Biology Semester 1 PDF

MANIPAL INSTITUTE OF TECHNOLOGY BIOLOGY FOR ENGINEERS COURSE PLAN Department : Biotechnology Course Name & code : Biology for Engineers, BIO 1071 Semester & branch : B. Tech First Semester Common to All bra...

MANIPAL INSTITUTE OF TECHNOLOGY BIOLOGY FOR ENGINEERS COURSE PLAN Department : Biotechnology Course Name & code : Biology for Engineers, BIO 1071 Semester & branch : B. Tech First Semester Common to All branches No of contact hours/week : 3 Hours, Total 36 Hours Course Outcomes (Cos) At the end of this course, the student should be able to: CO1: Interpret the buildings blocks of life by analyzing the elements, chemical bonding and macromolecules of living systems CO2: Infer the flow of information in living systems through simple genetic experiments CO3: Illustrate DNA as a dynamic information storage molecule CO4: Assess the biological organization from micro-level to macro-level biological systems as well as to understand evolution as a tool for improvising existing life forms CO5: Integrate the concepts of biology in solving complex engineering problems COURSE PLAN Lectures Topics COs 1 Introducing the topic Bioinspiration: Examples of bioinspiration models used in 2 5 engineering. Building blocks of life: Elements of life and their bonding 1 3 ability, importance of carbon, elemental replacement Different types of bonds and interactions in biological 4 systems, 5 Water and phospholipids as well as their importance in the survival of life, 6 Macromolecules such as carbohydrates 7 Proteins, their structures 8 Enzymes Mendel’s logics, Flow of information in living systems: 9 Mendelian model 10 Monohybrid and Law of Segregation, Law of dominance 11 Dihybrid cross, Law of independent assortment Testing the mendelian model – Monohybrid and Dihybrid 2 12 Test cross Morgan concept on location of factors, recombination, 13 crossing over 14 Recombination frequency, Map distance 15 Pedigree analysis Information storage and maintenance in living systems: 16 Discovery of DNA, Griffiths transformation experiment, Avery and Oswald Experiment 17 Hershey and Chase Experiment 18 Structure of DNA and RNA, Chargaff’s rule 19 Meselson and Stahl experiment 3 20 DNA copying mechanism (DNA Replication) 21 Proof reading, Kornberg experiment 22 RNA synthesis and processing (Transcription) 23 Genetic code 24 Protein synthesis (Translation) Communications: Neural and humoral , Autonomic nervous 25 system, action potentials Organization and Evolution of living systems: Biological 26 hierarchies, modularity and incremental change, Darwins Model, Lawmark’s theory 4 27 Evidences of Evolution – Fossils, Embryonic evidence Evidences of Evolution – Types of Mutations and Sickle cell 28 Anemia, Chemical evolution – globin and porphyrin rings Cooperation: Symbiosis, co-evolution, communal benefit, 29 predators and parasites. 30 Vaccination 5 31 Bioinspired Designs- Approach and Methodology 32 Bioinspiration case study: Natures moisture harvesters 33 Bioinspiration case study: Shock absorption  Bioinspiration case study: Multimodal locomotion, 34 Biopropulsion Bioinspiration case study: Robotic designs, aerial–aquatic 35 robotic platforms 36 Summarizing the Course Reference Books: David M. Hillis; Craig H. Heller; Sally D. Hacker; David W. Hall and Marta J., 2020. Life, the science of Biology, 12th edition. Sinauer Associates, Inc USA. ISBN 9781319307059 Urry, Cain; Wasserman ; Minorsky and Orr., 2021. Campbell Biology, 12th edition, Pearson Publications, USA. ISBN 9780134154121 Johnson AT, 2010. Biology for Engineers, CRC Press Inc., USA, ISBN 9781420077636 Name and Signature of Course Co-ordinator: Name Signature of Head of the Department First observation for inheritance being related to a metabolic pathway Archibald Garrod was an English physician. He observed that many children exhibited a symptom - the urine turns dark brown immediately after urination, i.e. when exposed to air. Further analysis indicated that the frequency of the disease was more common in children of consanguineous (within the family marriage e.g. Cousin-Cousin, uncle-niece) marriages. Simultaneously, Garrod found the concepts involved in rediscovery of Mendelian inheritance inspiring. A pedigree chart allowed Garrod to determine that the couples had a recessive allele causing the child to be homozygous recessive. Biochemical composition of the urine was investigated by Garrod and observed the following pattern for normal individuals or heterozygous individuals. TYROSINE: hormone produced by thyroid gland that produces a lot of brain chemicals / hormones. So in homozygous recessive cases the reaction is blocked. This was an indication that inheritance is responsible for turning the urine black. Garrod speculated this fact, but was unable to identify the enzyme or the gene. However an exact confirmation required several years of study. In 1958, the enzyme was identified –homogentisic acid oxidase and in 1996 the gene was identified. Chromosomes contain both proteins and DNA: What is the evidence that which chemical component carries the genetic information? Chromosome is a combination of two chemicals: DNA and Proteins: The chromosome is a dynamic structure in the sense that it condenses and expands during various stages of the cell cycle. Chromosome is a mixture of two different components (i) DNA and (ii) proteins in higher quantity compared to DNA. In fact, DNA is bound to proteins. This unique combination accounts for dynamicity of the structure. What we see or represent for a 1 chromosome is the most condensed state of chromatin fibers (DNA fiber). This can be visually seen during the metaphase of the cell division (Fig 1). Figure 1: Dynamicity of the chromatin fibers – they expand and contract according to the stage of the cell cycle: M=Mitotic phase (Division phase), G1 and G2 are gap phases and synthesis of the raw materials occurs during the Synthesis (S phase). [Figure adapted from Sadava et al, Life: The science of Biology, 9th edition, Page 211, Fig 11.8] The circumstantial evidences and logic to assume that DNA is the genetic material: Living creatures exhibit a great diversity. Similar traits are observed in living forms of the same kind (species), while differences are observed between different species. It means that the genetic composition of living forms of one kind differs from that of the other kind. This exactly means their amount will differ. So can we prove it? This theory was proven by Robert Feulgen, who developed a red colored dye which binds to DNA. It stains DNA material red inside the nucleus. So the intensity of the red color is an approximate estimate of the DNA it contains. This dye is known as Feulgen stain. The Feulgen staining techniques presented the following information: It was in the right position (inside the nucleus) and the color intensity varied between two species. The need of more cause and effect evidence! The Feulgen staining only provided a circumstantial evidence. We should prove with a cause and effect situation that DNA carries the genetic information and not the proteins. How to do it? 2 Frederick Griffith was a physician from England. He was working with bacteria, which are visible only under a microscope. Pneumonia was taking many lives during his time. So he wanted to develop a vaccine for pneumonia. He found that there exists two forms (strains) of the bacteria which causes pneumonia, Streptococcus pneumonia. These strains are: Smooth (S) and Rough (R) forms. Smooth forms care capable of causing the disease, while rough forms do not cause the disease. The reason is that the smooth forms are hidden inside a proteinaceous cover, so it can cheat the firewall (The immune system), while rough forms are not able to utilize that trick, as they lack the protein coat. Hence the firewall will definitely catch and eliminate them. Now he planned and executed the experiments as illustrated in figure 2. Figure 2: The experiments conducted by Griffith with the bacteria and mouse. [Figure adapted from Sadava et al, Life: The science of Biology, 9th edition, Page 268, Fig 13.2]. The above figure illustrates that in the experiment 4the material present in the S form transforms the material present in the R form. So we can say that some transforming principle is responsible for this change from an R form to S form of bacteria. How to identify this transforming principle? The scientific group led by Oswald Avery of Rockefeller University cracked this problem. Their experiment is illustrated in Figure 3. 3 Figure 3: Identifying the “transforming principle”. [Figure adapted from Sadava et al, Life: The science of Biology, 9th edition, Page 269, Fig 13.1] The above work was published without much impact in 1944 because, many were not aware of the fact that DNA is complex enough to give the diverse output. Moreover many were still wondering whether microscopic small creatures, like bacteria, has genes in it. 4 The impact of this work was intensified after another experimental work published in 1952 by Alfred Hershey and Martha Chase at Carnegie Laboratory of Genetics. They were trying to determine whether DNA or protein contains the genetic material by using a bacteriophage (a virus that attacks and kills the bacteria). Why they have selected a virus? Because virus is composed of just two components that we are trying to sort, the protein cover and the DNA inside it (Figure 4). Figure 4: Hershey and Chase experiment. [Figure adapted from Sadava et al, Life: The science of Biology, 9th edition, Page 271, Fig 13.4] 5 DNA structure: Figure 1- Timeline of events in the discovery of DNA structure. Image courtesy www.genscript.com The race for DNA structure: The structure of DNA remained elusive until experimental evidence of many types were considered together in a theoretical framework. Figure 1 indicates the various experiments which acted as steps towards the discovery of the correct DNA structure. The most crucial evidence was obtained using X-ray crystallography. Some chemical substances, when they are isolated and purified, can be made to form crystals. The positions of atoms in a crystallized substance can be inferred from the diffraction pattern of X- rays passing through the substance. The events that provided information about this vital molecule are described in the following text. Chemical composition of DNA: Biochemists knew that DNA was a polymer of nucleotides. Each nucleotide consists of a molecule of the sugar deoxyribose, a phosphate group, and a nitrogen containing base. each nucleotide contains:- - sugar deoxyribose - a phosphate group - a nitrogen containing base Figure 2- Chemical composition of DNA monomers. The only differences among the four nucleotides of DNA are their nitrogenous bases: the purines adenine (A) and guanine (G), and the pyrimidines cytosine (C) and thymine (T). Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. In 1950, biochemist Erwin Chargaff reported that DNA from many different species—and from different sources within a single organism— exhibits certain regularities. In almost all DNA, the following rule holds: The amount of adenine equals the amount of thymine (A= T), and the amount of guanine equals the amount of cytosine (G = C). Difference between pyrimidines and purines is as follows PYRIMIDINES: Are 6 member molecules with 2 nitrogen atoms PURINES: Are 9 member molecules with 2 nitrogen atoms Figure 3- Chargaff's rule- In DNA, total abundance of purines is equal to total abundance of pyrimidines. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. In 1952, Rosalind Franklin was able to obtain an X-ray diffraction pattern for certain DNA fibers. This experiment provided the greatest help required by the scientists to deduce the DNA structure. Figure 4- The positions of atoms in a crystallized chemical substance can be inferred by the pattern of diffraction of X rays passed through it. The pattern of DNA is both highly regular and repetitive. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. Around the same time, Linus Pauling proposed a triple stranded helical structure for DNA. Linus Pauling had discovered the helical nature of protein folding and deduced that the same folding pattern may be followed by DNA. The structure proposed by Linus Pauling had the phosphate groups of the nucleotides facing inside the helical core. However, such a structure would result in the phosphate group repulsion (due to the negatively charged oxygen groups). Almost unbelievable that the man who had such a command over chemical bonds would get this wrong. Figure 5- DNA structure as proposed by Linus Pauling (Top view). The negatively charged oxygen atoms repel each other and would cause the strands to disassociate. Image courtesy- http://www.dnai.org/  Double stranded structure discovery by Watson and Crick: The English physicist Francis Crick and the American geneticist James D. Watson, who were both then at the Cavendish Laboratory of Cambridge University, used model building to solve the structure of DNA. Watson and Crick attempted to combine all that had been learned so far about DNA structure into a single coherent model. Rosalind Franklin’s crystallography results (see Figure 4) convinced Watson and Crick that the DNA molecule must be helical (cylindrically spiral). Density measurements and previous model building results suggested that there are two polynucleotide chains in the molecule. Modeling studies also showed that the strands run in opposite directions, that is, they are antiparallel; that two strands would not fit together in the model if they were parallel. nitrogen bases form hydrogen bonds phosphate groups don't form hydrogen bonds Figure 6- DNA model proposed by Watson and Crick made several assumptions. The nucleotide bases are on the interior of the two strands, with a sugar-phosphate backbone on the outside. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. Figure 7-To satisfy Chargaff’s rule (purines = pyrimidines), a purine on one strand is always paired with a pyrimidine on the opposite strand. These base pairs (A-T and G-C) have the same width down the double helix, a uniformity shown by x-ray diffraction. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition.  Figure 8- In late February of 1953, Crick and Watson built a model out of tin that established the general structure of DNA. This structure explained all the known chemical properties of DNA, and it opened the door to understanding its biological functions. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. Important properties of DNA structure: 1. The double stranded helix has a uniform diameter 2. The two strands rum in opposite direction (antiparallel). 3. The backbone of each strand is made up of sugar phosphate groups linked by phosphodiester bonds 4. The two strands are held together by hydrogen bonding between the nitrogenous bases. Meselson and Stahl experiment: This experiment was instrumental in proving that DNA follows a semiconservative model of replication. A cell while undergoing division requires that old cell to produce copies of DNA that can be transferred to the new cells. The new cells receive a copy of the parent cell’s DNA. Figure 9- Watson and Crick suggested a semiconservative model of replication, wherein each parental strand acts as a template for synthesizing a new complementary strand. In this model, each daughter molecules consists of one old strand (from parent molecule) and one newly synthesized strand. Image courtesy- www.dnai.org Meselson and Stahl made clever use of radiolabelled (15N) heavy isotope of nucleotides and a density gradient of Cesium chloride (CsCl) to provide evidence for the semiconservative model of replication. They collected some of the bacteria after each division and extracted DNA from the samples. To separate the DNA from the cells at different generation on basis of density, they developed a density gradient solution in a test tube using CsCl. They found that the density gradient was different in each bacterial generation:  At the time of the transfer to the 14N medium, the DNA was uniformly labeled with 15N, and hence formed a single band corresponding with dense DNA. After one generation in the 14N medium, when the DNA had been duplicated once, all the DNA was of intermediate density. After two generations, there were two equally large DNA bands: one of low density and one of intermediate density. In samples from subsequent generations, the proportion of low-density DNA increased steadily. Figure 10- Meselson and Stahl experiment to prove that DNA replicates in a semiconservative manner. The researchers grew another E. coli culture on 15N medium, then transferred it to normal 14N medium and allowed the bacteria to continue growth. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. The results of this experiment can be explained only by the semiconservative model of DNA replication. In the first round of DNA replication in the 14N medium, the strands of the double helix—both heavy with 15 N—separated. Each strand then acted as the template for a second strand, which contained only 14N and hence was less dense. Each double helix then consisted of one 15N strand and one 14N strand, and was of intermediate density. In the second replication, the 14N-containing strands directed the synthesis of partners with 14N, creating low-density DNA, and the 15N strands formed new 14N partners. The crucial observation demonstrating the semiconservative model was that intermediate-density DNA (15N–14N) appeared in the first generation and continued to appear in subsequent generations. With the other models, the results would have been quite different: If conservative replication had occurred, the first generation would have had both high-density DNA (15N–15N) and low-density DNA (14N–14N), but no intermediate density DNA. If dispersive replication had occurred, the density of the new DNA would have been intermediate, but DNA of this density would not continue to appear in subsequent generations. Figure 11- Monomer of DNA (nucleotide monophosphate). The monomers exist within the strand in monophosphate form. Figure 12- During the formation of a phosphodiester bond, the incoming monomers are in nucleotide triphosphate form. The cleavage of the beta and gamma phosphate provides the energy needed for phophodiester bond formation. This reaction is catalyzed by DNA polymerase. Figure 13- Nitrogenous bases of DNA and RNA. Uracil is present in RNA instead of Thymine.  Figure 14- Hydrogen bonding between the nitrogenous bases of DNA. Figure 15- The purines (A and G) pair with the pyrimidines (T and C, respectively) to form base pairs that are equal in size and resemble the rungs on a ladder whose sides are formed by the sugar–phosphate backbones. The deoxyribose sugar (left) is where the 3′ and 5′ carbons are located. The two strands are antiparallel. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. This concludes the chase for discovery of DNA structure. The next section describes the process of DNA replication. KORNBERG ARTHUR was the first to discover: - - how monomers of DNA (deoxyribonucleic acid) duplicate within bacterial cells. -devised a cell free method of replicating DNA Kornberg, Arthur, an American physician and biochemist, was the first to discover how monomers of deoxyribonucleic acid (DNA) duplicate within bacterial cells and also the first to devise a cell free method for replicating DNA. For these achievements he shared the 1959 Nobel Prize in physiology. Arthur Kornberg isolated a new enzyme from E. coli, “DNA polymerase”, which had the property to assemble nucleotides and manufacture DNA. The cell free setup for replicating DNA was developed in vitro (in a test tube) by providing a pool of free nucleotides, a DNA primer (he used calf thymus DNA), a source of magnesium ions, and ATP. Kornberg used DNA polymerase to verify one of the essential elements of the Watson - Crick Model of DNA structure: DNA is always polymerized in the 5´ to 3´ direction (H-CH2 sugar phosphate bonds to H-O sugar phosphate bond; new nucleotides are added at the 3´ end). The findings of Kornberg experiment provided conclusive evidence that the double stranded helical model provided by Watson- Crick was accurate. Kornberg designed the following experiment to determine the growing end for DNA replication process The reaction used certain key ingredients as follows- 1. Labelled nucleotides (contained the radioactive phosphorus isotope 32P) 2. DNA primer (he used calf thymus DNA), 3. a source of magnesium ions, and ATP The procedure for the assignment is as follows: Initiation of the reaction using unlabelled nucleotide as the nucleotide precursor. Add radioactive (32P) nucleotide for a brief period, and then quickly stop the reaction. At the completion of the experiment, Kornberg observed that 32P nucleotides attached only to the 3’-OH end of the growing strand. The results of the experiment clearly indicated that the newly synthesized strand grows at the 3’-OH end. DNA replication: Semiconservative DNA replication in the cell involves a number of different enzymes and other proteins. It takes place in two general steps: The DNA double helix is unwound to separate the two template strands and make them available for new base pairing. As new nucleotides form complementary base pairs with template DNA, they are covalently linked together by phosphodiester bonds, forming a polymer whose base sequence is complementary to the bases in the template strand. The process of replication occurs within a region called the replication bubble, which contains all the enzymes required for replication and the DNA strands to be replicated. The replication bubble consists of two replication forks, in which the synthesis of DNA proceeds in the two opposite directions. Figure 19- Replication bubble with two replication forks proceeding in opposite directions Replication is carried out due to the efficient working of various enzymes involved in DNA replication. DNA is replicated through the interaction of the template strand with a huge protein complex called the replication complex, which contains at least four proteins, including DNA polymerase. All chromosomes have at least one region called the origin of replication (ori), to which the replication complex binds with high specificity. The first event at the origin of replication is the localized unwinding and separation (denaturation) of the DNA strands. There are several forces that hold the two strands together, including hydrogen bonding and the hydrophobic interactions of the bases. An enzyme called DNA helicase uses energy from ATP hydrolysis to unwind and separate the strands. Proteins called single-strand binding proteins bind to the unwound strands to keep them from reassociating into a double helix. This process makes each of the two template strands available for complementary base pairing. Three types of DNA polymerase exist which assist in the process of DNA replication.  DNA polymerase I  DNA polymerase II  DNA polymerase III The function of these DNA polymerases is revealed as the process of DNA replication is studied further. The first DNA polymerase to act in the replication complex is DNA polymerase III, whose function is to extend the new strand. A DNA polymerase elongates a polynucleotide strand by covalently linking new nucleotides to a previously existing strand. However, it cannot start this process without a short “starter” strand, called a primer. In DNA replication, the primer is usually a short single strand of RNA (Figure 14). This RNA primer strand is complementary to the DNA template, and is synthesized one nucleotide at a time by an enzyme called a primase. The DNA polymerase III then adds nucleotides to the 3′ end of the primer and continues until the replication of that section of DNA has been completed. Thus the basic function of DNA polymerase III is to extend the new strand starting from one end of the RNA primer. DNA polymerase I (discovered by Arthur Kornberg) degrades the RNA primer, and adds DNA in its place. This action of DNA polymerase I causes the resulting new strand to have a small gap. This gap is filled in by DNA ligases. When DNA replication is complete, each new strand consists only of DNA. Figure 20- DNA polymerase requires a primer to initiate replication. Primase is the enzyme which provides an RNA primer. DNA polymerase attaches nucleotides to the end of this RNA primer and extends the new strand. Note: the new strand is DNA in nature and not RNA. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. The two daughter strands resulting from a double stranded parent grow differently. The DNA double helix is antiparallel in nature, therefore: One newly replicating strand (the leading strand) is oriented so that it can grow continuously at its 3′end as the fork opens up. The other new strand (the lagging strand) is oriented so that as the fork opens up, its exposed 3′end gets farther and farther away from the fork, and an unreplicated gap is formed. This gap would get bigger and bigger if there were not a special mechanism to overcome this problem. Synthesis of the lagging strand requires the synthesis of relatively small, discontinuous stretches of sequence. These discontinuous stretches are synthesized just as the leading strand is, by the addition of new nucleotides one at a time to the 3′ end of the new strand, but the synthesis of this new strand moves in the direction opposite to that in which the replication fork is moving. These stretches of new DNA are called Okazaki fragments (after their discoverer, the Japanese biochemist Reiji Okazaki). While the leading strand grows continuously “forward,” the lagging strand grows in shorter, “backward” stretches with gaps between them. A single primer is needed for synthesis of the leading strand, but each Okazaki fragment requires its own primer to be synthesized by the primase. DNA polymerase III then synthesizes an Okazaki fragment by adding nucleotides to one primer until it reaches the primer of the previous fragment. At this point, DNA polymerase I removes the old primer and replaces it with DNA. Left behind is a tiny nick—the final phosphodiester linkage between the adjacent Okazaki fragments is missing. The enzyme DNA ligase catalyzes the formation of that bond, linking the fragments and making the lagging strand whole.  Single strand binding protein Helicase Figure 21- Synthesis of the leading strand. Image courtesy- Biology, by Campbell et al. Figure 22- Synthesis of the lagging strand. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. Figure 23- Sliding DNA clamp increases the efficiency of polymerization by keeping the enzyme bound to the substrate, so the enzyme does not have to repeatedly bind to template and substrate. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. During DNA replication, the progress of the replication fork generates positive supercoils ahead of the replication machinery and negative supercoils behind it. The DNA can be supercoiled to such an extent that if left unchecked it could impede the progress of the protein machinery involved. This is prevented by DNA topoisomerase, which makes single-stranded nicks to relax the helix. Small circular chromosomes, such as those of bacteria (consisting of 1–4 million base pairs), have a single origin of replication. Two replication forks form at this ori, and as the DNA moves through the replication complex, the replication forks extend around the circle. Two interlocking circular DNA molecules are formed, and they are separated by an enzyme called DNA topoisomerase. DNA polymerases are very fast. In E. coli, replication can be as fast as 1,000 bases per second, and it takes 20–40 minutes to replicate the bacterium’s 4.7 million base pairs. Figure 24- Replication in a bacteria having circular DNA. Human DNA polymerases are slower than those of E. coli, and can replicate DNA at a rate of about 50 bases per second. Human chromosomes are much larger than those of bacteria (about 80 million base pairs) and linear. Large linear chromosomes such as those of humans contain hundreds of origins of replication. Numerous replication complexes bind to these sites at the same time and catalyze simultaneous replication. Thus there are many replication forks in eukaryotic DNA. Figure 25- Larger linear chromosomes, typical of nuclear DNA in eukaryotes, have many origins of replication. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. Activity of telomerase: Replication of the lagging strand occurs by the addition of Okazaki fragments to RNA primers. When the terminal RNA primer is removed, no DNA can be synthesized to replace it because there is no 3′end to extend. So the new chromosome has a bit of single-stranded DNA at each end. This situation activates a mechanism for cutting off the single stranded region, along with some of the intact double-stranded DNA. This is a part of DNA repair mechanism. Thus the chromosome becomes slightly shorter with each cell division. Figure 26- Removal of the RNA primer at the 3′ end of the template for the lagging strand leaves a region of DNA— the telomere— unreplicated. In continuously dividing cells, the enzyme telomerase binds to the 3′ end and extends the lagging strand of DNA, so the chromosome does not get shorter. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. An enzyme, appropriately called telomerase, catalyzes the addition of any lost telomeric sequences. Telomerase contains an RNA sequence that acts as a template for the telomeric DNA repeat sequence. DNA Replication proofreading: DNA must be accurately replicated and faithfully maintained. The price of failure can be great; the accurate transmission of genetic information is essential for the functioning and even the life of a single cell or multicellular organism. Yet the replication of DNA is not perfectly accurate. So the problem arises in preserving life. DNA repair mechanisms help to preserve life. DNA polymerases initially make significant numbers of mistakes in assembling polynucleotide strands. Without DNA repair, the observed error rate of one for every 105 bases replicated would result in about 60,000 mutations every time a human cell divided. Fortunately, our cells can repair damaged nucleotides and DNA replication errors, so that very few errors end up in the replicated DNA. Cells have at least three DNA repair mechanisms at their disposal: A proofreading mechanism corrects errors in replication as DNA polymerase makes them. A mismatch repair mechanism scans DNA immediately after it has been replicated and corrects any base- pairing mismatches. An excision repair mechanism removes abnormal bases that have formed because of chemical damage and replaces them with functional bases. Most DNA polymerases perform a proofreading function each time they introduce a new nucleotide into a growing DNA strand. When a DNA polymerase recognizes a mispairing of bases, it removes the improperly introduced nucleotide and tries again. The error rate for this process is only about 1 in 10,000 repaired base pairs, and it lowers the overall error rate for replication to about one error in every 1010 bases replicated. Figure 27- Proofreading activity during DNA replication. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. After the DNA has been replicated, a second set of proteins surveys the newly replicated molecule and looks for mismatched base pairs that were missed in proofreading. Mismatch repair mechanism might detect an A-C base pair instead of an A-T pair. The repair mechanism “knows” whether the A-C pair should be repaired by removing the C and replacing it with T or by removing the A and replacing it with G (it can detect the “wrong” base)because a DNA strand is chemically modified some time after replication. In prokaryotes, methyl groups (—CH3) are added to some adenines. In eukaryotes, cytosine bases are methylated. Immediately after replication, methylation has not yet occurred on the newly replicated strand, so the new strand is “marked” (distinguished by being unmethylated) as the one in which errors should be corrected. When mismatch repair fails, DNA sequences are altered. One form of colon cancer arises in part from a failure of mismatch repair. Excision repair mechanisms deal with damage due to high-energy radiation, chemicals from the environment, and random spontaneous chemical reactions. Individuals who suffer from a condition known as xeroderma pigmentosum lack an excision repair mechanism that normally corrects the damage caused by ultraviolet radiation. They can develop skin cancers after even a brief exposure to sunlight. Figure 28- DNA repair mechanisms. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition.  Transcription RNA (ribonucleic acid) is a key intermediary between a DNA sequence and a polypeptide. RNA is an informational polynucleotide similar to DNA, but it differs from DNA in three ways: RNA generally consists of only one polynucleotide strand. The sugar molecule found in RNA is ribose, rather than the deoxyribose found in DNA. Although three of the nitrogenous bases (adenine, guanine, and cytosine) in RNA are identical to those in DNA, the fourth base in RNA is uracil (U), which is similar to thymine but lacks the methyl (—CH3) group In the process of RNA synthesis, the information contained in DNA is transcribed into RNA. During transcription, the information in a DNA sequence (a gene) is copied into a complementary RNA sequence. The process occurs in the nucleus and the resulting RNA is carried to the cytoplasm, where the protein synthesis occurs. Figure 1- Sites of transcription and translation (protein synthesis) in a eukaryotic cell. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. Figure 2- The nucleotide Thymine (present only in DNA) is replaced by Uracil (present only in RNA). The pairing of the ribonucleotides obeys the same complementary base-pairing rules as in DNA, except that adenine pairs with uracil instead of thymine. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. 1 Single-stranded RNA can fold into complex shapes by internal base pairing. Three types of RNA participate in protein synthesis: Messenger RNA (mRNA) carries a copy of a gene sequence in DNA to the site of protein synthesis at the ribosome. Transfer RNA (tRNA) carries amino acids to the ribosome for assembly into polypeptides. Ribosomal RNA (rRNA) catalyzes peptide bond formation and provides a structural framework for the ribosome. Figure 3- Types of RNA. Transcription is responsible for the synthesis of mRNA, tRNA and ribosomal RNA (rRNA), who play important roles in protein synthesis. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. Transcription requires several components: A DNA template for complementary base pairing; one of the two strands of DNA The appropriate nucleoside triphosphates (ATP, GTP, CTP, and UTP) to act as substrates An RNA polymerase enzyme- Like DNA polymerases, RNA polymerases are processive; that is, a single enzyme–template binding event results in the polymerization of hundreds of RNA bases. But unlike DNA polymerases, RNA polymerases do not require a primer and do not have a proofreading function. Transcription occurs in three stages: a) initiation, b) elongation, and c) termination a) INITIATION- Transcription begins with initiation, which requires a promoter, a special sequence of DNA to which the RNA polymerase recognizes as a start site and binds very tightly. Eukaryotic genes generally have one promoter each, while in prokaryotes and viruses, several genes often share one promoter. Promoters are important control sequences that “tell” the RNA polymerase two things: 2  Where to start transcription Which strand of DNA to transcribe (which of the two strands of DNA will act as template for producing a single RNA strand) Part of each promoter is the initiation site, where transcription begins. Groups of nucleotides lying “upstream” from the initiation site (5′ on the non-template strand, and 3′ on the template strand) help the RNA polymerase bind. Figure 4- Initiation of RNA synthesis by RNA polymerase. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. b) ELONGATION- Once RNA polymerase has bound to the promoter, it begins the process of elongation. RNA polymerase unwinds the DNA about 10 base pairs at a time and reads the template strand in the 3′-to-5′direction. Like DNA polymerase, RNA polymerase adds new nucleotides to the 3′ end of the growing strand, but does not require a primer to get this process started. The RNA transcript produced is antiparallel to the DNA template strand. Because RNA polymerases do not proofread, transcription errors occur at a rate of one for every 104 to 105 bases. Because many copies of RNA are made, however, and because they often have only a relatively short life span, these errors are not as potentially harmful as mutations in DNA. Figure 5- Successive addition of ribonucleotides to the 3' growing end of the newly synthesized RNA transcript. 3  c) TERMINATION- Just as initiation sites in the DNA template strand specify the starting point for transcription, particular base sequences specify its termination. For some genes, the newly formed transcript falls away from the DNA template and the RNA polymerase. For others, a helper protein pulls the transcript away. Figure 6- Process of elongation and termination in transcription of RNA. Image courtesy- Sadava et al, Life: The science of Biology, 9th edition. Difference in transcription between Prokaryotes and Eukaryotes  Initiation: In bacterial cells, the holoenzyme (RNA polymerase plus sigma) recognizes and binds directly to sequences in the promoter. In eukaryotic cells, promoter recognition is carried out by accessory proteins (transcription factors) that bind to the promoter and then recruit a specific RNA polymerase (I, II or III) to the promoter. 4  RNA processing: In prokaryotes, several adjacent genes sometimes share one promoter; however, in eukaryotes, each gene has its own promoter, which usually precedes the coding region. Eukaryotic genes undergo a systematic process called RNA processing to produce a mature mRNA from pre mRNA. Eukaryotic genes may contain noncoding base sequences, called introns (intervening regions). One or more introns may be interspersed with the coding sequences, which are called exons (expressed regions). Both introns and exons appear in the primary mRNA transcript, called pre- mRNA, but the introns are removed by the time the mature mRNA—the mRNA that will be translated—leaves the nucleus (figure 1). Pre-mRNA processing involves cutting introns out of the pre-mRNA transcript and splicing together the remaining exon transcripts. Eukaryotic gene transcripts are processed before translation: The primary transcript of a eukaryotic gene is modified in several ways before it leaves the nucleus: both ends of the pre mRNA are modified, and the introns are removed. 5  MODIFICATION AT BOTH ENDS Two steps in the processing of pre mRNA take place in the nucleus, one at each end of the molecule. A G cap is added to the 5′ end of the pre-mRNA as it is transcribed. The G cap is chemically modified (methylated) guanosine triphosphate (GTP). It facilitates the binding of mRNA to the ribosome for translation, and it protects the mRNA from being digested by ribonucleases that break down RNAs. Figure 7- Addition of 5' cap. Image courtesy- Genetics- : A Conceptual Approach; by Benjamin A. Pierce 6 Figure 8- Addition of 50 to 250 adenine nucleotides at the 3 end is called Polyadenylation, which occurs after transcription is completed. Image courtesy- Genetics- : A Conceptual Approach; by Benjamin A. Pierce A poly A tail is added to the 3′ end of the pre-mRNA at the end of transcription. In both prokaryotic and eukaryotic genes, transcription begins at a DNA sequence that is upstream (to the “left” on the DNA) of the first codon (i.e., at the promoter), and ends downstream (to the “right” on the DNA) of the termination codon. In eukaryotes, there is usually a “polyadenylation” sequence (AAUAAA) near the 3′ end of the pre-mRNA, after the last codon. This sequence acts as a signal for an enzyme to cut the pre mRNA. Immediately after this cleavage, another enzyme adds 100 to 300 adenine nucleotides (a “poly A” sequence) to the 3′ end of the pre-mRNA. This “tail” may assist in the export of the mRNA from the nucleus and is important for mRNA stability. 7 Splicing- The next step in the processing of eukaryotic pre-mRNA within the nucleus is removal of the introns. If these RNA sequences were not removed, a very different amino acid sequence, and possibly a nonfunctional protein, would result. A process called RNA splicing removes the introns and splices the exons together. Figure 9- The process of splicing beta globin gene. (UTR- untranslated region). Alternative splicing Figure 10- Alternative Splicing Results in Different mRNAs and Proteins In mammals, the protein tropomyosin is encoded by a gene that has 11 exons. Tropomyosin pre-mRNA is spliced differently in different tissues, resulting in five different forms of the protein. Alternate splicing is a mechanism in which the differential splicing of the same pre- mRNA gives rise to different proteins, which may have different functions. It can be a deliberate mechanism for generating a family of different proteins from a single gene. For example, a single pre-mRNA for the structural protein tropomyosin is spliced differently in five different tissues to give five different mature mRNAs. These mRNAs are translated into the five different forms of tropomyosin found in these tissues: skeletal muscle, smooth muscle, fibroblast, liver, and brain. 8  Translation Genetic code If genes are segments of DNA and if DNA is just a string of nucleotide pairs, then how does the sequence of nucleotide pairs dictate the sequence of amino acids in proteins? Simple logic tells us that, if nucleotide pairs are the “letters” in a code, then a combination of letters can form “words” representing different amino acids. We must ask how the code is read. How many letters in the RNA make up a word, or codon, and which specific codon or codons represent each specific amino acid. The logic is that the nucleotide code must be able to specify the placement of 20 amino acids. Since there are only four nucleotides, a code of single nucleotides would only represent four amino acids, such that A, C, G and U could be translated to encode amino acids. A doublet code could code for 16 amino acids (4 x 4). A triplet code could make a genetic code for 64 different combinations (4 X 4 X 4) genetic code and provide plenty of information in the DNA molecule to specify the placement of all 20 amino acids. Also, this genetic code is redundant in nature. After the start and stop codons, the remaining 60 codons are far more than enough to code for the other 19 amino acids— and indeed there are repeats (Figure 1). Thus we say that the genetic code is redundant; that is, an amino acid may be represented by more than one codon. Figure 1- Table of genetic code. Three letter code for amino acids. 1 Deciphering the genetic code: In 1961, Marshall Nirenberg and Heinrich Matthaei mixed poly(U) with the protein synthesizing machinery of E. coli in vitro and observed the formation of a protein! The main excitement centered on the question of the amino acid sequence of this protein. It proved to be polyphenylalanine—a string of phenylalanine molecules attached to form a polypeptide. This clearly meant that “words” consisting purely of U somehow caused the incorporation of phenylalanine. Figure 2- Nirenberg and Matthaei used a test- tube protein synthesis system to determine the amino acids specified by synthetic mRNAs of known codon composition. Image courtesy- Sadava et al, Life: The science of Biology, 7th edition. H. Gobind Khorana then conceived and carried out the experiment that decisively revealed the nature of the genetic code. He synthesized artificial messages more complex than Nierenberg’s and analyzed the resulting polypeptides. His data are shown below. “(XY)n” means “XYXYXY...”, and the resulting amino-acid couplet also repeats indefinitely (e.g., Ser-Leu-Ser-Leu-Ser-Leu...). Preparation for Translation: Linking RNAs, Amino Acids and Ribosomes The translation of mRNA into proteins requires a molecule that links the information contained in mRNA codons with specific amino acids in proteins. That function is performed by tRNA. Two key events must take place to ensure that the protein made is the one specified by mRNA:  tRNA must read mRNA correctly.  tRNA must carry the amino acid that is correct for its reading of the mRNA. Transfer RNAs carry specific amino acids and bind to specific codons The codon in mRNA and the amino acid in a protein are related by way of an adapter—a specific tRNA with an attached amino acid. For each of the 20 amino acids, there is at least one specific type (species) of tRNA molecule. 2 The tRNA molecule has three functions: It carries (“charged”) an amino acid, it associates with mRNA molecules, and it interacts with ribosomes. At the 3′ end of every tRNA molecule is a site to which its specific amino acid binds covalently. The charging of each tRNA with its correct amino acid is achieved by a family of activating enzymes, known more formally as aminoacyl-tRNA synthetases At about the midpoint of tRNA is a group of three bases, called the anticodon that constitutes the site of complementary base pairing (hydrogen bonding) with mRNA. Each tRNA species has a unique anticodon, which is complementary to the mRNA codon for that tRNAs amino acid. At contact, the codon and the anticodon are antiparallel to each other. As an example of this process, consider the amino acid arginine:  The DNA coding region for arginine is 3′-GCC-5′, which is transcribed, by complementary base pairing, to the mRNA codon 5′-CGG-3′.  That mRNA codon binds by complementary base pairing to a tRNA with the anticodon 3′- GCC-5′, which is charged with arginine. Figure 3- tRNA with a specific anticodon for arginine interacts with one arginine amino acid. This is called an activated tRNA. Activated tRNA specifically recognizes the codon on mRNA and produces hydrogen bonds at the site of anticodon-codon interaction. (Note the anticodon and codon are complementary to each other). 3 Ribosomes act as the workbench for translation: Ribosomes are required for the translation of the genetic information in mRNA into a polypeptide chain. Each ribosome consists of two subunits, a large one and a small one. In eukaryotes, the large subunit consists of three different molecules of rRNA and about 45 different protein molecules, arranged in a precise pattern. The ribosomes of prokaryotes are somewhat smaller than those of eukaryotes, and their ribosomal proteins and RNAs are different. Figure 4- Ribosome Structure Each ribosome consists of a large and a small subunit. The subunits remain separate when they are not in use for protein synthesis. Its structure enables it to hold the mRNA and charged tRNAs in the right positions, thus allowing the growing polypeptide to be assembled efficiently. Image courtesy- Sadava et al, Life: The science of Biology, 7th edition. A given ribosome does not specifically produce just one kind of protein. A ribosome can use any mRNA and all species of charged tRNAs, and thus can be used to make many different polypeptide products. On the large subunit of the ribosome are four sites to which tRNA binds (Figure 4). A charged tRNA traverses these four sites:  The T (transfer) site  The A (amino acid) site  The P (polypeptide) site  The E (exit) site An important role of the ribosome is to make sure that the mRNA–tRNA interactions are precise: that is, that a charged tRNA with the correct anticodon (e.g., 3′-UAC-5′) binds to the appropriate codon in mRNA (e.g., 5′-AUG-3′). When this occurs, hydrogen bonds form between the base pairs. But these hydrogen bonds are not enough to hold the tRNA in place. The rRNA of the small ribosomal subunit plays a role in validating the three-base-pair match. If hydrogen bonds have not formed between all three base pairs, the tRNA must be the wrong one for that mRNA codon, and that tRNA is ejected from the ribosome. 4 Translation Process: RNA-Directed Polypeptide Synthesis Like transcription, translation occurs in three steps: initiation, elongation, and termination. Initiation: The translation of mRNA begins with the formation of an initiation complex, which consists of a charged tRNA bearing what will be the first amino acid of the polypeptide chain and a small ribosomal subunit, both bound to the mRNA. The rRNA of the small ribosomal subunit binds to a complementary ribosome recognition sequence on the mRNA. This sequence is “upstream” (toward the 5′ end) of the actual start codon that begins translation. The mRNA start codon in the genetic code is AUG. The anticodon of a methionine charged tRNA binds to this start codon by complementary base pairing to form the initiation complex. Thus the first amino acid in the chain is always methionine. Figure 5- Initiation of translation begins with formation of an initiation complex (step 2). Image courtesy- Sadava et al, Life: The science of Biology, 7th edition. Elongation: The polypeptide elongates from the N terminus. A charged tRNA whose anticodon is complementary to the second codon on the mRNA now enters the open A site of the large ribosomal subunit. The large subunit then catalyzes two reactions: 5  It breaks the bond between the tRNA in the P site and its amino acid.  It catalyzes the formation of a peptide bond between that amino acid and the one attached to the tRNA in the A site. Because the large subunit performs these two actions, it is said to have peptidyl transferase activity. In this way, methionine (the amino acid in the P site) becomes the N terminus of the new protein. The second amino acid is now bound to methionine, but remains attached to its tRNA by its carboxyl group (—COOH) in the A site. Figure 6- The incoming charged tRNA recognizes the specific codon on the mRNA and enters into the A site. Peptidyl transferase activity of the large subunit causes the transfer of amino acid on the first tRNA (at P site) on the second tRNA (at A site) and a peptide bond is formed between these amino acids. Image courtesy- Sadava et al, Life: The science of Biology, 7th edition. After the first tRNA releases its methionine, it dissociates from the ribosome, returning to the cytosol to become charged with another methionine. The second tRNA, now bearing a dipeptide, is shifted to the P site as the ribosome moves one codon along the mRNA in the 5′-to-3′ direction. The elongation process continues, and the polypeptide chain grows, as the steps are repeated. Elongation factors assist the elongation of a polypeptide chain. 6  Figure 7- Elongation of polypeptide: (a) The next charged tRNA enters the open A site. (b) Its amino acid forms a peptide bond with the amino acid chain in the P site, so that it picks up the growing polypeptide chain from the tRNA in the P site. (c) The tRNA in the P site. Image courtesy- Sadava et al, Life: The science of Biology, 7th edition. Termination: The elongation cycle ends, and translation is terminated, when a stop codon—UAA, UAG, or UGA—enters the A site. These codons encode no amino acids, nor they bind tRNAs. Rather, they bind a protein release factor, which hydrolyzes the bond between the polypeptide and the tRNA in the P site. The newly completed protein thereupon separates from the ribosome. Its C terminus is the last amino acid to join the chain. Its N terminus, at least initially, is methionine, as a consequence of the AUG start codon. In its amino acid sequence, it contains information specifying its conformation, as well as its ultimate cellular destination. 7 Figure 8- Events of termination of polypeptide chain. Image courtesy- Sadava et al, Life: The science of Biology, 7th edition. Figure 9- Signals that start and stop transcription and Translation. These act as a boundary for the mRNA and protein synthesis. Image courtesy- Sadava et al, Life: The science of Biology, 7th edition. 8  01: BIOLOGICAL Hierarchy (Ref: Korn RW, 2005. The Emergence Principle in Biological Hierarchies, Biology and Philosophy (2005) 20:137 151) (Biological hierarchies are integrated. Each hierarchy constrains members at lower level. Structure and function are correlated at all levels of biological organization. The function is achieved by a coordinated action. Novel properties appear at each levels of hierarchy. Life is sustained by survival and reproduction) Solar system is familiar to all of us. We know that the sun and a planet impose equal gravitational pull on each other. It is the mass difference makes them distinct so that one orbits the other. Hence a planet with small mass is restrained more by the sun. This is also true for planet and its moon. What we can infer from this integration is that an entity at a level constrains members at a lower level. The strength of constraints becoming progressively weaker as we descend in the organization. In living systems, cells are held together by a greater density of covalent and hydrogen bonds of tissue features than these tissue features are held together by organ features and organ features are held together by organismal features. Thus a hierarchical model complexity A simple biological hierarchy is represented below Hierarchical Description Example Unit Molecules Groups of atoms, smallest unit of most Carbohydrate, Protein, DNA chemical compounds Cell Basic biological unit Epidermal cell, Parenchyma cell, Blood cell Tissue A group of similar cells Muscle tissue, Nerve tissue Organ A structure that is composed of different Liver, leaf, eye tissues System Functional unit made up of correlated and Digestive system, Photosynthetic semi-independent parts system Organism Any living thing Animal, Plant or a microbe Population or Similar individual organisms (species) in a Asiatic Lion population in Gir forests Colony specific locality of Gujarat, India; E. coli population in the mouth Biome Major regional community of organisms Grassland biome, Desert biome, defined by the habitat and determined by the Ocean biome interaction of the substrate, climate, flora and fauna Ecosystem A collection that includes all the biotic Marine ecosystem, Himalayan organisms and abiotic components of the total ecosystem environment Biosphere The part of earth that contains all the All ecosystems of Earth ecosystems In a hierarchical relationships in the living systems, we can observe many features or characters. They are summarized below: 1. The principal feature of a biological hierarchy is that the constraints imparted by each of the component 2. Biological hierarchies can undergo decomposition like that of a solar system. Applying a little perturbation energy removes the top levels and as the amount of energy is increased, progressively lower levels are uncoupled 3. A hierarchy can be of two types structural and functional. Structural hierarchy is simpler and can be explained by the forces operating within the system (E.g. Cells are organized into tissues, Structure of proteins). We feel energetic when we have a soft drink. This is a functional hierarchy, cells are influenced by the sugar supply from outside. An animal  cell or plant cell responding to a hormone secreted from outside is another example. Functional hierarchy is also constrained by the mental state regulated by the nervous system. Based on these facts functional hierarchies are more complex to explain. Hence structure and function are correlated at all levels of biological organization 4. Living hierarchies are composed of sub-hierarchies: E.g. Atoms are built into macromolecules like enzymes. These enzymes are indeed a sub-hierarchy i.e. a chemical sub-hierarchy [Other examples: macromolecules self-assemble into cells (cellular sub- hierarchy), cells differentiate into organisms (specialization sub-hierarchy) and organisms form populations by mating patterns (evolution sub-hierarchy).] 5. A pendulum clock simply explains a hierarchical concept. None of its parts can tell time, but a clock as a whole can. Similarly is the living system. The coordinated actions of constrained parts fitting together toward a complex goal. Thus it is it is obvious that the whole is greater than the sum of its parts. 6. A painter begins a part of his whole painting. Later the painting work is elaborated according to the relative size and orientation of the first part. Novel properties that appear at each level of the biological hierarchy as a result of interactions among components at the lower levels. After finishing, the paint dries into the final constrained system. Now the painter assumes that the painting is sufficient to stand by itself as a novel one. Similarly novel properties that appear at each level of the biological hierarchy as a result of interactions among components at the lower levels. Principles of Biology (Ref: Johnson, AT, 2011. Biology for engineers, CRC Press) Biology is a very complex science, since living things are very complex. The study of biology requires inter-disciplinary approach. There are several things to imbibe for other branches of science including engineering. To study biology we need to understand what is happening inside at each hierarchical level. Apart from these we should also look into the surrounding physical, chemical and biological environment. We can develop the principles of biology at this context: 1. The primary goal of life is survival and reproduction [genetic material survives for next generation] 2. Living things are constantly changing [evolves gradually]  3. Long-term changes occur in a species only if there is a reproductive advantage [territorial establishment, mating with strongest and fit partner] 4. Life is redundant 5. Co-existence of species requires that each adapts to a different ecological niche [zebra and wild beast] 6. Attributes passed from one generation to the next require an information legacy [inheritance] 7. Each distinguishing biological trait is made valuable by its cost [species invests some energy in attracting a preferred mate e.g. Dancing of male peacock] 8. An individual is a product of both its genetic code and its environment [influence of environment rabbit coloration] 9. Life is conservative [a species evolves from an existing one] 10. Living things use simple building blocks with complex interactions [polymers proteins, polysaccharides and nucleic acids] 11. Extremes are not tolerated well by living things, nor do living things create extreme conditions. [Life will exploit its environment to the maximum extent as possible E.g. bacteria in hot spring] Life was considered only in terms of physics and chemistry till the recent past. Now it is known to have a third aspect of information that along with the descendant constraints in its hierarchical organization 03: SYMBIOSIS, COEVOLUTION, COMMUNAL BENEFIT, COMMENSALISM AND PARASITISM [Ref: Reece at al., 2011. Campbell Biology, Pearson; Johnson, AT, 2011. Biology for engineers, CRC Press) (Biological units cooperates resulting in an interaction and relationship. This has created different forms and levels of interaction for maximum exploitation of the resources. Organisms are benefited from a communal life style.) Biological units cooperate with other biological units resulting in an interaction and relationship. This makes an effectively functioning whole organism. The gills gather oxygen, the heart circulates blood, the muscle locomote, the mouth ingests food, the gut digests food, the excretory system eliminates wastes and the liver processes biochemicals. In plants also the biological units cooperate. The root hairs absorb water and nutrients, the xylem and phloem transport materials, the leaves fixes energy from solar photons and cells at various locations emit chemicals for communication. Symbiosis: This is a relationship between dissimilar organisms for the benefit of both the partners. Hence this is a mutualism. This is a +/+ interaction. We can see lot of examples from the environment (1) The association between hermit crab and sea anemone. The anemone attaches to the c the anemone and defended by the stinging cells of anemone (2) Lichens: This is a composite organism. The partners are green algae and fungus. The fungus gains oxygen and carbohydrates from the photosynthetic green alga. The alga gains water, carbon dioxide and mineral salts from the fungus. The fungus also provides protection from desiccation. (3) Mitochondria and chloroplast: It is believed that mitochondria and chloroplasts evolved from prokaryotes that became residents in a larger host cell in an attempt to exploit environment by few biochemical mechanisms.  (Image credit: http://evolution.berkeley.edu/evolibrary/article/history_24) Coevolution: In this type of example two or more species have developed a mutual dependence that is very profound and essential. Many species of flowering plants coevolved with specific pollinators. A perfect example can be seen in the case of the Madagascar orchid and its pollinator moth. The orchid produces nectar at the base of a foot long spur. When Charles Darwin saw this orchid for the first time, he predicted the existence of a moth with a proboscis (tongue) long enough to reach that nectar. Later this moth was discovered. (Image credit: http://zooblogogy.tumblr.com/post/39029261422/during-his-trip-to-madagascar- charles-darwin) Another example of coevolution is the Trematolobelia singularis, a flower found in Hawaii. The flowers are borne in clusters with distinct curve exactly fits the beak of Hawaiian nectar-eating Communal benefit: Look at the following interaction in which when a single ant cannot bridge the gap between two leaves to be used in a nest, the worker ants arrange themselves in chains and pull together to close the gap. The entire community is benefited from this behavior. (Image credit: https://www.catersnews.com/viewstory.php?id=1788) Bacteria and their communal behavior: Biofilms are the complex, multilayered, multispecies consortia of microbes. These aggregations form sticky and persistent coatings on surfaces. Biofilms are more resistant to some physical forces like a shear flow. It also well tolerates antimicrobial agents at concentrations much higher than an individual bacteria. Bacteria within biofilms may also be better adapted to withstand nutrient deprivation, pH changes, oxygen radicals, disinfectants and antibiotics than planktonic bacteria. Biofilm formation is also a mechanism that enables bacteria to remain within a favorable environmental niche. By living together, they can specialize and divide the labor. Hence biofilms are interactive communities. They also provide an opportunity with higher rates of gene transfer. Therefore biofilm formation is a communal behavior of many bacteria Surgical equipment and catheters are susceptible to biofilm formation by bacteria. This is a great threat. It will be more severe if the bacteria in the biofilm is drug resistant. Commensalism: This is an interaction of +/o type. This is an interaction between species that benefits one of the species but neither harms nor helps the other. Cowbirds and cattle egrets feed on insects flushed out the grass by a grazing cattle. The birds increases their feeding rates by following an herbivore and clearly benefit from the association. On the other hand the cattle is unaffected or not benefited from the association. However, cattle may sometimes derive some Parasitism: Parasitism is an interaction in which one organism is benefited, while the other is harmed. Therefore this is a +/- symbiotic interaction. The organism benefited is known as the parasite and the affected organism is called the host. The host is harmed in this process. Parasites can be endoparasites (E.g. Round worms) or ectoparasites (E.g. Ticks and Mites).  Communications: Neural and humoral, autonomous nervous sytem Brain is acting as the control center of animals. It is interesting to see how communications are made between central nervous system and immune cells. It happens in three routes which can act as parallel. The illustration is as follows Pathways involved in the immune-to-brain communication. Three pathways participate in the immune-to-brain communication: humoral, neural and cellular (leukocyte) routes. Macrophages sense the presence of pathogens through chemical mechanism. Infections and injury lead to inflammation. This activates signalling pathways. “Neurons communicate with each other through electrical and chemical signals, The electrical signal, or action potential, runs from the cell body area to the axon terminals, through a thin fiber called axon. Some of these axons can be very long and most of them are very short. The electrical signal that runs along the axon is based on ion movement. The speed of the signal transmission is influenced by an insulating layer called myelin, Myelin is a fatty layer formed and its main purpose is to insulate the neuron’s axon. This prevent neuronal impulses from spreading in unwanted directions. The lipid-rich myelin sheath, therefore, acts as an insulator, offering high transverse resistance and only allowing a current to flow along with the segments. Myelin has properties of low capacitance and high electrical resistance which means it can act as an insulator The brain is one the most complicated machine. Its function is to receive and send signals. It happens through the nervous system. The general organization of the nervous system is as follows The signals received are of different types and has to be processed separately. Further the signals are received and communicated through different structural organizations (tissues/bones etc) The living systems has solved this issue with the help of modifying the structure of neurons. Thus we have different types of neurons  Evolution Introduction Evolution means change over a period of time. The idea that living beings may have evolved from simple compounds is a fascinating concept. Evolution is the process by which modern organisms have descended from ancient organisms. In other words, species are not constant, they change over time. The change observed so that the population is better adapted to their environment. The study of evolution provides an insight into the investigation for nature of life, origins of life, diversity of various living beings and the similarities and differences in their structure and function. The origin of life has different theories and these theories are uncertain. The major theories for the origin of life are: 1) Special creation This theory is supported by most religions, civilizations. The basis of this theory is that life was created by a supernatural power at a particular time. While this theological approach concentrates on the reason behind creation of beings scientific theories concentrate on the how these beings came into existence. There is no intellectual conflict between scientific and theological theories as they are mutually exclusive realms of thought. 2) Spontaneous creation The theory suggested that life arose from non-living matter. This theory wa highly popular and coexisted with the special creation theory. Aristotle (384-322 BC) believed in this theory and said that life did not arise just from pre-existing parents but also from by spontaneous generation due to natural forces. This theory fell from favor as more advancements in science. In 1688, Redi observed that the little worms which arise in decaying flesh were fly larvae. He supported the idea of biogenesis, which states that life can arise only from pre-existing life. In 1765, Lazzaro Spallanzani observed that vegetables would not support growth of other life forms after intense heat treatment and sealing. Based on Spallanzani’s work Louis Pasteur designed several experiments and finally disapproved the theory of spontaneous creation. 3) Cosmozoan This theory does not suggest a mechanism for origin of life but favors the idea that life on earth has an extraterrestrial origin. In 1908, Arrhenius proposed the cosmozoan or panspermia theory. This theory assumed the existence of advanced civilization on other planets in our galaxy and life on earth and many other planets were infected from these advanced civilized planets. 4) Biochemical evolution As per this theory, life arose as per the chemical and physical laws. In 1923, Oparin suggested that from the simple compound like nitrides, oxides, ammonia, methane many complex organic compounds were formed gradually under the influence of electric charges, ultra-violet rays. The accumulation of the simple compounds in the oceans resulted in the production of the primeval soup from which life could have arisen. In 1953, Stanley Miller a graduate student of Harold Urey designed an apparatus for stimulating condition prevalent on earth at the time of abiogenic evolution of organic substances. The apparatus has a spark chamber with two electrodes, a flask for boiling and a condenser. Miller used a mixture of methane ammonia, hydrogen and water. The mixture was exposed to electric discharges, following by condensation and then boiling. It was continued for 18 days. Miller was able to identify 15 amino acids, organic acid, ribose sugar and purine, adenine. Several theories were propounded to explain the evolution. Lamarck’s theory of evolution Jean Baptiste Lamarck was a French naturalist who proposed a theory based on inheritance of acquired characteristics the offspring then adapt further, advancing evolution of the species. He explained that the use and disuse of certain abilities led to the organism to gain or lose the ability. In support of Lamark’s theory, some of the characters indeed passed from parents to offspring like development of strong biceps muscles in blacksmith, elongated body and loss of limbs in snakes due to continuous creeping through the holes and crevices, migration of both the eyes towards the upper side in flat fishes living on the bottom of sea, lengthening of neck in the giraffe due to its continuous use in reaching to the leaves and fruits of high rise tree. This theory put more importance on need of the animal and considers it strong enough to device ways to form organs needed for adaptation. This theory was discredited as the use or disuse of all the abilities does not cause transfer abilities to next generation (eg. healthy parents need not always have healthy children). The experiments carried out by August Weismann proved to be a major criticism against Lamarkism. He had cut off the tails of rats for about 80 generations, but tailless offsprings were never born, Theory of Natural selection: In June 1831, the H.M.S. Beagle set sail from England and 22 year-old Charles Darwin took up an unpaid position on this voyage. Darwin had begun his studies as a medical student, then became a divinity student at Cambridge. But neither field excited him, much to his father’s disappointment. Darwin become interested in geology and spent some time studying geology informally. After three years of surveying the South American coast, the Beagle reached San Cristobal (Chatham) in September 1835. The Beagle spent 5 weeks in the Galapagos. The voyage helped Darwin to observe the variety of differences which occurred in the same species on these different islands. Also, he observed completely different species exclusive to some islands. Thus Darwin’s greatest scientific contribution was that he could provide a logical insight into how and why evolution occurred. Charles Darwin propounded the theory of Natural selection. When there are differences in organism’s abilities to survive and reproduce based upon inheritable traits natural selection takes place. As per Thomas Malthus, every generation in a species, more offspring are produced than actually survive due to limited resources. Survival of any individual is not random, and it depends on hereditary factors. Those individuals with favorable inheritable traits will survive and reproduce. Those with less favorable inheritable traits will be eliminated. This will lead to a gradual change in the entire population, favorable hereditary variations accumulating over time and the species will change. Darwin devoted 20 years in generating evidence to support his ideas. Wallace wrote to Darwin telling him his ideas on natural selection. This geared Darwin into publishing his ideas. Thomas Wallace and Darwin agreed to publish similtaneous papers. Darwin's book, The Origin of Species, was an immediate sensation. Darwin has described his views on evolution as follows: “Thus, from the war of nature, from famine and death, the most exalted object which we are capable of conceiving, namely, the production of higher animals, directly follows. There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.” There are several observed cases of Natural selection. 1. Insects resistance to insecticides Insecticides are sprayed on crops to protect them from attack of various insects. Some insects which are resistant to the insecticides, survive the use of insecticides on crops. Thus their progeny flourishes, while the others which are susceptible will be killed by the insecticides. This is a result of genetic variability in the population of insects. Those with the beneficial genetic makeup will survive and flourish. 2. Bacterial resistance to antibiotics Antibiotics are targeted against bacteria. Some bacteria possess the antibiotic resistance gene in their plasmid. They can survive even in the presence of antibiotics. Bacteria have the capacity to transfer the plasmid to other bacteria by transformation. Therefore all the bacteria with the plasmid having antibiotic resistance gene survive in the presence of antibiotic. 3. Increased frequency of sickle cell anemia in Africans. The protein in red blood cells (RBCs) that transports oxygen from the lung to metabolically active tissues, like muscle, where it is needed. The discovery of haemoglobin S (HbS) by Linus Pauling and colleagues in 1949 was the first demonstration that the production of an abnormal protein could be the cause of a genetic disorder. In 1956, Vernon Ingram identified the abnormality in the amino acid sequence of the β-globin chain (β6Glu→Val). This abnormality resulted in the normal concave cells gaining a sickled appearance. Figure 1- The structure of hemoglobin protein in the RBCs. Sickle cell anemia id produced due to mutation event in the beta chain of hemoglobin. Figure 2- The abnormal cells of RBC as seen in Sickle cell Disease (SCD) compared with the normal RBCs. The sickle shape of the abnormal cells obstructs the blood flow and causes blood blockage in the thin capillaries causing extreme pain. Figure 3- The gene for the beta chain of hemoglobin in normal RBCs codes for glutamic acid, which is hydrophilic in nature. The mutation in the gene coding for beta chain changes the codon on the mRNA to code for valine instead of glutamic acid. Valine is hydrophobic in nature. Figure 4-Basic pathophysiological mechanism of sickle cell disease: the polymerization of deoxy-HbS. The replacement of a glutamic acid by a valine residue at position 6 in the β-globin polypeptide chain characterizes the abnormal haemoglobin of SCD: HbS. The presence of hydrophobic valine in the beta chain acts as a hydrophobic pocket to which the other hydrophobic residues (phenylalanine and leucine) in the beta chain bind. At low oxygen pressure, deoxy-HbS polymerises and gets organised in long polymer fibres that deform, stiffen, and weaken the red blood cell Inheritance of sickle cell anemia  The character of having a sickle cell is recessively inherited and follows the Mendelian pattern of inheritance for a recessive train. The normal cell phenotype is dominant. Figure 5- Inheritance of sickle cell disease. hbA stands for normal RBC gene and hbS stands for sickle shaped RBC gene. The recessive trait of a RBC being sickle shaped is not expressed phenotypically in a heterozygous individual. The phenotype of a sickle cell is expressed in a homozygous recessive individual. Thus the trait follows Mendelian inheritance pattern for a recessive character. The sickle cell eventually bursts and dies. Under low oxygen conditions (high altitude or after rigorous exercise), a heterozygous individual for the sickle cell trait, RBCs start showing the sickled phenotype. These heterozygous individuals realize oxygen scarcity in their cells under such conditions as the sickling of cells reduces the oxygen carrying capacity of RBCs. Sickle cell and resistance to malaria: The reduced oxygen carrying capacity gives the heterozygous individual protection against malaria. Malaria pathogen completes a part of its early life cycle in the RBCs. The early stages of the malaria pathogen’s development requires oxygen to complete its life cycle. Since in the heterozygous individuals the RBCs have a low capacity to carry oxygen, the malaria pathogen is not able to survive. Thus, the heterozygous and homozygous recessive individuals are protected from malaria. Figure 6- SCD and malaria resistance. Evolution to protect against death by malaria: The effect of natural selection is evident in the distribution of the sickle cell trait in areas where malaria is found to be indigenous. Thus, hinting that the process of evolution may have used the sickle cell trait as a protection against malaria, in these regions. Figure 7- Geographic distribution of malaria and the appearance of sickle cell trait. Darwin’s theory of natural selection was had one major loophole. The theory could not explain the inheritance of traits from one generation to next. Existence of vestigial organs could not be explained using natural selection. Overspecialisation of some structures like antlers and tusks of elephants becomes a hindrance to these organisms. This fact that these structures that were hindrance to the organism being inherited could not be explained. Importance of Population genetics: Natural selection is understood on observing the changes which occur in a population rather than in an individual. Technically, evolution results from the change in gene frequencies within a population overtime. Therefore, in order to understand evolution, it would be important to describe those events that change gene frequencies in a population. Darwin could not explain how adaptive inheritable traits are passed on. Biologists did not have a good understanding of the genetic details of how natural selection works until the field of transmission genetics was established in the early 1900s. At that time, the rediscovery of Gregor Mendel’s publications paved the way for the development in the 1930s and 1940s of the field of population genetics. As the principles of evolution were integrated with the principles of modern genetics during this period, a new understanding of evolutionary biology—known as the Modern Synthesis—emerged. This was when biologists began to study mechanistic aspects of evolution as well as the broad evolutionary patterns that were so evident in nature. There are several evidence for evolution: 1. Fossil evidence: Fossils are the preserved remains of ancient organisms. The remains of the organisms can be found in preserved form in sap, mineral replacement, in ice, or traces e.g. footprints, molds. Fossils demonstrate the existence of intermediate forms of species, thus demonstrating evolution. The given figure shows how the ancient whales spent more time immersed, hence their nostrils where at the tip of the nose. Over the years, as they migrated to seas, the nostrils occupied a space higher on the skull. At present, whales can break the surface of sea because their nostrils are on the top beginning of Figure 8- Ancient whales spent more time immersed, hence their nostrils where at the tip of the the skull. nose. Over the years, as they migrated to seas, the nostrils occupied a space higher on the skull. At present, whales can break the surface of sea because their nostrils are on the top beginning of the skull.  2. Embryonic evidence: The embryonic stages of various organisms share similar features for eg. the duck and chick embryo both have presence of webbed feet (Fig. 2). The later stages of development in the chick embryo causes the death of the layer in the interdigital zone since the chick has no use of webbed feet in its habitat. Figure 9- The embryo of duck and chick share a common structure initially. The molding of limbs in duck and chick embryo 3. Genetic evidence: The DNA sequences in a gene family are usually different from one another. As long as at least one member encodes a functional protein, the other members may mutate in ways that change the functions of the proteins they encode. For evolution, the availability of multiple copies of a gene allows for selection of mutations that provide advantages under certain circumstances. If a mutated gene is useful, it may be selected for in succeeding generations. If the mutated gene is a total loss (pseudogene), the functional copy is still there to carry out its role. The presence of pseudogenes is an evidence of evolution in the gene. The gene family encoding the globins is a good example of the gene families found in vertebrates (Fig. 3). These proteins are found in hemoglobin and Figure 11- A pathway for evolution of globin genes. (1) It is thought10-Evolution Figure that the modern globin of globin gene has evolved from an gene myoglobin (an oxygen-binding protein present in muscle). The ancestral form as the result of fusion between two of the globin exons. (2) A primitive globin gene has one exon. (3) Duplication globin genes all arose long ago from a single common of the globin gene followed by (4) a mutation that produced two differ