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Exam 3 Flashcards

1
Q

Viruses do more than cause diease such as?

A
  • Vital members of aquatic
    ecosystems.
  • It can be used to destroy
    cancer cells and pathogenic
    bacteria. -Phage therapy
  • Bacteriophages in human guts
    may regulate bacterial
    microbiome.
  • Important model organisms.
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2
Q

Hershey and Chase Experiment ( 1952)

A

This was the experiment that allowed the determinaiton of DNA as the genetic material.
This was done by radio labels of bacteriophages the compounds like sulfur in proteins was labled and phosphorus in DNA.
The bacteriphases were manipulated via transduciton mechanism and tracking the genetic materia being passed on they found that DNA was the radio labeled material being moved into bacteria.

DNA is the genetic material.

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3
Q

What are the 7 characteristics that make something living?

A

-Growth and Development
-Respond to enviroment
-Cellular
-metabolism
-homeostatsis
-heredity
reproduce

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4
Q

Does a virus really follow the 7 characteristics of being alive?

A

Viruses can only complete 2 of the 7 under very specific conditions. So no they arent alive.
They can reproduce and pass on heredityary material. But they can only accomplish this within a host cell. It does not change over time.

dont have ribosomes cant sequnce gene to be in tree of life

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5
Q

What is a virus?

A

Acellular infectious agents
* Obligate intracellular parasites

They infect all types of cells
* Bacteria
* Archaea
* Eukaryotes

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6
Q

other acelluar infectious agent

A

Viroids
satelites
prions

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7
Q

viroids

A

small single-stranded circular RNA
* Only plant pathogens

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8
Q

satellites

A

viruses that co-infect with another
virus
* They cannot replicate on their own and depend on
a helper virus
* Example: hepatitis D, helper hepatitis B

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9
Q

prions

A

proteinaceous infectious particles
* Small misfolded proteins
* Cause neurodegenerative diseases
* Example: Mad cow disease

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10
Q

Virus particle composition

A

Covering- Capsid ( envelope)
Central Core ( nucleic acid , matrix proteins , enzymes)

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11
Q

Virion Structure Covering

A

Capsid - proteins
* Protects the nucleic acid
* Involved in host cell recognition, binding,
and release of nucleic acids into host cell

Envelope – lipids
* Not all viruses are enveloped
* Host membranes
* Viral proteins replace host proteins
* Usually, from host cell

Spike proteins

Non-envelope virus are considered naked

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12
Q

Virion Structure Central core

A

Nucleic Acids (viral genome)
* DNA or RNA

Proteins
* Vary by type of virus
* Viral proteins/enzymes encoded by viral
genome

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13
Q

Basic Structure of capsids

A

Icosahedral
* Radial symmetry; based
on an icosahedron

Filamentous
* Helical symmetry,
Flexible

Complex
* Amorphous Viruses
* No symmetry

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14
Q

Viral Genome

A

Dont follow the Central Dogma
- Baltimore classification system ( based on how to get into mRNA)
1.dsDNA
2.ssDNA
3.dsRNA
4.ssRNA(+)
5.ssRNA(-)
6.ssRNA-RT
7.dsDNA-RT

Viruses force cells to make viral genome which then has a high muation rate.

positive sense can work as mRNA

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15
Q

General viral multiplication

A
  1. Attachment (adsorption)
  2. Entry into the host cell
    (penetration)
  3. Synthesis
  4. Assembly
  5. Release
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16
Q

Viral attachment

A

Step with specificity
* Host Range

Envelope/Capsid proteins
bind with specific receptors
in the host cell membrane.

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17
Q

viral entry to the host cell

A
  • Depends on the virus
    A. Inject nucleic acids
    B. Receptor-mediated
    endocytosis
    C. Viral envelope fuses with the
    host cell’s membrane
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18
Q

Viral synthesis

A
  • Steps and location depend
    on the viral genome
  • Virus uses host cell
    machinery to make more
    copies of itself
  • High mutation rate! ( our cells dont know how to make viruses)
  • Trick DNA viruses tend to go to nucleus and RNA tend to remain in cytoplasm
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19
Q

Where does the Assembly of viruses occur for EUK and Prok

A

Prok
- cytoplasm

Euk
* Depending on virus
* Nucleus
* Cytoplasm
* ER/Golgi

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20
Q

release of viruses

A
  • Depends on the virus

A. Cell lysis – naked viruses
B. Budding - enveloped viruses
* Cell membrane
* ER/Golgi
* Other

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21
Q

Viral Infections in animals

A
  • acute infection
    Infection leads to lysis of cell (ex.influenza)
  • latent infection
    Infection leads to a dormant virus within a cell ( ex. HIV ,Herpes simplex) later activation with symptoms coming and going. Long term.
  • chronic infection
    infection has a very slowly replicaiton time and damamage isnt present till much later. persistent viral infection ( Hepatatis B )
  • transformation into malignat cell
    viral infection turns cells into cancer or malignant cells ( HPV)

Epstein-Barr both persistent and infections

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22
Q

Describe why it is difficult to generate antiviral drugs.

A

Targeting bacteria means we target strucutres that help bacteria grow but viruses arent like bacteria.

Antiviral agents are hard to discover.
* What can be targeted?

Viruses are unique.
* There is no one medication that will target all viruses.

Antiviral agents may have severe side effects.
* Some drugs may target the host cell structures. (Not ideal!)
* Metabolized by liver.

Viral genomes mutate quickly, even faster than bacteria.
* No one antiviral agent will work for long.

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23
Q

What are the differences between types of genome in viruses?

A

It variation comes on how many steps it takes to make mRNA from the starting genomic material of the virus

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24
Q

How do group 1 and group 2 viruses replicated their genome?

A

-Single and double stranded DNA follow central dogma

dsDNA-Transcription -mRNA - translation- Protein
- viral or host RNA polymerases are resposible for transcription
- translation is possible due to host ribosomes
- -viral and host DNA polymerase respobile replicaiton

ssDNA(+)- make compliment strand-dsDNA-Transcription -mRNA - translation- Protein
- viral or host RNA polymerases are resposible for transcription
- translation is possible due to host ribosomes
- -viral and host DNA polymerase respobile replicaiton

most found in nucleus

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25
HPV
* Causes warts or cancerous lesions * Direct contact-sexual * dsDNA * Icosachaedral capsid * Naked
26
What is the replication cycle of HPV?
**Receptor**: Extracellular Matrix proteins of Keratinocytes **Entry**: Endocytosis **Synthesis/Assembly**: Nucleus, then cytoplasm **Release**: Lysis* - note that when you have uninfected epithelium cells outer most cells are dead and compact but infected by HPV will interupt gene expresssion and not die which can lead to cancerous cells.
27
RNA viruses and the classes
**Group 3**: dsRNA **Group 4**: ssRNA(+) **Group 5**: ssRNA (-) **Group 6**: ssRNA-RT | most of them found in cytoplasm with a exception of influenza
28
What are unique proteins that allow for RNA replication onlly found in viruses?
RNA-dependent RNA-Polymerases(RdRp)
29
RNA virus synthesis of group 3
dsRNA-**Transcription**-(+)mRNA-**Translation**-Protein-**Assembly ** - Uses host Ribosomes - replicaiton of the + mRNA is done by RdRp - dsRNA is then packaged in capsid protein
30
RNA viruses synthesis of group 4
(+)ssRNA-**Translation**-Protein - Replication of the (-)ssRNA using RdRp which is then replicated to make the (+)ssRNA which can be packaged in the capsid - during the replication of ssRNA leads to high error and high mutation rate which explains the many strains of virus - host cell ribosomes are using for translation
31
RNA viruses synthesis of group 5
(-)ssRNA-**Replication**-(+)ssRNA-**Translation**-protein-**assembly** - RdRp used in making the (+)ssRNA and to make the (-)ssRNA that will be packaged - ribosomes from host cell
32
SARS-CoV-2
* Causes Covid-19 * Direct transmission- Respiratory route * Helical capsid * ssRNA+ * Enveloped *** Receptor**: ACE2-receptor in host cells **Entry**: Endocytosis * **Synthesis/Assembly:** Cytoplasm and ER/Golgi) * ***Release***: Exocytosis | ACE2-receptors
33
Ebola
* Causes Hemorrhagic Fever * Direct transmission-bodily fluids * Helical capsid * ssRNA- * Enveloped * **Receptor**: C-type lectins (cell adhesion, immune response, apoptosis) * **Entry**: Endocytosis * **Synthesis/Assembly**: Cytoplasm * **Release**: Budding
34
Influenza Virus
* Causes influenza or flu * Direct transmission-Respiratory route * Pleomorphic capsid * ssRNA- * Enveloped * **Receptor**: Sialic acid receptors * **Entry**: Endocytosis * **Synthesis**: Viral RNA in nucleus * translation in cytoplasm * **Assembly**: Cytoplasm/Golgi * **Release**: Budding | exception virus that will go into the nucleus for assembly
35
Measles
- Helical capsid - ssRNA(-) - enveloped - entry: membrane fusion - synthesis/assembly :cytoplasm - release: budding - receptor: CD46 ( all nucleated cells) - SLAM immune cells - nectin-4 respiratory tract epithelium **Complicaitons ** * Pneumonia * Encephalitis * Subacute sclerosing panencephalitis: rare but fatal brain infection years after infection * Immune suppression * Hearing loss - cognitive impariment - seizures - death - highly transmisible Ro=18
36
RNA viruses syntehesis group 6
(+)ssRNA-**Reverse Transcription**-(-)ssDNA-**Replication**-dsDNA-**Transcription**-Protein-**Assembly** * ssRNA * Reverse transcriptase( viral protein only ) * dsDNA is integrated into the host’s DNA and serves as a template for mRNA synthesis and positive-strand RNA genome synthesis. - host cell ribosomes used in translation - RNA pol from host
37
HIV
* Causes AIDS * Direct transmission-Parenteral and sexual contact * Cone-shaped capsid * ssRNA Retrovirus (RT) * Enveloped * **Receptor**: CD4+ receptor (only found in T-cells) *** Entry**: Envelope fusion * **Synthesis/Assembly**: Cytoplasm- Nucleus-Cytoplasm * **Infection result**: Latent infection or Acute *** Release**: Budding
38
potential drug targets for the 6 groups of viruses.
**Group 1 and 2**: DNA and RNA viral polymerases **Group 3 , 4 , 5**: RdRp **Group 6**: RT , Integrase ,Protease
39
metabolism
Is the process of using Energy, Carbon , Electrons to make ATP which can be used to do Chemical work—synthesis of complex molecules (anabolism) Transport work—take up nutrients, eliminate wastes, and maintain ion balances Mechanical work—cell motility and movement of structures within cells | make and use ATP
40
catabolism
breaking down sources of energy which allows the creation of ATP
41
anabolism
the use of ATP to generate large molecules
42
What is ATP and its role?
* Adenosine triphosphate * Nucleotide * Precursor to DNA and RNA * Energy carrier/Activated carrier
43
Substrate Level phosphorylation
Enzyme-substrate The enzyme will phosphorylation allows the formation of ATP
44
Oxidative Phosphorylation
Oxidation-Reduction (Redox) reaction Happens in a membrane, the variety of mebrane proteins that have affinity to electrons transport it. This then lands in electron acceptor molecule. Thorught this process a Proton gradient is generated on one side of the membrane. The cell will then want to move these proton via a protein like ATP synthase that mechanism will phosphorylate and form ATP.
45
Photophosphorylation
Light energy is used to create ATP same idea that the electrons will create proton gradient that is used to activate ATP synthase that phosphoyrlate and make ATP
46
Oxidation reduction reactions play a critical role in energy conservation
* Donates electron (oxidation reaction). Low energy * Accepts electron (reduction reaction). High energy
47
another energy activated carrier
NADH * Nucleotide * Nicotinamide adenine dinucleotide + hydrogen * Oxidation-reduction (redox) reactions * Electron carrier * Accepts electrons – energy full (NADH) * Donates electrons - release energy (NAD) FADH * Nucleotide * Flavin Adenine Dinucleotide + Hydrogen * Oxidation-reduction (redox) reactions * Electron carrier * Accepts electrons – energy full (FADH) * Donates electrons - release energy (FAD)
48
The chemical reactions in cells are organized into pathways
* Each reaction of a pathway is catalyzed by an enzyme * Linear * Starting molecule and end product defined. * Branching * Can yield more than one product. * Cyclic * All molecules are considered intermediates.
49
Common metabolic pathways
- Glycolysis ( linear pathway Glucose creates 4 ATP and 2 pyruvate - Krebs/Citric/TCA ( cyclic pathway) Pyruvate forms NAHD FADH2 - ETC (sequential redox reaction) eventually will form ATP
50
How are biochemical pathways regulated
* Transcriptional level * Translational level * Post-translational level
51
Essential Nutrients for a bacterial cell
Nutrients Macronutrients * CHONPS (Organic or inorganic) * Growth factors Micronutrients * Trace elements
52
Phototroph
Light absorption captures energy.
53
Chemotroph
Chemical molecules yield energy.
54
Types of energy sources
Carbon source Energy source Electron source
55
Carbon sources
Autotrophs Heterotrophs
56
Energy Source
Phototrophs Chemotrophs
57
Electron source
Lithotrophs Organotrophs
58
Autotrophs
CO2 is fixed and assembled into organic molecules.
59
Heterotrophs
Preformed organic molecules are acquired and assembled into new organic molecules.
60
Lithotrophs
Inorganic molecules donate electrons.
61
Organotrophs
Organic molecules donate electrons.
62
Chemoheterotrophs
• Organic material: energy, electrons, and carbon • Dead organic material: decomposer/saprophytes • Living organic material: pathogen • Oxygen plays an important role in ATP generation.
63
What are the steps to aerobic respiration metabolism
1.Glycolysis = 2 ATP and NADH 2.Krebs Cycle= CO2 , ATP FADH , NADH 3. ETC using O2 for electron acceptor = ATP and H20 Overall release 36-38 ATP
64
What are the steps to anaerobic respiration
1.Glycolysis = 2 ATP and NADH 2.Krebs Cycle= CO2 , ATP FADH , NADH 3. ETC using non-O2 groups like SO4, NO3, CO3 for electron acceptor = ATP and H20 Overall release 2-36 ATP
65
Why is aerobic respiration more efficient at making ATP
Based on electron affinity charts glucose is great at giving up electrons and oxygen is great at receiving electrons making their use in aerobic respiration more efficient compared to other modalities.
66
What are the steps to fermentation metabolism?
1.Glycolysis= 2ATP and NADH 2. Fermentation Overall 2 ATP formed
67
Why are euk cells more efficient at ATP production than prok.
Prokaryotic cells tend to rely on the proton motive force created by ATP synthase for other factors like flagella to ration and even secondary transport. Comparatively EUK cells have secondary mechanism that take care of that meaning more ATP can be made .
68
Obligate aerobes and metabolism
Aerobic- yes Anaerobic - no Fermentation- no
69
Facultative anerobes and metabolism
Aerobic- yes Anaerobic - yes Fermentation- yes
70
Microaerophile and metabolism
Aerobic- yes Anaerobic - yes Fermentation- no
71
Aerotolerant anaerobe
Aerobic- no Anaerobic - yes Fermentation- yes
72
Strict anaerobe
Aerobic- no Anaerobic - yes Fermentation- yes
73
Identify which nutritional types utilize the electron transport chain.
All types except rhodopsin based and only fermenting organisms
74
Fermentation
* No Krebs * No ETC * Anaerobic * Three possible products Acid Ethanol Gas
75
types of fermentation.
Homolactic ethanolic heterolactic mixed acid | pyruvate as the starting material
76
homolactic
- 2 lactic acid - no ethanol - no gas | dairy products
77
ethanolic
- no acid - 2 ethanol - 2CO2 | alcoholic beverages
78
heterolactic
- 1 lactic acid - 1 ethanol - 1 CO2 | sourdough
79
mixed-acid
- acetate,formate , lactate, succinate - ethanol - CO2/H2 | swiss chesse
80
How do microbes utilize fermentation?
* Some microbes switch between respiration and fermentation. * Some microbes can only do fermentation ex.Lactic acid bacteria
81
Chemolithoautotroph
* Inorganic molecules: energy, electrons, and carbon * All chemolithotrophs are prokaryotes * Some may switch between nutritional types - primary producers
82
Describe how chemolithotrophs generate ATP and NADH.
Through the electron trasnport chain -using various sources of electron donors and acceptros the most common acceptor is O2 ex. methanogens
83
oxidizing bacteria.
Chemolithotrophs ( electron donors) Iron Oxidizing Bacteria Sulfur Oxidizing Bacteria Nitrogen Oxidizing Bacteria (nitrifiying) Hydrogen Oxidizing Bacteria
84
reducing bacteria
Anaerobic respiration ( electron acceptors) Iron reducing bacteria sulfur reducing bacteria nitorgen reducing bacteria (denitrifying) hydrogen reducing bacteria
85
How do chemolithoauthrophs make macromolecules?
Biosynthesis/ anabolism by taking Carbon source such as CO2 and doing carbon fixation using ATP they can produce macromolecules usualy a type of sugar
86
where does glycolysis happen
Euk- cytoplasm Prok -cytoplasm
87
where does krebs occur
Euk- mitochondria Prok - Cytoplasm
88
where does ETC happen
Euk- Inner membrane Prok- cell membrane
89
Phototrophy
Photophosphorylation * Light: energy source
90
Diversity of Phototrophic microorganism
**Eukaryotes** Multicellular green, brown, and red algae; unicellular protists (for example, euglenoids, dinoflagellates, diatoms) **Bacteria** Cyanobacteria, green sulfur bacteria, green nonsulfur bacteria, purple sulfur bacteria, purple nonsulfur bacteria, heliobacteria, acidobacteria **Archaea** Halophiles
91
Types of phototrophy
pigment based rhodopsopsin based
92
Rhodopsin-Based
* Bacterio (archae) rhodopsin Retinal-Based Proton Pumps Purple in color * No ETC, but create proton motive force * Consume organic compounds * Mostly aerobic * Photoorganoheterotrophs Energy: light Carbon/electrons: organic molecules * Mostly aerobic
93
Pigment-based
* Photolithoautotrophs * Chlorophyll pigment Oxygenic photosynthesis Plants, algae, cyanobacteria * Bacteriochlorophyll pigment Anoxygenic photosynthesis Prokaryotes, not cyanobacteria
94
Oxygenic photosynthesis
* Energy: light * Electrons: Water * Carbon: CO2 * Pigment: Chlorophyll * Plants, algae, cyanobacteria
95
Anoxygenic photsynthesis
* Energy: light * Electrons: not water * Carbon: CO2 * Pigment: Bacteriochlorophyll * All other photosynthetic bacteria purple bacteria green bacteria
96
Purple Bacteria
**Purple sulfur bacteria** * Anaerobes * Electron donor – H2, H2S, S Sulfur granules in cells * Autotrophs CO2 fixation **Purple non-sulfur bacteria** * Most are heterotrophs * Electron donor Organotrophs – organic compounds Lithotrophs - H2, reduced sulfur compounds**
97
Green Bacteria
**Green sulfur bacteria** * Anaerobes * Electron donor – H2, H2S Accumulates sulfur outside the cell * Autotrophs CO2 fixation **Green non-sulfur bacteria** * Facultative anaerobes Anaerobic – phototrophs (H2S, H2) Aerobic- heterotrophs Aerobic and dark - chemoheterotrophs
98
Mention which nutritional types perform carbon fixation.
Chemoautotrophs photoautotrophs
99
Mention the carbon fixation processes and which organisms perform them
The use of ATP and NADH used to make sugars and organic molecules **Bacteria:** cynobacteria, purple bacteria , chemolithotrophs,green sulfur bacteria , sulfate reducers , green non sulfur **Archae:** sulfur oxidizers , methanogens , aerobic sulfur oxidizers **Eukaryotes:** Plants and algae

Microbiology (4 decks)

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