BEN/BIO/CEN/CHE/PHY 635 HW 2 Solutions 1) DNA vs. RNA (7 points). DNA and RNA use a similar building plan and some of the same building blocks. But there are also distinct chemical and structural differences. Using every source available to you (internet, library, grandmother etc. but ideally not fellow class members), try to answer the following questions: a. Please describe at least 3 major differences between the two molecules. (3 points) b. Consider a single strand of DNA with the nucleotide sequence GATACA. Considering the concept of complementary base pairing, what is the complimentary DNA strand (the strand that would bind/match perfectly with this piece of DNA)? (2 points) c. Now consider the process of transcription where the strand GATACA is translated into an RNA molecule. Again, thinking in terms of complementary base paring. What is the resulting RNA strand? (2 points) Solution: a) Comparison chart DNA Stands For DeoxyriboNucleicAcid. RiboNucleicAcid. Definition A nucleic acid that contains the genetic instructions used in the development and functioning of all modern living organisms. DNA's genes are expressed, or manifested, through the proteins that its nucleotides produce with the help of RNA. Function Structure Base Pairing Location The blueprint of biological guidelines that a living organism must follow to exist and remain functional. Medium of long-term, stable storage and transmission of genetic information. Double-stranded. It has two nucleotide strands which consist of its phosphate group, five-carbon sugar (the stable 2-deoxyribose), and four nitrogen-containing nucleobases: adenine, thymine, cytosine, and guanine. Adenine links to thymine (A-T) and cytosine links to guanine (C-G). DNA is found in the nucleus of a cell and in mitochondria. RNA The information found in DNA determines which traits are to be created, activated, or deactivated, while the various forms of RNA do the work. Helps carry out DNA's blueprint guidelines. Transfers genetic code needed for the creation of proteins from the nucleus to the ribosome. Single-stranded. Like DNA, RNA is composed of its phosphate group, five-carbon sugar (the less stable ribose), and four nitrogencontaining nucleobases: adenine, uracil (not thymine), guanine, and cytosine. Adenine links to uracil (A-U) and cytosine links to guanine (C-G). Depending on the type of RNA, this molecule is found in a cell's nucleus, its cytoplasm, and its ribosome. Stability Deoxyribose sugar in DNA is less reactive because of C- H bonds. Stable in alkaline conditions. DNA has smaller grooves, which makes it harder for enzymes to "attack." Ribose sugar is more reactive because of C- OH (hydroxyl) bonds. Not stable in alkaline conditions. RNA has larger grooves, which makes it easier to be "attacked" by enzymes. Propagation DNA is self-replicating. RNA is synthesized from DNA when needed. Unique Features The helix geometry of DNA is of B-Form. DNA is protected in the nucleus, as it is tightly packed. DNA can be damaged by exposure to ultra-violet rays. From: http://www.diffen.com/difference/dna_vs_rna Give yourself 3 points for at least 3 differences mentioned and explained The helix geometry of RNA is of A-Form. RNA strands are continually made, broken down and reused. RNA is more resistant to damage by Ultra-violet rays.
b) Because of the base pairing in DNA of A-T and C-G the complementary strand to GATACA is CTATGT. 2 points for getting the DNA complementary strand right. c) For RNA the thymine is replaced by uracil so the complementary RNA strand to GATACA is thus: CUAUGU. 2 points for getting the RNA complementary strand right 2) RNA. (6 points) There are several different kinds of RNA molecules in a cell. What are they and what particular purpose do they have? Solution: There is a huge number of different RNA s in living cells. A pretty exhaustive list with links to further explanations are given at : http://en.wikipedia.org/wiki/list_of_rnas The most important are mrna, trna and rrna, Messenger RNA (mrna) is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. Transfer RNA (trna) is an adaptor molecule composed of RNA, typically 73 to 94 nucleotides in length, that serves as the physical link between the nucleotide sequence of nucleic acids and the amino acid sequence of proteins. It does this by carrying an amino acid to the ribosome as directed by a three-nucleotide sequence (codon) in a messenger RNA (mrna). Ribosomal ribonucleic acid (rrna) is the RNA component of the ribosome, and is essential for protein synthesis in all living organisms. It constitutes the predominant material within the ribosome, which is approximately 60% rrna and 40% protein by weight. 1 point for name and one for explanation for each of the 3 main types of RNA molecules. Extra point for additional RNA types! 3) Proteins. (6 points) Assume that a typical protein has 100 amino acids and a ballpark molecular weight for an amino acid is 100 g/mol. In humans about 60% of all weight is solid material. Of all the solid material about 30% is protein. How many protein molecules are present per 70 kilograms (i.e., average weight of a human) of hydrated animal cells? If a protein s typical dimension is 10 Angstroms (1 A = 10-8 cm), could the distance between Pittsburgh and Los Angeles be spanned by aligning the protein molecules end-to-end? Solution: A weight of a 70kg person that is due to protein is given by 70kg*0.3*0.6 = 12.6 kg. The average weight of a protein with 100 amino acid is given by multiplying 100 with the average weight of an amino acid thus 100x100g/mol = 10kg/mol. So the number of such average proteins in the average body is 12.6 kg/ (10 kg/mol) = 1.26 mol. Since a mol corresponds to 6.022 10 23 objects (in this case proteins) the 1.26mol translate into : 1.26 mol * 6.022 10 23 proteins/mol = 7.588 10 23 proteins. Thus, an average human contains about 7.6 10 23 proteins. A protein is about 10 Angstroms in size (10-9 m), which means if all these proteins were laid end to
end the total length would be 7.6 10 23 protein molecules * 10-9 m/prot molecule /1000m/km = 7.6x10 11 km, which will get one from California and back quite easily. 6 points for getting the whole question right. Make use of partial credit(s) and subtract no more than 1 point total if you got the right solution conceptually, but made some calculation mistake 4) Structure of fatty acids. (4 points) Use the following structures to answer the questions below: A HO O B HO O H C CH D C O HO SOLUTION: a. Which fatty acid has the lowest melting point? Please explain.( 2 points) b. Which fatty acid has the highest melting point? Please explain. (2 points) a) In general the rule is that a lipid will have freely moving hydrocarbon chains, i.e. is fluid, when it melts. This happens at an higher temperature the more saturated the chain is and the longer it is. The most unsaturated chain I s C which therefore has the lowest melting point. b) For the reason laid out in a) fatty acid A) has the highest melting point. 2 points for each: one for making the right call, the other for the right reasoning. 5) Lipids. (5 points) After DNA, RNA and proteins lipids are the 4 th large class of molecules in living cells. Here are some basic questions to ponder: SOLUTION a. What is the definition of a lipid?( 1 points) b. How do fatty acids (such as those in problem 2) relate to lipids. What other structural groups of lipids can you name and describe? ( 2 points) c. What are the main subtypes of membrane lipids? ( 2 points) a) Lipids are a group of naturally occurring molecules that include fats, waxes, sterols, fatsoluble vitamins (such as vitamins A, D, E, and K), monoglycerides, diglycerides, triglycerides, phospholipids, and others. Lipids may be broadly defined as hydrophobic or amphiphilic small molecules; the amphiphilic nature of some lipids allows them to form structures such as vesicles, multilamellar/unilamellar liposomes, or membranes in an aqueous environment. b) There is the glycerol or sphingosine backbone to which the fatty acid(s) attach and then a polar head group that consist either of a phosphate group plus an additional group in the case of the Phospholipids or a Mono or disaccharide in the case to the Glycolipids.
c) As can be seen on the diagram below the main membrane forming lipid subtypes are Phospholipids consisting of Glycerophospholipids and Sphingolipids and the group of Glycolipids consisting of Sphingolipids with sugar containing head groups and Galactolipids. In archaea membranes are formed by ether lipids. 6) Ebola (9 points). The Ebola outbreak in West Africa is of great concern to the Health Organizations around the globe. If an infection with the Ebola virus leads to the outbreak of the disease (Ebola virus disease (EVD) or Ebola hemorrhagic fever (EHF) the fatality rate is currently a depressing 60%, usually because of multiple organ dysfunction syndrome (MODS). With what we learned so far and a bit extra legwork we can probably understand some of the basics of this disease.. Solution: ai) A virus is a small infectious agent that replicates only inside the living cells of other organisms. Viruses can infect all types of life forms, from animals and plants to bacteria and archaea. Virus particles (known as virions) consist of two or three parts: i) the genetic material made from either DNA or RNA, long molecules that carry genetic information; ii) a protein coat that protects these genes; and in some cases iii) an envelope of lipids that surrounds the protein coat when they are outside a cell. ( 1 point) aii) Replication cycle ( 3 points for a decent description of the replication cycle) Viral populations do not grow through cell division, because they are acellular. Instead, they use the machinery and metabolism of a host cell to produce multiple copies of themselves, and they assemble in the cell.
A typical virus replication cycle Some bacteriophages inject their genomes into bacterial cells (not to scale) The life cycle of viruses differs greatly between species but there are six basic stages in the life cycle of viruses: Attachment is a specific binding between viral capsid proteins and specific receptors on the host cellular surface. This specificity determines the host range of a virus. For example, HIV infects a limited range of human leucocytes. This is because its surface protein, gp120, specifically interacts with the CD4 molecule a chemokine receptor which is most commonly found on the surface of CD4+ T-Cells. This mechanism has evolved to favor those viruses that infect only cells in which they are capable of replication. Attachment to the receptor can induce the viral envelope protein to undergo changes that results in the fusion of viral and cellular membranes, or changes of nonenveloped virus surface proteins that allow the virus to enter.
Penetration follows attachment: Virions enter the host cell through receptor-mediated endocytosis or membrane fusion. This is often called viral entry. The infection of plant and fungal cells is different from that of animal cells. Plants have a rigid cell wall made of cellulose, and fungi one of chitin, so most viruses can get inside these cells only after trauma to the cell wall. However, nearly all plant viruses (such as tobacco mosaic virus) can also move directly from cell to cell, in the form of single-stranded nucleoprotein complexes, through pores called plasmodesmata. Bacteria, like plants, have strong cell walls that a virus must breach to infect the cell. However, given that bacterial cell walls are much less thick than plant cell walls due to their much smaller size, some viruses have evolved mechanisms that inject their genome into the bacterial cell across the cell wall, while the viral capsid remains outside. Uncoating is a process in which the viral capsid is removed: This may be by degradation by viral enzymes or host enzymes or by simple dissociation; the end-result is the releasing of the viral genomic nucleic acid. Replication of viruses involves primarily multiplication of the genome. Replication involves synthesis of viral messenger RNA (mrna) from "early" genes (with exceptions for positive sense RNA viruses), viral protein synthesis, possible assembly of viral proteins, then viral genome replication mediated by early or regulatory protein expression. This may be followed, for complex viruses with larger genomes, by one or more further rounds of mrna synthesis: "late" gene expression is, in general, of structural or virion proteins. Following the structure-mediated self-assembly of the virus particles, some modification of the proteins often occurs. In viruses such as HIV, this modification (sometimes called maturation) occurs after the virus has been released from the host cell. ] Viruses can be released from the host cell by lysis, a process that kills the cell by bursting its membrane and cell wall if present: This is a feature of many bacterial and some animal viruses. Some viruses undergo a lysogenic cycle where the viral genome is incorporated by genetic recombination into a specific place in the host's chromosome. The viral genome is then known as a "provirus" or, in the case of bacteriophages a "prophage". Whenever the host divides, the viral genome is also replicated. The viral genome is mostly silent within the host; however, at some point, the provirus or prophage may give rise to active virus, which may lyse the host cells. Enveloped viruses (e.g., HIV) typically are released from the host cell by budding. During this process the virus acquires its envelope, which is a modified piece of the host's plasma or other, internal membrane.
The genetic material within virus particles, and the method by which the material is replicated, varies considerably between different types of viruses. (from http://en.wikipedia.org/wiki/virus#replication_cycle ) b) Endothelia cells line the interior surface of blood vessels and lymphatic vessels, forming an interface between circulating blood or lymph in the interior and the rest of the vessel wall. Cells of this type that are in direct contact with blood are called vascular endothelial cells, whereas those in direct contact with lymph are known as lymphatic endothelial cells. Phagocytes are cells that protect the body by ingesting (phagocytosing) harmful foreign particles, bacteria, and dead or dying cells. They are essential for fighting infections and for subsequent immunity. Many of them live in the blood. Monocytes are a type of white blood cells (leukocytes). They are the largest of all leukocytes. They are part of the innate immune system of vertebrates including all mammals (humans included), birds, reptiles, and fish. A hepatocyte is a cell of the main tissue of the liver. Hepatocytes make up 70-85% of the liver's cytoplasmic mass and are involved in protein synthesis, protein storage, transformation of carbohydrates, synthesis of cholesterol, bile salts and phospholipids and the detoxification, modification, and excretion of exogenous and endogenous substances. 0.5 points each for a decent definition for each of the three cell types. c) The structure 3CSY (shown below) is of the trimetric ebola virus glycoprotein attached to an antibody against it. ( 1 point) d) The hope could be that by developing a compound based either on the specific antibody or the structure of the trimmer, one gains an agent that blocks the usage of this protein for further viral proliferation. ( 1 point) e) ( 1 point)