Differences between Prokaryotic and Eukaryotic Cells - Assignment Example

 1. Complete the following table to outline the structural differences between prokaryotic and eukaryotic cells. (12 marks) Property Prokaryotes Eukaryotes Nucleus Absent. The genetic material can be found in an area called the nucleoid. Present. Nucleus is one of the membrane organelles of a eukaryotic cell, and it specifically contains the cell’s genetic material and the proteins that allow replication and transcription of DNA. Cell size 0.5 - 5 µm in diameter 10 – 100 µm in diameter Internal membranes Absent The eukaryotic cell contains many membrane organelles. The double-membraned ones are the nucleus, mitochondria and chloroplasts (for phototrophic cells), while the others are lysosomes, vacuoles, etc. Cytoskeleton Strictly for proton-powered motility Either microtubules, microfilaments and intermediate filament, performing roles in reproduction, motility, and structure. Organization of DNA Not encapsulated by a membrane organelle. Usually organized in a single, circular bacterial chromosome. The replication mechanism is prone to mutations. Arranged in multiple chromosomes, which is contained within the nucleus. Corrective mechanisms are available to prevent the occurrence of mutations. Reproduction Binary fission, wherein the splitting of the cell into two follows immediately after DNA replication. Mitosis, which begins with cell preparation and DNA replication (prophase), followed by the migration of chromosomes in the middle of the cell (metaphase), continuing with distribution of chromosomes to two opposite sides of the cell (anaphase), and ending with cytosol and plasma membrane division (telophase). 2. Describe the basic composition of viruses. Are they considered to be living? Why/Why not? (3 marks) A virus particle is composed of nucleic acid, either double-stranded or single-stranded, with a surrounding protein coat and a possible membrane envelope. Because they cannot survive outside a cell it parasitizes, viruses are not considered living. 3. A girl who consumes cyanide dies immediately because ATP production ceases. This medical problem involves the improper functioning of an organelle. Which organelle is affected? Is it underactive or overactive? (2 marks) The mitochondrion, specifically its cytochrome oxidase, is affected in cyanide poisoning. Without this enzyme, the electron chain transport seizes, and ATP production does not occur. 4. Draw a diagram of a phospholipid bilayer that indicates its overall structure and that includes the structures of the three types of proteins that are found in membranes. Discuss the mobility of lipids and proteins in the membrane. (8 marks) The mobility of the membrane is dependent on the cholesterol also imbedded in the membrane. The presence of these molecules results to decreased interaction among phospholipids, and increased fluidity of the membrane. Temperature also affects membrane fluidity, such that higher temperatures cause fluidity of the membrane, while colder temperatures make the phospholipid bilayer less mobile. 1. Previous scientific evidence is a catalyst for new scientific discoveries. How did Hershey and Chase demonstrate that DNA is the genetic material of viruses following the statement by R.M. Herriott (1951) that “A virus may act like a little hypodermic needle full of transforming principles”? (10 marks) First experiment: a. They grew bacteriophages in vitro, using radiolabeled amino acids to stain the virus’ protein coat. b. These phages were allowed to infect the bacteria. The phages inject the DNA into the cell, leaving the radiolabeled coat outside the bacteria. c. The newly formed phages did not contain radioactivity Second experiment: a. They grew bacteriophages in vitro, using radiolabeled deoxyribonucleotides to stain the virus’ DNA. b. These phages were allowed to infect the bacteria. The phages inject the radiolabeled DNA into the cell, leaving coat outside the bacteria. c. The newly formed phages contain radioactivity 2. Complete the following table: (6 marks) Enzyme Function in DNA replication DNA polymerase III The enzyme that adds corresponding nucleotides (adenosine to thymine and guanine to cytosine, vice versa) onto the template strand in its 5’ to 3’ direction in order to make the daughter strand, attaching one nucleotide at a time to the latter’s 5’ end. Helicase The enzyme which untwists the double stranded DNA at the replication forks, making the two separated strands available as template strands. Primase The enzyme that produces the primer, an RNA chain which attaches onto the 3’ end of the template strand exposed by the replication bubble. Gyrase DNA polymerase I The enzyme that replaces the primer with its DNA counterpart once the DNA replication in the replication bubble is complete. Like DNA polymerase III, it adds nucleotides one by one to the 5’ end of the primer. DNA ligase The enzyme that attaches the Okazaki fragments together to form the lagging strand of DNA replication. 3. What is linkage? Do linked alleles normally assort independently? (3 marks) Linkage is the phenomenon in which genes located near each other on the same chromosome stay together even after genetic crosses. Such genes are thus referred to as linked genes. It is thus more likely for the parental phenotype of two linked genes to be inherited by the testcross of an F1 dihybrid. This means that linked alleles cannot assort independently from each other. 4. Outline the process of transcription. You may use a diagram to illustrate your description. With regards to RNA polymerase, how does transcription differ between prokaryotes and eukaryotes? (10 marks) Transcription is the process of synthesizing messenger RNA (mRNA) from template DNA. There are three stages of transcription. In the initiation phase, the RNA polymerase first binds to the promoter region of the DNA, and separates the strands of the double helix to put together RNA nucleotides complementary to the DNA template in a 5’ to 3’ fashion. In contrast to DNA polymerase, it can initiate RNA elongation without a primer. The RNA transcript is then released from the DNA template. 5. What three modifications does eukaryotic mRNA receive during processing? What is the name of the molecular complex that carries out splicing? (4 marks) In RNA processing, both the 5’ and 3’ ends of the pre-mRNA are altered. Particularly, the 5’ end receives a modified guanine nucleotide after addition of the first 20-40 nucleotides during RNA elongation. On the other hand, the 3’ end of the pre-mRNA is added with a polyadenylation signal, AAUAAA, and poly-A tail, which is a 50-250 long RNA chain of purely adenine nucleotides. In addition, certain interior sections of the RNA strand, called introns, are removed, and the remaining ones, referred to as exons, are spliced together. The spliceasome binds to certain sites along an intron to facilitate the latter’s release and degradation and the joining together of the two exons flanked by the removed intron. 6. For each of the following statements, indicate which of the following descriptions apply. Note: The descriptions may apply to more than one of these gene types. (7 marks) OG: oncogene PO: proto-oncogene TS: tumour-suppressor gene PO a. found in normal cells TS b. could code for a normal growth factor OG, PO c. found in cancer cells OG d. found only in cancer cells OG e. its presence can cause cancer TS f. its absence can cause cancer PO g. can be found in both normal cells and cancer cells 7. Tetracycline is an effective antibiotic because it inhibits protein synthesis. The action mechanism is binding the 30s ribosomal subunit in bacteria, thereby preventing the docking of amino-acylated tRNA. With your knowledge of the translation process, explain how tetracycline would prevent protein synthesis.(5 marks) If a drug acts by preventing the docking of the amino acid-transporting amino-acylated tRNA, proteins, which are important in all cellular processes, cannot be formed since there is no way by which amino acids can be delivered to initiate elongation of the polypeptide. Thus, without proteins, processes such as DNA replication and ATP production cannot push through, and the bacterial cells cannot prosper because cells cannot divide without new DNA and energy to power it. 8. Outline how proteins are targeted to the mitochondria and chloroplasts. Since mitochondria and chloroplasts contain their own DNA and protein-synthesis machinery, why must proteins be sorted to these organelles? (5 marks) Although mitochondria and chloroplasts contain their own genetic material and protein synthesis machinery, much of it is used in the production of rRNAs and tRNAs. Most of their proteins are thus produced in the cytosol. After which, they enter the organelles through these steps. 1. formation of the polypeptide with N-terminal matrix-targeting uptake sequence 2. the polypeptide is transported by mitochondrial import stimulating factor 2. the polypeptide binds with mitochondrial outer-membrane receptors through the uptake sequence 9. Outline all of the elements of the lac operon, and describe how the operon reacts to increases and decreases in lactose concentration. (10 marks) An operon is composed of the operator, the promoter, and the coding gene. The operator, situated within the promoter or between the promoter and the enzyme-coding region, regulates the binding of the RNA polymerase to the gene and the subsequent synthesis of corresponding mRNA. This binding is controlled by regulatory proteins, which either switches on or off the process. Regulatory proteins are encoded by genes located upstream to the promoter region of the gene it controls. The lac operon is an inducible operon that contains the gene for the lactose metabolizing B-galactosidase. This means that RNA polymerase binding to its operator is usually switched off. The lacI is the regulatory gene that codes for an allosteric repressor protein that can switch off B-galactosidase production by binding to the operator. The translation of the repressor protein is active by itself, and allolactose, the inducer, is needed to prevent the protein from binding to the operator of lac operon. 10. Discuss the role of alternative splicing as a mechanism of post-transcriptional control. How does alternative splicing contribute to diversity? What factors influence how splicing patterns are determined? (5 marks) Alternative RNA splicing is the mechanism by which a single gene can encode for more than one kind of polypeptide, depending on which segments are retained during RNA processing. Even if only a few DNA are encoded to proteins, the number of proteins is still greater than the genes. It also makes possible the existence of complex organisms even if it has similar DNA sequence as that of a less complex species. Factors such as the promoter structure, tissue-specific splicing factors, stress, protein expression levels, and phosphorylation can all influence the splicing patterns. 11. The drug colchicine was formerly used to treat gout. Now, other drugs with a similar function are being considered for the treatment of cancer. What cytoskeletal component do colchicines affect, and why would drugs that target this component be effective at treating cancer? (5 marks) Colchicine acts by disrupting microtubules. Denaturation of this cytoskeleton prevents the anaphase stage of mitosis, which depends on tubule formation. Without this cytoskeleton, mitosis cannot push through, and cells cannot divide. 12. Outline the process of muscle contraction. (10 marks) a. The myosin head binds with ATP, and thus detaches from the thin filament. b. When the ATP is hydrolysed to ADP and inorganic phosphate, the released energy allows binding of the myosin head with the thin filament, thus forming a cross-bridge. c. When the ADP and inorganic phosphate are released from the myosin, the head bends, sliding the thin filament towards the center of the sarcomere. Collectively, this sliding of thin filaments is observed as muscle contraction. 13. Read the following article and answer the questions below. This article can be found in the Scientific American Current Issues supplement included in your course package, or via the online journal databases in the AU Library. Nielsen, P. (2008). A new molecule of life? Scientific American, 299(6), 64-71. a. What is a PNA? Describe the chemical composition of a PNA. How does a PNA bind to DNA and RNA? (6 marks) The peptic nucleic acid is a synthetic hybrid of a stable polypeptide backbone (instead of a phosphate-sugar backbone) carrying a chain of nucleotides. The DNA or RNA strand of PNA binds to the specific nucleic acid sequence, in single-stranded or double-stranded state, to which it is complementary with. b. Considering the composition of a PNA, what advantages do these molecules have over antisense DNA and RNA molecules? (3 marks) PNA has the advantage of binding over both DNA and RNA, a stronger affinity to its target, and greater chemical stability. c. Outline in detail how a PNA regulates the expression of a gene. (5 marks) 1. In blocking the transcription phase, PNA can block to the gene sequence in single-strand form, preventing it to be transcribed. In addition, it can bind with the sequence at the double-strand form to expose the sequence to transcription enzymes. Likewise, PNA can prevent translation of an mRNA by binding to it before reaching the ribosomes. d. Give an example of how a PNA can be used to treat a medical condition. (3 marks) Many medical conditions have been associated with abnormally high or low amounts of a certain protein or enzyme. PNA can treat this condition by either initiating transcription in those with enzyme or hormone deficiencies, or preventing protein production in those with abnormally high levels of a protein. e. Explain how PNAs may be used to construct artificial life forms. (3 marks) A protocell has been proposed to be made from a PNA, esters and light-sensitive molecules enclosed in a self-assembling membrane. The light sensitive molecules derive from sunlight the energy to form more membrane from esters. Complementary PNA fragments can come from an external source, bind to the outer surface of the membrane, and migrate toward the protocell’s interior to form a new PNA strand. When the protocell is large enough, it divides into two. 5. For each of the following statements, indicate which of the following states applies. Note: Two of the statements have more than one correct answer. (5 marks) D: simple diffusion F: facilitated diffusion A: active transport N: none of the above F, A a. requires the presence of an integral membrane protein A b. involves proteins called ATPases D c. applies only to small, nonpolar solutes N d. applies only to ions D, F e. transport can occur in either direction across the membrane, depending on the prevailing concentration gradient 6. Describe how action potentials are propagated along a myelinated axon, and include a diagram to illustrate the mechanism. How does the process differ in unmyelinated axons? (10 marks) a. Action potential is generated by the inward flux on Na+ at one location (blue arrows). b. The depolarization spreads to the neighboring regions of the membrane, thus initiating the action potential. The spread of action potential is much faster in myelinated axons as it is in unmyelinated ones, because in the former, the sodium channels are restricted to gaps in the myelin sheath, referred to as nodes of Ranvier. 7. Hypertension, or high blood pressure, is often treated with compounds called beta-blockers, which block -adrenergic receptors throughout the body. Why do you think beta-blockers are effective in reducing blood pressure? (4 marks) In the sympathetic nervous system, catecholamines such as epinephrine are the neurotransmitters that bind to adrenergic receptors. Upon binding, a flight-or-fight response, which includes blood vessel constriction and increased heart rate, is initiated. Such changes result to an increase in blood pressure. Beta-blockers prevent the binding of catecholamines like epinephrine to beta-adrenergic receptors. If present, it prevents sympathetic response and increased blood pressure. 8. Distinguish among the following processes: exocytosis, receptor-mediated endocytosis, and phagocytosis. (6 marks) characteristics exocytosis Receptor-mediated endocytosis phagocytosis Intake or release of substances by the cell? Release intake Intake Where does the vesicle come from? Golgi apparatus Plasma membrane Plasma membrane What does it take in/release? Large molecules, such as proteins and polysaccharides cholesterol Cell What is produced after? Extracellular proteins and polysaccharides Coated vesicle Food vacuole 9. Outline the functions of the rough endoplasmic reticulum and the smooth endoplasmic reticulum. On which of the two are ribosomes present? (5 marks) smooth Rough ribosomes absent present function Lipid synthesis, carbohydrate metabolism, drug and poison detoxification, calcium ion storage Facilitates proper folding of secretory proteins, mostly glycoproteins, separates protein meant for excretion to those that will remain in the cytosol, membrane factory of the cell 10. Distinguish between glycolysis and gluconeogenesis. How are these two pathways coordinately regulated? How does the concentration of ATP affect each pathway? (5 marks) Glycolysis is the breakdown of 6-carbon glucose into a simple 3-carbon pyruvate, which further undergoes processing to extract energy from this molecule. In contrast, gluconeogenesis is the production of glucose. The concentration of ATP is significant in determining whether glucose catabolism or production will be conducted. Since ATP is the measure of energy in the cell, depleted ATP leads to its production through glycolysis and subsequent processes, while excess ATP results to gluconeogenesis 11. How is NAD+ regenerated through fermentation? (5 marks) In alcohol fermentation, NAD+ is regenerated by using the electrons in NADH to reduce acetaldehyde to ethanol. On the other hand, in lactic acid fermentation, pyruvate is reduced to lactic acid. 12. Define oxidative phosphorylation, and explain how the free energy of oxidation of NADH and FADH2 is used to synthesize ATP. (7 marks) Oxidative phosphorylation is a means of producing ATP from high-energy storage the mitochondrion can use to phosphorylate ADP to become ATP. The NADH and FADH2 are essential molecules as they pass the electrons from glucose to the electron transport chain. As the electrons are passed from enzyme to enzyme within the chain, protons are being pumped against the electrochemical gradient. The protons then pass through the ATP synthase to restore the resting potential of the membrane, 13. What are the light-dependent and light-independent reactions of photosynthesis? What is the function of chlorophyll, and what makes this pigment unique? (5 marks) Light-dependent Light-independent function Converts solar energy to ATP and NADPH Uses the energy from ATP and NADPH to reduce CO2 to sugar Reactions Electron flow Calvin cycle Chlorophyll is an important pigment that harvests solar energy from sunlight to power the conversion of CO2 to sugar. It absorbs colors, optimally violet-blue and red, except green. This is why plants are green in color. 14. What are the substrates and products of the Calvin cycle? (3 marks) The Calvin cycle uses the energy from ATP and NADPH to reduce CO2 to sugar. 15. Read the following article and answer the questions below. This article can be found in the Scientific American Current Issues supplement included in your course package, or via the online journal databases in the AU Library. Deretic, V., & Klionsky, D. (2008). How cells clean house. Scientific American, 298(5), 74–81. a. Define autophagy. What organelle carries out this function? (3 marks) Autophagy is the engulfment by autophagosome of bits of cytoplasm, bacteria and viruses for degradation and recycling. b. Describe a medical condition that results from the inability of cells to carry out autophagy. (3 marks) Chron’s disease is an inflammatory bowel disease that is caused by the increased microbial flora in the gut, which grows uncontrollably due to defective autophagy. c. Outline the process of autophagy in detail. You may use a diagram to illustrate what occurs. (8 marks) 1. Induction: many extraneous signals can stimulate autophagosome. 2. Nucleation: various cytoplasmic molecules merge to form a double-membraned phagophore 3. Expansion and Cargo Recognition: the phagophore then engulfs cytoplasmic contents 4. Protein recycling: the resulting autophagosome releases its membrane proteins for future use. 5. Fusion: the autophagosome fuses with lysosome 6. Digestion of the materials by autophagolysosome 7. The resulting building blocks are recycled. d. Give an example of an organism that can exploit autophagy for its own survival, and explain how this is accomplished. (3 marks) Legionella pneumophila is a bacterial species known to readily enter the cell. Upon autophagy of this bacterium, however, it prevents formation of autophagolysosome and degradation. Thus, it uses autophagosome as a haven of bacterial replication. e. Explain the possible link between autophagy and lifespan. (3 marks) Although mitosis goes as long as we live for cells such as the skin, it may not be the case in some cells, such as neurons. The only way such cell can prevent harmful materials from accumulating and causing its death is to tap autophagosomes to engulf these substances. Reference Reece, Jane, et al. Campbell Biology. 9th ed. San Francisco, CA: Pearson Benjamin Cummings. Read More