General Biology REVIEW OF GENETICS GENETICS - - Study of inheritance and variation HEREDITY - Is the passing of traits from parents to off-spring. Is the differences among individuals Gregor Johann Mendel Father of Genetics Discovered the fundamental laws of inheritance through his work on pea plants. - - Unit of inherited characteristics from parents to off-spring Deoxyribonucleic acid Genetic materials or the genetic blueprint of an organism Basis for protein production Basic unit: nucleotide which composed of a deoxyribose sugar, phosphate group, nucleobase Characteristics Double helix Bases Purines Pyrimidines Adenine Guanine Thymine Cytosine Adenine Cytosine RNA Ribonucleic acid Version of DNA used in protein synthesis Characteristics Single strand Bases Adenine Guanine Cytosine Uracil Guanine Uracil DOMINANT - Has two identical alleles - Has non-identical alleles PHENOTYPE - Observable trait of an individual - Genetic make-up of an organism PUREBRED Guanine Thymine - - GENOTYPE DNA - Characteristics represented in an individual HETEROZYGOUS GENES - - HOMOZYGOUS GREGOR MENDEL - Allele is fully or partially masked by its partner. This is fully expressed only when it is paired with another recessive allele. ALLELES VARIATION - RECESSIVE Adenine Cytosine Allele masks the expression of its partner on the allelic pair. Thus, it is expressed trait. - An organism that possesses homozygous characteristics HYBRID - An organism that possesses characteristics resulting from its heterozygous alleles. MENDELIAN GENETICS 1. Law of Dominance - if two alleles differ, the dominant allele will be fully expressed while the recessive allele will have no noticeable effect. 2. Law of Segregation – the two alleles for a specific characteristics segregate during meiosis 3. Law of Independent Assortment – the pair of alleles segregates independently NON-MENDELIAN GENETICS 1. Incomplete Dominance – results when two dominant alleles combine to form a phenotype that is in between those to alleles. The expressed trait is not characteristic of the original alleles 2. Codominance – results when two dominant alleles combine and both characteristics are expressed and are discernible (ex. ABO blood groups) 3. Multiple Alleles – more than 2 alleles for a give locus or traits. Dominance hierarchy is important. 4. Sex-linked – genes for specific trait are carried by sex chromosomes of organisms. - Expressive to male - Found in x chromosomes - Dominant in female but more expressive in male PEDIGREE ANALYSIS - - - An ancestral relationship A diagram that shows the phenotype and genotype for a particular organisms and its ancestors. The traits that’s been transmitted from parents to offspring. Common in human family to track disease Involved genes Used to determine the mode of inheritance Important to basic research and counseling Sum and Product Rule DNA REPLICATION - - - - The replication of a DNA molecules begins at special sites, origin of replication. In bacteria, this is a specific sequence of nucleotides that is recognized by the replication enzymes. These enzymes separate the strands, forming a replication “bubble”. Replication proceeds in both directions until the entire molecule is copied. In eukaryotes, there may be hundreds or thousands of origin sites per chromosomes. At the origin sites, DNA strands separate, forming a replication “bubble” with replication forks at each end. The replication bubbles elongate as the DNA is replicated, and eventually fuse. In the circular chromosome of E. coli and many other bacteria, only one origin of replication is present. The parental strands separate at the origin, forming a replication bubble with two forks. Replications proceeds in both directions until the forks meet on the other side, resulting in two daughter DNA molecules. In each linear chromosome, DNA replication begins when replication bubbles form at many sites along the giant DNA molecule. The bubbles expand as replication proceeds in both directions. Eventually the bubbles fuse and synthesis of the daughter strands is complete. - - - - - - - - - - DNA polymerase catalyze the elongation of new DNA at a replication fork. As nucleotides align with complementary bases along the template strand they are added to the growing end of the new strand by the polymerase. The rate of elongation is about 500 nucleotides per second in bacteria and 50 per second in human cells. In E. coli, two different DNA polymerases are involved in replication: DNA polymerase I DNA polymerase III - - - Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate. Each has a nitrogenous base, deoxyribose, and a triphosphate tail. ATP is a nucleoside triphosphate with ribose instead of deoxyribose. Like ATP, the triphosphate monomers used for DNA synthesis are chemically reactive, partly because their triphosphate tails have an unstable cluster of negative charge. The strands in the double helix are parallel. The sugar-phosphate backbones run in opposite directions. Each DNA strands has a 3’ end with a free hydroxyl group attached to deoxyribose and a 5’ end with a free phosphate group attached to deoxyribose. The 5’ -> 3’ direction of one strand runs counter to the 3’ -> 5’ direction of the other strand. DNA polymerases can only add nucleotides to the free 3’ end of a growing strand. A new DNA strand can only elongate in the 5’ -> 3’ direction. Incorporation of a nucleotide into a DNA strand DNA polymerase catalyzes the addition of a nucleoside triphosphate to the 3’ end of the growing DNA strand, with the release of 2 phosphates. Along one template strand, DNA polymerase III can synthesize a complementary strand continuously by elongating the new DNA in the mandatory 5’ -> 3’ direction. The DNA strand made by this mechanism is called the leading strand (continuous). The other parental strand (5’ -> 3’ into the fork), the lagging strand (discontinuous), is copied away from the fork. Unlike the leading strand, which elongates continuously, the lagging strand is synthesized as a series of short segments called Okazaki fragments. Okazaki fragments are about 1,000 – 2,000 nucleotides long in E.coli 100 – 200 nucleotides long in eukaryotes Another enzyme, DNA ligase, eventually joins the sugar-phosphate backbones of the Okazaki fragments to form a single DNA strand. DNA polymerase cannot initiate synthesis of a polynucleotide. They can only add nucleotides to the 3’ end of an existing chain that is base-paired with the template strand. The initial nucleotide chain is called a primer. In the initiation of the replication of cellular DNA, the primer is a short stretch of RNA with an available 3’ end. The primer is 5 – 10 nucleotides long in eukaryotes. Primase, an RNA polymerase, links ribonucleotides that are complementary to the DNA template into the primer. - RNA Polymerases can start an RNA chain from a single template strand. TOPOISOMERASE - - Breaks, swivels, and rejoins the parental DNA ahead of the replication fork, relieving the strain caused by unwinding. HELICASE - - TRANSCRIPTION AND TRANSLATION - Unwinds and separates the parental DNA strands. Untwists the double helix and separates the DNA template strands at the replication forks. SINGLE-STRAND BINDING PROTEIN - Stabilize the unwound parental strands. Keep the unpaired template strands apart during replication. - After formation of the primer, DNA pol III adds a deoxyribonucleotide to the 3’ end of the RNA primer and continues adding DNA nucleotides to the growing DNA strand according to the basepairing rules. Returning to the original problem at the replication fork, the leading strand requires the formation of only a single primer as the replication fork continues to separate. For synthesis of the lagging strand, each Okazaki fragment must be primed separately. Another DNA polymerase, DNA polymerase I, replaces the RNA nucleotides of primers with DNA versions, adding them one by one onto the 3’ end of the adjacent Okazaki fragment. The primers are converted to DNA before DNA ligase joins the fragments together. In addition to primase, DNA polymerases, and DNA ligases several other proteins have prominent roles in DNA synthesis. To summarize, at the replication fork, the leading strand is copied continuously into the fork from a single primer, The lagging strand is copied away from the fork in short segments, each requiring a new primer. If there is an incorrect pairing, the enzymes remove the wrong nucleotide and then resumes synthesis. The final error rate is only one per ten billion nucleotides. FUNCTIONS OF RNA rRNA – ribosomal RNA makes up about 60% of ribosomal structure. mRNA - messenger RNA record information from DNA and carry it to ribosomes. tRNA – transfer RNA delivers amino acids to proteins at the ribosome to extend the chain. TRANSCRIPTION - - - - - - - - Synthesis of leading and lagging strand occur concurrently and the same rate. The lagging strand is so named because its synthesis is delayed slightly relative to synthesis of the leading strand, each new fragment of the lagging strand cannot be started until enough template has been exposed at the replication fork. Enzymes proofread DNA during its replication and repair damage in existing DNA. Mistakes during the initial pairing of template nucleotides and complementary nucleotides occur at a rate of one error per 100,000 base pairs. DNA polymerase proofreads each new nucleotide against the template nucleotide as soon as it is added. - The synthesis of mRNA from a DNA template Occurs in the 5’ -> 3’ direction Involves RNA polymerase mRNA, tRNA, rRNA, must all be transmitted for protein synthesis to take place 1. INITIATION - RNA polymerase binds to the promoter site - Promoter means the region of DNA when RNA polymerase attaches and initiates transcription - Determines which strand of DNA will serve as the template - RNA polymerase – hooks together RNA nucleotides as they base pair along the DNA template - Transcription Unit – area of DNA that will serve as the template - Transcription Initiation Complex – the area where the transcription factors and RNA polymerase are bound to the promoter - TATA box – promoter DNA sequence - The actual sequence is 5’- TATAA – 3’ - TATA box is the RNA polymerase binding site After polymerase is bound to the promoter DNA, the two DNA strands unwind and the enzyme starts transcribing the template strand. 2. RNA STRAND ELONGATION - RNA polymerase moves along DNA template - It unwinds 10 – 20 DNA bases at a time - RNA polymerase adds nucleotides in the 5’ -> 3’ direction - As RNA polymerase moves along , the DNA double helix reforms - The new section of RNA ‘peels away’ as the double helix reforms 3. TERMINATION - Transcription stops when RNA polymerase reaches a section of DNA called the terminator - Terminator sequence – AAUAAA - Next, the RNA strand is released and RNA polymerase dissociates from the DNA - The RNA strand will go through more processing SENSE VS ANTI SENSE DNA STRANDS - The DNA double helix has two strands - Only one of them is transcribed The transcribed strand is the antisense strand The non-transcribed strand is the sense strand RNA is complementary to the antisense strand The 5’ end of the RNA nucleotides are added to the 3’ end of the growing chain RNA nucleotides… TRANSLATION - Forming of a polypeptide Uses mRNA as a template for amino acids sequence 4 steps (initiation, elongation, translocation and termination) Begins after mRNA enters cytoplasm Uses tRNA (the interpreter of mRNA) RIBOSOMES - Made of proteins and rRNA Each has a large and small sub unit Each has three binding sites for tRNA on its surface Each has one binding site for mRNA Facilitates codon and anticodon bonding Component of ribosomes are made in the nucleus and exported to the cytoplasm where they join to form one functional unit 3 tRNA binding sites A site – holds trna that is carrying the next amino acid to be added P site - holds trna that is carrying the growing polypeptide chain E site - where discharged trna’s leave the ribosome TRNA - Is transcribed in the nucleus and must enter the cytoplasm - Trna molecules are used repeatedly - Each trna molecule links to particular mrna codon with a particular amino acids - When trna arrives at the ribosome it has a specific amino acid on one end an anticodon on the other - Anticodons (trna) bound to codond (mrna) 1. INITIATION - Brings together mrna, trna ( with 1st amino acid) and ribosomal sub units - Small ribosomal sub unit binds to mrna and an initiator trna - Strart codon – AUG - Start anticodon – UAC - Small ribosomal sub unit attaches to the 5’ end of mrna - Downstream from the 5’ end is the start codon AUG (mrna) - The anticodon UAC carries the amino acid methionine - After the union of mrna, trna, and small sub unit the large ribosomal subunit attaches - Initiation is complete - The initiator trna and amino acid will sit in the P site of the large ribosomal subunit - The A site will remain vacant and ready for the aminoacyl-trna. ELONGATION - - GENETIC CODE - Four RNA nucleotides are arranged 20 different ways to make 20 different amino acids Nucleotide bases exist in triplets Triplets of bases are the smallest units that can code for an amino acid 3 bases = 1 co don = 1 amino acid There are 64 possible code Most of the 20 amino acids have between 2 and 4 possible codes The mRNA base triplets In translation the codons are decoded into amino acids that make a polypeptide chain It takes 300 nucleotides to code for a polypeptide made of 100 amino acids 61 of 64 codons code for amino acids Codon AUG starts translation The three ‘unaccounted for’ codons act as stop codons (end translation) DNA Antisense ACCAAACCG mRNA (transcription) UGGUUUGGC Polypeptide (translation) Trp – Phe – Gly - Amino acids are added one by one to the first amino acid (remember, the goal is to make a polypeptide Step 1 – (codon recognition) a. Mrna codon in the A site forms hydrogen bonds with the trna anticodon Step 2 – peptide bond information a. The ribosome catalyzes the formation of the peptide bonds between the amino acids (the one already in place and the one being added) b. The polypeptide extending from the P site moves to the A site to attach to the new amino acid TRANSLOCATION - The trna with the polypeptide chain in the A site is translocated to the P site Trna at the P site moves to the E site and leaves the ribosomes The ribosomes moves down the mrna in the 5’ 3’ direction TERMINATION - Happens at the stop codon Stop codons are UAA, UAG, UGA (they do not code for amino acid) The polyeptide is freed from the ribosome and the rest of the translation assembly, comes apart. HISTORY OF LIFE ON EARTH - EVOLUTION - Change in a species through time ORIGIN OF LIFE IN THE 1920s 1. A.I. Oparin of Russia 2. John B. S. Haldane of England - They proposed a hypothesis on the probable origin of life a. Atmosphere of Early Earth must have contained methane (CH4), ammonia (NH4), hydrogen (H2) and water vapor. b. Chemical reactions in said mixture of gases must have produced organic molecules and this could have given rise of the first living cells. 30 YEARS LATER 1. Harold C. Urey – proposed a model of the atmosphere of early earth similar to Oparin and Haldane hypothesis on the probable origin of life. In 1952, he suggested an experiment to explore the origin of life under conditions of his model of Earth’s primodial atmosphere. 1953 - Miller – Urey experiment Theory of chemical evolution Stanley Lloyd Miller – American chemist 1. Source of energy for the formation of the first organic molecules must have been gigantic fishes of lightning that must have constantly agitated the atmosphere of early earth 2. Source of energy must have been the abundant supply of ultra violet radiation that could have reached Earth without an ozone shield to stop it THEORIES AND HYPOTHESES ON HOW LIFE STARTED HERE ON EARTH DIVINE CREATION – life forms may have been placed on Earth by super natural or divine forces - The hypothesis that a divine god created life is at the core of most major religions. EXTRATERESTRIAL ORIGIN – this hypothesis also referred as panspermia, proposes that meteors or comic dusts may have carried significant amounts of complex organic molecule to earth, kicking off the evolution of life. - It is hypothesized that an early source of carbonaceous material is extraterrestrial, although not yet proven. SPONTANEOUS ORIGIN – most scientist accept the hypothesis od spontaneous generation. - That life evolved from inanimate matter associations among molecules become more and more complex. As changes in molecules increased in their stability initiate more and more complex associations, culminating in the evolution of cells. MNAY IDEAS HAVE BEEN DEVELOPED BASED ON SPONTANEOUS ORIGIN a. At the Ocean’s edge – life may arise from the constantly forming bubbles at the edge of the ocean as suggested by some scientist. b. Deep in the Earth’s crust – life may have formed as by-product of volcanic activity where sulfuric minerals, iron and nickel recombine. - Gunter Wachtershauser in 1988 and fellow scientist shows that these chemical recombinations can form precursors of amino acids which can be later linked to peptides. c. Under frozen oceans – just like Jupiter’s moon, Europa. It is hypothesized that life originated under a frozen ocean. d. Within Clay – the silicate surface chemistry was hypothesized by some researchers, emphasizing the positive charges of clay surfaces that may attract organic molecules and providing potential catalytic surface whre life chemistry may have occurred. e. At deep sea vent – another hypothesis that life originated at deep sea vents where the necessary prebiotic molecules are synthesized by metal sulfides in the vents. The positive charge f sulfides may have attracted the negative charge of biological molecules. AGE OF EARTH - - The Earth is approximately 4.6 billion years old. Life on Earth arose around 3.5 billion years ago. Over Earth’s vast history both gradual and catastrophic processes have produced enormous changes. Man could have been first appeared about 100150 thousand years ago as shown by artifactual evidences in various site. WHAT WAS THE EARTH LIKE MILLION YEARS AGO? a. b. c. d. Earth is covered with thick blanket of ice Lots of volcanoes and high mountains Large organisms roamed the land The atmosphere did not have high oxygen content e. Asteroids/meteors frequently hit the surface f. The lands moved a lot or the continents were a little closer to each other g. Volcanic eruptions h. A little bit warmer i. Plants were bigger j. Humans were not yet around GEOLOGICAL TIME SCALE - - A tabular presentation of the history of life based on geologist’s study of rocks and the fossils they contain. All the pieces of information about Earth are arranged chronologically from the oldest (at the bottom of the table) to the most recent (at the top of the table). EON – largest division of the geologic timescale; spans hundreds to thousands of million years ago. ERA – division in era that span time periods of tens to hundreds of million years ago. PERIOD – a division of geologic history that spans no more than one hundred million years. EPOCH – the smallest division of the geologic time scale characterized by distinctive organisms. GEOLOGIC TIME RECORD - - A tabular representation of the major divisions of the Earth’s history. The time intervals are divided and described from the longest to the shortest as EONS, ERAS, PERIODS and EPOCHS. Each period has an approximated time frame and characterized by distinctive features (events and organisms). FOUR ERAS - - - Precambrian Paleozoic Cambrian Ordovician Silurian Devonian Carboniferous Permian Mesozoic Triassic Jurassic Cretaceous Cenozoic Tertiary Quarternary PALEONTOLOGY FOSSILS - FOUR EONS - Hadean Archean Proterozoic Phanerozoic Paleozoic Mesozoic Cenozoic Is the study of the remains of organisms of the past. Evidences of organisms that lived in the past. They can be actual remains like bones, teeth, shells, leaves, seeds, spores, or traces of past activities such as animal burrows, nests and dinosaur footprints or even the ripples created on a prehistoric shore. 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 Absolute Dating RELATIVE DATING I. II. III. Based upon the study of layer of rocks Does not tell the exact age: only compare fossils as older or younger, depends on their position in rock layer. Fossils in the uppermost rock layer/strata are younger while those in the lowermost deposition are the oldest. HOW RELATIVE AGE IS DETERMINED? 1. LAW OF SUPERPOSITION - If a layer of rock is undisturbed, the fossils found on upper layers are younger than those found in lower layers of rock. However, because the Earth is active, rocks move and may disturb the layer making this process not highly accurate. - - RULES OF RELATIVE DATING A. Law of Superposition – sedimentary layers are deposited in a specific time, youngest rocks on top, oldest rocks at the bottom. B. Law of original Horizontality – deposition of rocks happens horizontally, tilting, folding or breaking happened recently. C. 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. 2. ABSOLUTE DATING - Determine the actual age of the fossil through radiometric dating, using radioactive isotopes carbon-14 and potassium-40. Considers the half-life or the time it takes for half of the atoms of the radioactive element to decay. - The decay products of radioactive isotopes are stable atoms. - Radio Carbon Dating – dating organic matter up to around 70,000 years old. - C-14 because it is based on the radioactive isotope of carbon. - C-14 meaning its mass is 14 atomic mass units is produced in nature by cosmic rays bombardment of nitrogen atoms in the atmosphere. - Radiocarbon dating has flaws, scientist discovered that the production of carbon-14 in nature is not exactly constant, thus some corrections in the age of fossil remains had to be made. DESCENT WITH MODIFICATION: A DARWINIAN VIEW OF LIFE CHARLES DARWIN - 1809 – 1882 Western England After graduation he joined the crew of the survey ship HMS Beagle as ship naturalist and conversation companion to Captain Robert Fitzroy. VOYAGE OF THE BEAGLE - December 1831 22 years old he left England as naturalist aboard the HMS Beagle for 5-year voyage around the world. DURING THE 5-YEAR VOYAGE IF THE BEAGLE - - - Freedom to explore on shore Collected thousands of specimens of the exotic and diverse flora and fauna of South America. Darwin’s observations challenged his belief that species do not change over time. His observation of geological formation and species variation led him to propose by which species arise and change. This process is known as evolution. He proposed that genetic change occurs in a species over time, which leads to their genetic and phylogenetic differences. The process is due to natural, not supernatural forces. EVOLUTION - - As descent with modification proposing that Earth’s many species are descendants of ancestral species that were very different from those alive today. Evolution can also be defined as a change in the genetic composition of a population overtime. Evolution is both pattern and a process. Pattern of evolutionary change is revealed in observations about the natural world. Process of evolution consists of the mechanisms that have produced the diversity and unity of living things. ARISTOTLE - - 384 – 322 B.C.E. Arranged life forms on a scale of increasing complexity and can be arranged based on their order of increasing complexity. Aristotle: The Scale of Nature Greek philosopher Father of biology Organized all things according to their Psyche (a kind of soul) Vegetative Psyche (lowest – you exist) Animate Psyche (middle – you move) Rationale Psyche (highest – you think) Problems: Anthropocentric, subjective, unable to prove existence of these Psyches. CAROLUS LINNAEUS - - MISSION: CHART THE SOUTH AMERICA COASTLINE - He noted that plants and animals of South America were very different from those of Europe. While on the Beagle, he read the Lyell’s Principles of Geology. - Swedish botanist May 27, 1707 Father of taxonomy Widely known for two contributions – classification and binomial nomenclature of organisms. Classified nature into kingdoms, classes, orders, general and species, which exist till today with some changes. Named 4,400 animal species and 7,700 plant species through his binomial nomenclature, a two-part scientific name in Latin for every species. - Was appointed Chief Royal Physician in 1747 and Knighted by King of Sweden in 1758 Founder of taxonomy in 1735 Science of grouping and naming Sought to discover order in the diversity of life “for the greater glory of God” Each creature was special – no evolutionary link Devised classification system based on morphology (form and structure) Binomial nomenclature – naming system that gives organisms a two part scientific name – Genos species and classifying species into hierarchy of increasingly complex category. IDEAS ABOUT CHANGE OVERTIME - JEAN BAPTISTE LAMARCK - - BARON GEORGE CUVIER - - 1769 – 1832 Father of paleontology Examining rock strata in Paris Basin He noted that the older the strata, the more dissimilar the fossils. He recognized that extinction had been a common occurrence in the history of life. Advocate catastrophism, speculating that boundaries between strata were due to local floods or droughts that destroyed the species then present. He suggested that the denuded areas were later repopulated by species immigrating from unaffected. - - - - ERASMUS DARWIN - - Darwin’s grandfather Changes in animals during development, animal breeding by humans and the presence of vestigial structures. He thought that species might evolve but he offered no mechanism. - - CHARLES LYELL - 1797 – 1875 “uniformitarianism” Geological processes that shaped Earth are still operating at the same rate. His book entitled Beagle Voyage. HUTTON AND LYELL OBSERVATIONS AND THEORIES HAD A STRONG INFLUENCE ON DARWIN 1. If geologic changes result from slow, continuous processes rather than sudden events, then the earth must be far older than the few thousand estimated by theologies from biblical references. 2. Slow and subtle processes persisting for long periods of time can also act on living organisms, producing substantial change over a long period of time. - 1766 – 1834 Economist Wrote essay on population growth 1744 – 1828 Published a theory of evolution based on his observation of fossil invertebrates in the collections on the Natural History of Museum of Paris. By comparing fossils and current species, found what appeared to be several lines of descent. Each line of descent was a chronological series of older to younger fossils, leading to a modern species. Explained two principles: use and disuse Use and disuse was the concept that body parts that are used extensively become larger and stronger, while those that are not used deteriorate. The inheritance of acquired characteristics stated that modifications acquired during the life of an organisms can be passed on to off spring. Ex. The long neck of giraffe. Though that evolutionary change was driven by innate drive of organisms. Theory was a visionary attempt to explain the fossil record and the current diversity of life with recognition of gradual evolutionary change. Modern genetics has provided no evidence that acquired characteristics can be inherited in the way proposed by Lamarck. Acquired traits such as bodybuilders bigger biceps do not change the genes transmitted through gametes to offspring. A comparison of Lamarck’s and Darwin’s theories of evolution. a. Jean-Baptiste de Lamarck’s proposal of the inheritance of acquired characteristics. b. Charles Darwin’s theory of natural selection. JAMES HUTTON - THOMAS MALTUS - Studied the factors that influence the growth and decline of human populations. Published an essay on the Principle of Population. He proposed that the size of human population is limited only by quantity of resources (food, water, and shelter. 1762 – 1797 “GRADUALISM” Proposed a theory of slow, uniform geological change. He explained that the earth is subject to slow but continuous cycles of rock formation and erosion produces dirt and rock debris that is washed into rivers, transported to the oceans and deposited in thick layers, which converted over time into sedimentary rocks which often contain fossils. CHARLES DARWIN THEORY OF EVOLUTION - Formulated hypotheses concerning evolution after taking a 5-year voyage as a naturalist aboard the ship HMS Beagle. - His hypotheses were that descent with modification from a common ancestor does occur and that natural selection results in adaptation to the environment. BIOGEOGRAPHICAL OBSERVATION BIOGEOGRAPHY – study of geographical distribution of organisms through the world. - - - - - - The distribution of species and the make-up of groups in different regions provide hints about past geological events. Darwin spent a month of observing life on the Galapagos Islands (a group of young volcanic islands 900 km west of the South America) Each island has a different rainfall and vegetation and its own unique assortment of plant and animal species. Although animals on Galapagos resemble species on the South American main land, many species were found no where else in the world = ENDEMIC. Darwin collected 13 species of finches in Galapagos Islands. Adaptations to the specific foods available on their home to different environments. Darwin explained that adaptations arise by Natural Selection, a process in which individuals with certain inherited characteristics leave more offspring than individuals with other characteristics. Darwin’s focus on ADAPTATION. immaculate logic and on avalanche of supporting evidence. EVOLUTION – descent with modification. - - - - - - - ADAPTATION - Any inherited characteristics that increases an organism’s chance of survival and reproduction in specific environment. - Darwin’s had developed the major features of his theory of Natural Selection as mechanisms for evolution. Darwin wrote a long essay on the origin of species and natural selection. - Alfred Russel Wallace, another naturalist working in the west indies, wrote an essay describing his work that summarized of some ideas Darwin had been thinking about for 25 years. Suddenly Darwin had incentive to publish the results of his work. 1859 - - - - 1858 - OVER PRODUCTION OF OFFSPRING - 1844 - WHAT IS DARWIN’S THEORY - 1840’s All organisms are related through descent from a common ancestor that lived in the remote past. As a result, organisms share many characteristics, explaining the unity of life. Over evolutionary time, the descendants of the common ancestor have accumulated diverse modifications or adaptations that allow them to survive and reproduce in specific habitats. Over a long periods of time, descent with modification has led to the rich diversity of life we see today. Closely related species, the twigs on a common branch of tree, shared the same line of descent until their recent divergence from common ancestor. Viewed from the perspective of descent with modification, the history of life is like a tree, with multiple branches from a common trunk. Linnaeus recognized that some organisms resemble each other more closely than others, but he did not explain these similarities by evolution. Linnaeus’s taxonomic scheme fit well with Darwin’s theory. To Darwin, the Linnaean hierarchy, reflected the branching history of the tree of life. Organisms at various taxonomic level are united through descent from common ancestor. - - Capacity to over produce seems characteristics of all species. STRUGGLE FOR EXISTANCE means that member of each species must compete for food, space and other resources. GENETIC VARIATIONS is found naturally in all populations. Some organisms in a population are less likely to survive. Ability of an individual to survive and reproduce in its specific environment = FITNESS. SURVIVAL OF THE FITTEST = organisms which are better adopted to the environment tend to produce more offspring than organisms without those traits. Overtime, Natural Selection results in changes in the inherited characteristics of a population. These changes increased a species fitness in its environment. IMPORTANT TO REMEMBER: On The Origin of Species by Means of Natural Selection presented evidence and proposed a mechanism for evolution that he called Natural Selection. The theory of evolution by natural selection was presented in the origin of species with - Populations evolve not individual. Natural Selection only works on heritable traits. A trait that is favorable in one environment may be useless or detrimental in another. - - Descent with modification suggest that each species has descended with changes from other species overtime. This idea suggests that all living species are related to each other and that all species, living and extinct, share a common ancestor. - EVIDENCES The theory that all organisms share a common ancestor is supported by many lines of evidence: - Fossil record Biogeographic distribution Anatomical evidence Biochemical evidence Evidence from Developmental Biology Molecular homologies Artificial Selection BIOGEOGRAPHY - - Are the remains and traces of past life or any other direct evidence of past life. - - - - - - - A paleontologist discovered fossilized remains of Tiktaalik roseae, nicknamed the “fish a pod” because it is the transitional form between fish and four-legged animals, the tetrapods. Mix of fish like and tetrapod- like features. Fossils such as Tiktaalik provide evidence that the evolution of new groups involves the modification of pre-existing features in older groups. The evolutionary transition from one form to another anatomical transitions during the evolution of whales. TRANSITIONAL FOSSILS Tortoises adapted to different habitats as they spread from the mainland to the different islands. DIVERGENT EVOLUTION – ADAPTIVE RADIATION. If Darwin’s theory is correct you would also expect to find different species living in far apart geographic regions but similar habitats becoming more alike as they adopt to similar environments. BOTH LIVE IN THE FOREST ECOSYSTEMS -sugar glider in Australia is a marsupial more closely related to kangaroos than North American. -flying squirrel because its ancestors were marsupials. -whales and sharks have similar body design even though they are very different organisms (one is fish and one is mammal) because they have independently adapted to living in a similar environment. CONVERGENT EVOLUTION BIOGEOGRAPHICAL EVIDENCE - 2004 - The beaks of Galapagos finches have adopted to eating a variety of foods. GALAPAGOS TORTOISES FOSSIL RECORD Provides evidence that organisms have changed overtime. - Constitute the strongest proof that species do change. a. The remains of ancient life found in the oldest rocks are fewer and more primitive that those found in younger rocks. Ex. Earliest fossils: Prokaryotes (blue-green bacteria) appeared 3.4 to 3.6 billion years ago. Findings: very simple forms of life lived in the past and over millions of years, probably gave the rise to many kinds of organism with more complex body structures. b. The remains of many ancient plants and animals show structural similarities to certain organisms that live today. Although none is exactly the same as the living species, also, fossils found in younger rocks are not found in much older rocks. Findings: imply that ancestral forms gradually evolved over millions of years and gave rise to offspring that are no longer exactly like themselves. Each type of marsupial in Australia is adapted to different way of life. All the marsupials in Australia presumably evolved from a common ancestor that entered Australia some 60 million years ago. Sugar glider, wombat, kangaroo – placenta. GALAPAGOS FINCHES FOSSIL - Such as Ambulocetus and Basilosaurus, support the hypothesis that modern whales evolved from terrestrial ancestors that walked on four limbs. These fossils show gradual reduction in the hand limb and a movement of the nasal opening from the tip of the nose to the top of the head, both adaptations to living in water. - Biogeographical differences provided evidence that variability in a single, ancestral population can lead to adaptation to different environments through the forces of natural selection. Competition for resources appears to produce some of the pressure that leads to diversification. SIMILARITIES IN STRUCTURE - - Structures that are similar because of a common ancestor are known as homologous structures. Organisms which undergo similar structure have close evolutionary tree. HOMOLOGOUS STRUCTURES - Forelimbs of all mammals share the same arrangement of bones that can be traced to same embryological origin. - Evolution explains why certain characteristics in related species have an underlying similarity. AMNION – bag of waters, the extraembryonic membrain of birds, reptiles and mammals, which lines the chorion and contains the fetus and the amniotic fluid. VESTIGIAL ORGANS – some homologous structures are vestigial and have no useful function even though they are still present. - - FUNCTIONS OF HOX GENE - Ex. Hipbones and pelvis in whales, cecum (appendix) in humans, legs in skink - - Most mammals have a pouch between their small and large intestines that contains bacteria to digest plants called cecum. In humans the cecum is shrunken and unused. It is our appendix. EMBRYOLOGY - Development of vertebrate embryos follows same path. Fish, salamander, tortoise, chicken, rabbit, human SIMILARITIES IN DEVELOPMENTAL CHANGES - - - Series of changes in body structure that an animal goes through from egg to adult. Organisms which undergo similar developmental changes have close evolutionary ties. Some groups of undifferentiated cells develop in the same order to produce the same tissues and organs of all vertebrates, suggesting that they can evolved from a common ancestor. Human embryo has a tail at 4 weeks which disappear at 8 weeks. If organisms evolved from ancestors in which that part functioned, the gene code to make the part would still be there even though it doesn’t work. If the organ is not vital to survival, then natural selection would not cause its eliminations. BIOCHEMICAL EVOLUTION - - - All living organisms use the same basic biochemical molecules including DNA, RNA, and ATP. Organisms use a triplet nucleic acid code in their DNA to encode for 1 to 20 amino acids that will form their proteins. The sequence of amino acids of some proteins is similar across the tree of life. The sequence of amino acids in the human version of cytochrome c, a protein essential to cellular respiration, is remarkably similar to that yeast. EVIDENCES FROM DEVELOPMENTAL BIOLOGY - It appears that life’s vast diversity has come about by a set of regulatory genes that control the activity of other genes involve in the development. Hox or homeobox, genes orchestrate the development of the body plan in all animals, from invertebrates to humans. All animals share a hox gene common ancestor, but the number and type of hox h=genes vary among animal groups. A change in the timing and duration of the expression of Hox genes that control the number and type of vertebrae can produce the spinal column of a chicken or the longer spinal column of a snake. MOLECULAR HOMOLOGIES - All life forms share same genetic machinery (DNA and RNA) Universal genetic code Important genes share highly conserved sequences Similarities in DNA and protein sequences suggest relatedness Similarities in karyotypes suggest an evolutionary relationship. Chimpanzees has 2 smaller chromosomes pairs we don’t have. Humans have 1 larger chromosome pair. Humans 46, Chimpanzees 48 ARTIFICIAL SELECTION - Works nature provides the variation through mutation and sexual reproduction and human select those traits that they find useful. CHARLES DARWIN THEORY OF EVOLUTION - - - Darwin observed that populations, not individuals, evolve but he could not explain how traits change overtime. Now we know that genes interact with the environment to determine traits the diversity of a population is linked to the genetic diversity of individuals within that population. Because genes and traits are linked, evolution is really about genetic, or more specifically, evolution is the change in allele frequencies in a population over time. GENES POPULATION EVOLUTION MICROEVOLUTION – revolutionary change within populations. POPULATION – a group of organisms of a single species living together in the same geographic area. ALLELE – genes governing variation of the same character that occupy corresponding positions on homologous chromosomes. ALLELE FREQUENCIES – portion of specific allele in the population, the percentage of each allele in a population’s gene pool. GENE POOL – the alleles of all genes in all individuals in a population. HARDY-WEINBERG PRINCIPLE – can measure the genotype frequencies of a non-evolving population. P2 + 2pq + q2 = 1 - HARDY-WEINBERG EQUILIBRIUM - A population in which allele frequencies do not change over time. A stable, non-evolving state. A constancy of gene pool allele frequencies that remains stable from generation to generation if certain conditions are met. HARDY-WEINBERG PRINCIPLE APPLIES - - - Only if the following conditions are met: 1. No mutation – no new alleles can arise by mutation. 2. No migration – no new members (and their alleles) can join the population, and no existing members can leave the population. 3. Large gene pool - the population is very large. 4. Random mating – individuals select mates at random mate choice is not biased by genotypes or phenotypes. 5. No selection – the process of natural selection does not favor on genotype over another. - Because these conditions are rarely met, a change in allele frequencies is likely. - When gene pool frequencies change, micro evolution occurs. - Deviations from Hardy-Weinberg equilibrium allow us to detect micro-evolutionary shifts. Mutation occurs when the DNA sequences has changed. - - NON-RANDOM MATING - - MUTATION - Occurs when DNA sequence has changed. Which can serve as a source of new genetic variation. MIGRATION - - - Gene flow is the movement of alleles between populations. Gene flow occurs when plants or animals migrate, or more specifically their gametes move between populations. When gene flow brings a new or rare allele into a population, the allele frequency in the next generation changes. Gene flow in plants may result when the pollen from one plant fertilizes plant in another population. SMALL POPULATION SIZE - - Genetic drift is when chance events cause allele frequencies to change. Both the bottle neck effect and founder effect result from the loss of genetic variation within the population. Genetic drifts refer to changes in the allele frequencies of a gene pool due to chance events such events remove individuals, and their genes from a population at a random without regard for genotype or phenotype. Genetic drift occur when, by chance, only certain members of a population reproduce and pass on their alleles to the next generation. A natural disaster can cause the allele frequencies of the next generation’s gene pool to be different from these of the previous generation. Genetic drift can be powerful force for evolutionary change especially in small populations. The smaller the population, the more genetic drift impacts in the allele frequencies. A large population can suddenly become very small. A bottleneck effect is a type of genetic drift in which the loss of diversity is due to natural disaster, disease, overhunting, overharvesting. A founder effect, another type of genetic drift is similar to bottleneck effect except that genetic variation is lost when a few individuals break away from a large population to found a new population. - - Alone does not cause allele frequencies to change. However, does affect how the alleles in the gene pool assort into genotypes, thus affecting the phenotypes in a population. In a randomly mating population, the alleles in the gene pool assort at random. When mating is non-random, gametes and thus alleles assort according to mating behavior. Type of non-random mating, called assortative mating, occurs when an individual chose a mate with a preferred trait, such as particular coat color, feather length, or body size. Assortative mating brings together alleles for these traits more often, then would happen by chance. NATURAL SELECTION - - - - - A population in Hardy-Weinberg equilibrium has phenotypes that are equally likely to survive and reproduce. One genotype does not have an advantage over another but in nature some phenotypes do have a reproductive advantage. Individual who have an advantageous phenotype often pass on the allele for those trait to their offspring. Overtime, selection for this advantageous trait increases the frequency of the alleles associated with it, while other alleles decreases. Most of the traits of evolutionary significance are polygenic, controlled by many years. Natural selection favors the most adaptive variant for a given environment. 3 types of Natural Selection 1. Stabilizing selection – the intermediate variation is the most adaptive, as is found in human birth weight. 2. Directional selection – either of the extreme phenotypes is favored, as when body size increases overtime. 3. Disruptive selection – two or more extreme phenotypes are adaptive, the curve from two peaks, as when British land snails have one of two different banding patterns of shell color. SEXUAL SELECTION - - - - About reproductive success, or fitness. Males produce many sperm and complete to inseminate females. Females produce few eggs and are selective about their mates. Traits that promote reproductive success, such as sexual dimorphism, are shaped by sexual selection. Cost benefit analysis helps a male determine if it is worth competing for males. Dominance hierarchies provide dominant males greater reproductive opportunities than lowerranking males. A territory is defended with specific behaviors known as territoriality. Biological differences between the sexes may promote certain mating behaviors because they increase fitness. MAINTENANCE OF DIVERSITY - - - Despite constant natural selection, genetic diversity is maintained. Mutations and recombination still occur, gene flow among small populations can introduce new alleles, and natural selection itself sometimes results in variation. In sexually reproducing diploid organisms, the heterozygote acts as a repository for recessive alleles whose frequency is low. In regard to the sickle-cell disease, the heterozygote is more fit in areas where malaria occurs, in this is known as the heterozygote advantage.
