Ch. 7 And 8 Flashcards
Composition of a Bacterial Cell
70% water
15% proteins
7% nucleic acid
3% carbohydrates
2% lipids
3% organic materials
How do cells take in Iron?
Since iron is insoluble, making uptake difficult, microorganisms secrete siderophores. They solubilize iron and take it to the cytoplasm of the microorganisms.
- Fe+2
- found in rocks and soil
- needed by cytochromes (respiratory proteins)
Methanogenesis
- Chemoautotrophs produce methane (CH4) - swamp gas - by reducing CO2 by using H2 under anaerobic conditions
- methane is released but becomes crystallizes due to immense pressure
Extracellular enzymes
- enzymes that are released by an organism into their environment
- saprobes have rigid cell wall and can’t engulf large food particles
- therefore, they release enzymes outside of their cell to digest food molecules into smaller pieces that can then be transported into the cell
Facultative Parasite
Some non pathogenic saprobes can adapt and invade a susceptible host rather than solely feeding off the environment
Ectoparasites
Parasites that live on the body
Endoparasites
Parasites that live in organs and tissues
Intracellular parasites
Parasites that live within cells
- most extreme!
Autotroph
A microorganisms that requires only inorganic nutrients and whose main carbon source is CO2
Heterotroph
An organism that relies on organic compounds for its carbon and energy needs
Organic Carbon
Found only in nature through living things
Fastidious
Refers to bacteria that require strict narrow , nutritional or environmental conditions for growth because they lack genetic and metabolic mechanisms to synthesize compounds for survival
Macronutrients
- Required in large quantities
- play principal roles in cell structure and metabolism
- sugars (carbs) and amino acids (proteins)
Micronutrients\Trace Elements
- Required in small quantities
- involved in enzyme function and maintenance of protein structure
- manganese, zinc, nickel
Growth Factor
An organic compound such as a vitamin or amino acid that must be provide in the diet to facilitate growth
- amino acids, purines, pyrimidines
Photoautotroph:
- sunlight as energy
- ex: photosynthetic organism, algae, plants, Cyanobacteria
Chemoautotroph:
- simple inorganic compounds for energy
- archaea, methanogens, and deep-sea vent bacteria
Chemoheterotroph
- metabolically convert the nutrients from other organisms
- Protozoa, fungi, animals, some bacteria
Two Types of Chemoheterotrophs
- Saprobes: free living microorganisms that feed on organic debris from dead organisms (opportunistic pathogens and facultative parasites, fungi, bacteria)
- Symbiotic Microbes: obtain organic matter from living organisms by deriving nutrients from host (pathogens and parasites)
Parasites
An organism that lives on or within another organism from which it obtains nutrients and receives protection - produces of some degree of harm to host
Obligate parasite
Parasites that are so dependent on their host that they are unable to grow outside of host
Passive Transport
- Substances exist in a Gradient and and move from areas of high concentration to low concentration
- does not require energy
- ex: diffusion, osmosis, facilitated diffusion
What is the difference between osmosis and diffusion?
Diffusion: movement of any molecule from high to low concentration
Osmosis: movement of solvent (water) through a semi-permeable membrane from high to low concentration
Active transport
- requires energy and carrier proteins to transport molecules from areas of low concentration to high concentration
Group Translocation
Substances being transported are altered during transfer across a plasma membrane
- sometimes used to transport sugars while simultaneously adding phosphate molecules to a activate them for the metabolic cycle
Reactive Oxygen Species
Toxic oxygen products released once oxygen is utilized
- superoxide (CO2-)
- peroxide (H2O2)
- hydroxyl radicals (OH-) - most dangerous
Protection against Toxic Oxygen
- utilize enzymes to convert superoxide ions into less harmful oxygen gas (superoxide dismutase and catalase)
Halophile
A microbe that needs a high concentration of salt for growth
Osmophile
An organism that tolerates a high salt concentration
Osmotolerant
- facultative halophile
- adapt to both high and normal salt concentrations
Xerophile
Organisms that can grow and reproduce in conditions with low availability of water
Acidophile
Organisms that thrive under highly acidic condition
Neutrophile
- Organisms that live in a range of 5.5-8 pH
- live in soil, freshwater, plant and animal bodies
Alkalinophile
Found in hot pools and soils that have a high level of basic materials
Psychrophile
An organism that thrives at low temps (0-15 degrees C)
Psychrotolerant
Organisms that can survive as 0 degrees C but prefers temps that are greater than 20 degrees C
Mesophile
Organisms that grow at intermediate temperatures between 20 and 40 degrees C
Thermophile
Organisms that thrive at temperatures between 50 and 80 degrees Celsius
Hyperthermophile
An organism that thrives at temperatures of 80 degrees C or higher
Aerobe
An organism that loves and grows in presence of oxygen
Facultative anaerobe
An aerobe that doesn’t require oxygen for its metabolism and is capable to growth in its absence - utilizes aerobic respiration when oxygen is present but can adapt to an anaerobic mode of metabolism like fermentation
Aerotolerant
Anaerobes that don’t need oxygen but can survive in its presence
Anaerobe
Organisms that can’t tolerate oxygen in their environment so they perform respiration without it - lack metabolic enzymes to process toxic oxygen
Microaerophile
An aerobic bacterium that requires oxygen at a concentration of less than that in the atmosphere
Barophile
Microorganisms that thrives under high pressure
- usually hydrostatic
- deep sea
Sessile
- Permanently attached, unable to move freely,
- could mean permanent attachment to substrate or base
Planktonic
Free loving bacteria - able to float or move
Symbiosis
Two organisms that live together in a close partnership
Symbiont
Refers to an organism living in symbiosis
Halobiont
A collection of closely related species that from a discrete ecological unit
Niche
Totality of adaptations organisms make to their habitat
- environmental factors affect the functions of metabolic enzymes
- ex: temp, oxygen, osmotic pressure, barometric pressure
Obligate Mutualism
Organisms that are so intimately associated that require each other to survive
Ex: Termites would not be able to digest wood if endosymbiotic protists like trichonympha did not exist
Ex: Root nodules on a legume have nitrogen fixing endosymbiotic bacteria that supply the plant with usable nitrogen and provide a nurturing habitat for the bacteria
NonObligate Mutualism
Organisms interact at the cellular level for mutual benefit, but they can be separated and live apart (cooperation)
Ex: Protozoan engulfs the algae but absorbs the nutrients they release and shelters them
Ex: Plant supplies nutrients to a fungus and the fungus protects the plant against drying out and insects
Commensalism
An unequal relationship when one benefits and the other is unharmed
Parasitism
A microbe invades the sterile regions of host and occupies its tissues and cells, causing some degree of harm/or damage
Ex: Mosquitoes are blood sucking ectoparasites of humans that carry their own parasites that cause malaria, and those parasites can be transmitted to humans through the blood sucking
Syntrophy
Microbes that share a habitat feed off substances that are released by other organisms
Ex: A dust mite lives in human settings and feeds off dead skin cells
Ammensalism
One member of an association produces a substance that harms or kills another
- Ex: Ants have complex symbiotic relationships that involve mutualism and amensalism with fungi and bacteria. The amensalism part is where the ants cultivate actinomycetes to protect their habitat from microbial pests
Competition
Occurs when microorganisms are sharing a space and are competing for nutrients
Ex: an organism uses up a vital nutrient to grow faster and dominate the habitat
Ex: microbes releasing inhibitory chemicals into the environment to inhibit or kill other microbes
Bio elements
Basic requirements for life: carbon, hydrogen, oxygen, phosphorus, potassium, nitrogen, sulfur, calcium iron, sodium, chlorine, magnesium
Biofilms
Result when organisms attach to a substrate by some form of extra-cellular material that binds them together in complex organized layers
- dominate the structure of natural environment on earth
- communicate and cooperate in the formation and function of biofilms (quorum sensing)
Benefits of biofilms
Microorganisms growing as biofilms are significantly less susceptible to antibiotics and host defenses than the planktonic form of that same organism
Quorum Sensing
A phenomenon occurring among microbes in a biofilm in which the members signal each other and coordinate function
- microbes are attracted to a surface and settle down, this stimulates the cells to secrete a slimy or adhesive matrix that binds them to the substrate - these attached cells release inducer molecules that accumulate to cell population growth - they monitor their population - inducer molecules stimulate specific genes on their chromosome to begin expression
Catabolic
larger molecules are broken down into smaller molecules through releasing energy
- exergonic
Anabolic
Biosynthesis; larger molecules are built from smaller ones, which forms cell structures
- Endergonic
Enzymes
A protein biocatalyst that facilitates metabolic reactions
- increases rate if chemical reactions without becoming part of the product or being consumed
- increase rate of molecule breakdown
How to overcome activation energy
- increase reactant concentration to increase rate of molecular collisions
- increasing thermal energy to increase molecular velocity
- add a catalyst (enzyme) which binds to the substrate (reactant) at the active site
Simple enzymes
Contain only proteins
Conjugated enzymes
AKA: Haloenzyme
- contain both a protein and non-protein portion (apoenzyme and cofactor)
Apoenzyme
The protein portion of an enzyme
Cofactor and coenzyme
- accessory to apoenzymes and the non protein portion of Haloenzymes
- Coenzymes: an organic cofactor that works with the apoenzyme to alter a substrate
- Cofactor: inorganic metals help being active site and substrate closed together
- essential to catalytic activity
How do enzymes lower activation energy?
- increase concentration of substrates at active site of enzyme
- orient substrates properly with respect to each other in order to form transition state complex
- induced fit model for enzyme substrate interaction
Competitive Inhibition
Substrate that resembles the normal substrate - competes with substrate for the active site
Allosteric Inhibition
Form of competitive inhibition in special types of enzymes with two binding sites: regulatory and allosteric
- negative feedback can slow enzymatic activity
- binding of molecules other than the substrate in the regulatory site
- sometimes the regulatory molecule is in the product of the enzymatic reaction
Non competitive Inhibition
Inhibitor binds to the entire enzyme-substrate complex and protects the enzyme from completing its cation on the substrate
Types of reactions
Linear: the product of one reaction is often the reactant for the next - forming a linear chain of reactions
Cyclic: starting molecule is regenerated to initiate another turn of the cycle
Branched: adds branches to molecule
Oxidoreductase
Transfers electrons from one substrate to another
Dehydrogenase
Transfers hydrogen from one compound to another
Transferases
Transfers functional groups from one substrate to another
Hydrolysase
Cleves bonds or molecules with the addition of water
Lyase
Add groups to or remove groups from double bonded substrates
Isomerase
Change a substrate into its isomeric form. An isomer is a compound that has the same molecular formula as another compound, but differs in arrangement of atoms.
Synthase
Enzymes that catalyze the formation of large molecules
- ex: fatty acid synthase, makes one component of triglycerides
Ligase
Binds DNA fragments during replication
Making ATP
Energy that is released during catabolic processes is used to make ATP
- through phosphorylation
Substrate Level Phosphorylation
ADP or GTP is phosphorylated by a substrate to produce ATP or GTP
Oxidative Phosphorylation
Phosphorylation of ADP to ATP using the free energy produced from redox reactions in the electron transport
ATP Hydrolysis
Catabolic process where chemical energy that is stored in ATP phosphate binds is released after water is used to split the binds
Glycolysis
Breakdown of glucose to pyruvic/lactic acid during fermentation - anaerobic (no oxygen consumed)
- synthesizes ATP to produce NADH and create pyruvic acid
- glucose metabolism is an essential energy source for all cells - specifically for the brain and red blood cells
- 10 step process that ends with 2 molecules of pyruvate and 2 net ATP molecules
Glycolysis Summary
- input: 2 ATP, 2 NAD+, One Glucose
- output: 4 ATP (2 net), 2 NADH, 2 pyruvate
- glucose phosphorylated by ATP
- converted to its isomeric form
- second ATP is used to phosphorylate the first carbon of fructose-6-phosphate -> fructose-1, 6 diphosphate
- those are split into two 3 carbon fragments (G3P and DHAP)
- DHAP is converted to G3P -each G3P molecule is involved in a single oxidation-reduction reaction
- 1 ATP and 3 phosphoglyceric acid is produced when one of the high energy phosphates diphosphoglyceric acid is donated to ADP through substrate level phosphorylation
- 3 phosphoglyceric acid becomes 2 phosphoglyceric acid when phosphates shift
- water molecule from 2 phosphoglyceric acid is removed so it becomes PEPA (phosphoenolpuruvic acid)
- PEPA gives up its high energy phosphate bond to produce ATP through substrate level phosphorylation-which creates pyruvic acid as one of its products
Pyruvic Acid to Acetyl CoA prior to Krebs
NAD+ is reduced and CO2 molecule is removed (decarboxylation)
Krebs Cycle
Metabolic cycle that is linked to glycolysis and receives acetyl groups generated when pyruvic acid is decarboxylated, it provides NADH, FADH2, and ATP
Krebs Cycle Summary
Input: 2 carbon component of acetyl CoA
Output: 4 carbon, 6 NADH, 2 FADH2, 2 ATP
Electron Transport Chain
Electron carrying molecules transfer energy-rich electrons and protons to molecular oxygen - energy is extracted and conserved in the form of ATP
- occurs in the mitochondria in eukaryotes
- special carriers receive electrons from reduced carriers (NADH, FADH2) generated by glycolysis and Krebs
- series of redox reactions
- ATP formation is through oxidative phosphorylation
- Complex I, III, IV pump protons from matrix into inter membrane space, creating a charged gradient - with each redox exchange, energy levels lesson - free energy is captured and processed by ATP Synthase complexes within the cristae
Alcoholic Fermentation
Inputs: glucose, ADP, Phosphate
outputs: ethanol, CO2, 2 ATP
Lactic Acid Fermentation
Inputs: glucose, ADP, Phosphate
Outputs: lactate, 2 ATP
Antibiotics: Cell wall damage and lysis
Penicillins, cephalosporins, bacitracin, vancomycin
Antibiotics: inhibit protein synthesis
Aminoglycosides Macrolides, Erythromycin, Tetracyclines, Chloramphenicol
Antibiotics: block DNA replication
- Fluor-quinolones
- end in floxacin
Antibiotics: stops mRNA synthesis
Rifampin
Antibiotics: inhibit folic acid synthesis
Sulfa Drugs, Trimethoprim
