Micro Exam 4

• In stringent response, idling ribosomes stimulate _____ and decreases the affinity of ___ ________ for _____ of ____ genes

  production of ppGpp; RNA polymerase; promoters; rRNA
• What are the four steps of the stringent response?

  -Amino acid deficienct results in idling ribosome

  -RelA is activated and synthesizes ppGpp

  -ppGpp interacts with beta subunit of RNA polymerase. Affinity for promoters of rRNA genes decreases

  -less rRNA is made = fewer ribosomes made
• What does the stringent response allow bacteria to do?


  It is a mechanism of stress response that allows the cell to focus on amino acid synthesis (ppGpp signals low AA) instead of growth and division in order to survive
• What is a riboswitch? What is its function?

  mRNA that binds a ligand (small molecule)

  -mRNA binding to a ligand impacts completion of transcription or mRNA translation ability
• What are examples of ligands?

  Vitamins, metals, nucleotides, and amino acids
• Where are riboswitches located?

  non-coding regions of mRNA and serve as sensors of small molecules (ligands)

  -binds to specific areas with a small range of concentrations to regulate genes related to its own metabolism, use, or transport
• Riboswitches play a crucial role in gene regulation by

  responding to specific molecules and adjusting the production of proteins accordingly (RNA-based regulation)
• For a lysine binding riboswitch, what happens when the lysine is bound vs not bound?

  -Bound: translation will NOT occur

  -Not Bound: translation occurs
• What are the two types of regulatory RNA molecules?

  -Small RNA (sRNA): encoded by intergenic regions (between genes)

  -cis-antisense RNA (asRNA): transcribed from DNA strand opposite the mRNA-encoding template strand
• How do regulatory RNA molecules typically affect gene expression?


  Post transcriptionally

  -either by binding to complementary targets of transcripts (stimulate or prevent translation) OR by interacting with proteins
• Small regulatory RNA are generally how long in length?

  100-200 nt
• What are the benefits of using regulatory RNA?

  -cheap (don't require a lot of work/resources)

  -diffuse rapidly

  -act on pre-existing messages
• What can sRNA do? How does it do it?


  -can inhibit translation

  -they interact with the ribosome binding site (RBS) (shine-delagarno sequence) to make it unavailable to the ribosome
• How can sRNA promote translation? Without sRNA, what happens to the RBS?

  -it provides an alternate base-pairing partner for the 5' UTR strand = prevents the concealment of the RBS

  -w/o sRNA, 5' UTR mRNA is SELF-complimentary and the RBS is concealed by default
• How is sRNA capable of promoting mRNA degradation?

  is an alternate base pairing for the mRNA, once bound, RNase III targets the double stranded RNA (mRNA + sRNA)
• What are the steps for sRNA in order to promote mRNA stability? What is the result?

  -sRNA-mRNA base pairing

  -RNase III targets the sRNA-mRNA duplex (splitting into two strands)

  -the two smaller strands are now more stable than one larger strand
• What do cells require energy to do?

  grow, maintain, chemotaxis
• What are the two ways cells gain energy?

  Phototrophy- absorb light energy and convert it to chemical energy

  Chemotrophy- catabolism of high energy compound to a lower energy product through oxidation reduction reactions
• What are the two subcategories of Phototrophy? What do they mean?

  Anoxygenic: light energy is used to photolyse a reduced compound other than water (ex: H2S)

  Oxygenic: light energy is used to photolyse H2O to release the oxygen
• What are the two subcategories of Chemotrophy? What do they mean?


  Lithotroph: oxidize inorganic chemicals (H2, H2S, NH4+, Fe2+) (ex: nitrifying bacteria)

  Organotroph: oxidize organic compounds (sugars)
• What is the formula for Gibbs free energy? What value is favorable?

  Formula: ΔG = ΔH - TΔS Favorable value: Negative
• What is enthalpy?

  Heat absorbed or released by the rxn
• what is entropy?

  disorder; (-) = more order; (+) = more order
• What are the standard conditions for ΔG*?


  Temperature = 298K

  Pressure = 1 atm

  Concentrations = 1 M
• What are the three factors that influence ΔG?


  -changes in enthalpy or entropy

  -concentrations of products and reactants

  -environmental factors
• How do cells harness energy released from the metabolism of glucose? (2 ways)


  -Multi-step rxns

  -utilize energy carriers
• What are the energy carriers of the cell?

  ATP, NADH, FADH2
• What are energy carriers?

  molecules that gain or release small amounts of energy in reversible rxns
• What are the three ways that ATP can transfer energy to cell processes?

  -Hydrolysis-releasing phosphate (Pi)

  -Hydrolysis-releasing pyrophosphate (PPi)

  -phosphorylation of an organic molecule
• Some energy carriers also transfer ___

  electrons
• What is an electron donor/acceptor?


  -E donor: reducing agent

  -E acceptor: oxidizing agent
• What carrier carries more energy than ATP?

  Nicotinamide adenine dinucleotide (NADH)

  (NAD+ = oxidized form) (NADH = reduced form)
• What is the process of electrons going from the EMP pathway to the ETC?


  -EMP pathway -> NAD+ (empty dump truck) -> ETC

  --EMP pathway -> NADH+ H+ (loaded dump truck) -> ETC
• Catabolic pathways require ______. Those then ____ the Ea of the transition state.

  enzymes; lower
• What are the substrates catalyzed by microbes?

  -Polysaccharides: (broken down to disaccharides, and then to monosaccharides; sugar and sugar derivatives, such as amines and acids, are catabolized to pyruvate)

  -Pyruvate/other intermed. products of sugar catabolism: fermented or further catabolized to CO2 and H2O via the TCA cycle

  -Lipids and AA: catabolized to glycerol and acetate & other metabolic intermeds

  -Aromatic compounds: such as lignin and benzoate derivatives, are catabolized to acetate through different pathways such as the catechol pathway.
• What are the two major metabolic pathways?

  Fermentation and Respiration
• What is fermentation?


  partial breakdown of organic food w/o net electron transfer to an INORGANIC terminal electron acceptor
• What is respiration?


  complete breakdown of ORGANIC molecules w/ electron transfer to a terminal electron acceptor such as O2
• What are the three ways bacteria and archaea use to breakdown glucose?


  -1. Embden-Meyerhof-Parnas (EMP)2. Entner-Doudoroff (ED)3. Pentose Phosphate Pathway
• What are the characteristics of the EMP Pathway?

  -most common method of glucose metabolism

  -energy investment stage follows by energy extraction

  -occurs in the cytoplasm

  -can occur in presence or absence of oxygen