1.1 Cellular foundations

1.1 Cellular foundations

1. The study of biochemistry shows how the molecules that constitute living organisms interact to mantain life

   • Features that make living organisms unique
     • A great chemical complexity and microscopic organization (cells- polymers-structure)
     • Important systems to mantain the equilibrium with its surroundings (mechanical, chemical, osmotic and electrical work)
     • A variety of functions that regulate the interactions between the organism´s components to create life
     • Each organism has a defense mechanism to can adapt to their environment
     • A capacity for self-replication and self-assembly
     • Ability to evolve
   • Biochemistry describes in molecular terms the structure, mechanisms and chemical process shared by all organisms

2. CELL STRUCTURE (the structural and functional units of all living organisms)

   • Plasma membrane
     • Lipids and protein molecules
     • Is a barrier to the free passage of inorganic ions
       • transport proteins
   • Cytoplasm
     • Cytosol
       • Proteasomes (degrade proteins no longer needed by the cell)
       • Ribosomes (protein synthesis)
       • Coenzymes (compounds to many enzyme-catalized reactions)
       • Metabolites (intermediate in degradative pathways)
     • is enclosed by the plasma membrane
   • Nucleus or Nucleoid (where the genome is stored and replicated
     • Eukaryotes (with nuclear membrane)
     • Prokaryotes (without nuclear membrane)

3. Domains of life

   • Archea(peptidoglycan) and Bacteria(pseudopeptidoglycan)
     • Aerobic (with oxygen)
     • Anaerobic (without oxygen)
     • Ways to obtain energy to do work
       • Phototrophs (light)
         • Autotrophs(from C02)
         • Heterotrophs(from organic compounds)
       • Chemotrophs(oxidation of fuels)
         • Lithotrophs (inorganic compounds)
         • Organotrophs (organic fuels)
     • contain cytosol, nucleoid and plasmids
       • Example of bacteria (E COLLI)
     • Single-celled microorganisms
   • Eukarya
     • Their organelles can be isolated for study
       • Claude, Duve and Palade developed methods for separating organelles from the cytosol (diferential centrifugation)
     • CYTOSKELETON (protein filaments crisscrossing the eukaryotic cell forming the interlocking 3 dimensional meshwork)
       • 3 types
         • Actin filaments
         • Microtubules
         • Intermediate filaments
       • Structure and organization to the cytoplasm and shape to the cell
       • Exocytosis (out) and Endocytosis (in)
         • pathways between cytoplasm and surrounding médium
     • Cells build Supramolecular structures
       • Structural hierarchy in the molecular organization of cells
         • 1.Monomeric units (nucleotides, aminoacids, etc)
           • Nucleic acids (monomeric subunits) are joined by covalent bonds
             • In supramolecular complexes macromolécules are held together by noncovalent interactions
               • Hydrogen bonds
               • ionic interactions
               • hydrophobic interactions
               • van der Waals interactions
         • 2. Macromolecules ( DNA, proteins, etc)
         • 3. Supramolecular complexes (Chromatin, cell wall, etc)
         • 4. Cell and its organelles

4. THE FOUNDATIONS OF BIOCHEMISTRY

   • 1.2 Chemical foundations
     • Biochemistry explain biológic form and función in chemical terms
       • Lavoisier compounds of carbon, oxygen, nitrogen, phosporus
       • Abundant in living organisms: Hydrogen, Oxygen, Nitrogen and Carbon
         • other essential, minor amounts
       • biochemical unity: universality of chemical intermediates & transformations
     • Carbon is versatile (size, shape, composition) and forms stable bonds
       • Biomolecules are derivatives of Hydrocarbons with different funcional groups
         • characteristics of compound: chemistry of funciotional group and disposition in space
       • Cells metabolome
         • Secondary metabolites (plants)
           • nicotine, quanine, morphine, caffeine
         • Ocurrence= Evolutionary conservation of metabolic pathways
         • central metabolites
           • aminoacids, nuecleotides, sugars, carboxylic acids
             • Micro- mili molar concentration
             • Water soluble
             • Polar
     • Macromolecules
       • Informational
         • Proteins
           • enzimes, structural, receptors and transporters
           • amino acids
         • Nucleic acids
           • DNA, RNA
           • genetic information
       • Polysaccharides
         • sugars
         • energy, structure, recognition elements
       • Lipids
         • small, not macro- associate noncovalently to large structures
         • hydrophobic, hydrocarbon derivatives
         • structural, energy, pigments, intracellular signals
     • Stereochemistry
       • 3D space arrangement of atoms
         • Configuration
           • breakage of bonds
             • Stereoisomers
               • Geometric/ cis-trans isomers
               • chiral centers
                 • enantiomers (mirror
                   • racemic mixture (equimolar, no rotation)
                 • Diasteromers (not mirror)
         • Conformation
           • bonds don't break
     • stereochemically correct interacciones
       • stereospecificity
   • 1.3 Physical foundations
     • Goal of Biochemistry
     • Living organisms exist in a dynamic steady, never at equilibrium with their surroundings
       • Molecules and ions are different in organims surroundings
         • small molecules, macromolecules, supramolecular, complexes
     • Organisms transform energy and matter from their surroundings
       • Universe
       • System
         • Isolated
         • Closed
         • Open
     • The flow of electrons provides energy for organisms
       • Energy from sunlight
         • Reactions involved in electron flow are oxidation-reduction reactions
     • Creating a mantaining order requires work and energy
       • Second law of thermodynamics
         • Endergonic reactions
         • Exergonic reactions
     • Energy coupling links reactions in biology
       • Central issue in bioenergetics
     • Keq and G° are measures of a reaction's tendency to proceed spontaneously.
       • The tendency of a chemical reaction to go to completion can be expressed as an equilobrium constant
         • A large value of Keq means the reaction tenis to proceed until the reactants are almost completely converted into the products
           • Bibliography: Lehninger, A. (2013). Lehninger principles of biochemistry (pp. 1-36). New York.
             • Karen Analy Chávez Bracamontes A01205591
               • Diego Antonio Vargas Vanegas A01205045
                 • Sofia Chufan de la Cuadra A01209015
                   • Martha Ximena Rico Santana A01209160
         • G is a fuction of the standard free energy change G
     • Enzymes promote sequences of chemical reactions
       • Every chemical reaction in a cell ocres at a significant rate because of the presence of enzymes
       • Organized into many sequences of consecutive reactions, called pathways
         • Anabolism
         • Catabolism
           • Cellular metabolism
     • Metabolism is regulated to achieve balance and economic
       • Key and science in each metabolic pathway are regulated so that each type of precursor moleculeis produced in a quantify appropiate to the current requerimients of the cell
   • 1.4 Genetic foundations
     • Living cells have the ability to reproduce themselves
       • Inherited traits
         • Genetic information that means that the organisms have nearly the same size, shape and infernal structure
           • It depends in the genetic material (DNA)
             • DNA is a sequence of monomerics subunits (nucleotides)
               • In a linear polymer encodes the instructions for forming all other cellular components
                 • The genetic information needs to be in a stable form with a mínimum of errors
                   • All of this depends in the complementary structure between the two strands of DNA
                     • For each daughter cell needs two DNA strands for the synthesis of a new
                       • If the synthesis has a damage in one strand the other one can asure the information
     • DNA encoded in a linear sequence of desoxyribonucleotide subunits
       • The expression of the message (protein) results in a tridimensional cell determinanted by it aminoacid sequence
         • Proteins associates with other macromolecules to create supramolecules
   • 1.5 Evolutionary foundations
     • 1.Dobzhansk's generalization says that all modern organisms have a common evolutionary progenitor with a series of small changes (mutations).
       • This mutations are transmited to the new generation.
         • This changes can be benefit or not in order to an organism or cell survive in an environment
           • The new organisms have new compunds
     • 2.Organic compunds like basic biomolecules are found in specific part of the planet
       • There is a hypothesis, these compounds were created by some natural forces which helped first living organism to acquire organic compunds
     • 3.Nucleic acids encode the genetic information
       • Specifies the structure of enzymes, and enzymes catalyze the replication and repair of nucleic acids, which came first DNA or protein?
         • The answer is RNA preceded both, RNA molecules can act as catalysts in their own formation
           • In the protein synthesizing, RNA molecules catalyze the formation of peptide bonds
     • 4.Early unicellular acquired the ability to obtain energy from their enviroment
       • A remarkable evolutionary event was the development of pigments in order to capture the energy of light from sun (photosynthesis).
         • With this event the amount of oxygen increased, as a result the anaerobic cells died
     • 5.Earliest eukaryotic cells had three major changes
       • a. The DNA amount increased, so the mechanism changed into a compactly form with specific proteins.
         • b. The size of the cell was bigger a system intracellular membranes was developed
           • c. Early eukaryotic cell developed a photosynthetic bacteria to form endosymbiotic
     • 6. As a result of the information on the molecular antomy of cells, it's posible analyze the evolutionary process
       • The sequence of genome
         • Study the similiarity from the simplest to the most complex organism
           • Two genes share sequence similiarities are homologous sequences and the proteins are homologs
             • Two homologous genes occur in the same species they are paralogous and protein are paralogs
               • In different species are orthologous and proteins orthologs (protein with the same function in both species)
         • When the genome is fully determined each gene is assigned a function (DNA synthesis, protein synthesis...)
           • The complexity of the organism determines the proportion of its genes that encodes genes involved in the regulation of cellular processes