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Lecture 4 Information What are the jobs of an organism Large scale o Survival o Find food o Reproduce Small scale o Take in nutrients o Convert them to energy o Expel wastes Commonalities across many organisms System to pass down information o DNA RNA Genetic code to interpret information and convert it to proteins Way to keep information protected Set of genes to accomplish goals of organism Typical Information System Stability constancy of information content Fidelity accuracy of information readout Entropy degradation of information content Redundancy number of information copies Information flow similar in organisms Central Dogma o DNA RNA Protein work in the system Several differences between DNA and RNA RNA uses uracil while DNA uses thymadine Ribose OH group is more reactive than deoxyribose H group o Therefore RNA can be more easily degraded RNA Less stable more error prone No redundancy single strand Autocatalytic DNA More stable less error prone Not autocatalytic DNA is a stable way to store information It is carried by RNA and converted into proteins Proteins do the enzymatic Inherent redundancy double strand complementary Information is stored in DNA codes for enzymes which need to do biological work Tom Cech Search for RNA Splicing Enzyme Nobel Prize for the discovery of catalytic properties of RNA RNA has no constraints due to it s a single strand can interact with other parts of itself multiple structures and this allows RNA to be a catalyst just like proteins discovery of Ribozymes Noticed RNA splicing and wanted to search for the protein responsible since all enzymes are proteins o No evidence of associative protein find RNA self splicing and ability to serve as a catalyst Primitive Genetic Material RNA as first information storage system in organisms RNA world o RNA carries genetic information o RNA can catalyze reactions like proteins o Selection will favor variants with effective replication DNA RNA Proteins Central Dogma not true for every organism Some RNA based Some are RNA based and inject RNA into a cell No true for every organism Convert it to DNA with a reverse transcriptase and integrate it into host genome But is true for the vast majority of organisms Order from Non order Boundary helpful for information systems o Protection from surroundings o Control access to information Phospholipid Structure o Polar head hydrophilic o Nonpolar tail hydrophobic How did earliest early life forms create boundaries o Bilayer formation through molecular self assembly Genetic code used to convert mRNA to amino acids Genetic code is common to nearly all organisms The code is likely very old and arose in the universal common ancestor Biological Energy Flow Energy flows into world as light o Does chemical and physical work o Leaves as heat Energy balance o Energy in Energy out Organisms do not create energy o They transform it Light is highly usable energy heat is not Energy flows from usable to unsable form Using Energy G H T S Biological enery balance 1st Law of Thermodynamics o H 0 energy is conserved Total energy in the universe is neither created nor destroyed in any process but it can be transformed from one form to another OR Total energy of the initial state of a biological process is equal to the total energy of its final state Reaction direction 2nd Law of Thermodynamics G 0 o Spontaneous reactions requiring no additional energy proceed in the direction that reduces free energy G or the useful energy available to do chemical work AND Spontaneous processes requiring no additional energy proceed in the direction that increases entropy in the universe Organisms use energy to maintain order Inside the cell has many organized structures Outside there is total disorder Genome Storage Genome stores the solutions i e molecular mechanisms that organisms have evolved to harness using thermodynamics Genomic information passed on from one generation to the next What is a genome Genome genes chromosomes o 1920 Hans Winkler Genome is the full complement of DNA molecules possessed by an organism o More than all genes Brown Genetics A Molecular Approach What else is in a genome besides genes Regulatory DNA promoters enhancers ncRNAs Spacers Introns intergenic regions telomeres Junk Pseudogenes Repetitive DNA What is genomics Analyze o Information contained in genomes o How that information is expressed o How that information differs between individuals or organisms Model Organisms Share genes and genetic pathways with humans Understand human genes based on studying the function of those genes based on studying the function on those genes in models Common genomic heritage for core functions in all organisms Number of Genes does not keep increasing as genome size increases Why does the rest of the genome get bigger This suggests that there is a core set of genes that all organisms need but they don t need an infinite number Note Those common to eukaryotes and prokaryotes must be critical to being a functioning organism Example Tilapia o First genome to be sequences using only next generation sequencing methods o Annotation predicting where genes are in the respective genome requires finding the coding exons within the larger Human Gene Heritage Cichlid Fish Genome genome Evolving Prokaryotic Genomes Genome size reflects metabolic complexity 90 of the genome encodes for proteins Incredible genetic diversity each prokaryotic species contains up to 15 unique genes in its genome Significant proportion of the genome is acquired from other often distantly related species via lateral gene transfer Evolving Eukaryotic Genomes Genomes size does not correlate with developmental complexity Much larger genomes but mostly non coding for proteins For example 2 of human genomes codes for proteins but over 50 consists of repeating sequences o Remainder is introns regulatory sequences etc Lateral gene transfer is much less common though there are plenty of examples Major source of genomic innovation duplication of genes chromosomes or entire Summary Organisms share common origin genetic code and central dogma Genomes reflect genetic adaptations to particular environmental circumstances o Molecular mechanisms for solving the challenges facing organisms Genomes reflect history o Acquisition of genes based on descent from a common ancestor o Acquisition of genes based on lateral gene transfer from other parts of the phylogenetic tree particularly in prokaryotes o Accumulation of changes within a


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UMD BSCI 207 - Lecture 4 – Information

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