MICR 271 Exam Flash Cards

Which theory supports the connection between prokaryotes and eukaryotes?

The endosymbiont theory

What are some differences between eukaryotic and prokaryotic cells in terms of genetic material storage?

Eukaryote:

• presence of a membrane-enclosed nucleus

Prokaryote:

• presence of a nucleoid

What are the 3 domains of life?

Bacteria, Archaea and Eukaryota

True or false: Eukaryotes and Archaea have a common ancestor.

true.

What is the endosymbiont hypothesis?

The hypothesis states that eukaryotes evolved from prokaryotes, based in the similarities found between bacteria and mitochondria.

What is the archezoan scenario?

• Hypothesizes that a primitive amitochondrial eukaryote cell phagocytosed an alpha-proteobacterium.

• The complexity of the eukaryotic cell and its defining features emerged BEFORE the mitochondrial symbiosis.

This theory has fallen out of favour.

What is the symbiogenesis scenario?

Hypothesized that the complexity of the eukaryotic cell and its defining features emerged AFTER the mitochondrial symbiosis.

What is phylogeny?

The evolutionary history of a group of organisms.

What does the distance between the branch points (of the tree of life) of two species indicate?

How similar their phylogenetic relationship are.

What were the old phylogenetic trees based on?

comparing rRNA

What is the phylogenomic tree of life based on?

comparing entire genomes

What differentiates the the tree of life from the web of life?

The web of life acknowledges the interconnectedness of all the domains of life. This is caused by horizontal gene transfer.

What is a virus? And what are their 3 main components?

They are small infectious agents.

• Genetic material

• Capsid

• Lipid Envelope

What is the first virus theory?

• Proposes that viruses are ancestral to cells.

• Viruses evolved from mixtures of macromolecules before the first cells on Earth appeared.

• It states that viruses existed as self-replicating units in a pre-cellular world.

What is the escape theory?

• The view that cells came before viruses.

• It proposes that viruses are derived from bits of cellular RNA and/or DNA fragments that leaked or “escaped” from cells.

• When DNA or RNA fragments acquire a protein coat they can become independent entities with the ability to interact with other cells.

What is the reduction theory?

The view that cells came before viruses. It proposes that viruses come from small primordial cells that lost cellular elements over the course if evolution, but maintained their genetic material and certain elements needed for replication.

True or false: The origin of viruses is well established.

False.

True or false: Viral genes represent a relatively small proportion of the total genetic diversity on earth.

False

True or False: Viruses are dependent upon their host cells in order to replicate.

True

True or false: Viruses have an important role in carrying genetic information between different species.

True

What is the hierarchy of bacteria taxa (in order)?

Kingdom, Phylum, Class, Order, Family, Genus, Species

What is the hierarchy of viral taxa (in order)?

Order, Family, Genus, Species

What are extremophiles?

Organisms that live in harsh environments

What is selective pressure?

Any phenomenon in the environment of an organism that impacts the fitness of the organism in that environment.

What is actinobacteria?

Group of gram-positive bacteria that are aerobic and mostly found in soil

What are Bacteroidetes?

Diverse gram-negative phylum which have colonized virtually all types of habitats on earth.

What are firmicutes?

Phylum of bacteria which are gram-positive and can often form endospores.

What are proteobacteria?

Major gram-negative phylum, includes a diverse array of bacteria

What is the difference between commensal and pathogenic bacteria?

Pathogenic bacteria: Bacteria that has the ability to cause infection. Some of these bacteria are opportunistic pathogens.

Commensal bacteria: non-pathogenic, they have a symbiotic relationship with the host.

What are the two ways genetic diversity is acquired?

Mutations and gene transfer/genetic recombination.

What are the 3 ways gene transfer occurs in bacteria?

• Transformation

• Conjugation

• Transduction

What is transformation?

The uptake of naked genetic material from the surrounding environment.

What is conjugation?

The direct transfer of genetic material from one bacterial cell to another

What’s transduction?

The process in which bacterial DNA is moved from one bacterium to another by a virus, often a bacteriophage.

What’s transposition?

A “jumping” of genes from one chromosomal location to another within an organism.

What are the 4 mechanisms of resistance of bacteria to antibiotics? Explain each briefly.

• Target protection: production of a protein that disrupts the interaction between an antibiotic and its target

• Target modification: alteration of amino acid sequences in target sites in bacteria

• Prevention of intracellular antibiotic accumulation: increased expression of bacterial efflux mechanisms which result in increased ability of bacteria to remove antibiotics from cell

• Antibiotic detoxification: Increased ability of bacteria to alter or degrade antibiotic, which reduces antibiotic effect

What are 4 reasons for increased antibiotic resistance?

• Long term use of

• Antibiotics are often inappropriately used

• Over the counter courses of antibiotics are taken when they are not needed

• Antibiotics can be inappropriately prescribed

True or False: Without the selective pressure exerted by the use of antibiotics, human pathogens would not have acquired resistance so readily.

True

What is herd immunity?

General immunity to a pathogen in a population based in the acquired immunity to it by a high proportion of members over time.

What are functionally similar structures of all three microbes?

A) Pili, Flagella, and spikes

B) Cytoplasmic membrane, plasma membrane, and protein coat

C) Nucleoid, nuclear envelope, and nucleic acid

B) Cytoplasmic membrane, plasma membrane, and protein coat

Which type of organism has the largest genome?

A) Eukaryotic cell

B) Bacterial cell

C) Virus particle

A) Eukaryotic cell

What are the 2 main virus structures?

Nonenveloped virus and enveloped virus

What is a non-enveloped virus?

The simplest virion, it consists of a capsid made of protein assembled around the nucleic acid (DNA or RNA).

What is an enveloped virus?

Surrounded by a lipid membrane (envelope) that consists of lipids and carbohydrates and embedded viral proteins. Sometimes they also have spikes on their exterior.

What is a virus called that infects bacteria?

Bacteriophage

What are the 3 different types of phage structures?

• Tailed Phage

• P22 Phage

• M13 Phage

What is the 1st step of the bacteriophage assembly line?

Infection: The phage attaches to the surface of he bacterial cell and injects its viral genetic material into the bacterium

What is the 2nd step of the bacteriophage assembly line?

Replication of viral genetic information: the viral genetic information replicates using host cell machinery

What is the 3rd step of the bacteriophage assembly line?

Production of viral proteins: host machinery makes the component parts of new phage

What is the 4th step of the bacteriophage assembly line?

Assembly of viruses: Using the component parts, new phages are created

What is the 5th step of the bacteriophage assembly line?

Lysis of the bacterium: the bacterium cell wall degrades and new phages are released. Lysis of the bacterial cell wall is accomplished by the phage protein lysin.

What’s the difference between lytic and lysogenic infection?

• Lytic destroys (lyse) the cell membrane as the phages escape the cell

• Lysogenic reuses the same cell to incorporate phage DNA, where it is passed on to new generations of the host cell until it goes into the lytic cycle

How do non-enveloped viruses infect host cells?

• They enter the host cell by binding to a receptor on the cell surface.

• They are taken into the host cell by endocytosis and the capsid is subsequently degraded.

• Releasing the viral genome that is transported to the nucleus for replication.

What is the 1st step of a nonenveloped viral infection?

Adsorption: the virus binds to a host receptor at the cell surface

What is the 2nd step of a nonenveloped viral infection?

Endocytosis: the virus is taken into the host cell via endocytosis

What is the 3rd step of a nonenveloped viral infection?

Capsid destruction: the viral genome is released into the cytoplasm after degradation of the viral capsid

What is the 4th step of a nonenveloped viral infection?

Genome replication: the viral genome is replicated inside the host cell nucleus and transcribed to direct viral protein synthesis

What is the 5th step of a nonenveloped viral infection?

Assembly: The viral proteins are synthesized, modified, and assembled with the viral genome to form new viral particles

What is the 6th step of a nonenveloped viral infection?

Release: Progeny viruses are released from cell upon lysis of host cell

What are the 2 basic bacterial structures?

Gram-positive and gram-negative

What are the cell wall components of a gram-positive bacteria?

• Teichoic and lipoteichoic acid: help maintain the structure and contribute a net negative charge to the cell wall

• Size of periplasmic space: much smaller in gram-positive

What are the characteristics of gram-positive bacteria?

• The cell wall provides structural, but not barrier, functions

• contains a thick peptidoglycan layer that is anchored to the cytoplasmic membrane

• Traps crystal violet-iodine complex of gram stain

What are the characteristics of gram-negative bacteria?

• Thin peptidoglycan layer anchored to the cytoplasmic and outer membrane

• Functions as a barrier

• IS more of a pink-red colour when stained

What are the cell wall components of a gram-negative bacteria?

• Size of periplasmic space: much larger in gram-negative

• Outer membrane: asymmetrical bilayer containing proteins, lipoproteins and lipopolysaccharides.

What are the 3 regions of the lipopolysaccharide?

• O-Antigen

• Core

• Lipid A

Explain the process of the gram staining procedure

1. Begin with heat fixed cells

2. Flood the slide with crystal violet dye for 1 minute

3. Add iodine solution for 20 sec

4. Wash slide with alcohol for 20 sec

5. Counterstain with safranin

Gam-positive will appear purple and gram-negative will appear pink-red.

What are key components of facilitated diffusion?

• Molecules move from an area of high concentration to low via a carrier molecule

• No energy required

• Moves along concentration gradient

What are the key components of primary active transport?

• Molecules are moved from an area of low concentration to high.

• Requires energy (ATP)

• Moves against concentration gradient

What are the key components of secondary active transport?

• Utilizes the movement of one molecule down its concentration gradient ro facilitate the transport of a second molecule against its concentration gradient.

• No energy required

What are the key components of group translocation?

• An organic molecule is transported across the membrane into the cell in conjunction with chemical modification

What are the key components of iron uptake? (2 different ways)

1. Transferrin and iron can cross the outer membrane as a complex, and the iron then passes through the inner membrane alone (no energy required)

2. Once the iron-siderophores complex reaches the cell surface, it binds to a siderophore-receptor protein and the whole complex is transported via multiple steps into the cytoplasm.

What are inclusion bodies?

small protein aggregates

What are catboxysomes?

microcompartments in the bacterial cytoplasm containing enzymes involved in carbon fixation

What is the 1st step of bacterial endospore formation?

Vegetative bacterium, a symmetrically dividing cellular form

What is the 2nd step of bacterial endospore formation?

Asymmetric division of the cell results in two compartments. The largest compartment is the mother cell and the small compartment is the forespore

What is the 3rd step of bacterial endospore formation?

Peptidoglycan within the septum between the 2 compartments is degraded and the forespore is engulfed by the mother cell, forming a cell within a cell

What is the 4th step of bacterial endospore formation?

The cortex, a thick layer of specialized peptidoglycan is formed

What is the 5th step of bacterial endospore formation?

Coat synthesis begins. The endospore coat is composed of proteins that provide much of the chemical and enzymatic resistance to degradation

What is the 6th step of bacterial endospore formation?

Coat synthesis is completed, and there is an increase in refractility and heat resistance

What is the 7th step of bacterial endospore formation?

Lysis of the mother cell liberates the endospore

What are the 2 types of motility structures?

• Flagella: used to move in liquid environments

• Pili: used to move on solid surfaces by twitching

What are the 4 arrangements of bacterial flagella?

1. Peritrichous: Multiple flagella all around the bacteria

2. Single/polar: Singular flagella

3. Lophotrichous: Tufts of flagella at one end of the bacteria

4. Bipolar: Singular flagella on each end of the bacterial

True of False: some archaea form monolayers rather than bilayers

true

What are the 2 ways HIV interacts with the host cell?

• Nonspecifically with negatively charged proteins on the host cell surface

• Specifically with host receptor proteins, such as CD4

What are the 2 steps to the adenovirus binding?

1. The virus attaches to the surface of host cell

2. Binding of of integrins and endocytosis

What are the 4 steps to biofilm formation?

1. Target cell interaction

2. Adherence

3. Biofilm formation

4. Target cell lysis

True or False: bacterial pili are used by bacteriophages for their own adherence to bacterial cells

True

What are the 3 steps for pilus-specific bacteriophage?

1. Attachment: attaches to bacterial pili

2. Retraction: retraction of the pili brings the phage in close proximity with the bacterial cell

3. Uncoating and penetration: interacts with membrane proteins or use the pili to directly inject the phage genetic material into the cell

What does the innate immune system do?

The innate immune system produces a nonspecific response, surveilling the body for foreign invaders and eliminating them.

What does the adaptive immune system do?

The adaptive immune system will initiate a specific response using specialized immune cells to eliminate and prevent the growth of the pathogen.

What are the 4 steps (phases) of the bacterial growth curve plot?

1. Lag phase

2. Exponential (Logarithmic) phase

3. Stationary Phase

4. Decline/death phase

Describe the lag phase.

• The bacteria adapt to the growth conditions

• The bacteria are maturing but not dividing yet

Describe the exponential phase.

Period characterized by cell doubling

Describe the stationary phase.

• The growth rate and death rate are equal

• It shows are linear in the graph because of he depletion of nutrients and build-up of waste products

Describe the decline/death phase.

Bacteria die or become smaller due to lack of nutrients and accumulation of deleterious mutations

What is a plate assay?

A method used to quantify. microbes

What is the first step of a plating assay?

Serial dilution: takes a known volume of the stock and place it into a known volume of distilled water.

What is the second step of a plating assay?

Serial dilution again: takes a known volume of the stock and place it into a known volume of distilled water.

What is the third step of a plating assay?

Serial dilution is repeated until the desired dilution is reached.

What is the fourth step of a plating assay?

They are put onto an agar plate (the more concentrated the stock, the more plaques or colonies that form.