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Chapter 1 - Coggle Diagram

- - - - types include...
        
        isolated systems that exchange neither matter nor energy with their surroundings
        
        closed systems that exchange energy but not matter with their surroundings
        
        open systems that exchange both energy and matter with their surroundings
    - - organisms extract energy from their surroundings in one of two ways:
        
        chemotrophs: C6H12O6 + 6O --> 6CO2 + 6H2O + energy (energy-yielding oxidation of glucose)
        
        photoautotrophs: 6CO2 + 6H2O --light--> C6H12O6 + 6O2 (light-driven reduction of CO2)
      - in oxidation-reduction reactions, one reactant is oxidized as another is reduced
  - - - enthalpy is represented by H and is heat content, roughly reflecting the number and kinds of bonds
      - free energy is represent as G and equals H - TS, where H represents enthalpy, T represents absolute temperature, and S represents entropy
      - entropy is represented as S and represents the randomness or disorder of the components of a chemical system
      - free energy change is represented by the equation deltaG = deltaH - T deltaS, where deltaH is negative for a reaction that releases heat, and deltaS is positive for a reaction that increases the system's randomness
  - - - Keq = [C]eq^c [D]eq^d / [A]eq^a [B]eq^b
    - - deltaG = deltaG° + RT ln ([C]eq^c [D]eq^d / [A]eq^a [B]eq^b) where R is the gas constant and T is the absolute temperature
  - - - drives ATP synthesis
      - produces the reduced electron carrier NAD(P)H
- - - - changes the instructions for a cellular componentQ
      - can be beneficial
  - - - biological evolution began more than three and a half billion years ago
        
        lipid vessicles containing organic compounds and self-replicating RNA gave rise to protocells
        
        protocells with the greatest capacity for self-replication became more numerous
    - - earliest cells probably obtained energy from inorganic fuels such as ferrous sulfide and ferrous carbonate
      - photosynthetic processes...
        
        ...arose from evolutoin
        
        ...use pigments that capture energy of light from the sun and reduce CO2 to organic compounds
      - atmosphere became richer in O2 with the rise of O2- producing photosynthetic bacteria
  - - - evolution of the chromosome
      - evolution of the nucleus
      - formation of endosymbiotic associations between early eukaryotic cells and aerobic or photosynthetic bacteria
  - - - can approximate the proportion of the genome dedicated to a specific process
      - genes involved in regulation of cellular processes tend to increase with organism complexity
- - - - thin, flexible, hydrophobic barrier around the cell that defines the periphery of the cell
      - composed of lipid and protein molecules
      - contains embedded proteins and carbohydrates
        
        for example, transport proteins, receptor proteins, and membrane enzymes
    - - the internal volume enclosed by the plasma membrane
      - composed of cytosol and a variety of suspended particles such as mitochondria, chloroplasts, ribosomes, and proteasomes
        
        cytosol
        
        highly concentrated solution
        
        contains enzymes, RNA, amino acids, nucleotides, metabolites, coenzymes, and inorganic ions
      - mostly water; hydrophilic
      - acts as a reducing environment
    - - bacteria and archaea store their genome in a nucleoid
      - genome
        
        complete set of genes
        
        composed of DNA
      - eukaryotes store their genome in a membrane-enclosed nucleus
  - - - animal and plant cells 5-100 micrometers in diameter
      - unicellular microorganisms 1-2 micrometers long
    - - as size increases. surface-to volume ratio decreases
  - - - endoplasmic reticulum and golgi complexes play central roles in the synthesis and processing of lipids and membrane proteins
      - peroxisomes are the site of the oxidation of very-long-chain fatty acids and detoxification of reactive oxygen species
      - lysosomes are filled with digestive enzymes
      - granules or droplets containing stored nutrient
      - mitochondria act as the site of most of the energy-extracting reactions of the cell
    - - plant cells...
        
        are larger at 10-100 micrometers
        
        have unique structures including...
        
        chloroplasts
        
        starch granules
        
        thylakoids
        
        cell walls
        
        vacuoles
        
        plasmodesmata
        
        glyoxysomes
      - animal cells...
        
        are smaller at 5-30 micrometers
        
        have unique structures including...
        
        lysosomes
  - - - Gently disrupt cells or tissues by physical shear to rupture the plasma membrane
      - Centrifuge the homogenate
  - - - filaments comprising cytoskeleton undergo constant disassembly into their protein subunits and reassembly into filaments
      - cytoskeleton is a 3D network of protein filaments in eukaryotic cells (actin filaments, microtubules, intermediate filaments)
    - - involve membrane fusion and fission
      - provide paths between the cytoplasm and the surrounding medium
  - - - chromatin
      - plasma membrane
      - cell wall
    - - hydrogen bonds
      - ionic interactions
      - van der Waals interactions
      - hydrophobic effect
- - - - carbon atoms have a characteristic tetrahedral arrangement of their four single bonds
      - free rotation around each single bond
      - limited rotation about the axis of a double bond
  - - - common amino acids
      - nucleotides
      - sugars and their phosphorylated derivatives
      - mono- di- and tricarboxylic acids
  - - - proteins
        
        long polymers of amino acids that can function as enzymes, structural elements, signal receptors, and transporters
        
        proteome refers to the sum of all proteins functioning in a cell, and proteomics is the systematic characterization of this protein complement under a specific set of conditions
      - nucleic acids
        
        DNA and RNA, polymers of nucleotides that store and transmit genetic information
        
        some RNA molecules have structural and catalytic roles in supramolecular complexes
      - polysaccharides
        
        polymers of simple sugars that act as energy-rich fuel stores
        
        act as rigid structural components of cell walls in plants and bacteria
        
        extracellular recognition elements that bind to proteins on other cells
        
        glycome is the entire complement of carbohydrate-containing molecules
      - lipid molecules
        
        are water-insoluble hydrocarbon derivatives
        
        act as:
        
        structural components of membranes
        
        energy-rich fuel stores
        
        pigments
        
        intracellular signals
        
        lipidome is the lipid containing molecules in a cell
  - - - enantiomers are stereoisomers that are mirror images of each other
        
        enantiomers have nearly identical chemical reactivities but differ in optical activity
        
        a racemic mixture is an equimolar solution of two enantiomers and shows no optical rotation
      - chiral centers are asymmetric carbons
        
        a molecule can have 2^n stereoisomers, where n is the number of chiral centers
        
        stereoisomers are named using the RS system
      - diasteromers are stereoisomers that are not mirror images of eachother
    - - organisms are stereospecific
      - if we consumed L-glucose instead of D-glucose, we could not process it
- - - - aerobic...
        
        ...organisms transfer electrons from fuel to O2 for energy
        
        ...environments have a plentiful supply of O2
      - anaerobic...
        
        ...environments are devoid of O2
        
        ...organisms transfer electrons to nitrate, sulfate, or CO2 for energy
        
        obligate anaerobes die when exposed to O2
        
        facultative anaerobes can live with or without O2
    - - Gram-negative bacteria have an outer membrane composed of a lipid bilayer
      - Gram-positive bacteria are colored by Gram's stain, have a thick peptidoglycan layer outside the plasma membrane, and lack an outer membrane
      - Archaea have a layer of peptidoglycan or protein that confers rigidity on their cell envelopes
  - - - phototrophs trap and use sunlight
      - chemotrophs derive energy from oxidation of a chemical fuel
    - - autotrophs can synthesize all their biomolecules directly from CO2
      - heterotrophs require some preformed organic nutrients made by other organisms
- - - - encodes the instructions for forming all other cellular components
      - provides a template to produce identical DNA molecules
      - the structure DNA allows its replication and repair with near-perfect fidelity
      - deoxyribonucleotides are the monomeric subunits that make up the DNA polymer
        
        each deoxyribonucleotide in one strand pairs specifically with complementary deoxyribonucleotide in the opposite strand
        
        strands are held together by hydrogen bonds
    - - native conformation is the precise 3D structure of a protein and is crucial to protein function