B&A ch.3 and 4

What are the three domains of life?

Bacteria, Archaea, Eukarya

Division of cocci in __ plane(s) produces?

A) one

B) two

C) three

D) many

A) streptococci

B) tetrads

C) sarcinae (cubes)

D) staphylococci

What are the two main bacterial morphologies?

Cocci (spheres) and bacilli (rods)

What are..?

1. Coccobacilli

2. Vibrio

3. Spirilla/spirochates

1. Very short rods, slightly longer than their diameter

2. Curved/comma shaped bacilli

3. Very long vibrio bacillus twisted/coiled around a central axis

Is it possible that cocci were initially derived from bacilli? Explain.

bacilli consist of a long tube/rod and two ½ sphere caps, and grow in length until they divide. Over time, this gene for growing in length may have been lost leaving only the two ½ sphere caps which make up a whole sphere, or coccus

Division of bacilli only occurs in __ plane(s)

division of bacilli only occurs in one plane, meaning they can only form chains of varying lengths (bacillus, diplobacilli, streptobacilli)

what are filaments?

filaments are single celled very long bacilli that have stopped dividing normally and form a long threadlike structures that sometimes branch

1. What are..

A) Vertical/aerial mycelia?

B) Substrate mycelia?

2. Provide an example of a bacterial genus that produces both substrate mycelia and aerial mycelia/spores?

3. Provide an example of a bacterial genus that produces substrate mycelia only?

1. 
   

A) Filaments that grow upward and can bear spores that serve dispersive/reproductive functions

B) Filaments that grow on or into substrate, do not produce spores

2. Streptomyces

3. Actinomyces

1. Where is a bacterium’s genome located?

2. What form does a bacterium’s genome take?

3. Does bacterial cccDNA have an origin of replication?

1. the nucleoid

2. Bacteria typically have a singular circular DNA molecule but can also have linear DNA in multiple molecules

3. Yes

1. What is the range of genome size for bacteria?

2. What is the genome size of E. coli?

3. What does Mbp refer to?

4. Approximately how many base pairs per gene in bacteria?

1. 0.7Mbp to 12Mbp

2. 4.5Mbp

3. Mbp stands for mega base pairs, 1Mbp=1 million base pairs, so E.coli has 4.5 million base pairs

4. Approximately 1000 base pairs per gene in bacteria, so E.coli has ~4500 genes

CCC stands for __, which refers to the shape of __

covalently closed circular, DNA in bacteria also called cccDNA

What is a Svedberg unit (S)?

A unit of measurement based on how fast a particle settles when spun in a centrifuge, reflecting not just the mass of the particle but its shape, size and density

• In bacteria and archaea (prokaryotes), ribosomes are _S, consisting of a larger _S subunit and a smaller _S subunit.

• In eukaryotes, ribosomes are _S, consisting of a larger _S subunit and a smaller _S subunit.

• In bacteria and archaea (prokaryotes), ribosomes are 70S, consisting of a larger 50S subunit and a smaller 30S subunit.

• In eukaryotes, ribosomes are 80S, consisting of a larger 60S subunit and a smaller 40S subunit.

1. What does the 50S subunit of a ribosome contain in prokaryotes? (3)

2. What does the 30S subunit of a ribosome contain in prokaryotes? (2)

3. Approximately how many proteins are found in a bacterial ribosome?

1. 23S rRNA, 5S rRNA, ~30 proteins

2. 16S rRNA, ~20 proteins

3. ~50

How can the 50S and 30S subunits of a prokaryotic ribosome add up to 70S?

Svedberg units do not add up mathematically due to the fact that S is based on not just mass but size, shape etc… the complete ribosome sediments (settles in a centrifuge) faster than its individual subunits do combined

1. Ribosomes are sites of…? (2)

2. The more ribosomes a bacterial cell has, the __ (faster, slower) the cell grows

1. Protein synthesis and action site for many antibodies

2. The more ribosomes a bacterial cell has, the faster the cell grows

Name 6 cytoplasmic inclusions for storage of excess nutrients and 2 cytoplasmic inclusions that do not function in nutrient storage

5 inclusions that function in nutrient storage are lipids, glycogen, polyhydroxyalkanoates (PHA), protein, polyphosphates and sulfur.

2 inclusions that do not function in nutrient storage are gas vacuoles and magnetosomes

Describe the primary stored resource for each of the 6 cytoplasmic inclusions that function in nutrient storage

• PHA, lipids and glycogen (polymerized glucose) all store carbon and hydrogen to be used as fuel in ATP production.

• Sulfur is stored as an electron source for respiration (intracellularly in cytoplasm or on the outer surface of the cell wall depending on species).

• Polyphosphates store excess phosphorous as a building block for DNA, RNA and ATP.

• Protein inclusions store excess amino acids or can have specialized functions.

What are polyhydroxyalkanoates (PHA)?

A type of lipid-like storage material for carbon and energy/fuel for ATP production

How can we see cytoplasmic inclusions?

Cytoplasm and cytoplasmic inclusions have different refractive indexes than cytoplasm, which helps us see them

What are the two types of magnetosome granules? What is the function of magnetosomes?

Magnetosomes are inclusions of magnetic iron oxide or magnetic iron sulfide granules surrounded by a lipid layer and allow for certain specialized bacterial species to orient themselves according to Earth’s magnetic fields

If __ (magnetosomes, flagella) act as the steering wheel of a car, __ (magnetosomes, flagella) act as the engine

If magnetosomes act as the steering wheel of a car, flagella act as the engine

What is the function of gas vacuoles

Gas vacuoles are accumulations of small, protein lined gas vesicles which allow cells to modify buoyancy to adjust depth in water

What are endospores?

• Endospores are structures found within vegetative cells which form in response to nutrient starvation

• Endospores are for survival- resistant to heat, radiation, chemicals, heavy metals, desiccation etc…

1. What happens when a nutrients become available to an endospore?

2. What happens to a vegetative cells when nutrients are limited? Name a common limiting nutrienT

1. When nutrients become available to an endospore, it germinates (takes up water and swells) to form a vegetative cell which has the capacity to reproduce unlike endospores

2. When nutrients such as nitrogen are limited, a vegetative cell forms a single endospore as it senses a decrease in necessary nutrients. Eventually the vegetative cell lyses, releases the more resistant endospore

1. Does the endospore or vegetative cells produce toxins?

2. Can endospores be stained?

3. Are endospores the same as spores produced by vertical/aerial mycelia? Why or why not

1. The vegetative cell produces toxins in certain harmful bacterial species

2. No, endospores cannot be stained

3. Endospores are not the same as spores produced by vertical/aerial mycelia. Only one endospore forms per cell under stress and they function in survival. Many spores form from vertical mycelia and they function in reproduction/dispersion of the species

What is Darwin’s dust? What can it tell us about endospores?

Darwin took some dust from the deck of his ship home in a closed jar and forgot about it…many years later, the jar, stored in the British museum was opened and the spores were able to germinate. This is just an example of how long endospores can remain dormant for, they have been shown to remain in dormancy for thousands of years while maintaining the ability to germinate into a vegetative cell

Bacillus and Clostridium are both genuses that produce endospores

• which genus is aerobic and which is anaerobic?

• Name two species of bacillus and the conditions they cause

• Name one species of clostridium and the condition it causes

• Bacillus is an aerobe while clostridium is an anaerobe

• Bacillus anthracis causes anthrax, Bacillus cereus causes a type of food poisoning

• Clostridium botulinum causes botulism (this is why a proper seal is so important in safe canning to prevent aerobic bacteria from producing toxins, growth of anaerobic bacteria like C.botulinum cannot be prevented by the lack of oxygen)

Explain in detail the function of the FtsZ protein

FtsZ is a cytoskeletal protein found in all bacteria and archaea that plays a necessary role in cell division. After replication (which FtsZ has nothing to do with), DNA partitions (moves to poles of the cell) and FtsZ monomers and other small units polymerize to form a Z-ring next to the inner membrane on the cell’s equatorial plane. Polymerized FtsZ is anchored to the inner membrane by membrane proteins. The Z-ring contracts by slowly depolymerizing to form progressively smaller rings, slowly separating the cytoplasm of the daughter cells. A peptidoglycan septum forms and attaches to the rest of the cell wall, separating the contents of the daughter cells and then splitting through an unknown process to form the two separate daughter cells

Are flagella found in bacilli or cocci?

Flagella are only found in bacilli

Label and describe each type of flagellar arrangement

Aphitrichous- no flagella

Monotrichous - one polar flagellum

Aphitrichous - two polar flagella, one on each end

Lophotrichous - many polar flagella on one end

Peritrichous - many flagella everywhere

How do flagella function?

Flagella consist of a filament connected to a basal body with a hook-like region. The basal body acts as a motor, converting chemical potential energy in the form of proton motive force (proton gradient, similar to functioning of ATP synthase) into kinetic energy (movement)

Can motile bacteria move towards or away from stimuli? Provide 3 examples

Yes, motile bacteria can move towards or away from stimuli

1. Chemotactic bacteria can sense chemical gradients and move accordingly

2. Phototactic bacteria can sense light sources and move accordingly

3. Magnetotactic bacteria contain magnetosomes and can sense/orient themselves according to Earth’s magnetic field

1. What are the two types of movement using flagella?

2. Which type of movement is longer in duration for meaningful movement according to a gradient?

1. Running (counterclockwise rotation of flagella, straight motion) and tumbling (clockwise rotation of flagella, rotation)

2. Length of runs increase and length of tumbles decrease

What are pili?

• Pili are thin protein tubes that help attach the cell to a surface.

• Specialized pili called the F pilus or sex pilus can be used for exchange of genetic material between cells

Through the term pili is generally interchangeable with fimbrae, there are some differences. Explain

Pili tend to be longer and thicker than fimbriae, fimbriae are not involved with exchange of genetic material, fimbriae are much more abundant than pili

Name 3 functions of the (inner) membrane

• contains the cytoplasm, separating it from the outside environment

• Acts as a border controlling entry and exit from the cell

• Nearly all metabolic functions rely on plasma membrane, whether they use the membrane or are located in it

What are the two main types of proteins found in (inner) membranes? Do eukaryotes or prokaryotes like bacteria have proportionally more membrane proteins and why?

• Membrane spanning proteins/integral proteins are embedded in the membrane, peripheral proteins are associated with either side of the membrane

• Prokaryotes like bacteria have proportionally more membrane proteins in their cell membrane due to the fact that they do not have membrane bound organelles, and all metabolic functions relying on a plasma membrane must take place in the cell membrane

Membrane lipids in bacteria are mostly phospholipids that contain which 3 components?

Glycerol, phosphate head group, 2 fatty acid tails

What form of glycerol is found in bacteria? What form of glycerol is found in archaea?

Glycerol-3-phosphate is found in bacteria while glycerol-1-phosphate is found in archaea

1. Are fatty acid tails in bacterial phospholipids usually on the longer or shorter end? How many carbons do they typically consist of?

2. Name 2 examples of “weird fatty” acid tails bacteria may have?

1. Fatty acid tails in bacterial phospholipids often have 14, 16, or 18 carbons but tend to be on the shorter side (closer to 14C)

2. Odd number of carbons, two terminal methyl groups (iso-FA) instead of one

What is the archaeal equivalent of fatty acid tails in bacterial phospholipids?

Isoprenoid based hydrocarbons which exist in multiples of 5 (ex. 5C, 10C, 15C) and can be branched

Explain what the instability of membranes containing both glycerol-3-phosphate and glycerol-1-phosphate tells us about evolution of bacteria and archaea

Glycerol-3-phosphate along with glycerol-3-phosphate dehydrogenase are only found in bacteria while glycerol-1-phosphate and glycerol-1-phosphate dehydrogenase are only found in archaea, and these enzymes are probably not related. While the simplest explanation is that cells arose only once due to their complexity, the fact that G1P and G3P cannot coexist in a membrane and that the corresponding enzymes are unrelated supports the hypothesis that bacteria and archaea evolved independently

What are two mechanisms that maintain membrane fluidity in bacteria? Explain each mechanism

1. Degree of unsaturation → varies with temperature. For example under low temperatures to prevent crystallization and subsequent loss of fluidity, degree of unsaturation increases as unsaturated fatty acids are kinked and interfere with crystalline structure

2. presence of hopinoids → bacterial equivalent of cholesterol, make up 1-5% of bacterial membranes and are stable to acid, alkaline and high temperatures

In bacteria, __ bonds connect the phosphate group to glycerol and glycerol to each fatty acid tail. In archaea, __ bonds connect the phosphate group to glycerol and glycerol to each isoprenoid-based hydrocarbon tail

Ester, ether

Why do archaea use ether bonds instead of using ester bonds like bacteria?

Archaea tend to live in much more extreme environments than bacteria. Ether linkages are much more thermodynamically stable and are much less sensitive to pH than ester linkages

What characteristic found in the large 60S subunit of eukaryotic rRNA can also be found in archaea?

5.8S rRNA

Are archaeal proteins involved in processes like transcription and DNA replication more like in eukaryotes or bacteria?

Eukaryotes

While bacterial cell walls are made of _, some archaeal cells contain a similar material called _

Peptidoglycan, pseudomurein

Name two major and two minor phyla of archaea

Major: Euryarchaeota, crenarchaeota

Minor: nanoarchaeota, korarchaeota

Crenarchaeota (4)

• Known strains are thermophilic or hypothermophilic

• Usually acidophiles

• Uncultivated representatives are widespread

• Found in polar and temperate marine water, soil, sediment

Provide three examples of Crenarchaeota

• thermoproteus is a big group within the phylum, possibly one of the earliest forms of cellular life (at 70-97 Celsius)

• Pylorobus are found by underwater volcanoes, up to 113 Celsius

• Sulfolobus grows at pH 2

Euryarchaeota, provide 3 examples of characteristics found within groups in this phylum

Euryarchaeota are widespread and diverse, includes methanogens (which produce methane as a byproduct of energy metabolism), extreme halophiles (salty environments) and thermophiles (hot environments)

Nanoarchaeota

Minor phylum of archaea, includes Nanoarchaeum equitans (smallest microorganism)

Korarcheaota

Minor phylum of archaea, uncultivatable (cannot be grown in a lab)

Briefly describe TACK, DPAAN and Asgard superphyla

TACK

• Several groups of related and very branched archaea

DPAAN

• includes Nanoarchaeota and are generally obligate symbionts

Asgard

• known only from DNA isolated from marine waters and reassembled through complex techniques

• Includes closest known relative of eukaryotes Heimdallarchaeia

How are phospholipids arranged in membranes?

Phospholipids are arranged so that the hydrophilic/polar head groups are close to water and the hydrophobic/nonpolar FA tails are away from the water

Name 7 possible functions of membrane proteins

Photosynthesis, respiration, ATP generation, movement of solutes, motility, sensing, DNA replication

1. What are plasma membranes permeable to?

2. What are plasma membranes impermeable to?

1. Most small and nonpolar molecules (ex. glycerol, ethanol, fatty acids), gases (ex. CO2, O2)

2. Large molecules (ex. Proteins, DNA), small polar/hydrophilic molecules (amino acids, sugars) and electrically charged (metal ions)

What is passive transport? Which two ways can passive transport occur?

Movement of compounds through the membrane from a region of high concentration to a region of low concentration (along concentration gradient) without energy requirements. Passive transport can occur by diffusion through the membrane or with help from a protein which binds to the compound and allows it to cross the membrane with no energy cost (facilitated diffusion)

What is active transport?

Active transport moves compounds against the concentration gradient from an area of low concentration to an area of high concentration using ATP or proton motive force

Name and describe 5 forms of active transport

1. Symport transporters use proton motive force to move a proton and a compound into the cell

2. Antiport transporters use proton motive force to move a compound into the cell and a proton out of the cell

3. Group translocation uses ATP and adds a phosphate group to the transported compound

4. ABC (ATP binding cassette) transporters are family of proteins that use ATP hydrolysis for transport

5. Efflux pumps use ATP to transport toxic compounds and natural antimicrobial products out of the cell

1. How do bacterial cell walls manage to be tough but also expandable/contractable?

2. How many molecules do bacterial cell walls consist of?

3. Why is it important that cell walls combat osmotic pressure?

1. Covalent bonding in peptidoglycan structure allows for flexibility

2. The cell wall of a bacterium consists of one large molecule, possibly one of the largest found in nature

3. Osmotic pressure can cause lysis or plasmolysis of a cell

What is lysozyme?

Lysozyme is an enzyme found in our eyes in saliva that causes bacteria to lyse by breaking bonds in peptidoglycan

What forms peptidoglycan’s backbone?

A dimer/ disaccharide repeat of two sugars: N-acetyl glucosamine and N-acetyl muramic acid connected by glycosidic bonds

Does NAM or NAG have a short polymer attached to it? Which amino acids are in this polymer?

NAM has a short polymer attached to it consisting of L-alinine, D-glutamic acid, AAx (number of possible amino acids), D alanine, D alanine (cut off)