Unit 4 6A.pdf

# Pathogens and their characteristics This section provides an overview of various pathogens, focusing on viruses and bacteria, detailing their structures, genetic material, and classifications. ### 1.1 Viruses Viruses are among the smallest organisms, though they are not considered cells. They are comprised of genetic material and proteins that direct the host cell's biochemical processes [5](#page=5). #### 1.1.1 General viral structure All viruses possess a protein coat, known as a capsid, which is made up of repeating protein subunits called capsomeres. Within the capsid lies the virus's genetic material, which can be either DNA or RNA. Additionally, viruses have virus attachment particles (VAPs), which are specific proteins (antigens) that bind to target proteins on the host cell's surface membrane. Some viruses are also surrounded by a lipid envelope, derived from the host cell's membranes, which aids in the transfer of viral components to host cells without rendering them vulnerable; however, not all viruses have this envelope [1](#page=1) [5](#page=5). #### 1.1.2 Classification of viruses Viruses are primarily classified based on their genetic material: * **DNA viruses**: These viruses utilize DNA as their genetic material. The viral DNA serves as a template for the synthesis of new viral DNA and messenger RNA (mRNA) for the production of viral proteins. Examples include smallpox viruses, adenoviruses, and bacteriophages [1](#page=1) [5](#page=5). * **RNA viruses**: These viruses have RNA as their genetic material. They are more prone to mutation than DNA viruses, partly due to having only a single strand of RNA. RNA viruses do not produce DNA. Examples include Tobacco Mosaic Viruses (TMV), Ebola fever, polio, measles, and influenza [1](#page=1) [5](#page=5). #### 1.1.3 Special types of viruses * **Retroviruses**: A specialized category of RNA viruses that have a unique replication cycle. They control the host cell to produce DNA that corresponds to their viral RNA genome. This viral DNA is then inserted into the host cell's DNA. This process is facilitated by an enzyme called reverse transcriptase, which is synthesized during the retrovirus's life cycle. Human Immunodeficiency Virus (HIV), the virus that causes AIDS, is a well-known example of a retrovirus [1](#page=1). * **Provirus**: Refers to viral DNA that has been integrated into the host cell's genome during the lysogenic pathway of viral reproduction. This state allows the virus to remain latent within the host cell, where it can exist without adversely affecting the host during a period known as lysogeny [1](#page=1). #### 1.1.4 Viral reproduction and cell damage * **Lysis**: This refers to the bursting of host cells, often due to the action of enzymes like lysozyme [1](#page=1). * **Exocytosis**: An energy-requiring process by which a vesicle within the cell fuses with the cell's surface membrane, releasing its contents to the outside of the cell [1](#page=1). ### 1.2 Bacteria Bacteria are single-celled microorganisms that possess a distinct cellular structure [4](#page=4). #### 1.2.1 Common bacterial structures All bacteria share the following components: * **Cell wall**: Contains peptidoglycan. Gram-positive bacteria have a thicker layer of peptidoglycan in their cell walls, whereas Gram-negative bacteria have a thinner cell wall, which can cause staining to leak out [4](#page=4). * **Cell surface membrane**: Encloses the cytoplasm [4](#page=4). * **Nucleoid**: Contains a single, circular strand of DNA [4](#page=4). * **70S ribosomes**: Sites for protein synthesis [4](#page=4). #### 1.2.2 Optional bacterial structures Some bacteria may also possess additional structures: * **Pili**: Threadlike projections extending from the cell wall that enable bacteria to attach to other cells or surfaces [4](#page=4). * **Flagella**: Used for locomotion [4](#page=4). * **Capsule/slime layer**: A sticky substance located outside the cell wall that provides protection [4](#page=4). * **Mesosomes**: Internal extensions of the cell membrane that fold into the cytoplasm and are involved in respiration [4](#page=4). * **Plasmids**: Small, circular pieces of DNA that are separate from the main chromosomal DNA and often code for specific characteristics of the bacterial phenotype [1](#page=1) [4](#page=4). ### 1.3 Pathogens and disease Pathogens are defined as microorganisms that cause diseases [1](#page=1). #### 1.3.1 Transmission of pathogens * **Vector**: A living organism or an environmental factor that transmits pathogens from one host to another [1](#page=1). --- # Viral and bacterial reproduction and infection cycles This topic details the distinct mechanisms by which viruses and bacteria replicate and infect host organisms, covering viral lytic and lysogenic pathways, bacterial binary fission, and bacterial growth phases [6](#page=6) [8](#page=8) [9](#page=9). ### 2.1 Viral infection cycles Viruses are obligate intracellular parasites that require a host cell to replicate. They employ different strategies to achieve this, broadly categorized into the lytic and lysogenic pathways [6](#page=6). #### 2.1.1 Retroviruses Retroviruses are a special type of RNA virus characterized by their use of the enzyme reverse transcriptase [6](#page=6). * **Structure:** They possess a protein capsid and a lipid envelope [6](#page=6). * **Replication Mechanism:** Their single strand of viral RNA directs the synthesis of reverse transcriptase. This enzyme is crucial as it transcribes viral RNA into DNA, a process opposite to the host cell's normal transcription (DNA to RNA) [6](#page=6). * **Integration and Latency:** The synthesized viral DNA is then inserted into the host cell's DNA, becoming a provirus. This proviral DNA acts as a template for producing messenger RNA (mRNA) and viral proteins [6](#page=6). * **Long-term Infection:** The integration of viral DNA into the host genome allows for persistent, long-term infections, as the viral genetic material is replicated along with the host's DNA during cell division [6](#page=6). * **Example:** Human immunodeficiency virus (HIV) is a well-known example of a retrovirus [6](#page=6). #### 2.1.2 Lysogenic pathway The lysogenic pathway is a mode of viral replication characteristic of retroviruses and DNA viruses, allowing for a latent period of infection [6](#page=6). 1. **Provirus Integration:** The viral DNA is inserted into the host cell's genome [6](#page=6). 2. **Repressor Protein Action:** Viral genes code for a repressor protein that inhibits the transcription and translation of other viral genes, effectively preventing the production of new viral components [6](#page=6). 3. **Latency and Replication:** As the host cell replicates its own DNA, the integrated viral DNA is also copied, leading to a state of latency where the virus is dormant within the host [6](#page=6). 4. **Activation:** Viruses in the lysogenic state can become activated and transition to the lytic pathway. This activation can be triggered by cellular damage or a depletion of nutrients within the host cell [6](#page=6). #### 2.1.3 Lytic pathway The lytic pathway is a more direct and destructive mode of viral replication that culminates in the lysis of the host cell [6](#page=6). 1. **Viral Component Synthesis:** Viral DNA is replicated to produce numerous copies of new viral genetic material [6](#page=6). 2. **Assembly:** These replicated viral components, along with synthesized viral proteins, are assembled into mature, infectious virus particles within the host cell [6](#page=6). 3. **Lysis and Release:** The host cell ultimately bursts (lysis), releasing a large number of progeny viruses into the environment [6](#page=6). 4. **Infection of New Hosts:** These released viruses are then free to infect new, susceptible host cells, initiating further rounds of infection [6](#page=6). 5. **Disease Manifestation:** The lytic pathway typically results in observable disease symptoms due to the widespread damage and death of host cells [6](#page=6). ### 2.2 Bacterial reproduction and growth Bacteria primarily reproduce asexually through a process called binary fission. Their growth can be characterized by distinct phases represented in a bacterial growth curve [8](#page=8) [9](#page=9). #### 2.2.1 Binary fission Binary fission is the fundamental mechanism by which bacteria multiply [8](#page=8). * **Process:** Once a bacterium reaches a certain size, it undergoes DNA replication. The DNA can be held in place by mesosomes, if present. The cell then elongates and divides into two identical daughter cells [8](#page=8). * **Generation Time:** The time required for a bacterial cell to divide into two is known as the generation time [8](#page=8). #### 2.2.2 Bacterial growth curves Bacterial growth is often depicted graphically as a growth curve, which illustrates the changes in the number of viable bacterial cells over time. A logarithmic scale is typically used for the y-axis because the difference in cell numbers between the smallest and largest populations can be extremely large, making a linear scale impractical. This logarithmic representation also makes it easier to assess the rate of bacterial growth and the steepness of the growth gradient [8](#page=8). The bacterial growth curve is typically divided into four distinct phases [9](#page=9): * **Lag phase:** In this initial phase, bacteria are adapting to their new environment. Their reproduction rate is low as they adjust their metabolic machinery [9](#page=9). * **Log/exponential phase:** During this phase, bacteria exhibit their maximum growth rate. Cells repeatedly double within a given time period, utilizing available nutrients [9](#page=9). * **Stationary phase:** At this point, the total growth rate becomes zero. The rate of cell division is equal to the rate at which cells are dying. This equilibrium is usually reached due to limited nutrient availability or the accumulation of toxic waste products [9](#page=9). * **Death/decline phase:** In the final phase, reproduction has nearly ceased. The death rate of cells begins to increase, leading to a net decrease in the viable bacterial population [9](#page=9). #### 2.2.3 Exponential growth rate calculation To quantify the rate of bacterial population increase, an exponential growth rate can be calculated. The formula provided is [8](#page=8): $$k = \frac{\log_{10}N_t - \log_{10}N_0}{\log_{10}2 \times t}$$ Where: * $k$ represents the specific growth rate constant. * $N_t$ is the number of bacteria at time $t$. * $N_0$ is the initial number of bacteria. * $t$ is the time elapsed [8](#page=8). > **Tip:** Understanding the bacterial growth curve is crucial for fields like food preservation, antibiotic treatment, and industrial fermentation, as it dictates the optimal conditions and timing for manipulating bacterial populations. --- # Methods for culturing and measuring microbial growth This section outlines essential techniques for growing and quantifying microorganisms, covering aseptic practices, growth media, and various measurement methods [10](#page=10). ### 3.1 Purpose of microbial techniques Microorganisms are typically only visible under a microscope. To culture them effectively, they require specific conditions such as oxygen, nutrients, an optimal pH, and a favourable temperature. Culturing must be done with care due to the risk of mutations that could lead to pathogenic strains, or contamination of the investigated culture by pathogenic bacteria [10](#page=10). ### 3.2 Aseptic techniques Aseptic techniques are crucial to prevent the contamination of cultures and to stop microorganisms from escaping into the environment. Key practices include [10](#page=10): * Washing hands thoroughly [10](#page=10). * Sterilising all equipment and disinfecting surfaces with ethanol before culturing [10](#page=10). * Using a Bunsen burner to heat the air, which kills any microorganisms present [10](#page=10). * Keeping cultures contained within the laboratory [10](#page=10). * Sealing cultures in plastic bags and sterilising them at high temperature and pressure before disposal [10](#page=10). ### 3.3 Culturing steps Culturing microorganisms involves providing the organism with the correct type of nutrients to facilitate growth. This is achieved using nutrient growth media (singular: medium), which contain carbon, nitrogen, and minerals. Media can be in liquid form, known as nutrient broth or liquid culture, or solid form, known as nutrient agar [10](#page=10) [2](#page=2). #### 3.3.1 Nutrient media * **Nutrient broth:** A liquid nutrient medium used for culturing microorganisms in flasks, test tubes, or bottles. Growing microorganisms in a nutrient broth is referred to as liquid culture [2](#page=2). * **Nutrient agar:** A jelly-like substance extracted from seaweed, used as a solid nutrient for culturing microorganisms, commonly in petri dishes. Nutrient agar can be heated to 90°C without becoming liquid and is inexpensive [10](#page=10) [2](#page=2). * **Selective medium:** A growth medium containing a very specific mixture of nutrients, designed so that only a particular type of microorganism will grow on it. Selective media are useful for identifying mutant strains, microorganisms resistant to antibiotics, or genetically modified organisms. An example is YM (yeast mould) medium [10](#page=10) [2](#page=2). #### 3.3.2 Inoculation Inoculation is the process of transferring microorganisms into a culture medium under sterile conditions [2](#page=2). ### 3.4 Measuring microbial growth Several methods can be employed to measure the growth of bacterial and fungal cultures. #### 3.4.1 Cell counts using a haemocytometer The haemocytometer is a specialised, thick microscope slide with a rectangular chamber that holds a standard volume, often 0.1 mm³. This chamber is engraved with a grid of lines. To count bacteria and single-celled fungi in a nutrient broth using a haemocytometer and a light microscope [11](#page=11) [2](#page=2): 1. A sample of the bacterial culture is placed on the slide [11](#page=11). 2. The apparatus is viewed under a light microscope [11](#page=11). 3. Cells within each square of the grid are counted [11](#page=11). 4. Cells touching the top and right lines are counted, while those touching the bottom and left lines are not [11](#page=11). This method allows for the determination of the total viable cell count, which is a measure of the number of living cells in a specific volume of a culture [11](#page=11) [2](#page=2). #### 3.4.2 Optical methods (turbidity) Turbidimetry is a method of measuring the concentration of a substance by quantifying the amount of light that passes through it. A culture solution becomes more turbid (opaque due to suspended matter) as the number of cells increases. This means more light is absorbed and less light is transmitted. Therefore, higher turbidity indicates a greater presence of microorganisms. Calibration can be performed by measuring the turbidity of various samples and correlating it with cell counts obtained from a haemocytometer to establish a relationship between turbidity and cell number. A created calibration curve can then be used to estimate the number of microorganisms by simply measuring turbidity [11](#page=11) [2](#page=2). #### 3.4.3 Dilution plating Dilution plating is used to count only the total viable cells in a culture. This method is based on the principle that each visible colony on an agar plate has developed from a single, viable microorganism. The original culture is diluted in stages until a point is reached where the number of colonies on the plate is countable. The total viable count is calculated using the formula [11](#page=11) [2](#page=2): $$ \text{Total viable count} = \text{number of colonies} \times \text{dilution factor} $$ It is recommended to use two or more plates per dilution and calculate the mean number of colonies for accuracy. The accuracy of this method can be cross-checked by using a haemocytometer on the original culture [11](#page=11). #### 3.4.4 Area and mass of fungi For fungi, growth can be assessed by measuring the diameter of individual areas of mycelium. This method is useful for comparing growth rates under different conditions to determine optimum growth conditions. The process involves culturing petri dishes at various temperatures, with several dishes at each temperature. The diameter of each fungal colony is measured after a specific period, and the mean diameter for each temperature is calculated. The conditions that yield the largest mean diameter are considered optimal [12](#page=12). --- # Mechanisms of disease transmission and defense This topic outlines the diverse ways pathogens spread between hosts and details the body's multifaceted defense systems against them. ### 4.1 Mechanisms of disease transmission Pathogens can spread through a variety of methods, utilizing different vectors and modes of contact. #### 4.1.1 Vectors Vectors are living organisms that transmit infections from one host to another. * **Examples:** Mosquitoes are common vectors for diseases such as malaria, dengue, and yellow fever [13](#page=13). #### 4.1.2 Inhalation Inhalation involves the expulsion of droplets from the respiratory tract through actions like coughing, sneezing, or talking, which can then be inhaled by others. * **Examples:** This mode of transmission is responsible for diseases like influenza, measles, and tuberculosis [13](#page=13). #### 4.1.3 Ingestion Ingestion typically occurs when pathogens contaminate food, often through fecal matter. This is a primary route for gut-related diseases. * **Infection Risk:** Consuming undercooked or raw food increases the risk of infection. * **Examples:** Salmonella poisoning, diarrhea, and hepatitis A are commonly transmitted through ingestion [13](#page=13). #### 4.1.4 Fomites Fomites are inanimate objects that can carry pathogens from one host to another. * **Examples:** Common fomites include towels, bedding, and personal items like cosmetics. Staphylococcus, a bacterium causing skin infections, can spread via fomites [13](#page=13). #### 4.1.5 Direct contact Direct contact involves the transmission of pathogens through physical touch, particularly relevant for skin diseases and sexually transmitted infections. * **Examples:** Impetigo is a common skin infection spread through direct contact, especially in young children. Sexually transmitted diseases like HIV, gonorrhea, syphilis, and Ebola also spread through direct contact via mucous membrane passage [13](#page=13). #### 4.1.6 Inoculation Inoculation is the direct entry of pathogens into the body through breaks in the skin, such as cuts, wounds, bites, or injections. * **Rapid Infection:** This method bypasses external defenses, allowing pathogens to reach tissues or the bloodstream directly, leading to rapid infection. * **Examples:** Hepatitis B, HIV, rabies, and tetanus can be transmitted through inoculation [13](#page=13). ### 4.2 Body's defense mechanisms The body possesses multiple layers of defense to prevent and combat pathogen invasion. #### 4.2.1 Epithelial defenses The skin and linings of internal tracts provide physical and chemical barriers. ##### 4.2.1.1 Skin The skin acts as a primary physical barrier. * **Keratin:** This impenetrable fibrous protein forms a robust physical barrier. * **Sebum:** The oily substance secreted by the skin contains chemicals that inhibit microbial growth. * **Natural Skin Flora:** Commensal microorganisms residing on the skin compete with foreign microbes, preventing them from establishing infections [14](#page=14). ##### 4.2.1.2 Surfaces of internal tubes and ducts Lining the respiratory, digestive, and urinary systems, these surfaces employ several defense strategies. * **Mucus Secretion:** Mucus traps pathogens and contains lysozymes, enzymes that effectively digest microbes, particularly gram-positive bacteria. * **Cilia:** Hair-like structures that beat rhythmically to move mucus, along with trapped pathogens, out of the tracts. * **White Blood Cells:** These cells patrol epithelial surfaces, engulfing and digesting pathogens. * **Examples of Secretions:** Sweat, oils, saliva, tears, and mucus all contribute to defense [14](#page=14). ##### 4.2.1.3 Gut defenses The gastrointestinal tract has specialized defenses against ingested pathogens. * **Polypeptides:** Produced in salivary glands, these peptides help destroy bacteria. * **Hydrochloric Acid:** The highly acidic environment of the stomach (pH 2) kills many pathogens ingested with food or drink [14](#page=14). * **Natural Flora:** The gut's resident microbial community competes with and inhibits the growth of harmful pathogens. * **Vomiting:** This reflex effectively expels many ingested microorganisms from the digestive system [14](#page=14). --- # Pathogenesis and specific diseases: Tuberculosis and HIV/AIDS This section explores how pathogens cause disease and details the pathogenesis, transmission, and symptoms of tuberculosis and HIV/AIDS. ### 5.1 General principles of pathogenesis Pathogens can cause disease through various mechanisms, including the production of toxins and invasion of host tissues [15](#page=15). #### 5.1.1 Bacterial toxins Bacteria produce two main types of toxins: endotoxins and exotoxins [15](#page=15). * **Endotoxins:** These are lipopolysaccharides found on the outer layer of gram-negative bacteria's cell walls. The lipid component of lipopolysaccharides acts as a toxin by stimulating an immune response, primarily affecting the area around the bacterial infection. While endotoxins themselves may not cause fatal diseases, their effects, such as diarrhea and vomiting, can lead to dehydration [15](#page=15). * **Exotoxins:** These are soluble proteins released by bacteria as they metabolize and reproduce within host cells. Exotoxins can be produced by both gram-positive and gram-negative bacteria and have more profound effects than endotoxins, including causing internal bleeding, damaging cell membranes, interfering with neurotransmitters, and directly poisoning cells. They are considered more dangerous and potentially fatal than endotoxins, though they rarely cause fever [15](#page=15). #### 5.1.2 Host tissue invasion Bacteria can invade host tissues, causing direct cell damage. The host organism's response to this invasion and cell damage is often what leads to the disease. In many cases, cell damage is further exacerbated by the production of exotoxins or the presence of endotoxins within the bacterial cell walls [15](#page=15). > **Tip:** Differentiating between the effects of endotoxins and exotoxins is crucial for understanding the clinical presentation and treatment of bacterial infections. ### 5.2 Tuberculosis (TB) Tuberculosis is a disease caused by the bacterium *Mycobacterium tuberculosis* [15](#page=15). #### 5.2.1 Transmission * Infection can occur through drinking contaminated milk or close contact with infected cattle [15](#page=15). * It primarily spreads via droplet infection, meaning pathogens enter the lungs when people breathe, cough, or sneeze near each other [15](#page=15). * Tuberculosis is most common among individuals with compromised immune systems [15](#page=15). #### 5.2.2 Symptoms * Tuberculosis primarily affects the respiratory system, specifically the lungs [15](#page=15). * It suppresses the immune system, reducing the body's ability to fight the disease [15](#page=15). * Common symptoms include weakness and coughing up blood [15](#page=15). #### 5.2.3 Disease progression * **Primary infection:** This is the initial stage where *M. tuberculosis* is inhaled into the lungs and multiplies slowly. In individuals with a healthy immune system, a localized inflammatory response forms a mass of tissue called a tubercle, containing dead bacteria and macrophages. After approximately eight weeks, the immune system typically controls the bacteria, inflammation subsides, and lung tissue heals. Primary TB infections often occur in childhood and many resolve without the individual realizing they were infected. However, *M. tuberculosis* can adapt by forming a thick, waxy outer layer to protect itself from macrophage enzymes, allowing bacteria to remain dormant within tubercles [15](#page=15) [16](#page=16) [3](#page=3). * **Latent TB:** In this stage, individuals show no symptoms and cannot spread the disease [16](#page=16). * **Active TB:** In this stage, individuals exhibit symptoms and can transmit the disease. Symptoms of active TB include fever, night sweats, loss of appetite, and weight loss [16](#page=16). #### 5.2.4 Diagnosis and Treatment * **Testing:** A sputum test is used to diagnose tuberculosis [16](#page=16). * **Treatment:** Antibiotics are prescribed for several months to treat the infection [16](#page=16). #### 5.2.5 Control measures * Avoiding crowded areas helps prevent the spread of infection [16](#page=16). * Pasteurization of milk (heating it to a high temperature) kills harmful bacteria [16](#page=16). * Immunization plays a role in control [16](#page=16). * Improving living standards, including healthy nutrition, contributes to better health outcomes [16](#page=16). ### 5.3 Human Immunodeficiency Virus (HIV) and Acquired Immunodeficiency Syndrome (AIDS) HIV is a retrovirus that causes AIDS [3](#page=3). #### 5.3.1 HIV * HIV is a virus that attacks immune cells, primarily T helper cells, thereby weakening the immune system. This makes the body susceptible to secondary opportunistic pathogens, such as TB, pneumonia, and Kaposi's sarcoma [17](#page=17). * A person infected with HIV is considered HIV positive, which is determined by a blood test showing the presence of HIV antibodies (or antigens) [17](#page=17) [3](#page=3). #### 5.3.2 Transmission of HIV HIV is transmitted through direct exchange of body fluids [17](#page=17): * Unprotected sexual intercourse [17](#page=17). * Use of infected or contaminated blood products [17](#page=17). * Sharing needles during drug abuse [17](#page=17). * From mother to fetus during early pregnancy, at birth, or through breastfeeding [17](#page=17). #### 5.3.3 AIDS Acquired Immunodeficiency Syndrome (AIDS) is the disease that results from the destruction of T helper cells due to HIV infection [3](#page=3). * **Symptoms:** Symptoms of AIDS can include fevers, persistent diarrhea, and significant weight loss. Deaths from AIDS are typically due to secondary infections that the compromised immune system cannot combat [17](#page=17). #### 5.3.4 Stages of HIV infection and progression to AIDS The progression of HIV infection is typically categorized into stages: * **Stage 1: Acute HIV syndrome:** This occurs in the first few weeks of infection. Some individuals may experience flu-like symptoms such as fever and swollen glands, while others remain asymptomatic. During this stage, there is a rapid increase in the virus's presence in the blood. After 3 to 12 weeks, HIV antibodies appear, and the person tests HIV positive [18](#page=18). * **Stage 2: Asymptomatic/Chronic stage:** Early symptoms disappear, and HIV continues to replicate within T helper cells. This replication helps keep the virus somewhat under control, allowing individuals to remain asymptomatic for extended periods, sometimes for many years, especially with effective antiretroviral drugs. However, over time, the immune system is slowly weakened, and secondary infections begin to develop as the immune system becomes less capable of managing pathogens [18](#page=18). * **Stage 3: Symptomatic disease:** The number of viruses in the body increases, and the T helper cell count drops significantly, often from 500 to 200 cells per cubic millimeter of blood. Patients begin to develop noticeable symptoms such as weight loss, diarrhea, and night sweats [18](#page=18). * **Stage 4: Advanced AIDS:** Without treatment, this stage can lead to severe conditions like dementia, cancer, TB, and cryptococcal meningitis, ultimately resulting in death [18](#page=18). > **Example:** A person in Stage 3 of HIV infection might experience severe weight loss and chronic diarrhea due to opportunistic infections like *Pneumocystis jirovecii* pneumonia, which their weakened immune system cannot effectively fight off. #### 5.3.5 Prevention of HIV Preventing the spread of HIV involves several key practices: * Limiting sexual partners to one [18](#page=18). * Using condoms to prevent the transmission of the virus during sexual activity [18](#page=18). * Using clean needles if injecting drugs [18](#page=18). #### 5.3.6 Role of Retrovirology Retroviruses, like HIV, have a unique replication cycle [7](#page=7): 1. The virus enters an animal cell [7](#page=7). 2. Viral RNA enters the host cell's cytoplasm [7](#page=7). 3. A viral enzyme called reverse transcriptase converts the RNA into DNA [7](#page=7). 4. The viral DNA then enters the host cell's nucleus and integrates into the host DNA [7](#page=7). 5. The host cell's machinery transcribes the viral genome into RNA and proteins [7](#page=7). 6. New viruses assemble and are released from the cell, often by exocytosis [7](#page=7). > **Tip:** Understanding the retroviral life cycle is key to developing antiretroviral drugs that target specific steps in this process, such as reverse transcriptase inhibitors. --- ## Common mistakes to avoid - Review all topics thoroughly before exams - Pay attention to formulas and key definitions - Practice with examples provided in each section - Don't memorize without understanding the underlying concepts

| Term | Definition | |------|------------| | Pathogen | A microorganism, such as a bacterium or virus, that can cause disease. | | Tobacco Mosaic Virus (TMV) | A virus that infects tobacco plants and related species, causing a mosaic pattern on leaves which can reduce crop yield. | | Capsid | The protein shell that encloses the genetic material of a virus. | | Capsomeres | Repeating protein subunits that form the capsid of a virus. | | Virus attachment particles (VAPs) | Specific proteins on the surface of a virus that bind to target proteins on the host cell membrane, facilitating entry. | | Envelope | An outer layer surrounding the capsid of some viruses, derived from the host cell membrane. | | DNA viruses | Viruses that possess DNA as their genetic material. | | RNA viruses | Viruses that possess RNA as their genetic material. | | Lysis | The process by which a cell bursts open, often due to the action of lysozyme or viral replication. | | Retrovirus | A type of RNA virus that uses reverse transcriptase to convert its RNA genome into DNA, which is then integrated into the host cell's DNA. | | Reverse transcriptase | An enzyme characteristic of retroviruses that synthesizes DNA from an RNA template. | | Human immunodeficiency virus (HIV) | A retrovirus that attacks the immune system, leading to Acquired Immunodeficiency Syndrome (AIDS). | | Plasmid | A small, circular, extrachromosomal DNA molecule found in bacteria, which can carry genes for specific traits. | | Vector | An organism or factor that transmits a pathogen from one host to another. | | Provirus | The genetic material of a virus, such as DNA, that has been integrated into the genome of a host cell. | | Latent | A state in which a virus is present within a host cell but is not actively replicating or causing disease. | | Lysogeny | A phase in the viral life cycle where the viral DNA integrates into the host cell's chromosome and replicates along with it, without immediately causing lysis. | | Exocytosis | A cellular process where vesicles containing substances fuse with the cell membrane to release their contents outside the cell. | | Sterile | Free from all living microorganisms and their spores. | | Nutrient medium | A substance, either liquid (broth) or solid (agar), that provides the necessary nutrients for the growth of microorganisms. | | Nutrient broth | A liquid medium used for culturing microorganisms. | | Liquid culture | The cultivation of microorganisms in a liquid nutrient medium. | | Nutrient agar | A solid medium derived from seaweed, used for growing microorganisms, typically in Petri dishes. | | Selective medium | A growth medium containing specific nutrients or inhibitors that allow only particular types of microorganisms to grow. | | Inoculation | The process of introducing microorganisms into a culture medium under sterile conditions. | | Haemocytometer | A specialized counting chamber on a microscope slide used for determining the concentration of cells in a liquid. | | Turbidimetry | A method used to measure the concentration of a substance in a liquid by quantifying the amount of light that passes through it. | | Turbid | Having suspended matter that makes a liquid opaque or cloudy. | | Dilution plating | A technique for estimating the number of viable microorganisms in a sample by diluting it and plating serial dilutions on agar. | | Total viable cell count | The number of living cells capable of growth and reproduction present in a specific volume of a culture. | | Communicable | Capable of being transmitted from one organism to another. | | Bacterial flora | The community of microorganisms that live in or on a specific part of the body. | | Sebum | An oily secretion of the sebaceous glands that helps protect the skin and inhibit microbial growth. | | Lysozymes | Enzymes found in bodily secretions that can break down the cell walls of bacteria. | | Endotoxins | Lipopolysaccharides forming part of the outer membrane of Gram-negative bacteria, which can cause toxic effects when released. | | Exotoxins | Soluble toxic proteins produced and secreted by bacteria. | | Lipopolysaccharides | Complex molecules composed of lipids and polysaccharides, found in the outer membrane of Gram-negative bacteria. | | Primary infection | The initial infection of a host by a pathogen, often occurring without prior exposure or immunity. | | Tubercule | A small, localized mass of inflamed tissue formed in response to infection, typically containing dead cells and microorganisms. | | Acquired Immunodeficiency Syndrome (AIDS) | A chronic, potentially life-threatening condition caused by the Human Immunodeficiency Virus (HIV) that damages the immune system. | | HIV positive | Indicating the presence of antibodies to HIV in the blood, signifying infection with the virus. | | Anti-retroviral drugs | Medications used to treat infections caused by retroviruses, such as HIV. | | Peptidoglycan | A polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of bacteria, providing structural rigidity. | | Nucleoid | The irregularly shaped region within a prokaryotic cell that contains its genetic material, usually a single circular chromosome. | | 70S ribosomes | Ribosomes found in prokaryotic cells, responsible for protein synthesis. | | Pili | Hair-like appendages on the surface of bacteria used for attachment to surfaces or other cells. | | Flagella | Whip-like appendages used by microorganisms for locomotion. | | Capsule/ slime layer | An outer layer of polysaccharide or protein that surrounds the cell wall of some bacteria, providing protection and aiding in attachment. | | Mesosomes | Inward folds of the bacterial cell membrane that may be involved in respiration or DNA replication. | | Gram positive | A classification of bacteria that retain crystal violet dye during Gram staining, typically due to a thick peptidoglycan layer. | | Gram negative | A classification of bacteria that do not retain crystal violet dye during Gram staining and are counterstained pink, typically due to a thin peptidoglycan layer and an outer membrane. | | Nucleic acids | Molecules such as DNA and RNA that carry genetic information. | | Lipid envelope | A membrane derived from the host cell that surrounds the capsid of some viruses, aiding in entry and evasion of the immune system. | | bacteriophages | Viruses that infect and replicate within bacteria. | | Ebola fever | An infectious disease caused by the Ebola virus, characterized by severe hemorrhagic fever. | | Polio | A highly infectious viral disease that can cause paralysis. | | Measles | A highly contagious viral illness that causes a widespread rash and fever. | | Influenza | A contagious respiratory illness caused by influenza viruses. | | Lysogenic Pathway | A mode of viral replication where the viral genome integrates into the host cell's genome and is replicated along with it, potentially remaining dormant for extended periods. | | Lyctic Pathway | A mode of viral replication where the virus replicates rapidly within the host cell, leading to cell lysis and the release of new viruses. | | Autolysis | The self-digestion of a cell by its own enzymes. | | Binary fission | A type of asexual reproduction in which a parent cell divides into two or more identical daughter cells. | | Generation time | The time it takes for a population of cells to double in number through cell division. | | Logarithmic scale | A scale in which values are represented by logarithms, used to display a large range of numbers or to visualize exponential growth. | | Exponential growth rate | The rate at which a population of organisms increases exponentially, where the number of individuals increases by a constant factor over constant time intervals. | | Bacterial Growth Curve | A graphical representation of the changes in the number of living bacterial cells over time during culture. | | Lag Phase | The initial phase of the bacterial growth curve where bacteria adapt to a new environment, showing little to no growth. | | Log/exponential Phase | The phase of the bacterial growth curve characterized by rapid and exponential increase in cell population due to maximum growth rate. | | Stationary Phase | The phase of the bacterial growth curve where the rate of cell division equals the rate of cell death, resulting in a plateau in population size. | | Death/ decline Phase | The final phase of the bacterial growth curve where the rate of cell death exceeds the rate of cell division, leading to a decrease in population size. | | Microbial Techniques | Methods used for the study, culturing, and manipulation of microorganisms. | | Aseptic Techniques | Procedures performed under sterile conditions to prevent contamination of cultures by unwanted microorganisms and to prevent the escape of microorganisms into the environment. | | Nutrient growth medium | A substance providing essential nutrients for microbial growth. | | Nutrient agar | A solid growth medium derived from seaweed, commonly used for bacterial cultures. | | Selective media | Growth media designed to favor the growth of certain microorganisms while inhibiting others. | | Yeast mould medium (YM) | A type of nutrient medium commonly used for the cultivation of yeasts and molds. | | Cell counts | Methods used to determine the number of cells in a sample, often using a haemocytometer or microscope. | | Optical methods (turbidity) | Techniques that measure the cloudiness or turbidity of a liquid culture to estimate the number of microorganisms present, based on light scattering or absorption. | | Calibration curve | A graph used to determine the concentration of a substance by comparing measurements to known concentrations. | | Dilution Plating | A technique used to count viable cells by serially diluting a sample and plating it on agar, where each colony is assumed to have arisen from a single cell. | | Dilution factor | The ratio of the original volume to the final volume after dilution, used in calculating cell counts. | | Area & mass of fungi | Methods for assessing fungal growth by measuring the diameter of mycelial areas or the dry mass of the fungal culture. | | Mycelium | The vegetative part of a fungus, consisting of a network of fine white filaments (hyphae). | | Vectors | Living organisms that transmit infectious pathogens from one host to another. | | Inhalation | The process of breathing in, which can transmit airborne pathogens. | | Ingestion | The process of taking food or drink into the body, which can transmit pathogens through contaminated food or water. | | Fomites | Inanimate objects that can carry and transmit pathogens. | | Direct contact | Transmission of pathogens through physical touch between individuals. | | Sexually transmitted diseases (STDs) | Infections passed from one person to another through sexual contact. | | Mucous membranes | Thin membranes that line body cavities and secrete mucus, serving as a barrier and a route for infection. | | Inoculation | The introduction of microorganisms into the body, typically through the skin via cuts, wounds, bites, or injections. | | Epithelial Defenses | Protective mechanisms provided by epithelial tissues, such as the skin and linings of internal organs. | | Keratin | A tough, fibrous protein that forms the structural component of hair, nails, and the outer layer of skin. | | Natural skin flora | The community of microorganisms that normally reside on the skin, often providing protection against pathogenic microbes. | | Cilia | Tiny, hair-like projections on the surface of cells that beat rhythmically to move substances along. | | White blood cells | Cells of the immune system that defend the body against infection and disease. | | Polypeptides | Short chains of amino acids produced by glands, some of which have antimicrobial properties. | | Hydrochloric acid (HCl) | A strong acid found in the stomach that helps kill ingested pathogens. | | Vomiting | The forceful expulsion of the contents of the stomach through the mouth, which can help remove ingested pathogens. | | Host tissue invasion | The process by which bacteria penetrate and damage the tissues of a host organism. | | Tuberculosis (TB) | An infectious disease usually caused by Mycobacterium tuberculosis that primarily affects the lungs. | | Mycobacterium tuberculosis | The bacterium that causes tuberculosis. | | Sputum test | A laboratory test performed on a sample of mucus coughed up from the lungs to detect the presence of infectious agents, such as tuberculosis bacteria. | | Antibiotics | Drugs used to treat bacterial infections. | | Pasteurization | A process of heating a liquid to a specific temperature for a set amount of time to kill harmful microorganisms. | | Immunization | The process of making an individual immune to a particular disease, usually through vaccination. | | Latent TB | A form of tuberculosis infection where the bacteria are present in the body but are inactive and do not cause symptoms or spread to others. | | Active TB | A form of tuberculosis infection where the bacteria are actively multiplying, causing symptoms and potentially spreading to others. | | Primary infection | The initial occurrence of an infection in a host. | | Tubercule | A localized collection of immune cells and dead tissue formed in response to infection, particularly tuberculosis. | | Macrophages | Large phagocytic cells of the immune system that engulf and digest cellular debris, foreign substances, microbes, cancer cells, and dead cells. | | Fever | An elevation of body temperature above the normal range, often a symptom of infection or illness. | | Night sweats | Excessive sweating during sleep, often associated with fever or certain medical conditions. | | Loss of appetite | A reduced desire to eat. | | Loss of weight | A reduction in body mass. | | HIV | Human Immunodeficiency Virus, a retrovirus that attacks the immune system. | | Immune cells | Cells of the immune system that protect the body from infection and disease. | | Secondary opportunistic pathogens | Microorganisms that cause disease in individuals with weakened immune systems. | | Kaposi’s sarcoma | A type of cancer that develops from the cells that line lymph or blood vessels. | | HIV positive | A status indicating the presence of HIV antibodies, meaning an individual has been infected with the virus. | | Antigens | Substances that trigger an immune response, often found on the surface of pathogens. | | AIDS | Acquired Immunodeficiency Syndrome, the advanced stage of HIV infection that severely damages the immune system. | | Acute HIV syndrome | The initial stage of HIV infection, characterized by flu-like symptoms and a rapid increase in virus levels in the blood. | | Asymptomatic/ Chronic stage | A phase of HIV infection where early symptoms disappear, and the virus replicates slowly, potentially lasting for many years. | | T helper cells | A type of white blood cell that plays a crucial role in the immune system by coordinating immune responses. | | Antiretroviral drugs | Medications used to manage HIV infection by suppressing viral replication. | | Symptomatic disease | A stage of illness where distinct symptoms become apparent. | | Advanced Aids | The final stage of AIDS, characterized by severe immune deficiency and opportunistic infections or cancers. | | Dementia | A chronic or persistent condition of mental illness or organic brain disorder characterized by loss of memory, personality changes, and impaired reasoning. | | Cryptococcal meningitis | A serious fungal infection of the membranes covering the brain and spinal cord. |