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Unit 3: Microbiology, lecture scraps;, Ames test, Transcription, image,…

- - - - Small acid soluble proteins protect DNA, provide carbon + energy
  - - - G+ (gram positive) = thick level of peptidoglycan, so sticks well to the pigment
      - G-(gram negative) = an outer membrane
      - Structure unique to prokaryotes (Archaea = pseudo-peptidoglucan)
      - NAG = N-acetyl glucosamine. NAM = N-acetyl muramic acid
      - Cell membranes
        
        3. Energy conservation
        
        Hydrogen ion creates a gradient that can enter the cell, the process of which creates ATP
        
        2. Protein anchor
        
        Membrane transporters
        
        Example of taking up nutrients
        
        Requires energy
        
        Group translocation
        
        Bring sugars into the cell
        
        20 systems in E. coli
        
        Links first and last steps of glycolysis 1)
        
        Simple transport
        
        Lactose symporter
        
        Na+ antiporter
        
        Protons (H+) movement creates a gradient
        
        2 more items...
        
        ABC transporters
        
        Proline, maltose, Zn, Fe
        
        ATP binding cassete
        
        1. Permeability barrier
        
        can diffuse: small molecules, water
        
        cannot diffuse: ATP out of the cell!
        
        Very selective!
        
        Even small ions (ie H+, K+ and Na+) do not diffuse freely
        
        3 main functions
  - - - Flagellar motility
        
        Chemotaxis/Phototaxis
        
        Ability to swim toward/away from a particular chemical/light source
        
        Allow bacteria to swim. Composed of flagellin protein subunits - different than eukaryotic flagella/cilia
        
        Their energy source
        
        Rotates instead of beat (some clocked at 100,000 rpm)
        
        this isn't entirely understood by science
        
        Run and tumble phenotype
        
        If they find an attractant...
        
        Bacterium can control the run and tumble mechanism by sensing molecules in the membrane of cells.
      - https://www.youtube.com/watch?v=8IJRzcPC9wg
      - Surface to volume ratio limits the size of cells
      - Divides quickly- fasted recorded is 8 minutes. Rapid reproduction rate, eg E.coli divides every twenty minutes
      - Fimbriae - Pillus/Pili
        
        Smaller than flagella (~7nm in diameter, shorter)
        
        Microbe-microbe + host-microbe interactions
        
        Allows bacteria to adhere to surfaces
        
        Transfer of genetic information through conjugation/mating using direct contact
      - Capsule
        
        Made of polysaccharide and/or protein
        
        Functions
        
        Attach to surfaces
        
        Prevent phagocytosis by host immune cells
        
        Prevents drying (dessication)
        
        Glycocalyx - slime layer
    - - Reproduce asexually by binary fission
  - - - Haystacks with channels for water and
        nutrient flow and waste disposal
    - - – Lungs of cystic fibrosis patients
      - – Alginate capsule
      - – Resistant to chemical treatment
      - – Ultimately end up killing the patient
    - - Enzyme retention
      - Resistances
      - Competition (between biofilms)
      - Cooperation
    - - Flagella are essential for biofilm formulation
- - - - each of these molecules are polymers, building blocks.
      - each provides a template for the next step
      - The errors in these processes that take place are what allows evolution
      - Which process can tolerate more errors?
        
        Perhaps replication?
        
        Repair mechanisms
        
        Perhaps transcription?
        
        While replication is more 'permanent'
        
        Error repair mechanisms
        
        DNA polymerase has a 1 error in a million
        
        Proofreading reduces rate by
      - One gene encodes one enzyme
      - TBH this unit is just IB biology topics 2 and 7(HL) use those notes
        
        Structure of DNA
        
        Replication + PCR, Transcription, Translation
      - Coupled transcription and translation
        
        Coupled transcription-translation (CTT) is a hallmark of prokaryotic gene expression. CTT occurs when ribosomes associate with and initiate translation of mRNAs whose transcription has not yet concluded, therefore forming “RNAP.mRNA.ribosome” complexes. CTT is a well-documented phenomenon that is involved in important gene regulation processes
  - - - ie genes are necessary to lead to a specific phenotype ie the trait of having a bacteria that makes us sick
- - - - Multiple genes controlled my the same operon
      - Genes necessary for life production are found in operons
    - - Bacteria has the ability to respond to tetracycline? It will only want to respond to this operator when exposed to it. Therefore, this thingy prevents the gene from being activated.
        
        This thingy is TetR
      - Since antibiotics have always been around, bacteria has to respond
      - It is essentially textbook negative regulation.
- - - - 6mm = full resistance
      - Categories = resistant, intermediate, sensitive
  - - - Single base pair, limited to a single gene
      - One allele --> different allenle
    - - Horizontal gene transfer
        
        Major driver of molecular evolution in. the genetic world
      - Transformation
        
        Often involves plasmids
        
        Uptake of naked DNA
      - Conjugation
        
        Transfer of genetic information through direct cell-to-cell contact
        
        Chromosomal segments of DNA or plasmids can be transferred
        
        Evidence?
        
        Lederburg and Tatum, 1946 experiments
        
        met- bio aux
        
        Prototroph? Autotroph? Wtf happened here with met-, thr-
        
        Consists of several processes
        
        Origin of transfer is sequence of DNA to cut --> rolling circle replication
        
        Plasmid is restored in the recipient cell
        
        Probability of getting two mutations is far too low.
        
        How did we get d--- located genes to be transferred from a donor to a recipient if the origin of transfer was on a plasmid?
        
        Horizontal gene transfer = reproduction without sex
        
        Horizontal gene transfer enables bacteria to respond and adapt to their environment much more rapidly by acquiring large DNA sequences from another bacterium in a single transfer. Horizontal gene transfer is a process in which an organism transfers genetic material to another organism that is not its offspring
      - Transduction
        
        A virus infecting a bacterium is called a bacterio/phage
        
        It is abundant
        
        Transfer of genetic information using a virus as a medium
        
        Can transfer ~100,000 bp
        
        How do bacteriophages (acellular life) get their genetic information onto the next generation?
        
        Lytic cucle
        
        Lysogenic cycle
        
        More about bacteriophages; also called phages
        
        Auxotrophy - restore lysine auxotrophy to prototrophy
        
        Generalized Transduction
        
        Phage infects bacterium
        
        Injects DNA
        
        Packaging mistakes- some phage heads contain bacterial DNA, not phage DNA
        
        Transducing particle bursts out and infects a new host
      - How are these two connected?