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Western University
Biology 1001A
Tom Haffie

Lecture 2- HIV Independent Study Outcome 1. The general mechanisms by which vaccines protect against diseases. Vaccines create a cache of weapons for the immune system which u can deploy when needed. When pre-immunized you have forces in your body pre-trained to eliminate your enemies (pathogens) Antibodies are what makes vaccines work. 2. Why developing a vaccine against HIV is relatively challenging, compared to other diseases. Mutates extremely fast, has decoys to evade immune system, it attacks antibodies, and it can hide very well within immune system. HIV is highly variable, there are multiple variations. 3. Why people are encouraged to get a flu vaccine each year (as opposed to one time only). Mutations cause strains to constantly change yearly. Multiple strains develop each year and thus antibodies from the previous flu shot are unable to identify these new strains. The flu can also pass on to animals which can then recombine these diseases to re-affect humans. Lecture 2 – Lecture Outcomes General global distribution of HIV infections. Subsaharan Africa is very HIV Prevalent Reasons why HIV is more common in some parts of the world than others. Larger population, less education, not as sanitary, environmental factors, biological factors of that specific type of ethnic peoples. Factors that explain why no cure or universal vaccine has been developed for HIV/AIDS. The virus mutates extremely fast and is thus constantly dividing and always evolving. Enormous genetic diversity of HIV, its ability “to replicate unrelentingly despite everything the immune system can throw at it”, the fact that the immune system cannot protect against superinfection, and the fact that we do not currently know what constitutes an immune response to HIV. Reasons why viruses are not considered “alive”. They are not considered alive because they depend on the host cell in order to reproduce. They lack a metabolism of their own. Reasons why anti-viral drug therapies often have serious side effects. Anti-viral drug therapies have serious side effects because they rely on host cell to reproduce and metabolize and therefore viral drugs must also target these host cells (regular cells in humans) which damages the physiology of these cells Major steps in life cycle of HIV. HIV is a retrovirus and therefore has reverse transcription Viron enters cells Reverse transcription occurs RNA is reverse transcribed into DNA Integrase splices viral DNA into host DNA Transcription and translation occurs and new virons assemble and enter circulation The immune system then collapses Specific role of integrase and reverse transcriptase in retroviral life cycle. Reverse Transcriptase lacks a proof reading enzyme and therefore it is error prone with a super high mutation rate Integrase splices viral DNA into Host DNA Mechanism of action of AZT. AZT is an anti-viral drug that targets steps for making the HIV cells AZT attacks reverse transcriptase -halts progression -instead of grabbing T it instead grabs AZT which blocks the addition of strands Reasons why effectiveness of AZT decreases over time. Creation of HIV is very error prone and therefore mutations occur all the time. Some kind of new mutation may be resistant to AZT and because this mutations are not on purpose they can be pretty beneficial random errors. The AZT resistance is passed from parents to offspring and therefore only the resistant forms continue to reproduce. The mutations generated variation which is inherited Rationale for multi-drug (drug cocktail) approach to treating viral infections. There are many different areas of the cell creation which are targeted, resistance to one may not affect the others. Drug cocktails are a combination of these drugs which affect different area‟s of progression and therefore not its not affecting one without the other. Principles of evolution of HIV: variation, heritability, differential reproduction, change in genotype of population. ^ READ ABOVE QUESTIONS TO GET ANSWER Role of CCR5-Δ32 mutation in human resistance to HIV infection. CCR5 is a receptor that is expressed on white blood cells. The mutation of CCR5-32 is a deletion in this receptor for those who are homozygous of this allele. It causes a HUGE resistance to aids Global distribution of CCR5-Δ32 allele. It is common in Northern Europe Likely explanations of modern distribution of CCR5-Δ32 allele. Not as strong of a selection pressure , 1% have aids Provides other benefits against past selection pressures. -------------------------------------------------------------------------------------------------------------------- Lecture 3 – Origin of Life (Independent Study Outcomes) 1. characteristics shared by all life All life is composed of cells which is the fundamental unit of all life. Life is defined by a list of attributes -They can harness and utilize energy -They can reproduce -They evolve -They have growth and development -They respond to stimuli -They exhibit homeostasis 2. in what way properties of life are "emergent". Properties of life are emergent because they come about or emerge from many simpler interactions and in itself do not have the properties found in higher levels. An example of this of how the ability to harness and utilize energy is not a property of molecules, proteins, or biological membranes itself but instead the ability emerges from the interactions of all three of these as a part of a metabolic process. 3. characteristics of the "habitable zone" of a solar system. A habitable zone is a region of space around the star where temperatures allow for liquid water. The presence of liquid water is a fundamental prerequisite for the development of life. Precise distance from the star that defines the habitable zone will vary depending on the type of star and amount of energy it emits. 4. conditions of a primitive Earth. Conditions of primordial earth consisted of an abundance of water vapour from evaporation of water at the surface as well as large quantities of hydrogen, carbon dioxide, ammonia, and methane. There was a complete absence of oxygen. 5. types of molecules that were, and were not, synthesized by the Millar-Urey experiment. In the miller urey experiment he placed components of a reductive atmosphere which included hydrogen, methane, ammonia, and water vapour. After running this over a high source of energy (electrodes) for a week, several organic compounds arose including urea, amino acids, and lactic, formic, and acetic acid. When cyanide and formaldehyde were added all building blocks of complex biological molecules were produced including amino acids, fatty acids, and purine and pyrimidine components of nucleic acid. As well several types of sugars were created as well as phospholipids which form lipid bilayers of biological membranes. 6. characteristics of mimivirus that suggest it should be considered to be alive. The mimivirus consists of a genome made up of more than 900 protein coding genes. It is able to get infected by another gene causing it to get infected…. something which characterizes its possibility of being alive. 7. characteristics of virophage. A virophage is able to infect the factory where viral particles are made in a virus. The virophage infects the viral factory and hijacks its machinery in order to replicate. It basically makes the host cell sick. It does what a parasite (bacterium) does and exploits its host for its own replication. Lecture 3 – Lecture Outcomes age of the Earth. The age of the earth is 4.5 billion years old age of start of life on Earth. 3.5 billion years on earth domains of life. The three domains of life are bacteria, archaea, and eurkaryotes. characteristics of LUCA Everything in life descended from a single population of identical organisms… everything derived from this one organism but that does not necessarily mean it is the first form of life. characteristics shared by all domains of life. All forms of life share fundamental biochemistry. They have DNA, ATP, Carbon, Phospholipid Bilyaer, Protiens. -Cells are made of lipids, g -Genetic system based on DNA, -Dna  Rna method for transfer of info -Common system of protein assembly -ATP for energy -Glucose and Glycolysis reason why the term “prokaryote” is inappropriate. Prokaryotes are an incorrect term because it suggests that is evolutionarily related. EX. Bacteria and Archaea are not related!!!! Pro also means before nucleus and there is no evidence which suggest that a nucleus is a derived figure ---- > Luca perhaps had a nuclear membrane. Basically it says „something without nucleus or came before nucleus‟ Certain level of complexity is lost. reductive evolution explanation for rise of bacteria and archaea. Bacteria and Archaea lack a lot of things eukaryotes have. They have less complexity  They got rid of it  REDUCTIVE EVOLUTION advantages of evolutionary simplification (streamlining). -Replicate Faster -Can grow and evolve faster -Can withstand and relish in harsh and extreme conditions -Can adapt rapidly to chaning environments relationship between homochirality and life Chirality is handedness. There is two optical isomers which have the exact same chemical and physical build.  Two molecules with identical molecular mass and chemical constituents but not super imposable (can lay or place over each other) The change is the position of atoms which can cause a completely different biological function. Life is homochiral, you don‟t use both forms only one. EX. We only use L-amino acids, or D- sugars. Binding sites on enzymes can only recognize one chiral partner BASICALLY EARLY LIFE HAD TO DECIDE WHICH AMINO ACIDS OR SUGARS (CHIRAL PARTNER) THAT THEY WOULD USE! reasons why we think RNA was the first of the three molecules of the Central Dogma to evolve. Rna is relatively simple in that it can confer info (get translated) and can even act as a structural or functional specimenCatalyst There are genes on DNA which make m-RNA (proteins), t-RNA(translation), and r-RNA(build ribosomes) The gene which made the tree of life is an rRNA gene, force that drives RNA folding. RNA is a single stranded but cane produce 3D structure It uses Hydrogen bonds to fold elaborately characteristics of a ribozyme. RNA‟S are catalytic  ribozymes (Biological Catalysts) -Precursor t-RNA processing -Intron excision -m-RNA processing a ribonucleic acid that acts as a catalyst in the same way that a protein based enzyme would. mechanism whereby a ribozyme cleaves RNA. Ribonuclease P is the mechanism in which ribozyme cleaves RNA The precursor t-RNA which is used for translation needs to be chopped off and fit into a ribozyme. It cuts RNA and Cleaves it. characteristics of amino transferase activity. aka PEPTIDYL TRANSFERASE activity. -Forms peptide bonds between adjacent amino acids using tRNAs during the translation process of protein biosynthesis. It is carried about by the ribosome. -Its activity is carried out by r-RNAwhich Is a ribozyme reasons why a ribosome is considered a ribozyme. 2/3‟rd of a ribosome is an RNA (Protien association  Ribonucleic Protein advantage that protein has over RNA as a catalyst. Proteins vs RNA 20 aa VS 4 bases Diversity advantage that DNA has over RNA as a repository for genetic information. in DNA the uracil is replaced by thymine  CU mutation is common DNA IS more stable and less error prone over RNA in which replication is never perfect chemical basis for the advantage that DNA has over RNA as a repository for genetic information. In RNA there is a hydroxyl group on the left which breaks down more easily because it removes structure of ribose and can shift DNA has a deoxyribose group which is a lot more stable and 2 strands can form thus conveying the same genetic info on both strands  LESS OF A MISTAKE BECAUSE THERE IS TWO COPIES. Lecture 4 – Biodiversity (Independent Study Outcome) 1. significance of "tree thinking" to evolutionary theory Tree thinking is important to evolution theory because evolution theory has constantly been changing over the last 150 years, but the concept of the tree of life is central. The idea of common ancestry is the solidifying principle of evolution and this is best shown through phylogeny. 2. most recent common ancestor of two or more groups, given a phylogenetic tree The most recent common ancestor of two or more groups would be represented by an internal node which basically diverges into two or more lineages of a species. 3. which groups are more versus less closely related to one another, given a phylogenetic tree The groups which are more closely related would perhaps be the ones whom share a more recent common ancestor vs a more deep rooted or further away common ancestor. Overall though every species is related by one single common ancestor whether or not there are other ancestral forms after and therefore everything is related and some point. It really depends on how recent this was 4. whether rotating internal nodes on a phylogenetic tree changes the information conveyed Rotating internal nodes on phylogenetic trees does not make a difference because the relationships amongst these internal nodes are the same no matter where they are moved. The order of the branching is what makes the significant different not the varying placements of internal nodes. 5. contemporary and ancestral species on a phylogenetic tree contemporary species are species that are alive in present day and are represented by the tips which are called terminal nodes consistent of the outer tips or branches whereas ancestral species are species which no longer exist and are represented by internal nodes which are basically a recent common ancestor of these contemporary species. Lecture 4 – Lecture Outcomes most recent common ancestor (MRCA) for a given group(s), given a phylogenetic tree. The most recent common ancestor given a group on a phylogenetic tree is the rendezvous point or the internal node in which there was a species who had diverged into the branches or terminal nodes. why the idea that “humans are descended from chimps” is inaccurate. Humans did not directly descend from chimps. They are not considered our common ancestor but in fact something that branched off from our most recent common ancestor. The chimpanzee and bonobos are our most closely related group. Our mrca may have not been similar to either but they indefinitely evolved. order of main branching events in tree of life (dates not testable). 1. MRCA of all humans, and chimps 2. Last shared a common ancestor which led to gorillas, MRCA of African great apes 3. MRCA is before gorillas, MRCA of all great apes 4. MRCA of all apes (gibbons) 5/6. OLD/NEW world monkeys. There existed a lineage which gave rise to new world monkey made it from Africa to south America 7. Tarsiers = nocturnal species with big ass eyes 8. MCRA OF ALL PRIMATES  lemurs and Larises 10. Rodents and rabbits, > 2000 rodent species OH SHIT METEORITE MASS EXTINCTION 11. Laurasitaheres – 85 m years ago 14. Marsupials convergent evolution as they lived in similar environments and selection pressures act on both marsupial and non-marsupial species 15. Monotremes Egg laying mammals 16. Birds are reptiles and closely related to snaked. REPTILES, should include birds. 17. Other vertebrates  MRCA OF ALL TETRAPODS (340 MYA) 18-22. Longfish coellacantsn (Ray-finned fish, Sharks)  These fish are no more closely related to others than they are to us 26. Protosoma (anthropods, gastropods, and insects)  1 million described species, first approx of all animals are insects 34-36. Fury, amoebozans, plants, either unicellular or multicellularity (evolved many times) 38. ARCHEA  MRCA of all eurkaryoes, and was prokaryotic meaning it had no cell membrane and was thus unicellular. 39. BACTERIA  NOW WE AT LUCA BITCH cause of global catastrophe associated with mass extinction 65 mya. End Cretaceous mass extinction. May have been a meteorite with enough dust to change the temperature on earth causing most dinosaurs to go extinct. relative species richness of protostome vs. deuterostome animals The major difference between protostomes and deuterostomes are how they develop in the early embryo stages. In protostomes the mouth opening is the first to be formed later followed by the anus. In deuterostomes the anus forms first followed by the mouth. Protostomes include the phyla Mollusca, Annelida and Arthropoda. Deterostomes include the phyla Echinodermata, Hemichordata and Chordata. why some traditional groupings of organisms (“reptiles”, “fish”) do not reflect evolutionary relationships Birds which are in fact reptiles are more closely related to snaked and have a transition period in which they evolved from dinosaur like species. Fish is a type of species which is no more related to other species of fish then they are to us as they have evolved many times and may have a MRCA with tetrapods closer to that of an MRCA with other fish species. distribution of multi-cellularity in tree of life. Everything after r-34,35,36. In this stage did fury, amoebozans, plants exists which were either unicellular or multicellular. The idea of multicellularity evolved several times. why estimating numbers of species is uncertain. There are many undiscovered species for several reasons. Only 1.2 million species have been identifies which is 10% of all species. Perhaps there are environment humans cannot explore, or there are just undiscovered areas consistent of species. role of similarities due to common descent (eg DNA genome) vs. convergence (eg eyes) in constructing a phylogenetic tree. Common descent vs convergent evolution causes discrepancies in phylogenetic trees. There are many similarities of species not only through common descent. Convergent evolution is how different species have evolved many similar characteristics and traits independent of each other through perhaps similar selection pressures. This does not necessarily mean that they are related through common descent (shared DNA genome) Lecture 5 – Why Evolution is True 1. how Darwin's theory of evolution differed from that proposed by Lamarck Lamark made 4 contributions to the theory of evolution 1.He proposed all species changed through time 2. He recognized that changes are passed from one generation to the next 3. He suggested that organisms change in response to their environments 4. He also hypothesized that the existence of specific mechanisms that caused evolutionary change Principle of use and disuse: body parts grow in proportion to how much they are used, unused structures get weaker Inheritance of Acquired Characteristics: changes that an animal acquires during their lifetime are inherited by its offspring.  DARWIN SAYS NATURAL SELECTION CAUSES CHANGE Darwin differs from Lamark because he provided purely physical rather than spiritual explanations about the origins of biological diversity. He also recognized that evolutionary changes occur in groups of organisms rather than individuals  some members of a group survive and produce more successfully than others. -Darwin also also described evolution as a multistage process.  Variation arises within groups, natural selection eliminates unsuccessful variations, and the next generation inherits the successful variations. 2. meaning of catastrophism, gradualism, uniformitarianism Catastrophism- Each layer of fossils represented the remains of organisms that had died in some sort of local catastrophe. Different species then recolonized and then another local catastrophe occurred, in which they formed a different set of fossils in the next layer Gradualism – The earth changed ever so slowly over its history. Uniformitarianism - Geological processes that sculpted earth’s surface over long periods of time, such as volcanic eruptions, earthquakes, erosion, and the formation and movement of glaciers are exactly the same as processes observed today. 3. difference between relative versus absolute ages of rock formations and the fossils they contain Relative ages - Sediments found in any one place form distinctive strata (layers) that usually differ in colour, mineral composition, particle size, and thickness. If undisturbed by geological processes do they reveal the order in which they formed with the youngest layers on top. Fossils found in the same layer(strata) typically represented organisms which lived and died at around the same time in the past. Sequences of fossils from lowest (oldest) to highest ( newest) represented relative ages of organisms. PROVIDES A GEOLOGICAL TIMESCALE Relative age does not tell how old something is but tells us in what order events have happened Relative- the age of a rock or fossil compared to the surrounding rocks and fossil Absolute Ages – Instead of providing a geological timescale radiometric dating using isotopes cab allow actual ages (with error bars) to be associated with different rock layers. 4. approximate age of a fossil or rock formation, given the half-life of a radioisotope and the proportion of starting isotope that has decayed rocks containing isotopes can be dated when amount of isotopes can be measured, and the rates of decay are known. This approach is limited by the half life of the isotope which is the amount of time it takes for the initial amount of isotope to decay into more stable elements. 5. why most living things never form fossils Most living things never form fossils because the soft remains or organisms are quickly consumed by scavengers or decomposed by microorganisms. Fossils are usually able to preserve details of most hard structures such as bones, teeth, and shells of animals or wood, leaves, or pollen of plants. Fossils also rarely form in habitats where sediments do not accumulate (mountain forests) or where soils are acidic (many forests). Fossils also do not last forever. (erosion) Lecture 5 Outcomes characteristics of a scientific theory -An assumption which is based on limited knowledge… a conjecture or a coherent set of testable hypothesis that attempt to explain facts about the natural world. When is such a theory considered true and scientific ? Well when there is an assertion which there is so much evidence that it wud be pretty fucked up to deny that shit. You can test such theories by attempting to falsify it.  Theories graduate to facthood after repeated attempts to falsify/disprove them. components of the theory of evolution 1. EVOLUTION HAPPENS BITCH!!!! Prime example is how allele frequencies in a population change from one generation to the next overtime like such as that of HIV evolving from a susceptible to resistant form ADAPTIVE EVOLUTION ALTHO SOMETIMES THIS SHIT IS RANDO. 2. Gradualism Evolution doesn’t proceed rapidly but instead it takes several forms of small changes. Natural selection is cumulative in how small changes add up to very drastic ones. 3.Speciation Lineages diverge into multiple lineages, basically everything on earth comes from a common ancestor. If speciation never happened we’d all be the fucking same…… AND BE SOME KIND OF PERFECTED FOR OF LUCA. 4. Common Ancestry (all life is fucking related SHIT) Any two groups of species have a traceable lineage with a common ancestor. 5. Most evolutionary change results from Natural Selection. Adaptive change: things are better adapted to environment Non-Adaptive change: Cheetah’s going through a population bottleneck (outbreak of disease) and therefore a loss of genetic variation occurs and they do not become better adapted. 6. EVOLUTION OCCURS IN POPULATIONS NOT INDIVIDUALS. populations change but individuals do not adjust in response to natural selection you need a variable population (varying traits)  ones with reproductive advantages continue to reproduce while the shitty ones die off. Population changes because some individuals are better and continue to pass on their traits. evidence for "descent with modification" -Homologies -Intermediates in fossil records -Vestigial Traits -Fossil evidence that lineages split(speciation) -Direct observation of Evolution Examples of homology and why they support the idea of evolution Homologies support the idea of common ancestry which is a component of the theory of evolution There are structural, developmental, and molecular similarities between varying organisms of the past and present. -Inherited arrangement of bones -There are similarities two species which are not explainable through shared function but instead have correlation to common ancestry. EX. DOLPHINS HAVE HIND LEGS WHICH GROW IN DEVELOPMENTAL STAGE BUT THEN DISSAPPEAR WHEN BORN. Transitional forms link related groups. Examples of vestigial traits and why they support the idea of evolution Vestigial traits are traits which serve no purpose  rudimental eyes, or appendix in humans. Vestigial traits demonstrate the idea that at some time organisms may have contained this particular vestigial trait at one point and in the present they are now not used. role of fossil record as evidence for evolution Fossil evidence is able to show modification of species through intermediates in fossil records. Intermediates are fossil records of organisms in transitional stage meaning, they may be a cross-over of two different species. Lecture 6 – Genome Variations ISO 1. meaning of "C-value". The c-value refers to the amount of DNA in pictograms contained within a haploid nucleus (gamete) or half the amount in a diploid somatic cell of a eukaryotic organism. C-value and genome size are used interchangeably and therefore when using c-value for polyploids it may refer to two or more genomes contained within the nucleus. 2. "paradox" or "enigma" associated with C values The paradox or enigma associated with the C-values refers to complex puzzle surrounding the extensive variation in nuclear genome size among eukaryote species. (why some eukaryotic species are more or less complex than others) Why a large genome size has no correlation on complexity of OGRANISM. EX some single celled protists have genomes much larger than that of humans. 3. meaning of haploid (n) and diploid (2n) Haploid means that there is one copy of each chromosome in the nuclei whereas diploid means two copies of each chromosome in the nuclei. Haploid  Micro-organisms. 4. relationship between C and n as measures of genome size. The ploidy relates to the number of sets of the genome 5. proportion of the human genome that codes for protein. Less than 2%. 24% are introns which are non-coding spacers. Rest of DNA (3/4) is basically occupies spaces between the gene.  some is functional and includes regulatory sequences such as promoters and enhancers but most of it >50% consists of repeated sequences with no function. Lecture Outcomes – Genomic Variation non-nuclear genomes in typical plant and animal cells. Plants have 3 different types of genomes, 2 of which are non-nuclear. The non-nuclear genome is the mitochondria and the chloroplast. trend in C value from prokaryotic vs. eukaryotic cells. The trend in C-value is that simpler organisms tend to have less need for genes and less need for DNA  THIS IS WHAT US NIGGAS THOUGHT IN HIGHSCHOOL. Bacteria and Archaea genomes are relatively smaller but overall protostomes have a lot of of variability and at a certain point these trends don’t really exist. relationship between C value and organismal complexity An organisms complexity literally has nothing to do with the genome size and how m any genes are within the genome. The amount of DNA does not relate to organismal complexity. Why such differing genomes then?  we don’t know. C-ENIGMA/PARADOX. relationship between C value and ploidy Ploidy refers to the number of sets of chromosomes. Ex. 3N … 3.N distribution of linear vs. circular chromosomes in the various domains of life. Eukaryotes have linear chromosomes whereas bacteria and archaea have circular chromosomes. Mitochondria and Chloroplasts also have circular chromosomes. role of nucleosomes in DNA packaging in chromosomes DNA is winded around nucleosomes. (basic unit of DNA packaging) A segment of DNA is wound on sequence of around 8 histone protein cores. It packages the DNA tightly. General trends in costs of DNA sequencing The cost of DNA sequencing gets relatively cheaper every year as it becomes easier to assemble a genome. Moore’s law states every 2 years computing power increases and as computing power increases there is a relation to completing a complete genome. relative distribution of various components of genome sequence ("junk" vs. essential DNA) Over 50 % of genome does not code for shit.  Lots of transposons (Mobile DNA), viruses, and dead genes (pseudogenes). 10%  Introns  non coding DNA 10%  Essential DNA, and of this 10 .. only 2% code for proteins. 25%  Uknown. Lecture 7 - Independent Study Outcomes 1. purine and pyrimidine base-pairing in DNA/RNA DNA consists of four different nucleotides which consist of a 5 carbon deoxyribose group, a phosphate group, and one of four bases A-C-T-G. The purines consists of the two bases known as adenine and guanine which are nitrogenous bases built from a pair of fused rings of carbon and nitrogen atoms.  Pyrimidine consists of the two bases know and cytosine and thymine which are built from a single carbon ring. The number of purines equals the number of pyrimidine’s A=T, G=C *chargaff’s rules+ 2. outcome of the classic Meselson and Stahl experiment The outcome of the classic Meelson and Stahl experiment was to demonstrate that DNA replication was semi-conservative. They figured this out by distinguishing parental DNA molecules from newly synthesized DNA molecules. 3. direction of movement of DNA polymerase on the template strand Each DNA strand has two distinct ends consisting of a 5’ end and a 3’ end. DNA has an anti-parallel nature and therefore 5’ end is opposite of the 3’ end of the other. DNA polymerase can only add a nucleotide on a 3’ end of an existing nucleotide chain. As a new DNA strand Is assembled, a 3’ hydroxyl group is always exposed at its newest end , the oldest end has an exposed 5’ phosphate. 4. meaning of semi-conservative, semi-discontinuous, leading and lagging strand Semi-Conservative  Hydrogen bonds between two strands break allowing them to unwind and separate. Each strand then acts as a template for the synthesis of its partner. When replication is complete there are two double helices, each with one strand derived from parental molecule base- paired with a newly synthesized one. Each of the new two double helices consists of identical base-pair sequences as the parental DNA. Semi-Discontinuous  Descriptive of the replication of DNA in which the parent strand that is exposed from its 3'-end towards its 5'-end is used as a template for continuous synthesis of a new strand, but the parent strand that is exposed from its 5'-end towards its 3'-end is used as a template for synthesis of short discontinuous segments of DNA, called Okazaki fragments. These Okazaki fragments are covalently linked into a single continuous polynucleotide chain. Leading Strands: - Newly synthesized DNA strand made in the direction of DNA unwinding, which is created by leading strand template. Lagging Strands: -Strand synthesized discontinuously in the opposite direction is called the lagging strand, which is created by the lagging strand template. 5. general action of proteins in Fig. 12.15. Helicase – Unwinds DNA Helix. Primase – Assembles RNA primers in the 5’ TO 3’ direction. (new strand) SSBP – Stabilizes single stranded DNA to prevent the two strands at replication fork from winding back together Topoisomerase – Avoids twisting of DNA ahead of the replication fork (circular DNA) by cutting the DNA, turning the DNA on one side of the break in the direction opposite to that of the twisting force, and then rejoining. DNA Polymerase 3 – Main replication enzyme in E.COLi; extends RNA primer by adding DNA nucleotides to it DNA Polymerase 1 – E-coli enzyme that uses its 5’ to 3’ exonuclease activity to remove RNA of previously synthesized okazaki fragments and uses its 5’ to 3’ polymerization activity to replace RNA nucleotides with DNA nucleotides. Sliding Clamp- Tethers DNA Polymerase 3 to the DNA template making replication more efficient DNA Ligase – Seals nick left between adjacent bases after RNA primer replaced with DNA Lecture 7 – Lecture Outcomes basic structure of double-stranded DNA Polymer making up strand of DNA has on the 5’ end a phosphate group and on the 3’ Carbon it has a hydroxyl group. The two strands of double helix run anti-parallel. components necessary for DNA synthesis DNA synthesis occurs in the S Phase of interphase after G1 Phase. Necessary for DNA synthesis is a large selection of enzyme and proteins which help catalyze and enable the process of DNA replication. Helicase unwinds the double stranded DNA, which then makes a replication fork. A Very necessary component for DNA synthesis is DNA polymerase 3 which can ONLY BUILD from the free 3’ end of the template strand with the hydroxyl group. direction of elongation of a given DNA strand 3’  5’ (left to right on leading strand) In discontinuous replication which is in the opposite direction of the unwinded DNA strand does it go from right to left structure of a replication bubble relationship between replicated DNA and metaphase chromosomes Our chromosomes have hundreds of origins for replication with multiples firing all at once. It starts at the g1 phase for prepare for growth. At s phase DNA replication occurs. G2 phase no occurs where the chromosomes are different than that which started at g1 phase.  the daughter molecules are compacted around nucleosomes (2 double stranded DNA MOLECULES). This is what gives shape to the X SHAPED metaphase chromosomes, it replicates into two identical molecules attached by the centromere. why chromosomes shorten at each replication In order to change RNA to DNA, there must be another DNA strand in front of the RNA primer. This happens at all the sites of the lagging strand, but it doesn't happen at the end where the last RNA primer is attached. Ultimately, that RNA is destroyed by enzymes that degrade RNA left on the DNA. Thus, a section of telomeres is lost during each cycle of replication at the 5' end of lagging strand.  Ends of linear chromosomes o Repetitive DNA sequence: TTAGGG in vertebrates o Specialized proteins o Form a "capped" end structure Telomeres are specialized structures that are essential for protecting chrom
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