Lecture Notes: Viruses, Bacteria, & Archaea (2024-2025) PDF

BIOLOGY 1 ASB0204 Topic 10: Viruses, Bacteria and Archaea Dr. Nur Akmal Ishak Dr. Ezyana Kamal Bahrin Biology Unit, Centre for Foundation Studies in Science of Universiti Putra Malaysia (ASPut...

BIOLOGY 1 ASB0204 Topic 10: Viruses, Bacteria and Archaea Dr. Nur Akmal Ishak Dr. Ezyana Kamal Bahrin Biology Unit, Centre for Foundation Studies in Science of Universiti Putra Malaysia (ASPutra), Universiti Putra Malaysia  The Invisible Us – The Human Microbiome in Health and Disease Microbiome is the community of microorganisms (such as fungi, bacteria and viruses) that exists in a particular environment. The latest study from the American Academy of Microbiology estimates each human ecosystem contains around 100 trillion cells of microorganisms and just 37 trillion human cells. 2  COURSE OUTLINE 01 02 03 04 Viruses The The The Prokaryotes Bacteria Archaea Learning Outcomes By the end of this lecture, you will be able to: 1. Explain the basic structure and life cycle of virus. 2. Explain the basic structure and characteristic of bacteria and archaea. 3. Relate the importance of microorganisms in life.  Lesson 01 Viruses The Structure of Virus Virus is a very small (~ 20 – 300 nm). Virus can be characterized by their: ❑size and shape (helical, polyhedral, complex) ❑presence or absence of outer envelope ❑type of nucleic acid (DNA/RNA) 6 The Structure of Virus Each type has at least two parts: Covering and Inner Core Capsid (protein coat) Outer layer composed of protein subunits Covering called capsomers. Envelope (not found in all viruses) Virus particle Some viruses have an outer membranous envelope surrounding the capsid. Nucleic acid core (DNA or RNA) Inner core surrounded by a capsid. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Various proteins (E.g. enzymes) 24.1 The status & Structure of Viruses Further reading: page 500-502 7 Examples of DNA Viruses TEM 80,000X TEM 90,000X Adenovirus: DNA virus with a polyhedral capsid T-even bacteriophage: DNA virus with a polyhedral and a fiber at each corner. head and a helical tail. fiber protein capsid fiber protein unit DNA neck tail sheath capsid DNA tail fiber pins base plate a. b. 8 a: © Dr. Hans Gelderblom/Visuals Unlimited; b: © Eye of Science/Photo Researchers, Inc. Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Examples of RNA Viruses c. d. TEM 500,000X 20nm Influenza virus: RNA virus with a spherical capsid Tobacco mosaic virus: RNA virus with a helical Surrounded by an envelope with spikes. capsid. spikes capsid RNA RNA envelope capsid Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 9 c: © Dr. O. Bradfute/Peter Arnold/Photolibrary; d: © K.G. Murti/Visuals Unlimited Characteristics of Viruses: 1. Parasitic Nature of Virus Viruses are obligate intracellular parasitic: ❑ Can reproduce only within host cells using resources of a host. ❑ Incapable to replicate its own genetic material. ❑ Once inside a living/host cell, they hijacks the cell’s protein synthesis machinery to replicate nucleic acids, capsids, viral enzyme. 10 Obligate: restricted to a particular function or mode of life. Characteristics of Viruses: HOST SPECIFIC 2. Viruses are host specific Viruses infect specific types Tobacco mosaic virus Rabies of organisms (bacteria, plants, fungi, animals etc.). What determines the specificity of a virus for a host cell? Host specific : tobacco plant Host specific : mammals Determined by structure of HIV Hepatitis molecules in naked capsid/spikes on virus, lock and key with a receptor on a host cells at the outer surface. Host specific : white blood cells Host specific : liver cells 11  Reproductive Cycles of Bacteriophages: 1. Lytic cycle Bacteriophages : viruses that infect bacteria ✔ Virus injects DNA into the host cells ✔ Host cell start copying viral DNA and making capsid and accessory parts ✔ Then, cell lyses (burst) releasing the viruses to infect other cells 12 Reproductive Cycles of Bacteriophages: 2. Lysogenic cycle ✔ After DNA is insert, it is integrated into host cell’s DNA with no destruction of the host DNA. Viral reproduction ✔ Phage is latent (existing in hidden/dormant) and does not occur latent viral DNA is called prophage. immediately but may occur in ✔ The prophage is replicated along with host DNA the future. (lysogenic cells). ✔ Lysogenic cells carry a copy of the prophage genome. ✔ Certain environmental factor (UV radiation, nutrients availability, chemical treatment, etc) can induce prophage to reenter the lytic stage. 13  phage 1. Lytic and lysogenic cycles of Bacteriophage 1. ATTACHMENT Phage attaches to cell surface of bacterium. Phage bind to specific host cells based on host- specific match between phage and host cell receptors. 14 14  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1.1. ATTACHMENT ATTACHMENT Phage attaches Capsid to cell combines withsurface of bacterium. receptor. bacterial nucleic acid cell wall bacterial capsid DNA 2. PENETRATION LYTIC Viral DNA enters host. Virus injects CYCLE its genome into the cytoplasm of host cell. viral DNA 15 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1. ATTACHMENT 1. ATTACHMENT Phage attaches Capsid to cellwith combines surface of bacterium. receptor. bacterial nucleic acid cell wall bacterial capsid DNA 2. PENETRATION Viral DNA enters host. LYTIC viral DNA CYCLE New viral 3. BIOSYNTHESIS components are Viral components are synthesized. synthesized using host cell’s machinery and 16 energy.  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1. ATTACHMENT 1. ATTACHMENT Phage attaches Capsid to cell combines surface with of bacterium. receptor. bacterial nucleic acid cell wall bacterial DNA capsid 2. PENETRATION Viral DNA enters host. LYTIC CYCLE viral DNA 4. MATURATION 3. BIOSYNTHESIS Assembly of viral components. Viral components are synthesized. Viral components are assembled into new viruses. 17  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1. ATTACHMENT 1. ATTACHMENT Phage attaches Capsid to cellwith combines surface of bacterium. receptor. bacterial nucleic acid cell wall bacterial DNA capsid New viruses 5. RELEASE 2. PENETRATION New viruses leave host cell. Viral DNA enters host. exit host cell through lysis or budding in order to infect LYTIC viral DNA new host cells. CYCLE 4. MATURATION 3. BIOSYNTHESIS Assembly of viral components. Viral components are synthesized. 18  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1. ATTACHMENT 1. ATTACHMENT Phage attaches Capsid to cell combines withsurface of bacterium. receptor. bacterial nucleic acid cell wall bacterial DNA capsid 5. RELEASE 2. PENETRATION New viruses leave host cell. Viral DNA enters host. INTEGRATION Viral DNA is integrated into bacterial DNA and then is passed on when bacteria reproduce. LYTIC viral DNA viral CYCLE DNA LYSOGENI 4. MATURATION Assembly of viral components. 3. BIOSYNTHESIS Viral components are synthesized. C CYCLE 19  1. ATTACHMENT 1. ATTACHMENT Phage attaches to cell surface of 24.3 Viral Replication Capsid bacterium.combines with receptor. bacterial Can you differentiate lytic and nucleic acid cell wall lysogenic cycles? bacterial DNA capsid Further reading: page 503 di 5. RELEASE 2. PENETRATION New viruses leave host cell. Viral DNA enters host. INTEGRATION Viral DNA is integrated into bacterial DNA and then is passed on when bacteria reproduce. LYTIC viral DNA CYCLE viral DNA LYSOGENI 4. MATURATION 3. BIOSYNTHESIS C Assembly of viral components. Viral components are synthesized. CYCLE prophage 20 daughter cells © Eye of Science/Science Source 2. Reproductive Cycle of Retrovirus Animal ricus Entry Attachment Capsid and Animal virus nucleic acid is attaches to host- release into host cell cell receptor. cytoplasm. Enveloped viruses Capsid is fuse with animal removed by cell’s plasma enzymes. membrane. Uncoating releases viral DNA or RNA 22  Reverse transcription Retroviruses contain reverse transcriptase (Example: HIV, the virus that causes AIDS). Carries out reverse transcription from RNA to copy of DNA (cDNA) cDNA becomes integrated into host DNA. Replicated when host DNA is replicates (cell division). HIV may remain in the host genome latent for years. 23  Biosynthesis Maturation Release How antiviral drugs are developed? These 3 steps are the same as bacteriophage but Read page 510 & 511 in the case of HIV, it is released by budding from 24 the plasma membrane.  Summary of Virus Subtopic Structure of Virus HOW VIRUS REPRODUCED? 1 Lytic cycles of Bacteriophage ✔ Covering: Capsid & Envelope Attachment (A) Penetration (P) Biosynthesis (B) Maturation (M) ✔ Inner core: Nucleic acid Release (R) core (DNA or RNA) & various protein 2 Lytic and lysogenic cycles of Bacteriophage Characteristics of Virus A P Integration (I) B M R ✔ Parasitic Nature of Virus: obligate intracellular 3 Life cycle of retroviruses parasitic. A P Reverse transcription (RT) B ✔ Viruses are host specific M R 25  Lesson 02 The Prokaryotes The Structure of Prokaryotes (include bacteria and archaea) The length ranges from 1 to 5 µm. Most prokaryotes are unicellular. Lack a membrane-bounded nucleus and organelles. contains ribosomes and storage granules. Most prokaryotes have cell wall. To support and maintain its shape The cell wall is made up from peptidoglycan. However, peptidoglycan is absent in archaea. structure of pro 27  Many prokaryote species produce a capsule/slime layer that surrounds the cell wall. Made of polysaccharide or protein. Protect the bacteria against phagocytosis (eg: Streptococcus pneumoniae). Use to attach to surfaces such as rocks, plant roots and human teeth. - reproduction Fimbriae and pili is for attach to cell surfaces and transmitting DNA between bacteria. 29  Prokaryotic Cell Shapes Bacteria can be further classified in terms of their three basic shapes: Spiral (spirilli) Rod (bacilli) Round (cocci) 30  Prokaryote Reproduction Prokaryotes reproduce asexually by binary fission. required lo pick up Genetic material can be exchanged among prokaryotes and resulting dua from genetic recombination. final bactering Transduction Conjugation Transformation ⮚ Occurs when ⮚ Conjugation pilus forms ⮚ Occurs when 31 bacteriophages carry between two cells bacterium picks up free portions of bacterial ⮚ Donor cell passes DNA pieces of DNA from DNA from one cell to to recipient cell through other prokaryotes another virus as vectors the pilus ⮚ Becomes incorporated ⮚ Serve as vectors into genome  lesson 03 The Bacteria  The Bacteria Most bacterial cells are protected by a cell wall. -Contains peptidoglycan Bacteria are commonly differentiated using the Gram stain procedure. When washed after staining: Gram-positive bacteria retain dye and appear purple Gram-negative bacteria do not retain dye and appear pink Gram-negative bacteria have a second plasma membrane which blocks antibiotic drugs, making infections difficult to treat. 33 The difference is dependent on the construction of the cell wall.  is peptidoglycan purple - at first both after hav purple introducing pink stain, has pink, only gramit gram It) hav purple for membrane pink plasma purple for peptidoglycon 34 Gram-negative (pink) Gram-positive (purple) thin peptidoglycan layer thick peptidoglycan layer Bacterial Oxygen Requirements Oxygen requirements Obligate Obligate Facultative aerobes anaerobes anaerobes unable to grow in the presence of free oxygen 35 able to grow in either unable to grow in the the presence or absence of free absence of free oxygen oxygen Examples: Botulism, gas gangrene, and tetanus Modes of Nutrition Mode of nutrition Energy source Description Autotroph Photoautotroph Sunlight Use energy from sunlight to synthesize organic compounds. eg: cyanobacteria Chemoautotroph Inorganic chemicals Obtain energy by oxidizing inorganic chemical y does not use carbora substances such as ammonia or hydrogen sulfide. Heterotroph Photoheterotroph Sunlight Obtain their carbon from other organism but use chlorophyll and other photosynthetic pigments to trap sunlight energy. eg: purple nonsulfur bacteria Chemoheterotro Organic compounds depend on organic molecules for both carbon and ph energy. eg: decomposer and pathogenic bacteria  Prokaryote Relationships with Other Organisms Prokaryotes interact with other organisms in both beneficial and harmful ways. Commensalism Mutualism Refer to page 529 and Parasitism discuss on this topic. 37  ⮚ Commensalism One population modifies the environment in such a way that a second population benefits. Obligate anaerobes live in our intestine because bacterium E. coli uses up oxygen. ⮚ Mutualism Both species benefit from association. Mutualistic bacteria live in human intestines and release vitamins K and B12 which help produce blood components. 38 ⮚ Parasitism Parasite benefits at host expense; disease- causing bacteria are called pathogens Many form endospores  Prokaryote Relationships with Other Organisms Prokaryotes interact with other organisms in both beneficial and harmful ways. Commensalism Mutualism Refer to page 529 and Parasitism discuss on this topic. 39 Bacteria and Disease 40  Endospore-forming Bacterium Some bacteria form resistant endospores under unfavorable conditions. Examples: Bacillus spp.and Clostridium spp. Endospores can survive without nutrients. Resistant to: ultraviolet radiation, desiccation, high temperature, extreme freezing 41 and chemical disinfectants. Endospores can be destroyed by burning or by autoclaving. The endospore of Clostridium tetani Antibiotics Antibiotics Inhibit protein Inhibit cell wall biosynthesis biosynthesis Penicillin Affect bacterial but Erythromycin Tetracycline Ampicillin not animal cells Fluroquinolone Bacterial resistance to antibiotics is increasing. Refer to page 535 and discuss on this topic. 42  lesson 04 The Archaea  The Archaea Archaea were formerly considered bacteria. Other differences: Archaea do not have peptidoglycan in their cell walls like the bacteria. Archaea are biochemically more like eukarya than bacteria. Archaea are now thought to be more 44 closely related to eukarya than to bacteria.  Many live in harsh conditions: Methanogens Produce methane from hydrogen gas and carbon dioxide. Commonly found in the guts of animals, deep layers of marine sediment, hydrothermal vents, and wetlands. course title 45 course title 46 46  Eldra Solomon Charles Martin Diana W. Martin Linda R. Berg Chapter 24 Viruses and Subviral Agents Chapter 25 Bacteria and Archaea References:  THE END https://youtu.be/73c1RIqi0uw?si=4a4nutL18 ejGIZiJ course title