Concepts of Evolution and DNA in Biology

Concepts of Evolution and DNA in Biology Because the fossil record did not exhibit Darwins predicted slow and gradual evolution with transitional forms, some paleontologists sought to find a theory of evolution where, changes in populations might occur too rapidly to leave many transitional fossils (see Figure from Gould and Eldredge 1977 . In 1972, Gould and Eldredge proposed the theory of punctuated equilibrium where most evolution takes place in small populations over relatively rapid geological time periods. By reducing the numerical size of the transitional population and the number of years for which it exists, punctuated equilibrium greatly limits the number of organisms bearing transitional characteristics. Since many organisms are not fossilized, this increases the likelihood that transitional forms would not be fossilized. One strength of this theory is that Gould and Eldredge claim it is predicted by population genetics. But what are the implications of punctuated equilibrium? Under punctuated equilibrium, species usually change little as, gradual change is not the normal state of a species. Large populations may experience, minor adaptive modifications of fluctuating effect through time but will rarely transform in toto to something fundamentally new. This is called stasis. But small peripheral populations may allow for more change at a quicker rate. Gould argued that most macroevolutionary change takes place in such populations during speciation such that there is insufficient time for the transitional forms to be fossilized: Speciation, the process of macroevolution, is a process of branching. And this branching â‚ ¬Ã‚ ¦ is so rapid in geological translation (thousands of years at most compared with millions for the duration of most fossil species) that its results should generally lie on a bedding plane, not through the thick sedimentary sequence of a long hillslope. What is meant by phylogeny? Give an account on phylogeny of humans. Ans- The context of evolutionary biology is phylogeny, the connections between all groups of organisms as understood by ancestor/descendant relationships. Not only is phylogeny important for understanding paleontology, but paleontology in turn contributes to phylogeny. Many groups of organisms are now extinct, and without their fossils we would not have as clear a picture of how modern life is interrelated. We express the relationships among groups of organisms through diagrams called cladograms, which are like genealogies of species. Phylogenetics, the science of phylogeny, is one part of the larger field of systematics, which also includes taxonomy. Taxonomy is the science of naming and classifying the diversity of organisms. In humans- it is used to the transfer of genes. In general, organisms can inherit genes in two ways: vertical gene transfer and horizontal gene transfer. Vertical gene transfer is the passage of genes from parent to offspring, and horizontal gene transfer or lateral gene transfer occurs when genes jump between unrelated organisms, a common phenomenon in prokaryotes. Horizontal gene transfer has complicated the determination of phylogenies of organisms, and inconsistencies in phylogeny have been reported among specific groups of organisms depending on the genes used to construct evolutionary trees. Carl Woese came up with the three-domain theory of life (eubacteria, archaea and eukaryotes) based on his discovery that the genes encoding ribosomal RNA are ancient and distributed over all lineages of life with little or no horizontal gene transfer. Therefore, rRNAs are commonly recommended as molecular clocks for reconstructing phylogenies. This has been particularly useful for the phylogeny of microorganisms, to which the species concept does not apply and which are too morphologically simple to be classified based on phenotypic traits. DNA is genetic material. Describe two classical experiments to support this statement. Ans- Clarification came during the First World War. During the war, hundreds of thousands of servicemen died from pneumonia, a lung infection caused by the baceterium Streptococcus pneumoniae. In the early 1920s, a young British army medical officer named Frederick Griffith began studying Streptococcus pneumoniae in his laboratory in the hopes of developing a vaccine against it. As so often happens in scientific research, Griffith never found what he was looking for (there is still no vaccine for pneumonia), but instead, he made one of the most important discoveries in the field of biology: a phenomenon he called transformation. Dr. Griffith had isolated two strains of S. pneumoniae, one of which was pathogenic (meaning it causes sickness or death, in this case, pneumonia), and one which was innocuous or harmless. The pathogenic strain looked smooth under a microscope due to a protective coat surrounding the bacteria and so he named this strain S, for smooth. The harmless strain of S. pneumoniae lacked the protective coat and appeared rough under a microscope, so he named it R, for rough . Dr. Griffith observed that if he injected some of the S strain of S. pneumoniae into mice, they would get sick with the symptoms of pneumonia and die, while mice injected with the R strain did not become sick. Next, Griffith noticed that if he applied to the S strain of bacteria, then injected them into mice, the mice would no longer get sick and die. He thus hypothesized that excessive heat kills the bacteria, something that other scientists, including Louis Pasteur, had already shown with other types of bacteria. However, Dr. Griffith didnt stop there he decided to try something: he mixed living R bacteria (which are not pathogenic) with heat-killed S bacteria, then he injected the mixture into mice. Surprisingly, the mice got pneumonia infections and eventually died (Figure 3). Dr. Griffith examined samples from these sick mice and saw living S bacteria. This meant that either the S bacteria came back to life, an unlikely scenario, or the live R strain was somehow transformed into the S strain. Thus, after repeating this experiment many times, Dr. Griffith named this phenomenon transformation. This discovery was significant because it showed that organisms can somehow be genetically re-programmed into a slightly different version of themselves. One strain of bacteria, in this case the R strain of S. pneumoniae, can be changed into something else, presumably because of the transfer of genetic material from a donor, in this case the heat-killed S strain. Scientists around the world began repeating this experiment, but in slightly different ways, trying to discover exactly what was happening. It became clear that, when the S bacteria are killed by heat, they break open and many substances are released. Something in this mixture can be absorbed by living bacteria, leading to a genetic transformation. But because the mixture contains protein, RNA, DNA, lipids, and carbohydrates, the question remained which molecule is the transforming agent? This question was examined in several ways, most famously by three scientists working at The Rockefeller Institute (now Rockefeller University) in New York: Oswald Avery, Colin MacLeod, and Maclyn McCarty. These scientists did almost exactly what Griffith did in his experiments but with the following changes. First, after heat-killing the S strain of bacteria, the mixture was separated into six test tubes. Thus, each of the test tubes would contain the unknown transforming agent. A different enzyme was then added to each tube except one the control which received nothing. To the other five tubes, one of the following enzymes was added: RNase, an enzyme that destroys RNA; protease, an enzyme that destroys protein; DNase, an enzyme that destroys DNA; lipase, an enzyme that destroys lipids; or a combination of enzymes that break down carbohydrates. The theory behind this experiment was that if the transforming agent was, for example, protein the transforming agent would be destroyed in the test tube containing protease, but not the others. Thus, whatever the transforming agents was, the liquid in one of the tubes would no longer be able to transform the S. pneumonia strains. When they did this, the result was both dramatic and clear. The liquid from the tubes that received RNase, protease, lipase, and the carbohydrate-digesting enzymes was still able to transform the R strain of pneumonia into the S strain. However, the liquid that was treated with DNase completely lost the ability to transform the bacteria . Thus, it was apparent that the transforming agent in the liquid was DNA. To further demonstrate this, the scientists took liquid extracted from heat-killed S. pneumoniae (S strain) and subjected it to extensive preparation and purification, isolating only the pure DNA from the mixture. This pure DNA was also able to transform the R strain into the S strain and generate pathogenic S. pneumoniae. These results provided powerful evidence that DNA, and not protein, was actually the genetic material inside of living cells. PART-B Do the two strands of DNA duplex carry the same genetic information? Explain. Ans:- No,the two strands of dna duplex carry different information ,because  complementary  base pairs  binding to form a  double helix.The two chains are wound round each other and linked together by hydrogen bonds between specific complementary bases to form a spiral ladder-shaped moleculeThe stabilization of  duplex  (double-stranded) DNA is also dependent on base stacking. The planar, rigid bases stack on top of one another, much like a stack of coins. Since the two purine.pyrimidine pairs (A.T and C.G) have the same width, the bases stack in a rather uniform fashion. Stacking near the center of the helix affords protection from chemical and environmental attack. Both hydrophobic interactions andvan der Waals forces  hold bases together in stacking interactions. About half the stability of the DNA helix comes from hydrogen bonding, while base stacking provides much of the rest. What is the difference between Z and B- DNAs? ANS:- Z-DNA  is one of the many possible double helical structures of  DNA. It is a left-handed double helical structure in which the double helix winds to the left in a zig-zag pattern. alternating  purine-pyrimidine  sequence (especially poly(dGC)2), negative  DNA supercoiling  or high salt and some  cations  (all at physiological temperature, 37 °C, and pH 7.3-7.4). Z-DNA can form a junction (called a B-to-Z junction box) in a structure which involves the extrusion of a base pair.  The Z-DNA conformation has been difficult to study because it does not exist as a stable feature of the double helix. Instead, it is a transient structure that is occasionally induced by biological activity and then quickly disappears. B-DNA It is an antiparallel double helix.It is a right-handed helix. The base-pairs are perpendicular to the axis of the helix. (Actually, they are very slightly tilted at an angle of 4 degrees)The axis of the helix passes through the centre of the base pairs.Each base pair is rotated by 36 degrees from the adjacent base pair.The base-pairs are stacked 0.34 nm apart from one another.The double helix repeats every 3.4 nm, i.e. the pitch of the double helix is 3.4 nm.B-DNA has two distinct grooves: a MAJOR groove; and, a MINOR groove. These grooves form as a consequence of the fact that the beta-glycosidic bonds of the two bases in each base pair are attached on the same edge. However, because the axis of the helix passes through the centre of the base pairs, both grooves are similar in depth. 6. What is the role of RNA in DNA replication? ANS:- RNA WAS NEED TO INTIATE THE TRANSCRIPTION PROCESS.   On the lagging strand, primase builds an RNA primer in short bursts. DNA polymerase is then able to use the free 3 OH group on the RNA primer to synthesize DNA in the 5 † Ã¢â‚¬â„¢ 3 direction. The RNA fragments are then removed (different mechanisms are used in eukaryotes and prokaryotes) and new deoxyribonucleotides are added to fill the gaps where the RNA was present. DNA ligase is then able to ligate the deoxyribonucleotides together, completing the synthesis of the lagging strand. This rna primer was a short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementarystrand.