Exam 4.1

• How do physical requirements (pH, temperature, oxygen, etc.) impact a microbe?

  Each condition has a min/max and optimal growth conditions
• What (chemical requirements) macromolecules does a culture need to grow successfully?

  *Carbon 50%

  *Oxygen 20%

  *Nitrogen 14%

  *Carbohydrates, proteins, lipids, nucleic acids
• How does a microbiologist supply a culture with each macromolecule?

  Using media/agar
• What categories of culture media do microbiologists use?

  *Chemically defined medium: types and quantities of nutrients are known

  *Complex medium: know types of nutrients in it, but not quantities

  *Living medium: use one type of cell to support the growth of another cell

  *Selective media: allow some type of bacteria to grow, while killing others

  *Differential media: allow many microbes to grow, but will change in appearance due to biochem properties

  *Fastidious: microbes are those that require external growth factors (ex. metals, vitamins, blood, etc)
• Why is water so important to biological organisms?

  *It's polar (can bond with 4 neighboring molecules, excellent dissolving medium, is a natural reactant/product, H-bonds acts as temp buffer)
• What is the difference between organic and inorganic molecules?

  *Organic: always contain C and H

  *Inorganic: usually lack C, can have C if no H
• What are the four groups of macromolecules, their differences, their uses and their structures?

  *Carbohydrates: sugars/starches, C, H, and O

  *Lipids: fats/waxes, C, H and O, glycerol head linked to fatty acid tails (ester linkage), phospholipids, steroids

  *Proteins: C, H, O, N, and sometimes S, enzymes, transporters, flagella/pili, toxins, made of amino acids, amino acids are joined by peptide bonds through dehydration synthesis

  *Nucleic acids: DNA double-stranded (deoxyribose), RNA single-stranded (ribose), made of nucleotides (N-base, sugar, P group), nucleosides (N-base, sugar)
• Spherical

  Coccus (cocci)
• Rod

  Bacillus (bacilli)
• Curved rod

  Vibrio
• Club

  Coryneform
• Helical

  Spirillum
• Monomorphic

  Consistent cell morphology
• Pleomorphic

  Inconsistent cell morphology
• Single cells

  Solitary
• Doubles

  Diplo + cell morph
• Chains

  Strepto + cell morph
• Irregular clusters

  Staphylo + cell morph
• Four (one plane)

  Tetrads
• Four (two planes)

  Sarcinae
• What is the function and structure of the glycocalyx?

  *Thick coating of polysaccharides (and sometimes polypeptides)

  *Capsule: neat and consistent shape

  *Slime layer: inconsistent shape, loosely adhered to cell

  *Helps cells evade the immune system, can form biofilm, carbohydrate reserve
• What are the functions of bacterial flagella, fimbrae and pili?

  *Flagella: propel the bacteria (run and tumble), motility, taxis (find light or nutrients), made of: filament, hook, basal body (1 basal body per membrane)

  *Fimbrae: adhesion, short hair-like protein fibers

  *Pili: motility (twitching or gliding), conjugation
• What are the differences between Gram-positive and Gram-negative cell walls?

  *Gram + cells have a very thick layer of PG in the plasma/cytoplasmic membrane, gram - cells have a very thin layer of PG in the plasma/cytoplasmic membrane

  *Gram + have teichoic acid in cell wall, gram - have LPS in cell wall
• Know the theory behind the Gram stain.

  *Crystal violet: primary stain

  *Grams iodine: mordant/fixant

  *EtOH: decolorizer

  *Safranin: secondary stain/counterstain

  *Water: decolorizer

  *Malachite green: primary stain

  *Acid-fast/gram + cells turn... red

  *Non acid-fast /gram - cells turn...blue
• What is the structure of the CM? How is it constructed?

  Lipid bilayer (polar heads, fatty acid chains in tails)
• Why do bacteria produce endospores? Which bacteria produce them?

  *For survival --> will occur when the cell is stressed

  *Bacillus and Clostridium produce them (100 genera)
• What are some characteristics of endospores that are useful for identification?

  *Part of cell: central, terminal, subterminal

  *Shape: swollen, non-swollen

  *Shape: elliptical, round
• What is the endosymbiotic theory?

  *Theory that eukaryotic organelles (mitochondria and chloroplasts) from ancient free living prokaryotes
• What are the differences between anabolism and catabolism?

  *Anabolism: building molecules, endergonic (absorbs heat)

  *Catabolism: breaking down molecules, exergonic (releases heat)
• What are enzymes, cofactors and coenzymes?

  *Enzymes: biological catalysts, proteins (usually) encoded by genes

  *Cofactors: non-protein component

  *Coenzyme: non-protein component (organic)
• How do enzymes aid metabolism (+ steps)?

  *Speed up chemical reactions

  1. Substrate contacts the active site

  2. Complex is formed

  3. Products are formed

  4. Products are released

  5. Enzyme is unchanged (can be used again)
• What is redox, and what molecules are commonly involved?

  *Oxidation and reduction

  *OIL RIG

  *Use e- from H (dehydrogenation)

  *NAD+ is a common e- carrier --> becomes NADH after accepting the e-
• What are the major methods for ATP generation?

  Substrate-level phosphorylation and oxidative phosphorylation
• What is the difference between aerobic respiration, anaerobic respiration and fermentation?

  Aerobic respiration take place in the cytoplasm (glycolysis) and mitochondria (krebs and ETC). *Anaerobic respiration takes places only in the cytoplasm

  *Fermentation belongs to the anaerobic respiration and it takes place in the cytoplasm only
• What is the goal of glycolysis, Krebs cycle and the electron transport chain?

  *Glycolysis goals: generate ATP + NADH

  *Krebs cycle: generate NADH + FADH2 to power ETC, generate small amount of ATP

  *ETC: Generate ATP, replenish supply of NAD+ and FAD for glycolysis + Krebs cycle
• What is chemiosmosis, and how is it used to generate ATP?

  *Chemiosmosis produces energy in the form of ATP

  *E- passes through the ETC, causes H+ excess which get passed through ATP synthase (makes ATP)
• What is the goal of the Calvin-Benson cycle? Why was it once called the "dark reactions"?

  *Goal: can be used to fix C in any organism, makes glucose

  *Was called the dark reactions because it doesn't need energy from the sun to occur
• What is the difference between a genotype and a phenotype?

  *Genotype: genes of an organism

  *Phenotype: expression of the genes
• Why is DNA replication known as semi-conservative?

  Half of the DNA is old and half is newly synthesized DNA
• What are the substrates and products of transcription?

  *First: RNA polymerase binds to the promoter

  *RNA polymerase begins transcribing DNA into RNA (works in the 5' to 3' direction) > adds RNA nucleotides one base at a time (breaks apart two strands and starts inserting complementary pairs)

  *Ends when RNA polymerase reaches the terminator --> RNA molecule is released + leaves the DNA molecule

  *RNA --> synthesis of RNA from a DNA template