the biggest reasons is that ATP generates the efficient amount of energy - the amount of energy that takes care of most of the bodies needs. Also, smaller energy is more versatile in that it can simply add together to get larger amounts of energy whereas, other molecules may generate too much energy and the superflous will be loss as heat. Also, ATP can be recycle through ADP by the body, which makes it very efficient and versatile
What are the ethical dilemas with gene expression studies concerning humans?
One of the common methods of gene expression studies is to disrupt a gene and observe the consequences. This has highly questionable ethics if done to humans, because the gene disruption is potentially very damaging. Sometimes this can be avoided by finding similar genes in other organisms and observing the disruption of the gene (although this is perhaps just as unethical depending on the organism). A solution to this is to obserce correlation between genotype and phenotype across a wide population and extrapolate conclusions from that. This avoids the ethical problems of manipulating genetic material for ill effects while still gathering data on the effects of genes, although the data is much more noisy.
You load an electrophoresis tray with DNA. You know the DNA sequences in Lane 1 are larger than the sequences in Lane 2, but the results show that there are two bands in Lane 1, one that moved less than Lane 2 and one that moved far more than Lane 2. Explain a possible reason why this occured.
One possible reason is that sometimes if the restriction enzymes do not fully snip up a DNA sample, the plasmid will remain intact in a super-coiled form, which moves faster through the gel than linearized DNA.
Some people argue that being vegetarian is beneficial to the environment because it is more energy efficient (for the environment, not the individual) to eat plants rather than meat. What is the basis for this argument?
Only 10-25% of energy is passed to on each level of the food chain. Animals are 1-2 times higher than plants, so it requires a significantly higher amount of overall energy for humans to get the same amount of energy from meat as they would from a plant.
What properties of oxygen make it a good electron "collector" in the electron transport chain?
Oxygen is a good electron acceptor because it is highly electronegative and readily available. If oxygen is not present, anaerobic organisms will use other compounds as electron acceptors, but using oxygen makes the electron transport chain more efficient in producing ATP.
Explain oxygen's chemical role in the rise of life on Earth.
Oxygen was likely created as a waste product by early autotrophs. It tends to react with any element or compound less electronegative than itself, which in the case of Earth, meant that it reacted with almost everything. The growing supply of oxygen on Earth gave rise to opportunistic aerobic bacteria that over time developed into almost all the non-plant life on Earth.
Why might PCR be useful in forensics?
PCR is useful in forensices for amplifying DNA found at crime scenes, however it will amplify any and all DNA found.
Why is photosynthesis much like cellular respiration in reverse?
Photosynthesis gains its electromembrane gradient through the energy from the sun and uses that energy to create macromolecules. Cellular respiration takes macromolecules and break them down to create its electromembrane gradient and then energy.
What is so unique about the relative energy levels of the reactants and products of photosynthesis?
Photosynthesis is the only known process that can take low-energy carbon and convert it into high-energy carbohydrates. Typically, organisms can only break down substances to lower-energy forms.
Explain how photosynthesis is linked to the evolution of aerobic respiration.
Plants decompose water in order to gain hydrogen ions and low-energy electrons. This porduces oxygen as a byproduct. Organisms evolved aerobic respiration in order to survive in the high-oxygen environment created by early autotrophs' photosynthesizing.
What differences might you expect between a plant from a low light environment and a plant from a high light environment?
Plants in low light environments typically try to make the most efficient use of the light that they receive. They likely have a balance of chlorophyls to make optimum use of the spectrum. Plants in high light environments may have problems with excessive light and could have adaptations to limit the light intake. Examples of this are physical adaptations such as the use of caretenoids as inhibitors, exterior coatings on the plant to block incoming light, and orienting leaves to reduce the effective surface area of light intake.
Describe ways in which plants are able to protect themselves from too much light.
Plants protect themselves from too much light by carrying out multiple actions. Some plants curl their leaves edges and some plants can turn turn white to reflect the light. Caretenoids also play a large role in protecting plants from too much light by carrying out the process of quenching and dissapating light through heat.
Why do plants not require animals in order to survive?
Plants use aerobic aspiration in addition to photosynthesis and can therefore recycle their own carbon dioxide.
What is the difference between positive and negative gene regulation by proteins?
Positive gene regulation involves a protein binding to the DNA and increasing the likelihood of transcription, whereas in negative gene regulation, a protein binds to the DNA to inhibit or lower the likelihood of transcription.
What is one reason restriction fragments are inserted into plasmids as opposed to direclty into bacterial nucleoli?
Possible reasons include not disrupting any genes the bacterium needs to function and because plasmids are transferred easily between bacteria.
How does prokaryotic and eukaryotic RNA polymerase differ?
Prokaryotes only use one type of RNA polymerase during transcription. This differs from eukaryotes, which use multiple types of RNA polymerase to transcribe DNA.
Explain how the fact that eukaryotic cells are compartmentalized and prokaryotic cells are not affects the cells' capacity for gene regulation.
Prokaryotic DNA is transcribed and translated in the same area of the cell, so gene regulation takes place when the DNA operators or promoters are repressed or activated. In eukaryotes, genes can be regulated at several different stages in the process of gene expression. For example, transcription can be regulated by histone proteins changing charge, and translation can be blocked by miRNA binding with the mRNA.
Do you think that the color of the light shown on the leaves of a plant could affect the plant's growth? Describe an experiment to test this idea, and give a justified answer.
Put several plants in dark boxes shut out from light under identitcal conditions. Light up different colored bulbs in each of the boxes for 12 hours to simulate daylight. Water equally every day. Measure growth in inches after each week (growth as determined by the height of the plant). Answer: The reason a white light works best is because chlorophyll absorbs red and the green light is reflected (which is why we see leaves as green). Not all light will treat the plant equally.blue light
What is the structural difference between dideoxynucleotide and deoxynucleotide, and why is dideoxynucleotide's main property especially useful?
Rather than having a hydroxyl group on the 3' carbon, dideoxynucleotide has a hydrogen group there. Dideoxynucleotide's ability to prevent any more nucleotides being added on is helpful because it can end PCR reactions.
What is one way to speed up an equilibrium reaction?
Remove products as they are created. This will keep the reaction always chasing a moving equilibrium point.
What are restriction enzymes naturally used for and why are they useful to scientists?
Restriction enzymes are used in bacteria to cut out foreign DNA sequences that have made their way into the plasmid. They are useful to scientists because they can cut open specific sites in plasmids so that a gene of interest can be pasted in. The bacteria will then be used to harvest more copies of the gene or the protein it makes.
How might riboswitches be used to combat bacterial infections in the future?
Riboswitches are responsible for regulating and controlling protein production in RNA. If an antibacterial agent could alter or replace a target bacteria's riboswitches, it could critically impair that bacteria's ability to generate protein and destroy it.
If human DNA is almost completely identical, how can criminal investigators use DNA to solve crimes?
STRs, or short tandem repeats, occur with varying frequencies in different individuals. Even though two people have the same gene, the STR pattern will be unique.
In Photosynthesis I, why is it important to have a wide variety of pigments?
Since each pigment is specific to a particular wavelength of light, having a diversity of pigment types allows the plant to gain energy from a variety of wavelengths. As a result, the plant will be able to capture more energy from light.
How do you know when a process of fermentation is complete?
Some of the ways to check the process of fermentationinclude measuring the pH or level of gas in the substance. Fermentation increases the acidity of the substance, so monitoring pH levels will show how far along the substance is fermented. Alcohol fermentation also releases carbon dioxide as a byproduct that can be measured to track fermentation.
What are some pros and cons of letting people access DNA testing without restrictions?
Some pros are that it may be cheaper and easier than getting testing through a doctor and knowing risk factors may help people make positive life changes. Some cons are that people may incorrectly interpret or make assumptions based on their results if they don't have a medical professional's guidance.
Humans breath oxygen, why would we need to use anaerobic respiration for energy?
Sometimes while we are working out very hard our muscles will use anaerobic respiration because we can't supply them oxygen fast enough to produce the energy they need. The process used is called lactic acid fermentation.
How is it adapative for stomata to be located on the underside of leaves?
Stomata are located there because if they were on the top, they would be in direct contact with sunlight, which would cause increased loss of water, even with closed guard cells.
How can the supercoiling of DNA regulate the expression of genes?
Supercoiling can render parts of the DNA physically inaccessible to transcription processes
Explain what supercoiling is and how this has caused confusing gel electrophoresous results.
Supercoiling is the process that occurs when large DNA molecules are wound up very tightly. Supercoiling can lead to confusing gel electropheresis results because these DNA molecules move through the gel faster than linear molecular strings, making them seem smaller than they actually are.
Describe supercoiling and explain why it is important in the sucess of life.
Supercoiling packs DNA nicely within a nucleus of a cell. Without supercoiling, DNA would not be able to fit within a cell and DNA duplication would be increasily difficult for the enzymes that do so.
Given what we know about enzyme structure, why is Taq polymerase used in PCR versus E.coli polymerase?
Taq polymerase comes from an organism that lives at high temperatures and therefore won't denature during PCR, unlike polymerase from other organisms.
What would happen if a restriction enzyme only needs to recognize one nucleotide in order to proceed cutting?
That restriction enzyme would cut DNA at any instance that it finds that nucleotide, resulting in a very dissolved DNA.
What is the purpose of the Calvin cycle
The Calvin cycle takes carbon from the air and turns it into sugar
Our muscles can survive without oxygen on anaerobic respiration for a good amount of time, nevertheless we cannot survive this long in the absence of oxygen. Why is this?
The brain requires a constant supply of ATP from aerobic cellular respiration and damages easily in absence of oxygen.
How would an average plant react to being placed in a room with only blue light? Red light? Green light?
The chlorophyl in an average plant absorbs red and blue light, and reflects green light. As such, in the red and blue rooms, the plant would be intaking slightly less light, but should still be able to survive. In the green room, the plant would be taking in very little energy and shouldn't survive.
Why is it so dangerous, from a cellular perspective, for the temperature of a human body to deviate by more than 20°F from equilbrium (approximately 98°F)?
The enzymes that maintain homeostasis in human cells have adapted to work optimally at human body temperature. The further human body temperature strays from this ideal temperature, the less effective the enzymes will be at catalyzing essential reactions in cells. If body temperature strays far enough from equilibrium, enzymes will no longer be able to maintain homeostasis and cells will begin to die.
What is the key difference between the lock and key model and the induced fit model?
The induced fit model calls for enzyme conformation to the subtrate while the lock and key model is more static and neither the subtrate nor the enzyme change shape.
How does the "induced fit" model differ from the "lock-and-key" model? Can you guess why this distinction is important for understanding enzyme function?
The lock-and-key model states that the active site of an enzyme does not change, and is specific the enzyme's substrate. The induced-fit model states that bonding between the enzyme and its substrate cause the enzyme to change the shape of its active site, resulting in a closer fit between the enzyme's active site and its substrate. In terms of understanding an enzyme's function, the induced-fit model accounts for the fact that an enzyme can accomodate both the substrate and its products (before they are released by the enzyme), whereas the lock-and-key model states that the shape of the active site remains unchanged. Since product(s) will differ in shape from the original substrate, the induced fit model explains how an enzyme can "hold on" to a substrate while the substrate is being modified -- the active site is always changing.
What is the main difference between prokaryotic and eukaryotic gene expression and why do think this difference exists?
The main difference is that eukaryotes have 3 different kinds of RNA polymerase while prokaryotes have only one. The reason for this is most likely that prokaryotes do not have membrane enclosed organelles or a nucleus.
If fermentation is so inneficient, why do cells still do it?
The major reason is due to exercising. In the absense of oxygen, normal cellular respiration can not occur. Therefore, the cells use fermentation to make more NAD+ which allows glycolosis to continually happen and produce more ATP. However, in place of pyruvate, lactic acid is produced (which causes that burning sensation in your muscles when you work out).
Describe the actual mechanism that makes riboswitches more valuable than their predecessors in such applications.
The mechanism that makes them great candidates for such drugs is the ability of their aptamer region to switch, depending on the existence of a ligand. By switching, a terminator stem-loop is created and transcription cannot occur. Thus in a less-magnified scope, riboswitches can shut down bacteria while maintaining that bacteria do not develop resistances. Bacteria are unable to do so, because this is a physical change that cannot be overridden by enzyme or cell wall mutations.
What factors must engineers and scientists keep in mind when designing a molecule to competitively inhibit the function of an enzyme?
The molecule designed to fit into the active site shouldn't neccesarilly be designed to fit like a key into a lock. Instead, the molecule can bend and twist in order to make the most efficient series of bonds with the enzyme in question.
Explain the relationship between catabolic and anabolic reactions.
The molecules broken down by catabolic reactions form products that are used to form other products via anabolic reactions.
What would happen to an organism that could not generate NAD+ or FAD?
The organism would not be able to process glucose, since NAD+ is necessary for glycolysis to occur. This would prevent it from producing ATP and cause it to die.
Explain the purpose of pigments in the light-harvesting center under normal lighting conditions.
The pigments are strictly and uniquely structured to pass light energy, using a process of excited electrons, towards the site of photosynthetic reactions with minimal light/heat dissipation.
For plants, certain wavelengths of light are more beneficial than others. How might plants grown in the presence of purple light differ from plants grown in the presence of green light?
The plants grown in the presence of purple light will grow larger, as they are able to capture more energy from their light source. The plants grown in the presence of green light will not grow as quickly.
A lot of food we eat are genetically modified to contain more vitamins. Once the desired target sequence that expresses the vitamin gene is inserted into the Ti plasmid, what are the two ways that the recombinat plasmid is inserted into the plant?
The plasmid could be inserted into plants cells, and the plant could grow from those reproducing cells. It could also be inserted into a specific type of bacteria, which is then used to infect plants, causing the plants to reproduce infected cells.
Why are dideoxynucleotides important?
The polymerase enzyme cannot add nucleotides to these bases, so they form a cap for the synthsized DNA. It is often fluorescently labelled.
Describe the product of PCR and explain the importance of temperature in this process. "
The process of PCR results in large quantities of copies of a specific gene sequence. Temperature plays a significant role in the process because each step in the PCR process occurs at a different temperature. Different temperatures facilitate different steps of the reaction. For example, denaturation happens at hot temperatures.
How does the desert kangaroo rat survive without drinking water?
The rat uses the water produced by respiration to survive. By eating, it is able to produce the water it needs.
How does the cell keep itself from being destroyed by the release of energy?
The reactions that release energy require an activation energy, which prevents them from happening all at once. Also, there is a many-step process to release all the energy present in glucose.
What is the importance of a start codon other than the fact that it shows RNA polymerase where to start coding?
The start codon is especially important because it sets the reading frame for the rest of the gene eg. if the frame were shifted one to the left or right, an entirely different polypeptide would be formed.
Decomposing results with an increase in entropy. Can you think of any biological event that results with a decrease in entropy? Describe this event and explain why (local) entropy would decrease.
Theoretically, the universal entropy never decreases, however the following are some examples of "iffy" decreases in entropy: Water Freezing, the moments just before the Big Bang, gasses cooling these would all mean a decrease in entropy because the system is either slowing or less particles are going crazy
Hidden stops are codons that are 1 spot shift away from being a stop codon. What do you think the purpose of these codons are?
They serve to stop translation earlier in case of a frameshift mutation.
Explain the interaction of transcription factors and operons in gene expression.
Transcription factors are proteins that bind with the operons on the DNA to alter the expression of the gene/s in the operon. The transcription factor can be a repressor, in that the binding of the protein to the operator inhibits RNA polymerase from binding to the promoter. The protein can also be an activator protein and the binding to the operator allows for the binding of RNA polymerase to the promoter
Even though humans are much larger than the organisms they feed on, they only absorb .01% of the sun's energy that the original producer created. Explain how they can maintain a larger physique while getting such a small amount of energy from the sun.
We must eat a lot more than the other organisms relative to our mass in order to sustain our energy consumption.
Why would scientists not change the genome and would rather send in "naked DNA?" (Hint: Think of the Bubble Boy)
When changing the genome, besides having moral questions, scientists found that sometimes altering the genome could cause bad side effects such as being near the gene which causes other diseases, such as leukemia.
When is yeast a better choice than bacteria for expressing a cloned gene?
When eukaryotic genes are transcribed, the resulting mRNA undergoes processing, and some sections, introns, may be cut out. Prokaryotes do not process mRNA, so if the introns could interfere with gene expression, then a eukaryotic cell needs to be used. Yeast is commonly used in this case.
Why might supercoiled DNA be a problem while trying to use the Sanger method to sequence DNA?
When supercoiled DNA goes through the electrophoresis process, it acts as a strand of DNA that is much smaller than it is. The Sanger method uses gel electrophoresis to determine the order of nucleotides based on the size of the DNA. As a result, supercoiled DNA would cause a piece of DNA to appear smaller than it is, which would cause errors when reading the order of nucleotides in the strand.
Describe a likely outcome of a bacterial cloning procedure performed in an antibacterial-free environment.
Without an antibiotic, replication of both the bacteria with and without the target plasmid will take place. Scientists will be largely unable to differentiate between desirable and undesirable bacteria. In the case of insulin (or similar) production, the yield will be less resources (nutrients, space, etc.) will be wasted growing unwanted bacteria.
What would happen if there were no energy storage molecules in an organism?
Without energy storage molecules, the reactions would tend towards equilibrium since all reactions are reversible. Also, endothermic reactions would not have an energy source for powering the reaction. This would lead to the organism not maintaining metabolism and simply equilibrating with the immediate environment.
Why do competitive inhibitors raise K_m without changing v_max?
v_max doesn't change because if the substrate concentration is high enough, the inhibitor's presence is insignificant. K_m is the substrate concentration necessary for the rate to reach v_max/2, and K_m rises because the substrate is competing with the inhibitor, so the substrate concentration needed to reach a certain reaction rate is higher than it would be without the inhibitor.
Give an example of how riboswitches can be potentially used for drug design.
we can make drugs that target the binding sites that are regulated by the riboswitches to repress transcription.