Microbio Test 3

Fermentation

the completion of catabolism without the electron transport system and a terminal electron acceptor.

Phototrophy

yields energy from light absorption

Baltimore Virus Classification

•The genome composition and mechanisms of replication and mRNA expression define seven fundamental groups of viral species: •Group I: Double-stranded DNA viruses •Group II: Single-stranded DNA viruses •Group III: Double-stranded RNA viruses •Group IV: (+) single-stranded RNA viruses •Group V: (-) single-stranded RNA viruses •Group VI: RNA retroviruses •Group VII: DNA pararetroviruses

Lysogenic

•the active reproduction of the virus is modulated such that virions are produced and released, but the cell lives

Electron donor

a reducing agent

Types of capsid proteins that protect the viral nucleic acid

1. Symmetrical 2. Asymmetrical 3. Bacteriophage

Swiss cheese involved which two fermentation stages

- Stage 1: Lactobacillus ferments lactose into lactic acid - Stage 2: Propionibacterium converts lactate to propionate, acetate, and CO2

Standard conditions for delta G

- Temp = 298 K (25C) - Pressure = 1 atm - Concentrations = 1 M In living cells, the conditions for delta G' are the same PLUS ph 7

Is smallpox really gone?

1. There are two reserves of smallpox (CDC and Russia) 2. People are able to artificially recreate it 3. Smallpox can live in permifrost - climate change is an issue.

reduction potential

a measure of the tendency of a molecule to accept electrons

Mrs. Karwah

- Time Person of the year in 2014 - Died in 2017, bled out during pregnancy

Marine viruses

- huge role in cycling of food molecules - infect phytoplankton, releasing their minerals in the upper water where they are available to phototrophs - Viral shunt - *recycle organic matter*

Endogenous Virus

- permanently integrated into a host chromosome -May direct its own reproduction (lysogenic) or may be "latent", rarely lytic

Virion

- primarily extracellular, prior to "infection" - basically *inert*, no reproduction or metabolic activity

Lytic

- the active reproduction of the virus leads to a breakdown of cellular integrity and the cell comes apart or explodes - Usually results in a massive release of virions

Methanogenesis

- the reduction of CO2 and other single-carbon compounds to methane. Generates energy - provides niches for methanotrophs.

Provirus

- viral genome is temporarily integrated into a host chromosome - Usually directs its own reproduction with the host's "assistance" - Usually "lysogenic", may be lytic

Virus Structure (Phospholipid membrane)

- virion may be enveloped by a phospholipid membrane (ex: herpes, HIV) - membrane may be derived from host cell membrane OR intracellular membraneous structure (ex: golgi, ER) - may contains proteins from host or virus

HIV stats 2019

- 37.9 million people estimated to be living with HIV infection globally, about 1.8 million were newly infected, and about 1 million died of HIV-related causes - 15% that were affected were unaware of their status - About 75 million infected, about 35 million dead since beginning of epidemic

Hepatitis C epidemiology

- About 75% of those chronically infected were born between 1945-1965 - People in the 1945-1965 birth cohort are five times more likely to be infected with HCV than others - About 50% of people with chronic infections live in ten states, with five of those states in Appalachia - Highest rate of current infections occurring in 20-29 year-old age group

Some observations about viruses

- All known cellular organisms can be infected by viruses. - Not all viral infections cause a recognized disease (e.g., annelloviruses) - "Virome" - Some viral infections that cause disease also stimulate immunity from infection by other (worse) diseases (e.g., cowpox preventing smallpox).

ETS examples

- Anaerobic respiration - Lithotrophy and methanogenesis - Phototrophy

Denitrification

- Dissimilatory reduction of NO3- to N2 (stepwise with specialized respiratory proteins, different species can do all or some) - Most are heterotrophic - NO3- comes from urea and general nitrogen-rich waste from residents, businesses. Also an agricultural pollutant - in both cases need to remove excess bioavailable N from the system.

TSE's

- Experimentally transmissible - Cause central nervous system degeneration - No inflammation or inflammatory processes - Loss of motor coordination - Behavioral changes - Spongiform brain lesions

Influenza

- Four types: A, B C, D - Type A and B responsible for "flu"

HIV attachment and host cell entry

- HIV binds to the CD4 receptor of T lymphocytes together with chemokine receptor CCR5 - envelope and host membrane fuse, HIV core enters cytoplasm - HIV core then dissolves and releases its contents - Reverse Transcriptase copies the RNA genome to DNA

Vaccine effectiveness

- Highly variable - Normally 40-50% - 2004-2005 flu season was the least effective (10%) followed by 2014-2015 (19%)

Flu vaccines

- Injectable - Inhaled mist - Trivalent - 2 A, 1 B - Quadrivalent - 2 A, 2 B

Prions

- Intended to describe an abnormal form of a normal protein that could catalyze the formation of additional abnormal proteins (beta-pleated sheets). - A protease-resistant protein (PrP) was found in experimental scrapie models - Problem: disease could be transmitted experimentally with no detectable PrP, and PrP could be present without clinical disease or the ability to experimentally transmit disease

Replication Complexes

- Intracellular viruses - Replication of viral nucleic acids and proteins using host's energy production mechanisms and either the host's or its own replication mechanisms - usually "lytic"

Oncogenic viruses

- Many human cancers are caused by oncogenic viruses (Epstein-Barr, hepatitis C) - Oncogenic viruses "transform" the host cell, causing it to lose growth control.

Death of CD4+ T cells

- Permissive CD4+ cells allow for virion production and release without cell lysis - Non-permissive CD4+ cells allow for "replication" activities, but not virion formation due to abortive transcription and translation - Accumulation of defective virus products results in pyroptic response by other immuno-competent cells and tissues

Viroids

- Plant pathogens - Circular, single-stranded RNA, 250-400 nucleotides - No protein coat - Do not code for protein - Use host RNA Polymerase II (normally for making mRNA from DNA) - Rolling circle replication - Transmitted by insects, leaf contact, and injury

Replication cycle of HIV

- Retroviral mRNAs are exported to the cytoplasm for translation. - Envelope proteins are translated at the ER and exported to the cell membrane. - Retroviruses are assembled at the cell membrane, where virions are released without cell lysis. - Alternatively, the accumulation of retroviral proteins in the cell membrane leads to cell fusion, forming syncytia.

Why do different kinds of reactions use different energy carriers?

-Different redox levels -Different amounts of energy -Regulation and specificity

Symmetrical capsid proteins

-Icosahedral (e.g., Herpes, HIV) -Filamentous (e.g., Ebola)

Bacteriophage capsid proteins

-May be symmetrical or asymmetrical -May be tailed

Who does CO2 fixation (reductive pentose phosphate cycle)?

-Oxygenic phototrophic bacteria -Chloroplasts of algae and plants -Facultatively anaerobic purple bacteria -Lithoautotrophic bacteria

Asymmetrical capsid proteins

-RNA may be coated with protein (e.g., influenza) -DNA may stabilize itself through covalent bonding of ends and be enveloped by nucleocapsid proteins (e.g., vaccinia)

Whats different about the reductive, or reverse, TCA cycle?

-Uses 4-5 A T Ps to fix four molecules of C O 2 and generate one oxaloacetate -Reduction (addition of 2H + 2e-) is performed by NADPH or NADH and by reduced ferredoxin (FDH 2).

Chemolithotrophy

-e- from inorganic compounds

Virus structure (DNA and RNA)

-nucleic acid (DNA or RNA) - DNA may be single or double stranded -ssDNA is "+" or sense. - RNA may be single or double stranded - ssRNA can be "+" or "-"

Anabolic function of TCA cycle

-α-ketoglutarate is used to make certain amino acids -Oxaloacetate is aminated to form aspartate, entering pathways to purines and pyrimidines

3 things RNA transcriptase does with HIV

1. DNA synthesis from RNA template 2. RNA degradation 3. DNA-dependent DNA synthesis

3 main types of catabolic pathways

1. Fermentation 2. Respiration 3. Photoheterotrophy

3 main catabolic pathways

1. Fermentation: partial breakdown of organic food without net electron transfer or an inorganic terminal electron acceptor. 2.Respiration: complete breakdown of organic molecules with electron transfer to a terminal electron acceptor such as O2 3.Photoheterotrophy: catabolism is conducted with a "boost" from light.

Bacteria's 3 main routes to catabolize glucose

1. Glycolysis or Embden-Meyerhof-Parnas (EMP) pathway 2. Entner-Doudoroff (ED) pathway 3. Pentose phosphate pathway (PPP)

Influenze subtype A: based on which two proteins?

1. Hemagglutinin (18 variations, attachment) 2. Neuraminidase (11 variations, replication/release)

3 ways ATP can transfer energy to cell processes

1. Hydrolysis-releasing phosphate (Pi) 2. Hydrolysis-releasing pyrophosphate (PPi) 3. Phosphorylation of an organic molecule

mechanisms of oncogenesis include:

1. Insertion of an oncogene into the host genome 2. Integration of the entire viral genome 3. Expression of viral proteins that interfere with host cell cycle regulation

Factors that determine delta G

1. Intrinsic properties of a reaction (changes in delta H and S) 2. Concentrations of reactants and products 3. Environmental factors

3 major classes of prokaryotic energy-acquiring processing using an ETS:

1. Organotrophy (or chemoorganotrophy) 2. Lithotrophy (or chemolithotrophy) 3. Phototrophy

What is the origin of virus?

1. Some are so simple in structure and function that it is impossible to tell - primordial soup?2. Some are very complex and contain genes and accessory proteins that are similar to those found in eukaryotic cells 3. Some are intermediate and appear to be derived from prokaryotes

Virus 4 States of Being

1. Virion 2. Replication complexes 3. Provirus 4. Endogenous Virus

Etiology

1. cause, origin specifically: the cause of a disease. 2. a branch of knowledge concerned with causes specifically: a branch of medical science concerned with the causes and origins of diseases.

Biosynthetic strategies to control energetic and genomic costs:

1. regulation 2. competition and predation 3. genome loss and cooperation

A respiratory electron transport system includes at least three functional components:

1.An initial substrate oxidoreductase (or dehydrogenase) 2.A mobile electron carrier 3.A terminal oxidase

Product of Glycolysis (EMP)

2 ATP and 2 NADH

Product of ED pathway

2 pyruvate, 1 ATP, 1 NADH, 1 NADPH

Virus

A relatively small infectious agent that replicates in unicellular and multicellular organismsS

Product of Pentose Phosphate Pathway

ATP and 2 NADPH

Most fermentations do not generate __________

ATP beyond that produced by substrate-level phosphorylation

What is the electron flow in ETS in E. coli under aerobic conditions? A)ATP -> NDH-1 protein complex -> Quinone pool -> Cytochrome protein -> ½ O2 B)NADH -> NDH-1 protein complex -> Quinone pool -> Cytochrome protein -> ½ O2 C)NADH NDH-1 protein complex -> Quinone pool -> Cytochrome protein -> ATP

B)NADH -> NDH-1 protein complex -> Quinone pool -> Cytochrome protein -> ½ O2

Step curve

Batch culture of viruses generates this

Why are we aware of viruses?

Because of... Ebola, marburg, lassa, hanta, rabies, smallpox, influenza, and COVID-19!

Gut Virome

Best understood phage community - Phages limit bacterial numbers to levels the human immune system can tolerate - phages modulate immune system activity by suppressing T cell activation and tumor formation - phages attack biofilms

ATP synthesis can be generated by which mechanisms: A) pH difference across the membrane only B) Charge difference across the membrane only C) Either pH or charge difference

C) Either pH or charge difference

What cells does HIV infect?

CD4+ T helper cells

Function of enzymes

Catalyze biological reactions. Lower the activation energy to speed up a reaction

Which two pathways form 6-phosphogluconate

ED and PP pathway

Substrates for biosynthesis come from _____________ and ____________

Glycolysis and TCA cycle. 1. Succinyl-CoA 2. Glycerol-3-phosphate 3. pyruvate (which is also seen in catabolism)

"Coliphages"

Gut bacteriophages are part of a microbial community that modulates human digestion, the immune system and mental health

Does HIV infection cause AIDS?

Infection with HIV Causes Severe Immuno-deficiency due to CD4+ T Cell Death That Allows Opportunistic Pathogens to Cause AIDS-Related Diseases

Antigenic drift

Influenza viruses continually develop small mutations through replication "mistakes" that can lead to new phenotypes with respect to infectious capabilities. If two different strains of influenza virus infect a host simultaneously, their segments can re-assort to generate a novel hybrid strain

Energy carriers

Molecules that gain or release small amounts of energy in reversible reactions ex) NADH and ATP

where did HIV come from?

Monkeys, most likely through consumption of "bushmeat" - which is basically eating whatever animal they could find in the bush.

Anaplerotic reactions

Reactions that replenish depleted tricarboxylic acid cycle intermediates.

Lithotrophy

Some organotrophs have alternative oxidoreductases that conduct this by oxidizing H2 or Fe2

xyloglucans

Sugar derivative. Foods such as lettuce and tomatoes are made of this

T/F: most microbes can make their own amino acids and bases?

TRUE

What is "alive"?

The property or quality that distinguishes living organisms from dead organisms and inanimate matter, manifested in functions such as *metabolism, growth, reproduction, and response to stimuli or adaptation* to an environment that originates from within the organism.

BSE epidemiology

The study supports previous evidence of aetiological similarities between BSE and scrapie of sheep

How do biosynthesis pathways compare to catabolism pathways?

They are the same, but reversed! But now *NADPH* is used instead of NADH.

Bacteriophage

Viruses that infect bacteria. - *are used as alternatives to antibiotics!!!*

Chemotrophy

Yields energy from electron transfer between chemicals. 1.Chemoorganotrophy 2.Chemolithotrophy

ATP contains

a base (adenine), a sugar (ribose) and three phosphates. ATP always forms a complex with magnesium.

Syndrome

a collection of clinical signs and symptoms that are correlated with each other.

Polyketides

a diverse group of metabolites that include the broad-spectrum antibiotic erythromycin. Synthesized by a modular enzyme. Each malonyl group has a unique R group - allows them to form a variety of compounds!!

The net equation for alcoholic fermentation is: Glucose + 2 ADP + 2 Pi → ______________ a) 2 ethanol + 2 CO2 + 2 ATP b) ethanol + lactic acid + CO2 + 2 ATP c) 2 ethanol + 2 acetic acid + 2 ATP d) 3 ethanol + 2 ATP

a) 2 ethanol + 2 CO2 + 2 ATP

Which of the following are synthesized via a branched pathway involving chorismate? a)Fatty acids b)Purines and pyrimidines c)Aromatic amino acids d)Polyketide antibiotics

a) Aromatic amino acids

A branch of medical science concerned with the causes and origins of diseases is called: a) Etiology b) Ethiopiology c) Ophthalmology d) Etymology e) Astigmatology

a) Etiology

Which carbon source and reactant below would produce the largest free energy change? (Table 13.5) a) Glucose; O2 b) Ethanol; O2 c) Glucose, NO3- d) Acetate; NO3-

a) Glucose; O2

Transmissible spongiform encephalopathy (TSE) refers to what kind of disease? Select one: a) Holes are formed in brain tissue, may involve malformed proteins but the disease agent is not fully known b) Deterioration of muscle tissue by unknown agent c) Deterioration of brain tissue and nervous system cells by a virus d) Formation of plaques in any organ tissue as a result of a virus

a) Holes are formed in brain tissue, may involve malformed proteins but the disease agent is not fully known

What is TRUE about marine viruses? Select one: a) They are highly abundant and diverse, but not well characterized b) They are all pathogenic to humans c) They are all non-pathogenic to humans d) They have all been identified and well-characterized

a) They are highly abundant and diverse, but not well characterized

Since the beginning of the AIDS epidemic about 35 million people have died Select one: a) True b) False

a) True

Ms Karwah: Select one: a) All of these b) was an Ebola survivor c) was a Time magazine person of the year in 2014 for her work in support of other Ebola victims d) died in 2017 of blood loss during childbirth because no one would help her due to the stigma of her having had Ebola

a) all of these

The Baltimore classification of viruses is based on the: a) All of these b) Genome composition c) Origin of envelope d) Mechanism of replication e) Mechanism of mRNA expression

a) all of these

The Influenza A virus genome has: Select one: a) eight RNA segments that code for 10 proteins. b) nine DNA segments that code for nine proteins c) seven RNA segments that code for 9 proteins d) seven RNA segments that code for 10 proteins

a) eight RNA segments that code for 10 proteins.

In anaplerotic reactions, a) intermediates in a pathway are regenerated. b) nutrients are imported from the environment. c) molecules targeted for breakdown are salvaged for anabolism. d) proteins are synthesized to help cells survive anaerobic conditions.

a) intermediates in a pathway are regenerated.

What is *NOT* true about the polio virus? Select one: a) It is transmitted by coughing b) It infects human neurons and intestinal epithelium c) It has oral-fecal transmission d) It causes a flaccid paralysis e) Recovery is possible with massive support

a) it is transmitted by coughing

SARS-CoV-2 virus is a Select one: a) ssRNA virus b) dsRNA virus c) dsDNA virus d) ssDNA virus e) retrovirus

a) ssRNA virus

In EMP glycolysis, glucose is activated through ________ to fructose-6-bisphosphate. A)Two substrate phosphorylations by ATP B)One substrate phosphorylation by ATP C)Release of 2 ATP and 2NADH D)Coupling to proton motive force

a) two substrate phosphorylations by ATP

Which infectious agent is identified by the nucleic acid genome being the entire infectious particle? Select one: a) viroids b) prions c) viruses d) bacteria

a) viroids

Which intermediate of the Calvin cycle is exported to make glucose? a)Glyceraldehyde 3-phosphate (G3P) b)Ribulose 1,5-bisphosphate c)Ribulose 5-phosphate d)Rubisco

a)Glyceraldehyde 3-phosphate (G3P)

Energy

ability to do work

Photoautotrophy

absorption with CO2 fixation

Photoheterotrophy

absorption without CO2 fixation

Electron acceptor

an oxidizing agent

Which of the following is the reducing cofactor typically used in biosynthesis? a)NADH b)NADPH c)FAD d)FADH2

b) NADPH

Fermentation can be defined as: a) Partial breakdown of organic food with the use of an electron transport system b) Partial breakdown of organic food without the use of an electron transport system c) Complete breakdown of organic food with the use of an electron transport system d) Complete breakdown of organic food without the use of an electron transport system

b) Partial breakdown of organic food without the use of an electron transport system

The term __________ refers to the heat energy absorbed or released, whereas __________ is a measure of disorder or randomness. a) enthalpy; free energy b) enthalpy; entropy c) entropy; enthalpy d) entropy; free energy e) free energy; entropy

b) enthalpy; entropy

Terminal electron acceptors in anaerobic respiration include all of the following EXCEPT a)nitrous oxide. b)hydrogen sulfide. c)nitrate. d)sulfate.

b) hydrogen sulfide

Catabolism

breakdown of complex molecules into smaller ones

Biosynthesis (anabolism)

building of complex molecules. Requires essential elements, reduction (using NADPH), and energy.

Which metabolic pathway produces NADPH but NOT NADH? a)Entner-Doudoroff pathway b)Embden-Meyerhoff-Parnas pathway c)Pentose-phosphate pathway d)Two of the above e)All of the above

c) Pentose-phosphate pathway

Reduction potential is defined as the tendency for a molecule to a) release H+ in solution. b )release O H- in solution. c) accept electrons. d) donate electrons.

c) accept electrons

Cells use multiple energy carriers for all of these reasons *except*: a) Different redox levels of different reactions b) Different amounts of energy for different reactions c) To absorb light energy d) Regulation and specificity

c) to absorb light energy

All of the following statements about fatty acid biosynthesis are true EXCEPT a)It involves successive condensations of malonyl-ACP. b)A dehydratase is used to generate an unsaturated bond. c)NADH is used as reducing agent. d)The initial step involves addition of CO2 to acetyl-CoA.

c)NADH is used as reducing agent.

Location of TCA in prokaryotes

cytoplasm

Standard conditions for ΔGo include which of the following? a) Concentrations = 1 M b) Pressure = 1 atm c) Temperature = 37C d) A and B e) All of the above

d) A and B

Chemotrophy yields ______ from electron transfer between chemical compounds, while phototrophy yields ________ from light absorption. a) Energy; electrons b) Carbon; energy c) Electrons; carbon d) Energy; energy

d) Energy; energy

Helicobacter pylori is a Gram-negative bacterium. Where would its ETS be embedded? a) In the cell wall b) In the periplasm c) In the cytoplasmic membrane d) In the inner membrane e) None of the above

d) In the inner membrane

What is the net result from one acetyl-CoA molecule entering the TCA cycle? a)2 ATP, 2 N A D H, 2 F A D H2 b)1 ATP, 1 N A D H, 2 F A D H2 c)2 ATP, 3 N A D H, 1 F A D H2 d)1 ATP, 2 N A D H, 1 F A D H2 e)1 ATP, 3 N A D H, 1 F A D H2

e) 1 ATP, 3 NADH, 1 FADH2

The proton motive force drives which of the following processes in bacteria? a) ATP biosynthesis from ADP and P i b) Flagellar rotation c) Nutrient uptake d) Two of the above e) All of the above

e) All of the above ATP biosynthesis from ADP and Pi, Flagellar rotation, Nutrient uptake

The acquisition of energy by oxidation of inorganic electron donors is best defined as a)phototrophy. b)auxotrophy. c)autotrophy. d)heterotrophy. e)lithotrophy.

e) lithotrophy.

§Which of the following pathways is a route for C O2 fixation? a)Reductive acetyl-CoA pathway b)Reductive, or reverse, TCA cycle c)3-hydroxypropionate cycle d)Choices A and B e)Choices A, B, and C

e)Choices A, B, and C - Reductive acetyl-CoA pathway - Reductive, or reverse, TCA cycle - AND 3-hydroxypropionate cycle

Most bacteria assimilate NH4+ into which two amino acids? a)Alanine and arginine b)Leucine and lysine c)Aspartate and asparagine d)Proline and phenylalanine e)Glutamate and glutamine

e)Glutamate and glutamine

Chemoorganotrophy

e- from organic compounds

Recrudescence

getting well and then it comes back worse than it was before. This has happened with COVID-19

Influenze A virus

highly virulent and lyses infected cells with little or no latent state

How are bacteriophages cultured?

in batch culture (liquid) or isolated plaques on a bacterial lawn (plate)

The cellular levels of glutamate and glutamine act as...

indicators of nitrogen availability And these are used in other pathways of amino acid synthesis

2. Lithotrophy (or chemolithotrophy)

involves inorganic electron donors and inorganic or organic terminal acceptors

3. Phototrophy

involves light capture by chlorophyll, usually coupled to splitting of H2S or H2O or organic molecules

1. Organotrophy (or chemoorganotrophy)

involves organic electron donors and inorganic or organic terminal electron acceptors

HIV evolution

it is the most rapidly evolving pathogen known

Biosynthesis of fatty acids is a ________ process.

iterative - starts with NADPH and malonyl-ACP as reducing agent

Entropy

measure of the disorder or randomness of a system

Location of TCA in eukaryotes

mitochondria

Microbes transfer energy by ___________ ____________

moving electrons

Latent

no viral reproduction

Disease

pathophysiological response to internal or external factors.

the ETC generates a _______ ______ _______ that drives protons across the membrane

proton motive force

Glucose catabolism connects with the TCA cycle through...

pyruvate breakdown to acetyl-CoA and C O2

Anabolism

reactions that build cells