Prokaryotes and Viruses - Biology 11 - Sekulovich

Taxonomy

The classification and organization of the tree of life. These classification methods are constantly changing, and recent technological advances in genome sequencing have helped us better understand how to organize life evolutionarily.

Dichotomous Key

A tool used for the identification of species, consisting of a set of "conditions" that help organize different organisms.

Kind of like a book (animal disctionary)

Domain

The highest taxonomic rank in the hierarchical biological classification system, above kingdom. Examples include Eukarya, Bacteria, and Archaea.

Kingdom

A taxonomic rank below domain and above phylum. Examples include Animalia and Eubacteria.

Phylum

A taxonomic rank below kingdom and above class. An example is Chordata.

Class

A taxonomic rank below phylum and above order. An example is Mammalia.

Order

A taxonomic rank below class and above family. An example is Carnivora.

Family

A taxonomic rank below order and above genus. An example is Canidae.

Genus

A taxonomic rank below family and above species. In binomial nomenclature, the genus name is capitalized and comes before the species name. An example is Vulpes.

Species

A taxonomic rank below genus, representing a group of organisms that can interbreed and produce fertile offspring. In binomial nomenclature, the species name is lowercase and comes after the genus name. An example is vulpes.

Binomial Nomenclature

The system of naming species using two parts: the genus name followed by the species name.

Both parts must be italicized, with the genus capitalized and the species lowercase. Example: Aptenodytes forsteri.

Describe Earth 4.6 billion years ago. What made up the atmosphere?

Formed 4.6 billion years ago, initially extremely uninhabitable with no protection from the sun's harmful radiation. The early atmosphere contained water vapor, carbon monoxide (CO), carbon dioxide , hydrogen , and nitrogen

When did liquid water form on earth? How did the first organic compounds get energy?

Water formed on the surface of the Earth approximately 3.8 billion years ago.

These early prokaryotes were heterotrophs that obtained food and energy from organic molecules and were anaerobes, meaning they lived without oxygen.

Stromatolites

Special rock-like structures (fossils) produced by bacteria such as cyanobacteria, well established 3.4 billion years ago. They are signs of the first autotrophs.

Autotrophs

Organisms that produce their own food.

When did photosynthesis begin? (like what year) And what did it help create in the atmosphere?

Evolved 2.2 billion years ago, conducted with oxygen as a by-product, which helped create ozone in the atmosphere.

How did eukaryotic cells come to be?

Evolved 1.4-1.6 billion years ago. Aerobic organisms utilized oxygen in their metabolic pathways. This was the time that mitochondria and chloroplasts (prokaryotes themselves) evolved from being single-celled organisms to an organelle in a Eukaryote.

What is the Endosymbiosis Theory

A theory explaining the origin of eukaryotic cells from prokaryotic organisms. Evidence includes the double-membrane around both mitochondria and chloroplasts, as well as both containing their own DNA.

What is a virus? Size? Structure?

Generally considered non-living, smaller than the smallest cell (20-400nm). They have a non-cellular structure, lacking organelles, cytoplasm, or a cell membrane. They contain a protein coat called a capsid and a nucleic acid core containing either DNA or RNA (not both).

What is a Caspid? Protective Envelope? (Virus)

CASPID: The protein coat that encloses the nucleic acid of a virus.

PROTECTIVE ENVELOPE: An outer membrane coat that surrounds the protein coat or capsid in some viruses (e.g., influenza virus, Herpes Simplex virus).

What are the 4 virus shapes? What do they look like?

HELICAL: Like a hollow cylinder

POLYHEDRAL: Capsid is multifaceted, often icosahedral. Think of it like a 3-d multi sided shape

ENVELOPED: Circular shape with pointy things (COVID)

COMPLEX: A virus shape that is neither helical, polyhedral, nor enveloped, looks insanely goofy like a skyscraper

Why does Viral Taxonomy Exist? What do Family/ Genus names end in?

Basically just describe Viral Taxonomy

Viruses do not belong to any kingdom. They are not "living" (they are)

Family names end in -viridae, and genus names end in -virus.

Viral species share the same genetic information and ecological niche host; common names are used for species, and subspecies are designated by a number.

How would you identify a virus? Run through the steps

1. Does it have RNA or DNA?

2. Does it have or not have an ENVELOPE?

3. What is its Caspid Shape (Virus Shape)

4. What Host do they infect?

What is a Surface Marker/ Receptor Site? How are they connected

SURFACE MARKER-A specific marker on the surface of a virus that allows it to recognize and attach to a receptor site on a host cell it can infect.

RECEPTOR SITE -A specific site on a cell's surface that a virus's surface marker can match with, allowing the virus to infect the cell.

What is a parasite? How are viruses parasites? What is a host cell?

PARASITE - Organisms that are harmful to the host organism upon which they depend.

Viruses are obligate intracellular parasites, meaning they only reproduce when inside a host cell.

HOST CELL - The specific cell type that a virus infects and uses for reproduction. Viruses are inactive outside of host cells.

Lytic Cycle/ Lyse (Verb)

LYTIC CYCLE - A type of viral reproduction cycle that is short and can be overcome. The viral DNA takes over the host cell's machinery, replicates, assembles new phages, and then lyses (breaks open) the cell, releasing new viruses.

LYSE- To burst or break open a cell

EXPLODING PROCESS

Lysogenic Cycle

A type of viral reproduction cycle where the viral DNA integrates into the bacterial chromosome, becoming a prophage, and remains inactive in the host for long periods of time. The bacterium reproduces, copying the prophage and transmitting it to daughter cells. Occasionally, the prophage exits the chromosome, initiating a lytic cycle. Example: Mono or chickenpox.

SPAWN CAMPING THE WHOLE GAME

Vaccine

A weakened form of a virus that introduces the immune system to the virus, allowing the body to better fight off the full-blown virus when exposed.

Vector Control

Measures taken to prevent the spreading of a virus (COVID QUARANTINE YKYK)

EXAMPLES: Staying home when sick, covering one's mouth when coughing, washing hands frequently, avoiding contact with bodily fluids, and controlling mosquito populations (e.g., for West Nile virus).

What is an Antiviral Medication?

Specific drug treatments for certain viruses that do not cure the virus but can slow and inhibit its multiplication. They do not work against viral infections. Example: medication for HIV.

What is gene therapy?

A therapeutic technique where scientists explore using viruses to transport DNA and RNA into cells. Viral genetic material is replaced with new DNA, potentially used to cure genetic diseases.

What is a Prokaryote? What does it lack (Compare to Eukaryotuic) ? What is its size?

A single-celled organism that lacks a membrane-bound nucleus and other membrane-bound organelles. Their genetic material is located in the cytoplasm within a nucleoid region. They are very small (1-10um), unicellular, and the most abundant organisms on Earth, found everywhere.

What is Domain Bacteria? (Think Tree of Life)

One of the two domains consisting entirely of prokaryotes. It is the largest of the two domains and includes a wide range of organisms found in fresh/salt water, on land, and in the bodies of humans and other eukaryotes.

Domain Archaea (Tree of Life) - What is it and how does it differ from bacteria?

One of the two domains consisting entirely of prokaryotes. Under a microscope, they look similar to bacteria, but their cell walls lack peptidoglycan, and their cell membranes contain different lipids.

Their DNA sequences are more closely related to eukaryotes than those of bacteria. Many live in extremely harsh environments.

What are the Kingdoms Eubacteria and Archeabacteria?

EUBACTERIA: A kingdom within Domain Bacteria. (Often used synonymously with bacteria in older classification systems).

ARCHAEBACTERIA: A kingdom within Domain Archaea. (Often used synonymously with archaea in older classification systems).

What is an endospore?

Structures formed by some bacteria when growth conditions become unfavorable.

A bacterium produces a thick internal wall around its DNA, allowing it to remain dormant for months. It is not a true form of reproduction.

Its the tiny sac that contains DNA

Mesosome

Invaginations of the plasma membrane in prokaryotes that can form into vesicles.

Flagellum (Prokaryote)

A whip-like tail structure that some prokaryotes use for movement.

What are the different shapes of bacteria? What are their plurals?

COCCUS: Spherical-shaped bacteria. Plural: Cocci. (Btw they can form in multiple pairs)

BACILLUS: Rod-shaped bacteria. Plural: Bacilli.

SPIRILLUM: Spiral-shaped bacteria. Plural: Spirilla.

SPIROCHETES: A type of spiral-shaped bacteria, typically longer and more flexible than spirilla.

What is an autotroph? Photoautotrophs Chemoautotrophs?

AUTOTROPHS: Bacteria that make their own food

PHOTOAUTOTROPH: Autotrophs that use light energy from the sun and the process of photosynthesis to convert light energy into carbon compounds (their own food).

CHEMOAUTOTROPH: Autotrophs that use energy released by chemical reactions (e.g., involving ammonia, hydrogen sulphide) to make food.

Heterotrophs

Organisms that obtain energy from the food they eat through processes like aerobic respiration or fermentation. They are consumers.

Aerobic Respiration AND Fermentation

AEROBIC RESPIRATION: A metabolic process that uses oxygen to produce energy from food.

FERMENTATION: An anaerobic metabolic process that breaks down organic molecules to produce energy in the absence of oxygen.

What is a Decomposer/ Parasite?

DECOMPOSER: A prokaryote that obtains food from DEAD organisms.

PARASITE: A prokaryote that obtains food from LIVING organisms.

Binary Fission

The most common form of asexual reproduction in prokaryotes where a single cell grows and divides into two identical daughter cells. It involves DNA replication, the movement of origins to opposite ends of the cell, and the formation of a cross-wall.

Origin of Replication (Binary Fission)

The specific spot on a prokaryote's chromosome where the copying of DNA by replication enzymes begins during binary fission. It is the first part of the DNA to be copied.

Replication Forks

Its when the DNA double helix unwinds and unzips and forms a Y-shape

Conjugation

A form of sexual reproduction in prokaryotes where two prokaryotes approach each other, a small bridge forms between them, and genetic material is exchanged before the cells divide.

Spore Formation (Bacteria)

A process where many bacteria form spores when growth conditions become unfavorable.

It is not a true form of reproduction. The bacterium produces a thick internal wall around the DNA, allowing it to remain dormant for months.

Capsule (Bacteria)

An outer layer that protects the bacterial cell from damage. It is not found in all bacteria.

Cell Wall (Bacteria)

A rigid layer composed of peptidoglycan (a polysaccharide and protein) that surrounds the plasma membrane in bacteria. It helps maintain overall cell shape and protects from injury.

Plasma Membrane (Bacteria)

A lipid bilayer that transports ions, nutrients, and waste into and out of the cell.

Peptidoglycan

The primary component of the bacterial cell wall, composed of polysaccharides and proteins.

Gut Flora

Bacteria in the human gut- Many bacteria vital for the maintenance of human health, particularly in the digestive tract.

The majority live in the large intestine and break down certain nutrients, such as carbohydrates, that humans cannot digest. E. coli is an example.

E. coli

A type of bacteria found in the digestive tract gut flora that breaks down carbohydrates.

Nitrogen Fixation

The conversion of atmospheric nitrogen (N2) into useful forms like ammonia (NH3 ) or nitrates (NO3 ), a process carried out by certain bacteria.

Cyanobacteria

A type of bacteria important in food chains and involved in nitrogen fixation and the production of oxygen through photosynthesis. They are also responsible for forming stromatolites.

Actinomycetes

A type of bacteria mentioned as an example of organisms important in food chains and decomposition.

Obligate Anaerobes

Obligate anaerobes are microorganisms, typically bacteria, that cannot survive in the presence of oxygen

IF OXYGEN, THEY DIE

How is bacterial growth measured?

Measured as an increase in the number of bacteria rather than the size of individual cells, representing the growth of a cluster of bacteria. It is exponential, leading to rapidly increasing populations.

How fast does bacteria populations increase? How often do they double? What is this growth called?

A pattern of bacterial growth where populations increase very rapidly. Under good conditions, bacteria can divide as often as every 20 minutes, meaning one cell can lead to over a million cells in less than 8 hours.

EXPONENTIAL GROWTH

Antibiotics

Medications that destroy or slow the growth/reproduction of bacteria. They do not work against viral infections. Overuse can lead to antibiotic resistance.

Antibiotic Resistance

The ability of bacteria to withstand the effects of an antibiotic. It can arise from a mutation in a bacterium, leading to resistant strains.

Compare and contrast the Domains Bacteria and Archaea.

While both are prokaryotes (lacking a nucleus and membrane-bound organelles), Bacteria have cell walls containing peptidoglycan, while Archaea lack peptidoglycan and have different membrane lipids. Archaea are also known for thriving in extreme environments, and their DNA sequences are more closely related to eukaryotes than to bacteria.

Describe the major differences between the Lytic Cycle and the Lysogenic Cycle of viral reproduction.

The Lytic Cycle is a short, active cycle where the virus immediately replicates, lyses the host cell, and releases new viruses, leading to acute symptoms. The Lysogenic Cycle involves viral DNA integrating into the host's chromosome (as a prophage), remaining dormant for long periods, and replicating with the host cell before potentially entering a lytic phase.

Explain the hierarchical organization of the "tree of life" using the classification system from Domain to Species.

The tree of life is organized hierarchically starting from the broadest category, Domain, which contains Kingdoms. Kingdoms are divided into Phyla, then Classes, Orders, Families, Genera, and finally, the most specific category, Species. Each level becomes more specific, grouping organisms with increasingly shared characteristics.

Describe the key internal and external structures of a typical prokaryotic cell.

A typical prokaryotic cell is unicellular and lacks a nucleus and membrane-bound organelles. Its genetic material (DNA) is found in the cytoplasm within a nucleoid region. External structures may include a cell wall (often with peptidoglycan in bacteria), a plasma membrane, a capsule (for protection), and flagella for movement. Some also have mesosomes (invaginations of the plasma membrane) and can form endospores.

Compare and contrast the three main ways prokaryotes obtain energy: photoautotrophs, chemoautotrophs, and heterotrophs.

Photoautotrophs use light energy (photosynthesis) to produce their own food. Chemoautotrophs use energy from chemical reactions to synthesize food. Heterotrophs obtain energy by consuming organic molecules from other organisms, either through aerobic respiration or fermentation.

Outline the significant evolutionary milestones on early Earth that led to the development of more complex life forms.

Major milestones include: formation of liquid water (3.8 bya); production of first organic compounds; appearance of first prokaryotic fossils (3.5 bya, as heterotrophic anaerobes); establishment of stromatolites and first autotrophs (3.4 bya); evolution of modern oxygenic photosynthesis (2.2 bya), leading to ozone formation; and the evolution of eukaryotic cells (1.4-1.6 bya) through endosymbiosis.

Explain why antibiotics are an effective treatment for bacterial infections but are completely ineffective against viral infections.

Antibiotics target specific structures or processes unique to bacterial cells, such as cell wall synthesis, bacterial ribosomes, or specific metabolic pathways. Viruses, being non-cellular and relying on host cell machinery for reproduction, lack these bacterial targets, rendering antibiotics useless against them.

Describe the process of binary fission in prokaryotes, highlighting how genetic material is distributed to daughter cells.

Binary fission is an asexual reproduction process. The single circular chromosome replicates, starting at the origin of replication and proceeding in both directions. As replication continues, the two origins move to opposite ends of the elongating cell, pulling the newly copied chromosomes apart. A cross-wall then forms, and the cell divides into two genetically identical daughter cells.

Explain the concept of "antibiotic resistance" and how the overuse of antibiotics contributes to its development.

Antibiotic resistance occurs when bacteria evolve the ability to survive exposure to antibiotics that would normally kill them or inhibit their growth. Overuse of antibiotics creates a strong selective pressure, eliminating susceptible bacteria and allowing naturally resistant strains to survive, multiply, and become dominant, making infections harder to treat.

Anaerobe

an organism that grows without air, or requires oxygen-free conditions to live.

What are some benefits/ uses for bacteria? (Name 5)

1. Bacteria is vital for maintaining human health (Gut Flora)

2. Bacteria decays and decomposition of dead and waste materials

3. Bacteria in digestive tract BREAK DOWN K AND B VITAMINS

4. Bacteria helps make COTTAGE CHEESE AND BUTTERMILK (makes ts sour) and bacteria and CABBAGE makes VINEGAR AND SAUERKRAUT

5. Bacteria can be used to digest petroleum and human waste products

7. Bacteria can hep synthesize drugs and chemicals

7. Bacteria can be adapted to extreme environmetns and make heat stable enzymes - helps make medicine, food, and industrial chemistry

Bacteriophage

A bacteriophage, often called a phage, is a virus that specifically infects and replicates WITHIN BACTERIA

The name literally means "bacteria eater." They are the most abundant biological entities on Earth and are being researched for their potential to combat antibiotic-resistant bacterial infections.

Morphology

Morphology is the study of the form and structure of animals and plants

Tetrad

Group of 4 chromosomes during Pro phase 1