📖Molecular biology of the cell

May 4, 2021

authors: Alberts, Bruce and Johnson, Alexander D. and Lewis, Julian and Morgan, David and Raff, Martin and Roberts, Keith, and Walter, Peter
year: 2015

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 $\ce{O}$ $O$ is strongly attractive for electrons (electronegative) and $\ce{H}$ $H$ —weakly. So the whole $\ce{H2O}$ $H X_{2} O$ 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 $\ce{H+}$ —proton; $\ce{H3O+}$ —hydronium ion
- p.46 acid—substance that releases protons when it dissolved in water, thus forming $\ce{H3O+}$
- p.46 $\ce{H2O + H2O <=> H3O+ + OH-}$ $H X_{2} O + H X_{2} O H X_{3} O X^{+} + OH X^{-}$
  - 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 ( $\ce{-NH2}$ ). $\ce{-NH2 + H2O -> -NH3+ + OH-}$
- 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:

$\ce{-CH3}$	methyl
$\ce{-OH}$	hydroxyl
$\ce{-COOH}$	carboxyl
$\ce{-C=O}$	carbonyl
$\ce{-PO3^2-}$	phosphate
$\ce{-SH}$	sulfhydryl
$\ce{-NH2}$	amino

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 = $\ce{$monomer$ -> $polymer$ + H2O}$ (energetically unfavorable)
- hydrolisis = $\ce{$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 carrier	group carried in high-energy linkage
ATP	phosphate
NADH, NADPH, FADH_2	electrons and hydrogen
Acetyl CoA	Acetyl group
Carboxylated biotin	Carboxyl group
S-Adenosyl methionine (SAM-e)	Methyl group
Uridine diphosphate glucose	Glucose

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 $\ce{{pyruvate} → CO2 + {acetyl CoA} + NADH}$ (happens in mitochondria)
- $\ce{{acetyl group} → CO2 + H2O}$
- 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

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