Biology 2010 Lecture Notes

Unit 3. Metabolism

This page was last updated July 2, 2003

Some key words and phrases

  1. A brief review of chemistry for biologists
    1. atoms and elements
      1. subatomic particles: protons, neutrons, electrons
      2. atomic number vs atomic weight (atomic mass)
      3. isotopes and radioisotopes
        1. types of radiation: alpha particles, beta particles, positrons
        2. units: counts, rads, and rems
        3. half-life
        4. biological significance and use:  medical procedures, metabolic tracers, dating
    2. interactions between atoms -- compounds and molecules
      1. electron configuration
        1. energy shells subshells; orbitals
        2. valence electrons
      2. covalent vs ionic interactions
      3. polar vs non-polar molecules
      4. schematic representations
    3. interactions between compounds and molecules
      1. hydrophobic/hydrophilic interactions with water
        1. basic properties of water (based on polarity of molecule)
          1. cohesive and adhesive
          2. relatively high surface tension
          3. relatively high specific heat, heat of fusion, heat of vaporization
        2. interactions with nonpolar compounds -- hydrophobic compounds
        3. interactions with polar and ionic compounds -- hydrophilic compounds and aqueous solutions
          1. process of forming a solution
          2. concentrations of solutions
            1. grams (milligrams) per deciliter
            2. molarity --moles per liter of solution
          3. acidic and basic (alkaline) solutions
            1. pH scale
            2. buffers
    4. Organic molecules--the most important elements for biology are carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur; of these carbon is the most fundamental, providing the basic structure of organic molecules
      1. important factors in determining the structure of organic molecules
        1. number of carbons
        2. bonding: single, double, and triple bonds
        3. isomers: structural vs geometric vs stereo (enantiomers)
          1. in theory, sugars can be either left-handed or right-handed; in practice, right-handed sugars predominate in biological systems
          2. in theory, amino acids can be either left-handed or right-handed; in practice, left-handed amino acids predominate in biological systems
        4. presence of functional groups (pp. 54)
          1. hydrogen and hydrocarbons (basic group)
          2. hydroxyl groups (O-H) define alcohols
          3. carbonyl groups (C=O) define aldehydes and ketones
          4. carboxyl groups (COOH) define the carboxylic organic acids
          5. amino groups (NH2) define amides, amino acids
          6. sulfhydryl group (SH)
          7. phosphate group (PO4)
        5. polymers and macromolecules
          1. monomers
          2. dehydration (condensation) vs. hydrolysis reactions
      2. Major groups of organic molecules of biological significance
        1. hydrocarbons
        2. lipids = hydrophobic carbon compounds
          1. fats (triglycerides)
            1. glycerol & fatty acids
            2. mono-,di-, & triglycerides
            3. saturated vs unsaturated fats and fatty acids
          2. phospholipids
          3. steroids
            1. unique ring structure
            2. important examples
              1. cholesterol
              2. testosterone & estrogen
        3. carbohydrates (sugars and starches)
          1. monosaccharides = lots of hydroxyls and one carbonyl group
            1. important considerations
              1. number of carbons
              2. arrangement & position of functional groups
              3. ring vs straight form
            2. important monosaccharides
              1. glucose, galactose, and fructose--energy sources
              2. ribose, deoxyribose--parts of nucleic acids
            3. disaccharides
              1. form by condensation of two monosaccharides
                1. alpha and beta linkages
              2. important disaccharides: sucrose, lactose, maltose--energy storage & transport
            4. polysaccharides
              1. form by condensation of many monosaccharides
              2. important polysaccharides
                1. glycogen & starch--energy storage
                2. cellulose--structure
        4. proteins = chains of amino acids
          1. types of amino acids (see table on p. 69 or the image library)
          2. amino and carboxyl groups
          3. hydrophobic or hydrophilic side chains
          4. peptide bond
          5. important factors contributing to shapes of proteins
            1. amino acid sequence
            2. twisting around the peptide bonds: alpha-helix, beta-sheet
            3. interaction with surroundings: globular shapes
              1. denaturation
              2. disulfide bridges
            4. interactions with other proteins
          6. functions of proteins
            1. structure: tubulin, actin, collagen, elastin
            2. receptors
            3. molecular gates
            4. communication
            5. antibodies
            6. catalysts (enzymes)
            7. note that the function depends on the precise 3-D structure of the protein
        5. nucleic acids = chains of nucleotides
          1. ribose-based nucleotides vs deoxyribose-based nucleotides
          2. structure of DNA
            1. double-stranded
              1. nucleotides within a strand held together by linkages between phosphates and deoxyribose (the so-called sugar-phosphate backbone)
              2. the two strands are joined by hydrogen bonds between complementary bases
  2. The chemistry of cell membranes.
    1. functions of the cell membrane
      1. boundary
        1. controls passage of chemicals--this is most noticeable in the resting potential of a membrane
        2. don't want the permanent exclusion of chemicals--we need a variable means of passage
      2. holds cells together
      3. binding spots for cytoskeleton
      4. help cells recognize each other
      5. functions in growth and division
    2. implications for structure
      1. want something rather loosely put together (not rigid like plastic)
      2. need to perform many functions, vary the functions over time
      3. probably want more than one kind of molecule in membrane
    3. actual chemical structure
      1. phospholipid bilayer
        1. amphipathic - hydrophobic/hydrophilic
        2. fluid in plane (flip-flops rare) because loose bonding
        3. fluidity depends on nature of the phospholipids
        4. allows free passage of nonpolar molecules (diffusion), but blocks polar and ionic compounds
        5. allows membranes to unite
      2. embedded and associated proteins
        1. allow for controllable passage
          1. facilitated diffusion -- protein carriers
          2. active transport --protein carrier plus energy
            1. activation with phosphate (direct)
              1. example - sodium-potassium pump
            2. indirect - energized membrane
              1. example - proton pump powers other activity
          3. the movement of water
            1. diffusion process
            2. movement from hypotonic to hypertonic site
            3. note: concept of total water potential as the sum of osmotic, hydrostatic, and matric potentials
              1. example: turgor pressure in plants
        2. attachment of the cytoskeleton
        3. exocytosis & endocytosis (receptor- mediated)
          1. export or import large molecules
      3. glycolipids and glycoproteins
        1. communication & recognition
  3. Chemical reactions and metabolism.
    1. chemical reactions
      1. reactants (substrates) and products
      2. oxidation and reduction (redox reactions)
      3. chemical equilibrium
    2. energy concerns
      1. what is energy
      2. total energy versus free energy; entropy
      3. endergonic vs exergonic reactions
      4. energy of activation and the role of catalysts
      5. laws of thermodynamics
    3. metabolic pathways
      1. cyclic vs linear pathways
      2. catabolic vs anabolic pathways
    4. role of membranes
      1. localize reactions
      2. store chemical energy
        1. example: bacterial flagella
        2. example: cell membrane potentials
    5. role of proteins -- in essence control metabolism through their activity as enzymes; cells are distinguished by the activity of their enzymes
      1. what enzymes do
        1. reduce activation energy
        2. couple reactions
          1. ATP to ADP and inorganic phosphate -- provides energy
          2. NADH to NAD -- provides energy and electrons
        3. how enzymes work
          1. induced-fit model
        4. enzyme activity affected by
          1. environment (pH, temperature, salinity, etc.)
          2. presence or absence of cofactors (inorganic--minerals) and coenzymes (organic--vitamins)
          3. concentration of substrate (Lucy)
          4. concentration of inhibitors
            1. non-competitive vs competitive inhibitors (McDonalds)
          5. concentration of activators

More terms

  1. The Laws of Thermodynamics
    1. First Law - matter/energy is neither created nor destroyed in chemical reactions - only its form changes
    2. Second Law - in any change of form, the quality of the energy does not increase (it probably decreases)
      1. Second Law (alternate form) entropy increases in closed systems
    3. implications: must account for every atom and every calorie in any chemical reaction
      1. perpetual motion machines are not possible
  2. ATP and metabolism
    1. importance
      1. source of energy
      2. used to charge membranes
    2. sources of ATP -- unstable at room temperature so must be constantly reformed in the cell; two basic processes used to make ATP have been identified
      1. substrate-level phosphorylation -- phosphate group transferred directly from an energized molecule to ADP; simple to understand, but not used as much as the next method
      2. electron transport phosphorylation (chemiosmosis)
        1. requires a membrane, an electron donor, an electron acceptor, and an electron transport chain between the donor and the acceptor
          1. the transport chain is composed of special molecules (quinones and iron-containing proteins like cytochromes) in the membrane
        2. also requires the enzyme ATP-synthetase
        3. process
          1. electrons are donated to the electron transport chain
          2. electrons move down the chain in series of redox reactions
          3. proton gradient (pH gradient) across the membrane is created as the electrons move down the electron transport chain
          4. the energy stored in the proton gradient is used by ATP synthetase to convert ADP + Pi to ATP
    3. examples of electron transport phosphorylation
      1. anaerobic bacteria
        1. many do not perform electron transport respiration
        2. for those that do
          1. the process is called anaerobic respiration
          2. membrane is usually the cell membrane and H+ ions are pumped out
          3. the electron donor is NADH or FADH2 or some other organic compound
          4. the electron acceptors can be one of any number of compounds or ions; the most common are nitrate, sulfate, ferric iron (Fe+3), and carbonate
          5. less than 2 ATP produced per electron donor
      2. aerobic bacteria
        1. membrane equals cell membrane, H+ ions pumped out
        2. electron donor is NADH or FADH2, makes NAD+ or FAD
        3. electron acceptor is O2, makes water
        4. roughly 2 to 3 ATP per NADH molecule
      3. mitochondria
        1. membrane equals inner membrane of mitochondria, H+ ions pumped into space petween membranes
        2. the transport chain includes 5 cytochromes, 2 iron-sulfur proteins, and a lipid called ubiquinone
        3. electron donor is NADH or FADH2, makes NAD+ or FAD
        4. electron acceptor is O2, makes water
        5. roughly 3 ATP per NADH molecule, 2 per FADH2 molecule
      4. purple sulfur bacteria (light reactions of anoxygenic photosynthesis)
        1. more complex endergonic reaction, requires light to supply energy
        2. review the basics of light & pigments
          1. light = photons with associated wavelengths
          2. pigments absorb special wavelengths; electrons are excited to higher energy shell
            1. absorption spectra vs action spectra
            2. photosynthetic pigments
              1. bacteriochlorophylls and chlorophylls a & b -- nitrogen-based cages (porphyrin rings) that trap magnesium atoms
              2. xanthophylls and beta carotene (carotenoids)
        3. process
          1. light energy is absorbed and transferred to the reaction center; electron leaves the reaction center for electron transport chain (quinone plus cytochromes); moves down electron transport chain back to an oxidized reaction center; during  process H+ gradient formed across membrane--energy used to make ATP
          2. donor is bacteriochlorophyll
          3. acceptor is bacteriochlorophyll
          4. electron transport chain with quinone and cytochromes
      5. chloroplasts (photosynthesis I, the light reactions)
        1. process
          1. occurs in the thylakoids of chloroplasts
          2. pigments include chlorophyll a, other chlorophylls, and carotenoids
          3. pigments are arranged into reactions centers and antenna
            1. two types: RC680 = P680 = PSII and RC700 = P700 = PSI
            2. each reaction center has an associated electron transport chain
          4. two possible mechanisms, both operating simultaneously
            1. cyclic photophosphorylation (similar to what happens in purple sulfure bacteria; not as important in plants)
              1. light strikes P700
              2. electrons move to ETC (2 cytochromes and plastocyanin)
              3. ETC directs electrons to P700 (completing the cycle)
              4. proton gradient forms allowing ATP (only) to be made
            2. non-cyclic photophosphorylation (algae and higher plants)
              1. light strikes P680 and P700 more or less simultaneously
              2. electrons move from both reaction centers to their electron transport chains
              3. ETC from P700 directs electrons to NAD+, the acceptor making NADPH; includes ferredoxin and NADP reductase (not the same ETC as in cyclic flow)
              4. ETC from P680 directs electrons to P700, filling the gap left by the electrons leaving P700 (this ETC contains plstoquinone, 2 cytochromes, and plastocyanin--some of the same molecules as in cyclic ETC)
              5. electrons are ripped from H2O to fill the gap left by the electrons leaving P680 - oxygen is produced as a waste product
              6. as electrons move down their respective ETC's, proton gradient is formed, allowing the production of ATP
              7. SUMMARY - non-cyclic photophosphorylation acts as giant chemiosmotic system
                1. membrane = thylakoids
                2. electron donor = water, makes oxygen
                3. ETC includes two reactions centers with special chlorophyll molecules
                4. electron acceptor = NADP+, makes NADPH (equivalent to NADH)
                5. 2 to 3 ATP molecules made along with each NADPH
  3. Storing the energy from the light reactionss
    1. problem - ATP and NADH are very unstable so need to store the energy in a safer form (such as glucose)
      1. process of energy storage = dark reactions or Calvin-Benson cycle
        1. carbon fixation step
          1. react 6 CO2 & 6 RuBP to get 6 6-C sugars
        2. energy storage
          1. 6 6-carbon sugars split to form 12 PGA (3-C)
          2. 12 PGA are energized & reduced to form 12 PGAL
            1. costs 12 ATP and 12 NADPH
          3. 2 PGAL available to form 1 glucose
        3. regeneration -- other 10 PGALS go through complex series of reactions to form 6 new RuBP's to continue the cycle
          1. 4 PGALs join to make 2 six-carbon molecules (=phosphofructose)
          2. 2 PGALs join with the 2 P-fructoses to make 2 four-carbon

          3. molecules (erythrose) and 2 five-carbon molecules (xylulose)
          4. 2 PGALs join with 2 erythroses to make 2 seven-carbon

          5. molecules (sedheptulose)
          6. 2 PGALs join with 2 sedheptuloses to make 4 five-carbon

          7. molecules (2 ribose and 2 xylulose)
          8. all 6 five-carbon molecules are rearranged and energized to form 6 ribulose bisphosphate molecules
            1. cost an additional 6 ATP
        4. total cost of 1 glucose - 18 ATP and 12 NADPH
          1. equivalent to 54 ATP (compare 36-38 ATP recovered in

          2. aerobic cellular respiration)
      2. C4 metabolism: problem with Calvin-Benson cycle: RuBP carboxylase mistakes O2 for CO2 in some situations (O2 is a competitive inhibitor); as the result, some plants have evolved an lternate method of fixing CO2 called C4 metabolism
        1. process
          1. CO2 reacts with PEP to form oxaloacetate
          2. oxaloacetate is transferred to special cells and converted into CO2 & a 3-C molecule
          3. CO2 reacts with RuBP in the special cells and the Calvin-Benson cycle continues
  4. Using carbohydrates, fats, and proteins for energy
    1. purpose - convert energy in organics to energy in ATP
    2. involves both substrate-level phosphorylation & electron transport phosphorylation
    3. proceeds through 4 steps (if use glucose as substrate)
      1. glycolysis - split glucose to form pyruvate in cytoplasm
        1. energize glucose - costs 2 ATP
        2. energized glucose splits to form two PGALs
        3. PGALs are oxidized & de-energized to form two PGAs
          1. gain 2 NADH and 2 ATP
        4. PGAs rearranged to form 2 PEP
        5. PEPs de-energized to form 2 pyruvate
          1. gain 2 ATP
      2. bridge step - capture pyruvate
        1. pyruvate moves to mitochondrion and reacts with coenzyme A to form acetyl-CoA
          1. gain 1 CO2 and 1 NADH for each pyruvate
      3. Krebs cycle - finish removing energy
        1. acetyl-CoA & oxaloacetate react to form citrate & CoA
        2. citrate is decarboxylated & oxidized to form alpha-ketoglutarate
          1. gain 1 CO2 and 1 NADH
        3. alpha-ketoglutarate is decarboxylated, oxidized, and de-energized to form succinate
          1. gain 1 CO2, 1 NADH, and 1 ATP
        4. succinate is oxidized and rearranged to form malate
          1. gain 1 FADH2
        5. malate is rearranged and oxidized to form oxaloacetate
          1. gain 1 NADH
      4. electron transport phosphorylation
        1. converts energy in NADH and FADH2 to energy in ATP through electron transport phosphorylation
          1. donor = NADH or FADH2
          2. electron transport chain in cristae of mitochondria
          3. acceptor = oxygen (this is why we need oxygen)
    4. results of aerobic respiration
      1. 1 glucose molecule converted to 6 CO2
      2. initially 4 ATP, 10 NADH, and 2 FADH2 produced
        1. 10 NADH can be converted to 30 ATP in oxidative phosphorylation (costs oxygen)
        2. 2 FADH2 converted to 4 ATP in oxidative phosphorylation (also costs oxygen)
    5. NOTE: if no O2 must do something else to regenerate NAD+ for glycolysis
      1. anaerobic respiration - use another acceptor
      2. fermentation - waste NADH to continue with glycolysis alone
        1. many fermentations possible
          1. ethanolic fermentation
          2. lactic acid fermentation
        2. result in net gain of only 2 ATP from each molecule of glucose
    6. NOTE: using molecules other than glucose
      1. polysaccharides - convert to glucose first
      2. fats - convert to fatty acids and glycerol
        1. glycerol can be converted to PGAL
        2. fatty acids are broken into pieces two carbons long, forming acetyl-CoA for use in the Krebs cycle; process is known as beta-oxidation of fatty acids
          1. beta-oxidation costs 2 ATP to get started, but then gains 1 FADH and 1 NADH in the process of forming acetyl-CoA
          2. in humans acetyl-CoA is transported from the liver to active cells as ketone bodies; in active cells it is converted back to acetyl-CoA and used in the Krebs cycle
      3. proteins - convert to amino acids, then deaminate, leaving a carbon skeleton; the carbon skeleton can be coverted to pyruvate, acetyl-CoA, oxaloacetate, alpha-ketoglutarate, or some other molecule in glycolysis and the Krebs cycle
        1. in humans, the ammonia produced during deamination is converted by the liver to urea
    7. NOTE: it is possible to interconvert many of these molecules
      1. excess glucose can be used to make polysaccharides or lipids; to make lipids some of the glucose is converted to PGAL and then to glycerol, other glucose molecules are converted to acetyl-CoA and then to fatty acids
      2. excess amino acids can be used to make some of the scarse amino acids by transferring the amino group to one of the molecules in glycolysis or the Krebs cycle
        1. humans can not do this well--for example, we cannot make lysine from carbon skeletons and amino groups, we must get it from our food; the same is true of the other essential amino acids
  5. excess fat and amino acids can also be used to make glucose, but only the glycerol from the fat and only those amino acids with a PGAL skeleton; this process is called gluconeogenesis

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