DNA Structure and Properties PDF

DNA STRUCTURE AND PROPERTIES DNA (DEOXYRIBONUCLEIC ACID) The hereditary material in humans and almost all other organisms. Carries genetic material of an organism. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in t...

DNA STRUCTURE AND PROPERTIES DNA (DEOXYRIBONUCLEIC ACID) The hereditary material in humans and almost all other organisms. Carries genetic material of an organism. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria (where it is called mitochondrial DNA or mtDNA). Chloroplast also contains DNA. COMPONENTS OF A NUCLEOTIDE Phosphate Pentose sugar Nitrogenous base THE NITROGENOUS BASES (DNA) Divided into two groups: a. PYRIMIDINES (Thymine and Cytosine) b. PURINES (Adenine and Guanine) SALIENT FEATURES OF THE DOUBLE- HELIX STRUCTURE OF DNA: It is made of two polynucleotide chains, where the backbone is constituted by sugar-phosphate, and the bases project inside. The two chains have anti- parallel polarity. It means, if one chain has the polarity 5’ 3’, the other has 3’ 5’.  The bases in two strands are paired through hydrogen bond (h-bonds) forming base pairs (bp). Adenine forms two hydrogen bonds with thymine from opposite strand and vice-versa. Similarly, guanine is bonded with cytosine with three h- bonds. Based on the observation of Erwin Chargaff that for a double stranded DNA, the ratios between adenine and thymine; and guanine and Cytosine are constant and equals one. CHARGAFF’S RULE The amount of adenine = the amount of thymine. The amount of cytosine = the amount of guanine. This rule indicated that the DNA is symmetrical. THE CENTRAL DOGMA OF MOLECULAR BIOLOGY A theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein THE CENTRAL DOGMA OF MOLECULAR BIOLOGY Replication creates new copies of DNA. Transcription creates an RNA using DNA information. Translation creates a protein using RNA information. DNA REPLICATION DNA replication is the process of producing two identical replicas from one original DNA molecule. This biological process occurs in all living organisms as basis of biological inheritance. DNA REPLICATION DNA replication is semi- conservative. Each newly synthesized molecule contains 1 “parent template” strand and 1 new “daughter” strand. KEY ENZYMES IN DNA REPLICATION ENZYME FUNCTION Helicase Unwinds the DNA double helix at the replication fork Primase Provides starting point of RNA for DNA polymerase to begin synthesis of new DNA strand DNA Polymerase Adds new nucleotides to 3’ end of elongating strand. Dismantles RNA primer. Proofreading and error correction. DNA Ligase Re-anneals the semi-conservative strands and joins Okazaki fragments of the lagging strands. Topoisomerase Relaxes the supercoiled nature of the DNA. Single-strand Binding Bind to ssDNA and prevent the DNA double helix from re- (SSB) Proteins annealing after DNA helicase unwinds, thus maintaining the strand separation. TRANSCRIPTION This process involves the synthesis of mRNA from DNA. The DNA code is transferred to mRNA inside the nucleus. TRANSLATION The process of reading the RNA sequence of an mRNA and creating the amino acid sequence of a protein. VARIATIONS naturally occurring genetic differences among individuals of the same species. MENDEL’S LAWS OF INHERITANCE MENDEL’S 1ST LAW OF INHERITANCE: Law of Dominance The law of dominance states that in a heterozygous pair of alleles, one trait will conceal the presence of another trait for the same characteristics. The dominant allele masks the recessive allele. MENDEL’S 2ND LAW OF INHERITANCE: Law of Segregation This law explains that the pair of alleles segregate from each other during gamete formation (meiosis) so that only one allele will be present in each gamete. MENDEL’S 3RD LAW OF INHERITANCE: Law of Independent Assortment This law states that the alleles of two (or more) different genes gets sorted into gametes independently of one another. It also states that during fertilization, the genes come together again to form new set of combinations. MENDEL’S 3RD LAW OF INHERITANCE: Law of Independent Assortment MONOHYBRID CROSS DIHYBRID CROSS  NON-MENDELIAN PATTERNS OF INHERITANCE  Non Mendelian Patterns of Inheritance Multiple Alleles  The majority of human genes are thought to have more than two normal versions, or alleles. Traits controlled by a single gene with more than two alleles are called multiple allele traits.  An example is ABO blood type. Your blood type refers to which of certain proteins called antigens are found on your red blood cells. There are three common alleles for this trait, which are represented by the letters A, B, and O. ABO blood group Phenotype Antigens on Red Plasma Genotypes (blood group) Blood Cells Antibodies A IAIA , IAIO A Anti-B B IBIB , IBIO B Anti-A AB I AI B A and B None o I OI O None Anti-A and Anti-B  Non Mendelian Patterns of Inheritance  There are six possible ABO genotypes, because the three alleles.  The A and B alleles are dominant to the O allele. As a result, both AA and AO genotypes have the same phenotype, with the A antigen in their blood (type A blood). Similarly, both BB and BO genotypes have the same phenotype, with the B antigen in their blood (type B blood). No antigen is associated with the O allele, so people with the OO genotype have no antigens for ABO blood type in their blood (type O blood).  Non Mendelian Patterns of Inheritance Codominance  Another example that is non- Mendelian is codominance which describes a situation in which both alleles are expressed at the same time.  Codominance occurs when two alleles for a gene are expressed equally in the phenotype of heterozygotes.  Look at the genotype AB in the ABO blood group table. Alleles A and B for ABO blood type are neither dominant nor recessive to one another.  Non Mendelian Patterns of Inheritance Incomplete Dominance Another relationship that may occur between alleles for the same gene is incomplete dominance. This occurs when the dominant allele is not completely dominant. In this case, an intermediate phenotype results in heterozygotes who inherit both alleles.  Non Mendelian Patterns of Inheritance Polygenic Traits  Many human traits are controlled by more than one gene. These traits are called polygenic traits.  The alleles of each gene have a minor additive effect on the phenotype. There are many possible combinations of alleles, especially if each gene has multiple alleles. Therefore, a whole continuum of phenotypes is possible.  Human height, complexion or skin color, eye color, and hair color are examples of polygenic traits.  Non Mendelian Patterns of Inheritance Pleiotropy  Some genes affect more than one phenotypic trait. This is called pleiotropy.  There are numerous examples of pleiotropy in humans. They generally involve important proteins that are needed for the normal development or functioning of more than one organ system.  Non Mendelian Patterns of Inheritance Epistasis  Some genes affect the expression of other genes, this is called epistasis.  Epistasis is similar to dominance, except that it occurs between different genes, rather than between different alleles for the same gene. What is the Geologic Time Scale? The geologic time scale (GTS) is a record that depicts Earth’s history and at the same time, the order of life from 2500 million years ago (mya) to the present. GTS divides up the history of the earth based on life-forms that have existed during specific times since the creation of the planet. These divisions are called geochronologic units.  The Geologic Time Scale is divided by the following divisions: ✓Eons: Longest subdivision; based on the abundance of certain fossils ✓Eras: Next to longest subdivision; marked by major changes in the fossil record ✓Periods: Based on types of life existing at the time ✓Epochs: Shortest subdivision; marked by differences in life forms and can vary from continent to continent. 38 39 40 Major Groups of Organisms That Existed in the Early Years 41 A. Early Invertebrates (Cambrian Period, 442-488 mya and Ordovician Period, 448-444 mya) Brachiopods- lived in shells resembling those of clams or cockles, and animals with jointed, external skeletons known as arthropods—the ancestors of insects, spiders, and crustaceans. Trilobites, Anomalocaris, Pikaia gracilens 42 B. Early Coral Reefs, Fishes, Vascular Plants Silurian Period (444-416 mya) Crinoids, brachiopods, oldest known fossils of coral reefs. jawless fish, appearances of both the first known freshwater fish and the appearance of jawed fish, early vascular plants such as Cooksonia Devonian Period (416-359 mya) Placoderms (the armored fishes) Bony fishes (e.g. Ray-finned fish) Lobe-finned fish (fleshy pectoral and pelvic fins articulating to the shoulder or pelvis by a single bone (humerus or femur), which was powered by muscles within the fin itself) Lycophytes, horsetails, and ferns First tetrapods and insects 43 C. Amphibians, Origins of Reptiles, First Seed Plants Carboniferous Period (359-299 mya), famous for its vast swamp forests, which swamps produced the coal from which the term Carboniferous, or "carbon-bearing," is derived. Ferns and fernlike trees; giant horsetails, called calamites; club mosses, or lycopods, such as Lepidodendron and Sigillaria; seed ferns; and cordaites, or primitive conifers Early amphibians had had large skulls, small trunks, and stocky limbs (e.g. Calligenethlon, Carbonerpeton, and Diplovertebron) Earliest reptiles, the captorhinid Hylonomus 44 D. Reptiles (Dinosaurs), First Angiosperms, First Mammals Mesozoic Era (Triassic, Jurassic, Cretaceous Period, 251-65.5 mya) Marine reptiles such as Ichthyosaurus (with dolphin-like appearance Dominance of big predators, the Dinosaurs, which became extinct in between Cretaceous-Tertiary periods 45 E. Mammals Cenozoic Era (65.5 – present) First primates and rodents, apes and the first appearance of Homo sapiens (humans) 46 How are natural selection and survival of the fittest related? Because some survive better than others, natural selection tends to eliminate less fit characteristics. The fittest are those with favorable traits adapted to a specific environment. For example, camels and cactuses are adapted to live in dry places like desert. This is because camels are capable of storing large amount of water on their back. Similarly, cacti store water on their fleshy tissues that prevent them from dehydration. Other plants and animals which lack traits similar to camels and cactuses cannot live as well in such excessively dry places. 54 Evidence of Evolution 55  Evidence to support the theory of evolution came from different areas of science. Evidence of evolution are divided into two groups: direct and indirect. 56 Direct Evidence Fossil provides direct evidence for evolution because it can tell what has happened. In other words, it can prove that change in time has occurred. When certain fossils are arranged in the order of how old they are, we can make a direct comparison of their body structures. Through these fossil experts can confirm that species are not fixed but can evolve into other species over time. 57 Table 1. Types of Fossils Type of Fossil Description Examples Molds Impression made in a substrate = Shells negative image of an organism Casts When a mold is filled in Bones and teeth Petrified Organic material is converted into Petrified trees, Coal balls stone (fossilized plants and their tissues, in round ball shape) Original Preserved wholly (frozen in ice, Wooly mammoth; remains/true fossils trapped in tar pits, dried inside Amber from Baltic Sea caves or encased in amber) region Carbon Film Carbon impression in sedimentary Leaf impression on rock rocks Trace/Ichnofossils Record the movements and Trackways, toothmarks, behaviors of the organism burrows and nests 58 DATING FOSSILS Knowing the age of a fossil can help a scientist establish its position in the geologic time scale and find its relationship with the other fossils. There are two ways to measure the age of a fossil: relative dating and absolute dating. RELATIVE DATING ABSOLUTE DATING ✓Based upon the study of layer of rocks ✓Determines the actual age of the fossil ✓Through radiometric dating, using ✓Does not tell the exact age: only radioactive isotopes carbon-14 and compare fossils as older or younger, potassium-40 depends on their position in rock layer ✓Considers the half-life or the time it takes for half of the atoms of the ✓Fossils in the uppermost rock layer/ radioactive element to decay strata are younger while those in the ✓The decay products of radioactive lowermost deposition are oldest isotopes is stable atoms. Rules of Relative Dating 1. LAW OF SUPERPOSITION: Sedimentary layers are deposited in a specific time- youngest rocks on top, oldest rocks at the bottom 2. LAW OF ORIGINAL HORIZONTALITY: Deposition of rocks happen horizontally- tilting, folding or breaking happened recently 3. LAW OF CROSS-CUTTING RELATIONSHIPS: If an igneous intrusion or a fault cuts through existing rocks, the intrusion/fault is YOUNGER than the rock it cuts through. INDEX FOSSILS (guide fossils/ indicator fossils/ zone fossils): fossils from short-lived organisms that lived in many places; used to define and identify geologic periods 60 Indirect Evidence Indirect evidence is something that does not involve actual observation of evolution but for which we can infer that evolution has taken place. Many scientists considered genetics, comparative anatomy, embryology, and biogeography as indirect evidence for evolution. 61 a. Comparative Anatomy Comparing the anatomy and the development of organisms reveals a unity of plan among those that are closely related. The more body structures that two species have in common, the more closely they are related. It supports the idea of “descent from a common ancestor”. This includes: Homologous structures Analogous structures Vestigial structures 62  Similar structures in different species irrespective of their functions are called homologous structures. Homology seems to indicate descent from common ancestor. The skeletons on the limbs of vertebrates are homologous structures. 63  Analogous structures are structures, which are different in appearance but have the same function. Analogy does not indicate common ancestry. Examples of analogous structures are the legs of insects and mammals, and wings of butterflies and birds. 64  Vestigial structures are anatomical features that are usually reduced and have no function in many organisms. These are organs that were once functional in the ancestors of the species but are only remnants in the present species. For example, skeletal limbs found in some snakes have no known use to these animals. In humans, appendix is thought to have no use, but in other mammals it aids in the digestion of cellulose. 65 b. Genetics and Molecular Biology Living things shared several similar biochemical molecules, such as DNA, ATP, amino acids, and enzymes. This finding supports descent from a common ancestor. The more closely related organisms are the more similar is their biochemical makeup. 66  c. Biogeography Biogeography is the study of the distributions of organisms. Darwin’s trip around South America allowed him to observe the diversity of organisms in different areas and the resemblance of such species of birds and tortoises in an island to nearby mainland. Darwin believed that the group of animals in each island is adapted to a different way of life. The common ancestors of these organisms had come from one locale, spreading out into other accessible areas. 67 d. Embryological Development The unity of plan shared by vertebrates extends to their embryological development. The embryonic development of all vertebrates shows remarkable similarities. At some time during development, all vertebrates have a supporting dorsal rod, called a notochord, and exhibit paired pharyngeal pouches. This could indicate that an organism passes through some of the embryonic stages that its ancestors passed through. Then several modifications happen in ways appropriate to an organism’s final form. 68  Look closely at the illustration below. What similarities do you observe among the five vertebrates (fish, salamander, tortoise, chicken and human)? 69 How can evolution or change in gene pool occur? Gene pool pertains to genetic composition of individuals in a population. In real life, animals migrate and find other mates, genes continually mutate, and nature allows the fittest organisms to survive. When these conditions happen, evolution has occurred. 70 a. Non-random mating By non-random mating, we mean that sexual selection is not merely by chance. Individual’s choice of mate is influenced by some physical and behavioral characteristics. For example, white rabbits preferentially mate with rabbits of their own color. In humans, tall women prefer tall men rather than short men. Inbreeding, which is commonly observed in plants and in some kinds of animals, is a very good example of non-random mating. Inbreeding in plants is sometimes called self- fertilization. Animals like dogs, rats, cats, rabbits, pigs, and many other animals practice inbreeding. Inbreeding can result to a population whose members are alike in appearance, fitness, and lifestyles. 71 b. Mutation The organism’s appearance is dictated by the information stored in its chromosomes. So, if the chromosome’s structure or gene composition is changed, the appearance of the organism will also be changed. Any change in the structure of chromosomes and gene composition is called mutation. 72 What causes mutation? There are several agents for mutation (mutagens) like ultraviolet radiation and hazardous chemicals in the environment. These mutagens can change the information stored in individuals’ chromosomes or genes. Therefore, when mutation occurs, the appearance of individuals in the population changes, and the gene pool becomes different from the original population. 73 c. Genetic drift Genetic drift means change in gene pool due to chance alone. Unpredictable disasters or accidents such as earthquakes, floods, fires and diseases can reduce or totally eliminate certain traits in the population. Let’s say flood wiped out a population of ants. No matter how good the ants are adapted to its environment, they could be killed by such event. In this situation, the survival or death of individuals in the population has nothing to do with their fitness. 74  Genetic drift is also observed when a harmful insecticide has killed a big population of fruit fly, leaving a few members with particular trait. The next generation of fruit flies will inherit only the trait present in the survivors. The success of this trait is due to chance but not because it is the fittest trait. 75 d. Gene flow Gene flow occurs when individuals migrate from one population to another. Gene flow increases variations in the population. An effective sharing of traits happens when one migrates and interbreeds with the individuals of newly found population. Often, this results to an increase in the intermediate phenotypes in the population. presentation title 76 e. Natural selection Nature selects which trait will survive and which will not. These organisms with favorable traits, meaning those who are best suited in the environment, have a better chance of survival. The survivors pass on the favorable traits to their offspring, then after many generations, the population will produce organisms with traits that are very different from their ancestors. 77  Systems of Classification and the Species Concept ANNIE MAE Z. CANARIA Subject Teacher SYSTEMATICS TAXONOMY CLASSIFICATION the study of the science of the process of biological diversity identifying, arranging organisms, which focuses on naming, and both living and extinct, the evolutionary classifying into groups based on history of organisms based similar characteristics organisms on natural relationships 80 Linnaean System of Classification Developed by Swedish botanist Carolus Linnaeus in the 1700s. He grouped together organisms that shared obvious physical traits, such as number of legs or shape of leaves. For his contribution, Linnaeus is known as the “father of taxonomy”. 81  The Linnaean system of classification consists of a hierarchy of groupings, called taxa (singular, taxon). Taxa range from the kingdom to the species. The kingdom is the largest and most inclusive grouping. It consists of organisms that share just a few basic similarities. Examples are the plant and animal kingdoms. The species is the smallest and most exclusive grouping. It consists of organisms that are similar enough to produce fertile offspring together. Closely related species are grouped together in a genus. 82 Binomial Nomenclature A method in naming organisms developed by Carolus Linnaeus. Two-word Latin name consisting of the genus name and the species name. (e.g. Homo sapiens) Latin is the language used in binomial nomenclature, mainly because the language is unchanging and is historically the language used in science and education at that time. 83  Species Concepts 20XX Presentation title 84 What constitute a species? For centuries, scientists distinguished one species from another based on the morphological differences, internally and externally. However, there are organisms belonging to different species that can nearly identical, while some members of the same species can look very different. These pairs are examples of organisms look the same but belong to different species. a.) Cactus (Cereus cv.) and Euphorbia (Euphorbia lactea); and b.) Monarch butterfly (Danaus plexippus) and Viceroy butterfly (Limenitis archippus) 85 The following are the different species concepts: 1. Typological/morphological species concept 2. Biological species concept 3. Evolutionary species concept 4. Phylogenetic species concept 86 Typological/morphological species concept This is based on the idea that each species is a distinct group of organisms that shares certain characteristics, which distinguish them from the other species. According to Aristotle, species are unchanging, distinct and a natural group of organisms. Organisms with variations from the known characteristics of the species are considered as different species. 87 Biological species concept This concept came from evolutionary biologists, Theodosius Dobzhansky and Ernst Mayr. According to them, a species is a group of organisms that can interbreed and produce fertile offspring. However, there are limitations to this concept. For an instance, there are animal and plant species belonging to different species that can interbred and produce fertile offspring. Also, this concept does not account for extinct species or species that reproduce asexually. 88 20XX Presentation title 89 90 Evolutionary species concept According to this concept, a species is a single lineage of ancestor-descendant sequence of populations with distinct identity and evolutionary tendencies. If two or more groups evolved independently from an ancestral population these are considered different species. 91