Exam 2 Microbiology

Virion

a 10-400nm, complete virus particle that contains nucleic acid (DNA or RNA)

Capsid

a protein coat that encloses and protects the nucleic acid and is made of proteins called protomers.

enveloped virus

a full complete virion that has a lipid layer outside the capsid

Naked virus

a full complete virion: nucleic acid, and a capsid

Describe the structure of a viral envelope.

Viral envelopes are membranous structures made of lipids with embedded carbohydrates and proteins, with spikes that help the virion attach to a host cells.

How are viral envelopes formed?

They are formed from the host cell’s lipids, carbs, and the proteins that are encoded in the viral genome.

What are viruses?

Viruses are non-living, acellular, unable to replicate or reproduce on their own, exist both extracellularly and intracellularly, don’t make DNA, proteins, or RNA, and are infectious agents that cause major diseases in all cell types (archaeal, bacterial, and eukaryotic).

What are spikes also known as….

peplomers

Spikes

envelope proteins that project out the virion that can be used to ID viruses.

What are the five steps of the virus life cycle in order?

Attachment(adsorption), entry, synthesis, assembly, and release

What are the different virion symmetries?

A helical capsid is a hollow tube with protein walls, the capsid assembles around the helical RNA or DNA genome. An icosahedral capsid is a 3-D structure with 20 triangular faces, and ring-shaped units called capsomers. Capsids with complex symmetry have Binal symmetry which is an icosahedral head and helical tail.

Explain the basic molecular events that take place during attachment.

molecules on the outside of the virus (ligands) interact with molecules on the outside of the cell (receptors)

What can receptors dictate?

specificity, host species, tissues and cell types

What are the receptors on bacterial host cells?

LPS, teichoic acid, flagella and pili

What are the receptors for Eukaryotic cells?

immune system receptors

Explain the basic molecular events that take place during Entry.

The viral genome is injected into the cytoplasm or the entire nucleocapsid enters the host cells: enveloped viruses fuse to the host cell membranes and release nucleocapsids followed by the uncoating step where the capsid is degraded, and the genome is released. Naked viruses enter by endocytosis, nucleocapsid enters the endosome, where it is uncoated, and the viral genome is released.

What do you need to create viruses?

nucleic acids and proteins

Explain the basic molecular events that take place during Synthesis.

The virus uses the host cells machinery for the synthesis of viral nucleic acids and the viral proteins, early protein and late proteins.

What is the function of early proteins?

to help take over the cell

What is the function of late proteins?

functions in assembly and release of newly made viruses

Explain the basic molecular events that take place during Assembly.

New nucleocapsids are made, and can be assembled in the cytoplasm, nucleus, or virus factories.

Explain the basic molecular events that take place during Release.

Some viruses lyse their host cells for release, lysosome, and holin, viruses are released by budding, which can create viral envelopes, or some viruses aren’t released to the environment, but to the new host cells.

The protein coat or shell that surrounds a virion's nucleic acid is called a/an _____.

capsid

True or False, All viruses have a viral envelope.

False

Virulent phage

A type of bacteriophage and virus that kills the host cell immediately after multiplying, and only has one option which is the lytic cycle.

Temperate phage

The second type of bacteriophage where a virus can adopt another type of life cycle rather than immediately kill its host cell and has two options, lysogenic cycle, and lysogenic conversion. Can also undergo induction.

Oncovirus

a virus that causes cancer

What is a bacteriophage?

a virus that infects bacteria

Lysogenic conversion

Can change the phenotype of the host cell

Induction

a bacteriophage switches from the lysogenic cycle to the lytic cycle

What are the ring-shaped units in an icosahedral capsid called?

capsomers

What does icosahedral mean?

20 sides/faces

What are the molecules on the outside of the virus called?

ligands

What are the molecules on the outside of a host cell called?

receptors

Where can virions be assembled in?

the cytoplasm, nucleus, or virus factories

What are envelopes made of?

the spikes from synthesis

Describe the lytic cycle.

A bacteriophage immediately begins replicating upon entering a bacterial host, assembles new virions, and destroys the bacterial cell to release these virions.

Describe the lysogenic cycle.

Phage injects its DNA into the cytoplasm, the phage then integrates into the hosts chromosome, then Prophage DNA is copied when the cells divide

How does a temperate phage undergo induction?

After the prophage DNA is copied when the cells divide, if it is exposed to stress, the phage’s DNA is removed from the host’s chromosome creating the start of the lytic cycle.

What advantages does the lysogenic cycle give to temperate phages?

The viral genome stays around even if the host is dormant, and it ensures viruses still have host cells to infect when virus numbers are high.

What happens when viruses infect animal host cells?

lyse host cells, cause persistent infections: latent or chronic, transform host cells into a malignant cancer cell

What is a Latent infection?

virus will ultimately lyse host cells

What is a chronic infection?

virus will slowly release new virions and allow the host cell to live

How can an oncovirus cause cancer?

They create proteins that inactivate tumor suppressors and then the cells divide continuously which then leads to cancer.

What 3 things do all organisms require?

sources of energy, electrons for redox reactions, and carbon

What is aerobic respiration?

the breakdown of sugar to carbon dioxide using oxygen

What are examples of energy sources (ATP)?

chemoorganotroph, chemolithotroph, phototroph

What are fueling reactions?

ATP, reducing power, precursor metabolites

What are examples of carbon sources (Precursor metabolites).

autotrophs and heterotrophs

What are examples of electron sources (reducing power electrons)?

organotroph and lithotroph

What are the inputs and outputs of glycolysis?

inputs are 1 glucose molecule, 2 NAD+, 4 ADP, and 2 ATP

outputs are 2 pyruvates, 2NADH and 2ATP

What are the inputs and outputs of one TCA/Krebs Cycle?

inputs are 1 Acetyl CoA, 3NAD+ 1FAD, and 1 ADP

outputs are 2 CO2, 3NADH, 1FADH2, and 1ATP

What is pyruvate converted to before entering the TCA/Krebs cycle?

acetyl-CoA which generates 1 NADH and 1 carbon dioxide (CO2)

One glucose molecule generates how many ATP via substrate-level phosphorylation during the TCA/Krebs cycle?

two

Which part of aerobic respiration generates the most ATP?

ETC (Electron transport chain)

What are the outputs for the TCA/Kreb cycle for 1 glucose molecule?

4 CO2, 6 NADH, 2FADH2, 2ATP

How much ATP does the ETC produce?

28-32 ATP

How does the ETC create ATP?

It creates a high-to-low proton gradient that powers ATP synthase which generates ATP.

What are the inputs and outputs of the ETC?

inputs are 10 NADH and 2 FADH2

output is 28 ATP

Why might aerobic respiration yield less ATP in bacterial cells than in eukaryotes?

The bacteria cycle yields less ATP because energy is used to power flagella. Also, the process is shorter and has different carriers than eukaryotic cells.

What are the similarities between aerobic and anaerobic respiration?

sugar is oxidized, ATP is created, electron carriers (NADH and FADH2) are reduced

What are the differences between aerobic and anaerobic respiration?

Aerobic respiration makes 32-34 ATP, while anaerobic respiration makes 3 ATP. The terminal acceptors in anaerobic respiration have less positive reduction potentials than O2.

What are the 4 unifying themes of fermentation?

No oxygen is needed, pyruvate is used as an electron acceptor, NADH is oxidized to NAD+, and there is no ETC (no large ATP yield)

How are fermentation pathways named?

they are named after the alcohol or acid production

What are the 3 types of fermentation?

Lactic acid fermentation, Ethanol fermentation, and Mixed acid fermentation

Lactic acid fermentation is

pyruvate to lactate (lactic acid)

Ethanol fermentation is

Pyruvate to ethanol and carbon dioxide

Mixed acid fermentation is

pyruvate to ethanol and a mixture of other acids

How can microbes use complex carbohydrates, lipids and proteins in catabolic reactions?

The bacteria use these sugars, fats, and proteins to create energy and areas to store energy. These catabolic reactions are then used to break down large molecules outside the bacteria cell and then brought in, in small individual forms.

Where in our body can we perform lactic acid fermentation?

in our muscles

Define biogeochemical cycle

the recycling of inorganic matter between living organisms and their nonliving environment

Define bioremediation

using microbes to remove contaminants from the environment

What is the role of microbes in the carbon cycle?

Cyanobacteria can do photosynthesis which “fix” inorganic carbon into organic carbon. Then bacteria and archaea degrade hydrocarbons to carbon dioxide.

What are methanogens?

archaea that produce methane as a byproduct of anaerobic respiration

What are methanotrophs?

bacteria (order Rhizobiales) and archaea that use methane as a source of carbon

What is the role of microbes in the nitrogen cycle?

Cyanobacteria and Rhizobium “fix” inorganic nitrogen into ammonia through ammonification, nitrification, and denitrification.

What is ammonification in the nitrogen cycle?

organic nitrogen (nitrogenous waste), poop, is broken down into ammonia

What is nitrification in the nitrogen cycle?

Proteobacteria and archaea take ammonia and turn it into nitrite and then nitrate.

What is denitrification in the nitrogen cycle?

Pseudomonas and Clostridium bacteria turn nitrate into nitrogen gas

What is the role of microbes in the sulfur cycle?

Gut bacteria breaks down organic sulfur into hydrogen sulfide

Name two examples of how microbes can be used in bioremediation

sewage treatment and to degrade or contain oil spills

What does binary mean?

two

what does fission mean?

separation

What is binary fission

one cell separates into two identical cells

What is the cell cycle?

a complete sequence of events from the formation of a new cell to the next division

What are the 3 phases of the cell cycle?

period of growth, chromosome replication and partitioning, and cytokinesis

Which of the following cytoskeletal proteins is involved in assembly of the Z-ring and, ultimately, cytokinesis in during the bacterial cell cycle?

FtsZ

What are the two Par proteins and their functions?

ParA binds to ParB and pulls the chromosome toward pole and ParB binds to the chromosome.

Outline the molecular events that take place during the bacterial cell cycle.

First is chromosome replication, the cell elongates, Par proteins partition/separate chromosomes from each other, and then FtsZ creates a Z-ring/belt that pinches inward to create new cells.

What environmental factor affect microbial growth?

temperature, pH, oxygen concentration, and solutes and water

What are the different phases of bacterial growth in a lab?

First is the lag phase: cells are stressed and don’t divide but make materials, second is the exponential phase where lots of nutrients are used to supply the rapid cell division. Third is the stationary phase where cells stop dividing to conserve energy as nutrients deplete. Lastly, the death phase where cells run out of nutrients, and they drown in their own waste and die.

What is bacteria’s main source of energy?

sugar

Define Obligate aerobe and anaerobe

obligate aerobes need oxygen to survive while obligate anaerobes need NO oxygen

Define facultative anaerobe

can do both aerobic and anaerobic respiration

Define halophile

salt loving

Define mesophile and thermophile

mesophiles are medium-loving temperatures like 37 degrees Celsius. Thermophiles are heat-loving temperatures like 65 degrees Celsius.

Define acidophile, neutrophile, and alkaliphile

Acidophile is acid-loving with a pH less than 7. Neutrophiles are average acid-loving with a pH equal to 7. Alkaliphiles like a pH greater than 7 (9.5)

When are bacterial cells dividing at the highest rate? When are bacterial cells not dividing?

Bacterial cells are dividing at the highest rate in the log/exponential phase and not dividing in the lag, stationary, and death phases.

When are nutrients at their highest? When are nutrients at their lowest?

Nutrients are at their highest in the lag phase and their lowest in the stationary and death phases.

When are waste products at their highest? When are waste products at their lowest?

Waste products are at their highest in the death phase and lowest in the lag phase.