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FA12
| Question | Answer |
|---|---|
| What is a microbe? | a living organism that requires a microscope to be seen; each contains in its genome the capacity to reproduce its own kind |
| Microbes include members of which three domains of life? | bacteria (prokaryotes), archaea (prokaryotes), and eukaryotes (algae and plants, fungi and animals, and protists) |
| What were the 3 essential breakthroughs in studying microbes? | sterile culture (debunked spontaneous generation), petri plates and pure cultures, and microscopes |
| How do you classify microbes? | Isolate; BEFORE: shape, biochemical activities (grow in different media), environmental requirements (temp, pressure), and other phenotypes (spore formation, pathogenicity) /// NOW: DNA sequence |
| How do you choose a gene to be an "evolutionary chronometer?" | the gene must be present in all organisms and be conserved enough to make an alignment |
| What is a characteristic of the 16S ribosomal RNA (rRNA) gene that makes it ideal for comparison? | The level of mutation in rRNA is very low because the proper function of ribosomes is essential for protein synthesis |
| According to Lynn Margulis, how did eukaryotes cells contain mitochondria and chloroplasts? | She proposed these organelles evolved by endosymbiosis from prokaryotes. Ultimately leading to a single organism whose formally independent members are now incapable of independent existence. |
| In which characteristics are bacteria and archaea similar? | morphology, lack of a membrane enclosed nucleus, and metabolic reactions |
| In which characteristics are archaea and eukarya similar? | protein synthesis, transcription, and DNA replication |
| What functions does the cell membrane serve? | It consists of phospholipids, transporter proteins, and other molecules. It prevents cytoplasmic proteins from leaking out. It maintains a gradient of ions and nutrients through transporters |
| What is the purpose of the cell wall? | The cell wall is a rigid structure composed of polysaccharides linked covalently by peptides. It prevents osmotic lysis by withstanding turgor pressure that builds up from osmotic pressure, and determines the shape of the cell |
| What are the components of a cell envelope? | Cell membrane + cell wall + outer membrane (if one is present) |
| What are the components of the cell wall for gram positive bacteria? | A thick peptidoglycan layer and a cytoplasmic membrane |
| What are the components of the cell wall for gram negative bacteria? | outer membrane, a periplasm with a thin peptidoglycan layer within, and a cytoplasmic membrane |
| What are the different results of the gram stain? | Gram positive retain the crystal violet stain because of their thicker cell wall while gram negative bacteria do not |
| Describe the procedure for the gram stain. | Add methanol to fix cells to the surface. Add crystal violet stain, which binds to peptidoglycan. Add iodine, which binds the stain to gram positive cells. Wash with ethanol (stain is removed from gram negative cells). Add counterstain (safranin) |
| What purpose does iodine and ethanol serve in the gram stain? | Iodine is a mordant and forms complexes with the positively charged CV molecules trapped within the cell. It binds the stain to gram-positive cells. Ethanol decolorizes by removing loosely bound CV-I |
| What are most bacterial cell walls made up of? | Peptidoglycan aka murein. A glycan (a polysaccharide) attached to short cross-linked oligopeptides |
| What does the peptidoglycan structure contain? | It is composed of 2 sugar derivatives N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) and some special AA. Diaminopimelic acid (DAP) is sometimes attached to NAM |
| Describe the structure of peptidoglycan | It consists of parallel polymers of disaccharides (glycan chains) cross-linked with peptides. The sugar component consists of alternating linked NAG and NAM. A short peptide chain w/ various AA is attached to NAM. The peptide chains form cross bridges |
| What forms the cross-links in the peptidoglycan structure? | Lysine or diaminopimelic acid (DAP) |
| NAM and DAP have been detected in bacteria and archaea. True or False? | False. NAM and DAP have never been detected in archaea |
| What does lysozyme do to peptidoglycan? | It cuts and breaks the glycosidic bonds between NAG and NAM in PG, thereby weakening the cell wall |
| Compare the effects on lysozyme on PG in a low solute solution versus an isotonic solute solution. | Low solute solution: water enters the cell and results in lysis. Isotonic solute solution: results in a protoplast |
| What happens to light in fluorescence microscopy? | Incident light is absorbed and reemitted at a lower energy, thus longer wavelength |
| Describe characteristics of the archaeal cell wall. | No peptidoglycan (resistant to lysozyme and antibiotics that destroy PG or prevent its synthesis). Typically no outer membrane. It has pseudopeptidoglycan. Has S-layer |
| What are S-layers? | Paracrystalline surface layer. It consists of protein or glycoprotein. |
| What are the components of a gram positive cell envelope? | Capsule made of polysaccharides. S-layer made of protein. Thick cell wall (AA cross-links in peptidoglycan and teichoic acids for strength). Plasma membrane |
| What are teichoic acids? | Acid substance embedded in the cell wall. Chains of phosphodiester-linked glycerol or ribitol, w/ sugars or AA linked in the middle. Responsible for the strong (-) charge of cell surface. Reinforces cell wall. Binds divalent cations transported into cell |
| Describe the components of a gram negative outer membrane. | Outer membrane containing LPS. Periplasm with lipoproteins and peptidoglycan layer. Inner membrane |
| What is the function of the outer membrane on a gram negative bacteria? | It confers defensive abilities and toxigenic properties on many pathogens. |
| What is murein lipoprotein? | It is attached to 3 fatty acid side chains. It is a lipoprotein that connects the outer membrane to the peptide bridges of the cell wall |
| What are the components of the gram negative LPS? | Lipid part: lipid A (contains glucosamine phosphate dimer and fatty acids); Polysaccharide portion: core-polysaccharide and o-polysaccharide// LPS is unique to bacteria |
| Describe characteristics of O-polysaccharide and the core-polysaccharide of the gram negative LPS | The o-polysaccharide is a long, variable carbohydrate chain. It excludes hydrophobic region and elicits an immune response. The core-polysaccharide is a non-varying linker. |
| What function does the Lipid A part of the gram negative LPS serve? | It acts as a membrane anchor. When exposed, it is toxic. |
| What are porins? | It is a protein of the outer membrane of gram-negative bacteria. It has a distinctive cylinder of beta sheets and transports sugars and peptides. |
| What do periplasmic proteins do? | They are subject to fluctuations in pH and salt conc due to the outer membrane being porous to ions. They help refold proteins unfolded by oxidizing agents. |
| What is in the periplasm? | envirionmental sensors, binding proteins, degradative enzymes, and solutes metabolites |
| What does the mycobacterial cell envelopes contain? | membrane lipids (mycolic acids) and unusual sugars (arabinogalactans) |
| What are mycolic acids? | It is an unusual membrane lipid in mycobacterial cell envelopes. It gives a waxy coating on the cell surface, making them resistant to drying. It has the thickest cell walls known. Hard to take up nutrients. Super slow growers |
| What inhibits peptide cross-linking in the cell walls? | Vancomycin and penicillin |
| Summarize the synthesis of peptidoglycan in cell walls. | AA are added to UDP-NAM. The NAM-pentapeptide is transferred to bactoprenol (membrane situated lipid molecule). UDP is released. NAG is linked to NAM. Bactoprenol carries NAG-NAM to the outer side of the membrane. Transglycoslation. Transpeptidation |
| What does transglycoslase do? | It attaches the new disaccharide units (NAM-NAG) to an existing peptidoglycan chain |
| What does transpeptidase do? | It links 2 peptide side chains in the polypetidoglycan cell wall. |
| What are some antibiotics for cell walls and how do the target it? | Vancomycin binds to transpeptidase substrate. Penicillin binds to PBPs, inhibiting peptide crosslinks. Lysozyme breaks down PG. Bacitracin blocks PG synthesis by binding to the bactoprenol lipid and inhibiting dephosphorylation |
| What is the purpose of the capsule? | Some gram positive bacteria have them. It is a sugar (polysaccharide) coating that can protect against phagocytosis and may contribute to virulence and help cells stick to surfaces |
| What are the functions of the cytoplasmic membrane? | Permeability barrier (prevents leakage, regulates in/out), protein anchor, and energy conservation |
| Which substances are freely permeable across the cell membrane? | hydrophobic molecules: oxygen, carbon dioxide, nitride |
| Which substances are slightly permeable across the cell membrane? | small, uncharged polar molecules: water, glycerol |
| Which substances are impermeable across the cell membrane? | large, uncharged polar molecules: glucose, sucrose, and ions: H+, Na+, HCO3-, Ca2+, Cl-, Mg2+, K+ |
| Membranes consist mainly of: | phospholipids (glycerol with ester links to two fatty acids and a phosphoryl head group)and proteins |
| What does amphipathic refer to? | The fatty acid hydrocarbon tails are hydrophobic and the phosphate head is hydrophilic |
| What is a bilayer? | two layers of phospholipids (called leaflets) whose hydrocarbon fatty acid tails face the interior of the bilayer and whose charged phospholipid head groups face the cytoplasm or extracellular environment |
| What are characteristics of unsaturated chains? | C=C bond that causes a kink in the chain. Kinked chains don't pack as closely and the membrane is more fluid. Enhanced fluidity improves the function of the membrane at low temps |
| Organisms produce more unsaturated fatty acids in which conditions? | high pressure and low temperature. They actively change the lipid composition to prevent "freezing" |
| What are hopanoids or hopanes? | Planar molecules that fill gaps between hydrocarbon chains in membranes. It is the equivalent of sterols in eukaryotic membranes |
| What are characteristics of bacteria membranes? | ester linkage, glycerol 3 phosphate backbone, fatty acyl chains, and form lipid bilayers |
| What are characteristics of archaea membranes? | ether linkage between glycerol and fatty acids, glycerol 1 phosphate backbone, phytanyl (isoprenoid) chains, and form bilayers or monolayers |
| What are terpenoids and what do they do? | Hydrocarbon chains are branched terpenoids (polymeric structures derived from isoprene - every 4th carbon extends a methyl branch). The branches strengthen the membrane by limiting movement of the hydrocarbon chains |
| What is the difference between integral membrane proteins and peripheral membrane proteins? | Integral membrane proteins are firmly embedded whereas peripheral ones are not embedded but associate strongly |
| What are characteristics of membrane embedded proteins? | hydrophobic portion (soluble within membrane).Several alpha helices thread back and forth through membrane.Other peptide regions extend outside the membrane, containing charged and polar AA. Combo of hydrophobic+hydrophilic regions lock protein into place |
| Are bacteria or archaea more suited for high temperature environments and why? | Bacteria has ester-linked lipids and the lipid bilayer would come apart at high temps. Archaea have ether-linked lipids w/ branched hydrocarbon tails that can fuse together and form a tetraether monolayer that won't melt at high temps |
| How do flagellas assemble? | MS/C ring assembles 1st in the cytoplasmic membrane, then other rings, then the hook, then the cap. Flagellin molecules flow through the hook to form the filament at the terminus. A protein "cap" exists at the end of the growing flagellum |
| What do cap proteins do in flagellar assembly? | They assist flagellin molecules that have come up the channel to organize at the flagellum termini to form new filament |
| Name 3 cell wall antibiotics: | penicillin, vancomycin, and bactitracin |
| How does penicillin block peptidoglycan synthesis? | It targets penicillin binding proteins (PBP) by binding to transglycosylase and transpeptidase enezymes (PBP), and prevents their activities. It inhibits peptide cross-linking |
| How does vancomycin block peptidoglycan synthesis? | It binds to the D-Ala D-Ala terminal end of the disaccharide unit and prevents the action of transglycosylase and transpeptidase. It inhibits peptide cross-linking |
| How does bactitracin inhibit peptidoglycan synthesis? | It binds to the bactoprenol lipid carrier molecule that transports monomeric units of PG across the cell membrane and to the growing chain. It binds to and inhibits dephosphorylation of bactoprenol,thereby preventing the carrier from accepting new UDP-NAM |
| What are the differences in the lipids in bacteria and archaea? | Lipids in bacteria are ester linked and have fatty acid tails. Lipids in archaea are branched hydrocarbon chains ether-linked to glycerol |
| What protein are pili made out of? | Pilin |
| What are 3 functions of pili? | 1) DNA transfer between organisms 2) Binding to surfaces 3) motility |
| What are sex pili used for? | They are involved in conjugation (a form of genetic exchange): attach a "male" donor cell to a "female" recipient cell for transfer of DNA |
| How does twitching motility work? | It is flagella-independent motility over moist surfaces that is usually jerky and done by type IV pili. It occurs by extension, tethering, and then retraction of polar type IV pili (similar to a grappling hook) |
| What do Mot proteins do? | Mot proteins are in the cytoplasmic membrane and generate torque to drive and rotate the flagellum. Proteon translocation create electrostatis forces on the charges in the rotor ring proteins, causing the rotor to spin |
| What do fli proteins do? | They are the motor switch in the flagellar motor. Forward and reverse in response to cellular signals |
| What does the basal body of the flagellar motor consist of? | It is a rod and a series of rings that anchor the flagellum to the cell wall and the cytoplasmic membrane |
| What happens when the bacterial flagellum rotates clockwise? | The flagella spread out = tumbling motion. Changes the direction |
| What happens when the bacterial flagellum rotates counter-clockwise? | It flagella bundle behind the cell and push it forward = runs. No change in direction |
| What are the functions of tubulin? | chromosome segregation, vesicle transport, and motility (cilia and flagellum) |
| What are FtsZ, TubZ, and PhuZ used for? | Cell division (nearly universal in bacteria), plasmid segregation (found on large plasmids of bacillus and in several archaea), and phage replication (found on large bacteriophage) respectively |
| What are the 3 systems that regulate cell division in bacteria? | NO (nucleoid occlusion), Min, and MipZ |
| What is nucleoid occlusion? | It prevents division over the nucleoid. The noc protein binds to DNA and inhibits FtsZ assembly |
| What does the Min system in gram negative bacteria do? | It prevents division near the cell poles. MinC/MinD oscillate back and forth, with the lowest time averaged concentration in the middle. It prevents division over the genome |
| How does Min function in Bacillus? | NO oscillation. MinC/MinD and otheres (DivVA) form an "inhibitor sandwich" on either side of the cell division site to prevent FtsZ from assembling new rings nearby. It prevents division at the poles |
| How does the MipZ system work? | MipZ inhibits FtsZ assembly everywhere except the middle |
| What do PhuZ filaments do? | They center the replicating phage DNA in the center of the cell |
| What are the functions of actin? | growth and cytokinesis, motility, remodeling, chromatin reorganization, and transcription |
| What are MreB, FtsA, MamK, and ParM used for? | They are Actin-like Proteins (ALPS). MreB = cell shape determination. FtsA = cell division. MamK = magnetosome organization/formation. ParM = plasmid partitioning (plasmid R1). AlfA = plasmid partitioning (plasmid pLS32) |
| What is MreB used for? | It is essential in many rod shaped bacteria. It controls cell shape and interacts with proteins that synthesize the cell wall |
| What are the two ways in which bacteria store carbon? | Polyhydroxybutyric acid (PHB) causes the production of large granules in the cytoplasm. Glycogen is a starch like glucose polymer that is a great source of energy |
| When are PHBs produced? | They are produced in times of carbon excess and then broken down for use as carbon skeletons for biosynthesis when needed |
| What are magnetosomes? | They are intracellular structures made by magnetotactic species: bacteria showing magnetically directed motility. All are gram negative and motile. These are small pockets of membrane filled with crystals of the magnetic mineral magnetite |
| What are gas vesicles used for? | They are used to increase buoyancy of prokaryotes living and floating within the water column by decreasing the density of cells. It is commonly in photosynthetic cyanobacteria and other planktonic species. Vesicles = spindle shaped gas-filled structures |
| What are thylakoids? | It consists of layers of folded sheets of membranes packed with photosynthetic proteins and electron carriers. They contain integral membrane proteins which play a role in light harvesting and the light-dependent reactions of photosynthesis |
| What are carboxysomes? | They are polyhedral protein covered bodies packed with the enzyme Rubisco for carbon dioxide fixation |
| What are the two types of gene transfer? | Vertical transmission (from parent to child) and horizontal transmission (transfer of small pieces of DNA from one cell to another) |
| What are nucleotides connected to each other by? | 5'-3' phosphodiester bonds |
| What does each nucleotide consist of? | phosphate group, 5-carbon sugar (deoxyribose), and nitrogenous base (purine = adenine and guanine. pyrimidine = cytosine and thymine) |
| The orientation of the DNA strand determined by what? | The presence of a free phosphate on the 5' end and a free hydroxyl on the 3' end |
| What are the two strands of DNA held together by? | Hydrogen bonding between a purine and a pyrimidine on opposite strands. Hydrogen bonding allows complementary base interactions (A pairs w/ T via 2 H bonds. G pairs w/ C via 3 H bonds) |
| The DNA double helix has grooves: a wide major groove and a narrow minor groove. What are they for? | These provide DNA-binding proteins access to base sequences buried in the center without the strands being separated. |
| Can bacterial DNA be supercoiled in the positive or negative direction? | Bacterial nucleoids are kept negatively supercoiled. The DNA is twisted about its axis in the opposite direction from that of the double helix |
| What are 2 topoisomerases and what are they used for? | Topoisomerase I is used to relieve supercoils. Gyrase uses energy to introduce negative supercoils. These 2 types of enzymes balance the amount of supercoiling of their DNA |
| What are the 2 parts of the flagella motor? | The non-rotating part called the stator (Mot proteins) and the rotating part (rotor) MS and C rings |
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midsummersaint
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