Chapter 5&6 lecture flashcards
Cells must accomplish 2 fundamental tasks to grow
- Synthesize new components = ANABOLISM
- Biosynthesis - Harvest energy = CATABOLISM
The sum total of chemical reactions of biosynthesis and energy-harvesting is termed?
Metabolism
Metabolism has 2 components
1) Catabolism
– Degradative reactions
– Produce energy from breaking down molecules
2) Anabolism
– Synthesis of cell components
– Require energy input
* Anabolic reactions utilize the energy produced from catabolic reactions
Metabolic pathways occur in sequence of chemical reactions
- Starting compound is converted to intermediate molecules and end products.
- Intermediates and end products can be used as precursor metabolites
- Metabolic pathways employ critical components to complete processes:
Enzymes
ATP
Chemical energy source
Electron carriers
Precursor metabolites
What is the role of enzymes?
– Enzymes facilitate each step of metabolic pathway
– They are generally proteins and act as catalysts
* Favors (does not accelerate) conversion of substrate to product
– Catalyze reactions by lowering activation energy
* Energy required to initiate a chemical reaction
Enzyme inhibitors
– Competitive inhibitors bind active site
– Allosteric inhibitors bind elsewhere causing shape of enzyme to change
Role of ATP
– Adenosine triphosphate (ATP) * Energy currency of cell – Negatively charged phosphate groups attached to adenosine molecule * Negative charges of phosphate repel each other & create unstable bond that is easily broken releasing energy – ATP created by 3 mechanisms: Substrate phosphorylation Oxidative phosphorylation Photophosphorylation
Substrate phosphorylation uses?
Chemical energy to add phosphate ion to molecule of ADP
Oxidative phosphorylation uses?
Energy from proton motive force to add phosphate ion to ADP
Photophosphorylation ultilizes?
Radiant energy from sun to convert ADP to ATP
Role of chemical energy source
- Energy source: Compound broken down to release energy, variety of compounds available, glucose most common organic molecule
Harvesting energy requires series of couples reactions
Oxidation-reduction reactions
Oxidation-reduction reactions
– Electrons transferred from one substance to another
* Compounds that LOSE electrons are oxidized (termed electron donor)
* Compounds that GAIN electrons are reduced (termed electron carrier)
– In reactions, electrons are removed
* Protons often follow, generally in the form of H+ ion
– H+ ion has one proton and no electron
Three different types of electron carriers
1) Nicotinamide adenine dinucleotide (NAD+)
2) Flavin adenine dinucleotide (FAD)
3) Nicotinamide adenine dinucleotide phosphate (NADP+)
Reduced forms of electron carriers represents?
Reducing power. - due to usable energy in bonds Reduced forms are: – NADH – FADH2 – NADPH
Precursor metabolites are?
– Intermediate products produced in catabolic pathways
– Used in anabolic pathways
* Serve as raw materials for construction of macromolecules
The key central metabolic pathways are?
– Glycolysis – Tricarboxylic acid cycle (TCA) – Electron Transport Chain – Fermentation – Pentose phosphate pathway
Central (metabolic) pathways are amphibolic and provide?
– Energy (ATP)
– Reducing power
– Precursor metabolites
Electrons move from one carrier to another, eventually to a?
Terminal e- acceptor
This chain (electron transport chain) allows protons to be pumped across the cell membrane of prokaryotes, a?
PROTON GRADIENT
Proton gradient provides energy to?
Phosphorylate ADP -> ATP
Respiration generates a?
Proton gradient
– Produces ATP by oxidative phosphorylation
– Used to power flagella and some active transport
Aerobic respiration
– Final electron acceptor is O2 (yields H2O)
– Uses Krebs (TCA) cycle
– More ATP generated = most effective
Anaerobic respiration
Anaerobic respiration
– Final electron acceptor is not Oxygen
– Uses modified Krebs (TCA) cycle, generating less reducing power
– Less ATP generated = less effective
Fermentation is?
1) For cells that cannot respire
2) Do not oxidize glucose completely
3) Produces less ATP than either form of respiration
4) Uses pyruvate, or other organic molecule as terminal electron acceptor
5) Process may produce acids, alcohols, and gases
The pentose phosphate pathway is?
1) Necessary for production of NADPH and certain precursor metabolites
2) NADPH is a coenzyme needed for synthesis of nucleotides and fats
3) Required for the production of nucleotides, glucose (via photosynthesis), and some amino acids
Photosynthetic metabolism in a nutshell
1) Generate chemical energy (ATP) from absorbing light
– Utilizes an electron transport chain
– Yields O2
2) Calvin Cycle (most common pathway of carbon fixation)
– “Fixes” atmospheric CO2 to generate organic compounds
– Use ATP to provide energy to cycle
– Yields sugar (fructose)
Prokaryotes divided based on oxygen requirements
1) Obligate aerobes
2) Obligate anaerobes
3) Facultative anaerobes
4) Microaerophiles
5) Aerotolerant anaerobes
Obligate aerobes (2 main points)
– Absolute requirement for oxygen
– Need oxygen to produce energy
Obligate anaerobes (2 main points)
– No multiplication in presence of oxygen
– May cause death
Facultative anaerobes (2 main points)
– Grow better with oxygen
– Use fermentation in absence of oxygen
Microaerophiles (2 main points)
– Require oxygen in lower concentrations
– Higher concentration inhibitory
Aerotolerant anaerobes (2 main points)
– Indifferent to oxygen, grow with or without
– Do not use oxygen to produce energy
Optimum temperature -5°C to 15°C
– Found in Arctic and Antarctic regions
Psychrophile
Temperatures in 20°C to 30°C range
* Important in food spoilage
Psychrotroph
Temperatures in 25°C to 45°C range
- More common
- Disease causing
Mesophile
Temperatures in 45°C to 70°C range
* Common in hot springs
Thermophiles
Temperatures in 70°C to 110°C range
- Usually members of Archaea
- Found in hydrothermal vents
Hyperthermophiles
Do not cause disease in humans because they cannot survive at body temps; some do cause food spoilage in refrigerators
Psychrophiles
Because normal body temp. is around 37 Degrees C, human pathogens are?
Mesophiles
Mesophiles that can survive brief periods at higher temps.
Thermoduric organisms.
Thermophiles & hyperthermophiles stabilize their proteins with extra?
Hydrogen & covalent bonds between amino acids
Heat-loving organisms do not cause disease because?
They “freeze” at body temps.
Organisms are sensitive to changes in acidity because hydrogen ions and hydroxyl ions interfere with hydrogen bonding w/in proteins and nucleic acids; as a result organisms have ranges of?
Acidity that they prefer & can tolerate
A pH below 7.0 is _______; the lower the pH value, the more ______ a substance is
Acidic
Alkaline pH values are?
Higher (basic) than 7.0
Most bacteria & protozoa, including most pathogens, grow best in what type of pH?
A narrow range around a neutral pH between 6.5 and 7.5. Such microbes are thus called neutrophiles
Some bacteria & many fungi are acidophiles which are?
Organisms that grow best in acidic habitats
Obligate acidophiles require an acidic environment & die if the pH approaches
7.0
The low pH of some cheeses act as what?
Preservative by preventing any further microbial growth. Other acidic foods, such as sauerkraut and dill pickles are also kept from spoiling because most organisms cannot tolerate their low pH
Multiply between pH of 5 to 8
– Maintain optimum near neutral
Neutrophiles
Thrive at pH below 5.5
– Maintains neutral internal pH, pumping out protons (H+)
Acidophiles
Grow at pH above 8.5
– Maintain neutral internal pH through sodium ion exchange
– Exchange sodium ion for external protons
Alkalophiles
Pumping of hydrogen ions in the electron transport chain generates what?
The gradient used by the ATP synthase complex to synthesis ATP
In addition to the protein complexes in the electron transport chain are?
Two mobile carries:
1) Ubiquinone
2) Cytochrome c
At the start of the electron chain ___ electrons are passed from?
2 electrons are passed from NADH into the NADH dehydrogenase protein complex. Coupled with this transfer is the pumping of one hydrogen ion for each electron
After the beginning of the electron transport chain where NADH passes 2 electrons and the pumping of one hydrogen ion for each electron what happens?
The two electrons are transferred to ubiquinone which moves the electrons to the next protein complex (cytochrome b-c1). Each electron is then passed from the complex (cytochrome b-c1) to the mobile cytochrome c which accepts one electron at a time. One hydrogen ion is pumped through the complex as each electron is transferred
Osmotolerant bacteria tolerate what?
high salt environments
Bacteria that require high salt for cell growth termed?
halophiles
All microorganisms require water for? not available in all environments
Water
In high salt environments bacteria increase?
internal solute concentration. Synthesize small organic molecules
Growth of prokaryotes depends on nutritional factors as well as physical environment.
Main factors to be considered are:
–Required elements
– Growth factors
– Energy sources
– Nutritional diversity
Required elements. Major elements
Carbon, oxygen, hydrogen, nitrogen, sulfur, phosphorus, potassium, magnesium, calcium and iron.
– Essential components for macromolecules
Organisms classified based on carbon usage
1) Heterotrophs– Use organic carbon as nutrient source
2) Autotrophs– Use inorganic carbon (CO2) as carbon source
Trace elements
Cobalt, zinc, copper, molybdenum and manganese.
– Required in minute amounts
Culture media can be liquid or solid
1) Liquid is broth media used for growing large numbers of bacteria
2) Solid media is broth media with addition of agar
- Agar marine algae extract
- Liquefies at temperatures above 95°C
- Solidifies at 45°C
- Remains solid at room temperature and body temperature
Bacteria grow in colonies on?
Solid media surface.
- All cells in colony descend from single cell
- Approximately 1 million cells produce 1 visible colony
The Growth Curve
– Characterized by 4 distinct phases:
1) Lag
2) Log (exponential)
3) Stationary
4) Death
Growth can be calculated
Nt=N0x2n
- (Nt ) number of cells in population
- (N0 ) original number of cells in the population
- (n) number of divisions
Some bacteria cannot synthesize some cell constituents
These must be added to growth environment. Referred to as growth factors
Organisms can display wide variety of factor requirements
Some need very few while others require many. These termed fastidious
Complex media
– Contains a variety of ingredients – There is no exact chemical formula for ingredients - Can be highly variable * Examples include: 1) Nutrient broth 2) Blood agar 3) Chocolate agar
Chemically defined media
– Composed of precise amounts of pure chemicals
– Generally not practical for routine laboratory use
- Invaluable in research
- Each batch is chemically identical
- Does not introduce experimental variable
Selective media
Inhibit the growth of unwanted organisms. Allow only sought after organisms to grow
Thayer-Martin agar– For isolation of N. gonorrhoeae is an example of?
Selective media
MacConkey agar–For isolation of Gram- negative bacteria is an example of?
Selective media
Contains substance that bacteria change in recognizable way
Differential media
Blood agar– Certain bacteria produce hemolysin to break down RBC. Hemolysis. This is an example of?
Differential media
MacConkey agar– Contains pH indicator to identify bacteria that produce acid. This is an example of?
Differential media
Culturing anaerobes
1) Some die in the presence of oxygen even if exposed for a short time
2) Incubated in anaerobe jar
- Chemical reaction converts atmospheric oxygen to water
- Organisms must be able to tolerate oxygen for brief period
3) Reducing agents in media achieve anaerobic environment
- Agents react with oxygen to eliminate it
- Sodium thioglycolate
4) Anaerobic chamber also used for cultivation
Streak-plate method
– Simplest and most commonly used in bacterial isolation
– Object is to reduce number of cells being spread
- Solid surface dilution
- Each successive spread decreases number of cells per streak
Measuring turbidity with a?
spectrophotometer.
– Measures light transmitted through sample
– Measure is inversely proportional to cell concentration
– Must be used in conjunction with other tests once to determine cell numbers
Reduction reactions are those in which electrons are added. The molecule that donates an electron is oxidized. If the electron is part of a hydrogen atom, an oxidation reaction is also called?
Dehydrogenation.
Apoenzymes are the portions of enzymes that may require one or more?
Cofactors such as inorganic ions or organic cofactors (also called coenzymes)
The combination of both apoenzyme and its cofactors is a?
Holoenzyme
Feedback inhibition (negative feedback) occurs when?
The final product of a series of reactions is an allosteric inhibitor of some previous step in the series. Thus, accumulation of the end-product “feeds-back” into the series a signal that stops the process
The pentose phosphate and Entner-Doudoroff pathways are alternative means for the catabolism of glucose that yield fewer ATP molecules than does glycolysis. However, they produce?
Precursor metabolites not produced in glycolysis
Two carbons from pyruvic acid join coenzyme A to form acetylcoenzyme A (acetyl-CoA), which then enters the Krebs cycle, a series of 8 enzymatic steps that transfer electrons from?
Acetyl-CoA to coenzymes NAD+ & FAD
Aerobes use oxygen atoms as final electron acceptors in their electron transport chains in a process known as aerobic respiration, whereas anaerobes use?
Other inorganic molecules (such as N03-, SO42-, and CO32-), or rarely an externally acquired organic molecule as the final electron acceptor in anaerobic respiration
A proton gradient is an electrochemical gradient of?
Hydrogen ions across a membrane. It has potential energy known as a proton motive force
Oxidative phosphorylation and photophosphorylation use?
Chemiosmosis
Catabolic process in which enzymes split pairs of hydrogenated carbon atoms from a fatty acid & join them to coenzyme A to form acetyl-CoA
Beta-oxidation
Secreted by microorganisms to digest proteins outside the microbes cell walls. The resulting amino acids are moved into the cell & used in anabolism, or deaminated and catabolized for energy
Proteases
Metabolic reactions that are reversible- they can operate catabolically or anabolically
Amphibolic reactions
Some cells are able to synthesis glucose from amino acids, glycerol, & fatty acids via a process called
Gluconeogenesis
Reactions involving adding an amine group from ammonia to a metabolite to make an amino acid.
Amination
Occurs when an amine group is transferred from one amino acid to another
Transamination
