Medical Microbiology FINAL EXAM Study material PDF

Med Micro: FINAL EXAM Study material Unit 1-3 Will Be On Exam Unit 1 Unit 1 Lecture 8/23/24 What is a microbe? Microorganism (things you can't see with the naked eye) Microbes are ubiquitous Our body allows for colonization of microbes in the...

Med Micro: FINAL EXAM Study material Unit 1-3 Will Be On Exam Unit 1 Unit 1 Lecture 8/23/24 What is a microbe? Microorganism (things you can't see with the naked eye) Microbes are ubiquitous Our body allows for colonization of microbes in the gut but they keep other parts of the body sterile Terms that describe the relationships between species Mutualism- both species benefit Parasitism- one species benefits and the other is harmed Commensalism- one species benefits, other is not harmed History of infectious disease Florence Nightingale- she documented the significance of infection using quantitative approach This helped lead to epidemiology which is the study of disease Germ theory of disease: Koch establishes Bacillus anthracis as the cause of Anthrax (Koch showed that anthrax can be transmitted to rabbits using blood from infected animals and he characterized that bacteria as Bacillus anthracis). Koch postulates are used to determine if a particular microbe is the causative agent of a disease Steps in Koch postulates 1. The microbe is found in all cases of the disease but is absent from healthy individuals 2. Microbes are isolated from the diseased host and grown in pure culture  3. When the microbe is introduced into healthy, susceptible host, the same disease occurs 4. The same strain of microbe is obtained from the newly diseased host Pathogens can be divided into two pathogens Primary pathogens- cause disease in an otherwise healthy host. Opportunistic pathogens- not typically associated with disease Virulence- severity of disease associated with infection by a pathogen Filoviruses are extremely virulent pathogens. Infections commonly lead to death. LD50- evaluated by determining the amount of pathogen Invasion- growth inside of host cells (bacterial pathogen that has grown inside of the vacuole) Invasiveness- ability to spread in tissue (Clostridium that spreads through the gas filled spaces of muscle fibers) Host range- the species that a particular pathogen can infect ( Species that particular pathogen can infect) General mechanisms of Pathogenesis Avoidance (Avoid host defenses that are going to apart of a normal immune response)Adherence (They have to get inside the host and stick) Growth ( growth is associated with what's making an individual sick) Overview of pathogenesis Adherence: they must attach to their host Avoidance: they must avoid host defenses or rapid immune responses Gain nutrients from the host for growth Unit 1 Lecture 8-26-24 Pathogens- are microbes that cause disease Describing pathogens: primary or opportunistic Primary- can make a healthy individual sick Opportunistic- Immunocompromised state will get sick by pathogens Degree of virulence- how reliable does it make people ill Type of growth: -invasion (Invading cells) -invasiveness (spreading through tissues) -host range (can it affect only humans or animals) Fever is a sign of disease Phases of disease 1. Incubation 2. Prodromal- initial symptoms appear during this phase 3. Illness- high number of microbes compared to immune response of host 4. Decline- number of microbes go down 5. Convalescence- Symptoms of a disease- are things felt by the patient but difficult to measure. Signs of a disease - directly measurable or observable evidence of disease Localized infection- focal Widespread Infection- systemic Acute infection- appear rapidly Chronic infection - more slowly Nosocomial infection- acquired in hospital Iatrogenic- Transmitted by a health worker Infections may include multiple pathogens, or lead to secondary infections due to changing host defenses Modes of Transmission Indirect transmission- Microbes can be transmitted indirectly by inanimate objects (fomites), by vehicle transmission, or by an insect vector Direct transmission- Microbes can be transmitted by direct contact or by aerosolization Vehicle transmission- some microbes can be transmitted through contaminated fomites, food, water, or air Vertical transmission- Transmission of an infectious agent from an insect to its offspring Insect vectors- Microbes can be transmitted from animal to animal by insect vectors. Reservoirs are the primary source of a pathogen Zoonotic pathogens- can grown in animals or insects, as well as humans, and these hosts can act as the reservoir Carriers can harbor a pathogen without having disease symptoms Zika- cases have been reported around the world Endemic disease is present at a relatively constant level Epidemic disease indicates a large increase above the baseline level Pandemic disease is a worldwide epidemic Unit Lecture 8/28/24 Zika is acute infection Both direct and indirect Direct transmission- sex Indirect transmission- Mosquito vector Mother to fetus (vertical transmission) Portal of entry Vector borne illness- mosquito bites Portals of entry Entry via the eye- The conjunctiva is subject to infection by some organism carried there by fingers or air Oral route- Pathogens can be ingested (food-borne, waterborne, oral fecal). Respiratory route- Airborne pathogens can be inhaled Parenteral route- Pathogens can be injected into the bloodstream Genital or sexual transmission. Pathogens can enter via direct contact with genital mucosa or sexual transmission Entry through skin- skin can be colonized by some pathogens and penetrated by others. Wounds, too, offer pathogens access to the body’s interior. Influenza Portal of entry: Respiratory Why is the flu worse in the winter? during winter people spend more time indoors with the window sealed and they more likely to breathe the same air as somebody who has the virus, low levels of vitamin d and melatonin because days are shorter and it comprises our immune system, The virus survive better in cold climates and they can infect more people under those conditions. Youngest members of population and oldest people of the population when - are going to have some sort of immunocompromisation that is going to affect the way they handle the virus Young individuals like infants they don't have fully developed immune system Older individuals they have low thymic output when you get in your 60s Host Factors contributing to susceptibility to disease -Level of immunocompetence Influenced by age, genetics, behaviors (alcohol, smoking), disease Exposure to pathogens based on behaviors or occupations: healthcare, agricultural, recreation Emerging and re-emerging diseases Human activity increases exposure to the new vectors and reservoirs, population growth leading to deforestation and settlement Pathogen evolution may increase host range to include humans Areas of forest removal are associated with increased rate of malaria What effect might climate change have on exposure to vectors? Because climate change causes shifts in where people are living and where non human animals are living and they ultimately that leads to novel exposure to vectors that carry diseases that human may never had came in contact with before Microbial structures and Biomacromolecules Biomacromolecules create microbial structure and mediate all functions. Our immune system recognizes specific microbial biomacromolecules and the drug therapies we use are based on specific interactions with microbial biomacromolecules. We can distinguish eukaryotic and prokaryotic cells by their differences and similarities Differences: The eukaryotic has a clearly defined nucleus and the prokaryotic does not it has its chromosomal content that is free floating in the cell. Eukaryotic: Has membrane bounded organelles Prokaryotic doesn't have mitochondria Unit 1 Lecture 8-30-24 Microbial Structures and Biomacromolecules Biomacromolecules create microbial structures and mediate all functions of infection. Our immune system recognizes specific microbial biomacromolecules, and the drug therapies we use are based on specific interactions with microbial bio,macromolecules. Viruses are made of biomacromolecules Viruses cant replicate on their own Prokaryotes and Eukaryotes can replicate by binary fission or mitosis. Viruses are more simple in structure Carbohydrates are formed from saccharide monomers You can have various forms of these molecules ❖ You can have a straight chain form ❖ You can have alpha or beta glucose molecule ❖ You can use monosaccharides to go to disaccharides’ ❖ Polysaccharides provide important structural and energy storage molecules  ❖ Both are polymers of glucose, but differ in the type of glycosidic linkage between the monomers. Glycogen, produced in animals, is identical to starch, except that the branch points along the glucose polymer occur more frequently. Lipids ❖ Lipids are amphipathic molecules that assemble into layers in the presence of water ❖ Fatty acids have nonpolar hydrocarbon chains ❖ Phospholipids are made by linking fatty acids to polar head groups ❖ Phospholipids assemble into layers when water preferentially interacts with the head groups and not the non-polar fatty acids ❖ Cells produce phospholipids bilayers to form membrane barriers. DNA and RNA DNA is made of Adenine, Guanine, Cytosine, Thymine RNA uses Uracil instead of thymine Polynucleotides: nucleotides linked by phosphodiester bonds RNA: is single stranded DNA: is double stranded Genetic information is stored in the sequence of nucleotides in DNA This information is retrieved when it is copied into RNA and then used to direct the synthesis of specific proteins. DNA- serves as a template for RNA synthesis so you can continue to replicate and repair your DNA strands. Once you have RNA synthesis via transcription you can then synthesize protein via translation Proteins are assembled from amino acids which are linked together by peptide bonds Each amino acid has distinct properties Interactions between different regions of a polypeptide chain create characteristic helices and sheets. These fold into a final 3D shape which determines the function of that protein. Each protein has a unique series of amino acids, a unique shape and function Protein come in a wide variety of shapes that allow distinct functions There are as many as 2000 different proteins in a bacterial cell. Nucleoid region contains DNA Cytoplasm contain ribosome, peptide, rna Envelope contains lipopolysaccharide inner membrane The membrane provides a semipermeable barrier the cell regulate what comes inside and outside itself. Other functions include transport, secretion, environment, sensing, energy acquisition. The lipid bilayer of the cell membrane limits movement of molecules into and out of the cell. Study Guide Material: Zoey Lee ○ Unit 1: Study Questions Overview Of Microbes & Infectious Disease Identify the major types of microbes. What roles do they play in the biosphere? ○ Microbes → Living organism that requires microscope to be seen ○ Types of Microbes: Bacteria Algae Arachea Virus Eukaryotes Protists Fungi Protozoa ○ Biosphere → Found throughout Describe four ways that microbes are beneficial to humans. ○ Health Digestion Protection Food production Fermentation ○ Biotechnology Drugs Hormones Vaccines  ○ Bioremediation Detoxication? ○ Environment Energy capture → photosynthesis Geochemical cycling → Nitrogen fixation/cycle What types of relationships exist between species that live in the same place? ○ Symbiotic/symbiosis What are Koch's postulates? Why is the second step of his procedure critical to determining whether a microbe is the cause of a disease? ○ What are Koch’s Postulates 1. Microbe in all cases of disease, absent in healthy 2. Microbe isolation from host, grown in pure culture 3. Microbe in new host, same disease occurs 3. Same strain of microbe within new dead host ○ Why is the second step of his procedure critical to determining whether a microbe is the cause of a disease? If the microbe is unable to cause the same signs within the new host then that particular microbe is not the disease-causing factor By going the pure culture we are ruling out OTHER microbes & factors that COULD cause diseases Identify and define different categories of pathogens. What are the general steps in pathogen infection and how are they related to the symptoms/signs of disease? ○ Identify & Define Categories of Pathogens Pathogens → Organisms cause disease in host Primary Pathogens ○ Disease is fast-reacting Opportunistic Pathogens ○ Opportunity to strike, immune functioning ○ General Mechanisms 1. Adherence → Stick 2. Avoidance → Hide 3. Growth → Make ppl sick ○ General Steps in Pathogen Infection & How they are related to symtpoms/signs 1. Incubation Asymptomatic Adhering & Avoidance No sickness yet 2. Prodromal Increase microbes  Initial symptoms → Feeling off 3. Illness Clear distinction in microbes vs immune response Feeling the worst 4. Decline Immune responses start to beat the microbe rate Feeling better 5. Convalescent Feel perfectly fine BUT still are contagious Asymptomatic but still spreading microbes 6. Long term Reduce microbes Immune response = doubled and records microbe. Able to fight specific pathogen faster → Immune memory How would you describe infections in terms of timing of symptoms? Location of infection? Relationship to other infections? Source of infection? ○ How would you describe infections in terms of timing of symptoms? Acute Infections Infections in which symptoms develop rapidly; its course can be rapid/protracted ○ Symptoms appear rapidly Chronic Infections Symptoms develop gradually, weeks or months. Slow to resolve, 3+ months. ○ Symptoms develop slowly, resolve slowly Subacute Infections Symptoms take longer to develop but arise quickly compared to chronic Latent Infections Can occur AFTER acute infection; organism is present but symptoms don’t show till disease reappears. ○ Location Of Infections Focal Localized but spreads Systemic Widespread Mixed Multiple pathogens  Secondary infections Primary to secondary. Changing host defenses ○ Relationship to other infections Localized Stays in one place ○ Source Of Infection Nosocomial Infections → Acquired in-hospital Iatrogenic Infections → Transmitted by health care worker Provide at least two examples of direct and indirect transmission of a pathogen between individuals. Describe the relationship between pathogen resilience and disease transmission. ○ Examples & Explinaitons Indirect Transmission → Transmitted by inanimate objects (fomites) Sharing food Touching something after coughing ○ Vehicle Transmission → Insect to offspring Having babies ○ Insect Vector → Animal to animal/humans Caused by an insect vector Insect → Raccoon → Human Direct Transmission → Direct contact or by aerosolization Sneezing Influenza ○ Resilience & Disease Transmission Resilience → Withstands environmental stresses and survives LONGER even when outside a host. Higher chance of transmission opportunities Disease Transmission → Betters the spreading of the specific pathogen. Allowing for reproduction. Biomacromolecules, Cell Struc, Functions Name the different classes of biomacromolecules. List the monomer for each and explain how they are held together. What is the role of hydrogen bonding in each structure? List the functions of each class. Where are the different classes found in a bacterial cell? ○ Biomacromolecules → Microbial structure creatures + mediator for ALL functions Carbs → Glycosidic Linkage Proteins → Peptide Linkage  Nucleic Acids → Phosphodiester Linkage, sugar-phosphate backbone Lipids → Fatty Acid to polar head (glyceral) (Hydrophobic interactions?) ○ Name the different classes of biomacromolecules & Monomers + how they are held together Carbohydrates = True Polymers Structural Components ○ Monomers → Monosaccharides Glucose, Fructose, etc ○ Disaccharides → Joined together by hydroxal (OH) groups (hydrophilic) ○ Polysaccharides → Long chains help together by the glycosidic linkage (Binds carbs to one another) Functional Components ○ Provide important structural & energy storage ○ Can attach to certain lipids & proteins Polysaccharide Examples ○ Cellulose → Structural Support Polymers of glucose + glycosidic linkage Held together by hydrogen bonds Arranged on top of each other, like a wall Cell walls of plants ○ Starch → Energy Storage Monomers Polymers of glucose + glycosidic linkage Held together by glycosidic bonds Helical shape, branching. Found in potatoes Glycogen is the animal version, stored within muscles Proteins = True Polymers Monomers = Amino Acids ○ Linked together by the carboxyl groups (Peptide bonding) Oh → H → H2O REMOVED = Peptide link  ○ Amino Terminus OPPOSITE of Carboxyl terminal → Allows for the unique arrangement of amino acids, protein structure Polypeptides (proteins) ○ Assembled from amino acids and linked together by the peptide bonds ○ Each amino acid has a unique property which creates folding and characteristic of protein. ○ When these polypeptide chains interact with one another it can create helices OR sheets. Structures: Primary, secondary, tertiary, & quaternary ○ Primary structure: Amino Acid chains, no particular arrangement ○ Secondary structure: Linked by hydrogen bonds (not very strong) α → Alpha helix ß → Beta-pleated sheets ○ Tertiary structure: Alpha helix & Beta-pleated sheets create a 3D pattern. Linked by Disulfide bond → 2 sulfur groups Ionic bond → Negative & Positive charges ○ Quaternary Structure Consists of more than one polypeptide chain Functional Component: ○ Structural support, enzyme production, cell division, growth, etc Lipids = NOT true polymers Functional Components: ○ Fatty Acids: Energy storage molecules Building block of cell membranes Insulation  Membrane barriers Energy storage Cushion organs Protein channels within membrane Changes permeability Phospholipids: ○ Composed of 2 fatty acids connected to glycerol and phosphate group. This phosphate is negatively charged making the hydrophilic head and hydrophobic tails. ○ Assemble into laters when water interacts with hydrophilic head. Make selectable permeable membranes ○ Amphipathic molecules!!! Made up of Polar head → Hydrophilic Nonpolar tail → Hydrophobic Allows for the assembly of layers with the presence of water Composes membrane barriers Triglyceride ○ Phosphate group is REMOVED allowing for the addition of another fatty acids → 3 fatty acids to glycerol molecule ○ HYDROPHOBIC ○ Allows for additional energy storage Saturated Solid @ room temperature Single bond Unsaturated Liquid @ room temperature Double/Triple bond Nucleic Acids = True Polymers Functional Components: ○ Store & Transmit genetic information Nucleotides = Monomers ○ Composed of 5-carbon sugar, phosphate group, and NUCLEOBASE ○ Nucleobase → Variation  Purines = 2 rings Adenine (RNA & DNA) Guanine (RNA & DNA) Pyrimidines = 1 ring Cytosine (RNA & DNA) Thymine (DNA) Uracil (RNA) Polynucleotides ○ Linked by phosphodiester bonds. Creates a sugar-phosphate backbone 5’ & 3’ 5’ is the phosphate (H) → 3’ is the hydroxal (OH) ← ○ Ribose → RNA ○ Deoxyribose → DNA Structures ○ DNA → Replication Double helix Thymine Complementary pairing → Hydrogen bonds Genetic information is stored within the sequence of nucleotides ○ RNA → Protein Synthesis Single-stranded Uracil Genetic information is ‘copied’ into RNA which will be used for protein synthesis Amino acids → Polymers → Proteins What biomacromolecules are found in Ebola virus? (Outside research may be needed for this!) ○ Ebola Virus ALL biomacromolecules are found within Ebola virus They aren’t able to reproduce without a host What functions does the membrane provide for a bacterial cell? Describe the characteristics of molecules that cannot pass through a lipid bilayer. ○ Bacteria Membrane Functions Barriers & Protection Selective permeability Transport Structural Support  ○ Molecules CAN’T easily pass through lipid bilayer Size → Large Polarity → Uneven distribution of charges Charged → Na+, K+, Cl- Hydrophilic → Water-attracted molecules are hard to pass through a hydrophobic bilayer What is osmolarity and what effect does it have on cells? Under what conditions does a cell shrink? Under what conditions does it swell? ○ Osmolarity/Osmosis → Type of diffusion, dealing with the concentration gradients ○ Effects On Cells Isotonic No Change Equal amount of solute within cell and outside cell ○ Saline Solution/IV Hypertonic Shrinkage VERY salty Solute is greater outside cell compared to solute within cell Dehydration Hypotonic Blows Up Solute outside cell is LOW compared to solute within cell Water rapidly flows into cell and amount makes the cell burst What processes do cells use to bring nutrient molecules inside? What mechanisms are used to handle larger nutrient molecules? ○ Process Of Nutrients Within Cell Passive Transport Diffusion → High to low concentration Facilitated Diffusion → Specific transport proteins embedded within membrane. Semi-permeable. Active Transport Coupled Transport ○ NO ATP ○ Open channel & pick up off concentration gradient, moving against concentration gradient ○ Energy ion gradient to move against concentration gradient  ○ Piggybacking Symport: 2 molecules within cell For every sugar molecule you want within the cell you bring a salt molecule Antiport: 1 in and 1 out cell Trading Sugar in and Salt out ABC Transport ○ USES ATP DIRECTLY ○ Target molecules are bound to specific proteins which allow transport Endocytosis Receptors & Vesicles are engulfed and brought into the cell Cell engulf large molecule Vesicle Transport Large molecules enclosed within vesicle are fused with membrane Draw a cartoon of a peptidoglycan cell wall indicating the subunits of the glycan chains and showing the location of interchain crosslinks. Describe the function of the cell wall and identify an environmental condition where it is essential. Describe specifically what penicillin does that affects the cell wall. ○ Glycan Chains → Linked by peptide cross bridges Peptides = very strong proteins ○ Function Provides structural support & rigidity in cell wall ○ Environmental conditions Important for osmotic pressure regulation Allows the cell wall NOT to blow up during hypotonic osmosis ○ Penicillin Breaks apart the peptide cross bridges which then fully disrupts the cell wall. Breaking all the glycan chains Where is the genome found inside a bacterial cell? How is this structure formed and why is the formation of the structure necessary? ○ Found Genome is found within the nucleoid region ○ Structure Single, circular DNA molecules ○ Formation  Supercoiled to fit within the cell & protects genetic material Identify different bacterial cell shapes and "arrangements". What determines different arrangements? ○ Cell Shape → Dependent on cytoskeletal interaction with membrane Different Types Of Bacterial Shapes: Coccus → Circular Rod/Bacillus → Straight Vibrio → Whiplike/hairlike area at the end of rod Spirochete → Elongates, spaghetti ○ Bacterial Arrangement Determined by attachment of cells FOLLOWING division. Depends on where division plane changes between generations Strepto— ○ Straight chain ○ Plain division in the middle Sarcina— ○ Cube ○ Perpendicular plane Division in 2 planes North-South East-West Staphylo— ○ Grape-Like ○ Several different cross-sections ○ Everywhere What are the differences in envelope structure that distinguish Gram-positive and Gram- negative bacteria? ○ Gram-positive Outside → Inside Cell Peptidoglycan (cell wall) ** THICK Cell membrane ○ Gram-negative Outside → Inside Cell Outer membrane** Peptidoglycan Periplasmic Space Cell Membrane List the steps of the Gram staining procedure. If a sample has pink cells present at the end of the procedure, what does that tell you? Predict the  effect on your results if you leave out the alcohol wash, or if you forget the Safranin counter stain. ○ Steps Of Gram Staining 1. Add methanol (clear) 2. Add crystal violet stain (purple) 3. Add iodine (purple) 4. Wash w/ethanol (Gram+, purple; Gram-, clear) 5. Add safranin counterstain (Gram+, purple; Gram-, pink) List 3 extracellular appendages that might be found on a bacterial cell. What are they made out of? What are their functions? ○ Flagella: Made of: Flagellin protein. Function: Movement. ○ Pili (Fimbriae): Made of: Pilin protein. Function: Attachment to surfaces and other cells. ○ Capsules: Made of: Polysaccharides or proteins. Function: Protection against phagocytosis and desiccation. Where are flagella attached to bacterial cells? What is their source of energy? How are they controlled so that bacterial movement is non-random? ○ Attachment: Anchored in the cell membrane and cell wall. ○ Source of Energy: Proton motive force (protons moving across the membrane). ○ Control: Rotational movement is controlled by the direction of proton flow and response to environmental signals (chemotaxis). Draw both a bacterial and eukaryotic cell. Label at least 5 structures on both. What structures are involved in gene expression? Protein secretion? Digestion? Movement? ○ Bacterial Cell: Structures: Plasma membrane, cell wall, nucleoid, ribosomes, flagella. ○ Eukaryotic Cell: Structures: Plasma membrane, nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, ribosomes. ○ Gene Expression: Bacterial: Ribosomes, nucleoid. Eukaryotic: Nucleus (transcription), ribosomes (translation). ○ Protein Secretion: Bacterial: Membrane proteins and secretion systems.  Eukaryotic: Endoplasmic reticulum, Golgi apparatus, vesicles. ○ Digestion: Bacterial: Cytoplasm (some enzymatic activity). Eukaryotic: Lysosomes, endosomes. ○ Movement: Bacterial: Flagella. Eukaryotic: Cilia, flagella (more complex structure). Compare and contrast bacterial and eukaryotic cells – what characteristics do they share? What are their differences? ○ Shared Characteristics: Plasma membrane. DNA as genetic material. Ribosomes for protein synthesis. ○ Differences: Bacterial Cells: No nucleus. Single circular DNA molecule. Smaller size. Simple internal structure. ○ Eukaryotic Cells: Nucleus present. Multiple linear DNA molecules. Larger size. Complex internal organelles (e.g., mitochondria, endoplasmic reticulum). ○ Unit 2: Study Questions Microbial Growth What growth requirements are shared by all cells? What term describes a growth requirement that is specific to a species (not shared with most other species)? Describe how these specific growth requirements can be used in the identification of pathogens. Explain the relationship between an organism’s habitat and its growth requirements. What prediction would you make about a pathogen’s reservoir? ○ Growth Requirements + Terms Carbon → elements/nutrients Auto → CO2 fixed & assembled into organic molecules Hetero → Organic molecules catabolized and anabolized Energy Source Photo → Photosynthesizing Chemo → Electron donor oxidized ○ Organotrophy (aerobic)  Organic molecules donate to O2 ○ Oranotrophy (aneronic) Organic molecules donate to other molecules ○ Lithotrophy (aerobic) Inorganic molecules donate to O2 ○ Lithotrophy (anerboic) Inorganic molecules donate to other molecules ○ Identification Of Pathogen Organisms that are Autophototrophs will NOT be pathogens Heterochemotrophs WILL be pathogens ○ Habitat + Growth Requiremirements Habitats can be indicators of growth requirements such as carbon source, growth factors, and oxygen presence. Shigella, blood diarrhea, human intestine, NAD (nicotinamide) ○ What predictions can be made about the pathogen’s reservoir? Based on those relationships Oxygen Growth factors Aerobic VS anaerobic ○ Reservoir → where the organism can live and thrive Living host ○ Environment → Abitotic favors, ecosystem Soil Gut This is the kinda microbe Where can we find it in Reservoir → Glossary within the textbook What are the phases of growth of a bacterial population? How are the cells and the environmental conditions different in the different phases? What distinguishes continuous and batch culture? ○ Phases Of Growth Lag → Flat Line NOT dividing rapidly, Adhering & avoiding Getting comfortable with the environment Log (Exponential) → HUGE growth Positive increase in cell division  Nutrients & space at max Stationary → Platoe Constant Losing resources Higher toxicity Death → Decline (negative) Higher amount cells dying Negative Exponential ○ How are cells & environment conditions different in each phase? Lag Cells = getting used to environment/adhering + Few cells Environment = High nutrients + High space Log Cells = Used to environment + MANY cells Environment = Constant nutrients + Max space Stationary Cells = @ Threshold Environment = Max nutrients + Max space + Toxic products increase Death Cells = Depleting Environment = Maxed out + Resources low ○ What distinguishes continuous and batch culture? *** WITHIN SLIDES *** List 3 environmental parameters that change for a gastrointestinal pathogen as it is ingested. What terms are used to classify microbes based on their preferred habitat? ○ Environmental Parameters Change For Gastrointestinal Pathogen pH → Decrease Temperature → Change Osmolarity → Salt presence increases ○ Terms classifying microbes Temperature (4) Hyperthermophile ○ Above 80C/176F Thermophile ○ 50C/122F → 80C/176F *** Mesophile ○ 15C/59F → 45C/113F Psychrophile ○ BELOW 15C/59F pH (3) Alkaliphile  ○ Above 9 Basic Neutralophile ○ Between 5-8 Neutral Acidophile ○ Below 3 Acidic Osmolarity (1) Halophile ○ HIGH salt ○ Greater than 2 Describe 4 different ways that microbes can be classified in terms of their relationship to oxygen. Explain specifically how oxygen can be essential for some organisms and lethal for others. ○ Oxygen Strict Aerobe ONLY O2 Facultative Mircobe With Or Without O2 Microaerophile Small amount O2 Strict Anaerobe NO O2 What are the characteristics of a biofilm? What is the difference between a biofilm and a capsule? What advantage does a cell gain by living in a biofilm? What is the role of cell density in biofilm formation? ○ Characteristics Of Biofilms Community-based Work alongside together Exopolysaccharides Matrix Retains nutrients Protects cells from the environment Structural support for biofilm towers Substrate for more bacterial cells Highly resistant Surface Attachment Grow on solid surfaces ○ Catheter tubing ○ In-dwelling medical devices Adhere to surface Structure The complex community of microbes adhering to the surface forms a thick & sticky slime layer  Resistance Antibiotics Immune responses Difficult to treat ○ Difference Between Biofilm & Capsule Structural Differences Biofilm: ○ Multiple cellular communities ○ Numerous cells ○ Exopolysaccharides Matrix Capsule: ○ Tightly adherent coating ○ Made up of proteins → Glycocalyx ○ Defined layer of polysaccharides/proteins surrounding a singular microbial cell Provides protection Adhesion Function Biofilm: ○ Community-based ○ Enhance Survival Communication Sharing resources ○ Sharing energy accusations ○ Sharing information Sex Pili Capsule: ○ Protect individual cells ○ Prevent phagocytosis Phagocytosis → Specialized process where they ingest or engulf other cells or particles Special form of endocytosis First line of defense ○ Advantages Of Living In Biofilm Resistance Resilient to antibiotics Nutrients Available Trap nutrients More efficient exchange Cooperation Share resources Metabolic products  Protection Exopolysaccharide matrix Stability Microbial growth ○ Role Of Cell Density In Biofilm Formation Quorum Sensing Bacteria communicate through signaling molecules Density increases = produce signals to coordinate behavior ○ Biofilm formation Allows for the production of the biofilm ○ Way that bacteria cells can sense at least enough of cells around to start ramping up more. Qurum → Min amount of people within the meeting for the meeting to happen ○ Cell density → Positive feedback loop ATP → NEGATIVE FEEDBACK LOOP What are the characteristics of an endospore? What is its significance for those bacteria that produce them? How do environmental conditions influence biofilm and endospore formation? What is the role of biofilms and endospores in virulence and pathogenesis? ○ Characteristics Of Endospores Dormant Protective Coat Inactivity Genetic Material Everything from the mother cell ○ Significance For Bacteria Survival Survive environmental stressors Resistance to UV Dispersal Wind, water, and animal vectors, facilitate the spread of bacterial species Reactivation Favorable conditions ○ Moisture ○ Nutrients Germination Resuming normal metabolic activity ○ Environmental Conditions Influencing Biofilm & Endospore Formation Nutrients Overall availability ○ Limited nutrients → Endospore formation ○ High nutrients → Biofilm development Stress Factors Environmental ○ Endospores High temperature ○ Biofilm Cell density (more cells) Surface interaction Signal Molecules Communication ○ Biofilms Quorum sensing Cell density increase = change in promotion of biofilm development ○ Endospores Stress signals Harsh environment → High temperature No nutrients ○ Role Of Biofilms & Endospores In Virulence & Pathogenesis Biofilms Chronic Infections ○ Found on wounds/medical devices Protective Resistance to antibiotics Colonization ○ Adhere to host tissues/surfaces ○ Increase ability to establish infection Immune Evasion ○ Exopolysaccharide Matrix shields bacteria from the host immune system ○ Difficult for immune cells + antibodies reach bacteria Endospores Survival Of Pathogen  ○ Pathogenic bacteria survive in harsh environments until they are able to infect a host Transmission ○ Dormant in environment ○ Ready to germinate Get into the host Once it gets wet it'll reactivate ○ Cause disease when ingested/introduced into suitable host Resistance To Treatment ○ Resistant to disinfectants + antibiotics ○ Complicates treatment efforts → Allows for the weaponization of the pathogen ○ Contributing to the persistence + spreading of infection Bioenergetics Identify external sources of energy that are used by microbes, as well as energy carriers and other immediately available sources of energy that that microbial cells use for growth processes. Sources of energy Phototrophs use light Chemotrophs are oxidized Organotrophy: organic molecules donate e- Lithotrophy: inorganic molecules donate e- (iron nitrogen, etc) Energy Carries NADH, H+, FADH (ATP Synthesis and Glycolysis) Immediate available sources? Solar energy Primary producers→ Autotrophs Inorganic → Iron, nitrogen What determines enzyme specificity? What do enzymes do that enhances chemical reactions? ○ Enzyme specificity Binding Sites and shape Enzyme → chemical reactions ○ Reduces activation energy (uses less energy) Catabolysizes reaction Catabolic reactions = endergonic (takes energy) ○ Ice absorbing heat How is fermentation related to glycolysis? How is the production of fermentation products useful to the cell? ○ Relation to glycolysis  Generates little ATP Needs NAD+ ->NADH Doesn’t need O2 BUT can grow in the presence of O2 ○ Useful products to the cell? Pyruvate which allows regeneration of NAD Compare and contrast ATP, NADH, and co-­enzyme A. ○ NADH= energy carrier ○ ATP= energy bank ○ Co-enzyme A= attaches to acetyl which triggers Krebs cycle Compare and contrast the mechanism of ATP generation during fermentative growth and respiration. ○ Fermentation 2 ATP More waste products Can process in presence of O2 BUT does not use it Organic molecules=final e- acceptor ○ Respiration 34 ATP Requires Krebs cycle Uses ETS Inorganic AND O2 molecules=final e- acceptor Describe how oxygen is used in aerobic respiration. What are the metabolic sources of carbon dioxide and water? ○ O2 is final e- acceptor ○ CO2 is produced when pyruvate turnes into acetyl Co-A ○ H2O is a product of adp-> atp Draw a flow diagram, or make an outline of events, that shows movement of energy from food molecules (glucose) to ATP during respiration. Draw a second flow diagram that shows the movement of electrons during respiration starting with food molecules. How are these diagrams similar? How are they different? ○ Similarities?differences  Compare aerobic and anaerobic respiration: what is different about these catabolic processes? What are the specific requirements of cells growing by anaerobic respiration? ○ Aerobic respiration: Uses O2 as final e- acceptor ○ Anaerobic respiration: Uses anything BUT O2 as a final e- acceptor (NO3, CO3, SO4) ○ Requirement for anaerobic respiration: - Specific oxidoreductase to pull high energy e- from inorganic molecules For microbes that are growing by lithotrophy, what is their source of energy (give an example), and how is ATP made? ○ Inorganic sources of molecules are sources of energy ○ How ATP works: pulled e- from inorganic molecules to power protons to leave the cell and power proton gradient to make ATP Genome Replication, Mutation, PCR, Gene Expression How are the genome structures of prokaryotes and eukaryotes different? ○ Prokaryotes: Circular chromosome Nucleoid region NOT membrane-bound Plasmids Circular DNA molecules Carry genes → Antibiotic resistance ○ Eukaryotes: Linear chromosomes Membrane-Bound nucleus Chromatin Structure DNA wrapped around proteins → Complex called chromatin ○ Helps regulate gene expression & DNA replication Explain how "base pairing rules" are related to "semiconservative replication" of DNA. ○ Base pairing rules → Specific pairing nitrogenous bases in DNA Adenine - Thymine (DNA) → 2 Hydrogen Bonds Adenine - Uracil (RNA) Cytosine - Guanine → 3 Hydrogen Bonds ○ Semiconservative Replication The mechanism by which DNA is duplicated Two strands of double helix are separated The original strand serves as a template for the synthesis of new complementary strands ○ Relationship Between Base Pairing & Semiconservative Replication  Template Function Original DNA strand serves as a template during replication Base pairing rules ensure correct nucleotides are added to the new strands BASED on sequence of template strands ○ Parent strand → ATCG ○ Daughter strand → TAGC Complementary Strands End of replication, the new double helix consists of one original strand and one newly synthesized strand ○ Semiconservative replication Original= Parental Newly Synthesized = Daughter Each new DNA molecule retains one of original strands, maintaining genetic continuity & fidelity Accuracy & Fidelity Base pairing rules = accuracy of DNA replication Specificity pairing minimizes chance of error during replication ○ Reduce mutation ○ Ensure genetic information accurately copes and passes to the daughter cell Draw a DNA replication fork; identify the polynucleotides and protein components. Describe the specific roles of the individual protein components in DNA replication. ○ Replication Fork Structure → Two strands of DNA separated Leading Strand ○ 5’ to 3’ ○ TOWARD fork Lagging Strand ○ 3’ to 5’ ○ AWAY from fork ○ Created in segments → Okazaki Fragments Polynucleotides Repeating units of nucleotides ○ Adenine ○ Thymine ○ Cytosine  ○ Guanine Bases on leading + lagging will pair with complementary bases ○ A–T ○ C–G ○ Protein Components + Roles Helicase Unwinds double-strands @ replication fork Separating two strands by breaking hydrogen bonds between base pairs CREATES replication fork ○ Zipper → Opens and closes Primase Synthesizes short RNA primer provides starting point for DNA polymerase Primer is necessary because DNA polymerase CANNOT initiate synthesis on its own DNA polymerase Synthesize new DNA strands by adding nucleotides complementary to template strands Add nucleotides in 5’ to 3’ direction ○ Leading Strand Continuous synthesize of the leading strand ○ Lagging Strand Synthesizes Okazaki fragments in a discontinuous manner Fragments DNA Ligase Role: ○ Joins Okazaki fragments on lagging strand by sealing the nicks in sugar-phosphate backbone ○ Forming continuous DNA strand ○ Repair and Okazaki → Seller What specifically will happen if DNA polymerase is inaccurate during DNA synthesis? Explain how this inaccuracy might affect the organism. ○ Mutation ○ It can be beneficial, harmful, or irrelevant depending on what protein it makes Describe different types of mutations in physical and genetic terms. Provide examples of different causes of mutations. How will different types of mutations alter gene products? ○ Physical  Substitution: Replacing a singular nucleotide Deletion: Deleting a nucleotide from the sequence Insertion: Adding a nucleotide that was not there originally ○ Coding Missense: Changing the codon which changes the protein Nonsense: Replacing an amino acid that makes the protein nonfunctional Frameshift: shift in the reading frame changes the protein which usually makes protein nonfunctional What is meant by 'sensitivity' and 'specificity' in a detection assay? ○ Sensitivity: - The Polymerase Chain Reaction can detect small amounts of DNA ○ Specificity: - Recognize unique DNA Identify the individual steps of the PCR assay and describe what occurs during each step. ○ 1. Denaturation: Heating the DNA to unwind and split the strand ○ 2. Annealing: Adding in the new primers and cooling down the DNA to let the primers stick ○ 3. Extension: Taq polymerase duplicates DNA based on the new prime end Side note: Taq polymerase is generally from an extremophile How is DNA synthesis in the Polymerase Chain reaction similar to, or different from, DNA synthesis during genome replication in cells? ○ PCR Made in a lab ○ Genome replication Within cells