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MICRO TEST 2

Terms in this set (293)

Bioelements
basic requirements for life (carbon, hydrogen, oxygen, phosphorus, potassium, nitrogen, sulfur, calcium, iron, sodium, chlorine, magnesium)
essential nutrients
substance (element or compound) an organism must get from a source outside its cells
subgroups of essential nutrients
macronutrients and micronutrients
macronutrients
required in large quantities: play principle roles in cell structure and metabolism (proteins and carbs)
micronutrients or trace elements
required in small amounts; involved in enzyme function and maintenance of protein structure. (manganese, zinc, nickel)
organic nutrients
contain carbon and hydrogen atoms and are usually the products of living things.
-methane CH4, carbs, lipids, proteins, and nucleic acids.
inorganic nutrients
atom or molecule that contains a combination of atoms other than carbon and hydrogen
-Metals and their salts (magnesium sulfate, ferric nitrate, sodium phosphate), gases (oxygen, carbon dioxide) and water
chemical analysis breakdown of cell components
70% water
97% of dry cell weight is organic compounds (proteins most prevalent)
96% of cell is 6 elements CHOPSN
3% inorganic ions
irons
Fe2+
-comes from rocks and soil
-essential element for the structure of respiratory proteins (cytochromes)
Cytochromes
An iron-containing protein that is a component of electron transport chains in the mitochondria and chloroplasts of eukaryotic cells and the plasma membranes of prokaryotic cells
Siderophores
Take iron from host iron-binding proteins
Microorganisms require iron
true
ferric iron is very ___________ so uptake is difficult
insoluble
microorganism
Any organism of microscopic or submicroscopic size.
microorganisms secrete __________ to aid uptake of ferric iron, which transports iron ion to cell
siderophores
siderophores create a complex with _________ _____
ferric iron
What is the purpose of siderophore-ferric iron complex?
So the complex can be transported into the cell...there is no other way to better get iron into cell (iron uptake)
Classification of nutritional types are determined by?
(The fuel source) carbon source fuel vs energy source fuel
Carbon source nutritional types microorganisms
-Heterotroph (get carbon from other organisms)
-Autotroph (uses CO2 as source)
Energy source nutritional types microorganisms
-Chemotroph (gain energy from chemical compounds)
-Phototrophs (gain energy from -photosynthesis
Heterotophic chemoheterotrophs
1. saprobes
2. Parasites
Saprobes
-A type of chemoheterotroph
-Organisms that obtain food from decaying organic matter via aerobic respiration
-Metabolize the organic matter from dead organisms
-Fungi, bacteria, some decomposing protozoan
symbiotic microbes
-A type of chemoheterotroph
-Obtain organic matter from living organisms
-Parasites, commensals (many bacteria are), mutualistic microbes.
Photoheterotroph
-Obtain energy from sunlight or organic matter
-Purple and green photosynthetic bacteria
parasites
derive nutrients from host (pathogens, some are obligate parasites)
obligate parasites
unable to grow outside of a living host
Photoautotrophs
-Energy source is sunlight and CO2
-Photosynthetic organisms, such as plants, algae, and cyanobacteria
Chemoautotroph
-Obtain energy from simple inorganic chemicals
-only certain bacteria and archaea, such as methanogens and deep sea vent bacteria and all archea
Organic compounds (these are _____​_____ to get ATP from them)
​oxidized
Sun(____________​__ organic compounds to energize them)
​photooxidazes
Non living energy source environment 2 categories
photoautotroph
chemoautotroph
living energy source environment
chemoheterotroph
photoheterotroph
Chemoheterotrophs
-An organism that must consume organic molecules for both energy and carbon.
-Metabolic conversions of nutrients from other organisms for carbon and energy
-Protozoa, fungi, many bacteria, animals
-Saprobe
-Symbiotic microbes
How do bacteria get large food particles across their membrane since they can't use phagocytosis?
via exoenzymes
Exoenzymes
dissolve extracellular barriers and penetrate through or between cells
passive transport examples
-Does not require energy
-diffusion
-osmosis
-facilitated diffusion (solutes require carrier)
Passive Transport
does NOT require energy, substances exist in a gradient and move from areas of higher conc to lower conc
Diffusion osmosis
-exists in a state of random motion and is a property of atoms and molecules that exist in a state of random motion
-no energy needed
-form of passive transport
-qualities are: nonspecific Brownian movement and movement of small uncharged molecules across membranes high to low
facilitated diffusion
-Molecule binds to carrier protein in membrane and is carried across to the other side
-no energy needed
-passive
-carrier protein needed
-qualities: Molecules specific; transports both ways, Transports sugars, water, amino acids
active transport
Energy-requiring process that moves material across a cell membrane against a concentration difference high to low conc
- E required
-transporter required
-AGAINST the gradient
-pumps protons into space
-These protons are then a source of potential energy for other needed functions
active transport types
-carrier-mediated
-group translocation
-bulk transport
carrier mediated active transport
-Nature of transport: energy is needed, molecules don't need to exist in gradient, rate of transport is increased, may occur low to high or high to low against conc gradient
-carrier-mediated: atoms or molecules are pumped into or out of the cell by specialized receptors; driven by ATP or other high energy molecules
-qualities: Transports simple sugars, amino acids, inorganic ions (Na+, K+)
group translocation (active transport)
-Nature of transport: energy is needed, molecules don't need to exist in gradient, rate of transport is increased, may occur low to high or high to low against conc gradient
-Molecule is moved across membrane and simultaneously converted into a metabolically useful substance
-alters molecule
-Qualities: Alternate system for transporting nutrients (sugars, amino acids)
●Couple transport of nutrient while simultaneously activating it
○ Adding a phosphate energizes it (like how ATP is active butADP isn't really)
○ Glucose
●Specific molecule actively captured by protein carrier, thenaltered/activated
●Transport is coupled with synthesis to conserve energy
Bulk transport (active transport)
-Nature of transport: energy is needed, molecules don't need to exist in gradient, rate of transport is increased, may occur low to high or high to low against conc gradient
-Mass transport of large particles, cells, and liquids by engulfment and vesicle formation
-Qualities: endocytosis
ie: phagocytosis, pinocytosis (NOT IN BACTERIA)
Tonicity
the ability of a surrounding solution to cause a cell to gain or lose water
isotonic solution with cell wall
A solution in which the concentration of solutes is essentially equal to that of the cell which resides in the solution
hypotonic solution with cell wall
A solution in which the concentration of solutes is less than that of the cell that resides in the solution
hypertonic solution with cell wall
A solution in which the concentration of solutes is greater than that of the cell that resides in the solution
isotonic no cell wall
-Rates of diffusion are equal in both directions
-Diffusion will occur in default direction of net water movement
hypotonic no cell wall
Diffusion of water into cell causes swelling and cell may burst (osmolysis) if no mechanism exists to remove water
hypertonic no cell wall
Water diffusing out of the cell causes it to shrink and become distorted
(shrivels like a grape to raisin)
microbes can adapt
True
Environmental factors that influence microbes and affect the function of metabolic enzymes
-Temperature
-Oxygen requirements
-pH
-Osmotic pressure
-Barometric pressure
BOOPT
Niche
Totality of adaptations organisms make to their habitat.
cardinal temperatures
the range of temperatures for the growth of a given microbial species.
Minimun, maximum and optimum
minimum temperature
lowest temperature that permits a microbe's growth and metabolism
Temperature adaptation groups (3)
psychrophiles, mesophiles, thermophiles
Psychrophiles
optimum temperature below 15C; capable of growth at 0C
very cold
Grow best in the fridge (unlikemost)
Grow slowly in cold but well >20Staph auerus, Listeriamonocytogenes (food borne illnesses)
Enzymes that neutralize ROSs
-superoxide dismutase
-catalase/peroxidase
Reactive Oxygen Species (ROS)
A group of extremely reactive peroxides and oxygen-containing radicals that may contribute to cellular damage
-singlet oxygen 1O2
-superoxide ion O2-
-peroxide H2O2
-Hydroxyl radicals OH-
As oxygen is used it is turned into several toxic products called _________ _______ _______
reactive oxygen species (ROS)
Thermophiles
optimum temp greater than 45C
very hot
hypertherm
-Survive above 60

-Some bacteria and archaea
-80-121
-Thermusaquaticus makesenzyme to copyDNA at high temps(Taq polymerase)
Mesophiles
optimum temperature 20-40C; most human pathogens
Found in animals, plants, soil, water (in temperate, sub trop, and trop)
What happens when a micro is not capable of dealing with toxic oxygen?
forced to live in oxygen free habitats
Aerobes adaptations to oxygen requirements
Aerobes utilize oxygen and can detoxify it
-Adaptions:
Obligate aerobe,
Facultative anaerobe,
Microaerophile
Obligate aerobe
cannot grow without oxygen
+SOD
+Catalase
-Growth occurs in tube only where high concentrations of oxygen diffused into medium.
Facultative anaerobes
utilizes oxygen but can also grow in its absence (both)
+SOD (super oxide dismutase)
+Catalase
-Growth is best where most oxygen is present, but occurs throughout the tube
Microaerophile
Only need a very small amount of oxygen
+SOD
+/-Catalase (low levels)
Anaerobe oxygen requirement adaptations
-Anaerobes do not use oxygen
-Adaptations:
Obligate anaerobe,
Aerotolerant anaerobes
Obligate anaerobe
lacks the enzymes to detoxify oxygen so cannot survive in an oxygen environment
-Growth occurs only where there is no oxygen (bottom of tube)
strict anaerobes
an organism that cannot survive in an atmosphere of oxygen in any amount
-SOD
-Catalase
Aerotolerant anaerobes
do not utilize oxygen but can survive and grow in its presence
+SOD
--Growth occurs evenly, oxygen has no effect
Microaerophiles
-Only aerobic growth
-Oxygen is required in low concentrations
-Growth only occurs where there is very little oxygen present
-Can produce lethal amounts of toxic forms of oxygen if exposed to regular atmospheric oxygen
Oxygen requirement determination
-cultures with reducing media that contain O2- removing chemical like thioglycollate can help determine the O2 requirements of a microbe
-the relative position of growth (growth levels) of bacteria that differ in different O2 requirements in such culture media provides some indication of their adaptation to O2 use
Explain how many microorganisms use enzymes to neutralize toxic products ofoxygen gas and are thus able to survive in aerobic environments. (in other words,how do cells deal with oxygen?)
-Dangerous byproducts of oxygen
-Singlet oxygen builds up = toxic, dangerous
-Superoxide (super reactive O​2​)
-Peroxide H2O2
-Hydroxyl OH
-Conversion of superoxide
-Superoxide dismutase/SOD works to produce h202 (toxic to cells) and oxygen
-This dissociates into peroxide anions
-Then, H2o2 is degraded by either ​catase​ or peroxidase to break it down into water and non-toxic oxygen
Effects of pH (3) categories or microorganism
-Neutrophiles
-Acidophiles
-Alkalinophiles
Neutrophiles
Majority of microorganisms that prefer to grow in pH levels between 6 and 8
Acidophiles
grow in extremely acidic pH
Alkalinophiles
grow optimally in extreme alkaline pH levels
Osmotic categories (2 main types)
-Most microbes exist under hypotonic or isotonic conditions
-Osmophiles

-Osmotolerant
Osmophiles
-Require a high conc of salt (halophiles)
-Adaptation:
-Obligate halophiles grow optimally in solutions of 25% NaCl but require at least 9% NaCl (salt lakes and ponds)
-halobacterium
-halococcus
Osmotolerant
-Do not require high concentration of solute
-Adaptation:
-Faculative halophiles are remarkably resistant to salt
-staphylococcus aureus
Pressure category Barophiles
Just Barophiles
Barophiles
can survive under extreme pressures and will rupture if exposed to normal atmospheric pressure
Microbial relationships are dynamic not always fixed
True
Microbial relationships often depend on location and environmental factors and relationships can be influenced by "others"
True
Ecological Associations Among Microorganisms
symbiosis
mutualism
-obligate
-nonobligate
Commensalism
parasitism
Mutualism
A relationship between two species in which both species benefit
Obligate mutualism
one species cannot survive without the other; require each other to survive
Nonobligate mutualism
can be separated or live apart; still benefit each other when together just don't need it
Commensalism
A relationship between two organisms in which one organism benefits and the other is unaffected
Parasitism
A relationship between two organisms of different species where one benefits and the other is harmed
-Rickettsia and chlamydia bacteria
Non-symbiotic ecological associations
when organisms are free-living in a shared habitat
-syntrophy
-amensalism
Syntrophy
Also called 'cross-feeding'; a specialised form of mutualism where microbes sharing a habitat feed off substances released by another organism
-Azotobacter
-Cellulomonas
Amensalism
One member of an association produces a substance that harms or kills another
(antagonism, competition)
-Antibiosis
Biofilm microbial relationship
Biofilms result when organisms attach to a substrate but some form of extracellular matrix that binds them together in complex organized layers (organism is the film)
-Dominate the structure of most natural environments on earth
-Communicate and cooperate in the formation and function of biofilms (quorum sensing)
-They can colonize things easily
-Quórum sensingc.Occurs in self monitor of self density, genetic activationd.When biofilms start to form, Planktonic microbes go to surface and rest
-They settle down which stimulates cells to secret a slimy polysacch matrix
-Inducer molecules bind to substrate released and accumulate as cell grows ***sufficient number of inducers needed
-Inducers monitor size of population
-Quórum- critical # of cells
-Inducers enter biofilms and stim gene expression
quorum sensing
The ability of bacteria to sense the presence of other bacteria via secreted chemical signals.
Sessile
Describes an organism that remains attached to a surface for its entire life and does not move
It is a sessile world for many microbes
True
Tissue
A group of similar cells that perform the same function.
Organ
A collection of tissues that carry out a specialized function of the body
Organ system
group of organs that work together to perform a specific function
Interrelationships between microbes and humans
Human body is a rich habitat for symbiotic bacteria, fungi, and a few protozoa - normal microbial flora
Commensal, parasitic, and synergistic relationships
-These relationships are not fixed
Holobiont
the human host and all of its resident microbiota
What does growth refer to in microbiology?
Growth refers to an increase in population and reproduction not in actual individual physical size.
Cell cycle steps in Eukaryotes
Interphase
G1
S
G2

MITOSIS
CYTOKINESIS
Bacterial growth
1. Growth (nutrients and energy)
2. Chromosome replication and partitioning
3. Cytokinesis
Bacteria growth stage
1. A parent cell at the beginning of the cell cycle. What cannot be seen is the synthesis and activity gearing up for cell division (requires nutrients)
Bacteria chromosome replication and partitioning stage
2. Chromosome replication and cell enlargement. The parent cell duplicates the chromosome and synthesizes new structures that enlarge the cell in preparation for the daughter cells.
3. Chromosome division and septation. Chromosomes affix to the cytoskeleton and are separated into the forming cells. The cell lays down a septum that begins to wall off new cells. Other components (ribosomes) are equally distributed to the developing cells.
Cytokinesis growth steps
4. Completion of cell compartments. The septum is synthesized completley and the cell membrane patches itself so there are 2 separate cell chambers.
5. End of cell division cycle. Daughter cells are now independent units. Some species will separate completely and some will remain attached, forming chains or pairs.
Rate of population growth is exponential
True
Equation for calculating population size over time
Nf=(Ni)2^n
-Nf is total number of cells in population
-Ni is starting number of cells
-n is generation time
-2^n = number of cells in that generation
Population growth curve bacteria
Typically display a predictable growth pattern over time
Bacterial Growth Curve stages
1. Lag Phase
2. Exponential growth phase
3. Stationary phase
4. Death phase
Lag phase
"flat" period of adjustment, enlargement, little growth
Exponential growth phase
A period of maximum growth when cells have adequate nutrients and a favorable environment
Stationary Phase
Rate of cell growth quals rate of cell death caused by depleted nutrients and a favorable environment. Organic acids and pollutants excreted
Death phase
as limiting factors intensify, cells die exponentially
Indirect method to analyze population growth
Turbidometry
-most simple method
-Degree of cloudiness and turbidity (how clear, how much light can pass through) of the nutrient culture media reflects the relative population size.
Direct method to analyze population growth
Enumeration of bacteria:
-viable colony count
-direct cell count (manually or automated)
--Manual-counting number of cells in a sample microscopically
--Automated-Coulter counter or flow cytometer
Types of microbial growth media
-Culture media
-Defined or synthetic
-complex
Culture media
-Needed to grow, transport , and store microorganisms in the lab
-Culture media is solid or liquid preparation
-Must contain all the nutrients required by the organism for growth
-Classification
--chemical constituents from which they are made
--physical nature
--function
Basis for classification of culture media (6)
*Defined
*Synthetic
-Complex
-Chemical composition
-Physical nature
-Function
Basis for culture media classification
[chemical composition]
Types:
-defined (synthetic)
-complex
Basis for culture media classification
[physical nature]
Types:
-liquid
-semisolid
-solid
Basis for culture media classification
[function]
Types:
-supportive (general purpose)
-enriched
-selective
-differential
Examples of Defined Media
Common complex media examples
at least one ingredient is not chemically defined
media components (peptones)
protein hydrolysates prepared by partial digestion of various protein sources
media components (extracts)
aqueous extracts, usually of beef or yeast
media components (agar)
sulfated (& therefore not easily digested by bacteria) polysaccharide used to solidify liquid media; most microorganisms cannot degrade it
Functional types of media
-Supportive or general purpose media
ie: TSA
---Supports the growth of many microorganisms
-Enriched media
ie: Blood agar
---General purpose media supplemented by blood or other special nutrients
-Transport media
---Keeps microbe alive but doesn't support growth
-Selective
-Differential
Selective media
-Favor the growth of some microorganisms and inhibit growth of others
ie: MacConkey agar which selects for gram-negative bacteria
Differential Media
-Distinguish between different groups of microorganisms based on their biological characteristics
ie: Blood agar that determines hemolytic vs nonhemolytic bacteria
ie: MacConkey agar that shows lactose fermenters vs nonfermenters
Microbial growth
need resources and energy the proper environmental conditions and proper mechanics and assessment
Bacterium
a microscopic prokaryote
Bacteria
single-celled or noncellular spherical or spiral or rod-shaped organisms lacking chlorophyll that reproduce by fission
Bacterium produces
2 bacteria
Defined vs complex media
Defined media are usually composed of pure biochemicals off the shelf; complex mediausually contain complex materials of biological origin such as blood or milk or yeast extract or beef extract, the exact chemical composition of which is obviously undetermined.
The Metabolism of Microbes
-Nutrients are sources of energy like carbohydrates, proteins, lipids
-Catabolism releases energy as ATP with NADH that anabolism can use
-End products with reduced energy from Catabolism CO2 and H2O
-Anabolism uses energy ATP NADH to build from simple building blocks of sugars and amino acids
-Anabolism products are carbohydrates, proteins, lipids that can be used as a source of energy or to synthesize cell structures
Microbial metabolic diversity is needed
True
Metabolism
All chemical and physical working of a cell
2 chemical reaction types in metabolism
catabolism and anabolism
Catabolism
degradative; breaks the bonds of larger molecules forming smaller molecules; releases energy
Anabolism
biosynthesis; process that forms larger macromolecules from smaller molecules; requires energy input
Energy is defined as...
the capacity to do work while effecting change within a system
Thermodynamics
The study of energy transformations that occur in a collection of matter.
Chemical work
synthesis of complex molecules
Transport work
take up of nutrients, elimination of wastes, and maintenance of ion balances
Mechanical work
cell motility and movement of structures within cells
First law of thermodynamics
-Energy cannot be created or destroyed
-Total energy in the universe remains constant
--However, energy may be redistributed either within a system or between the system and its surroundings
Second law of thermodynamics
-Entropy
--Amount of disorder or randomness in a system
-Physical and chemical processes proceed in such a way that the disorder or randomness increases to the maximum possible
Role of ATP in metabolism
exergonic breakdown of ATP is coupled with endergonic reactions to make them more favorable
Exergonic reaction
Products favored...
A spontaneous chemical reaction in which there is a net release of free energy.
Endergonic reaction
Reactants favored...
A non-spontaneous chemical reaction in which free energy is absorbed from the surroundings.
Endergonic reactions are coupled with exergonic reactions to make reaction more ________
favorable
Endergonic exergonic coupling example
Endergonic: ATP --> ADP+Pi
Exergonic: any favorable reaction usually favors CO2 and H2O combustion run
Start with glucose...
Catabolism options (5)
-Aerobic respiration
-Anaerobic respiration
-Fermentation
-Photography
-Chemolithotrophy
Energy "currency"
ADP + Pi
ATP
(above cycle)
enzymes do not create reactions
True
enzyme's active site is unique foreach substrate
True
cofactors are either coenzymes or metal ions
True
Active site of an enzyme
the region of an enzyme that attaches to a substrate
Structure and classification of enzymes
Some enzymes are composed solely of one or more polypeptides. Some enzymes are composed of one or more polypeptides and nonprotein components
Enzyme protein catalysts
-High specificity for the reaction catalyzed and the molecules acted on
-substance that increases the rate of reaction without being permanently altered
Enzyme substrates
are the reacting molecules
Enzyme products
substances formed by reaction
Some enzymes are composed solely of one or more polypeptides
True
Some enzymes are composed of one or more polypeptides and nonprotein components
True
Enzyme structure
-simple
-conjugated
-holoenzymes
---apoenzyme
---cofactors
Simple enzymes
consist of protein alone
Conjugated enzymes or holoenzymes
-contain protein and nonprotein molecules
--apoenzyme is the protein portion
--cofactors are nonprotein portion
-----Inorganic elements (metal ions) Fe, Cu, Mg
-----Organic molecules (coenzymes)
coenzymes
An organic molecule that is a necessary participant in some enzymatic reactions; helps catalysis by donating or accepting electrons or functional groups; e.g., a vitamin, ATP, NAD+.
How do enzymes work?
-Activation energy (energy required to form the transition state complex) is lowered by enzyme and the result is a much faster reaction
How enzymes lower activation energy
-By increasing concentrations of substrates at active site of enzyme
-By orienting substrates properly with respect to each other in order to form the TS complex
-Induced fit model for enzyme-substrate interaction
enzyme induced fit model
Binding of a substrate within the active site causes conformational changes within the enzyme such that the number of interactions is increased
How are enzymes classified?
Based on the types of reactions they catalyze
Nature uses many levels or regulation to control metabolic pathways what is an example?
Post-translational modifications regulation: small molecules can bind (noncovalently) to a protein and affect its function. an example is feedback inhibition, in which the product of a metabolic pathway inhibits the first enzyme in the pathway.

The structure and function of a protein can be altered by covalent changes to the protein. These can be reversible (phosphorylation and dephosphorylation) or irreversible like (removal of amino acid residue)
Direct controls on the actions of enzymes
-Competitive inhibition
-Allosteric inhibition
-Noncompetitive inhibition
Competitive inhibition
substance that resembles the normal substrate competes with the substrate for the active site
Allosteric inhibition
form of noncompetitive inhibition in special types of enzymes with 2 binding sites (active and regulatory/allosteric site)
- Allosteric regulator binds to enzyme; inactivating
***Enzymes are regulated by negative feedback from the binding of molecules other than the substrate in the regulatory site
Noncompetitive inhibition (interruptor)
Inhibitor binds to the entire enzyme-substrate complex and prevents the enzyme from completing its action on the substrate
Many metabolic processes involve oxidation-reduction reactions (electron transfers)
True
Electron carriers are often used to transfer electrons from an electron donor to an electron acceptor
True
Transfer of electrons from a donor to an acceptor results in... (2)
-Can result in an energy release, which can be conserved and used to form ATP
-The more electrons a molecule has the more energy rich it is
Oxidation
is the loss of electrons
Reduction
is gain of electrons
Electrons shared in covalent bonds are rearranged
True
Electrons lose potential energy as they move closer to more electronegative atoms (oxygen)
True
Gibbs free energy
the energy of a system that is available to do work at a constant temperature and pressure
The greater the difference between the donors electronegativity and the acceptors electronegativity the more ???? is the ΔG
the more negative ΔG (Gibbs free energy)
-Reactants have more energy than the products so products becomes more stable (favorable)
-Free energy is released and reaction is therefore spontaneous
Donor and acceptor graphic
The energy in glucose is found in the the electrons in its bonds
True
What catabolic reactions start with glucose?
-Aerobic respiration
-Anaerobic respiration
-Fermentation
In metabolic reactions how do electrons move?
-Repeatedly accept and release electrons and hydrogen to facilitate the transfer of redox energy
-Most electron carriers are coenzymes
---NAD, FAD, Coenzyme A, and compounds of the respiratory chain.
"electron shuttle bus"
3 mechanisms of ATP synthesis
-Substrate-level phosphorylation
-Oxidative phosphorylation
-Photophosphorylation
Substrate-level phosphorylation
Transfer of phosphate group from a phosphorylated compound (substrate) directly to ADP
Oxidative phosphorylation
Series of redox reactions occurring during respiratory pathway
Photophosphorylation
in photosynthetic organisms, utilizing the energy of sunlight
Pathways of bioenergetics
Bioenergetics: study of the mechanisms of cellular energy release
-Includes catabolic and anabolic reactions
-Primary catabolism of fuels (glucose) proceeds through a series of three coupled pathways
1. Glycolysis
2. Kreb's cycle
3. Respiratory chain
Chemoorganotrophic fueling processes
(also called chemoheterotrophs)
-aerobic respiration
-anaerobic respiration
-fermentation
Metabolic strategies: Nutrient processing is varied, yet in many cases is based on three catabolic pathways that convert glucose to CO2 and yields energy (3)
-aerobic respiration
-anaerobic respiration
-fermentation
Aerobic respiration involves
-glycolysis
-Kreb cycle
-respiratory chain
-Oxygen is final electron acceptor (O2)
-38 ATP produced
Anaerobic respiration involves
-glycolysis
-Kreb cycle
-respiratory chain
-molecular oxygen is not the final electron acceptor
(SO42-, NO3-, CO32-)
-Number of ATP produced varies with microbe
Fermentation involves
-glycolysis
-organic compounds are the final electron acceptors (pyruvate, acetaldehyde)
-2 ATP produced
Glycolysis location
cytoplasm in both eukaryotic and prokaryotic cells
glycolysis products
2 pyruvate, 2 ATP, 2 NADH
Glycolysis Step 1
Two molecules of ATP and 2 phosphates are used to breakdown glucose into 2 molecules of PGAL
glycolysis step 2
- 2 NADH are produced.
- NADH, a coenzyme, forms when NAD+ combines with 2 energy rich electrons and H+(obtained from an intermediate molecule during the breakdown of glucose).
- NADH is an energy rich molecule
glycolysis step 3
Each phosphate group added in Steps 1 and 2 is removed and added to ADP, forming a total of 4 ATP molecules and 2 molecules of pyruvic acid
glycolysis step 4
A six-carbon intermedicate splits into two three-carbon intermediates
glycolysis step 5
A redox reaction generates NADH
The last step of glycolysis
he conversion of PEP to pyruvate
What happens to pyruvate after glycolysis?
-Can synthesize amino acids, sugars, fat metabolites (anabolic)
-Can lose a carbon and become acetyl cow to enter into Kreb's cycle (respiration)
-Can break down into acids, gas and acetaldehyde... acetaldehyde is used for fermentation and becomes Alcohol, Acetone, and 2-3-butanediol
Amphibolic
a metabolic pathway which has the characteristics of both anabolism and catabolism
Amphibolic pathways
Fermentation process
-Incomplete oxidation of glucose or other carbohydrates in the absence of oxygen
-Uses organic compounds as terminal electron acceptors
-Yields a small amount of ATP
-Production of ethyl alcohol by yeasts acting on glucose
-Formation of acid, gas and other products by the action of various bacteria on pyruvic acid
Fermentation graphic
Alcoholic and acetic formation graphic
Products of Pyruvate fermentation
Krebs cycle graphic
Where is potential energy stored in Krebs cycle
in the chemical bonds of acetyl CoA (processed glucose) in a step-by-step process, trapping it in the form of high-energyintermediate molecules.
Electron transport and Oxidative Phosphorylation
-Final processing of electrons and hydrogen
-Major generator of ATP
-Chain of redox carriers that receive electrons from reduced carriers (NADH and FADH2)
-ETS shuttles electrons down the chain, energy is released and subsequently captured and used by ATP synthase complexes to produce ATP (oxidative phosphorylation)
Electron transport and ATP synthesis in bacterial cell envelope graphic (see channel membrane proteins picking up electrons)
Overview of catabolic pathways graphic
Donor acceptor graphic
Incomplete healing of a tattoo led to a case of vibriosis because the tattoo site was a ______ of _______ for the Vibrio vulnificus bacterium.
port of entry
______ is the acquisition of chemical substances by organisms for use as an energy source or as building blocks of cellular structures.
nutrition
An organism which acquires energy by metabolizing the nutrients from other organisms is called a(n) ____________.
heterotroph
A __________ is an organism that uses the sun's light to provide the chemical energy to produce sugar for cellular respiration.
phototroph
A man succumbed to vibriosis due to a combination of swimming in the ocean before a tattoo was completely healed and an underlying condition of liver disease. In this case the tattoo was a ______ for the Vibrio vulnificus bacterium causing the infection.
portal of entry
An autotrophic organism that utilizes light for energy and carbon dioxide primarily as a carbon source is specifically termed a
photoautotroph
Which organism relies upon organic compounds for its carbon and energy needs?
heterotroph
_______ involves the complete breakdown of glucose to yield carbon dioxide, water, and energy in the form of ATP.
aerobic respiration
Which of the following cell structures is specialized for transport of materials into and out of the cell?
cell membrane
The speed and continuous movement of atoms and molecules is largely controlled by ________.
temperature
The principal energy-yielding pathway that involves the breakdown of glucose in the presence of oxygen is called
aerobic or cellular respiration
Organisms with cell walls become _______ in a hypotonic solution because the cell wall prevents them from bursting.
turgid
True or false: All atoms and molecules are in a constant state of movement that increases with temperature increases.
True
Autotroph
​produce energy needed to live on their own in the form of INorganic CO​2
Heterotroph
can't produce its own energy, and thus needs to get it from organiccompounds
Pinocytosis
cellular drinking
Endocytosis
​includes both pinocytosis and phagocytosis; involves wrapping amembrane around substance and bringing it into the cell
Phagocytosis
cellular eating via a phagocytic cell
Plasmolysis
​when a cell is placed in a hypertonic environment, this happens
Adaptation
​adjustment to a new environment with the help of random genetic changesin response to new environmental conditions
Pathogens
​any disease causing organisms
Nutrient
any substances from environment used for metabolism and growth
Fastidious bacteria
require STRICT, narrow nutritional or environmental conditions forgrowth
Bioelements
​any chemical found in molecules/compounds that make up livingorganisms. Encompassed by the acronym CHNOPS + Ca, Cl, Fe, K, Mg, Na
Obligate anaerobe
strict anaerobe - can't survive in an environment with oxygen
strict anaerobes
an organism that cannot survive in an atmosphere of oxygen
Bioelements
​any chemical found in molecules/compounds that make up livingorganisms. Encompassed by the acronym CHNOPS + Ca, Cl, Fe, K, Mg, Na
Essential nutrient
​a.k.a. Growth factor. Organic compounds that must be consumed inthe diet for growth. (Vitamins, amino acids, etc.)
Organic compound
​molecules containing carbon and hydrogen
Micronutrient
trace elements. Needed in small amounts for enzyme function andprotein structure maintenance.
Opportunistic pathogen
takes over a host when host immunity is compromised. P. aeruginosa
P. aeruginosa
What are some environmental conditions that influence microbial adaptations?
a. Nutrients from air water and bedrock i.Constant decomposition and synthesis b.Atmosphere is composed of nitrogen, oxygen, co2c.Sunlight for energy d.Temperature
Adaptation
Adjustment to a new environment with the help of random genetic changes in response to new environmental conditions.
Nutrient
any substances from environment used for metabolism and growth
Essential nutrient
​a.k.a. Growth factor. Organic compounds that must be consumed inthe diet for growth. (Vitamins, amino acids, etc.)
micronutrient
trace elements. Needed in small amounts for enzyme function andprotein structure maintenance.
opportunistic pathogens
takes over a host when host immunity is compromised.
P. aeruginosa
What are some environmental conditions that influence microbial adaptations?
a. Nutrients from air water and bedrock
i. Constant decomposition and synthesis
b. Atmosphere is composed of nitrogen, oxygen, co2
c. Sunlight for energy
d. Temperature
Cells are 70% water and 30% other substances. Of this 30%, what is the mostabundant organic compound in cells? What other nutritional materials are foundin a cell?
a. PROTEINS!!! (#1) (building block = amino acids)
b.Carbs, sugars, Lipids
c.Minerals, other inorganic compounds (primarily used as cofactors)
i.CHOPSN
1.Nitrogen
How might nutrients be categorized based on carbon content?
-Organic vs inorganic
-Organic nutrients are molecules that contain a framework of carbon and hydrogen-Ex: methan (CH4), large polymers of carbs lipids proteins
-***essential to structure and function of ALL living things
-Inorganic: lack either carbon or hydrogen in that combo
-Mineral deposits, metals, salts, gases (oxygen, ​carbon dioxide)!!!
What are two other major categories of essential nutrients to life? What are somefunctions of these elements? ***table 7.1!
-Macronutrients
---Needed in large amounts
---Very important roles in structure and metabolism
---Sugars, aa's with CHO
-----CO2: made in resp, used in photosynth
-----H is in water, which is a very important part of life (most abundant In all cells, solvent for reactions)
-----H ions for energy transfer and pH

-Micronutrients/trace elements
--Needed in smaller amounts
--Zn, Ni, Mn
--Enzyme function, protein structure maintenance
---Zinc: enzyme cofactor, regulates euk genes

-Bioelements - ​CHONPS​, K, Ca, Mg, Cl, Zn, Fe
--NH3 needed to make amino acids and nucleic acids in all organisms
--K = protein synth, membrane transport
--Na - maintain osmotic pressure
--IRON
---In rock and soil, structure for respiratory proteins(cytochromes)
---Charged, not very soluble, so bacteria acquire them via siderophores
An Isotonic vs hypertonic vs hypotonic environments: What would happen if a cell was placed in a hypotonic environment? Is this bad or good?
-Hypotonic = solute particle concentration much lower than the cell
-Water moves from low to high solute ... you want to dilute it
-The cell would swell
-This is actually ideal for most bacteria bc they have a rigid cell wall, thus allowing it to be turgid/fully extended and full
-Ideal since membranes are a site for many processes so you need to have a membrane that is not floppy
What is a common example of an organism that lives in a hypotonicenvironment? How does it survive?
-Amoeba -- lacks cell wall
-Has a water/contractile vacuole to pump out excess water
-If time: What would happen if it lacked a cell wall? it would lyse/explode
How can this concept be used advantageously by the food industry topreserve food?
Hypertonic solutions have a growth limiting effect on microbes by removing moisture (astronautfood, for example... or camping foods. It is dehydrated and stays good til you add water)-Salted hams, fish, preservatives
Although bioelements are important, there are some living things that do not havean absolute need for them.
False
Why can certain organisms not survive above their maximum temperature?
-Their enzymes and nucleic acids denature/become permanently deactivated
-Function best at a small range of an optimum temp
-Cardinal range: range of temps of microbial growth consisting of min, max, and optimum
Everything can detoxify except anaerobes
True
Why is it difficult for bacteria to uptake iron? Is iron important for bacterial growth (what do they use it for?) ? How do bacteria overcome this difficulty of iron uptake?
-Iron is very important for bacterial growth and it is essential for the structure of repiratory proteins (cytochromes)
-Uptake of the iron is difficult because Ferric ion is insoluble so bacteria can't easily takeit in
-Have siderophores = iron magnets, which just snag the iron and transport it across thecell membranes
Explain the difference between a capnophile and a barophile
Capnophiles: grow best at higher CO2 concentrations, normally in atmosphere
-Important for isolation of some clinical pathogens like Neisseria (gon, mnin),Brucella abortus, Strep pneumoniae
-Incubated in a healthy CO2 range
-CO2 is an essential nutrient for autotrophs to synthesize organic compounds
---Barophiles: Deep sea microbes that exist in pressures up to 1000x atmospheric pressure
What are the four environmental factors that influence microbial growth?
Temp, oxygen, pH, osmotic pressure...Misc: barometric pressure
The patient's culture results positive for Staphylococcus. The RN understands that the culture most likely required growth on a complex medium, consisting of
at least one ingredient that is not chemically defined.
A 65-year-old homeless male presents to an urgent care clinic with a deep laceration on his left arm. He states that he cut his arm on an old piece of scrap metal two days prior. His wound is red, tender, hot to the touch, and has yellow drainage. The RN collects a sample of the drainage and sends it to the laboratory for microbial analysis, per provider orders.Microscopic analysis revealed the presence of grapelike clusters of gram-positive cocci. The RN educates the patient that the species identification of the organism will require biochemical testing, which aids in microbial identification by providing information on cellular metabolism. Which of the following statements by the patient demonstrates understanding of the nurse's teaching?
Biochemical tests can determine the organism's nutrient requirements.
All of these statements are correct.
Biochemical tests can provide information about the microbe's mechanism for deriving energy.
Biochemical tests can provide information about products given off during growth.
Biochemical tests can determine the presence of enzymes in the sample.
An 85-year-old female in a long-term care facility is prescribed verapamil for blood pressure management twice daily. The medication is classified as a calcium channel blocker.The RN is familiar with the action of calcium channel blockers. By inhibiting the passage of calcium through ion channels, the drug targets which of the following processes?
Group of answer choices
passive transport
An 85-year-old female in a long-term care facility is prescribed verapamil for blood pressure management twice daily. The medication is classified as a calcium channel blocker.Which of the following is a characteristic of active transport?
Involves the use of carrier proteins
The hospital infectious disease team is involved with the study of a healthcare-associated infection that has spread to 10% of inpatients. The infected patients are exhibiting symptoms of severe abdominal cramping, diarrhea, nausea, and vomiting. The RN on the infectious disease team provides education to staff regarding the pattern of bacterial growth and methods of infection control.The period of growth between inoculation and when the cells adjust to their environment and begin growth at their maximum rate is called the ________.
lag phase
The hospital infectious disease team is involved with the study of a healthcare-associated infection that has spread to 10% of inpatients. The infected patients are exhibiting symptoms of severe abdominal cramping, diarrhea, nausea, and vomiting. The RN on the infectious disease team provides education to staff regarding the pattern of bacterial growth and methods of infection control.Which of the following is a characteristic of the death phase of bacterial growth?
The cells are not reproducing.
The hospital infectious disease team is involved with the study of a healthcare-associated infection that has spread to 10% of inpatients. The infected patients are exhibiting symptoms of severe abdominal cramping, diarrhea, nausea, and vomiting. The RN on the infectious disease team provides education to staff regarding the pattern of bacterial growth and methods of infection control.The most rapid increase in bacterial growth occurs during which of the following stages?
Exponential growth phase
The hospital infectious disease team is involved with the study of a healthcare-associated infection that has spread to 10% of inpatients. The infected patients are exhibiting symptoms of severe abdominal cramping, diarrhea, nausea, and vomiting. The RN on the infectious disease team provides education to staff regarding the pattern of bacterial growth and methods of infection control.
The RN educates the staff about the importance of timely symptom recognition and treatment of the infection. Which of the following statements by a hospital provider demonstrates a proper understanding of antimicrobial agents?
It is most effective to treat patients with antimicrobials in the lag phase of bacterial growth.
It is most effective to treat patients with antimicrobials during the stationary growth phase.
It is most effective to treat patients with antimicrobials in the exponential growth phase.
It is most effective to treat patients with antimicrobials during the death phase of bacterial growth.
A patient with anorexia nervosa is admitted to the hospital for medical treatment. The patient presents with severe malnutrition and evidence of organ dysfunction. Labs are drawn and continuous intravenous (IV) fluids are initiated.The RN educates the patient and her family about cellular metabolism. Which of the following processes is common to fermentation, anaerobic respiration, and aerobic respiration?
Glycolysis
A patient with anorexia nervosa is admitted to the hospital for medical treatment. The patient presents with severe malnutrition and evidence of organ dysfunction. Labs are drawn and continuous intravenous (IV) fluids are initiated.The RN instructs the patient that although bacterial cells can also undergo aerobic respiration, they differ from eukaryotic cells in that ________.
the Krebs cycle takes place in the mitochondrion in these cells
the electron transport chain is present in the plasma membrane of these cells
glycolysis takes place in the mitochondrion in these cells
they make less ATP in this process than eukaryotic cells
A newborn infant screening yields a positive result for biotinidase deficiency. The RN prepares education for the patient's parents regarding the role of enzymes in metabolism and this enzyme deficiency disorder.Which of the following statements, by the patient's mother, best represents an understanding of metabolism?
Metabolism involves all chemical reactions and physical workings of the cell.
Metabolism involves the consumption of energy for workings of the cell.
Metabolism involves the production of energy for workings of the cell.
Metabolism involves the production of enzymes.
A newborn infant screening yields a positive result for biotinidase deficiency. The RN prepares education for the patient's parents regarding the role of enzymes in metabolism and this enzyme deficiency disorder.All of the following are true of enzymes except ________.
enzymes create a chemical reaction
A 67-year-old patient with severe sepsis undergoes a full infectious workup upon admittance to the intensive care unit. Cultures of urine, blood, sputum, and cerebral spinal fluid are obtained. The cultures do not yield a specific organism, so further analysis of the sample is done to determine the characteristics of the microorganism. The organism's metabolic processes are analyzed in the lab.The organism is found to grow throughout the entire tube of broth media. Which of the following terms best describes the oxygen requirement of this organism?
Facultative anaerobe
A 67-year-old patient with severe sepsis undergoes a full infectious workup upon admittance to the intensive care unit. Cultures of urine, blood, sputum, and cerebral spinal fluid are obtained. The cultures do not yield a specific organism, so further analysis of the sample is done to determine the characteristics of the microorganism. The organism's metabolic processes are analyzed in the lab.The organism sample is further tested and found to grow in the absence of oxygen. Which of three main pathways of catabolism may this organism utilize to produce energy under these circumstances?
Fermentation and anaerobic respiration
A 67-year-old patient with severe sepsis undergoes a full infectious workup upon admittance to the intensive care unit. Cultures of urine, blood, sputum, and cerebral spinal fluid are obtained. The cultures do not yield a specific organism, so further analysis of the sample is done to determine the characteristics of the microorganism. The organism's metabolic processes are analyzed in the lab.Biochemical testing reveals that the organism further reduces nitrite to produce nitrous oxide. Based on this byproduct, which of the following is the most likely catabolic pathway utilized by this organism?
Group of answer choices
Aerobic respiration
Fermentation
Anaerobic respiration
Aerobic respiration, anaerobic respiration, and fermentation can all lead to the production of nitrous oxide
A 67-year-old patient with severe sepsis undergoes a full infectious workup upon admittance to the intensive care unit. Cultures of urine, blood, sputum, and cerebral spinal fluid are obtained. The cultures do not yield a specific organism, so further analysis of the sample is done to determine the characteristics of the microorganism. The organism's metabolic processes are analyzed in the lab.Which of the following statements properly characterizes the ATP yield from anaerobic respiration?
All of the choices are correct.
Anaerobic respiration produces 2-36 ATPs per glucose molecule.
Anaerobic respiration produces less ATP per glucose molecule than aerobic respiration at maximum net yield.
Anaerobic respiration at maximum net yield produces more ATP per glucose molecule than fermentation.
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