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MIC 401 Week One Lecture Notes

by: Hiba Naji

MIC 401 Week One Lecture Notes MIC 401

Marketplace > University at Buffalo > Microbiology > MIC 401 > MIC 401 Week One Lecture Notes
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Very detailed notes for week one material, lectures 1 and 2!
Biomedical Microbiology
Dr. Amy Jacobs
Class Notes
Microbiology, Mic 401
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This 19 page Class Notes was uploaded by Hiba Naji on Monday February 8, 2016. The Class Notes belongs to MIC 401 at University at Buffalo taught by Dr. Amy Jacobs in Spring 2016. Since its upload, it has received 86 views. For similar materials see Biomedical Microbiology in Microbiology at University at Buffalo.


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Date Created: 02/08/16
Lecture 1: Structure and Function of Bacteria  Microbiology is the study of microorganisms too small to be seen with the eye alone; you must use a microscope: o Microbes o Germs o Bugs  Types of microorganisms: o Bacteria o Fungi o Parasites o Viruses  All are capable of: o Causing disease o Being pathogenic- ability to cause an infection in the host human)  Basic Cell types: o Prokaryotic- early nucleus  Bacteria  Algae o Eukaryotic- true nucleus  Membrane bound nucleus  Animals  Fungi  Differ in cell structure and complexity  Similar- same metabolic reactions taking place, and are chemically similar.  Structural organization or prokaryotic cell: o Appendages- outermost part  Flagellum  Fimbriae (common pili)  Sex pillus o Cell Envelope- outer wrapping of bacterium  Exterior on cell wall you have glycocalyx (slime layer/capsule)  Cell wall  Membrane o Cytoplasm- interior of cell  Cellular pool  Nucleoid (chromatin body, chromosomes)  Plasmids  Ribosomes  Inclusion bodies/granules o Endospores  Appendages: o Flagellum- motility o Pili (fimbriae)- attachment factors  Flagellum- not all bacteria have flagellum. We classify bacteria as being mobile or non-mobile. They have different flagellum arrangements. o True directed movement---> moving toward food, moving away from danger o NOT Brownian motion: vibrating back and forth  Fimbriae/common pili- small hair like projections found on exterior of cell. Fimbriae comes from Latin term "fringe"- allow bacteria to attach to a surface. 100s of fimbriae, only 1-3 pili o Adhesion: advantageous for bacteria to get in body and be pathogenic. Once it attaches to a surface, it colonizes, grows, and replicates. It produces a variety of different factors that aids in its pathogenesis: toxins  If pathogenic, its virulent. Various factors that aid in its pathogenesis.  Sex pilus- longer pili found on exterior surface. Used for conjugation to have the transfer from one cell to another. Limiting factor for this to happen is the proximity of the 2 cells.  Cellular envelope- outer wrapping of bacteria o Consists of glycocalyx (slime layer and capsule) o They have similar composition (proteinpolysaccharide mix) o They differ:  Slime layer: slimy, not uniform in density, not tightly adhered to bacterium. Aids in attachment  Capsule: same basic composition, tightly adheres to surface of bacterium. If a bacteria has a capsule, its an antiphagocytic (first line of non specific host defense) inhibit the phagocyte, can't be destroyed or killed by enzymes within. Allows bacteria to survive.  They also both aid in loss of water and nutrients from bacteria and protect from the environment.  These are all virulent factors. Not all bacteria have these!!!  Cell wall- exoskeleton of cell- gives bacteria their shape o Rigid structure, protects bacteria from osmotic lysis  Differentiate between Gram positive and Gram negative with the Gram stain o Looking for differences in composition of cell wall o Common component shared by both Gram positive and Gram negative cell walls is the heteropolymer peptidoglycan. Both have this. o Peptidoglycan is made up of N-Acetylglucosamine (NAG) and N- Acetylmuramic acid (NAM) o Chains are cross linked by tetrapeptides between the acids that hold the whole structure together. This is referred to as interbridging  Key factors of Gram Positive cell wall: o Multiple layers of peptidoglycan (40 layers) 90% o Other 10% is acidic polysaccharides- teichoic and lipoteichoic acid o The acidic polysaccharides span the peptidoglycan layers, increases rigidity of cell wall and allows the transport of ions across cell wall  Key features of Gram Negative cell wall- more complex in nature o 3 layered cell wall  Outer membrane-largest component  1 layer of peptidoglycan  Periplasmic space o Outer and inner membrane have same basic composition- phospholipid bilayer  Phosphate head, lipid tail o Outer layer is exterior to single layer of peptidoglycan (1 layer) o Gram positive is more rigid, polysaccharides increase rigidity o Intercalated in outer membrane there's a porin protein channel.  Spans the whole phospholipid bilayer, so it has both hydrophobic and hydrophilic tendency  Purpose of this is to allow transport of materials from outside to inside irrelevant of their charge. Also, lipid polysaccharides intercalated there, and again hydrophobic/philic tendency and lipoprotein.  Lipoprotein is embedded in outer membrane but also attaches to single layer of peptidoglycan. Lipoprotein holds the whole fluid structure together. Cell membrane is known as fluid mosaic model because its selectively permeable and allows flow of materials in and out.  Said to be the anchor. Anchors the outer membrane firmly to the single layer of peptidoglycan. o Periplasmic space is found between the outer and inner membrane and within the periplasmic space if found the single layer of peptidoglycan. It is a selectively permeable barrier, bringing stuff from the outside to the inside. Within the periplasmic space is hydrolytic enzymes, and they break apart the 6 carbon sugar unit to single carbon monomers, which will be used for synthetic purposes and energy production that is taking place in the inner membrane.  WHAT TO REMEMBER: o Gram +/- share common composition of peptidoglycan  Know what it is, why it gives the bacteria cell rigidity (due to the cross linking or interbridging of glycan chains at the meriamic acids  What is more complex? Gram -  Gram - is considered to be a 3 unit entity. o What is the purpose of the periplasmic space?  Contains hydrolytic enzymes which breakdown the carbohydrates needed for synthetic reactions as single unit monomers for metabolism or synthesis of energy production.  Intermembrane has many names- cytoplasm, protoplasmic, inner, cellular o Primary purpose is that its useful for synthetic reactions o The cellular membrane is considered to be the bacterial analogue- for the synthetic reactions to take place in eukaryotic cells. o The inner membrane / cellular membrane is molded around the cytoplasm:  allows materials to be transported into the cytoplasm and transported out  Very thing, flexible layer  Made up of phospholipid bilayer  It is a curvature  Has fluid which allows materials to be transported across it.  Also has integral proteins embedded and spans the whole bilayer (has hydrophobic and hydrophilic tendencies)  Peripheral proteins which are more hydrophilic in nature.  Composition of membrane itself is variable  It is the site of many metabolic activities attributed to organelles in eukaryotes  Respiration and photosynthesis  Energy production of ATP  Transport systems (in and out)  Synthesis of cell components, lipids, secretion of exoenzymes and toxins  Toxins are produced when bacteria grow, the end product produced by the growth of the bacteria could be a toxin. This toxin aids in the pathogenesis of the bacteria ---> another virulent factor  (Exoenzymes go to periplasmic space in from bacteria or even further out for nutrient processing)  BASIC FUNCTION IS SYNTHETIC REACTIONS- TRANSPORT SYSTEMS AND SECRETION!!!  Cytoplasm: dense gelatinous material that contains many of the building blocks for synthetic reactions, and water (70-80% is water) o Found within the cytoplasm is the cell pool. o A complex mix of nutrients  Carbohydrates  Amino acids  Fatty acids  Inorganic ions o Components of the cell pool are the building blocks of metabolic reactions and sources of energy for catabolic reactions  Anabolism synthetic reactions require energy  Catabolic reactions degrade something and produce energy  Nucleoid/chromatin: nonuniform region, dense area, stringlike area in center. Concentrated to an irregular dense area in center of cell and consists of single double strand of DNA all coiled around. Can also be referred to as a nucleoid or nuclear region, and contains genetic information for structure and function, in contrast to eukaryotes, its not enclosed by a membrane. This the minimal amount of genetic material needed for cell survival. Single double stranded region, irregular in shape and in a dense area in center of cell.  Plasmids: extra component o Extra piece of chromosomal DNA o Found in most but not all bacteria. If they have a plasmid, it is advantageous to the bacteria. o Antibiotic resistance is usually coded for on a plasmid  This resistance can be transferred from 1 bacteria to another, even different types of bacteria because it can pass the plasmid. o Plasmids may also code for the production of certain toxins and enzymes.  Aid in pathogenesis, helps bacteria cause an infection in the host. o Plasmids function as either a selective advantage or protective trait  Ribosomes- free in cytoplasm or attached to inner membrane o Sight of protein synthesis (Inner membrane is bacterial analogue for synthesis)  Inclusion body/granules- storage granule during time of plenty o Bacteria stores 3 types of storage granules:  Organic: glycogen or starch  Lipid: polyhydroxybutyric acid  Inorganic: phosphate  Endospores (spores): mechanism of survival, not all produce spores o But very advantageous if they can because 1 bacteria cell will produce 1 spore under adverse conditions  Lack of food/water  Extreme temperatures or pH  Anything in environment that is not advantageous for bacteria to grow. o One spore can then convert back to one bacterial cell. (germination, growth of bacteria)  Growth is exponential o FOR GROWTH NOT REPRODUCTION- PROTECTS DNA INSIDE THERE (SURVIVAL) o Spores are dormant structures or resting structures  Waiting for appropriate time for cell to grow again. Lecture 2 Bacterial Growth and Metabolism Bacterial Growth: o Bacteria grow mostly by binary fission and most bacteria that cause disease in humans will grow in artificial culture media o Some notable exceptions:  Some bacteria like Legionella only grow on selective media  Some obligate intracellular pathogens (need cells or tissues to grow in)- Chlamydia  Some require animal models like Mycobacterium leprae which causes leprosy  Some never have been grown- like Treponema pallidium (causes syphilis, you don't need to know this) o Number of different things bacteria need to grow, the first of these is different nutrients:  Macronutrients:  N , H , CO , Carbon, PO , Fe, Sulfur, K , Ca , Mg +2and an 2 2 2 4 energy source (Most elemental- required in large amounts for most bacteria to grow. )  Micronutrients: +2 +2  Trace elements: Mn , Zn , Cobalt, Molybdenum, Nickel, Cu , Selenium  In addition there are a number of growth factors that bacteria need and these are like vitamins. They need these substrates in order to make things they are going to require later on.  P-aminobenzoic acid- precursor of folic acid  Folic acid- vitamin that is required for carbon metabolism  Biotin- fatty acid biosynthesis  Cobalamin (B )-12eduction of single carbons +  Nicotinic acid (niacin)- precursor of NAD  Riboflavin- Precursor of FMN (source for energry for bacteria)  Thiamine (B )-1decarboxylations  Pyridoxal group (B )-6amino acid formation o Their ability to use or not to use things we give them is a way to describe them.  Prototroph: A bacteria that can get all the nutritional requirements for growth from the micronutrients and macronutrients supplied (form the artificial medium we give them)  Fastidious: Some bacteria need more and have a complex and special nutrient requirements. They might require special vitamins or amino acids to grow. o In addition to nutrients they need some atmospheric gases  CO -2Some bacteria need it as a supplement for its growth, some don't  Oxygen- some really need it, some don’t.  Obligate Aerobes- they must have oxygen to grow.  Facultative aerobe- grow either with oxygen or without oxygen, you can refer to them as either facultative aerobe or anaerobe.  Obligate anaerobe- does ideally in absence of oxygen but may still be able to grow if oxygen is present. o When they are plated out onto medium they grow out in four different phases.  Lag phase - initial, beginning of growth  Numbers don’t increase much, stay kind of stationary.  Logarithmic (exponential phase)- great increase in numbers  Once they reach a threshold in time, they grow like wild fire in large amounts and increase is exponential fashion.  Stationary phase - no increase in number of bacteria  Once they hit a peak, they pretty much have used up all the nutrients in the medium and they plateau off.  Death- decline in bacterial numbers  After they really exhausted all there is, they die off in a logarithmic way as well. o Bacterial Metabolism  Bacterial cells are highly specialized energy transformers  The reason they need to more energy is to form new compounds, and the reason they need to make new compounds is to make new bacteria.  Metabolism refers to all the biochemical reactions in a cell.  Refers to taking any of the constituents around them and convert them into energy.  Generated by oxidation reactions of substrates.  To convert into energy, they react with their substrates to make ATP from ADP to store energy in the cell and to use it when they want to synthesize new compounds for the generation of their new progeny of new bacteria.  Energy ----> synthesize organic compounds needed by the cell  The energy they have must be adequate to synthesize their organic compounds for their bacteria. o Metabolic Classes of Bacteria  Heterotrophic  Essentialls all pathogenic bacteria  Obtain energy from organic compounds  We are organic in nature, and they are looking for organic substrates to make energy, most pathogenic bacteria are heterotrophic.  Photosynthetic - less pathogenic  Synthesize their own glucose from sun light activating it  Autotrophic - less pathogenic  They don’t need sunlight  They don’t need organic compounds  They get their energy from inorganic compounds like minerals and CO (di2 into arctic ice for to proce on other planets bacteria may still exist) o Same word- slightly different meanings  Aerobic growth refers to need for oxygen for growth  Aerobic respiration refers to oxygen acting as the final electron acceptor for metabolism o Metabolic Energy  Bacteria may generate energy by:  Aerobic respiration- Final electron acceptor ----> Oxygen  Anaerobic respiration  Final electron acceptor NOT oxygen  Fermentation  Photosynthesis o Aerobic Respiration  Major energy-producing mechanism for aerobes  Provides ATP + metabolic intermediates in order to make energy for itself and store it in order to reproduce.  Three major pathways - linked to one another  Glycolysis or Glycolytic pathway (Embden-Meyerhof)  Krebs cycle (Citric Acid Cycle)  Electron transport chain-oxidative phosphorylation DON’T MEMORIZE INTERMEDIATES  For all three pathways:  Glucose = most common substrate (used most commonl y, rarely other 6 carbon compounds are used)  The major energy source  Bacteria oxidize glucose  C 6 12+ 6O ----2> 6CO + 6H O2+ ener2y  1 molecule glucose ----> up to 38 molecules of ATP if done at the most efficient means  Oxygen is used because it is the final electron acceptor  When bacteria is making ATP from ADP, they are storing energy. When they cleave ADP from ATP energy is released.    1 glucose ----> 2 pyruvates  Net gain of +2 ATP’s  And NADH generated  Converted into more ATP  1 NADH can convert into ~3 ATP’s --- later on. o Krebs Cycle   Generates 2 NADH=Energy   1 glucose ----> 2 pyruvates     Respiratory process - uses O 2  Initial step - Pyruvate - is decarboxylated to CO and 2cetyl coenzyme A  2 NADH’s (converted into more ATP later on)  Later portion - cycle  Net gain of +2 ATP’s per molecule of glucose  And 6 more NADH (converted into more ATP later on)  And 2 FADH (c2nverted into more ATP later on) o Electron Transport + Oxidative Phosphorylation (place where NADH and FADH ge2 converted to more ATP) Series of electron transfers within the cytoplasmic membrane Generate ADP and ATP  Each NADH = 3 ATP’s  Each FADH = 2 ATP’s  Accomplished with cytochromes and enzymes that allow them to shuttle along  An electron is transferred from Molecule A to Molecule B.  Molecule A is oxidized and Molecule B is reduced.  Oxidized molecule lost an electron  Reduced molecule gained an electron  NADH and FADH carr2 electrons (e-) and protons (H+).  Generates energy for synthesizing ATP from ADP and phosphate (Pi).   Whole glycolytic pathway in one picture o Anaerobic Respiration- only difference between aerobic and anaerobic respiration is that the final acceptor is not oxygen.  Utilizes the same three pathways as aerobic respiration:  Glycolytic pathway  Krebs cycle  Electron transport - right at end, instead of oxygen molecule picking up terminal electron something else has to substitute for it.  But O 2s not the terminal electron acceptor  Instead, generally, oxygen containing salts, supplied in growth media:  -) Nitrate (NO 3  Sulfate (SO 4-2)  Carbonate (CO ) 3-2  Ferric iron (Fe )3  Produce energy by reducing substrate  Main difference, their may be a slight variability in the amount of ATP o Fermentation- lots of simplicity in difference that takes place  Pasteur- 1850’s  Studies led to discovery of anaerobic bacteria  Primarily anaerobic- used by anaerobic bateria (bacteria that do much better in absence of oxygen)  Organic compound - not O - is 2sed as a terminal electron acceptor (very less efficient)  Produces less energy, but… supports the bacteria  Supports anaerobic bacterial growth  Generates energy primarily using the glycolytic pathway  But:  -Not the Krebs cycle  -Not the electron transport chain  An enormous amount of energy is generated during those last two stages so ommiting them will decrease energy production by a lot.  Simple organic end-products formed from anaerobic dissimilation or metabolism of glucose  Pyruvate is left over and used to react to form other end products  End-products of bacteria  Lactic acid  Ethanol  Acetic acid  Butyric acid  Example + +  Pyruvic acid + 2 NADH H ----> lactic acid + NAD  All you get is 2 ATP from a molecule of glucose o Photosynthesis- used by bacteria to generate energy  Convert light to ATP  Not a feature of pathogenic bacteria o Summary:  Glucose +other CHO’s---> 1) Glycolysis ---> 2ATP +2NADH---->  2) Krebs cycle ---->2ATP + 8NADH + 2FADH --2>  NADH + FADH - e2ectron carriers ---->  3) Electron transport ----> 34 ATP  Possible molecules ATP = 38  Final electron acceptor ----> Oxygen  End products generated ----> CO + H2O 2  Micro-organisms - Aerobes +  Facultative organisms  Glucose +other CHO’s---> 1) Glycolysis ---> 2ATP +2NADH---->  2) Krebs cycle ---->2ATP + 8NADH + 2FADH ---> 2  NADH + FADH - e2ectron carriers ---->  3) Electron transport ----> variable # ATP  Possible molecules ATP ---> variable ---> less than 38  Final electron acceptor ----> Inorganic molecules - oxygen- containing salts  End products generated ----> hydrogen sulfide (H S);2nitrite; methane (CH ) 4  Micro-organisms - Aerobes + some facultative organisms  Glucose +other CHO’s---> Glycolysis ---> 2ATP + 2NADH  No incorporation of Krebs cycle or electron transport  Possible molecules ATP ---> 2  Final electron acceptor ----> organic molecules  End products generated ----> ethanol, butanol, lactic acid  Micro-organisms -  Facultative organisms  Obligate anaerobes o Universal Features Bacterial Energy Production  All major pathways use glucose or hexose catabolism  Chemical energy is conserved by formation of high energy compounds  ATP or ADP  Major source of PO is ATP or ADP 4  Not inorganic phosphates  For conservation of chemical energy  PO 4s renewed by kinases  Results in loss of energy  Also generates NADH and FADH 2  1 NADH = ~3 ATPs  1 FADH =2~2 ATPs  Serve as reducing equivalents  Potential energy generated for each pathway


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