Prelim 3 BioG 1440

facultative aerobes

bacteria and yeast

ROS

superoxide anion, hydrogen peroxide, hydroxyl radical

detoxification enzymes

superoxide dismutase, catalases, peroxidases

pathologies of OS

neurodegenerative disease, aging, depression injury

avoidance

anaerobes, particularly bacteria

diazotrophs

small subset of bacteria and archaea nitrogen protection:

nitrogen plant sep.

leghemoglobin- buffer oxygen low enough to allow nitrogenase to function, not so low to stop respiration

nitrogen space sep.

anabaena with heterocysts

nitrogen time sep.

crocosphaera watsonii

rubisco

initial step in co2 assimilation

phytoplankton

in surface waters of oceans, accounts for 50% of all photosynthetic co2 fixation despite only being about 2% of total plant carbon (more efficient)

common pH

bicarbonate

acidic pH

carbonic acid

basic pH

carbonate

morphological ccm

???

biochemical ccm

??? ccms:

cyanobacteria

carboxysomes (with high levels of rubisco and carbonic anhydrase)

algae

pyrenoids

c3

typical plant

c4

spatial, mesophyll cells bring in co2 and concentrate it in organic acids, which are provided to a second cell called the bundle sheath cell where calvin cycle occurs.

cam

time, co2 in night, calvin cycle in day, stomata only open at night reducing water lost by transpiration look up oxygen evolutionary steps

o2 carrier proteins

hemocyanin

o2 binding proteins that float free in hemolymph, 2 copper ions used (mollusks and some arthropods)

hemoglobin (Hb)

in many vertebrates and some insects

chloride bicarbonate anion exchanger

example of antiport, drives transport of carbonate anion across rbc into blood plasma

principal signal to increase respiration

decrease in blood pH blood pH decreases when co2 increases in tissues, detected my major blood vessels and medulla

dead space

approx 1/3 of each breath, not efficiently exchanged

peroxiredoxin

?

heme cofactor

central iron atom that carries o2 bound by iron on one side and nitrogen histamine on other, creating binding pocket for o2 in carrier protein myoglobin has much higher o2 affinity compared to hemoglobin

hyperbolic/simple binding curve

Mb

sigmoidal/s

shape binding curve- Hb, due to cooperative binding

hemoglobin is a tetramer

4 subunits (2 alpha, 2 beta)

Hb T state (tense)

binds hemoglobin, then allosteric change in shape to R

Hb R state (relaxed)

positive cooperatively allows much easier binding bc of higher affinity O2 effectors, increase O2 offloading into tissues by weakening activity of hemoglobin for o2

bohr effect

2,3 BPG

negative molecule, binds in center of tetramer between alpha and beta subunits, comes from isomerized 1,3-BPG from glycolysis as an offshoot, positive charged groups hold it in place.

H

pH, Hb binds to proton acting as a buffer so pH doesn’t drop at drastically as it otherwise would, binding also helps offloading to tissues

CO2

fetal Hb

h143 is no longer +, but neutral. this causes weaker 2,3-BPG binding, making the fetal Hb have a higher affinity for O2. O2 from maternal can be transferred to fetal more easily.

fetal Hb cell types

instead of beta subunit, has a gamma chain, which persists early after birth.

deoxyhemoglobin

Hb form that releases o2 (low affinity)

allosteric regulation

binding process alters shape and this o2 affinity, leading to sigmoidal curve

In was one of the earliest examples of

genetic disease (sickle cell anemia)

Hb was one of first proteins to

have a known sequence (molecular clocks)

parabronchus

in birds, have extensive air capillaries to increase the exchange of air with the bloodstream

cross

current- beds of capillaries run across the exchange surface to efficiently exchange (contrast to mixing in mammals in this chamber)

bar

headed goose- provided example of bird at high altitude, has an ADAPTATION that is a mutation of their Hb. Hb has a higher affinity for O2, as graph shifts to LEFT compared to related species. - o2 partial pressure is much lower at high altitudes, needs high affinity to be able to bind enough

living pathogens

bacteria, fungi, helminthes: PROLIFERATE

non living pathogens

viruses, prions: REPLICATE

resistance mechanisms

eliminate the parasite

tolerance mechanisms

endure damage of pathogen

susceptibility

determined by resistance and tolerance (hosts die when one is lacking)

mucosal and epithelial immunity

cells like body, exposed to outside, prevent initiation of infection

cellular and humoral immunity

block growth of pathogen / clear infection

cellular

eat or kill microbes or infected cells

humoral

diffusible molecules in ECF that interact with microbes to block them or kill them

epithelial and innate are encoded in

germline

adaptive immunity requires

somatic DNA recombination (multiple steps to generate, select, and amplify cells and effectors) mucosal physical: epithelial barrier, gelatinous mucus chemical: pH enzymatic: lysozymes, digestive enzymes innate cellular: phagocytosis humoral: antimicrobial peptides adaptive cellular: T cells and B cells (lymphocytes) humoral: antibodies

only rely on innate

invertebrates and protochordates

adaptive immunity organisms

cartilaginous fish, bony fish, amphibians, birds, tetrapods, mammals

agnathans

peculiar case, subcategory of vertebrates called JAWLESS vertebrates. do not have canonical adaptive immunity, but have a kind of adaptive response (adaptive-like immunity)

jawless and jawed

case of convergent evolution, two independent appearance of adaptive immunity

why is adaptive immunity not as broadly distributed

fairly recent innovation

NF

kB- transcription factor that is activated when a host detects an infection, this factor activate immune cells and transcribe immune effectors

DAMPs

damage associated molecular patterns, part of innate, recognize tissue damage, indirect

PAMPs

pathogen associated molecular patterns (non-self), innate, recognize FEW microbial patterns,

if you have PAMPs and DAMPs

innate response is activated

PRRs

pattern recognition receptors, receptor for innate immunity, activate innate response

antigens

recognize ALL domains (epitomes) that are non-self, trigger adaptive immunity

adaptive recognition of ANY NON

SELF- specific receptors like B-cell or T-cell (antibodies also interact)

phagocytosis

innate immune cells (phagocytes) 1. recognize pathogens 2. internalize microbe into a vacuole called a phagosome 3. phagosome acidifies the vesicle (low pH) 4. fuses with lysosomes (degrading enzymes) 5. generates oxygen species

mature form of phagosome

phagolysosome

antimicrobial peptides

example of a humoral effector molecule (innate), small, POSITIVELY CHARGED (catonic), bind to membrane of bacteria, amphipathic

bacterial membrane charge

negative

amphipathic

hydrophilic and hydrophobic part

when antimicrobial peptides insert in membrane

pore is formed, leading to bacterial lysis (bacterial cell destruction by membrane breakdown)

inflammation

activation of innate immunity leads to release of mediator molecules (cytokines, chemokines, histamine) that effect local circulatory system

4 cardinal signs of inflammation

tumor, rubor, calor, dolor (signs of an infection response is ongoing)

tumor

swelling (edema bc of vasodilation and leakage)

rubor

redness (more blood coming)

calor

heat (blood to skin surface)

dolor

pain (synthesized nerve cells)

why inflammation

so innate cells can use circulatory system to leave and do their job

Somatic dna recombination in jawless (agnathans)

gene conversion

Immune repretoire

huge diversity of effector molecules and recognition receptors to be able to bind any pathogen

Negative selection

subtract cells with receptors that recognize SELF

T lymphocyte cytotoxicity

in case of viral infection, cytotoxic T cell can bind to infected cell by a self non-self complex, and kill that infected cell

Self

nonself complex- MHC molecule that presents little bit of the foreign antigen (non self), exposing T cell to antigen

MHC

presents antigen

Perforin

???

Antibodies do…

neutralization, recruitment to complement, and opsonization

What generates antibodies

B lymphocytes, which generate SPECIFIC antibodies

Neutralization

antibodies bind inactive viruses and toxins, preventing them from reaching or entering cell

Recruitment to Complement

complex makes a pore formation (like antimicrobial peptides), where complements (proteins) can lysis bacteria

Opsonization

tagging microbes fro phagocytosis (boosting innate efficiency)

Ancestral antiviral immune processes

RNA interference and CRISPR

RNA interference (RNAi)

in all eukaryotes 1. virus replicates and generates dsRNA (likelihood of virus bc only usually found in viruses) 2. DICER is an enzyme that that immediately destroys the dsRNA into siRNA 3. siRNA are bound to RISC to be guides to find and degrade any RNA homologous

CRISPR

in bacteria, aims at eliminating DNA 1. bacteria captures fragments of DNA of invading bacteriophage into CRISPR locus 2. CRISPR locus is transcribed into RNA, where it can be integrated to Cas9 protein 3. RNA Cas9 complex can receive invader if has homologous to pieces of foreign DNA, binding and cleaving it

SIMPLE cell cell communication requires

contact, so info can be exchanged directly. molecules can be exchanged or signals, that alter cel activity with protein or gene expression changes

simple junction types

gap junctions (animals), plasmodesmata (plants)