Chapter 3: Gluconeogenesis and Transport

Chapter 3

• Gluconeogenesis involves making sugar from non-carbohydrate sources
• It is an anabolic pathway where a molecule is made by building larger molecules from smaller ones using energy
• Catabolic pathways break down larger molecules and release energy

Review of Transport

• Simple transport is passive and allows direct molecule transport across the cell membrane, from high to low concentration without energy
• Group translocation is a form of active transport using an energy-rich organic compound (not ATP) to transport a molecule across the cell membrane
• ABC transporters are proteins that use ATP energy to move substances across the cell membranes in bacteria, either bringing in essential nutrients or expelling waste and toxins, that play roles in nutrient uptake, waste removal, and antibiotic resistance
• Uniport involves of a single type of molecule or ion in one direction across the cell membrane
• Antiport involves two different types of molecules or ions in opposite directions across the cell membrane, where one substance is transported in while the other is transported out
• Symport events involves two or more different molecules or ions are moved across the cell membrane in the same direction simultaneously, typically using the energy of one molecule's gradient (often a proton or sodium ion) to move another molecule against its concentration gradient

Pentose Phosphate Pathway (PPP)

• PPP is primarily used for two important functions
• First, it produces NADPH, crucial for anabolic reactions like fatty acid and cholesterol synthesis, and protects the cell from oxidative damage
• Second, the pathway generates ribose-5-phosphate, a key building block for nucleotides needed to produce DNA and RNA
• While the PPP helps build molecules and depends on cell's catabolic needs, it is mainly an anabolic pathway

Cellular Respiration

• Cellular respiration breaks down glucose to produce ATP
• Glycolysis occurs in the cytoplasm, where one 6-carbon glucose molecule splits into two 3-carbon pyruvate molecules, producing 2 ATP
• In pyruvate oxidation, each pyruvate is turned into Acetyl-CoA, releasing 2 carbon atoms as carbon dioxide (CO2)
• Acetyl-CoA enters the Krebs cycle in the mitochondria, where more carbon is released as CO2, and energy is transferred to NADH and FADH2
• NADH and FADH2 help create a proton gradient that drives the production of about 28 ATP, with oxygen acting as the final electron acceptor to form water in the electron transport chain
• Overall, cellular respiration produces about 38 ATP from one glucose molecule
• If oxygen is unavailable, cells can switch to fermentation, which allows ATP production to continue via glycolysis, but only produces 2 ATP per glucose molecule, and regenerates NAD+ so glycolysis can keep going, but it results in byproducts like lactic acid or ethanol, depending on the organism

Krebs Cycle

• In the Krebs cycle, a 2-carbon Acetyl-CoA combines with a 4-carbon oxaloacetate to form a 6-carbon citrate molecule
• Citrate breaks down, releasing 2 carbon dioxide molecules (CO2) and transferring energy to molecules like NADH and FADH2
• Through the electron transport chain, these energy carriers produce more ATP
• Oxaloacetate is regenerated to allow the cycle to start over with another Acetyl-CoA

Catalysts

• A catalyst speeds up a chemical reaction without being consumed by lowering the activation energy required for the reaction
• Enzymes are biological catalysts, like amylase breaking down starches, or chemical catalysts, such as platinum

Endoenzymes and Exoenzymes

• Endoenzymes function inside the cell
• Exoenzymes are excreted by the cell and function outside the cell
• Endoenzymes are most common and are involved in glycolysis, the Kreb's cycle, and electron transport chain

Induced Fit Model

• Proposed by Daniel Koshland in 1958
• Suggests that when a substrate binds to an enzyme's active site, the enzyme's structure slightly changes to fit the substrate more snugly, optimizing the reaction

Reviewed Scientists

• Gustav Embden (1920s) contributed to the Embden-Meyerhof pathway, describing how glucose is broken down in glycolysis to produce ATP
• Willard Gibbs (1876) developed the concept of Gibbs free energy, crucial for understanding energy changes in chemical reactions
• Daniel Koshland (1958) proposed the induced fit model of enzyme action, showing that enzymes change shape when binding to substrates
• Michaelis and Menten (1913) created the Michaelis-Menten model, explaining enzyme kinetics and the relationship between enzyme activity and substrate concentration
• Paul Boyer (1970s) developed the binding change mechanism of ATP synthase, explaining ATP production during oxidative phosphorylation

Siderophores

• Molecules produced by bacteria, fungi, and plants
• Bind to iron and help transport it into cells, aiding iron acquisition for growth and metabolism

Organic and Inorganic Molecules

• Organic molecules contain carbon, usually bonded to hydrogen, oxygen, nitrogen, and sometimes sulfur or phosphorus
• Inorganic molecules do not have carbon-hydrogen bonds and are simpler
• If a molecule contains carbon, hydrogen, (and typically oxygen or nitrogen), it is likely organic
• If it lacks carbon-hydrogen bonds, it is inorganic

CHONPS, Macronutrients and Micronutrients

• CHONPS refers to the five key elements essential for life, including Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Phosphorus (P), and Sulfur (S)
• Macronutrients, CHONPS, are needed in large amounts for energy, growth, and cellular functions
• Micronutrients are needed in smaller amounts but are essential for enzyme activity, immune function, and other processes
• Trace elements are needed in very small amounts but are still essential for specific biochemical functions
• Vitamins are organic compounds essential for metabolism and function as coenzymes or antioxidants

Oxidation and Reduction

• Oxidation involves loss of electrons
• Reduction involves gain of electrons
• Oxidizing agent gains electrons and is reduced
• Reducing agent loses electrons and is oxidized

Carbon Dioxide

• The most oxidized form of carbon is carbon dioxide (CO2)
• Carbon in CO2 has an oxidation state of +4, which is the highest possible oxidation state for carbon in its stable compounds

Electron Transport Chain (ETC)

• ETC has four complexes: Complex I, Complex II, Complex III, and Complex IV
• NADH enters Complex I, donating electrons and helping pump protons, which leads to the production of 3 ATP
• FADH2 enters at Complex II, doesn't pump as many protons, so it only produces 2 ATP
• Because NADH enters at a more efficient complex, it results in more ATP than FADH2
• The final electron acceptor in cellular respiration is inorganic
• It is oxygen (O2), which accepts electrons at Complex IV in the electron transport chain, combining with protons (H+) to form water (H2O)
• Oxygen is an inorganic molecule and is thus the final acceptor

ATP synthase

• An enzyme found in the inner mitochondrial membrane (or plasma membrane in prokaryotes) that produces ATP
• Uses the energy from a proton gradient created by the electron transport chain
• Protons flow back into the matrix through ATP synthase, and the enzyme uses this energy to convert ADP and inorganic phosphate into ATP
• This process, known as chemiosmosis, is a key part of oxidative phosphorylation in cellular respiration

Chemoorganotrophs

• Most pathogenic microorganisms are chemoorganotrophs because they obtain energy from breaking down organic compounds, such as sugars and proteins, from their host
• They are also heterotrophs, relying on organic carbon sources for growth and survival since microbes do not produce their food

Phosphorylation

• Three types of phosphorylation
• Substrate-level phosphorylation occurs when a phosphate group is directly transferred from a high-energy substrate molecule to ADP to form ATP, happening during glycolysis and the Krebs cycle
• Oxidative phosphorylation occurs in the electron transport chain (ETC), where ATP is produced through the flow of electrons and protons across the mitochondrial membrane
• The energy from this proton gradient is used to synthesize ATP via ATP synthase, this process is part of cellular respiration and is much more efficient than substrate-level phosphorylation
• Photophosphorylation occurs in photosynthesis, where light energy is used to produce ATP from ADP and inorganic phosphate in the thylakoid membranes of chloroplasts
• Light energy excites electrons, which are then used to drive ATP synthesis
• Oxidative phosphorylation is more efficient than substrate-level phosphorylation because it produces far more ATP with the electron transport chain generating the majority of ATP in cellular respiration (around 30-32 ATP per glucose molecule)

Laws of Thermodynamics

• The First Law of Thermodynamics (Law of Energy Conservation) states that energy cannot be created or destroyed, only transformed from one form to another
• The Second Law of Thermodynamics states that the state of entropy of the entire universe, as an isolated system, will always increase over time, also changes in the entropy in the universe can never be negative
• -ΔG: Energy is released, the reaction is spontaneous, and the system becomes more stable (exergonic)
• +ΔG: Energy is required, the reaction is not spontaneous, and the system becomes less stable (endergonic)

Coenzymes

• Small, organic molecules that assist enzymes in their catalytic activity
• They often act as carriers of specific atoms or groups of atoms, such as electrons or functional groups, during biochemical reactions
• NAD+ (oxidized) → NADH (reduced): NAD+ accepts electrons and becomes NADH
• FAD (oxidized) → FADH2 (reduced): FAD accepts electrons and becomes FADH2
• CoA does not undergo redox changes but carries acetyl groups (as acetyl-CoA)
• NADP+ (oxidized) → NADPH (reduced): NADP+ accepts electrons and becomes NADPH

ATP

• ATP is short-lived because it is quickly used by cells for energy transfer and cellular processes
• To store energy longer-term, cells store it in molecules like glycogen (in animals) or starch (in plants), as well as in lipids (fats), which can be broken down when energy is needed

5 point essay

• During the electron transport chain (ETC), about 34 ATP are produced from one glucose molecule in cellular respiration
• In eukaryotes, the ETC occurs in the inner mitochondrial membrane, while in prokaryotes, it occurs in the plasma membrane
• NADH and FADH2 donate electrons to the complexes, with Complexes I, III, and IV acting as proton pumps, moving protons across the membrane to create a proton gradient
• This proton gradient generates a proton motive force (PMF), which stores energy
• ATP synthase uses this proton flow to produce ATP from ADP and inorganic phosphate through chemiosmosis, generating approximately 34 ATP per glucose molecule

Glucose Oxidation

• The glucose molecule is completely oxidized during the Krebs cycle (citric acid cycle)
• Six carbons in the original glucose molecule are released as carbon dioxide (CO2), with two carbons released per turn of the cycle
• Since the glucose molecule is broken down into two pyruvate molecules during glycolysis, the two pyruvates are then converted into two acetyl-CoA molecules before entering the Krebs cycle, where the carbon atoms are fully oxidized and released as CO2

Citric Acid Cycle

• After the citric acid cycle, the energy from the original glucose molecule is primarily stored in the form of NADH, FADH2, and ATP
• These molecules carry the high-energy electrons and will later be used in the electron transport chain to generate a larger amount of ATP
• Some energy is released as carbon dioxide (CO2)

Chapter 4 Equations

• Number of generations (n): n=t/g
• Generation time (g): g=t/n
• Division rate (v): v=1/g=(mu)

Enumerating Cells

• A method to enumerate cells is to perform a serial dilution followed by plating the diluted samples and counting colony-forming units (CFUs)

Limiting Microbes

• A physical method is to limit microbes on a surface with sterilization through heat or UV light

Cardinal Temperatures

• Minimum temperature: The lowest temperature an organism can grow at
• Optimum temperature: The temperature at which the organism grows best
• Maximum temperature: The highest temperature an organism can grow at
• Psychrophile: Organisms that grow best at low temperatures (0-20°C)
• Mesophile: Organisms that grow best at moderate temperatures (20-45°C)
• Thermophile: Organisms that grow best at high temperatures (45-70°C)
• Hyperthermophile: Organisms that grow best at very high temperatures (70°C+)
• Most pathogens are mesophiles because they grow best at human body temperature (37°C)

Membrane Changes

• Psychrophiles have more unsaturated fatty acids, while thermophiles and hyperthermophiles have more saturated fatty acids in their membranes to help maintain fluidity at extreme temperatures

Chemostat/Bioreactor

• A chemostat or bioreactor is an open system that continuously supplies fresh nutrients and removes waste to support continuous microbial growth

Growth Curve Stages

• Lag phase: The bacteria adapt to the environment with no growth
• Log phase: Exponential growth occurs
• Stationary phase: Growth rate equals death rate
• Death phase: Death rate exceeds growth rate

Diauxic Shift

• Occurs when a microorganism switches from using one carbon source to another, often when the preferred carbon source is exhausted, that happens during the log phase

Asexual Reproduction Types

• The types of asexual reproduction in microorganisms include binary fission, budding, fragmentation, and spore formation

Asexual vs. Sexual Reproduction

• Asexual reproduction is faster and produces genetically identical offspring
• Sexual reproduction is slower but allows for genetic diversity

Fission vs. Budding

• In fission, the parent cell divides into two equal daughter cells
• In budding, the new cell forms as a smaller outgrowth of the parent

Biofilm Formation Stages

• Attachment to a surface
• Microcolony formation
• Maturation of the biofilm
• Dispersion of cells

Complex vs. Chemically Defined Media

• Complex media contains undefined ingredients
• Chemically defined media contains known quantities of specific chemicals

Types of Media

• Growth media supports a wide range of organisms
• Media contains additional nutrients for fastidious organisms
• Selective media inhibits growth of some organisms while promoting others
• Differential media helps differentiate between organisms based on metabolic activities
• Enrichment media favors the growth of a specific group of organisms
• Selective and differential media combine both features

Precision and Accuracy

• Precision refers to the consistency of results
• Accuracy refers to how close the results are to the true value
• Precision without accuracy can occur if measurements are consistently wrong
• Accuracy without precision happens when results are correct on average but inconsistent

Quantitative vs. Qualitative Methods

• Quantitative methods include plate counts being precise but time-consuming, and turbidity measurements being fast but less accurate
• Qualitative methods include microscopic counts being fast but less accurate for low concentrations

pH Groups

• Neutrophiles grow best in neutral pH (6.5-7.5)
• Acidophiles grow best in acidic pH (below 5.5)
• Alkaliphiles grow best in basic pH (above 8.5)
• Neutrophiles contain most pathogens and thrive in the human body, which is neutral

Osmosis and Tonicity

• Isotonic: Equal solute concentration on both sides with no net water movement
• Hypertonic: More solutes outside the cell enables water movement out, causing cell shrinkage
• Hypotonic: Fewer solutes outside the cell enabling water movement in, causing cell swelling
• Some pathogens like Halobacterium can thrive in high-salt (hypertonic) environments

Oxygen Utilization

• Aerobes require oxygen and have enzymes like catalase and superoxide dismutase
• Anaerobes do not require oxygen and may have anaerobic enzymes
• Facultative anaerobes can grow with or without oxygen
• Microaerophiles require low levels of oxygen
• Aerotolerant anaerobes do not use oxygen but can tolerate it

Control Methods

• Physical methods include heat (sterilization, pasteurization), filtration, and UV radiation but may damage cells or surfaces
• Chemical methods utilize disinfectants, antiseptics, and antibiotics that are broad-spectrum, but have potential toxicity

Thomas Brock

• Known for discovering thermophilic bacteria in hot springs and for isolating the heat-stable enzyme Taq polymerase, used in PCR (Polymerase Chain Reaction)

Chapter 5 Virology Contributions

• Edward Jenner developed the first smallpox vaccine, pioneering the use of vaccination
• Louis Pasteur proposed the germ theory of disease and developed the rabies vaccine, contributing to the understanding of viruses
• Ivanovsky and Beijerinck discovered that tobacco mosaic disease was caused by a virus, marking the discovery of viruses as distinct from bacteria
• Rosalind Franklin provided X-ray crystallography images that helped reveal the structure of DNA, influencing the understanding of viral genomes
• Ruska and Knoll developed the electron microscope, which allowed for the visualization of viruses for the first time

Viruses vs Other Microbes

• Viruses cannot replicate on their own but require a host cell
• Their genomes can be made of DNA or RNA (not both), and they consist of a protein coat called a capsid, sometimes with an envelope
• Unlike bacteria and fungi, they don't have cellular structures

Lytic, Latent and Lysogeny

• Lytic is a viral replication cycle where the host cell is destroyed after virus production
• Latent viruses remain dormant in the host cell and can be activated later (typically animal viruses)
• Lysogeny viruses integrate into the host genome and replicates with it (typically bacteriophage)

Naked Viruses

• A naked virus lacks an envelope, consisting only of a protein coat (capsid) and its genetic material

Virion

• A complete, infectious viral particle that includes the genome and the capsid, and sometimes an envelope

Viral Envelope

• A viral envelope is a lipid membrane surrounding some viruses
• Derived from the host cell's membrane during virus release
• Not all viruses have envelopes; those that do include influenza and HIV aiding in entry into host cells

Virus Shapes and Capsomers

• Viruses can have shapes like icosahedral, helical, or complex
• For example, adenovirus is icosahedral with identical capsomers, while influenza is helical and has non-identical capsomers

Bacteriophage & Parts

• A bacteriophage is a virus that infects bacteria
• Study is the T4 bacteriophage
• The parts of a bacteriophage include the capsid, tail, and tail fibers
• The tail tube moves downward to inject viral DNA into the host

Virus Replication

• Animal viruses enter the host through fusion or endocytosis, while bacteriophages inject their DNA through the tail tube

Lytic vs Lysogenic/Latent viruses

• Lytic viruses destroy the host cell immediately after replication
• Lysogenic/latent viruses integrate their genome into the host's genome and can remain dormant

Virus Entry

• Animal viruses typically enter through fusion or endocytosis
• Bacteriophages attach to the surface and inject their genetic material

Transformation and Transduction

• Transformation is a process where a virus can alter the host's genetic material, making it cancerous (typically animal cells)
• Transduction is when a bacteriophage transfers bacterial genes from one bacterium to another

Pathogenicity Islands and Inclusion Bodies

• Pathogenicity islands are genetic regions in bacteria with genes for virulence factors and are often transferred by bacteriophages
• Inclusion bodies are abnormal structures within the cell formed during viral infection( e.g., Negri bodies in rabies)

Classification of viruses

• Acute virus: (e.g., Influenza); causes rapid infection and clearance
• Persistent Virus: (e.g., HIV); remains in the body for a long period
• Chronic Virus: (e.g., Hepatitis B); can cause long-term infections

Matrix Enzymes

• Enzymes used by viruses to help in replication and transcription
• RNA polymerase in the flu
• Tamiflu inhibits neuraminidase enzyme in influenza

Permissive Hosts

• A permissive host can support viral replication
• A nonpermissive host cannot

One-Step Growths

• The one-step growth curve has an eclipse phase, which is the period when viral particles are unassembled and not detectable

Early, Mid, and Late Proteins

• Early proteins are involved in taking over the host cell machinery
• Mid proteins help in viral DNA replication
• Late proteins are structural components of the virus

Cultivation of Viruses

• In vivo methods involve growing viruses in live animals or eggs, for the study of the virus in its natural host but are is expensive and involves ethical concerns
• In vitro methods uses cultured cells, which are less costly but may not fully replicate the viral behavior in a living organism
• Bacteriophages are typically cultured in bacterial cultures, while animal viruses require cultured mammalian cells

Viral Plaques

• Areas of cell destruction on a bacterial lawn caused by viral infection
• They form when bacteriophages lyse bacterial cells

Cytopathic Effects

• Visible changes in host cells due to viral infection, such as cell lysis or formation of syncytia (multinucleated cells) e.g., CPE of polio and herpes