BIOL 3270 Exam 1: What are Microbes Made of?

what are microbes?

single celled and very diversely shaped forms of life that include bacteria, archaea, yeast, viruses, etc and that are too small to be seen with the naked eye and are very diverse in shape (rods, balls, etc)

what gene is universal in bacteria?

16s rRNA

what are the 3 rules of microbiology?

1. microbes are very small

2. microbes are everywhere

3. microbes rule

what is the range of microbe sizes?

they can range from 0.4 microns (prochlorococcus marinus) to 100 microns (paramecium)

what is the significance of prochlorococcus marinus?

it is one of the smallest and most abundant bacterial cells and can perform photosynthesis to where it can fix CO2 and convert it into sugar and O2 -- it is responsible for 20% of the oxygen you breathe everyday

how do bacteria collectively constitute the major portion of biomass on earth?

carbon: equal to all plants on Earth; nitrogen: 10x all plants on Earth; phosphorus: 10x all plants on Earth

what is the significance of Bacillus infernus?

it was isolated from a 2-mile deep well meaning it was surviving with no light, no oxygen, high pressure, and high temperature

what is the significance of Yersinia pestis?

in 14th century killed a large population (black death)

do men or women have more diverse microbes on their fingertips?

women

What is the size of E. coli?

roughly 2 micrometer (microns) in length and 1 micron in diameter

what are extremophiles?

organisms that grow under extreme conditions including extreme temperatures, pressures, pH, salinity, radiation

what is the role of Deinococcus radiodurans as an extremophile?

Deinococcus radioduran (the toughest bacteria) can withstand 15,000 Gy and effectively protects against genomic/DNA damage upon radiation by repairing the shattered DNA after exposed (remember 10,000 Gy would kill a human)

what is the metabolic diversity of microbes?

they are able to fix carbon and nitrogen while living without the presence of plants or animals -- they are able to survive off of different nutrients in diverse environments

what shape does the name Coccus denote?

sphere (ex. streptococcus pneumoniae)

what shape does the name Bacillus denote?

rod (ex. bacillus anthracis)

what shape does the name Spirillum denote?

spiral (ex. spirillum minus)

why is morphology not a good predictor of the evolutionary relationship of microbes or the species they belong to?

there are not enough distinguishable traits between bacteria; i.e if two bacteria where spherical shapes we could still not predict how close they are in species

what sets the morphology of a particular species?

optimization for nutrient uptake, swimming motility in viscous environments, gliding motility

given that mitochondria originated from proteobacteria, would it resemble closeness to E.coli or B. anthracis?

E. Coli; mitochondria is homologous (shares common ancestry to E.coli)

is archaea closer to eukarya or prokarya?

eukarya as it splits before the root (last common ancestor)

why is bacterial shape limited?

shape is determined by the trade off between three tasks and those that are unusual shapes tend to not survive -- there is a reason for limited shapes

1. fastest for swimming

2. best for maneuverability

3. easiest to make

what are longer rods and curved structure shapes better for?

maneuverability

what are shorter rod shaped structures better for?

swimming mobility

what bacterial shape is easiest to make?

coccus, or a very tiny rod shape

what is the relationship of surface area and volume in cells?

when the spherical shape becomes smaller, the surface area becomes larger

why are some bacterial cells so large if a microbe should thrive better at small sizes?

some bacteria, including nitrate bacteria (Thiomargarita magnifica), may store energy with their large volume

what are the all advantages of being small for a microbe (prokaryotes)?

- larger surface area relative to cell volume than larger cells

- greater nutrient exchange per unit cell volume and allows microbe to flourish

- grow faster, less energy to needed and with larger surface area is still easily able to process nutrients

- can move things through diffusion without expending energy

- can divide and replicate faster than larger cells

how does the smallness of a microbe affect evolution and how does largeness not matter here?

each time a cell divides, its chromosome replicates which gives more chance for mutations to occur and greater evolutionary possibilities whereas larger cells are more likely to mask mutations

can larger microbes rely just on diffusion to move things ?

no, it would massive amounts of time to move nutrients/toxins out with just diffusion

- some parts of the cell would never see the nutrients

- expends actual energy to do this unlike small bacteria

what are some examples of larger bacterial cells?

thiomargarita namibiensis (contain vacuoles for nutrients) and thiomargarita magnifica (leaves of mango trees)

what are some of the organelles of bacteria?

cell wall, plasma membrane, cytoplasm, flagella, capsule, ribosomes

can bacterial cells that are 0.1-0.2 microns survive?

Many bacteria cells that are 0.1-0.2 microns in size often cannot contain all the necessary things (like a cell wall, flagella, capsules, etc) to function properly and often are supplied by their hosts. some also adapt as endospores while trying to conserve energy

what is the lower limit of cell size meaning what are all the things a living cell has to have and takes up space within the cell?

a chromosome, proteins to copy the chromosome and express genes, with a minimum of 300 genes to survive -- all of this stuff takes up space

what is the most abundant bacterial species?

pelagibacter ubique

what is the role of the cytoplasmic (cell) membrane of a bacterial cell?

a thin 6-8 nanometer wide barrier that surrounds the cell and separates the cytoplasm from the cell's environment

what are the distinctive features of the cell membrane?

a phospholipid bilayer (leaflets) that contains a hydrophobic fatty acid tails (hydrophobic core) and hydrophilic components (glycerol phosphate head, negatively charged, polar) with a fluid membrane

- contains an equal amount of phospholipids and proteins

what would happen if you added 70% ethanol (a strong solvent) to the cell membrane?

Will destroy the cell membrane - tails cannot interact with ethanol and will cause changes in the packing of tails because it is a solvent (means it can dissolve in water)

Ethanol: dissolves both polar and nonpolar substance and destroys the folded structure of proteins

what is the role of the cell membrane as a permeability barrier?

prevents leakage and functions as a gateway for transport of nutrients in and out of the cell because of their hydrophobic/hydrophilic features-- functions to keep water soluble proteins and other components within the cytoplasm

what is the role of the cell membrane as a protein anchor?

it is the site of many proteins involved in transport, bioenergetics, and chemotaxis -- involved in import/export of nutrients and toxins, and generation of ATP

what is the role of the cell membrane in energy conservation?

site of generation and use of the proton motive force (a way of conserving energy) -- since bacteria do not have mitochondria they are able to generate energy (ATP) on their cell membrane

why do polar (charges uneven) and charged molecules require specific protein transporters to pass through the cell membrane?

due to hydrophobic regions -- need very specific transporters for each molecule

how do small, uncharged molecules (O2, CO2, and H2O) pass through the membrane?

they easily permeate the membrane by diffusion

why do bacteria change their membrane lipid composition?

in response to different environments -- most common in fatty acid tails

what is the difference betweens saturated and unsaturated fatty acids?

saturated fatty acids contain no double bonds whereas unsaturated do contain double bonds with cis (same side) being more beneficial, creating a "kink" for increased membrane fluidity

how would E.coli bacteria respond to a cold environment?

it would take on unsaturated fatty acids to maintain its liquid form and prevent from being frozen in a cold environment -- essentially bacteria need to survive so will change forms based on environment

what are the role of hopanoids in bacteria?

insert themselves within the lipid bilayer and are stiffening agents that add strength to membranes by limiting the motion of phospholipid tails -- needed when bacteria move to a hot environment to prevent from over heating (become stiff)

describe the structure of cytoplasmic (membrane/transport) proteins.

the outer surface of cytoplasmic (membrane) proteins are hydrophilic as they are surrounded by water, but the inside forms a hydrophobic core

describe the function of membrane proteins.

- provide structural support through flagellum and anchor layers of the envelope

- detect environmental signals (acidity, temperature, and transporters that can release toxins)

- secrete virulent factors and signal molecules for exportation of toxins and signals across envelope

- substrate transport

- generation of energy through management of ion flux

what do membrane proteins require?

a hydrophobic portion that is soluble within the membrane

- several hydrophobic alpha helices through membrane

- peptide regions extend outside containing charged/polar amino acids that react with water

what is passive diffusion? give examples of molecules that would participate in this diffusion.

diffusion of a solute through a membrane down its concentration gradient without a transport protein

ex: small uncharged molecules including (O2, CO2, H2O) -- NOT large, polar, charged molecules

What is osmosis?

diffusion of water across a selectively permeable membrane where its aim is to maintain a concentration that is higher inside than outside the cell with the concentration of water therefore being lower inside than outside

what is osmotic pressure?

the pressure required to stop the flow of solvent molecules from a dilute solution to a concentrated solution through a semi-permeable membrane, as solvents like water, that pass from a dilute solution to a highly concentrated one inside the cell can actually cause the cell to burst

what ions require transport proteins (transporters)?

inorganic ions (Na+, Cl-, K+)

what are transport proteins?

proteins that obtain energy for active transport by cotransport of another substance down its gradient or by coupling to a chemical reaction

what is active transport?

transport from lower to higher concentration and requires energy

what is cardiolipin?

A double phospholipid linked by glycerol that increases in bacteria grown to starvation (lack of nutrients) or stationary phase

- concentrates in patches near cell poles

- "wedge" shape of narrow head and wide fatty acid for stabilization of polar membrane

- contributes to stability

what do bacteria do to unsaturated fatty acids during starvation and acid stress?

convert them to cyclopropane to decrease fluidity and increase stiffening for adaptation to osmotic stress, acidic pH, cold environments, etc

what are planar molecules?

they fill gaps between hydrocarbon chains and affect the packing of hydrophobic tails

and reinforce the membrane - includes cholesterol or hopanoids

(Both synthesized from same precursor molecules as archaea lipids)

Fit between fatty acid side chains and limit their motion - producing stiffness for

describe the difference between the archaeal and bacterial membrane

in the archaeal membrane there are ether links between the glycerol and fatty acids that are more stable than the ester links in bacterial cells which gives the reason to why some archaea grow at high temperatures

- archaea membranes also have branched terpenoids derived from isoprene which extends a methyl branch (limits the movement of hydrocarbon chains because side chains make the membrane more stiff)

what bonds allow archaeal cells to grow and thrive in high temperatures as compared to bacterial cells?

the membrane is attached through covalent bonds which stabilizes the membrane in high temperatures as opposed to in bacterial cells they are attached by hydrophobic forces

what is the upper temperature limit of archaeal membranes? do we need to know this?

microorganisms that use FeIII as an electron acceptor are key components of the deep hot biosphere where after after acception, FeIII is reduced to FeII

what is the pressure of a cell equivalent too?

car tire 32 PSI due to osmotic stress

what is the function of the cell wall?

support and protect the cell membrane from osmotic stress**

describe the cell wall of bacteria.

A single molecule peptidoglycan wall composed of disaccharides and amino acids that gives bacteria structural support. It has maximal volume with minimal surface area and is highly porous to ions and organic molecules (in gram negative bacteria). It is often a target for antibiotic treatment.

describe peptidoglycan.

Repeating framework of long glycan (disaccharide) chains cross-linked by 4 short peptide (amino acid) fragments -- transpeptidase does the cross linking

- joins two molecules with covalent bonds to create one single molecule *unique to bacteria

describe how cross bridges are formed in peptidoglycan

NAM forms amide link with amino terminus of short peptide -- the cross bridges are formed by removal of second D-alanine at end of the amino acid (peptide) chain to then form a covalent bond with the other peptide chain's NAM

how does peptidoglycan prevent osmotic shock within the bacterial cell?

in gram positive bacteria, the cell wall limits the volume of the closed cell by generating tugor pressure which presses the cell wall against the cell membrane, whereas in gram negative bacteria, the outer membrane tends to prevent a lot of osmotic shock

what carries out the process of the bonding of the two amino acid (peptide chains) groups?

transpeptidase

what is a target of transpeptidase?

antibiotics which bind to the terminal D-Ala-D-Ala and prevent removal of terminal D-alanine and therefore without removal, the two glycan chains with amino acid side chains cannot be covalently (peptide) bonded to rebuild the cell

what are the lysozymes role in bacteria and how does adding antibiotics affect the bacteria's growth?

lysozymes "destroy" their own cell wall by creating gaps in the chain, so that the cell can grow larger.

By adding antibiotics you can inhibit the transpeptidase and when the cell wall is broken they will not be able to repair and grow

In order for antibiotics to act properly the cells have to be actively growing (if they are not actively growing the peptidoglycan will already be covalently bonded) - if they are not growing the antibiotics will not kill the bacterial cells

why would some bacterial cells not have a cell wall?

high salinity in the environment, meaning if the outside of the cell already has a high salt concentration, meaning the inside is filled with more water, there would be no need for water to rush into the causing osmotic stress (if anything more water would need to be outside of the cell)

what are some examples of bacteria that does not have a cell wall?

intracellular bacteria (Rickettsia, Mycoplasmas)

Endosymbionts -- feed off hosts (Buchnera, Wolbachia)

mitochondria and chloroplasts (used to have it one)

what are inorganic vs organic molecules vs macromolecules?

inorganic = K+, Mg2+. and phosphate; store energy in the form of transmembrane gradients

vs

organic = phospholipids, enzyme cofactors, polyamines, lipids, sugars

vs

macromolecules = nucleic acids and proteins; contain information, catalyze reactions, and mediate transport

what is the Gram stain?

It is a test to determine if a bacteria is gram positive or gram negative based on the difference in cell wall structure

lay out the steps of a Gram stain

- Add methanol to denature proteins and fix cells to surface

- Add crystal violet stain (purple color)

- Add iodine, which binds stain to Gram positive cells

- Gram positive can trap the dyes better than Gram negative

- Iodine forms a complex with crystal violet

- Wash with ethanol to wash away crystal violet stain from Gram negative (because Gram positive cells will trap it)

- Add safranin counterstain (pink) to stain Gram negative cells so that there is a differentiation

describe Gram positive bacteria

contain multiple layers of peptidoglycan, but is still one molecule due to cross links; the peptidoglycan layers are reinforced by teichoic acids which have negative charges that retain the Gram stain

what are sortases in Gram positive bacteria?

responsible for covalently attaching specific proteins that help acquire specific nutrients needed by the bacterial cell

what is the S layer of Gram positive bacteria?

the protein membrane; multiple units of protein or glycoprotein; rigid but allows substances to pass through -- helps pathogens bind and attack host cells by allowing stuff out of cell

- protect cell from phagocytosis

- helps maintain cell structure

- those that do NOT have S layers can grow much faster using the energy that would have been used to create the S layer

give examples of Gram positive bacteria

Bacillus anthracis, Streptococcus Pneumoniae - Firmicutes phylum

describe Gram negative bacteria

contain a thin layer of peptidoglycan (thin cell wall), periplasmic space (containing the cell wall) and enzymes, and an outer membrane which contains the following:

- lipoproteins

- lipopolysaccharide (Lipid A, core polysaccharide, O-antigen)

- proteins

- polysaccharides

- porins

describe the lipoproteins found in the outer membrane of Gram-negative bacteria.

inward facing leaflet; connects the outer membrane to the peptide bridges of the cell wall

Describe Lipopolysaccharide (LPS) found in the outer membrane of Gram-negative bacteria.

outward facing leaflet that protects bacterial cells from the immune system of hosts after creating possibly lethal inflammatory responses

describe the Lipid A component of LPSs

a hydrophobic tail (remember its a lipid) used for anchoring and is recognized by immune system; endotoxic part of LPS

describe the O- antigen component of LPSs

*high variability* a repeat unit of sugars that is recognized by immune system and causes the host to release antibodies

- connects with core polysaccharide

- can establish infections in the host cell by changing O-antigen number to confuse immune system

- sugar chains protects from phagocytosis by host's immune system

what would happen if a cell had a deleted LPS gene?

the cell would die from attack by the host cell

describe the toll-like receptors that lipopolysaccharides are recognized by and what happens.

when recognized, LPSs can bind which triggers conformational changes in the intracellular domain and send a cascade of signals to the nucleus to make cytokines (trigger for immune system inflammation signals)

what does it mean that lipopolysaccharides are endotoxins?

they are toxins that are apart of the cell and those that can trigger a strong immune response which can damage your own tissue and cause sepsis -- LPS is recognized as an endotoxin due to its ability to trigger potent immune responses in host organisms. While this activation of the immune system can aid in bacterial clearance, Gram-negative bacteria have evolved mechanisms to exploit LPS-induced inflammation to their advantage. For example, excessive production of pro-inflammatory cytokines in response to LPS can lead to tissue damage and compromise the host's ability to combat infection effectively

when is an endotoxin harmless?

when the pathogen remains intact -- once lysed when the cell undergoes cell division, they can cause sepsis

what happens when something binds to the toll-like receptors?

a signal is sent to the nucleus to synthesize/release pro inflammatory cytokines

what is the function of the porins found on the outer membrane in Gram-negative bacteria?

they permit entry of nutrients such as sugars and peptides; contain a beta barrel conformation and have limited specificity meaning they allow passive uptake of molecules including derivative antibiotics like ampicillin to where those charged groups are attracted to the charged amino acid residues and is allowed entry

what is the periplasm in Gram negative bacteria?

home of the cell wall in Gram negative bacteria (between outer and cell membrane) -- contains enzymes and nutrient transporters

- subjected to pH fluctuations due to outer membrane containing porins that allow ions in that could potentially change the charge of the cell

why are antibiotics not very effective against Gram negative bacteria?

the outer membrane protects the cell wall from any destruction BUT adding amino groups to an antibiotic could potentially allow the transporters to transport it into the cell for destruction of the cell wall

what are capsules in bacteria and how do they aid in invasion of the immune system?

polysaccharide layers that assist in attachment to surfaces (including host cells) due to their own "sticky" surface. they aid in the invasion of the immune system and avoid phagocytosis by WBCs, enabling the pathogen to persist in the blood. they also resist desiccation (drying out) by trapping water and nutrients -- often used to distinguish between different bacterial species

what is Xanthan gum?

a bacterial capsule that appears slimy; found in things like salad dressing, toothpaste, sauce, etc to keep the oils and water stuck together -- luckily the bacteria in our digestive tract can digest this

what is caulobacter crescentus?

a gram negative bacteria that uses its stalk to stick to places where it has a holdfast and is able to stick to things very, very tightly

- has flagellum

- polysaccharides (used to stick) and proteins

where do caulobacter crecrenus live?

water streams/taps -- use their holdfast to cling to surfaces to not be washed away by the water -- can use their bending to grasp onto stuff to where 1 square inch can hold 10,000 pounds

what are bacterial fimbriae and pili?

filamentous, hairy protein structures on the cell surface that enable organisms to stick to surfaces, form biofilms, and form pellicules

how does bacterial pili (fimbriae) engage in bacterial sex?

pili bring cells together to facilitate genetic exchange (DNA) between cells which is called conjugation but do not depend on this to replicate and can replicate on their own

what are bacterial flagella?

long structures (mainly in proteobacteria) that extend beyond the cell to help cells swim and move towards nutrients AND away from danger; can move extremely fast

describe the flagella of Gram negative bacteria

contain a motor region with filaments; the tail is made up of a single protein that forms polymers and a hollow tube

- L ring anchors to outer membrane

- P ring anchors to peptidoglycan (cell wall)

- MS ring anchors to cell membrane