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78 Cards in this Set
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- Back
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What is catabolism
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Def: All decomposition reactions in a living organism; the breakdown of complex organic compounds into simpler ones.
It's exergonic reaction (release of heat). Catabolic reactions transfer energy from complex molecule to ATP The energy broken down gets trapped in ATP Most likely the breakage of covalent bonds |
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What is Anabolism
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Def: All synthesis reactions in a living organism; the building of complex organic molecules from simpler ones.
Source of all energy on earth (at least in medical micro class) comes from the sun. ATP powers the anabolic reaction. Anabolic reaction transfer energy from ATP to complex molecules. It is an endergonic reaction. |
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What is Metabolism
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Catabolism + Anabolism = Metabolism
Metabolic testing is also known as biochemical testing |
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How do Enzymes functions as catalysts
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Enzyme binds with a substrate in the active site to form an enzyme-substrate complex. An end product is produced and then the enzyme is released back into the environment.
- Enzyme remains unchanged in the reaction - Enzyme is not permanently altered - Enzyme speeds up the process. It catalyzes the reaction. The reaction can go up to 1 millionth of a second. - The enzyme is highly specific. |
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What is a Redux reaction
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-Hydrogen is the Electron source for most biological reactions
- All chemical reactions involve the transfer of electrons. - Oxidation - When a molecule loses an electron; biological oxidations are often dehydrogenations...the loss of a H(proton) - Reduction - when a molecule gains an electron; biological reduction are often hydrogenations. . .gain of a H(proton) - An oxidation reaction is always paired with a reduction reaction |
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What is Oxidation
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- When a molecule loses an electron; biological oxidations are often dehydrogenations.
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What is Reduction
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When a molecule gains an electron; biological reductions are often hydrogenations. . .gain of H(proton)
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What are Electron Carriers (Shuttles)
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- Electron carriers are electron acceptors: NAD+, FAD, NADP+
- In accepting an electron (or hydrogen), the electron carrier is "reduced"; it holds "reducing power" or energy - In losing an electron (or hydrogen), the celectron carrier is "oxidized"; it gives up energy |
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What are the oxidized and reduced forms of: NAD+, FAD, NADP+
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Oxidized: NAD+, FAD, NADP+
Reduced: NADH, FADH, NADPH - holds energy for later reactions |
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What is Phosphorylation
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3 ways to make ATP
1. substrate level phosphorylation; organic - energy comes from Carbon like tissues 2. Oxidative phosphorylation; organic 3. Photophosphorylation; photosynthetic - energy comes from sunlight |
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What are the pathways of Prokaryotic Glucose Catabolism
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Glucose - substrate of choice - its catabolism that gains the most energy for the cell
2 main pathways: Respiration and Fermentation |
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Describe the Characteristics of the Pathways for Prokaryotic Glucose Catabolism
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Respiration - always includes Kreb Cycle
Aerobic - Oxygen is the final electron acceptor: O2 is reduced Anaerobic - inorganic nitrate or sulfate - final electron acceptors: NO2 or SO4 are reduced ----------------------------------------- Fermentation - occurs in the absence of oxygen Various organic molecules are final electron acceptors CO2 is a type of end product E coli is capable of using both pathways. Anaerobic microbes are human pathogens. They can be both aerobic and anaerobic. |
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What is the favored energy source for Heterotrophs
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glucose
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What is Glycolysis
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Def: The main pathway for the oxidation of glucose to pyruvic acids; aka Embden-Meyerhof pathway
Pathway common to respiration and fermentation. It's the first step. Net result of glycolysis in the breakdown of glucose (6-C sugar) is 2 ATP & 2 3-C sugar) The ATPs are synthesized via substrate level phosphorylation. Energy for the phosphorylation come from the breakage of covalent bonds |
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What is the Krebs Cycle
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A pathway that converts 2-carbon compounds to CO2, transferring electrons to NAD+ and other carriers
Krebs Cycle "turns twice" for one glucose molecule catabolized After completion of 2 turns thru the Krebs cycle, all 6-carbons of the glucose have been "knocked off" as CO2 (decarboxylation) Pyruvic Acid loses a carbon to become Acetyl (2-Carbon). CoA binds w/Acetyl. Acetyl-CoA goes into the Krebs Cycle |
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Characteristics of Electron Transport Chain
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-occurs in the plasma membrane of prokaryotes & in the inner membrane of mitochondria for eukaryotes
-as H+ is pumped out of the cell, an electrogradient is produced inside/across the plasma membrane -protons release energy as they move down the gradient through the channel created by ATP synthase (protein) - The movement is called chemiosmosis |
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What is Chemiosmosis
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Def: a mechanism that uses a proton gradient across a cytoplasmic membrane to generate ATP
Chemiosmosis powers both: 1. oxidative phosphorylation of ATP 2. proton motive force for the rotation of bacterial flagella |
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Where do Metabolic Pathways take place for:
1. Glycolysis 2. Preparatory Step 3. Krebs Cycle 4. ETC |
Prokaryotes
1. Cytoplasm 2. Cytoplasm 3. Cytoplasm 4. Plasma membrane Eukaryotes 1. Cytoplasm 2. Cytoplasm 3. Mitochondrial matrix 4. Mitochondrial inner membrane |
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Describe Fermentation in Prokaryotes - follow one Glucose through fermentation
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- Gains energy for the cell from the oxidation of sugars
- Does not require oxygen (no Krebs Cycle or ETC) - Organic molecules are the final electron acceptors; results in organic acids and alcohol end-products - Substrate carbons may be "blown off" as gas - Far less efficient than respiration - net ATP gain: 2 (from Glycolysis for one glucose) Glycolysis In: Glucose Out: 2 pyruvates E carrier: 2 NADH Net ATP: 2 ATP Carbon end products: organic acids, organic alcohols, CO2, O2 |
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Describe the path of one glucose through respiration in prokaryotes
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- From one glucose, aerobic respiration in prokaryotes produces 38 ATPs. In eukaryotes, net 36 ATPs.
Glycolysis In: Glucose Out: 2 pyruvates E carrier: 2 NADH Net ATP: 2 ATP from substrate-level phosphorylation Krebs Cycle In: 2 pyruvates Out: 6 CO2 E carriers: 8 NADH, 2 FADH Net ATP: 2 ATP from substrate-level phosphorylation ETC In: 10 NADH, 2 FADH2, 6 O2, reducing power Out: H20 Net ATP: 34 ATPs |
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Describe the biochemical test for fermentation of sugars
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- Tests for the presence of enzymes which catabolizes sugars
- sugar catabolism produces acid and gas - pH indicator changes to yellow in the presence of acid - bubble in inverted Durham tube indicates gas production - peptone are added because they can serve as a substrate for ATP. It's not as efficient as using sugar. Peptone is the control. Allows one to know if the organism is actually growing. |
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What are photosynthesis and phosphorylation
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- Photophosphorylation - energy stored in bonds of ATP
- Oxygenic photosynthesis - conversion of light energy into chemical energy + oxygen; reverse of respiration 1. Respiration uses oxygen and sugars; produces CO2 and ATP 2. fermentation uses sugars; produces CO2, alcohol, ATP 3. photosynthesis uses CO2; produces O2, sugars, ATP |
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What is a Sterilant
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kills all viruses and infectious microorganisms including endospores
sterilant must eliminate endospore to be considered sterilant |
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What is a Disinfectant
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reduces the numbers of microorganisms
removes most of the pathogenic microbes reduces the number if microbes for inatimate objects |
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What is an Antiseptic
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removal of the largest number of microorganisms using chemicals for tissue
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What are the parameters of autoclaving
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it is the gold standard for instrument sterilization: 121.6 C for 15 min @ 15 psi
higher pressure equals higher temperature destroys endospores dirty instruments can mask and/or protect anything inside. Instruments have to be cleaned first, then it goes into autoclave |
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What are methods of eliminating microorganisms
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1. liquid filtration
2. Irradiation 3. Sterilization by Autoclave - steam under pressure 4. Chemical disinfectants for inatimate objects 5. Chemical antiseptics for tissues |
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What organism is a huge problem for hospitals
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Pseudomonas aeruginosa - resistant to lysol which is O-phenylphenol. It's a huge problem in burn wards. It can grow in an anaerobic environment.
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Characteristics of Chemical Sterilants
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The effective antimicrobial action of chemicals depends on:
- concentration - time of exposure - presence of extraneous organic matter - pH ----------------------------------------- Gaseous ethylene oxide - sterilant - useful to sterilize plastics & heat labile media Hydrogen peroxide - sterilant - high toxicity due to free radicals - used in deep puncture wounds cuz they bubbling gas gets the debris away Aldehydes: Cidex, formaldehyde - sterilants - 1 choice to destroy endospores and TB - medical equipment - used on dead tissue like in anatomy labs sodium hypochlorite (bleach) - disinfectant or sterilant (time and concentration dependent) - effective and cheap - water purification |
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Characteristics of Chemical Disinfectants
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At lower concentrations, they can sometimes be used as antiseptics
Phenolic compounds * Lysol, hexachlorophene, Triclosan * 2% Amphyl - common micro disinfectant -surface disinfectants -effective against TB -effects persist after application -may cause neurologic damage in infants Alcohols - 95% ethanol - disinfectant in aqueous solution - in gels, needs 62% to be effective - can be used as an antiseptic too Quarternary ammonium compounds (Quats) - disinfectant only - ineffective against TB and endospores - Pseudomonas grows in Quats Sodium hypochlorite (bleach) - disinfectant or sterilant (time and concentration dependent) - effective and cheap - water purification |
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Types of Antiseptics for Tissue
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Chlorhexidine
- antiseptic - low toxicity - ca be used as mouth rinse - most common surgical scrub and preoperative skin prep Some phenolic compounds - Triclosan Heavy Metals - Biocidal and antiseptic - Silver; zinc (Zicam) - prevents wound infection - burns, catheters Iodine - antiseptic - Betadine - Water purification Alcohols - Isopropanol - antiseptic - mostly mechanical rather than disinfectant when used as a antiseptic cuz it evaporates. Mechanical process refers to how it lifts the debris from the skin Surfactants (soap) - non-toxic enough to be used around food preparation - not antiseptic - doesn't kill microbes - mechanical action only - effective on transient microbes by lifting them off skin |
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What are the concerns for sewage plants
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- human pathogens in feces, etc.
- organic material (waste) in feces. |
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Why are organic waste as issue in sewage plants
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The number of microbes increase if the organic waste is not eliminated in the water before the water is dumped into oceans/lakes/etc. Microbes live off of organic waste. Microbes raise the Biological Oxygen Demand (BOD). This results in the loss of O2 in H2O. . .resulting in the death of fish and other aquatic life who need the O2.
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How do they test for human pathogens in sewage plants
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First use the Presumptive test for Coliforms (Enterobacter aerogenes and E.Coli). E aerogenes is non-fecal in origin. If positive, then use the Confirmed Test to test for Coliforms, specifically E coli using a differential and selective medium. Differential 'cause it differentiates btn Coliforms and non-Coliforms. Also selective because it selects for gram negative bacteria. High E. coli count implies contamination.
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What is the standard method for waste water treatment
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1. Primary Treatment gets 30% of organic waste out via screening/filtering of large objects. Affluent continues to a settling tank - heavier materials settle to the bottom of the tank as sludge. Oils float to the top and are skimmed off.
2. Secondary Treatment - remaining affluent, which has a lot of organic waste, is exposed to different microbes to reduce the BOD. Microbes consume the organic waste...biological reduction of organic material. This process occurs in aeration tanks. The microbes that are added/utilized are called "active sludge." 3. Tertiary treatment renders the water potable. For H2O to be potable, MPN must equal zero. |
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What are Coliforms
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Def: exclusively a group of microbes found in guts, but it also includes bacteria not found in guts such as Enterobacter aerogenes. It includes Gneg facultative & aerobic rods that ferment the sugar lactose at 35C for 48 hrs. Microbes produce acid and gas. Examples:
- E aerogens - we can expect to find environmental microbe - E coli - from human colons - high E coli implies contamination MPN = most probable number in 100 mL of water sample |
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Describe Bacterial Chromosone
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- single chromosone
- circular - double stranded DNA - supercoiled - DNA gyrase enzyme involved in supercoiling. DNA wound up tightly like a spring and then wound up again...supercoiled - most bacterial species have plasmids *** eukaryotic DNA organized around histones |
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Describe DNA double helix
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Base Pair Rules
A:T in DNA A:U in RNa G:C Strands are antiparallel and complementary. Sugar-phosphate backbone anti-parallel direction for both strands. Information is stored in the sequence of bases Sugar-phosphate backbone held together by covalent bonds Strands of DNA double helix held together by hydrogen bonds |
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Describe DNA replication in bacteria
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The parental strand is unwound by Helicase. Replication begins at the replication fork. Replication is ONLY in the 5' to 3' direction of the daughter strand. New neucleotide can only be added to the 3' hydroxyl group. One strand is continuous replication and the other strand is discontinuous replication. The DNA polymerase adds the complimentary nucleotides to growing DNA strand.
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What is Helicase
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It is an enzyme responsible for unwinding the DNA. It unwinds strands at the Point of Replication. It breaks bonds at the replication fork. It unzips the strands one by one.
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What is DNA polymerase
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It is an enzyme used in replication
Adds complimentary nucleotides to growing DNA strand It proofreads as it goes along; it's a very accurate enzyme. Only adds nucleotides to a free 3' hydroxyl group of the growing strand (the daughter strand) |
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What is RNA primase
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RNA primase used on the lagging strand during replication due to discontinuous growth of the lagging strand. It's the first enzyme that comes in to help with synthesis of the lagging strand.
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What is DNA ligase
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it joins the short DNA strands of the lagging strand. They need to be joined because it is discontinuous growth of the daughter strand. Grown can only go from the 5' to 3' direction
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What is replication
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Replication is the faithful copying of the parental DNA at the time of cell division. It ends the life of the parental cell. Parental cell divides itself into two daughter cells.
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What are the characteristics of replication of bacterial DNA
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1. faithful copying of the parental DNA during cell division. Parental cell dies and is left with two daughter cells
2. there are two replication forks in bacterial chromosome 3. replication is bidirectional in bacteria 4. daughter strands grow only in the 5' to 3' direction; there are leading and lagging strands. The leading strands has continues growth and addition of nucleotide added to the free 3' hydroxyl 5. lagging strand requires RNA primase and DNA ligase 6. it is a semiconservative process - each daughter has a DNA from the parental cell that serves as a template for replication 6. another replication can start while the previous one is still the process 7. replication fork is not static. it moves |
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Characteristics of RNA
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- plays a different role from DNA
- Different pentose (ribose) - Uracil in place of thymine - much shorter strands - single-stranded - Linear - never circularizes - less accuracy in its synthesis - short lived |
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What are Sigma Factors
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proteins responsible in gene expression regulation
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What does RNA polymerase do
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- recognizes the promoter region of the DNA
- reads DNA template in the 3' to 5' direction (synthesis of mRNA is in the 5' to 3' direction) - determines which of the two DNA strands serve as the template - when it reaches the terminator sequence, the mRNA falls off |
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what are the three types of RNAs
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1. mRNA
2. tRNA 3. rRNA |
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Characteristics of the "Universal Genetic Code"
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- 64 codons (61 sense codon and 3 non-sense codons) coding for 20 amino acids
- has redundancy/degeneracy - anti-codon found on the tRNA - binds with the codon on the mRNA via Hydrogen bonds |
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Characteristics of ribosome
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prokaryotic ribosome
- 70S (30S + 50S) eukaryotic ribosome - 80S (40S + 60S) tRNA and ribosome move along the mRNA via translocation (codon by codon) |
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What does RNA polymerase do
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- recognizes the promoter region of the DNA
- reads DNA template in the 3' to 5' direction (synthesis of mRNA is in the 5' to 3' direction) - determines which of the two DNA strands serve as the template - when it reaches the terminator sequence, the mRNA falls off |
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what are the three types of RNAs
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1. mRNA
2. tRNA 3. rRNA |
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Characteristics of the "Universal Genetic Code"
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- 64 codons (61 sense codon and 3 non-sense codons) coding for 20 amino acids
- has redundancy/degeneracy - anti-codon found on the tRNA - binds with the codon on the mRNA via Hydrogen bonds |
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Characteristics of ribosome
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prokaryotic ribosome
- 70S (30S + 50S) eukaryotic ribosome - 80S (40S + 60S) tRNA and ribosome move along the mRNA via translocation (codon by codon) |
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discuss the Lac Operon
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In normal conditions of the Lac operon, the repressor protein binds to operator region. It represses & blocks transcription of the gene. Why? Lactose is not the favored nutrient source. It is an allosteric inhibition binding. When lactose is present, the lactose (inducer) binds to the repressor protein allosterically. This unblocks the operator region to allow for transcription.
However, in order for RNA polymerase to bind to the promoter region, 2 things must occur: 1. activation 2. induction Activation occurs when activator binding site is activated/bound with cAMP-CAP complex. Induction - Occurs when lactose is present as a nutrient source high cAMP concentration implies low ATP/ADP concentration. Puts cells in a panic mode to find an alternative nutrient source other than glucose. If "induction" is required, this means the gene is normally turned off. Induction turns on the gene. |
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What are Mutations
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- alterations in the DNA
- Inheritable through all subsequent generations - consequences for the cell line based on nature of the mutation 1. deleterious - ends the cell line or decreases its survivability 2. no effect on cell line 3. beneficial - increases survivability |
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what is a missense mutation
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- faulty protein or
- normal protein; silent (degeneracy of code) |
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what is non-sense mutation
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incomplete protein
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what is a frameshift mutation
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- serious mutation, not a point mutation
- replication error (spontaneous mutation) which inserts or deletes one or more nucleotide pairs and thereby shifts the reading frame |
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What are mutagens and their characteristics
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Radiation
- UV radiation causes thymine dimers (occurs on the same strand) - Ionizing radiation (X rays and gamma rays) causes formation of ions that react with nucleotides Repair mechanism (enzymatic) - nucleotide excision - separation of thymine dimers |
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what are the 4 mechanisms in which bacteria get diversity through asexual reproduction - 4 naturally occurring gene transfers
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1. Transformation
2. Transduction 3. Conjugation 4. Transposons |
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What is transformation
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"naked" ssDNA transfer from the environment to the recipient cell
donor cell dies |
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What is transduction
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DNA transfer from donor to recipient cell by bacteriophage (virus)
donor cell dies |
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What is conjugation
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Transfer of F plasmid DNA from an F+ donor to F- recipient cell
requires extra-chromosomal plasmids, which is also part of the bacterial genome involves the use of a pilus donor cell lives |
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What is transposons
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Short segments of chromosomes which self-excise and insert at new location within the chromosome or within a new plasmid
done through a pilus; pilus gene carried on the plasmid conjugation can be seen in eukaryotic cells |
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what are the characteristics of plasmids
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1. extrachromosomal
2. circular 3. dsDNA 4. independently self-replicating 5. code for useful but non-essential traits |
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What are the characteristics of Restriction Enzymes (Endonucleases)
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1. naturally occurring in bacteria
2. each endonuclease cleaves DNA at a specific recognition site 3. produces restriction fragments (RFLPs) with stick ends 4. the number and length of each fragment produced depends upon the specific sequence of nucleotides in the source DNA recognition sites are palindromic |
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What is transposons
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Short segments of chromosomes which self-excise and insert at new location within the chromosome or within a new plasmid
done through a pilus; pilus gene carried on the plasmid conjugation can be seen in eukaryotic cells |
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what are the characteristics of plasmids
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1. extrachromosomal
2. circular 3. dsDNA 4. independently self-replicating 5. code for useful but non-essential traits |
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What are the characteristics of Restriction Enzymes (Endonucleases)
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1. naturally occurring in bacteria
2. each endonuclease cleaves DNA at a specific recognition site 3. produces restriction fragments (RFLPs) with stick ends 4. the number and length of each fragment produced depends upon the specific sequence of nucleotides in the source DNA recognition sites are palindromic |
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How does one engineer a gene vector
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1. digest vector DNA w/endonuclease
2. digest source DNA carrying gene of interest w/same endonuclease 3. Produce RFLPs from vector & source w/complementary sticky ends 4. anneal ends with DNA ligase 5. rDNA created The same endonuclease must be used throughout the process to ensure complementary sticky ends |
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What are the characteristics of Plasmid vector
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vector must be:
1. self-replicating 2. short; readily inserts into host cell; resist enzymatic degredation 3. carries gene marker 4. carries restriction sites |
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How does one engineer recombinant cells in vitro
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1. isolate DNA from donor cell
2. use the same endonuclease to cleave donor DNA and vector DNA 3. hybridize donor DNA with vector DNA to get a rDNA 4. inser rDNA into hose cell and clone |
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What are helminths
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Helminths are
1. eukaryotic parasites 2. three main types: 1. nematods (roundworms) 2. cestodes (tapeworms) 3. trematodes (flukes) |
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Types of Nematodes
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ascarids, hookworms, whipworms, pinworms, filariases, trichninas, threadworms
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Types of Cestodes
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pork tapeworms, beef tapeworms, fish tapeworms
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Trematodes
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lung flukes, liver flukes, blood flukes (schistosomes)
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