Microbio Exam 1 Flashcards
- Robert Koch
Robert Koch was a pioneering German physician and microbiologist known for his significant contributions to the field of microbiology, including the development of Koch’s Postulates.
Koch’s Postulates
4 critera used to determine whether a specific microorganism is the cause of a particular disease
Petri Dish
A Petri dish is a shallow, flat, cylindrical, lidded dish made of glass or transparent plastic. It is commonly used in laboratories for the cultivation and observation of microorganisms.
Plate Streaking (for Isolation)
Plate streaking is a microbiological technique used to isolate individual bacterial colonies from a mixed culture. It involves streaking a sample onto the surface of an agar plate to obtain separate colonies.
Media (Solid and Liquid)
Media, in microbiology, refer to substances or environments that provide nutrients and support the growth of microorganisms. They can be in either solid (agar) or liquid (broth) form.
Agar vs. Gelatin
Agar keeps form at 37C, while gelatin liquifies
This is the temp of incubation
Agar has more complex carbohydrates, which are more difficult for microbes to break down
Broth
Broth is a liquid medium used for the growth and cultivation of microorganisms. It provides a nutrient-rich environment to support microbial growth in suspension.
Differential Media (with Examples)
media contains specific indicators or substrates that allow different species of microorganisms to make distinct visible reactions. Examples include Blood Agar and MacConkey Agar.
Blood agar is a good differential medium because of the hemolytic activity on red blood cells.
Selective Media (Selection Methods)
Selective media are culture media designed to inhibit the growth of certain microorganisms while allowing the growth of others. Selection is achieved through the inclusion of specific chemicals or factors.
Complex Media
-composed of extracts, digests, or infusions from biological sources.
-support a wide range of microbes
Nutrient Media
Nutrient media are culture media that provide essential nutrients required for the growth of a variety of microorganisms. They are often used for general-purpose culturing.
Transport Media
Transport media are specialized media used to maintain the viability of clinical specimens during transport from the collection site to the laboratory. They help preserve the integrity of the sample.
Brightfield Microscopy
-specimens are viewed against a bright background.
-stained or unstained samples
Darkfield Microscopy
-oblique lighting to create contrast by illuminating specimens against a dark background.
-observes live, unstained specimens.
Phase Contrast Microscopy
enhances the contrast of transparent, unstained specimens by exploiting differences in the phase of light passing through the specimen.
Fluorescence Microscopy
Uses fluorescent dyes or proteins to label specific molecules or structures within a sample.
It enables the visualization of specific targets with high sensitivity.
Electron Microscopy
Advanced microscopy technique that uses a beam of electrons instead of visible light to achieve much higher resolution and magnification, allowing for detailed examination of subcellular structures.
Differential Stain
A differential stain is a staining technique that differentiates between different types of microorganisms or cellular structures based on their staining properties. The Gram stain and acid-fast stain are examples.
Gram Stain
The Gram stain is a widely used differential staining technique that classifies bacteria into Gram-positive and Gram-negative groups based on differences in cell wall composition.
Acid-Fast Stain
The acid-fast stain is a differential staining technique used to identify acid-fast bacteria, such as Mycobacterium species, which have a unique cell wall composition that resists decolorization during staining.
Cultivability of Microorganisms (Limitations of Microbial Culture)
Not all microorganisms can be easily cultured in the laboratory. Some require specific growth conditions or are uncultivable due to complex nutritional needs or symbiotic relationships.
Isolation of Organisms from Colonized Sites of the Body
Can be challenging due to
- Ethical concerns
- Complex Microbial Ecosystems
- Rely on culturing on artificial media, which can be biased. The body is far different than media is
Sterile Sites of the Body
Certain body sites, such as the bloodstream, cerebrospinal fluid, and internal organs, are normally sterile, meaning they should not contain microorganisms under healthy conditions.
Use of Media for Growth (Nutrient), Isolation (Selection), and Identification (Differential)
Nutrient media supports growth
Selective media inhibit unwanted microorganisms
Differential media help identify specific characteristics.
Limits of Resolution for Light Microscopy (Function of the Wavelength of Light)
The resolution of light microscopes is limited by the wavelength of visible light. Objects closer together than half the wavelength cannot be distinguished as separate.
Use of Acidic vs. Basic Stains (Use of Negative Staining)
Acidic stains (e.g., nigrosin) are repelled by bacterial cells, creating a dark background for visualization. This is the initial step in gram staining.
Basic stains (e.g., crystal violet) adhere to cells, providing contrast.
Brightfield vs. Darkfield Microscopy (Technique and Uses)
Brightfield microscopy uses transmitted light for standard observation, while darkfield microscopy employs oblique lighting to visualize transparent specimens like live bacteria.
Gram Stain vs. Acid-Fast Stain
Gram staining classifies bacteria into two broad groups based on cell wall characteristics (Gram-positive and Gram-negative),
Acid-fast staining specifically targets and identifies acid-fast bacteria with unique cell walls, such as Mycobacterium species.
Shape and Arrangement of Bacteria
Bacteria exhibit diverse shapes
cocci (spherical), bacilli (rod-shaped), and spirilla (spiral-shaped)
and arrangements (e.g., chains, clusters) that aid in their identification and classification.
Bacterial Culture Considerations (Temperature, Oxygen, Nutrients)
Bacterial culture success depends on factors like temperature (mesophilic, thermophilic), oxygen requirements (aerobic, anaerobic), and nutrient availability.
The Germ Theory of Disease and Its Relationship to Microscopy, Spontaneous Generation, Fermentation, and Koch’s Postulates
The Germ Theory of Disease revolutionized our understanding of infectious diseases. It built upon:
Advances in microscopy, which allowed scientists to observe microorganisms.
The refutation of spontaneous generation, the idea that life could arise from nonliving matter.
The understanding of fermentation as a microbial process.
Koch’s Postulates, which provided a framework for establishing the causal link between specific microorganisms and diseases. Koch’s work with anthrax and tuberculosis were pioneering examples.
Implications for Microbial Contamination in Various Body Locations
Different body locations have varying levels of microbial contamination:
Sterile sites (bloodstream, internal organs) should be free of microorganisms under healthy conditions.
Understanding contamination levels is crucial for:
Choosing appropriate lab techniques and culture media.
Isolating pathogens without interference from normal microbiota.
Identifying microbes in clinical samples accurately.
Peptidoglycan and Outer Membrane Structure (in Detail)
Peptidoglycan is a fundamental component of bacterial cell walls. Important details:
Gram-positive bacteria have a thick peptidoglycan layer.
Gram-negative bacteria have a thinner peptidoglycan layer and an outer membrane.
Outer membrane contains lipopolysaccharides (LPS), which are significant for immune responses and antibiotic resistance.
Bacterial Structures: Common to All Bacteria, Identification Aids, and Virulence Factors
Common structures include:
Cell wall, cytoplasmic membrane, cytoplasm, ribosomes, DNA.
Identification structures like flagella, pili, capsules, or spores.
Virulence factors, such as toxins, adhesins, and invasins, facilitate disease.
Parameters Defining a Bacterial Niche and Their Effects on Microbial Growth
Bacterial niche parameters include:
Temperature, pH, oxygen availability, nutrient sources, and competition.
Manipulating these conditions impacts:
Microbial growth, with temperature extremes causing reduced growth or death.
Adaptation to different environments and niches.
Comparison of Aerobic and Anaerobic Energy Metabolism
Differences between aerobic and anaerobic metabolism:
Aerobes use oxygen as the final electron acceptor in the electron transport chain, yielding more energy.
Anaerobes use alternative electron acceptors (e.g., nitrate, sulfate) or fermentation, yielding less energy.
Implications for energy production and adaptation to oxygen availability.
Comparison of Respiration vs. Fermentation
Respiration uses electron transport chains and can yield a higher amount of ATP, while fermentation relies on substrate-level phosphorylation (where ATP is synthesized directly) and produces less ATP.
The end products of these pathways differ. In respiration, the final electron acceptor is usually oxygen, leading to the production of water. In fermentation, the end products vary depending on the specific type of fermentation but do not involve the complete oxidation of glucose.
Respiration is more efficient in terms of energy generation per molecule of glucose, making it the preferred energy production pathway when oxygen is available. Fermentation is typically used by cells when oxygen is scarce or absent, despite its lower energy yield.
Cell Membrane
Also called plasma membrane
Phospholipid bilayer that surrounds the cell’s cytoplasm. Selevely permeable barrier, controlling entry/exit of ions, nutrients, waste.
Lipid Bilayer
The lipid bilayer consists of two layers of phospholipid molecules arranged in such a way that their hydrophobic tails are oriented inward while their hydrophilic heads face outward. This structure creates a dynamic and flexible membrane where various proteins, including transporters, receptors, and enzymes, are embedded. The lipid bilayer’s fluidity allows the membrane to adapt to changing conditions.
Semipermeable/Diffusion/Transport
A semipermeable membrane selectively allows certain substances to pass while restricting others based on factors such as size, charge, and solubility. Diffusion is the passive movement of molecules or ions from regions of higher concentration to lower concentration until equilibrium is reached. Transport, whether passive (facilitated diffusion) or active (active transport), involves the movement of specific molecules across the membrane through various mechanisms.
Cell Wall
The cell wall is a rigid and protective outer layer found in bacterial, plant, and fungal cells. In bacteria, it lies outside the cell membrane and contributes to cell shape, structural integrity, and protection against osmotic pressure. The composition and structure of the cell wall vary between bacterial groups, such as Gram-positive and Gram-negative bacteria.
Peptidoglycan
Peptidoglycan is a complex polymer found in the cell walls of most bacteria. It consists of repeating units of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) linked together, forming glycan chains. These chains are crosslinked by peptide bridges, creating a strong, flexible mesh-like structure surrounding the bacterial cell membrane.
NAG/NAM
N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) are sugar molecules that form the backbone of peptidoglycan in bacterial cell walls. They are connected in alternating fashion, creating the glycan chains of peptidoglycan.
Tetrapeptide Crosslinks
Tetrapeptide crosslinks are chemical bonds that connect the peptide chains of peptidoglycan strands in the bacterial cell wall. These crosslinks consist of four amino acids: L-alanine, D-alanine, D-glutamic acid, and meso-diaminopimelic acid (meso-DAP), or diaminopimelic acid (DAP).
Penicillin
Penicillin is a class of antibiotics that inhibits bacterial cell wall synthesis by targeting the enzymes involved in peptidoglycan crosslinking. It weakens the cell wall, making bacteria susceptible to osmotic lysis and cell death.
Lysozyme
Lysozyme is an enzyme found in various bodily secretions, such as tears and saliva, as well as in some immune cells. It targets and breaks down the peptidoglycan structure of bacterial cell walls.
Gram Negative / Gram Positive
Bacteria are classified into two major groups based on their response to the Gram stain. Gram-negative bacteria have a thinner peptidoglycan layer and an outer membrane, while Gram-positive bacteria have a thicker peptidoglycan layer but lack an outer membrane.
- Connection: Gram staining is a fundamental microbiological technique used to differentiate between these two groups based on cell wall characteristics.
Teichoic Acid
Teichoic acids are negatively charged polymers found in the cell walls of Gram-positive bacteria. They contribute to the overall negative charge of the cell surface and play roles in cell structure, adhesion, and ion transport.
Outer Membrane
The outer membrane is a distinctive feature of Gram-negative bacteria and forms an additional protective layer outside the thin peptidoglycan layer. It contains various proteins and lipopolysaccharides (LPS).
Lipopolysaccharide (LPS)
LPS is a major component of the outer membrane in Gram-negative bacteria. It consists of lipid A, a core oligosaccharide, and an O polysaccharide chain. Lipid A is responsible for the endotoxic properties of LPS.
Endotoxin / Septic Shock
Endotoxins are lipopolysaccharides (LPS) found in the outer membrane of Gram-negative bacteria. When released during bacterial cell death, they can trigger a severe immune response known as septic shock in the host.
O Polysaccharide
The O polysaccharide is the outermost portion of the lipopolysaccharide (LPS) molecule in Gram-negative bacteria. It exhibits high variability between different bacterial strains and contributes to antigenic diversity.
Porins
Porins are protein channels present in the outer membrane of Gram-negative bacteria. They allow the passive diffusion of small molecules, such as ions and nutrients, across the membrane.
Endospore
An endospore is a dormant and highly resistant structure formed by some bacterial species, enabling them to survive harsh conditions, including heat, desiccation, and radiation.
- Connection: Endospore formation is a survival strategy used by certain bacteria to withstand adverse environmental conditions, transforming into a dormant state until conditions become favorable again.
Glycocalyx
The glycocalyx is a protective sugar coat on the cell surface, which can take the form of a capsule or slime layer. It serves functions such as protection, adhesion, and immune evasion.
- Connection: Capsules, a type of glycocalyx, contribute to bacterial virulence by preventing phagocytosis, while slime layers play roles in biofilm formation and attachment.
Capsule
capsule is a well-defined and organized glycocalyx layer surrounding the bacterial cell. It provides protection against host defenses and enhances bacterial virulence.
Biofilm
A biofilm is a structured community of microorganisms embedded in a self-produced extracellular matrix. Biofilms can form on surfaces in various environments, including medical devices and natural habitats.
Biofilm formation often involves the production of a protective glycocalyx,
Autotroph
Autotrophs are organisms that can produce their own organic compounds, such as glucose, from inorganic sources like carbon dioxide and water.
They are the foundation of most ecosystems as they provide energy and organic matter for heterotrophs.
Examples of autotrophs include plants, algae, and some bacteria.
Heterotroph
- Heterotrophs are organisms that cannot synthesize their own organic compounds and rely on consuming other organisms or organic matter for energy and nutrients.
- They play a vital role in ecosystems as consumers and decomposers.
- Examples of heterotrophs include animals, fungi, and many bacteria.
Phototroph
1.Phototrophs are organisms that obtain energy from sunlight through the process of photosynthesis.
2. They convert solar energy into chemical energy stored in organic molecules.
3. Examples of phototrophs include plants, cyanobacteria, and some protists.
Chemotroph
- Chemotrophs are organisms that obtain energy by oxidizing chemical compounds, rather than relying on sunlight.
- They can use a variety of chemicals as energy sources, such as hydrogen sulfide, ammonia, or organic molecules.
- Examples of chemotrophs include certain bacteria and archaea.
Exoenzymes
Exoenzymes are enzymes secreted by microorganisms outside of their cells to break down complex organic
molecules into simpler forms.
They play a crucial role in the digestion of organic matter in the environment.
Exoenzymes are commonly produced by fungi and some bacteria.
Active Transport
Active transport is a cellular process that requires energy (usually ATP) to move molecules or ions against their concentration gradient.
It allows cells to accumulate essential substances even when they are scarce in the environment.
Examples of active transport include the sodium-potassium pump in animal cells
Group Translocation
Group translocation is a type of active transport where a molecule is chemically modified as it is transported into the cell.
This modification helps the cell concentrate the transported molecule inside.
Phosphotransferase systems (PTS) in bacteria are an example of group translocation.
Carrier-Mediated Transport
Carrier-mediated transport involves the use of specific carrier proteins to facilitate the movement of molecules across the cell membrane.
It is often used for the selective transport of ions and large polar molecules.
Glucose transporters (GLUT proteins) are examples of carrier-mediated transporters.
Osmosis
Osmosis is the passive movement of water molecules across a selectively permeable membrane from an area of lower solute concentration to an area of higher solute concentration.
It is crucial for maintaining the balance of water and solutes in cells.
Osmosis can lead to changes in cell volume if the surrounding solution has different osmotic pressures.
Aerobic
Aerobic organisms require oxygen for their metabolic processes, such as respiration.
They can generate more energy (ATP) compared to anaerobic organisms because oxygen is a highly efficient electron acceptor.
Examples of aerobic organisms include most animals and many bacteria.
Anaerobic
Anaerobic organisms can thrive in environments with little or no oxygen.
They often use alternative electron acceptors like nitrate or sulfate for respiration.
Anaerobic bacteria play a crucial role in processes such as fermentation and the breakdown of organic matter in oxygen-deprived conditions.
Halophiles
Halophiles are organisms that thrive in environments with high salt concentrations.
They have adapted mechanisms to prevent desiccation (dehydration) in salty conditions.
Examples of halophiles include some archaea and bacteria found in salt flats and salt mines.
Facultative
Facultative organisms can adapt to and grow in multiple environmental conditions.
They can switch between aerobic and anaerobic metabolism, or between different energy sources, depending on the environment.
E. coli is a well-known facultative bacterium
Bacteriocidal
Bacteriocidal agents are substances or treatments that kill bacteria.
They are used as disinfectants, antibiotics, or in food preservation to prevent bacterial growth.
Examples of bacteriocidal antibiotics include penicillin and streptomycin
Thermophile
Thermophiles are organisms adapted to high-temperature environments, often above 45°C.
They have specialized enzymes and cellular structures to withstand extreme heat.
Thermophiles are found in hot springs, deep-sea hydrothermal vents, and compost piles.
Psychrophile
Psychrophiles are organisms that thrive in cold environments, often at temperatures below 20°C.
They have enzymes that remain active in the cold and flexible cell membranes.
Psychrophiles can be found in polar regions, glaciers, and deep-sea environments.
Obligate
Obligate organisms have strict requirements for their survival and growth.
They cannot adapt to different environmental conditions.
An obligate aerobe, for example, must have oxygen to survive.
Superoxide Dismutase
Superoxide dismutase (SOD) is an enzyme that detoxifies superoxide radicals, which are harmful byproducts of oxygen metabolism.
It plays a crucial role in protecting cells from oxidative damage.
SOD is found in most aerobic organisms.
Catalase
Catalase is an enzyme that catalyzes the breakdown of hydrogen peroxide into water and oxygen.
It is important for preventing the buildup of toxic hydrogen peroxide in cells.
Catalase is found in many aerobic and facultative organisms.
Symbiotic
Symbiotic relationships involve the interaction between two different species living together in close proximity.
These relationships can be mutualistic, commensalistic, or parasitic.
Examples of symbiotic relationships include lichen (mutualism), gut bacteria (commensalism), and fleas on mammals (parasitism).
Commensalism
Commensalism is a type of symbiotic relationship where one organism benefits, and the other is neither helped nor harmed.
The organism benefiting is called the commensal, while the other is the host.
An example is barnacles attaching to the shells of turtles.
Mutualism
Mutualism is a type of symbiotic relationship where both organisms benefit from the association.
Each organism provides something the other needs, such as protection, nutrients, or services.
The relationship between bees and flowering plants is a classic example of mutualism.
Lag, Log, Stationary, Death (Phases of Growth)
Bacterial growth typically goes through four phases: lag phase (no growth), log (exponential) phase (rapid growth), stationary phase (growth equals death), and death phase (decline).
Each phase represents different growth rates and metabolic activities.
Monitoring these phases is important in microbiology and industrial processes.
Generation Time
Generation time is the time it takes for a population to double in size during the exponential growth phase.
It varies among different organisms and is influenced by environmental factors.
Generation time is used to assess the growth rate and reproductive capacity of microorganisms.
Environmental Niche
An environmental niche refers to the specific ecological role and habitat of a microorganism, including all the factors that influence its growth and behavior.
It encompasses physical factors like temperature and pH, as well as biotic factors like interactions with other organisms.
Understanding a microorganism’s niche is essential for predicting its behavior and survival in a particular environment.
Energy and Carbon Sources in a Niche
Energy sources are substances or processes that provide energy for microbial metabolism, such as sunlight or organic compounds.
Carbon sources are the compounds that microorganisms use to build their cellular structures and biomolecules.
Microorganisms can be classified based on their energy and carbon sources as phototrophs (light energy), chemotrophs (chemical energy), autotrophs (carbon from CO2), or heterotrophs (carbon from organic compounds).
Essential Nutrients and Their Role in Biomolecules
Essential nutrients are elements or molecules that microorganisms require for growth and metabolism but cannot synthesize themselves.
Common essential elements include carbon, nitrogen, phosphorus, sulfur, and various metals.
These nutrients are incorporated into biomolecules such as proteins, nucleic acids, and lipids, which are essential for cell function and structure.
Methods of Active Transport
Active transport mechanisms require energy (usually ATP) to move molecules against their concentration gradient.
Examples include the use of transport proteins, like pumps or carriers, to move ions and molecules into or out of the cell.
Active transport is essential for nutrient uptake and maintaining cellular homeostasis.
Osmotic Pressure and Role of Solutes (Salt) in Hyper/Hypo-tonic Environments
Osmotic pressure is the pressure exerted by the movement of water across a semipermeable membrane due to differences in solute concentration.
In a hypertonic environment (higher solute concentration outside the cell), water tends to leave the cell, leading to cell shrinkage.
In a hypotonic environment (lower solute concentration outside the cell), water tends to enter the cell, potentially causing cell swelling or bursting.
Bacteriostatic Properties of Salt and pH
High salt concentrations and low pH levels can act as bacteriostatic agents, inhibiting bacterial growth.
Salt can dehydrate bacterial cells by osmosis, disrupting their metabolism.
Low pH (acidic) conditions can denature proteins and damage cell membranes, leading to reduced bacterial growth.
Concept: Detoxification of Oxygen Free Radicals (Enzymes Involved
Detoxification of Oxygen Free Radicals (Enzymes Involved and Who Produces Them)
Superoxide dismutase (SOD) and catalase are enzymes involved in detoxifying oxygen free radicals.
SOD converts superoxide radicals into hydrogen peroxide, and catalase further breaks down hydrogen peroxide into water and oxygen.
These enzymes are produced by many aerobic and facultative organisms to protect against oxidative damage.
Other Organisms as Being Part of a Niche (and Helpful/Hurtful Interactions with Them)
Microorganisms often interact with other species in their niche, which can be helpful, harmful, or neutral.
Helpful interactions include mutualism (both benefit) and commensalism (one benefits, no harm to the other).
Harmful interactions include competition for resources and parasitism, where one organism benefits at the expense of another.
Stages of Bacterial Growth in a Closed System (and Implications for Antibiotic Sensitivity)
Bacterial growth in a closed system typically involves lag phase (slow growth), log phase (exponential growth), stationary phase (growth equals death), and death phase (decline).
Antibiotics are most effective during the log phase when bacteria are actively dividing and susceptible.
The stationary phase can be less sensitive to antibiotics due to reduced metabolic activity.
Individual Bacterial Quantification Methods and Their Limitations
Methods for quantifying bacterial populations include plate counts, turbidity measurement, and molecular techniques like qPCR.
Plate counts provide viable counts but take time and may underestimate some bacteria.
Turbidity measures optical density but doesn’t distinguish between live and dead cells. Molecular methods require specific genetic targets.
Nt = No * 2^n
The equation Nt = No * 2^n represents the formula for calculating bacterial population growth.
Nt is the final population size, No is the initial population size, and n represents the number of generations.
This formula illustrates how bacterial populations can double with each generation during exponential growth.
Apoenzyme
An apoenzyme is the protein component of an enzyme without its cofactor.
It is inactive by itself and requires the binding of a cofactor or coenzyme to become an active holoenzyme.
Apoenzymes are essential for catalyzing biochemical reactions.
Holoenzyme
A holoenzyme is the complete and active form of an enzyme.
It consists of the protein component (apoenzyme) and its associated cofactor or coenzyme.
Holoenzymes are essential for catalyzing specific biochemical reactions efficiently.
NAD, FAD, NADP
NAD (Nicotinamide Adenine Dinucleotide) and FAD (Flavin Adenine Dinucleotide) are coenzymes involved in redox reactions.
NADP (Nicotinamide Adenine Dinucleotide Phosphate) is a coenzyme involved in anabolic reactions.
These coenzymes play crucial roles in cellular energy metabolism.
Oxidation/Oxidized
Oxidation is a chemical reaction where a molecule loses electrons or gains oxygen.
An oxidized molecule has undergone this process and typically has higher energy levels.
Oxidation is a key step in energy release during catabolic reactions.
Reduction/Reduced
Reduction is a chemical reaction where a molecule gains electrons or loses oxygen.
A reduced molecule has lower energy levels and often stores energy.
Reduction is essential for energy storage during anabolic reactions.
Endergonic/Exergonic
Endergonic reactions require energy input to proceed and have a positive Gibbs free energy change (ΔG).
Exergonic reactions release energy and have a negative ΔG.
Endergonic reactions build complex molecules, while exergonic reactions break them down.
Catabolism
Catabolism refers to the metabolic processes that break down complex molecules into simpler ones.
It releases energy and provides substrates for anabolic reactions.
It is a exergonic process, and cellular respiration is an example of a catabolic and exergonic process.
Anabolism
Anabolism refers to the metabolic processes that build complex molecules from simpler ones.
It requires energy, typically from catabolic reactions.
Anabolism includes processes like protein synthesis and DNA replication.
This is a endergonic process.
Activation Energy
Activation energy is the energy required to initiate a chemical reaction.
Enzymes lower the activation energy, making reactions proceed more easily.
Lowering activation energy allows reactions to occur at lower temperatures in biological systems.
Allosteric Site
An allosteric site is a distinct binding site on an enzyme, separate from the active site.
Binding at the allosteric site can regulate the enzyme’s activity by either activating or inhibiting it.
Allosteric regulation is essential for controlling metabolic pathways.
ATP (Adenosine Triphosphate)
ATP is a molecule that stores and transfers energy within cells.
It consists of adenine, ribose, and three phosphate groups.
ATP is used as the primary energy currency for cellular processes.
Glycolysis
Glycolysis is a metabolic pathway that breaks down glucose into two molecules of pyruvate.
It occurs in the cytoplasm and produces ATP and NADH.
Glycolysis is the initial step in both aerobic and anaerobic respiration.
Krebs Cycle (Citric Acid Cycle)
The Krebs cycle is a series of chemical reactions that occur in the mitochondria.
It oxidizes acetyl-CoA to produce NADH, FADH2, and ATP.
The Krebs cycle is a central part of aerobic respiration.
Electron Transport
Electron transport is the final stage of aerobic respiration.
It takes place in the inner mitochondrial membrane and involves the transfer of electrons through protein complexes.
Electron transport generates a proton gradient used to produce ATP.
Fermentation
Fermentation is an anaerobic metabolic pathway that produces ATP without oxygen.
It involves the conversion of pyruvate to products such as lactate or ethanol.
Fermentation is less efficient than aerobic respiration in terms of ATP production.
Anaerobic Respiration
Anaerobic respiration is a metabolic process that uses electron acceptors other than oxygen.
It occurs in environments with low or no oxygen.
Examples include nitrate and sulfate reduction by bacteria.
Pyruvate
Pyruvate is a three-carbon compound produced during glycolysis.
It can be further metabolized to produce ATP or serve as a precursor for other molecules.
Under aerobic conditions, pyruvate enters the Krebs cycle; under anaerobic conditions, it can undergo fermentation.
Cytochrome Oxidase
Cytochrome oxidase is an enzyme involved in the electron transport chain during aerobic respiration.
It transfers electrons to oxygen, the final electron acceptor.
Cytochrome oxidase plays a critical role in the production of water from oxygen and electrons.
ATP Synthase
ATP synthase is an enzyme complex located in the inner mitochondrial membrane.
It generates ATP from ADP and inorganic phosphate (Pi) using the proton gradient created during electron transport.
ATP synthase is often called the “molecular turbine.”
Chemiosmotic Gradient
The chemiosmotic gradient is a difference in proton concentration and electrical charge across a membrane.
It is created during electron transport and used to drive ATP synthesis by ATP synthase.
The chemiosmotic gradient is a key aspect of energy coupling in cells.
Transamination
Transamination is a biochemical reaction that transfers an amino group (NH2) from one molecule to another.
It plays a vital role in amino acid metabolism and the synthesis of non-essential amino acids.
Transaminases are enzymes involved in transamination reactions.
Light (Photosynthesis) Reaction
The light reaction is the first stage of photosynthesis that occurs in the thylakoid membrane of chloroplasts.
It involves capturing light energy and converting it into chemical energy in the form of ATP and NADPH.
Oxygen is released as a byproduct of the light reaction.
Krebs Cycle (Dark Reaction)
The Krebs cycle is the second stage of photosynthesis that occurs in the stroma of chloroplasts.
It uses ATP and NADPH generated in the light reaction to fix carbon dioxide and produce glucose.
The Krebs cycle is an anabolic process that builds carbohydrates.
Oxidative Phosphorylation
Oxidative phosphorylation is the process in which ATP is synthesized using the energy generated by the electron transport chain.
It occurs in the inner mitochondrial membrane during aerobic respiration.
Protons flowing through ATP synthase drive the phosphorylation of ADP to ATP.
Protein Structure (Especially as it Pertains to Function and Regulation)
Protein structure is essential for its function and can be classified into primary, secondary, tertiary, and quaternary levels.
The primary structure is the linear sequence of amino acids, while the secondary structure involves folding into alpha helices or beta sheets.
Tertiary structure is the three-dimensional arrangement, and quaternary structure involves interactions between multiple protein subunits. Structure impacts function and regulation through active sites and binding sites.
Methods of Enzyme Regulation (Competitive/Allosteric/Synthesis)
Enzyme activity can be regulated through competitive inhibition, where a molecule competes with the substrate for the active site.
Allosteric regulation involves the binding of molecules at sites other than the active site, changing the enzyme’s shape and activity.
Enzyme synthesis and degradation control the overall enzyme concentration in the cell, affecting its availability for reactions.
Coupling of Catabolic and Anabolic Processes
Cells couple catabolic (energy-releasing) processes with anabolic (energy-consuming) processes to efficiently use energy.
ATP produced in catabolic pathways provides energy for anabolic reactions that build complex molecules.
This coupling ensures that energy is harnessed and utilized effectively within the cell.
Capturing Energy as Reduced Compounds
Energy in the form of electrons is captured and stored in reduced compounds like NADH and FADH2.
These reduced coenzymes carry high-energy electrons to the electron transport chain.
The energy released during electron transport is used to synthesize ATP.
Net ATP Production in Glycolysis, Kreb’s Cycle, and Electron Transport
Glycolysis generates a net of 2 ATP molecules per glucose molecule.
The Krebs cycle produces 2 ATP molecules per glucose molecule.
Electron transport chain yields approximately 28-32 ATP molecules per glucose molecule during aerobic respiration.
End Products of Catabolic Pathways (i.e., Glycolysis and Kreb’s Cycle)
The end products of glycolysis are two molecules of pyruvate, 2 ATP, and 2 NADH.
In the Krebs cycle, the end products include ATP, NADH, FADH2, and carbon dioxide (CO2).
These end products serve as substrates for subsequent stages of energy production.
Role of Pyruvate
Pyruvate is a key metabolite in both glycolysis and aerobic respiration.
Under aerobic conditions, pyruvate enters the Krebs cycle after being converted to acetyl-CoA.
Under anaerobic conditions, pyruvate can undergo fermentation to generate energy.
Differences Between Aerobic and Anaerobic Respiration
Aerobic respiration uses oxygen as the final electron acceptor in the electron transport chain, while anaerobic respiration uses other molecules.
Aerobic respiration produces more ATP per glucose molecule compared to anaerobic respiration.
Anaerobic respiration may produce end products like lactate or ethanol, while aerobic respiration produces water and CO2.
Purpose, Process, and End Products of Fermentation
Fermentation is an anaerobic process that regenerates NAD+ for glycolysis.
It involves the partial breakdown of glucose, resulting in end products like lactate (in lactic acid fermentation) or ethanol and CO2 (in alcoholic fermentation).
Fermentation allows glycolysis to continue in the absence of oxygen.
Interconversion of Amino Acids and Carbohydrates via the Kreb’s Cycle
The Krebs cycle can interconvert amino acids and carbohydrates.
Amino acids can be deaminated and their carbon skeletons used in the Krebs cycle for energy.
Gluconeogenesis allows some intermediates of the Krebs cycle to be used for glucose synthesis from non-carbohydrate sources.
Role of Electron Transport in the Creation of a Chemiosmotic Gradient (PMF) and Production of ATP
During electron transport, electrons move through protein complexes in the inner mitochondrial membrane.
Protons are pumped out of the mitochondrial matrix into the intermembrane space, creating a proton motive force (PMF).
ATP synthase uses the PMF to produce ATP as protons flow back into the matrix through the enzyme.
