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Biochem LCCW

LCCW Biochem Class w/ Straub

Microbiology: is the study of very small non-cellular particles and unicellular organisms called microorganisms/microbes.
What's included in the microorganisms/microbes that are in microbiology? viruses, bacteria, algae, protozoa and certain fungi
What do all the pioneers in microbio have in common? They are all dead.
What are the units of measurement? Micrometer and nanometer
What's the bacterial range of size? 0.2 micrometers to 5 micrometers
whats the smallest thing we can see with a light microscope? bacteria
T/F All bacteria are motile FALSE. Not all bacteria are motlie
What's the name of the ONLY motile thing in bacteria? Flagella
T/F all motile things can travel long distance FALSE. Not all motile bacteria can travel long distances
what are the 3 components to a bacterial flagellum? filament, a hook, and a basal body
Filament of Flagellum: is the rigid, helical structure that extends from the cell surface. it is composed of the protein FLAGELLIN arranged in helical chains so to form a hollow core.
Hook of flagellum: flexible coupling between the filament and the basal body
Basal body of flagellum: consists of rod and a series of rings that ANCHOR the flagellum to the cell wall and the cytoplasmic membrane. It acts as a ROTARY molecular motor, enabling the flagellum to rotate and propel the bacterium
Energy for rotation of the flagellum comes from what? The proton motive force generated by the electron transport chain of the bacteria
Monotrichous ONE - flagellar configuartion
Lophotrichous: MANY - flagellar configuration
Amphitrichous: BOTH poles - flagellar configuration
Peritrichous: RANDOM - flagellar configuration
Taxis: Is a motile response to an environmental stimulus.
Chemotaxis: Responds to chemicals. it is a reponse by the bacteria to chemical gradients of either attractants or repellents in the environment.
Phototaxis: Light
Osmotaxis: osmotic pressure
Aerotaxis: Air
Thermotaxis: Temperature
Chemical gradients are present (the GOOD ones): attractant based gradients will cause the bacteria to tumble less frequently as it moves UP the gradient.
Repellent based gradients (the BAD ones): Will cause tumbling down the gradient at increased speeds.
Chemotaxis is regulated by what? Chemoreceptor (in the cytoplasmic membrane or periplasm of bacterium bind chemical attractants or repellents)
PAMPs and MAMPs: immune system can protect against infection, it must be able to detect the presence of microorganisms (bacteria). Does this by recognizing molecules unique to microorganisms that are NOT associated with human cells.
PAMP: The protein flagellin in bacterial flagella is a PAMP that is recognized by defense cells of the body and triggers innate immune defense mechanisms such as inflammation, fever and phagocytosis
Axial Filaments: Internal Flagella found ONLY in spirochetes. Composed from 2-100+ axial fibrils/endoflagella
Pilus (Fimbriae): Non-motile appendage. They are thin, protein tubes originating from the cytoplasmic membrane. They are virtually ALL gram negative bacteria. Not in many gram positive bacteria.
Short attachment pili: aka "FIMBRIAE" -- usually quite numerous. Are organelles of adhesion allowing bacteria to colonize environmental surfaces or cells and resist flushing.
Long attachment pili: aka "F" or "Sex Pili" -- very few in number. Make more pili (?)
Glycocalyx: "cell envelope" - not always present on all species of bacteria. Divided into Slime layer and Capsule.
Slime Layer - Glycocalyx: polysaccharide coating. Covers the surface of the bacterial organism like a film, but is NOT firmly attached to the bacteria. They will often fall off the cell wall.
Pseudomonas species: Glide or slide along solid surfaces. can aid slightly in the adherence of bacteria to other structures (see also - slime layer)
Capsule - Glycocalyx: A gelatinous layer covering the entire bacterium. Polysaccharide, (except Bacillus anthracis)
Quelling reaction: In the presence of the homologous antibody, the capsule (glycocalyx) will swell greatly.
Capsular polysaccharides can be used as what? antigens in vaccines
Cell wall: considered the first true (outermost) structural component to ALL bacteria (except MYCOPLASMA -- no cell wall)
NAG and NAM: Repeating units. Repair of wall is continuous to prevent lysis
Peptidoglycan: (aka: murein) is a vast polymer consisting of interlocking chains of identical peptidoglycan monomers. Consists of 2 joined amino sugars (NAG and NAM)
Function of peptidoglycan: Prevent osmotic lysis
LPS: outer layer of the cell wall in gram negative bacteria and also serves as an endotoxin
Archaens: Have cell walls made of protein and hydrocarbons
Gram Positive: very THICK, single band of peptidyglycan
Gram negative: very thin band of peptidyglycan and band of lipopolysaccharide layer
Mycobacteria (acid fast) - contains large amounts of lipids such as mycolic acid
Archaens: Have cell walls made of protein (hydrocarbons)
Cell membrane: Lipid bi-layer with proteins, the only major chemical difference for most bacteria as compared to eukaryotic organism is a complete lack of sterols
Porins: channel proteins
Permeases: Protein Facilitators
Mycoplasma: Membrane contains sterols - NO CELL WALL
Mesosomes: invagination of the membrane (and more - pg 6, but not so important)
Membrane 5 Functions: Energy reactions, nutrient processing and synthesis, regulate transport, selective barrier, secretion
Protoplasm: Gelatinous solution made up of mostly water and the biochemical building blocks for synthesis activities (SCHNOP)
Chromosome: Single molecule - Haploid (= all genes are expressed)
All bacterial DNA is organized how? as a single set of double stranded DNA
Most bacteria are what shape? circular (no introns/extrons)
Plasmids: ALWAYS small circular double stranded DNA (always smaller than chromosome). Must be incorperated into chromosome in order to function. use is TOTALLY random.
What are the 4 spore producers? Bascillus, clostridium, sporosarcina, and coxiella
Which spore producers are gram positive? Bascillus, closridium, and sporosarcina
Which spore producers are gram negative? Coxiella (the ONLY gram negative one)
Sporalating inducers: heat, desiccation, freezing, changes in oxygen, radiation, chemicals and lack of nutrients
Structure of endospores? outer layer contains heat resistant chemicals such as calcium, and dipicolinic acid
Clostridium tetani: Tetinus (rust not necessary). Has to get into anaerobic environment in order to activate. puncture wounds, burns, etc
Clostridium botulinum: Anearobic organism found in food/canned goods. only active when can is vacuumed sealed. In uncooked foods.
Bacillus anthracis: Aerobic: Lack of nuetrients move from host to host by find/infext/killing and bleeding it out
What are the 4 types of Cocci? Staphyloccocus, streptococcus, tetrads and diplococci
Staphylococcus: Cluster
Streptococcus: Chains
Tetrads: squares of 4
Diplococci: pairs of 2
3 types of Bacilli: (cylindrical, club, or comma): Streptobacilli, Coccobacilli, and palisade
What are the 4 main types of bacterial shapes? cocci, bacilli, spirals/spirillia (stairs), and pleomorphic (no real set shape)
What are the 4 main types of unusual bacteria and are the gram negative or positive? All are gram-negative. Rickettsia, chlamydia, Mycoplasma and photosynthetic bacteria
Photosynthetic bacteria: contains photosynthetic pigments
Mycoplasma: NO cell wall. Can act as a commensal or a causative agent of pneumonia
Rickettsia: Leaky cell membrane
Chlamydia: They lack the enzymes required to many essential metabolic activities, in particular, they lack the ability to produce ATP molecules (aka. they are energy theifs and steal ATP)
What is king? GLUCOSE
T/F Aerobic Respiration and fermentation happen together True - they happen TOGETHER
Whats the most common pathway of Glycolysis? The Embden-Meyerhof Pathway (= 2 ATP produced)
What are the 3 major pathways (in prokaryotes) for glycolysis? Embden-meyerhof pathway, Phosphoketolase/Heterolactic pathway, and the Entner-Doudoroff pathway
Any questions about anything on pg 11...? A: they follow nder-myenhoff pathway and they're used to ID bacteria
The heterolactic (phosphoketolase) pathway: Rare and less effective then the Ender-meyerhof pathway because it only produces 1 ATP
The Entner-Doudoroff Pathway: Rare and only produces 1 ATP
Respiration must have what? Acetyl CoA convertion, TCA and ETC
What are the 4 essential structural or metabolic components needed for respiration (in addition to a pathway of glycolysis)? The TCA cycle, the ETS, and outside electron acceptor (Aerobic/Anaerobic respiration), and ATPase enzyme.
Anaerobic: No O2 needed
Aerobic: O2 required
Sulfate reduction: is not an alternative to the use of O2 as an electron acceptor. it is an obigatory process that occurs only under anaerobic conditions.
Polysaccharide capsules: (aka inclusions) are polymers of glucose and other sugars
Cell wall peptidoglycan (NAG and NAM) is derived from what? glucose phosphate
Bacterial Genetics (random facts): all are haploid, no introns/slicing, gene # is about 4,000, and most are circular
Helicase: unwinds DNA
Primase: Synthesizes RNA primers
Single strand Binding protein: Prevents DNA from interacting with components of nucleoplasm
DNA gyrase (topoisomerase): Prevents torque and super coiling affects
DNA polymerase III: Synthesize new DNA to be laid down behind primers
DNA polymerase I: Remove RNA primers and replaces them with DNA
DNA ligae: Joins fragments together
Semidiscontinuous replication: Leading and lagging strands, 3-->5 orientation, and okazaki fragments
Okasaki Fragments: Okazaki fragments are short, newly synthesized DNA fragments that are formed on the lagging template strand during DNA replication.
Telemorase: end of DNA (limit the number of replications within the DNA)
Constitutive enzymes: those are always present/ON (glycolytic enzymes).
Induction or Induced genes (4 steps/things): Always tied to dissacharade breakdown//inhibit protein produced in ACTIVE form//inactvated by substrate that genes supprece to break down// always tied to catalytic repression function of CAP.
End product Repression: Build up of cellular end products feedback to shut down the pathway
End product repression (3 step-ish things): more complicated breakdown// inhibit protein = INACTIVE form//activated by build up of end product. Genes turn off. NO CAP function!
No Glucose = CAP function. (<-- Glucose MUST be absent)
Heritable Stability: Resides in template directed, semi-conservative replication of DNA and RNA (no change)
Heritable variation: Achieved via mutation and/or recombination (ie changes in base sequence). Mutation will get passed on to all future generations
Spontaneous mutation: Random change in DNA arising from replication mustake or background radiation. MOST common mutation.
Induced mutation: results from exposure to a mutagen (chemical or physical mutagens)
Environmental selection: Genes only usable if it's been encountered by the environment before
Recombination: donation of DNA from one bacteria to another
conjugation is mostly gram neg or positive? Primarily gram negative
F-facotr (conjugation): Ability to form a pilus
Pilus/Pili? RANDOM. long tube that makes an attachment with another bacteria
R-Factor? resists factors (osmotic imbalance, acid, etc). attibuted ton conjugation. R-Factor is the most common.
T/F Plasmids, as long as they stay plasmids, are harmless? True
HFR strains? High frequency recombination strains
RTF's Resistant Transfer Factor: Plasmid with genetic info for F pilus and enzymes capable of neutralizing/inhibiting antibiotic activity
Intergeneric conjugation: seen among some enterobacteriaceae
Transformation: Environmental DNA
Transduction: Virus acts as a carrier
General transduction: Lytic - far more RANDOM. Destroys cell.
Specialized transduction: Lysogenic - More SPECIFIC for which gene is picked/selected
Transposons: Are a sequences of DNA that can move around to different positions within the genome of a single cell. ("jumping genes"). Fatal in humans.
Fastidious Bacteria: "picky eater" - these organisms lack the genetic and metabolic mechanisms to sythesize every organic compound they need to survive.
Nutritional categories are determined how? by sources of carbon and energy used.
Autotroph: Carbon source is INORGANIC
Heterotroph: Carbon source is ORGANIC
Temperature and bacteria: bacteria is unable to self-regulate temperature. Max and min Temp: highest and lowest temps that bacteria can still grow
Optimal temp: temp at which the fastest rate of metabolism and growth occur
Psycrophile: Cold loving bacteria 15C or below
Mesophile: Medium temp bacteria 10-50C (anything that lives in our bodies)
Thermophile: Head loving bacteria 45-150C
Environmental pH's? Acidophiles (acid lovers) and Alkaliphiles (alkaline lovers)
Osmotic pressure: Halophiles (salt lovers)
Microaerophilic: needs lower levels of O2
Strict Anaerobe: No O2 needed at all
Aerotolerant Anaerobe: Short brief periods in O2 environment
Symbiosis: A term used to denote 2 organisms living together in a close partnership
Mutalism: When organisms live in an obligatory but mutually beneficial relationship
Commensalism: The member called commensurable receives benefits, while its cohabitant is neither harmed nor benefitted
Parasitism: Is a relationship between 2 or more free-living organisms that befits them but is NOT necessary for their survival. is NOT SYMBIOSIS.
What are the 3 categories under symbiosis? mutualism, commensalism, and parasitism
Created by: walkingbyfaith09