Microbiology CH 1
ALL POLAR MOLECULES ARE _______ ALL NONPOLAR MOLECULES ARE _________________
hydrophilic; hydrophobic
What drives protein folding?
hydrophobic interactions
Describes a complex prokaryotic virus and complex eukaryotic virus.
1.) A complex prokaryotic virus has a capsid and nucleic acid genome, as well as a helical sheet and base plate. Tail fibers are used to attach to a host cell 2.) Complex eukaryotic virus ha s a protein capsid and nucleic acid genome. Also, has an envelope which is a membrane derived from host cell that is insulatory (B/C of hydrophobic tails) so that the virus cannot communicate with the outside environment. It uses spike proteins to facilitate attachment and allow for delivery of viral genome to the cytoplasm of the host cell.
Name the important and beneficial contributions of microbes
1.) Bacteria and yeast engage in competitive exclusion 2.) Help breakdown our food in our GI tract and provide us with the nutrients that we can uptake. 3.) Pink moss: fungal spores will germinate in the soil and create a symbiotic infection and creates an anaerobic env. to allow plant to use nitrogenous which can be incorporated readily into N using macromolecules 4.) In food, S.cerevisiae uses oxygen dependent metabolism to oxidize sugars into CO2 which will accumulate and cause bread to rise, in beer/wine it will oxidize simple sugars to ethanol. Yogurt/tofu, lactic acid building bacteria will ferment sugars into lactic acid 5.) Insulin comes from E. coli, Hep A vaccine uses bakers yeast to modify proteins.
What are the 3 types of investigation used in epidemiology?
1.) Descriptive 2.) Analytical 3.) Experimental
What are the three types of motility used?
1.) Flagella: used to propel protozoa in aquatic environments by moving in a whip like manner 2.) cillia (hair): coat the entire surface move back and forth in a coordinated way to allow the organism to move 3.) cytoplasmic extensions called pseudopods which extend, attach to surfaces , and pull organism in that direction
How to Carry out a gram stain
1.) Make a smear and allow it to dry 2.) Fixation through heat 3.) Add the primary stain (Crystal violet) so that it becomes purple 4.) Rinse with diH2O 5.) Add the mordant -Iodine- which adds a black color 6.) Go through decolorization using ethanol 7.) Add the counterstain - safranin-
What are the 8 subdisciplines of molecular biology?
1.) Medical microbiology: Study of host-pathogen interactions 2.) Agricultural microbiology: Study of soil microbes and their interactions with cash crops 3.) Industrial microbiology: The use of microbes for production of marketable products such as drugs, food etc. 4.) Aquatic microbiology: The study of microbial interactions in water environments. Essential for waste water treatment 5.) Microbial systematics: The classification of microorganisms. Use of rRNA sequencing has made this very popular 6.) Microbial physiology: The study of bacterial metabolism enhanced by advances in cultivation techniques 7.) Bacterial genetics: transmission of genetic informations through horizontal transfer or vertical transfer. Both of which contribute to microbial diversity. 8.) Genomics: Analysis of global changes in gene expression in response to environmental stimuli. This is widely used in biotechnology sectors.
What are the 3 classes of side chains?
1.) Polar: contains atoms with extremely different / electronegativities. Polar side chains will be hydrophilic and increasing their content will increase solubility. (Asn, Gln, Tyr, Ser, Thr) 2.) Charged: They are ionized in solution and therefore carry a charge Acidic: Asp, Glu (give up a proton in solution and acquire a net - charge) Basic: Arg, Lys, His (Accept a proton in solution and acquire a net + charge) 3.) Hydrophobic (allopathic): Found on the interior proteins play a major role in proton folding (Gly, Ala, Val, Leu, Ile, Phe, Met, Cys, Pro, Trp)
What are the different protein structures?
1.) Primary: A linear chain of amino acid that form a random coil. These are not common and readily fold into secondary structure 2.) Secondary: Formed through H bonding between the amine groups and the carbonyl oxygen in the peptide backbone of the protein. Can be folded back and forth to make a Beta pleated sheet or an alpha helix. 3.) Tertiary: The alpha helices will overlay the Beta pleated sheets giving the protein a specific function. The amine adjacent to the carboxylic acid in the structures will create an ionic bond and stabilize the structure. There are also adjacent methyl groups that will form hydrophobic interactions and contribute to stabilization. 4.) Quaternary: If a monomer protein is not active a complex formation between two different proteins will result in an active protein. ALL BONDS THAT STABILIZE 3 WORK HERE.
What percent of microbes never come into contact with humans? What is their role?
99.9%, important role in biogeochemical cycles.
What experiments were done against spontaneous generation
1668: Francesco Redi provided the first evidence against by putting spoiled meat into two flasks, one uncovered one covered. He left them for several days and found that maggots only appeared on the flask if it was open. DID NOT EXCLUDE THE POSSIBILITY OF SPONTANEOUS GENERATION OF BACTERIA. 1861 Louis Pasteur: put a non sterile liquid into a volumetric flask then manipulated the neck into an S shape. He then heated the liquid to sterilize it and forced the steam out of the open end. When the liquid cooled it remained sterile for a very long time UNTIL he tipped the flask and allowed the liquid to mix with microbes and dust that were trapped in the neck of the flask then the broth putrefied.
What is the function of the chloroplast?
carry out photosynthesis: convert co2 and light to sugars and oxygen
What is the central building block of ALL lipids?
A 3-C polyalcohol (glycerol) Lipids consist of 3 types of functional groups being attached to C-based atoms
Describe a simple viruses structure
A capsid made of protein will protect the genome (some type of nucleic acid, could be dsDNA, ssDNA, dsRNA, ssRNA.)
What are the components of a bacterial cell?
A cell wall composed of peptidoglycan is the outermost layer, within it is the plasma membrane Inside the membrane is the cytoplasm, ribosomes, and a nucleoid. The nucleoid is composed of closed circular chromosomes.
Describe the structure of algae
A cell wall made of cellulose encloses the entire cell. The following layer is the plasma membrane, inside is the golgi, nucleus, ER continuous with the nucleus, mitochondria, ribosomes, and chloroplast.
Describe the structure of fungi
A cell wall made of chitin envelops the entire cell. The next layer is the plasma membrane which surrounds the cytoplasm and all other components of the fungi. These include: nucleus, ER, golgi, ribosomes, and mitochondria.
How are the polypeptide bonds of proteins formed?
A condensation reaction with the remove the -OH and 1 H to create H2O. This results in a peptide bond.
What are Koch's postulates?
A set of guidelines to demonstrate that a specific pathogen causes specific disease symptoms 1.) Isolate organisms from animal and culture in vivo 2.) Infect a healthy animal and determine if the disease is reproduced 3.) isolate organisms from the infected animal and see if it is the same as what was isolated/cultured in step 1
What causes protein denaturation?
Acidic or alkalinity, high temperature etc. Urea can facilitate unfolding. If you remove the stress the protein can refold using chaperones.
What is an aldose?
An aldehyde sugar, identified by the carbonyl group (CO) at the end of a carbon skeleton (carbonyl oxygen is on the 1' C)
How are saturated and unsaturated fatty acids formed?
An unsaturated fatty acid is the result of an additional fatty acid being added to other -OH groups, this will result in a double bond between the two CH and a kink in the chain so that is branches off in a different direction. A saturated fatty acid has a single bond and does not branch off.
Who was the first person to visualize bacteria? How?
Antoni Von Leeuwenhoek in 1684, developed a simple microscope using a lens with high enough resolving power to make a 100x microscope. He placed a sample of pond water at the tip of a needle and used a screw to lower/elevate it to focus
How do we typically store monosaccharides?
As complex polysaccharides so that the bond can be easily broken for energy and the monosaccharides can be released for Energy metabolism
What types of linkages can occur via anomeric carbons?
Beta 1,4 glycosidic bond: The 1' C from 1 sugar is attached to the 4' C on another adjacent sugar. The hydroxyl group from the 1'C is above the plane Beta 1,6 glycosidic bond: The 1' C from 1 sugar is attached to the 6' C on an adjacent sugar. The hydroxyl group used to form the bond is above the plane. Alpha 1,4 glycosidic bond: The 1' C from 1 sugar is attached to the 4' C on another adjacent sugar. The hydroxyl group from the 1'C is beneath the plane Alpha 1,6 glycosidic bond: The 1' C from 1 sugar is attached to the 6' C on another adjacent sugar. The hydroxyl group from the 1'C is beneath the plane
When does sepsis occur?
Blunt force trauma to the stomach causes a rupture to the intestinal lining allowing for the release of gram - bacteria into the blood, the presence of LPS causes the symptoms and will bind to the receptors on the surface of macrophages to facilitate activation (septic shock)
What is the difference between glycogen and starch?
Both have long chains of alpha1,4 linkages joining sugars BUT glycogen has a number of branch points formed by alpha1,6 linkages.
How can ribose be turned into deoxyribose?
By removing the -OH on the 2' C hence the name DEOXYribose
What functional groups must be ionized to exist in biological systems?
Carboxylic acid Amine Phosphate Ester
What is Edward Jenner known for?
In 1796 Jenner produced the first successful vaccination for smallpox. Milkmaids were not susceptible to smallpox because they have been previously infected by cowpox a similar disease that caused localized pus filled blisters without the systemic infection. He injected an orphan with cowpox then smallpox and the orphan lived because the less severe cowpox caused him to build immunity.
Describe Louis Pasteur's contribution to the discovery of fermentation and pasteuration.
In 1864 Pasteur characterized S. cerevisiae and found that under anaerobic conditions it could convert sugar from fruits/grains into alcohol via fermentation. When being transported alcohol/meat etc. would often spoil, he examined the spoiled alcohol and found cells smaller than S. cerevisiae. He heated the alcohol enough to kill this bacteria -acetic-acid fermenting bacteria- without hurting the alcohol. This process of heating perishables to prevent spoiling by killing bacteria is called pasteurization.
How do microorganisms differ from higher eukaryotes?
In higher eukaryotes a single cell cannot function alone it must work with other to produce tissue, organs, etc.
What is the difference between alpha and beta configuration of a ring?
In the alpha configuration the hydroxyl on the 1' C is beneath the plane of the ring In the beta configuration the hydroxyl on the 1'C that was used for the nucleophilic attack is above the plane of the ring
What is the difference between Gram positive and Gram negative bacteria?
Gram + a thick layer of peptidoglycan (30-50 sheets make up the outer layer), they have a number of teichoic acid (composed of glycerol phosphate or ribitol phosphate with attached molecules of glucose or D-alanine. Individual alcohol molecules are then connected through phosphate groups to form long strands and then are covalently attached to peptidoglycan) Teichoic acid can bind metal ions. Also, have lipoteichoic acid LTA that go inward and facilitate stable association between the plasma membrane and the peptidoglycan. Here peptidoglycan is the result of: Alternating NAG and NAM that are joined by Beta1,4 linkage. Chains are linked together by a peptide crosslink Gram - The peptidoglycan layer here is much thinner (1-2 sheets) and there is an outer membrane surrounding it composed of a lipid bilayer. In the region facing the periplasm there is a variety of lipids , lipids facing the environment are attached to NAG-6-polyalcohol. Instead of a phosphate has a long polysaccharide chain (LPS lipopolysaccharide) Also, have a porin. Proteins that serve as channels allowing virtually any small hydrophilic substance to pass. The section between plasma and outer membrane is the periplasm
What is Martinus Beijerinck known for?
He developed the enrichment culture technique where microorganisms are isolated using highly selective media and incubation conditions that favor specific organisms. This allows us to isolate pure cultures He was also the first to identify viruses through the TMV ( tobacco mosaic virus) he did so by passing an extract from plants through a sterilization filter so that all cellular life is removed, he was able to find a virus smaller than bacterium that was somehow incorporated in the cells of the host plant.
What did Alexander Fleming discover?
He discovered antibiotics while studying staphylococcus aureus. A fungal colony grew and inhibited the growth of the staph bacterial colonies were smaller close to the fungal colony and there were none directly by it.
Which functional groups are hydrophilic and polar?
Hydroxyl group Ketone Aldehyde Carbonyl (C=O) Carboxylic Acid Amine Phosphate Ester Sulfhydryl
How does synthesis of nucleic acids occur
Nucleotide synthesis always occurs in the 5' --> 3' direction. When long chains of nucleotides are being formed they are delivered as a triphosphate, acid anhydride bonds are high energy when broken they release enough energy to facilitate the condensation reaction that allows for the attachment of the incoming nitrogenous nucleotide.
When does an acid anhydride bond occur?
Occurs when there is a condensation reaction between a carboxylic acid and phosphate resulting in a high energy bond that can be broken and release energy,
When does an ester linkage occur?
Occurs when there is a condensation reaction between a carboxylic acid group and a hydroxyl group. Results in a polar, soluble compound.
Who was the first epidemiologist? What subtype of epidemiology did he practice?
John Snow was the first descriptive epidemiologist, he gathered information and found commonality. He studied the cholera outbreak and analyzed the death records, information from victims and survivors etc. He realized that all infected got their water from one source and had them remove the water pump afterwards the number of cases of cholera decreased.
What is the theory of spontaneous generation?
Life arises -spontaneously generates- from dead matter (spoiled food)
What is LPS?
Lipopolysaccharide is the outer half of the outer membrane and is made of Lipid A, core polysaccharide and O antigen.. It is also called bacterial endotoxin Lipid A The core polysaccharide is conserved across species and attaches the lipopolysaccharide chain to phosphate on lipid A through an amine ester linkage. The species specific O-antigen is a variable external region
What experiments and observations were made in favor of spontaneous generation?
Maggots appear on spoiled meat, broth would get cloudy and stinky. 1745: John Needleman boiled broth to ensure that all life had been killed then he left it for days and found through microscopy that it was full of microorganisms so he argued that microorganisms had spontaneously generated.
When does an ether linkage occur?
Occurs when there is a condensation reaction between two hydroxyl groups this is used for lipid biosynthesis.
When does a phosphoanhydride linkage occur?
Occurs when there is a condensation reaction between two phosphate groups, it creates a high energy bond that can be broken and release energy
When does a thioester linkage occur?
Occurs when there is a condensation reactions between a carboxylic acid and a sulfhydryl group resulting in a polar compound. The thioester linkage is a high energy bond that can be broken and release energy to drive other reactions.
What functional group is nonpolar?
Methyl therefore it is insoluble in aqueous environments
What are enatomers?
Mirror images that can not be superimposed
What is a hexose sugar? Give an example
Monosaccharide with six carbon atoms in each molecule, such as glucose.
Is carbon soluble?
No, but we can add functional groups to one of the four bonds carbon is able to make to increase solubility.
Which functional group plays a large role in energy metabolism?
Phosphate ester
What is the germ theory of disease?
Proven by Robert Koch in 1876 with anthrax, the germ theory of disease shows that a specific bacteria produces diseases and can be replicated through a pure culture, not just infected blood. It was proven through Koch's postulates
Which nitrogenous bases are purines? pyrimidines?
Purines: G and A (2 ring) Pyrimidines: C, T, and U (1 ring)
What two forms can ribose exist as? How does it go from one to another
Ribose is an aldose. It can exist in the linear form OR, following a nucleophilic attack from the carbonyl O (1' ' C) to the 4' C it can become a ring
Who was the first person to visualize unicellular life? How did they do it?
Robert Hooke in 1665, developed a compound microscope (100x) using 2, 10x magnification lens. Was the first to see protists (fungal hyphae and spores)
Whats is the structure of an amino acid?
The basic structure of all 20 amino acids is the same, the side chains just differ.
What distinguishes algae from fungi?
The chloroplast, and its ability to undergo photosynthesis. Algae produces 40% of oxygen in aquatic atmosphere
What is a structural isomer?
Same number of atoms different structural arrangement such as ethanol (drunk) and dimethyl ether (death)
Describe the peptide cross link in gram + S. aureus.
The Gly creates a peptide cross bridge thatt allows for attachment of the 4 amino acid attached to NAM. the Lys on one will attach to the Gly on one end and the Lys on the other will attach to the Gly on the opposing end.
What causes the difference in color of gram -/+ bacteria?
The different structure of the cell wall. 1.) The crystal violet is applied and is present as indiv. molecules The Gram + bacteria has layers of peptidoglycan that are porous so that CV can easily penetrate BUT it can not cross the plasma membrane because lipids that line it are hydrophobic. The Gram - bacteria had an outer membrane that has hydrophobic lipids that do not allow the CV to cross and get to the peptidoglycan layer 2.) The mordant -I- is applied It again can cross the Gram + BUT NOT the Gram - In the Gram + it interact with CV to formed the CV-I complex which is a large aggregate This same aggregate is formed on the outer membrane of Gram- 3.) When we decolorize them with ethanol the CV-I complex is too large to get through the peptidoglycan so the pigment is stuck there but it is easily taken off the surface of gram - 4.) We add the counterstain -S- it will decorate the outer membrane of the gram - in the same way that CV did, and it will enter the peptidoglycan in gram + BUT because the purple is darker gram + appears purple and gram - appears red
What distinguishes algae from plants?
The lack of xylem and phloem
Describe the structure of a basic protozoa
The plasma membrane encloses within itself a mitochondria, golgi apparatus, endoplasmic reticulum, ribosomes, cytoplasm and the nucleus. Attached to the cytoplasmic membrane is the flagella which is used to propel the protozoa through its aqueous environment.
What is epidemiology?
The study of how and why outbreaks of a disease occurs. It involves identifying pathogens, their reservoir, and mode of transmission.
What is vitalism? What experiment/observation was made in favor of this theory?
The theory that for life to arie it needs vitalistic forces that are found in the air. When sealed off to air spontaneous generation will not occur. 1765 Lazzaro Spallanzani: boiled two broths left one covered and another uncovered found that the uncovered broth had microbes and argues that the fresh air had allowed bacteria from the environment to fall in and that this fresh air is required for spontaneous generation.
What is the difference between saturated and unsaturated fatty acids?
Unsaturated fatty acids are unable to be packed in so closely together because of the kinks, therefore they increase fluidity of the membrane. Saturated fatty acids lack any kinks and can pack together very closely and allows for van der waal dispersion forces to act on the saturated fatty acid chain. this leads to a dramatic loss of the mobility of the lipids in the membranes they create.
Why are fiber and cellulose not able to be broken down by animals?
They are both complex carbohydrates assembled by beta linkages that cannot be broken by enzymes in mammalian organisms. Cellulose has a structural role in animals for this very reason.
How are Gram positive and gram negative bacteria similar?
They are both synthesized via long repeating chains of two sugars (NAG and NAM) these chains are linked together through peptide chains between the NAM to make sheets.
Fungi are saprophytes - what does this mean?
They obtain their organic molecules from the environment and use them to synthesize proteins, nucleotides, and other macromolecules
How do fungi reproduce?
They replicate asexually through binary fission
How does bacteria reproduce?
Through binary fission an organism will duplicate it's genetic material, then divides into two separate cells.
How are lipids used for energy?
Triglycerides can be removed converting them into phospholipids which can be used for membrane metabolism, the fatty acids can be liberated for energy metabolism When triglycerides are liberated a fatty acid will be removed and a phosphate group will attach to the 3'C via a condensation reaction. This will allow for an acid anhydride bond to create a phospholipid bilayer of the membrane where the fluidity is determined by the content of saturated vs. unsaturated fat.
What kind of lipid is used for long term storage?
Triglycerides: consist of a fatty acid group that is attached to glycerol through an ester linkage. The ester linkage is the result of a condensation reaction between the two
True or False All protozoa are motile unicellular eukaryotes
True
What is Sergei Winogradsky known for?
Used Beijerinck enrichment culture techniques to discover chemoautotrophy (seen with H2S) and nitrogen fixation. He was able to characterize these processes.
What are the different kinds of chemical bonds discussed
Van der Waals interactions: Also known as transient dipole, this is due to a shift in the electron distribution due to random probability. The low electron density side with induce a dipole shift in another molecule so that it's high density side is attracted to the low density side of the first molecule. Ionic bonds: An electrostatic interaction between oppositely charged molecules or functional group H bonds: Form between H and an atom with high electronegativity that is attracted to the H via (+) and (-) dipoles Covalent bond: formed by the sharing of electrons to complete valence shells, this is the strongest bond and can force double or triple bonds hydrophobic interaction: occurs between long hydrocarbon chains where the non-polar regions of molecules will interact to prevent association with the aqueous environment.
Describe the peptide-cross link in gram - E. coli
a peptide-peptide cross bridge will occur between the Ala and DAP of two NAG-NAM.
What is the structure of a ribonucleotide?
a phosphate group attached to a pentose sugar attached to a nitrogenous base
Why are C-C covalent bonds so important?
because they are strong enough to be stable but can be broken if needed. This provides the versatility needed for life.
Are fungi unicellular or multicellular?
both
What is a geometric isomer?
isomers in which the order of atom bonding is the same but the arrangement of atoms in space is different. Resulting in cis and trans isomers
What is a microorganism?
a unicellular life form that functions independently from other cells, BUT communicates with other microorganisms through signaling molecules that promote signal transduction
What are the 3 types of RNA?
mRNA: transcription tRNA: delivery of amino acids to the ribosome rRNA: catalytic component of the ribosome
Algae are photoautotrophic - what does this mean?
organism that uses energy from sunlight to convert carbon dioxide and water to carbon compounds (sugar) and oxygen
What are complex carbohydrates?
polysaccharides, includes glycogen (animals) and starch (plants)
What is the cell wall of Archaea composed of?
pseudopeptidoglycan
What color will gram positive bacteria stain? gram negative?
purple Pink/red
Define metabolism
the chemical processes that occur within a living organism in order to maintain life. ENERGY PRODUCTION.
What is the role of nucleic acids?
transmit genetic information allows for production of protein