Midterm 1 study Q's Flashcards

1
Q

True or false: Microorganisms have adapted to every environment on earth.

A

True!

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2
Q

Hyperthermophiles can live in near _____ temperatures.

A

Hyperthermophiles can live in near boiling temperatures.

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3
Q

When the equilibrium falls between symbiotic communities, we can it ______.

When one species takes over the community, it can result in _______.

A

When the equilibrium falls between symbiotic communities, we can it dysbiosis.

When one species takes over the community, it can result in pathogenesis.

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4
Q

about how big is a bacteria?

A

1 μm

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5
Q

Viron vs Prion?

A

A virion is a complete virus particle that consists of genetic material, either DNA or RNA, surrounded by a protective protein coat called a capsid, and sometimes an outer lipid envelope. It is capable of infecting host cells to replicate and spread.

In contrast, a prion is an infectious agent made solely of misfolded protein without any genetic material. Prions cause diseases by inducing normal proteins in the host to misfold, leading to neurodegenerative conditions. While virions contain nucleic acids and can replicate, prions rely solely on protein misfolding to propagate.

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6
Q

1: How do bacteria know what shape they have to be?

2: What moulds their shape?

A

1: They know what shape they have to be due to their genetics, including the shape of their cell wall. Some bacteria can change their shape according to environmental stressors.

2:The shape of bacteria is primarily moulded by their cell wall, which is composed of peptidoglycan—a mesh-like structure that provides rigidity. The arrangement and cross-linking of peptidoglycan layers determine the overall shape, whether it be rod-like (bacilli), spherical (cocci), or spiral (spirilla).

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7
Q

True or false: all bacteria have a flagella

A

False. Not all bacteria have flagella. Flagella are specialized structures that some bacteria possess to aid in movement, but many bacteria lack flagella entirely. Bacteria can move in various ways, including through other means like pili or by using diffusion.

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8
Q

the cytoskeleton is composed of what macromolecule?

A

Proteins.

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8
Q

True or false: a standard bacteria contains ribosomes

A

True

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9
Q

true or false: the lipid bilayer has fluidity?

A

True. The lipid bilayer has fluidity, allowing its components (such as proteins and lipids) to move laterally within the membrane.

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10
Q

integral vs peripheral protein?

A

integral are embedded in the membrane, peripheral are attached to the membrane’s surface.

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11
Q

1: Phosphatidylglycerol structure?

2: Phosphatidyethalolamine structure?

A

1: Phosphatidylglycerol is made of glycerol ester linked to 2 fatty acids, and on its other side, a phosphoryl group linked to a terminal glyceride.

2: Phosphatidyethalolamine contains glycerol linked to 2 fatty acids, and a phosphoryl group with a terminal ethanolamine.

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12
Q

Identify the main shapes of bacteria

A

-A Coccus is a single circular bacterium.
–> Diplococcus (two)
–> Tetrad (four)
–>Streptococcus (chain)
–> Staphylcoccus (cluster)

-A single rod bacteria is a Bacillus
–> a chain is streptobaccillus.

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12
Q

Which of the following statements is true? Pay attention to the capitalized terms and their definition.

The PROPHAGE excised itself from the plant cell’s genome.

The uncoated virus, or VIRION, hijacked its host’s machinery.

This animal cell is a known host of fourteen different PHAGES.

The eukaryote could not eliminate its integrated PROVIRUS.

A

Answer: The eukaryote could not eliminate its integrated PROVIRUS.

Prophage refers to viral DNA integrated into a bacterial genome, not a plant cell’s genome. The statement about the prophage in a plant cell is incorrect.

Virion refers to the complete virus particle outside the host cell, not after uncoating and hijacking the host’s machinery. The use of “virion” here is incorrect.

Phages infect bacteria, not animal cells. The statement about an animal cell being a host of different phages is incorrect.

Provirus is the correct term for viral DNA integrated into a eukaryotic host genome, as in this case with a eukaryotic cell.

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13
Q

What are hopanoids?

are they just for bacteria?

A

they stick into the cell membrane and stabilize it.

Usually but not exclusively found in bacteria.

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14
Q

Describe the structure and function of the glycocalyx (capsule/slime layer)

A

Structure: Made of polysaccharide layers that may differ in rigidity and flexibility.
–>Two parts to it: the capsule layer and the smile layer.
–>Capsule layer is tightly attached, a tight matrix, visible if treated with India ink.
–>The slime layer is loosely attached and easily deformed.

FUNCTION:
–>helps attach to surfaces.
–>Protects against phagocytosis
–>prevents dehydration.

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15
Q

What does S-Layer do, what is it?

A
  • Additional protective layer found in gram-positive bacteria, gram negative baceria, and archaea.
  • It’s a crystalline layer of thick subunits consisting of protein or glycoprotein.
  • Helps Protect from OSMOTIC STRESS and may contribute to cell shape.
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16
Q

Fimbriae?

A
  • helps organism stick to surfaces
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17
Q

Pili?

A

Pili are hair-like appendages found on the surface of many bacteria. They are primarily involved in functions such as attachment to surfaces, motility, and gene transfer between bacteria (conjugation). Unlike flagella, pili are usually shorter and more rigid, and they can help bacteria adhere to host tissues or exchange genetic material through a process called bacterial conjugation.

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18
Q

How does the peptidoglycan layer differ between gram-negative and gram-positive bacteria?

A

Gram-negative: no actual molecules that link the two amino acid tetramers together.

Gram-positive: the amino acid tetramers are linked by a pentaglycine bridge (5 glycine molecules).

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19
Q

What are NAM and NAG?

A

the two sugars that make up peptidoglycan (peptidoglycan layer) in BACTERIA.
(bound together by Beta-1-4 linkages).

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20
Q

What enzyme can destroy the NAM and NAG sugar bonds in the peptidoglycan layer?

A

a lysozyme.

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21
Q

Why are bacteria excellent targets for antibiotics such as Penicillin and Vancomycin?

A

Because both of those antibiotics target the peptidoglycan layer of the bacteria, and that layer is unique to bacteria, so it would not affect our own cells.

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22
Q

Is the peptidoglycan layer the cell wall of the bacteria?

A

Yes, the peptidoglycan layer is the main component of the cell wall in most bacteria.
(it provides structural strength, maintains the cell’s shape, and protects it from osmotic pressure).

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23
Q

True or false: different bacteria synthesize their peptidoglycan cell walls from different locations depending on the bacteria.

A

TRUE!
The cell wall can have growth from different areas, depending on the bacteria.

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24
Q

what is a bacteriophage?

A

A bacteriophage (often called a phage) is a virus that infects and replicates within bacteria. They are highly specific to their bacterial hosts and are found in many environments, including soil, water, and even within living organisms.

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25
Q

Gram positive vs Gram negative bacteria?

A

Gram-Positive:
-S-layer
-Thick peptidoglycan layer
-cell membrane

Gram negative:
-Outer membrane
-Peptidoglycan
-inner membrane

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26
Q

do gram positive bacteria still have membrane proteins, even though their membrane is on the inside of the peptidoglycan layer?

A

Yes, Gram-positive bacteria still have membrane proteins in their cell membrane, even though it is located beneath the thick peptidoglycan layer.

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26
Q

Describe Acid-fast bacteria.

A

-They have a HYDROPHOBIC LAYER.

Acid-fast bacteria, such as Mycobacterium species, have a thick, waxy cell wall rich in mycolic acids. This waxy layer makes them resistant to typical staining methods, so they require a special acid-fast stain (like the Ziehl-Neelsen stain) to be identified. Once stained, they retain the dye even after being exposed to acidic decolorization, distinguishing them from non-acid-fast bacteria. Acid-fast bacteria are often associated with diseases like tuberculosis and leprosy.

27
Q

What are the 5 areas that antibiotics may target on a bacteria?

A

1: Cell wall (penicillin, vancomysin)

2: Plasma Membrane.

3: Ribosomes

4: Metabolic pathways

5: DNA & RNA synthesis

28
Q

Describe the structure, function, and biochemistry of the bacterial plasma (cytoplasmic) membrane.

A

Structure: regular cell membrane. Lipid bilayer, membrane proteins, has HOPENOIDS instead of cholesterol (as found in eukaryotes) to stabilize the membrane.

Function: Same as any other membrane.
-Passage of ions
-ATP production
-signal transduction

Biochemistry: The membrane is made of phospholipids, with a glycerol backbone, fatty acid tails (hydrophobic), and phosphate heads (hydrophilic). The presence of ether bonds in archaea vs. ester bonds in bacteria and eukaryotes is notable.

29
Q

Bacteria can have two possible different phospholipid types depending on their ________.

A

Bacteria can have two possible different phospholipid types depending on their environment.

(names on a different cue card).

30
Q

What are the 3 main roles of the bacterial cell membrane?

A

1: Permeability barrier (allows stuff in and out)

2: protein anchor (contains membrane proteins).

3: energy conservation (atp production, “proton motive force”)

31
Q

What are the 3 filaments in the BACTERIAL cytoskeleton?

A

FtsZ: Tubulin-like Protein. (think t for tubulin).

MreB: Actin-like protein.

Crescentin: filament-like protein.

32
Q

What shape is each of the bacterial cytoskeleton filaments?

A

FtsZ: Circular

MreB: coil-shaped

Crescentin: regular straight filament shape.

33
Q

What does the bacterial cytoskeleton do?

A

-Necessary for the movement of molecules within the cell (regular cytoskeleton stuff).

-Influences the shape of the cell (regular cytoskeleton stuff).

34
Q

What do the FtsZ, the MreB, and the Crescentin cytoskeleton filaments do?

A

FtsZ: Forms a ring at the future site of cell division, guiding the formation of the septum, which is crucial for bacterial cell division.
(so, guides growth of the septum).

MreB: determines the length of the cell.

Crescentin: curves the bacteria into a crescent shape.

35
Q

What is the nucleoid?

A

-The nucleoid region is where the cluster of the bacteria’s DNA is located (in the centre of the bacteria).

-Prokaryotes have this

-it’s obviously not enclosed by a membrane.

36
Q

Describe DNA replication of the bacteria’s circular chromosome at the Ori site.

A

1: The origin replicates, and two replisomes begin replicating.

2:

37
Q

In bacterial cells, the DNA is attached to the envelope at the _______________.

A

-In bacterial cells, the DNA is attached to the envelope at the origin of replication.

(this is where the circular chromosome will replicate from when DNA replication occurs.)

38
Q

In prokaryotes, why is translation coupled so closely with transcription?

A

Because the ribosomes will bind to the mRNA and begin translation into proteins before the mRNA has even finished transcribing the DNA.

39
Q

Describe the function of inclusions

A

-they are crytal-like structures that store energy and reduce osmotic stress.

-They store carbon based polymers, and also store glycogen and PHB

-Inclusions are specialized structures within bacterial cells that serve as storage sites for various substances. They can store nutrients, such as carbohydrates, lipids, and proteins, which the cell can use when needed, especially during periods of nutrient scarcity. Inclusions can also store waste products or byproducts of metabolism to prevent them from interfering with cellular processes. Overall, they help bacteria manage resources efficiently and adapt to changing environmental conditions.

40
Q

Describe the structure and function of endospores.

A

-Some bacterial cells can preserve their DNA genome into a little capsule like spore. This spore is essentially the bacteria’s “child” that it gives its energy to and then dies for.

a spore can withstand conditions that a vegetative cell cannot.

they do not metabolize

STRUCTURE: has a membrane around the DNA, a cortex, a protein coat (exosporium).

41
Q

Explain Parsing intracellular material

A

-Parsing intracellular material refers to the process by which cells sort, organize, and distribute the components within their internal environment. This involves breaking down complex molecules, transporting nutrients, and separating waste or unwanted materials. Cellular mechanisms, like endocytosis and vesicle transport, help move and process this intracellular content to maintain proper cell function and homeostasis.

-ParM is an actin-like protein that will push plasmids to each end of the new cells during cell division.

-Think PARTITIONNING, so splitting things equally among cells.

42
Q

Differentiate flagella, fimbriae, and pili

A

Flagella: Long tail structures used for movement. They rotate to propel the bacterium through liquid environments.
–>Bacteria use a rotary motion, eukaryotes use a whip-like motion!

Fimbriae: Short, hair-like projections that help bacteria attach to surfaces and each other. They are not used for movement but for adhesion.

Pilli: Similar to fimbriae but usually longer and less numerous. They can be involved in transferring genetic material between bacteria (conjugation) {SEX PILUS} and also help with attachment.

43
Q

Describe the different mechanisms used by bacteria for locomotion.

A

-Flagella: bacteria can move my rotating flagella. (helps with things like chemotaxis).

-Pili: Some bacteria use pili to “crawl” along surfaces in a process called twitching. Pili extend, attach to a surface, and then retract, pulling the bacterium forward.

-Gliding: Certain bacteria can glide along surfaces without the use of flagella or pili. The exact mechanism is not fully understood, but it may involve the secretion of a slimy layer or other surface proteins that reduce friction.

-Bacterial Corkscrew Movement: Spirochetes, a type of bacteria, move in a corkscrew fashion due to their unique flagella located within their outer membrane. This allows them to burrow through viscous environments, such as mud or tissue.

44
Q

Identify structures unique to bacteria.

A

1:Peptidoglycan Layer: A rigid layer that provides structural support to the cell wall.

2: Plasmids: Small, circular DNA molecules separate from the chromosomal DNA, often carrying antibiotic resistance genes.

3: Flagella: Tail-like structures used for movement, often with a simple structure compared to eukaryotic flagella.

4: Pili (or Fimbriae): Hair-like appendages used for attachment to surfaces and in conjugation.

5: Capsule: A protective outer layer made of polysaccharides that can help bacteria evade the immune system.

6: Endospores: Highly resistant structures that allow bacteria to survive harsh conditions.

7: Nucleoid Region: The area where the bacterial chromosome is located, not enclosed by a membrane.

45
Q
  • Describe the concept of asymmetry and its purpose using a few examples.
A

Asymmetry in bacteria refers to the unequal distribution of cellular components and structures. In Gram-negative bacteria, the outer membrane contains lipopolysaccharides that protect against antibiotics, while the inner membrane has a different lipid composition. Some bacteria have polar flagella that allow for directional swimming, enhancing their ability to move toward favorable conditions. Certain metabolic enzymes are localized to specific regions of the cell, optimizing metabolic processes. During cell division, asymmetry allows daughter cells to have different characteristics, impacting their adaptability. This asymmetrical organization is essential for bacteria’s survival and efficiency in diverse environments.

46
Q
  • Explain why archaea are considered a separate domain of life (this includes knowing how to distinguish organism evolutionarily)
A

-Metabolism like redox reaction = like bacteria.

-DNA & RNA machinery = like eukaryotes.

-gene regulation = like bacteria

-UNIQUE trait of ether-linked membranes, found naturally only in archaea.

-Single, circular genome = like bacteria

-Histones = like eukaryotes

-DNA replication enzymes = look like eukaryote ones.

-Cytoskeleton = similarities to bacteria and eukaryotes.

Archaea are considered a separate domain of life due to their unique genetic and biochemical characteristics that distinguish them from bacteria and eukaryotes. While they are both prokaryotic, archaea have distinct ribosomal RNA sequences, which indicate a different evolutionary lineage. Additionally, their cell membranes contain ether-linked lipids, unlike the ester-linked lipids found in bacteria and eukaryotes. Archaea also possess unique metabolic pathways and are often found in extreme environments, such as hot springs and salt lakes, further emphasizing their evolutionary divergence. These differences support the classification of archaea as a separate domain, highlighting their unique evolutionary history and adaptations.

47
Q

Describe the General shapes and characteristics of archaea

A

-Can live in extreme environments

-0.5 to 5 um.

-NO nucleus.

-is a prokaryote

-single, circular genome.

-some have gas vacuoles or carbon storage

-Shapes are the same as bacteria: cocci, bacilli, spirilla, filamentous

48
Q

Archaeal vs bacterial cell membrane?

A

Archaeal and bacterial cell membranes differ in several key ways. Archaeal membranes are made of ether-linked lipids and can form monolayers or bilayers, while bacterial membranes are always bilayers made of ester-linked lipids. Additionally, archaea use isoprene units in their lipids, whereas bacteria use straight-chain fatty acids. These differences contribute to the ability of archaea to survive in extreme environments.

49
Q

tell me about Cell wall structure of archaea.

A

-instead of peptidoglycan, SOME have pseudomurine mech.
(so just instead of peptidoglycan, basically same thing).

-the sugars are NAT and NAG (instead of NAG and NAM in bacteria), and they have glycosidic beta-1,3 bonds instead of the beta-1,4 ones in bacteria.

-some archaea have pseudomurein in their cell walls, while others have an S-layer.**

50
Q

what is an s-layer?

A

-usually outermost layer, resists osmotic pressure, more flexible than a peptidoglycan layer.

-made of protein or glycoprotein.

51
Q

Archaeal Plasma (cytoplasmic) membrane structure?

A

-structurally similar to membrane of bacteria and eukaryotes, but different lipid constituents.

-can form membranes with only a mono-layer. (more stable than a bilayer in hot environment)

-Isoprene chains instead of fatty acids.

-Ether linkages instead of ester linkage in bacteria and eukaryotes.

52
Q

what are Hami in archaea?

A

Hami are Archaeal “grappling hooks” that assist in surface attachment.

53
Q

Compare Archaella to flagella of bacteria or eukaryotes.

A

-simpler than flagella.

-uses ATP rather than proton motive force.

-rotating flagella (eukaryotes have whip-like flagella)

54
Q

Archaeal cytoskeleton

A

-Composed of:

TubZ (similar to FtsZ/tubulin)
determines cell length

Crenactin (like MreB/actin)
aids in septum formation during cytokinesis.

55
Q

Describe structures, metabolic pathways UNIQUE to archaeal cells

A

**Unique Structures:::

Pseudomurein - A cell wall component similar to peptidoglycan but distinct in composition.

S-layer - A protective outer layer made of proteins, found in many archaea.

Ether-linked lipids - Membrane lipids with ether bonds instead of ester bonds, providing stability in extreme environments.

Hami - Unique filamentous structures that help in adhesion to surfaces.

**Unique Metabolic Pathways:::

Methanogenesis - A process that produces methane as a metabolic byproduct, exclusive to methanogenic archaea.

Sulfur reduction - Some archaea can utilize sulfur as an electron acceptor in their energy metabolism.

Anaerobic ammonium oxidation (anammox) - A unique pathway used by some archaea for nitrogen cycling in oxygen-depleted environments.

Haloarchaea phototrophy - The use of light to drive ATP synthesis, using proteins like bacteriorhodopsin.

56
Q

Describe the structures and composition of viruses

A

-A capsid to enclose the genome

-a genome

-an envelope(optional)
–> Surface proteins may be found on envelope.

57
Q
  • Differentiate among bacteriophages, plant viruses, and animal viruses
A

Bacteriophage: A virus that infects Bacteria!!
–> Prophage integrates its genome into the bacteria’s genome.

Plant Virus: virus that infects plants.

Animal Virus: virus that infects animals.
–> Virus that integrates its genome into the animal’s DNA is a *provirus.
–>Pass the provirus onto your gametes and offspring = endogenous virus.

58
Q

Describe the general characteristics of viral life cycles and its different phases.

A
  1. attachment to cell, injects its genome.
  2. Viral DNA integrates into host’s DNA
  3. viral DNA uses the ribosomes to construct its proteins.

4: assembly and packaging of new viruses

5: cell lysis and release of new virions.

59
Q

Lytic vs Lysogenic cycle of viruses?

A

-weather it’s Lytic or Lysogenic depends on the environment.
–> typically, things that threaten the host cell’s survival trigger a LYTIC burst.

-lysogenic is where the DNA remains dormant in the host’s genome.

-Lytic is where it kills the cell and releases the virions.
–>As the virus replicates and assembles new virions, the internal pressure increases. Eventually, the production of viral proteins can also disrupt the host cell’s membrane. When the pressure becomes too great, or when the cell membrane integrity is compromised, the cell membrane ruptures, releasing the newly formed viruses into the surrounding environment.

60
Q

Describe how phages, using T4 as an example, deliver DNA into its host

A
  1. bacteriophage’s tail fibers bind to polysaccarides (ATTACHMENT).
  2. base of the tail contacts the cell wall surface.

3: T4 Lysozyme (enzyme that breaks down bacteria cell walls) drills a hole in cell wall.

4: Tail sheath contracts and pops our tail tube into the cell wall, which will reach the genome inside.

5: genome is excreted from tail tube, and is now within the cytoplasm.

61
Q

Describe the several mechanisms of defense bacteria have against viral infections

A

1: Genetic Resistance

2: Restriction endonucleases

3: CRISPR

62
Q

Explain the difference between a virulent and temperate virus

A

Virulent: Always kills host (always does lysis)

Temperate Virus: develops a long-term stable relationship with host, integrates it’s DNA into host’s genome. (does not try to kill host unless it needs to i guess).
–>Lysogen = host cell harboring a temperate virus.
–> Lysogeny = does not use the ribosomes to make its proteins, lays dormant, is passed to daughter cells.

63
Q

Describe Genetic Resistance.

(bacteria defence against virus)

A

Bacteria mutates and changes the surface molecules that the virus phage recognizes.

–> or it can produce a molecule to mask the phage’s target.

–> Con: the phage will adapt to recognize the new molecule.

SO bacically, trying to trick the phage into thinking this is the wrong spot so it won’t bind.

64
Q

Describe Restriction enzymes

A

-bacteria makes enzymes that will eat gene sequence that the virus secretes into it.

(a cat and mouse game, bacteriophage finds a way to override, bacteria makes a new one).

65
Q

Describe CRISPR.

A

–> Basically, bacteria can have these proteins that recognize the Virus gene sequences, and cut them out.
—>Bacteria must have been infected once before in order to have knowledge of these sequences of course.

CRISPR, or Clustered Regularly Interspaced Short Palindromic Repeats, is a part of the adaptive immune system in bacteria that provides protection against viral infections. In bacterial cells, CRISPR sequences contain snippets of DNA derived from previous viral invaders, which serve as a memory bank. When the bacteria encounter the same virus again, they use CRISPR-associated proteins, like Cas9, along with a guide RNA that matches the viral DNA to target and cut it. This process prevents the virus from successfully replicating within the bacterial cell, effectively acting as a defense mechanism against future infections.

66
Q

Describe the 3 mechanisms of entry utilized by animal viruses

A

1: Endocytosis of a non-enveloped virus.
(so, it gets the vacuole of the animal cell as it’s “membrane” instead while it’s in there.)

2: Membrane fusion of an enveloped virus.
(so, a virus that DOES have an envelope, will fuse that envelope with the cell’s membrane, and then let the naked virus capsule into the cell, and it just releases it’s DNA there.)

3: Endocytosis of an enveloped virus. (so, just it has an envelope and ALSO gets a vacuole around it from the animal cell membrane.)

67
Q
  • Describe the replication process of animal viruses (what is particular to animal infections)
A

Lytic cycle: Same basically as in bacteria. Host cell usually dies. (but they also can leave through exocytosis, which will sometimes leave the host alive).

Lysogenic cycle: same concept as for bacteria essentially.
DNA remains dormant, is sometimes passed onto offspring. It can choose to begin forming proteins and buildings viruses at some point though, if it needs/wants to.

68
Q

Explain what viral tropism is

A

ability to infect a particular tissue type within a host.

69
Q

Describe unique characteristics of retroviruses and latent viruses

A

Retroviruses: Use a reverse transcriptase to copy their genomic sequence.
(some RNA viruses can turn to retroviruses, in order to turn their genome to DNA)

Latent viruses: Latent viruses are viruses that can remain dormant within a host cell for extended periods without causing immediate harm or symptoms.
(latency period)