📖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+HX2OHX3OX++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+HX2ONHX3X++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 = monomerpolymer+HX2O\ce{$monomer$ -> $polymer$ + H2O} (energetically unfavorable)

    • hydrolisis = polymer+HX2Omonomer\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 pyruvateCOX2+acetyl CoA+NADH\ce{{pyruvate} → CO2 + {acetyl CoA} + NADH} (happens in mitochondria)

    • acetyl groupCOX2+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