Metabolism Flashcards by Lyssa Rose

Catabolism

Breaking down molecules
Hydrolysis
Exergonic

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Function as organic catalysts. Active sites bind to substrates, speed up but not used up in a chemical reaction. Genetically determined.

Enzymes

Lowers activation energy, lock and key relationship. End in -ase. Named after substrate or type of reactions catalyzed.

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Inactive if not bound to one or more of the nonprotein cofactors.

Apoenzyme

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Either inorganic ions or certain organic molecules called coenzymes (all coenzymes are either vitamins or contain vitamins

Cofactors

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The combination of a proteinaceous apoenzyme with one or more cofactors

Holoenzyme

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Nonprotein catalysts. A type of RNA that acts like an enzyme.

Ribozymes

Removes sections of RNA and splices them back together. Used experimentally to treat disease.

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Accelerate reaction rates without being permanently changed.

Catalysts.

Turnover number of substrate molecules converted per second is usually between 1-10,000

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Transported extracellularly when they break down large food molecules or harmful chemicals (penicillinase). Sometimes referred to as virulence factors; pathogens secrete things that help them colonize host tissue

Exoenzymes

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Retained intercellularly and function in metabolic pathways

Endoenzymes

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Catalytic cycle

Substrate+enzyme>
enzyme-substrate complex>
Product+enzyme

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Anabolism

Making molecules
Dehydration synthesis
Condensation
Endergonic

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Induced fit model

The enzyme adjusts slightly to the substrate following initial recognition

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Factors affecting enzyme activity?

Environment: temp, pH, enzyme and substrate concentrations

Enzyme inhibitors

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Activator+allosteric site?

Inhibitor+allosteric site?

Active conformation

Inactive conformation

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End product of a metabolic pathway inhibits the first enzyme

Feedback inhibition

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Redox reactions

Oxidation

Reduction

Partial or complete loss of electrons

Partial or complete gain of electrons reducing the positive charge

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ATP components

Adenine, nitrogenous base
Ribose, five carbon sugar
Chain of three phosphate groups

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Oxidation of glucose to pyruvic acid with the production of some ATP and energy containing NADH.

Glycolysis

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Oxidation of acetyl to CO2 with the production of some ATP and energy-containing FADH2

Krebs cycle, citric acid cycle

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Oxidation of NADH and FADH2 to produce lots of ATP

Electron transport chain and oxidative phosphorylation

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Glycolysis in eukaryotes

Electrons are transported from the cytoplasm across the mitochondria not matrix by use of 2 ATP which reduces the overall output of ATP in the cell to 36 ATP

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Glycolysis in prokaryotes

Glycolysis and the Kreb’s cycle occur in the cytosol so there is no loss of ATP, and cells have a net gain of 38 ATP.

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Found in the plasma membrane of bacteria, mitochondrial membrane of eukaryotes. Mostly proteins with metallic cofactors (prosthetic groups). From least electronegativity to highest. O2 final electron acceptor.

Carrier molecules in the pathway of electron transport. Generates a proton gradient, proton motive force.

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Coupling electron flow to ATP synthesis.

Chemiosmosis

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Synthesis of macromolecules utilizing intermediates of glycolysis and Kreb's cycle yielding amino acids, carbs, lipids, and nuclei acids

Amphibolic pathways

Conditions affecting microbial life?

Nutrients and energy sources, temperature, moisture, gases, osmotic pressure, pH, light, other organisms

Chemical substances are acquired from the environment and used for cell growth and metabolism

Nutrients

Required in relatively large quantities for structure and metabolism. These elements compromise 96% of the cell.

Macronutrients. Carbon, hydrogen, oxygen, nitrogen, phosphorous, sulfur.

Trace elements. Required in small quantities for enzyme and pigment structure/function.

Micronutrients

Contain carbon atoms and are usually the products of living things

Organic nutrients

A simple atom or molecule that has no carbon atom in its structure, with the exception of CO2

Inorganic nutrients

Obtain carbon from organic matter from other life forms

Heterotrophs

Obtain carbon from CO2 which is then converted into organic compound

Autotrophs

Carbon?

Used for all cellular structures and processes.

Nitrogen

Mostly in the form of N2, nitrogen gas from the atmosphere. Some bacteria can utilize it from other sources. Must be converted to NH3 to combine with carbon. Major component of proteins and nucleic acids.

Oxygen

From the atmosphere and/or organic salts (sulfates, phosphates, nitrates) Major component of organic compounds such as lipids, carbs, proteins

Hydrogen

Organic compounds such as H2O, salts, and certain naturally occurring gases Maintains pH, forms hydrogen bonds in macros, prime energy force in redox reactions of cellular respiration

Phosphorous

Inorganic phosphate (PO4), derived from phosphoric acid (H3PO4), found in rocks and oceanic mineral deposits Key component of nucleic acids, phospholipids in cell membranes and coenzymes.

Sulfur

Widely distributed in the environment in mineral form, as SO4, sulfides, hydrogen sulfide has, and elemental sulfur, found in organic substances like essential amino acids, certain vitamins. Structural stability and shape of proteins by forming unique covalent linkages called disulfide bonds.

Potassium

Essential to protein synthesis and membrane function

Sodium

Used in some types of cell transport

Calcium

Stabilizer of the cell wall and endospores of bacteria

Magnesium

Component of chlorophyll, stabilizer of membranes and ribosomes, important in cell energy reactions TSS, tampons absorb mag from the vaginal mucus, S. aureus produce the toxin for TSS

Iron

Component of cytochrome pigments (electron transport chain) High blood levels allow increased faster growth of bacteria, hemochromatosis a genetic disease of Europeans Low levels mean diphtheria bacillus produces its toxin, agent of bubonic plague, Yersinia pestis, more virulent, immune system compromised

Zinc

The fungus Aspergillus requires large amounts to produce aflatoxins, induce hepatoma, and related liver diseases

An organic compound such as an amino acid or a vitamin that cannot be synthesized by an organism and must be provided as a nutrient. Most parasites lack the ability to synthesize all needed organic compounds from raw materials

Growth factors

Use light and CO2

Photoautotroph Photosynthetic bacteria

Used electrons from reduced inorganic compounds and CO2

Chemoautotroph H, S, Fe, and nitrifying bacteria

Uses electrons from H atoms in organic compounds and organic compounds for Caron

Chemoheterotroph All animals, most fungi, Protozoa, bacteria

Cold loving, range from -15C to 15C, rarely pathogenic

Psychrophiles

Grow slowly at low temps, better at 20-30C, causes food spoilage, Listeria monocytogenes and S. aureus in fridges

Psychrotrophs

Moderate temp loving, from 10-50C, optimum temp at 20-40C. Most human pathogens prefer 30-40C

Mesophiles

Microbes that survive under short exposures to high temps. Contaminants of heated foods. Often cyst forming, spore forming, or thick walled organisms.

Thermoduric

Heat loving. Range is 45-85C. Most are spore forming species of Bacillus and Clostridium, a small number are pathogens.

Thermophiles

Archaea in deep sea and hydrothermal vents

Hyperthemophiles

Important respiratory has and powerful oxidizing agent that is toxic in many forms

Oxygen

Produced by phagocytes to kill invading bacteria. Its build up can damage and destroy a cell.

Singlet oxygen, 1O2.

Destructive, metabolic products of oxygen. Most cells are equipped with enzymes that neutralize these products, those that do not are anaerobic.

Superoxide ion (O2-), peroxides, hydroxides

Capable of growth in the absence of oxygen. Oxygen is metabolized by aerobic respiration when present. When absent it uses an anaerobic mode of metabolism.

Facultative anaerobe.

Do not utilize oxygen but survive in the presence of it because they can break down todo oxygen by alternate pathways.

Aertolerant anaerobes (facultative aerobes)

Requires a small amount of oxygen, less than 10%. Most live in places such as soil, water, or the body where they are not exposed directly to the atmosphere.

Microaerophiles. Lumpy jaw, syphillis, H. pylori

All microbes require some but these types grow best at higher CO2 levels than is normally present in the atmosphere. Candle jar special CO2 incubation procedures

Capnophiles Streptococcus pneumoniae

Optimum pH for most microbes

Between 6 and 8. Most human pathogens grow optimally from 6.4 to 7.5. Human blood is 7.35.

Bacteria that decompose urine create alkaline conditions since ammonium may be produce when urea is decomposed.

Alkalinophiles

Live in solutions that have a high solute concentration. Can grow and spoil food.

Osmophiles

Bacteria that live under high pressures, like deep-sea microbes.

Barophiles

One benefits from the obligate relationship, the other is neither harmed nor benefitted.

Commensalism.

One organism harms the other

Parasitism

Two organisms complementing each other to produce more pronounced effect than when one of them is present alone.

Synergism

One organism inhibits the other

Antagonism

Media with chemical components that are known with exact specifications.

Defined media.

Media with components that are not chemically analyzed but have been proven to support growth. Malt, soy, yeast extract

Complex media

Stores cultures for short periods of times, weeks. 2-4C

Refrigeration

Stores cultures for years -20C

Freezing

Stores cultures in liquid nitrogen stores indefinitely, -70C

Deep-freezing

Storing cultures in a freeze-drying process in vacuum, stores for decades. Vaccines.

Lyophilization

Newly inoculated cells require an adjustment period of enlargement and synthesis. The cells are not yet multiplying at their maximum rate. The population is sparse and dilute, sampling error.

Lag phase of growth

Period of maximum activity in microbial growth

Exponential growth phase

Microbial growth phase when factors become limited for additional growth because lack of food or space, as well as accumulation of wastes.

Stationary phase.

Microbial growth stage when limiting factors intensify, cell die at the rate they multiply.

Death phase

Direct methods of measuring bacterial growth

Standard Plate Count, membrane filtration, most probable number, direct microscopic count

Genetic method of recovering and identifying unculturable organisms, especially prokaryotes. More prok species have been added into data bases and refined their taxidermy in the process.

Genetic prospecting. Uses polymerase chain reaction

The study of the genes and inheritance. The sum total of genetic material of the cell.

Genetics Genome

Contain hundreds of genes that are composed of DNA. Found in nucleoid and plasmids in prokaryotes. In the nucleus and extra chromosomal DNA in mitochondria and chloroplasts in eukaryotes.

Chromosomes.

Specific segments of the DNA molecule that code for a protein associated with cell functions. Replicate. Transcribed as RNA. Specific peptides/proteins that function as enzymes, antibodies, or structural proteins.

Genes

Small molecules of circular DNA that replicate independently. Not essential for normal metabolism, growth, or reproduction.

Plasmids. Can confer survival advantages like fertility, resistance, bacteriocin factors, virulence plasmids.

Monomeric units that make up nucleic acids, DNA and RNA. Composed of pentode sugar, deoxyribose in DNA, ribose in RNA. Phosphate group. Nitrogenous bases.

Nucleotides.

Cytosine and thymine in DNA Cytosine and uracil in RNA

Pyrimidine nitrogenous bases

Adenine and guanine

Purine nitrogenous bases

Antiparallel strands with one strand running from 5' to 3' direction and the other running opposite from 3' to 5'

DNA. The 5' end bears a free PO4 group, 3' bears a free OH group. Two strands are held together by hydrogen bonds that dictate base pairing rule. A-T. G-C.

Organism's genetic makeup The expression of observable traits the genetic makeup puts out

Genotype Phenotype

A specific segment of DNA containing structural genes, promoter region, operator, and regulatory "I" gene

Operon Inducible operons like the lactose operon are normally off but are turned on by an inducer substrate. Repressive operons govern anabolism and are usually on, but can be shut off when the end product is no longer needed.

Dark repair or excision repair of mutations

Does not require light. Four important enzymes: Endonuclease cuts the sugar-phosphate backbone. Exonuclease removes the damaged nucleotides. DNA polymerase inserts correct bases. Ligase seals the backbone.

rRNA

Forms ribosomes

tRNA

delivers amino acids to ribosomes

mRNA

Carries information for making specific proteins from DNA to ribosomes