bimm 120 final part 2 - the old stuff

three laws of biology + corollaries

1) all living organisms obey the laws of thermodynamics

• corollary: temporary creation goes against 2nd law of thermodynamics (disorder and chaos increase)

• resource utilization decreases entropy

• corollary: an organism in equilibrium is dead

2) all living organisms consist of membrane-encased cells

• plasmids and viruses are not alive

• corollary: cell is only structure that can grow and divide fully on its own

• genetic instructions program cell growth, division, and sexual reproduction

3) all living organisms arose in an evolutionary process

• corollary: all living organisms contain homologous macromolecules (DNA, RNA, and proteins) that are derived from common ancestor

• corollary: genetic code is universal

know which codon position determines what

3 positions: P1, P2, P3

P1 = important for IDENTITY of amino acid

P2 = important for TYPE of amino acid (hydrophilic, hydrophobic, or semipolar)

P3 = wobble position, if important, only matters if position is purine (A/G) or pyrimidine (C/T/U)

• P2 dictates if P3 is important

negative selectivity principle

the negative selection principle states “what is least important changes the most”

wobble base-pairing

different codons can code for one nucleotide

• P3 allows specific alternate base pairing

• example: isoleucine can be coded by AUC, AUA, or AUU

• P3 = wobble base!

• EXCEPTION: in start codons, wobble is P1 (fMet/Met = AUG, GUG, UUG, CUG)

H-bond differences between A:T/U and C:G

rules:

1) more H-bonds can be formed between C:G than A:U/T

• C:G has 3 H-bonds, A:U/T has 2 H-bonds

2) bonds between tRNA and mRNA are stronger if the tRNA is a purine and the mRNA is a pyrimidine

(purines = A & G, pyrimidines = C, T, & U)

purines v. pyrimidines

purines: 2 aromatic rings, A & G bases

pyrimidines: 1 aromatic ring, C & T & U bases

primordial soup

set of conditions that allowed for the rise of nucleic acids, lipids, and other simple building blocks of life

• frozen argument: universal code set in stone and optimized and mutations are therefore deleterious

what is the benefit of redundancy in the genetic code?

multiple codons can code for the same AA, so a singular nucleotide mutation (polymorphism) has less of a chance to change the AA identity and cause a problem

what is the connection between the expression of a gene and the use of rare or common codons?

if a protein/gene is expressed at a high level, a lot of common codons are used

if a gene/protein is expressed at a low level, more rare codons are used

• more popular AAs have multiple codons that encode them, generally

• Trp and Met are the rarest AAs and are both coded by only one codon

what are episymbionts?

a symbiont that lives on the SURFACE of another organism for survival

• mode of association between microbes, especially CPR bacteria and DPANN archaea, which have small genomes and small size (nano)

• CPR bacteria attach to another, larger bacterium

• DPANN cannot survive on their own, associate with LARGER microbes

antigenic drift & shift

antigenic drift: gradual change in mutations leading to adaptations, large accumulation of point mutations over time leading to variation

antigenic shift: combination/exchange of genetic components from different viruses in the same host cell to make something new; recombination of genetic material

influenza basics

h1n1 = spanish flu, swine flu today

• birds/pigs/human crossover

• SEASONAL

h5n1 = humans are NOT immune

• avian flu

• currently not human-human transmissible

• not seasonal, in migratory birds all year long

universal vaccine not possible because strains mutate = yearly vaccine!

subtypes based on hemagglutinin (HA) and neuraminidase (NA)

• can all infect birds, all avian origin

coronaviruses: SARS-1 and SARS-2 basics

Severe Acute Respiratory Syndrome

• replicase, RNA-dependent RNA polymerase, does not have good proofreading capability = antigenic drift

• promotes viral recombination

• jumped from animals to humans

• spread by live markets and wet markets

• flu-like symptoms, fever, fatigue, difficulty breathing

• viral spike protein (S) binds to ACE2 cell surface receptors

coronavirus: MERS basics

Middle East Respiratory Syndrome

• caused by coronavirus, first recorded in Saudi Arabia

• flu-like symptoms, pneumonia

• deadlier than SARS and Covid-19, less contagious

• infection by direct contact with camel

diff pathogen types

virus = non-living organisms that rely on hijacking of the host cell to replicate, require antivirals (ex: SARS-CoV-2, SARS, CoV-1, MERS, HIV, Ebola)
bacteria = Salmonella, Listeria, Mycobacterium, etc., living microorganisms that can cause infectious diseases that can be cured by antibiotics (diseases = tuberculosis, pneumonia, typhoid fever, food poisoning)
prions = misfolded proteins that can cause nearby normal proteins to also fold incorrectly, cause degenerative diseases 

reservoir and intermediate hosts

flu:

• birds to pig/horse/cat/dog to human

coronavirus:

• SARS-1: bat to palm civet to human

• SARS-2: bats to raccoon dog/pangolin to human

mers:

• bats in Africa to camels to humans

bats are reservoirs: not infected, just carriers, commensal infection

virus recombination

influenza viruses have FAST evolution, multiple viral chromosomes allow recombination when infecting the same cell

virus “mixing bowls”

pigs are mixing bowls of influenza viruses, because pigs have 2 kinds of receptors, one targeted by bird virus & one targeted by human viruses

• pigs swap their genetic material and create novel more virulent strains

cooperation and competition role in evolution

cooperation = true driving force for survival and evolution

• symbiosis provided potential pathway for creation of more complex organisms

• no primordial life form could have a full complement of metabolic and biosynthetic catalytic proteins that would allow living organisms to reproduce in the presence of only abiotic sources

competition = natural selection, only AFTER DNA came together

Bdellovibrio exovorus (Bex) and bacteriovirus (Bba)

Bba grows in periplasm of the prey cell after penetrating the outer membrane of the host

• attack phase, outer membrane penetration, periplasmic growth phase (no division), final synchronous cell division paired with host cell lysis phase

Bex grows externally, often attached to the outer surface of the outer membrane of the host bacterium

• grows and divide by binary dission

both:

• Bex has a smaller genome than Bba

• have large numbers of pseudogenes and incomplete systems

• likely undergoing genome size reduction with a rapid loss of function

Asgard and DPANN archaea

Asgard archaea share a relatively close evolutionary relationship with eukaryote, then saw fusion of bacterial and archaeal cells

• Asgard archaea provided essential framework to explain origin of multi-cellular eukaryotes with their metabolic pathways

• EUKARYOTES BRANCHED OFF ASGARD ARCHAEA

DPANN archaea:

• found in extreme environments (heat, salinity, acidity)

• small genome, small cell size, limited metabolic abilities

• cannot make nucleotides, AAs, and lipids

• have outer membrane and unique surface attaching grappling hooks known as hami

• form biofilms & grow by making their own food

CPR bacteria

CPR = Candidate Phyla Radiation

• key biosynthetic pathways

• small genome, small cell size

• episymbiont

• slightly different genetic codes

• unusual ribosome compositions

• pili-like structures extend from CPR cell surfaces

metagenomics

the DNA of entire communities of bacteria are simultaneously sequenced without separation of the different species from each other

• google def: explore diverse species in an environment

lipid divide

isoprenoids = metabolites that are essential in all living organisms in all domains of life

• archaea make precursors via MVA pathway

• bacteria use nonhomologous MEP pathway to make precursors

MVA pathway was likely lost in bacteria

aerobes v. anaerobes

aerobe = oxygen-dependent

anaerobe = oxygen-independent

obligate v. facultative

obligate = MUST be a certain way

facultative = has a preference, but can survive either way

obligate anaerobe v. facultative anaerobe

obligate anaerobe: will NOT grow in oxygen

facultative anaerobe: can grow without oxygen, prefers having oxygen

• facultative FLIPS preferred (if anaerobe, prefers oxygen, if aerobe, prefers no oxygen)

homology

relatedness, descent from common ancestor

divergence

during evolution, those with common ancestor diverge genetically at some point to become diff species

analogy and convergent evolution

convergent evolution: similar habits/lifestyles = similar traits

• analogy: similarity of function between organisms with diff origins (ie. wings developed independently for moth and birds for function of flight)

ASD: basics

ASD = autism spectrum disorder

• multifactorial: genetic and environmental causes

• connection b/w gastrointestinal issues and ASD

• microbial products can cross the blood-brain barrier and cause differences in neurodevelopment = ASD

ASD: causes

• excessive inflammatory products, like IL-6

  • cause abnormal neuron outgrowth and retardation

  • need normal microbes to inhibit IL-6

• altered BBB lets inflammatory cytokines in = neuroinflammation

• disruption of mucosal microbiota

• dysbiosis!!! imbalance in microbiome composition

need microbiome healthy to strengthen intestinal barrier integrity

ASD: symptoms

• food selectivity: picky eater

  • consumption of particular diet alters gut microbiom to favor specific bacterial genera

  • less diverse diet reduces microbiome diversity

• deficits in social behavior

  • can be reversed by probiotics or microbiota recolonization

• GI issues: irritable bowel syndrome and Crohn’s disease

short chain fatty acids: bacterial products contribution to alleviating symptoms

microbiome metabolite = SCFAs

• can act on central nervous system via microbiota-gut-brain axis

• tryptophan can be converted into metabolite that generates neurotoxic products depending on changes to microbiome

main branches of immune system

the two protein networks for coordinating pathogen attacks & communication/regulation:

INNATE: general, fast, always there for you

• responds to antigen QUICKLY

ADAPTIVE: specific, slow, must be induced

neurotransmitters produced by gut bacteria

5HT: serotonin (80% of body’s total)

DA: dopamine

NA: noradrenaline, for bacteria eavesdropping

bacteriorhodopsin basics

• retinal-binding proteins that take light energy and pumps protons against the concentration gradient from cytoplasm to extracellular space

• converts light energy to chemical energy

• light-driven ion pump exclusive to ARCHAEA

bacteriorhodopsin & the photocycle

photocycle:

• initiated by photoisomerization of C13=C14 bond, starting a series of proton transfer between main structural elements of bacteriorhodopsin

• result = translocate SINGLE proton across membrane

bacteriorhodopsin & photocycle steps/elements:

• protonated Schiff’s Base (SBH+) transfers proton to primary acceptor D85 (extracellular)

• extracellular proton releasing complex (PRC) releases H+ to extracellular bulk

• primary proton donor gives H+ to SB on its D96 (cytoplasm)

• D85 transfers its proton to PRC

D = aspartate

what changes account for “reverse” proton transport?

• counterions orientation

  • inward pump = xenorhodopsin

  • incomplete SBH+ counterion = light-induced reorientation of SBH+ toward cytoplasmic side

• acts as channel: once proton gradient is created, ion concentration allows c-ring to be a channel to let protons back in

• reverse pump: F0/F1 ATPase can generate ATP by letting protons cross to interior membrane

basics of F0/F1 ATPase & its capabilities

• goal: pump protons to the other side of the membrane to create gradient, then make ATP when the protons come back

• F0 - a, b, c

• F1 - alpha, beta, delta, gamma, epsilon

• rotor = c-ring, epsilon, gamma

• stator: a, b, delta, alpha & beta

• ATP binds to beta, the catalytic subunits

  • ADP and phosphate bind, ATP made, ATP leaves

CW = build PMF, ATP hydrolysis

CCW = ATP synth, PMF lets protons flow back in

how is ATP synthesized?

binds to beta subunits that catalyze ATP synthesis WHEN ATPase rotates counter-clockwise

• pmf used as power for CCW rotation

basics of ParM, FtsZ, MreB

ParM: actin involved in plasmid segregation, forms helical polar filaments with dynamic instability

• polymerization pushes plasmids apart via spindle mechanism

FtsZ: prokaryotic tubulin homolog, main component of cell div machinery, assembles ring at center of cell

• summons other division machinery

• forms Z-ring

MreB: bacterial actin homolog, polymerizes, has ATPase

• conserved in rod-shaped bacteria

• non-polar filament, do NOT exhibit treadmilling

• amphipathic alpha-helix bind to negative curved membrane to guide peptidoglycan synthesis into ROD shape

where do cytoskeletal proteins localize?

cytoplasm

dynamic instability & its relationship to cytoskeletal polymerization/dissociation

dynamic instability = switch between periods of growth and periods of shrinkage

• GTP hydrolyzed = GDP bound - depolymerization

• GTP bound = growth, stabilizing cap for growth

treadmilling

polar filaments grow on one end (add subunits) and disassemble at the opposite end (take off subunits)

• monomers in the middle relatively fixed in space

• FtsZ protofilaments employ treadmilling, used to direct movement of peptidoglycan enzymes

MamK deets

• in magnetotactic bacteria (respond to Earth’s magnetic field)

• align magnetosomes (magnetic organelles) into chains for navigation

• forms stable, double-helical filaments; low ATPase activity likely accounts for their stability

different classes of transporters & what they do

channels: let things through, can be regulated by membrane potential or ligands

• aquaporin

• Na+ leak channel

cotransporters: transport 2 substrates together

• antiporter: substrates go opposite direction

• symporter: substrates go same direction

pumps: consume energy (ATP) to move substrates

• ATPases

CCW v. CW flagellar rotation and mobility

CCW = forward direction, all flagella move together

CW = tumbling and backwards movement

what determines the power source for flagellar motors?

flagella rotation driven by the proton motive force

• MotAB motor is the channel for protons

• MotAB accepts Na+ in some species

• movement of protons causes MotA to change conformation = power stroke = motor on

how are flagella assembled?

1) basal body

2) hook

3) filament

• components added to flagellum tip, travel through the hollow tube of the flagellum to tip

• eventually tail is capped by HAP2

what is the secretion system built into flagella?

type III secretory system, used to assemble the components of the flagellum outside of the membrane

types of motility: da basics

swimming: flagella

gliding: smooth, adhesive organelle allows bacteria to grab onto something, change shape with attachment to surface, then movement occurs when retraction conformation occurs

• powered by proton motive force

swarming: numerous flagella = swarm (elongated, more flagellated bacteria)

twitching: type IV pili

• cell propulsion = pilus extend, attach to surface, then retract

• powered by ATP hydrolysis

A. motility = adventurous motility

• polysaccharide secretion

• jet propulsion

S motility = social motility

• type of twitching with type IV pilus

how does flagellar localization/arrangement affect motility?

peritrichous flagella: E.coli and Salmonella

• synchronized many flagella

• CCW = smooth coordinated run

• CW = tumble

polar flagella:

• CCW = run

• CW = tumble/backwards

internal: spirochete, periplasmic flagella

• enables swimming in viscous fluids

• like swarming

differences between bacterial and archaeal flagellum assembly/architecture

archaeal flagellum not hollow, have signal peptides

• new subunits assembled at base

bacterial flagellum hollow tub

• new subunits assemble at tip

how does gliding/twitching motility differs from swimming?

gliding & twitching require bacteria to attach to surface via adhesion & pili respectively

• flagella do not attach to surface, just swim

buoyancy and “actin rockets”

• parasites like Listeria and Shigella use host cell actin for movement = actin rockets for propulsion

• gas-vesicle helps passive cells move vertically via buoyancy (can float or sink in fluid)

additional functions of pili and flagella for adhesion and infection

flagella and pili sense surface to adhere to, once adhere can form adhesions

• resistant to antibiotics

• adhesion leads to biofilm, biofilm aids survival and proliferation of bacteria = infections

e-pili and how they differ from other pili

e-pili = electrically conductive pili

• conductive in the absence of native metal cofactors or added metals

• conduits for long range e- transport to extracellular terminal e- acceptors or surface sensors

• pilin nanowires

how pathogenic bacteria react to contact/adhesion?

pathogenic bacteria

• adhesion can mean steady nutrient supply & enables injection of virulence factors

  • resist antibiotics

  • activatioon of virulence requires physically rigid surface

• biofilms formed, hard for immune system to eradicate

  • adhesion = initial biofilm stage

feedback loops & contact/adhesion with pathogenic bacteria

positive feedback loop: attachment is the path to the dark side

• attachment leads to virulence factor activity

• Vfr activity leads to immobility

• immobility leads to biofilm formation

• biofilm formation leads to attachment and more virulence

pseudomonas aeruginosa

opportunistic pathogen with either acute or chronic effects

• acute effects are cytotoxic, cause systemic infection and sepsis, common with infections of burns

• chronic effects are noncytotoxic, usually do not cause sepsis, but can cause cystic fibrosis

• polar flagella normally attach to a surface temporarily and then detaches, if it stays attached, irreversibly attached = flagella rotation halted

what changes occur in a cell when it experiences stress?

• reduction in motility

• expression of adhesins

• expression of virulence genes

• small molecule secondary messengers to ensure reliable signaling

• positive feedback loop results in robust transitions to virulent states

chemotaxis (Che) proteins: da basics

MCP = methylated chemotaxis protein

CheA = autokinase, phosphorylates itself on histidine residue

• transfers phosphate group to CheY

CheY = sensor that binds to basal region of flagellum & causes it to tumble (CW rotation)

CheB takes methyl group OFF MCP

• inactive but if phosphorylated by CheA, becomes methylesterase

CheR adds methyl to MCP

• constitutive creates methyl group on MCP

• methylase, always active

why is methylation is so important for chemotaxis? activation v. adaptation

activation requires phosphorylation

adaptation requires methylation

• receptor becomes less sensitive with time

• works via MCP

• MCP are methylated at a constant rate

• methylation decreases sensitivity

• fully methylated = insensitive

quorum sensing in relation to host eukaryotes

sensing of cell population density which can regulate gene expression

receptor placement and its relation to signal properties

hydrophobic signal molecule = cross membranes

• receptor inside

hydrophilic signal molecule = surface or uptake

• receptor on surface of cell

magnetosomes

membrane-enclosed vesicle

• filled with a single crystal on magnetite

• vesicle then brought iron via transport protein

• iron forms magnetic crystals, which are oriented in parallel inside the cell

• allow whole cell to act like a magnet

• SAME SIZE ACROSS EUKARYOTE, PROKARYOTE, AND ARCHAEA

carboxysomes

protein shells used to compartmentalize enzymes, found in all cyanobacteria

• used for CO2 fixation & chemitrophic generation of energy

nucleoids

chromosome of bacteria fills cell, not enclosed by membrane

• 1 (or 2) chromosomes plus plasmids, tightly folded

• contains all DNA

• not a nucleus because no membrane

cellulosomes

degrade cellulose, most common macromolecule on Earth

• protein machine, external to cytoplasm or periplasm

• scaffoldin contains cellulose-binding domains for binding and degrading cellulose

annammoxosomes

oxidizes ammonium to nitrite to generate energy, anaerobi ammonium oxidation machines

• has lipid bilayer, membrane-bound organelle

• ONLY in planctomycetes

acidocalcisomes

found in bacteria and eukaryotes

• spherical electron-dense, acidic organelles

• rich in calcium and polyphosphate

• osmoregulation

common strategies for establishing organelle boundaries

membranes: lipid bilayer!

protein shells: carboxysomes

liquid-liquid phase separation: few enzymes float around, they form hyperstructures that can exist temporarily or permanently, liquid-liquid phase separation

DNA packing strategies (!!!)

supercoiling

• makes DNA compact

• strains duplex to facilitate strand separation for initiation of DNA replication and transcription

• topo I relaxes DNA by breaking one strand

• topo II breaks two strands, generates supercoils, dimer, uses ATP

Mg2+ ions shield the negatively charged backbone

SMC = structural maintenance of chromosomes

• two domains bind DNA and bring it together

bending proteins: DNA binding proteins may or may not recognize specific sites

• bend DNA up to 180 degrees and may cluster together on DNA to bend it more

• highly abundant, essential collectively

know about what plays an indirect role in drug resistance

TolQRA plays a role in the transport of LPS (lipopolysaccharide that activates innate immune system) to the outer surface of the outer membrane

• so TolQRA is indirectly involved in drug resistance

MotAB (!!!)

secretion systems that use chemiosmosis with H+ to function

• motAB is the ion selector, rotor is flagellum

• FliG interacts directly with MotAB to produce torque

• in bacterial flagellum

TolQRA

TolQR and TolA are protein sets that form complexes

• plays a role in the transport of lipopolysaccharide to the outer surface of the outer membrane

• it is indirectly involved in drug resistance

which secretion systems use the same components?

type I: ATP-binding cassette

• inner: ABC, powered by ATP

• outer: OMF or OMP

type II:

• inner: Sec, tat, powered by GTP/ATP+pmf

• universal, found in all cellular organisms

• outer: MTB (or Secretin), powered by ATP or pmf (only OM component energized)

type III:

• fla/path, (flagellin exporter) powered by ATP+pmf

• outer: secretin, flagellar LP rings

type IV:

• inner: conj/vir, powered by ATP

• outer: vir

what components does ABC NOT connect to?

the ABC part is the inner membrane…MFP in the periplasm, OMF in outer membrane

• ABC transport unfolded proteins

basics in structure and function of ALL inner and outer membrane transport systems

inner membrane components require energy:

• GTP

• ATP

• ATP+pmf

outer membrane components generally do not require an energy source

additional cytoskeletal proteins mentioned and described

inner membrane components:

• Oxa1 (YidC): powered by translation or pmf

• MscL: forms very high-conductance channels, no direct power source

• Holins: no direct power source, commonly very bad for bacterial health

outer membrane components:

• type V: two-partner system

• AT-1, AT-

• OmpIP

gram-positive v. gram-neg bacteria

gram-positive only has one membrane

gram negative has inner membrane (then periplasm between) and outer membrane

• two membrane

chemotaxis & aerotaxis

chemotaxis = move toward/away chemical stimulus

aerotaxis = based on oxygen concentration

• obligate aerobes seek oxygen

• obligate anaerobes flee oxygen

• facultative anaerobes prefer oxygen, but can make do without

• microaerophiles seek a specific oxygen concentration

• aerotolerant microbes have no strong feelings one way or another

• oxygen detection via 2 independent MCPs

  • Aer: detects FAD (v. FADH2, reduced state) oxidation state

  • Tsr: detects pmf directly

common roles of virulence factors

adhesins: recognize and attach to surfaces

invasins: allow invasion into host cells

• essential in intracellular pathogens

proteases: break down proteins

toxins: lyse cells, stop critical cellular processes, induce aberrant signaling behavior

generally require secretion systems to translocate to host-ready areas