Study Guide for Lecture Exam #1 PDF

Ashkan General Microbiology​​ ​ ​ ​ ​ ​ ​ ​ ​ ​ E. Ininns Saddleback College​ Study Guide for Lecture Exam #1 The following questions will help you in reviewing the first few weekly quizzes and for Lecture Exam #1. You...

Ashkan General Microbiology​​ ​ ​ ​ ​ ​ ​ ​ ​ ​ E. Ininns Saddleback College​ Study Guide for Lecture Exam #1 The following questions will help you in reviewing the first few weekly quizzes and for Lecture Exam #1. You should be able to answer these questions after viewing the videos on each topic using the textbook as a supplemental resource. The exam will focus on material covered in lecture videos and in this study guide. Chapter #1: Introduction to Microbiology 1.​ List the major contributions made to microbiology by: Leeuwenhoek, Virchow, Koch, Pasteur, Lister, Semmelweis, Jenner, Ehrlich, Fleming, Watson and Crick (see textbook). ​ Leeuwenhoek: first to observe bacteria, improved design and quality of microscope. Made important drawings of the microorganisms ​ Virchow: introduced the concept of biogenesis: living cells can arise only from preexisting cells which refuted the theory of spontaneous generation ​ Koch: proved that microorganisms can cause disease (Koch’s postulate) ​ Pasteur: disproved spontaneous generation (belief that living organisms can arise from nonliving matter). ​ Semmelweis: Showed that handwashing with chlorinated lime solutions significantly reduced childbirth-related infections ​ Jenner: developed vaccine against smallpox (first vaccine) ​ Ehrlich: Used the first synthetic chemotherapeutic agent and first synthetic drug ​ Flemming: observed that penicillin fungi inhibited the growth of bacteria ​ Watson and Crick: discovered double-helix structure of DNA explaining how genetic information is stored and replicated 2.​ List and briefly describe the 5 types of organisms studied in Microbiology as outlined in the first lecture. ​ Virology: study of viruses - very small sub-microscopic -​ not true independent cells -​ obligate intracellular parasites -​ Ex: SARS-COV-2 ​ Bacteriology: study of bacteria -​ small self sufficient cells -​ have DNA but no nucleus or organelles -​ prokaryotic -​ Ex: Salmonella ​ Protozoology: study of protozoans -​ large true cells -​ true nuclei and organelles -​ eukaryotic -​ Giardia ​ Mycology: study of fungi -​ single cells (yeast) or multicellular (molds, mushrooms) -​ eukaryotic -​ Ex: Aspergillus ​ Parasitology: study of worms -​ large (macroscopic) -​ eukaryotic parasites -​ common in humans -​ ascaris 3.​ What are EIDs? List 5 examples of EIDs from the textbook.  Emerging Infectious Diseases (EID’s) are new or re-emerging diseases due to microbial evolution, human activity, or environment changes ​ Zika Virus Disease ​ Middle East Respiratory Syndrome (MERS) ​ Influenza ​ Antibiotic-Resistant infections ​ Ebola Virus Disease 4.​ List the 6 ways microorganisms help or benefit humans as described in lecture. ​ Photosynthetic Microbes: Base of all aquatic food web/chains produce oxygen and chemical energy ​ Nitrogen Fixing Microbes: Make nitrogen available to plants, animals needed for DNA, ATP, proteins etc. ​ Normal Flora: “Good” microbes; don’t (usually) cause disease some found in probiotics. Help by increasing digestion, produce vitamins, and compete with pathogens. ​ Food/Beverage/Drug Producing Microbes: Produce wine, beer, cheese, yogurt, bread, antibiotics etc.. ​ Genetically Engineered Microbes: Produce insulin, hormones, enzymes, clotting factors, more nutritious and pest resistant plants etc. GMOs (Genetically Modified Organisms). ​ Bioremediating Microbes: “living fix” for problems like; Sewage treatment, toxic oil clean-up. 5. ​ Define the following terms: pathogen, normal flora, theory of spontaneous generation, germ theory of disease, prion (see textbook). ​ Pathogen: A disease-causing organism ​ Normal microbiota/Normal flora: The microorganisms that colonize a host without causing disease ​ Theory of spontaneous generation: The idea that life could arise spontaneously from non-living matter ​ Germ theory of disease: the principle that microorganisms cause disease ​ Prion: an infectious agent consisting of a self-replicating protein, with no detectable nucleic acids Chapter # 2: Chemical Principles 1. ​ List the four most common elements in living organisms and their letter symbols. ​ Oxygen (O) ​ Carbon (C) ​ Hydrogen (H) ​ Nitrogen (N) 2. ​ List the names and characteristics of the three types of chemical bonds. ​ Ionic bonds: electrons are shared between atoms. ​ Covalent bonds: electrons are transferred between atoms. (charged ions, metal and nonmetals) ​ Hydrogen bonds: weak attraction between a hydrogen and an electronegative atom. (H,O,N,F) 3.​ Define the following types of reactions: synthesis/anabolic, decomposition/catabolic. ​ Synthesis reactions: A chemical reaction in which two or more atoms combine to form a new, larger molecule ​ Anabolic reaction: All synthesis reactions in a living organism; the building of complex organic molecules from simpler ones (typically requiring energy). ​ Decomposition reaction: A chemical reaction in which bonds are broken to produce smaller parts from a large molecule ​ Catabolic reaction: all decomposition reactions in a living organism the breakdown of complex organic compounds into simpler ones. 4.​ How do electron shells relate to bond formation? ​ Electron shells determine bond formation as atoms share, gain, or lose electrons to achieve a full outer shell, ensuring stability 5.​ Why is H20 described as a “polar” solvent? What types of compounds are soluble in water? ​ Because of its uneven charge distribution ​ Polar compounds are soluble in water (like dissolves like) 6.​ Know the formula for pH. Know which numbers on the pH scale are considered: acidic, neutral, basic/alkaline. ​ pH=-log[acid] ​ acidic: 7 ​ neutral: =7 7.​ Recognize the functional groups: hydroxyl (alcohol), amino, carboxyl, phosphate (see Table 2.4). ez 8.​ List the elements (atoms) found in all carbohydrates. What are the main functions of carbohydrates? Know the differences between and examples of monosaccharides, disaccharides, polysaccharides. ​ Ex: sugars, starches ​ Contain: CH2O ​ Function: energy, structure, signaling -​ Monosaccharide: single sugar unit -​ Disaccharide: two monosaccharides linked by glycosidic bond (sugar-O-sugar) -​ Polysaccharides: long chain of monosaccharides. Ex: cellulose, starch.(plants) -​ glucose + fructose = sucrose -​ glucose + galactose = lactose -​ glucose + glucose = maltose Glycogen (animals) dextran, peptidoglycan (bacteria) 9.​ List the elements (atoms) found in lipids, and how they differ from carbohydrates. Know the general characteristics, structures and functions of simple fats, phospholipids, and steroids. ​ Ex: fats, oils ​ Contain: CHO ​ Function: energy, structure, signaling, insoluble in H2O ​ Lipids: hydrophobic, energy-rich molecules with long hydrocarbon chains. Energy storage, hormone production, cell membrane structure ​ Carbohydrates: hydrophilic, composed of sugar units, used for primarily quick energy & structural support. ​ Simple fats: glycerol plus 1-3 fatty acids Simple fats ​ Structure: glycerol backbone with 1-3 fatty acid chains ​ Functions: Energy Storage, insulation and protection Phospholipids ​ Structure: Glycerol backbone, two fatty acid tails (hydrophobic), and a phosphate group (hydrophilic) ​ Functions: Major components of cell membranes, forming the lipid bilayer Steroids ​ Structure: 4 fused hydrocarbon rings ​ Functions: Hormone production (testosterone, estrogen..), cholesterol, bile salts (digestion) 10.​ List the elements (atoms) found in all amino acids and how amino acids are joined together to form proteins. Be able to recognize a peptide bond (see Figure 2.14). ​ Ex: hemoglobin, antibodies, enzyme ​ Contain: CHON(S) ​ Function: diverse ​ RECOGNIZE: Side group, Amino group, R group that all proteins have ​ Amino acids are joined together through a peptide bond (C-N) 11.​ List and define the four levels of structure found in proteins (see Figure 2.15). Is quaternary structure found in all proteins? What is a denatured protein?  ​ Not all proteins have a quaternary structure ​ Denatured Protein:protein that loses 3D structure and function due to heat, pH, salinity, or chemicals 12.​ List the elements (atoms) found in all nucleic acids. List the 3 main components of nucleotides. Know which bases are purines and pyrimidines. Know the differences between DNA and RNA. ​ Ex: DNA, RNA ​ Contain: CHONP ​ Function: genetic info ​ 3 components are nitrogenous base, pentose sugar, phosphate group ​ Purines: adenine, guanine (double ring) ​ Pyrimidines: Cytosine, thymine, uracil (single ring) ​ Differences: Structure: DNA: double-stranded helix RNA: single stranded helix ​ Sugar: DNA: Deoxyribose ​ RNA: Ribose ​ Bases: DNA: T→ A RNA: U→A ​ Function: DNA stores genetic info transfer and translates genetic info (mRNA, tRNA, rRNA) ​ Stability: DNA more stable, long-term storage RNA: less stable, temporary function 13. ​ Know the complementary base pairing rules. What holds complementary base pairs together? A—>T (2H) / C—>G (3H) (DNA) A—>U/C—>G (RNA) 14.​ Know what ATP stands for, and its function. Be able to recognize its structure. (see Figure 2.18). ATP: Adenosine Triphosphate, source of energy in a cell. Chapter #3: Microscopy 1.​ Know the standard unit of length measurement in the metric system. Know the meaning of the prefixes: nano (n), micro (u), milli (m), centi (c) and kilo (k). pico (p) 10^-12 nano (n) 10^-9 micro (µ) 10^-6 centi (c) 10^-2 kilo (k) 10^3 2.​ Know the general limits of resolution for: the unaided eye, light microscope, electron microscope. (see Figure 3.2). Define: refraction and refractive index. Know the purpose of oil used with the 1000X lens. unaided eye: >200µm light microscope: 10 nm-200 nm electron microscope: 10pm-100pm Refractive index: measure of light bending ability of a medium Refraction: bending of light as it passes from one medium to another with different density causing a change in its speed and direction 3.​ Know what dark field versus bright field microscopy is. Know the difference between TEM and SEM. Know an example where fluorescence microscopy could be used. Dark Field Microscopy: Used to examine live microorganisms that either are invisible in the ordinary light microscope cannot be stained by standard methods, or are so distorted by staining that their characteristics are obscured Bright Field Microscopy: Most microbes are colorless, transparent, dyes used to help visualize cells and structures. Light is good for stained samples. Fluorescence microscopy: used primarily in a diagnostic procedure called fluorescent - antibody (FA) technique, or immunofluorescence which is used to mark antibodies or pathogens with specific dyes PUT EXAMPLE PICTURES FOR THE FOLLOWING TEM (transmission electron microscopy): electron pass through sample, look inside thin samples to see internal structures in 2D SEM (Scanning Electron microscopy): electron bounces off the sample’s surface, shows surface details in 3D 4.​ Define and give an example of: a simple stain, differential stain, basic dye, acidic dye, negative stain. Simple Stain: use simple dye Differential Stain: A stain that distinguishes objects on the basis of reactions to the staining procedure Basic Dyes: (+ charge) stain cell structures ex: methylene blue, crystal violet, safranin Acidic Dyes (- charge) stain background (used in negative stain) ex: eosin, nigrosin 5.​ Describe the 3 types of specialty stains described in lecture (see Table 3.3). Capsules Stain: Capsules appears colorless because their polysaccharides repel dyes Endospores Stain: Uses heat to drive green dye into relatively impermeable spore walls Flagella Stain: Stains extremely thin motility structures Chapter #4: Prokaryotic and Eukaryotic Cells 1.​ List the major differences between prokaryotic and eukaryotic cells. Prokaryotic: -​ Cells without a membrane bound nucleus or organelles -​ 0.2 - 2 microns Ex: bacteria Eukaryotic: -​ Cells with a nucleus and membrane bound organelles -​ 10-100 microns Ex: animals, plants, fungi, algae etc… 2.​ List the common shapes and arrangements of bacteria. Cocci (spherical (singular : coccus) Bacilli: Straight rods (singular : bacillus) Spiral: bent or curved bacilli. Include: vibrios (slightly bent), Spirilla (more twisted), spirochetes (spring-like) Diplo: pairs Tetrads: groups of 4 Strepto: chains Staphylo: clusters 3.​ Define biofilm and know their beneficial functions for bacteria. Biofilms: mixed communities of bacteria on surfaces like teeth, sewer pipes, catheters. Difficult to disinfect 4.​ Draw a simple labeled diagram of the 2 main types of bacterial cell walls. (See Figure 4.13) ​ Make a table to highlight the major differences between the 2 cell wall types. Gram positive vs Gram negative cell wall 5.​ Be able to sketch a simple, labeled diagram of a cytoplasmic (cell) (plasma) membrane. (see Figure 4.14b) Know how cell membranes are fundamentally different from cell walls. 6.​ Define the following types of transport across the cell membrane: simple diffusion, osmosis, active transport, facilitated diffusion. Passive transport (requires no energy) -​ diffusion high to low (through the membrane) -​ Osmosis diffusion of H2O -​ facilitated requires no ATP but requires the help of an embedded protein in cell membrane (used for ions, sugars, and water) Active transport (requires energy) 7.​ Describe the basic function and structure of the following prokaryotic structures: ribosomes, metachromatic granules, endospores, flagella, pili, glycocalyx, capsules. Ribosomes: used for protein synthesis -​ composed of rRNA + proteins, 2 subunits: 50s +30s when joined together they are 70s different from the 80s ribosomes seen in eukaryotic cells. 70s are the target of antibiotics! Metachromatic granules: Function: Store phosphate reserves, which can be used for ATP production. Structure: Dense, irregularly shaped granules that stain red or blue with certain dyes (e.g., methylene blue). Endospores: highly protective prokaryote dormant stage formed under harsh conditions produced only in bacillus and clostridium. -​ 3 protective layers: -​ Core: made of dipicolinic acid, DNA, RNA, enzymes -​ Cortex: peptidoglycan -​ Coat: protein Flagella: Function: Enable movement by rotating like a propeller, allowing chemotaxis. Structure: Long, whip-like appendages composed of flagellin, anchored by a basal body in the cell membrane. Pili: Function: Aid in attachment to surfaces and in bacterial conjugation (DNA transfer). Structure: Short, hair-like protein projections extending from the cell surface. Glycocalyx: Function: Protects against desiccation, aids in adherence to surfaces, and helps evade immune responses. Structure: Gel-like outer layer made of polysaccharides or polypeptides, found outside the cell wall. Capsules: Function: Protects bacteria from phagocytosis and contributes to virulence. Structure: A well-organized, dense glycocalyx layer firmly attached to the cell wall. 8.​ List how prokaryotic and eukaryotic chromosomes are different from each other. ​ Define: plasmid, DNA supercoiling. Plasmid ​ A small, circular, double-stranded DNA molecule found in prokaryotes (and some eukaryotes). ​ It replicates independently of the chromosomal DNA. ​ Often carries antibiotic resistance genes or other beneficial traits. DNA Supercoiling ​ The process of twisting DNA to make it more compact. ​ Helps in DNA packaging, especially in prokaryotes that lack a nucleus. ​ Enzymes like DNA gyrase and topoisomerases regulate supercoiling. 9.​ Describe the basic function and structure of the following eukaryotic organelles: nucleus, endoplasmic reticulum, Golgi apparatus, lysosomes, mitochondria, chloroplasts. Nucleus ​ Function: Stores genetic material (DNA), controls cell activities, and regulates gene expression. ​ Structure: Surrounded by a double membrane (nuclear envelope) with nuclear pores; contains chromatin (DNA + proteins) and a nucleolus (site of ribosome production). Endoplasmic Reticulum (ER) ​ Function: Synthesizes proteins (rough ER) and lipids (smooth ER), transports molecules within the cell, and detoxifies chemicals. ​ Structure: A network of membranes connected to the nuclear envelope. ○​ Rough ER: Studded with ribosomes, involved in protein synthesis. ○​ Smooth ER: Lacks ribosomes, involved in lipid synthesis and detoxification. Golgi Apparatus ​ Function: Modifies, sorts, and packages proteins and lipids for transport (inside or outside the cell). ​ Structure: Stacks of flattened membrane sacs (cisternae), with vesicles budding off to transport materials. Lysosomes ​ Function: Digest and break down waste, pathogens, and damaged organelles using hydrolytic enzymes. ​ Structure: Membrane-bound vesicles containing digestive enzymes (acid hydrolases), with an acidic internal environment. Mitochondria ​ Function: Generate ATP through cellular respiration, providing energy for the cell. ​ Structure: Double membrane organelle with an inner membrane (folded into cristae to increase surface area) and a matrix containing enzymes and mitochondrial DNA. Chloroplasts (found in plants and algae) ​ Function: Conduct photosynthesis, converting sunlight into chemical energy (glucose). ​ Structure: Double membrane organelle containing thylakoids (stacked into grana), stroma (fluid-filled space), and chlorophyll (light-absorbing pigment). 10.​ List how eukaryotic plasma membranes, cell walls, ribosomes and flagella differ from prokaryotic ones. 11. ​ Define and give an example of endosymbiosis, ectosymbiosis. Endosymbiosis ​ Definition: A type of symbiotic relationship where one organism lives inside the cells or body of another. ​ Example: Mitochondria and chloroplasts in eukaryotic cells originated from ancient bacteria that were engulfed by a larger cell but remained functional (Endosymbiotic Theory). Ectosymbiosis ​ Definition: A symbiotic relationship where one organism lives on the surface of another, rather than inside. ​ Example: Barnacles on whales—barnacles attach to the whale’s skin, gaining mobility and access to food, while the whale is largely unaffected. Chapter #10: Identification and Classification of Microorganisms 1. ​ Define: taxonomy, phylogeny (systematics), binomial nomenclature. Taxonomy: science of grouping (classifying) organisms together based on shared characteristics Binomial nomenclature is a system of naming organisms using two Latinized names: genus (capitalized) and species(lowercase), e.g., Homo sapiens. 2. ​ List the taxonomic hierarchy and who is credited with developing it. Taxonomic Hierarchy (Largest to Smallest) 1.​ Domain 2.​ Kingdom 3.​ Phylum 4.​ Class 5.​ Order 6.​ Family 7.​ Genus  8.​ Species Developed by: Carl Linnaeus (18th century), known as the "Father of Taxonomy." 3.​ What contribution did Darwin make to taxonomy? Define: phenotype and genotype. Phenotype: Based on observable characteristics Genotype: Based on organisms genetics 4. ​ Describe the basics of the classification systems of Whittaker and Woese. Whittaker’s Five-Kingdom System (1969) Developed by: Robert Whittaker​ Key Idea: Classification based on cell type, nutrition, and organization. ​ Kingdoms: 1.​ Monera (prokaryotes – bacteria & archaea) 2.​ Protista (unicellular eukaryotes) 3.​ Fungi (heterotrophic, absorb nutrients) 4.​ Plantae (autotrophic, photosynthetic) 5.​ Animalia (heterotrophic, ingest food) Woese’s Three-Domain System (1990) Developed by: Carl Woese​ Key Idea: Classification based on rRNA differences and genetic analysis. ​ Domains: 1.​ Bacteria (true bacteria, prokaryotic, peptidoglycan cell walls) 2.​ Archaea (prokaryotic, extreme environments, no peptidoglycan) 3.​ Eukarya (all eukaryotic organisms – includes Protista, Fungi, Plantae, and Animalia) Woese’s system replaced the Monera kingdom by splitting it into Bacteria and Archaea due to fundamental genetic and biochemical differences. 5.​ What is Bergey's manual? 6.​ How are bacterial unknowns identified in Bio 15 lab? Define: dichotomous key A dichotomous key is a tool used to identify organisms based on a series of paired statements or questions that lead the user to the correct classification. Each step presents two contrasting choices (e.g., "Has wings / No wings") until the organism is identified. Example: 1.​ a) Has feathers → Go to 2​ b) No feathers → Go to 3 2.​ a) Can fly → Falco peregrinus (Peregrine Falcon)​ b) Cannot fly → Struthio camelus (Ostrich) 3.​ a) Has scales → Go to 4​ b) No scales → Go to 5 7.​ List and briefly describe the advanced bacterial identification methods used in more sophisticated reference and research labs. DNA Sequence Analysis & Hybridization Probes ​ Uses genetic sequencing to identify bacteria by comparing DNA sequences to known databases. rRNA Analysis, Ribotyping ​ Examines ribosomal RNA (rRNA) genes to classify bacteria, as these sequences are highly conserved. GC Content Expressed as % ​ Measures the percentage of guanine (G) and cytosine (C) in bacterial DNA to help differentiate species. DNA Chips, Microarray Tests ​ Uses small DNA fragments on a chip to detect the presence of bacterial genes through hybridization. DNA "Fingerprinting" ​ Analyzes genetic variations using techniques like Restriction Fragment Length Polymorphism (RFLP) to distinguish bacterial strains. Polymerase Chain Reaction (PCR) ​ Amplifies specific DNA sequences, making it easier to detect bacterial DNA, even in small samples. Membrane Fatty Acid Analysis ​ Identifies bacteria by analyzing the composition of their fatty acids, which vary by species. Phage Susceptibility Testing ​ Uses bacteriophages (viruses that infect bacteria) to determine bacterial identity based on their susceptibility to specific phages. Fluorescent in situ Hybridization (FISH) ​ Uses fluorescent probes that bind to specific bacterial DNA sequences, allowing visualization under a fluorescence microscope. Chapter #11: The Prokaryotes No formal questions on this chapter. Simply flip through the pages, look at the figures, and notice the enormous diversity in types of prokaryotes! Chapter 5: Microbial Metabolism (Students note: there will be NO questions on the exam regarding the following metabolic pathways: photosynthesis, anaerobic respiration, pentose phosphate pathway, Entner-Doudoroff pathway, or organic molecule biosynthesis) 1.​ Define: metabolism, anabolism, catabolism. How is ATP involved in the relationship between them? Metabolism: Sum of all chemical reactions in a cell or an organism Catabolism: large compounds broken down, energy releasing Anabolic: large compounds built up, energy required Energy (ATP) from catabolic reactions used to drive anabolic reactions 2.​ Recognize the structure of ATP (see Figure 2.18) and be able to identify its major components and the location of high energy bonds. 3.​ List and define the 3 types of phosphorylation reactions used to generate ATP. Substrate-Level Phosphorylation ​ Definition: ATP is generated by the direct transfer of a phosphate group from a high-energy substrate to ADP. ​ Example: Occurs in glycolysis and the Krebs cycle. Oxidative Phosphorylation ​ Definition: ATP is produced using energy from electrons transferred through the electron transport chain (ETC), with oxygen as the final electron acceptor. ​ Example: Occurs in cellular respiration in mitochondria. Photophosphorylation ​ Definition: ATP is generated using light energy to drive electron transport and ATP synthesis. ​ Example: Occurs in photosynthesis within chloroplasts (light-dependent reactions). 4.​ Know the difference between oxidation and reduction reactions. What do co-enzymes like NAD+ and FADH2 do in these reactions? How are some dietary vitamins related to these co-enzymes? (Table 5.2) Oxidation vs. Reduction Reactions ​ Oxidation: The loss of electrons (or hydrogen atoms) from a molecule, often releasing energy. ​ Reduction: The gain of electrons (or hydrogen atoms), storing energy in molecules. ​ Redox Reactions: These two processes occur together; one molecule is oxidized while another is reduced. Role of Coenzymes (NAD⁺ & FADH₂) in Redox Reactions ​ NAD⁺ (Nicotinamide Adenine Dinucleotide) ○​ Acts as an electron carrier, accepting electrons (reduced to NADH) during glycolysis and the Krebs cycle. ○​ NADH then donates these electrons to the electron transport chain (ETC) to generate ATP. ​ FAD (Flavin Adenine Dinucleotide) ○​ Functions similarly but carries two electrons and two protons when reduced to FADH₂. ○​ FADH₂ transfers electrons to the ETC at a slightly lower energy level than NADH, generating less ATP per molecule. Dietary Vitamins Related to These Coenzymes NAD⁺ is derived from vitamin B₃ (Niacin). FAD is derived from vitamin B₂ (Riboflavin). These vitamins are essential in metabolism because they help synthesize coenzymes required for redox reactions. 5.​ Describe what biochemical/metabolic pathways are. Biochemical/metabolic pathways are a series of sequential reactions. compound A converted to compound B converted to compound C converted to compound D. 6.​ List the key features of the structure and function of enzymes. Be able to describe Figure 5.2. 7.​ Define: active site, substrate, product, coenzyme, cofactor. Active Site ​ The specific region on an enzyme where the substrate binds and the chemical reaction occurs. Substrate ​ The reactant molecule that binds to the enzyme’s active site and undergoes a chemical reaction. Product ​ The final molecule(s) formed after the enzyme catalyzes the reaction. Coenzyme ​ A non-protein organic molecule (often derived from vitamins) that assists enzymes by transferring electrons, hydrogen atoms, or functional groups (e.g., NAD⁺, FAD, Coenzyme A). Cofactor ​ A nonprotein helper that enhances enzyme activity, which can be a metal ion (e.g., Mg²⁺, Zn²⁺, Fe²⁺) or an organic coenzyme. 8.​ Describe how pH, temperature and substrate concentration affect enzyme activity. Know the following types of enzyme inhibition: competitive, allosteric, and feedback inhibition. Factors Affecting Enzyme Activity 1.​ pH ○​ Each enzyme has an optimal pH where it functions best. ○​ Too acidic or too basic environments can denature the enzyme, altering its active site and reducing activity. 2.​ Temperature ○​ Enzyme activity increases with temperature up to an optimal point. ○​ Beyond the optimal temperature, enzymes denature (lose shape and function). ○​ At low temperatures, enzyme activity slows due to reduced molecular movement. 3.​ Substrate Concentration ○​ Higher substrate concentration increases enzyme activity up to a saturation point, where all enzyme active sites are occupied. ○​ Beyond this, adding more substrate does not increase reaction rate. Types of Enzyme Inhibition 1.​ Competitive Inhibition ○​ A molecule competes with the substrate for the active site. ○​ Can be overcome by increasing substrate concentration. ○​ Example: Drugs like sulfa antibiotics block bacterial enzyme activity. 2.​ Allosteric Inhibition (Non-Competitive) ○​ An inhibitor binds to an allosteric site (not the active site), causing a shape change in the enzyme, making the active site less effective. ○​ Cannot be overcome by adding more substrate. 3.​ Feedback Inhibition ○​ The end product of a metabolic pathway inhibits an earlier enzyme in the same pathway. ○​ Helps regulate overproduction and maintain homeostasis. ○​ Example: ATP inhibits enzymes in glycolysis when energy levels are high. 9.​ Write out the overall, balanced reaction for the complete oxidation of glucose to carbon dioxide and water (= aerobic respiration) in prokaryotes. ​ ​ C6​H12​O6​+6O2​→6CO2​+6H2​O+ATP (energy) Glucose oxidized Oxygen reduced 10.​ Know the starting and ending compounds for each of the following metabolic pathways in prokaryotes: glycolysis, Kreb's cycle (include preparatory step), and electron transport (see Figure 5.17). 1. Glycolysis ​ Starting Compound: Glucose (C₆H₁₂O₆) ​ Ending Compounds: ○​ 2 Pyruvate (C₃H₄O₃) ○​ 2 ATP (net gain) ○​ 2 NADH 2. Krebs Cycle (Including Preparatory Step) Preparatory Step (Pyruvate Oxidation) ​ Starting Compound: 2 Pyruvate (from glycolysis) ​ Ending Compounds: ○​ 2 Acetyl-CoA ○​ 2 CO₂ ○​ 2 NADH Krebs Cycle (Citric Acid Cycle) ​ Starting Compound: Acetyl-CoA (enters cycle by combining with oxaloacetate) ​ Ending Compounds (per 2 Acetyl-CoA): ○​ 4 CO₂ ○​ 2 ATP (via substrate-level phosphorylation) ○​ 6 NADH ○​ 2 FADH₂ 3. Electron Transport Chain (ETC) & Oxidative Phosphorylation ​ Starting Compounds: ○​ 10 NADH (from glycolysis + Krebs cycle) ○​ 2 FADH₂ ○​ O₂ (final electron acceptor) ​ Ending Compounds: ○​ ATP (~34 ATP molecules produced) ○​ H₂O (oxygen is reduced to water) ○​ NAD⁺ and FAD (recycled back to glycolysis and Krebs cycle) 11.​ What is fermentation? How is it different from respiration? 12.​ List the end products of the following fermentation pathways: alcoholic, mixed acid, lactic acid, butanediol. Know how fermentation end products are used in the identification of microbial unknowns. Use of Fermentation End Products in Microbial Identification ​ Biochemical tests detect fermentation products to distinguish bacteria. ​ Examples: ○​ Methyl Red (MR) Test: Detects mixed acid fermentation (positive for E. coli). ○​ Voges-Proskauer (VP) Test: Detects butanediol fermentation (positive for Enterobacter). ○​ Lactose Fermentation Test: Used to differentiate lactose fermenters (e.g., E. coli) from non-fermenters (e.g., Salmonella) on MacConkey agar. 13.​ Define: chemotrophs, phototrophs, chemoheterotrophs, chemoautotrophs, photoheterotrophs, photoautotrophs (see Figure 5.28). Definitions of Metabolic Classifications 1.​ Chemotrophs – Organisms that obtain energy from chemical compounds (organic or inorganic) rather than light. 2.​ Phototrophs – Organisms that obtain energy from light (photosynthesis). 3.​ Chemoheterotrophs – Use organic molecules for both energy and carbon sources. ○​ Example: Animals, fungi, most bacteria (E. coli). 4.​ Chemoautotrophs – Use inorganic compounds for energy and CO₂ as a carbon source. ○​ Example: Nitrifying bacteria (Nitrosomonas). 5.​ Photoheterotrophs – Use light for energy, but obtain carbon from organic compounds rather than CO₂. ○​ Example: Purple non-sulfur bacteria. 6.​ Photoautotrophs – Use light for energy and CO₂ as a carbon source (photosynthesis). ○​ Example: Plants, cyanobacteria (Anabaena).