Metabolism: Catabolism and Anabolism

Chapter 5

• Catabolism involves breaking down molecules, while anabolism involves building them.
• Metabolism encompasses all chemical reactions in an organism, including catabolism and anabolism.
• Catabolism releases energy (exergonic), while anabolism requires energy (endergonic).
• Amphibolic reactions can be either catabolic or anabolic, playing a role in both processes.
• Coenzymes assist enzymes in catalysis; alternate forms play different roles in metabolism.
• ATP structure includes adenine, ribose, and three phosphate groups; functions as the primary energy currency of the cell.
• Enzymes are proteins that catalyze biological reactions; their function is affected by temperature, pH, and substrate concentration.
• Denaturation is the loss of an enzyme's native structure, leading to loss of function.
• Activation energy is the energy required to start a reaction.
• Allosteric inhibition involves binding of an inhibitor to a site other than the active site.
• Competitive inhibition involves an inhibitor binding to the active site.
• Noncompetitive inhibition involves an inhibitor binding to a site other than the active site, altering the enzyme's shape.
• Feedback inhibition occurs when the product of a metabolic pathway inhibits an earlier step in the pathway.
• Sulfanilamide acts as a competitive inhibitor by blocking the active site of an enzyme involved in folic acid synthesis.
• Oxidation-reduction (redox) reactions involve the transfer of electrons; reducing power refers to the ability to donate electrons.
• NADH and FADH2 are coenzymes that carry electrons.
• Glycolysis is the breakdown of glucose into pyruvate; occurs in the cytoplasm of both prokaryotes and eukaryotes; starting substance is glucose, and products include ATP, NADH, and pyruvate.
• Acetyl-CoA synthesis converts pyruvate to acetyl-CoA; occurs in the cytoplasm of prokaryotes and the mitochondrial matrix of eukaryotes; requires pyruvate and produces acetyl-CoA, CO2, and NADH.
• Citric acid cycle oxidizes acetyl-CoA to produce ATP, NADH, and FADH2; occurs in the cytoplasm of prokaryotes and the mitochondrial matrix of eukaryotes; main products include CO2, ATP, NADH, and FADH2.
• Electron transport chain uses electron carriers to generate a proton gradient, which drives ATP synthesis; located in the cytoplasmic membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes.
• Chemiosmosis involves the movement of protons down their electrochemical gradient to generate ATP.
• Fermentation is an anaerobic process that regenerates NAD+ for glycolysis; alcoholic fermentation produces ethanol, while lactic acid fermentation produces lactic acid.

Chapter 6

• Fats are catabolized via beta-oxidation.
• Proteins are catabolized via deamination.
• Carbohydrate catabolism is central because it provides precursors for other metabolic pathways.
• Oxidative phosphorylation involves the electron transport chain and chemiosmosis.
• Substrate-level phosphorylation involves the direct transfer of a phosphate group from a substrate to ADP.
• Cells integrate and regulate metabolic functions through enzyme regulation, feedback inhibition, and hormonal control.
• Obligate aerobes require oxygen.
• Obligate anaerobes cannot tolerate oxygen.
• Facultative anaerobes can grow with or without oxygen.
• Aerotolerant anaerobes do not use oxygen but can tolerate its presence.
• Microaerophiles require low levels of oxygen.
• FTM (Fluid Thioglycollate Medium) is used to determine an organism's oxygen requirements.
• Enzymes like superoxide dismutase, catalase, and peroxidase protect against toxic forms of oxygen.
• Binary fission is the process of cell division in bacteria; differs from mitosis in that it does not involve the formation of a mitotic spindle.
• Binary fission results in two identical daughter cells.
• Nutritional requirements for growth include carbon, nitrogen, phosphorus, and other essential nutrients.
• Cells use these nutrients for building macromolecules and generating energy.
• Phases of microbial growth include lag, log, stationary, and death.
• During the lag phase, cells are adjusting to their environment.
• During the log phase, cells are growing exponentially.
• During the stationary phase, cell growth equals cell death.
• During the death phase, cell death exceeds cell growth.
• Trophic classification of microbes includes autotrophs (produce their own food) and heterotrophs (consume organic matter).
• Temperature, pH, and osmotic pressure affect microbial growth.
• Human pathogens typically require moderate temperature, neutral pH, and isotonic conditions.
• Logarithmic growth is exponential, while arithmetic growth is linear.
• Total number of cells in a population is calculated by multiplying the original number of cells by 2^n, where n is the number of generations.
• Singlet oxygen, superoxide radical, peroxide anion, and hydroxyl radical are toxic forms of oxygen.
• Superoxide dismutase, catalase, and peroxidase protect against these toxic forms of oxygen.

Chapter 7

• Biofilms are communities of microorganisms attached to a surface; clinically important because they are resistant to antibiotics and disinfectants.
• Quorum sensing is a process by which bacteria communicate and coordinate their behavior.
• Optimal growth conditions, defined media (precise chemical composition known), complex media (chemical composition not precisely known), differential media (distinguish between different microorganisms), selective media (inhibit growth of some microorganisms while allowing others to grow).
• Pure culture steps involve isolating a single type of microorganism; streak plate, pour plate, cfu (colony forming unit), axenic culture (pure culture), aseptic technique (preventing contamination).
• Cell count principles include colony forming unit (CFU), turbidity measurement, and viable count.
• Turbidity measurement is related to lab and use of spectrophotometer.
• A viable count measures the number of living cells in a sample.
• Ames test assesses the mutagenic potential of a chemical substance.
• Auxotroph is a mutant organism that requires a particular additional nutrient that the normal strain does not.
• Mutations can be silent, nonsense, frameshift, or missense.
• Nucleotides consist of a 5C sugar, phosphate group, and nitrogenous base.
• DNA contains deoxyribose, while RNA contains ribose.
• Genetic code is the set of rules by which information encoded in genetic material (DNA or RNA) is translated into proteins.
• Replication is the process of copying DNA.
• Transcription is the process of synthesizing RNA from a DNA template.
• Translation is the process of synthesizing protein from an RNA template.
• Enzymes and substrates required for replication include DNA polymerase, helicase, ligase, and nucleotides.
• Enzymes and substrates required for transcription include RNA polymerase, transcription factors, and nucleotides.
• Enzymes and substrates required for translation include ribosomes, tRNA, mRNA, and amino acids.
• DNA replication is semiconservative, meaning each new DNA molecule consists of one original strand and one new strand.
• Mutagens are agents that cause mutations; can lead to various results, including silent mutations, missense mutations, nonsense mutations, and frameshift mutations.
• Horizontal gene transfer involves the transfer of genetic material between organisms that are not parent and offspring.
• Transformation involves the uptake of naked DNA from the environment.
• Transduction involves the transfer of DNA by a virus.
• Conjugation involves the transfer of DNA between bacteria through direct contact.
• Bacterial pilus plays a role in conjugation by forming a bridge between cells.
• Prokaryotic chromosomes are circular and located in the cytoplasm, while eukaryotic chromosomes are linear and located in the nucleus.
• Plasmids are small, circular DNA molecules that are separate from the bacterial chromosome.
• F plasmid is a plasmid that carries genes for conjugation.
• Genetic recombination occurs when genetic material is exchanged between organisms; results in new combinations of genes.
• DNA polymerase has a lower proofreading error rate than RNA polymerase because DNA is more important to get right.
• Inducible operons are turned on in the presence of an inducer, while repressible operons are turned off in the presence of a repressor.
• Promoter is a region of DNA where RNA polymerase binds to initiate transcription.
• Lactose operon regulates the expression of genes involved in lactose metabolism; structure includes a promoter, operator, and structural genes; responds to lactose levels to maintain homeostasis.