📖Molecular Biology of the Cell

Alberts, Bruce and Johnson, Alexander D. and Lewis, Julian and Morgan, David and Raff, Martin and Roberts, Keith, and Walter, Peter

Chapter 1.

  • p.3 DNA—polymer, nucleotide—monomer
  • p.3 DNA nucleotide:
    • sugar (deoxyribose) + phosphate group
    • nucleobase (A, G, C, T)
  • p.3 nucleotide is assymetric
    • the phosphate group determines the directionality
    • so DNA is always read in the same order
  • p.3 two strands of DNA have opposite directionality
  • p.3 templated polymerization—one strand of DNA determines in which order a complementary strand is composed
  • p.4 the bond between bases is weak compared to sugar-phosphate link.
    • this allows strands to be pulled apart without breaking phosphates
  • p.4 DNA —(transcription)→ RNA —(translation)→ proteins
    • transcription is a form of templated polymerization
  • p.4 RNA
    • sugar (ribose instead of dioxyribose) + phosphate group
    • nucleobase (A, C, G, U)
  • p.5 RNA backbone is more flexible, so some parts of the molecule can bond to other part of the same molecule (AAAA–UUUU)
    • (can mRNA fold “inadvertenly?”)
  • p.5 protein—polymer, amino acid—monomer
  • p.6 there are 20 amino acids
  • p.7 codon—a triplet of nucleotides
    • codes 1 amino acid
  • p.7 gene—a region of DNA that is transcribed as a single unit
    • single protein
    • set of alternative protein variants
    • catalyctic, regulatory, or structured RNA molecule
  • p.7 besides genes, there are stretches of regulatory DNA
  • p.7 genome—complete DNA sequence
  • membranes
    • p.8 each cell is enclosed by plasma membrane
    • p.8 membranes consist of phospholipids
    • p.8 phospholipid has hydrophilic end (loves water, phoshate) and hydrophobic end (does not like water, hydrocarbon)
      • self-organizes in a bilayer to hide hydrocarbon and expose phosphate
  • p.8 cells produce molecules that self-assemble in the structures the cell needs
  • p.11 feeding:
    • organothrophic (other life)
    • photothrophic (sunlight)
    • lithothrophic (rock)
  • p.12 DNA, RNA, and protein are composed of just six elements: hydrogen, carbon, nitrogen, oxygen, sulfur, phosphorus
  • p.12 N and C from atmosphere are extremely unreactive. only some of the cells fix them to the form accessible for other living cells to consume
  • p.13 eukaryote—DNA inside nucleus (“eu”—“well,” “truly”; “karyon”—“kernel,” “nucleus”); prokaryote—no nucleus
    • prokaryotes are usually small (~few micrometers, up to 600)
  • p.14 most species cannot be cultured by standard laboratory techniques. at least 99% of prokaryotic species remain to be characterized
  • p.15 three major divisions (domains)
    • bacteria (eubacteria)
    • archaea (archaebacteria)
    • eukaryotes
  • p.15 some highly optimized/critical proteins are unlikely to evolve (as most of the changes lead to error and death). they are highly conserved. (e.g., ribosome)
    • (they can be used to track origins of species)
  • p.16 genetic innovation:
    • intragenic mutation
    • gene duplication
    • DNA segment shuffling
    • horizontal (intercellular) transfer
  • p.16 homologs = related genes
    • orthologs = evolved in different species
    • paralogs = evolved in one species (duplicate + mutate)
  • p.24 phagocytosis—engulfing/eating other cells
  • p.25 eukaryotes likely started as predators
    • (large, high mobility, able to engulf other cells)
  • p.25 all eukaryotes have (or had) mitochondria
  • p.26 as mytochondria, chloroplasts also have their own genome and almost certainly originated as photosynthetic bacteria, acquired by eukaryotes that already possessed mitochondria
  • p.39 unknown: how did the first cell membrane arise?

Chapter 2.

  • p.43 cells are 70% water
    • p.44 life chemistry depends on water properties (likely because life started in water)
  • p.43 atoms are linked by covalent bonds to form molecule; molecules can be held together by noncovalent bonds (which are much weaker)
  • p.44 O\ce{O} is strongly attractive for electrons (electronegative) and H\ce{H}—weakly. So the whole HX2O\ce{H2O} molecule has uneven distribution of electrons. That uneven distribution makes water molecules form hydrogen bond.
    • this bond is weak and is easily broken by random thermal motion, so this bond is very short-living, but there are many of them at any time
      • (this causes surface tension and makes water liquid)
  • p.44 hydrophobic molecules are uncharged and form no hydrogen bonds
  • p.94 noncovalent bonds
    • van der Waals attractions
    • electrostatic attractions
    • hydrogen bonds
    • hydrophobic forces (not strictly a force)
  • p.94 hydrogen bonds are formed when hydrogen is “sandwiched” between two electron-attracting atoms (usually O or N)
    • strongest when in a straight line
    • examples
      • in amino-acids to stabilize folded proteins
      • in nucleobases in DNA double helix
  • p.95 hydrophobic forces—water forces hydrohobic molecules close together
  • p.45 though one noncovalent bond is too weak, they can sum up over a surface of a molecule to hold two molecules together
  • acids/bases
    • p.46 HX+\ce{H+}—proton; HX3OX+\ce{H3O+}—hydronium ion
    • p.46 acid—substance that releases protons when it dissolved in water, thus forming HX3OX+\ce{H3O+}
    • p.46 HX2O+HX2OundefinedHX3OX++OHX\ce{H2O + H2O <=> H3O+ + OH-}
      • protons move freely from one molecule to another in water, thus water has pH 7.0 (10-7M — mol/l)
    • p.46 base (alkaline)—opposite of acid
      • aminogroup (NHX2\ce{-NH2}). NHX2+HX2OundefinedNHX3X++OHX\ce{-NH2 + H2O -> -NH3+ + OH-}
    • p.46 cells keep acidity close to pH7 (neutral) by keeping buffers: weak acids and bases that can release and take up protons near pH7, keeping the environment relatively constant
  • p.47 main chemical groups:
  • p.47 cells contain 4 major families of small molecules
    • sugars → polyscharides
    • fatty acids → fats, lipids, membranes
    • necleotides → nucleic acid
    • amino acids → proteins
  • p.49 condensation/hydrolisys
    • condensation = monomerundefinedpolymer+HX2O\ce{$monomer$ -> $polymer$ + H2O} (energetically unfavorable)
    • hydrolisis = polymer+HX2Oundefinedmonomer\ce{$polymer$ + H2O -> $monomer$} (energetically favorable)
  • p.52 metabolism = catabolic pathway (food to components) + anabolic pathway (or biosynthesis, component to molecules)
  • p.56 oxidation—removal of electrons, reduction—addition of electrons
    • oxidation and reduction always occur together
  • activated carriers
    • p.63 activated carrier (aka cofactor, aka coenzyme):
      • ATP
      • NADH
      • NADPH
      • there are other carriers
    • p.69 activated carriers often contain a nucleotide (usually, adinosine diphosphate). this might be a relic from RNA world, where it would be useful to bind to RNA enzymes
      • (or could they evolve from RNA?)
    • p.69
      activated carriergroup carried in high-energy linkage
      NADH, NADPH, FADH2electrons and hydrogen
      Acetyl CoAAcetyl group
      Carboxylated biotinCarboxyl group
      S-Adenosyl methionine (SAM-e)Methyl group
      Uridine diphosphate glucoseGlucose
    • p.70 many activated carriers require energy that is derived from ATP
    • p.74 ATP→ADP hydrolisis provides ΔG ~ -46–-54 kJ/mol.
      • there is another pathway with ΔG ~100kJ/mol (ATP → AMP + pyrophosphate (PPi))
  • p.73 head/tail polymerization
  • sugar oxidation
    • glycolysis is an oxidation of glucose that does not require oxygen
      • p.74 (pp.104–105) glycolysis = glucose + 2×ATP → 2×pyruvate + 4×ATP + 2×NADH
    • p.75 for aerobic cells, glycolysis is only the start of sugar oxidation
    • p.75 pyruvateundefinedCOX2+acetyl CoA+NADH\ce{{pyruvate} → CO2 + {acetyl CoA} + NADH} (happens in mitochondria)
    • acetyl groupundefinedCOX2+HX2O\ce{{acetyl group} → CO2 + H2O}
    • p.76 fermentation—anaerobic energy-yielding metabolic pathway involving the oxidation of organic molecules. Anaerobic glycolysis to the process whereby pyruvate is converted into lactate or ethanol, with the conversion of NADH to NAD+
    • energy storage
      • fat / glycogen (in animals) / starch (in plants)
      • fat is 2× more efficient storage of energy than glycogen. glycogen also binds more water, producing 6× actual difference