total of all chemical rxns in the cell

 divided into catabolism & anabolism

• Energy-producing rxns
• provide ready source of reducing power (electrons)
• generate precursors for biosynthesis
• biodegradation & production of ATP

• synthesis of complex organic molecules from simpler ones
• requires energy from fueling rxns
• biosynthesis & consumes ATP

• have representatives in all 5 nutritional types
• contribute to cycling of elements in ecosystem

A calorie is an energy unit. 

Define calorie:

Exergonic rxns: ΔG° is negative; proceeds    spontaneously

Endergonic rxns: ΔG° is positive; nonspontaneous

• high energy molecule
• exergonic breakdown of ATP coupled w/ endergonic rxns to make them more favorable
• ATP + H₂0 --> ADP + P_i + H⁺

transfer of electrons from a donor to an acceptor

• can result in energy release, which can be conserved & used to form ATP
• more electrons a molecule has, the more energy rich it is

the electron transport chain

first carrier is reduced & electrons moved to the next carrier and so on

• located in plasma membranes of chemoogranotrophs in bacteria & archaeal cells
• located in internal mitochondrial membranes in eukaryotic cells
• examples: NAD, NADP, & others

use iron to transfer electrons

(iron is part of a heme group)

• carry out rxns at physiological conditions so they proceed in a timely manner
• speed up rate @ which a rxn proceeds toward its final equilibrium 

• some composed solely of one or more polypeptides
• some have nonprotein components

energy required to form transition-state complex

(an enzyme speeds up by lowering activation energy)

• rate increases as substrate increases
• no further inc occurs after all enzyme molecules are saturated w/ substrate

• each enzyme has specific pH & temperature optima
• denaturation: loss of enzyme's structure & activity when temp & pH rise too much above optima

• binds enzymes at site other than active site
• changes enzyme's shape so that it becomes less active 

• RNA molecules that can catalyze rxns
• can catalyze peptide bond formation
• self-splicing

• important for conservation of energy & materials
• two major mechanisms: regulation of synthesis of particular enzyme (transciptional & translational) & direct stimulation or inhibition of activity of critical enzyme (post-translational)

two important reversible control measures:

1. allosteric regulation

2. covalent modification 

• most regulatory enzymes
• activity altered by small molecule

• binds non-covalently at regulatory site
• changes shape of enzyme & alters activity of catalytic site
• can either inc or dec enzyme activity

• reversible on & off switch
• addition or removal of a chemical group (phosphate, methyl, adenyl)

• respond to more stimuli in varied & sophisticated ways
• regulation of enzymes that catalyze covalent modification adds 2nd level

inhibition of one or more critical enzymes in a pathway regulates entire pathway

also called end-product inhibition

its own branch of the pathway &

the initial enzyme

• aerobic respiration
• anaerobic respiration
• fermentation

electron transport chain

as electrons pass through ETC to final electron acceptor, proton motive force (PMF) is generated & used to synthesize ATP

aerobic: final electron acceptor is oxygen

anaerobic: final electron acceptor is different exogenous acceptor such as NO^3-, SO₄^2-, CO₂. Fe³⁺, or SeO₄^2-

• uses organic electron acceptor
• no ETC; no proton motive force
• ATP synthesized only by substrate-level phosphorylation

glucose + 2ADP + 2P_i + 2NAD⁺

----------->

2 pyruvate + 2ATP + 2NADH + 2H⁺

• also called citric acid or Kreb's cycle
• common in aerobic bacteria, free living protozoa, most algae, & fungi
• major role is as source of carbon skeletons for use in biosynthesis

• for each acetyl-CoA molecule oxidized, TCA cycle generates:

-2 molecules of CO₂

-3 molecules of NADH

-one FADH₂

-one GTP = one ATP

• located in plasma membrane 
• some resemble mitochondrial ETC, but many are different 

• ETC organized so protons move outward from the mitochondrial matrix as electrons are transported down the chain
• proton expulsion during ET results in the formation of a conc. gradient of protons (pH gradient) & charge gradient
• combined chemical & electrical potential difference represent proton motive force (PMF)

Diffusion of protons back across membrane 

PMf drives ATP synthesis

• enzyme that uses PMF to catalyze ATP synthesis
• functions like rotary engine w/ conformational changes

• includes oxidation of NADH & FADH₂
• ATP produced by substrate level phosphorylation
• theoretical maximum total yield of ATP during aerobic respiration is 38 but actual number closer to 30

• amount of ATP produced during aerobic respiration varies depending on growth conditions & nature of ETC
• under anaerobic conditions, glycolysis only yields 2 ATP molecules

• uses electron carriers other than O₂
• generally yields less energy

• oxidation of NADH produced by glycolysis
• pyruvate or derivative used as endogenous electron acceptor 
• substrate only partially oxidized
• O₂ not needed
• oxidative phosphorylation does not occur (ATP formed only by substrate-level phosphorylation)

• many different carbohydrates can serve as energy source
• carbohydrates can be supplied externally or internally (from internal reserves)

Triglycerides

• common energy sources
• hydrolyzed to glycerol & fatty acids by lipases
• glycerol degraded via glycolytic pathways
• fatty acids often oxidized via B-oxidation pathway 

• removal of amino group from amino acid
• resulting organic acids converted to pyruvate, acetyl-CoA or TCA cycle intermediate (can be oxidized via TCA cycle & can be used for biosynthesis)

• energy from light trapped & converted to chemical energy
• a 2 part process

• light rxns in which light energy is trapped & converted to chemical energy
• dark rxns in which the energy produced in the light rxns is used to reduce CO₂ & synthesize cell constituents

• photosynthetic eukaryotes & cyanobacteria
• oxygen is generated & released into environment
• most important pigments are chlorophylls

• highly organized arrays of chlorophylls & accessory pigments
• captured light transferred to special rxn-center chlorophyll (directly involved in photosynthetic electron transport)

noncyclic electron flow (ATP + NADPH made; noncyclic photophosphorylation)

cyclic electron flow (ATP made; cyclic photophosphorylation)

• H₂O not used as an electron source so O₂ not produced
• only 1 photosystem involved
• uses bacteriochlorophylls & mechanisms to generate reducing pwr
• carried out by phototropic green & purple bacteria 

• some archaea used type of phototrophy that involves bacteriorhodopsin (a membrane protein which functions as light-driven proton pump)
• proton motive force generated
• ETC not involved

• using a carbon source & inorganic molecules, organisms synthesize new organelles & cells
• antibiotics inhibit anabolic pathways
• great deal of energy needed for anabolism

• macromolecules are synthesized from limited number of simple structural units (monomers)
• catabolic & anabolic pathways are not identical as some enzymes function in only one direction
• generation of precursor metabolites is critical step in anabolism
• carbon skeletons are used as starting substrates for biosynthetic pathways

consists of 3 phases

1. carboxylation phase

2. reduction phase

3. regeneration phase

three ATPs & two NADPHs are used during the incorporation of one CO₂

• catalyzed by enzyme ribulose 1,5-bisphosphate carboxylase (aka ribulose bisphosphate carboxylase/oxidase; rubisco)
• rubisco catalyzes addition of CO₂ to ribulose 1,5-bisphosphate (RuBP) forming 2 molecules of 3-phosphoglycerate

many precursor metabolites are used as starting substrates for synthesis of amino acids

• carbon skeleton is remodeled
• amino group & sometimes sulfur are added

Nitrogen 

• potential sources of nitrogen: ammonia, nitrate, or nitrogen (most cell use ammonia or nitrate)
• ammonia nitrogen easily incorporated into organic material b/c it is more reduced than other forms of inorganic nitrogen 

• used by bacteria to reduce nitrate to ammonia & then incorporate it into an organic form
• nitrate reduction to nitrite catalyzed by nitrate reductase 
• reduction of nitrite to ammonia catalyzed by nitrite reductase

• reduction of atmospheric nitrogen to ammonia
• catalyzed by nitrogenase (found onlyl in bacteria & archaea)

cyclic nitrogenous bases consisting of 2 joined rings 

adenine & guanine

cyclic nitrogenous bases consisting of single ring

uracil, cytosine, & thymine

can be found in nucleic acids as well as proteins, phospholipids, ATP, and some coenzymes

most common sources are inorganic phosphate & organic phosphate esters

incorporated through the formation of ATP by 

• phosphorylation
• oxidative phosphorylation
• substrate-level phosphorylation

• major required component in cell membranes
• most bacterial & eukaryotic lipids contain fatty acids

• all DNA present in a cell or virus
• bacteria & archaea generally have 1 set (haploid - 1N)
• eukaryotes have 2 sets (diploid - 2N)

• the pathway from DNA to RNA to protein is gene expression
• it is conserved in all cellular forms of life

• DNA stores genetic information
• information is duplicated by replication & is passed on to the next generation 

• transcription yields a ribonucleic acid (RNA) copy of specific gene
• translation uses info in messenger RNA to synthesize a polypeptide
• also involves activities of transfer RNA & ribosomal RNA

• the nitrogenous bases they contain 
• the sugars they contain
• whether they are single or double stranded

adenine, guanine, cytosine, & thymine

sugar is deoxyribose

• sugar phosphate backbone
• covalent bonds b/n the 3' hydroxyl of one sugar & a 5' hydroxyl of an adjacent sugar

• double-stranded helix
• base pairing: 

2H bonds-adenine (purine) & thymine (pyrimidine)

3H bonds-guanine (purine) & cytosine (pyrimidine)

• major & minor grooves form when the 2 strands twist around each other

adenine, guanine, cytosine, & uracil

sugar is ribose

phosphodiester bonds

most RNA molecules are single-stranded but some are double-stranded 

• messenger RNA (mRNA)
• ribosomal RNA (rRNA)
• transfer RNA (tRNA)

• polymers of amino acids linked by peptide bonds
• amino acids have central carbon with a C-terminal (carboxyl group), N-terminal (amino group), and side chains
• amino acids can be polar, non-polar, or charged depending on the side chain

• involves numerous proteins which help ensure accuracy 
• 2 strands separate w/ each serving as a template for synthesis of a complementary strand
• synthesis is semi-conservative in which each daughter cell obtains 1 old (parent) & 1 new strand

• Bacteria: DNA in most is circular; bidirectional replication from single origin & replication fork is where DNA is unwound
• Archaea: circuar but may have more than one origin  
• Eukaryotic: linear chromosome w/ many replication forks 

• Bacteria like E. Coli consists of at least 30 proteins
• Archaea has more similarities to eukaryotic replication machinery
• overall process similar in all

• DNA pol catalyzes synthesis of complementary strand of DNA
• DNA synthesis is in 5' --> 3' direction resulting w/ formation of a phosphodiester bond

• template that directs synthesis of complementary strand 
• a primer such as DNA or RNA strand
• Deoxyribonucleoside triphosphates (dNTPs) such as dATP, dTTP, dCTP, & dGTP 

• complex of 10 proteins 
• catalyze DNA synthesis
• proofreading for fidelity

DNA topoisomerase

introduces negative supercoiling to help compact bacterial chromosome

1. primase synthesizes RNA primer
2. lagging & leading strands are synthesized
3. DNA pol I removes RNA primers
4. Okazaki fragments are joined by DNA ligase

interlocked rings

form when the two circular daughter chromosomes do not separate

• basic unit of genetic info
• nucleic acid sequence that codes for a polypeptide, tRNA, or rRNA
• linear sequence of nucleotides w/ a fixed start point & end point
• codons are found in mRNA & code for single amino acids

• organization of codons such that they can be read to give rise to a gene product
• most do not overlap but the exception is some viruses which have overlapping reading frames