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Week 2 Lecture Notes

by: Cassidy Zirko

Week 2 Lecture Notes BCH 110

Marketplace > University of Montana > Biology > BCH 110 > Week 2 Lecture Notes
Cassidy Zirko

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About this Document

Covers origin of life, origin of cell and thermodynamics
Intro Biology for Biochemist
Scott Samuels
Class Notes
biochemistry, Biology
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This 5 page Class Notes was uploaded by Cassidy Zirko on Saturday February 6, 2016. The Class Notes belongs to BCH 110 at University of Montana taught by Scott Samuels in Spring 2016. Since its upload, it has received 20 views. For similar materials see Intro Biology for Biochemist in Biology at University of Montana.


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Date Created: 02/06/16
Biochemistry 110, Week 2 2/1/16 Origin of Life   Genetic information passed through a parent cell to a daughter cell   Big Bang: Theory for origin of Universe  o All matter  restricted to small amount of space before big bang  o Matter began to expand as result of big bang  o Temperature began to increase  o Only hydrogen and carbon were present   Earth  o Early atmosphere was different o No free oxygen  o No ozone so earth was bombarded with UV rays from sun   Miller­Urey Experiment  o Biomolecules ­ proteins and nucleic acids  o Arise under abiotic conditions from reactions of simple compounds   Macromolecules  o Large organized molecules  form structure and carry out activities of cell  o Polysaccharides (Sugar polymers)  extremely important  o Lipids( fats)  o Proteins (amino acids)  o Nucleic Acids (nucleotide polymer)   Polymers  o Derive from monomers  o Encode information  sequence of monomers  o Example: strand of DNA, polypeptide sequence and polysaccharide chain   5’ vs 3’ end – allow for directionality in sequence   Biomolecules and information  o Enzymes­ biocatalysts  most are proteins  o All reactions catalyzed by enzymes  o Catalytic activity depends on amino acid sequence  o Genetic code­ relationship between nucleotide sequence in nucleic acids, encodes  genetic information and amino acid sequence in proteins   Origin of Cells  o RNA World hypothesis   Ribozymes­ RNA with catalytic activity   Key event in life probably evolution of self replicating RNA   RNA both encoded with catalyzed its own replication originally   System evolved to encode for synthesis   RNA primarily genetic material   If RNA wasn’t first  like DNA was   20 different amino acids in RNA  greater range of activity   Viruses don’t usually use DNA to code  use RNA instead   Translating­ looking up of 2 amino acids catalyzed by RNA  Biochemistry 110, Week 2  Origin of life  o Key event­ evolution fo membranes separating cells from the environment  o Origin hypothesis evokes proteins or clay  o Double origin theory­ coding system and catalysis evolved separately  2/3/16   Cell  o Basic unit of life  o Biomembrane­ enclosed, semipermeable, respiratory chain, really complex  o Four main biomolecules: proteins, lipids, nucleic acids, polysaccharides  o Metabolism and energy transformations  o Membranes highly organized   Prokaryotes and Eukaryote  o Prokarytoes­ before the nucleus   Bacteria and archaea   Organized DNA in nucleoid   Has no nuclear membrane   Bacteria and organelles  o Eukaryotes: true nucleus   Well defined nucleus   Surrounded by a nuclear membrane   Similar to archaea molecular biology   Cytoplasm  o Viscous contents of cell contained when plasma membrane  o Very organized, cytoskeleton, cytol  o Cytosol­ aqueous part  o Cytoskeleton­ highly organized network of fibrous proteins that supports cell   Nucleus  o Hoses genome (DNA) site of replication and transcription  o Has a double membrane  o Nucleolus­ sit e of ribosomal RNA Synthesis  Mitochondria  o ATP­ energy, currency, production  o Two membranes (inner and outer) not double  o Inner membrane is foiled   ER  o Smooth and rough  o Rough has ribosomes  proteins  excreted from ER   Chloroplasts  o Photosynthesis, only in plants (ATP, sugar and oxygen production)  o Three membranes  one double membrane and an inner membrane  o Stackes of grana  preform photosynthesis   Golgi Complex  Biochemistry 110, Week 2 o Process and secreted and membrane protiens  o Like post office   Lysosomes  o Degradation of old cell components or ingested materials  o Low pH  acidic to denature proteins  o Degrade enzymes as well   Mitochondria and Chloroplasts  o Evolved from bacteria that were endocytosed (ingested)  o Contain their own bacterium – like genomes and ribosomes (make own proteins)  o Genomes vary in size  o Maternal DNA in mitochondria  o Pretty good idea of which bacterium was ingested  Mitochondria DNA  o Small genome  o Encodes own ribosomes for protein making  o Some energy production genes  o ATPase  making ATP and cell respiration  o Different mDNA have different genomes  o Mitochondria and nucleus collaborate on protein   Mitochondria and Chloroplasts  theory of endosymbiosis  o Evolved from bacteria that formed a symbiotic relationship with ancestral cell  o Genome  bacteria like (circular with no introns)  o Ribosomes are bacteria like (structure and function)  o Genomes moved to nucleus over evolutionary time period  o Ribosomes are small  o E. Coli classic Bacteria  o Mitochondria­ cant live on its own  given genes away   Domains of Life  o Five Kingdoms  o Monera, Protista, Fungi, Plantae, .Animalia  o Don’t reflect phylogenetic relationships reveled by molecular analyses  2/5/16 Energy, Enthalpy and Entropy   Reaction rate and reaction direction are different thermodynamically   Sun, oxidation of organic and inorganic molecules support life and living organisms   Photosynthesis and respiration  o Photosynthesis uses solar energy to synthesize sugars  o Cellular respiration oxidized sugars as foundation to produce energy and fixed  carbon  o Plants­ carbon dioxide and water form oxygen and sugar through calvin cycle and split oxygen and hydrogen to from water, uses sunlight energy   Animalia­ eat sugars and breakdown to form carbon dioxide from sugars and oxygen  o Energy used to do life  Biochemistry 110, Week 2  Oxidation and reduction (Redox)  o Oxidation reaction involve transfer of electron from donor to acceptor  o Oxidation: loss of electrons, substance losing electrons is the reducing reagent  o Reduction: gains electrons, Substance gaining electrons­ oxidizing agent  o Alkaline (lipids) most reduced carbon – CH2 o Carbon dioxide has the most oxidized carbon  o More bonds to oxygen make the carbon more oxidized  o Oxygen keeps most of the electrons because more electronegative then carbon   Release of Energy  o potential energy –reduced carbon  changes to kinetic energy by breaking bonds  o ATP  ADP and phosphate ion (lots of negative charges­ easy to separate because of charge repulsion   Chemical Equilibrium  o Rates of forwards and reverse reaction are equal  o No change in amount of products or reactants  o Equilibrium constant­ ratio of products to reactants at equilibrium  o Not effected by the rate of reaction  o Reaction rate described by equilibrium constant   Free Energy Change  ∆ o G determines the direction reaction  ∆ o G < 0­ reaction exergonic, releases energy and goes forward (forms  products)  ∆ o G=0,  reaction at equilibrium  ∆ o G >0, reaction is endergonic, needs energy reaction occurs backwards   Reaction rate  o Reaction rate determined by activation energy  o Activation energy increased by a catalysts   Activation energy  o Determines rate of reaction  o High energy transition state intermediate  o Reactants above products in an energy diagram is ­∆ G and a favorable  reaction  o Transition state ( not energetically favored)  o Catalyst stabilized and lower transition state  o Higher transition state  slower reaction   Catalysts  o Increase reaction rate  o Doesn’t change reaction direction  o Decreases activation energy   Enzymes  o Biological catalysts­ remain unchanged during a reaction  Biochemistry 110, Week 2 o Almost all reactions in a cell are catalyzed by enzymes  o Enzymes bid to substrates by multiple weak interactions  o Substrates are reactants  o Enzymes + substrates  products  o Decrease activation energy stabilizes transition states  o Enzymes can be both proteins and RNA  o Ribosomes ­  RNA enzyme   Life and Thermodynamics  o 1  law­ equivalence of heat and work (conservation of energy)  nd o 2  law­ heat doesn’t pass from a cooler to a hotter body, entropy of a closed  system can only increase  o Organization  takes energy  o Systems easily become disordered 


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