MIMG middy 1

CH: 1,2,3,5,6,7,9,10,11,12

what is the great oxidation event

2.4 BYO cyanobacteria started releasing oxygen into atmosphere

define microbiology

study of microorganisms that are unicellular, multicellular, and acellular

three categories of cellular organisms:

bacteria, archaea, eukaryotes

unicellular organisms:

bacteria and archaea

multicellular microorganisms:

fungi and protists

acellular microorganisms:

prions, viroids, satellites, and viruses

how old is earth and when did first life originate

4.5 BYO and in the first billion years

RNA world hypothesis

first self replicating entity was just RNA with a lipid bilayer around it

cellular organisms branching order

bacteria evolved first then eukaryotes and archaea diverged later

where did mitochondria and chloroplasts come from

bacterial endosymbiotes: when bacterias started living inside eachother and became symbiotic which evolved into a cell with organelles.

how do they figure out phylogenetic relatedness

sequencing with rRNA genes called small subunits and assessing the differences

explain distance method for making phylogenetic trees

use small subunit sequence to compare many organisms and see how close or far apart they are related

explain rooting phylogenetic trees

unrooted just shows relatedness but no common anscesstor. rooted trees have common ancestor. unrooted trees can be rooted by adding an outgroup

how are species named

two name system “Linnaeus” in the order Genius, species (italicized)

how do each celllar organism reproduce

eukaryotes sexually reproduce. bacteria and archaea use horizontal gene transfer

what did hooke do

made drawings of microbes and used a very simple microscope

what did leeuwenhoek do

forst to discribe microorganisms with a good microscope

explain the rebuttle of spontaneous generation.

first ppl thought living organisms spontaniously generated from nonliving organisms.then Redi proposed this was wrog using culture based experiments. then Pasteur shut it down even more with his swan neck flasks. then Cohn furthered this by establishing the classifications of microbes

what did chamberland do

made a bacterial filter which helped him discover viruses

list some subdiciplines of microbio

medical, public health, industrial, food, dairy, ecology, physiology, genetics

two most common shapes of bacteria

rods (bacilli) and spheres (cocci)

bacteria: what shapes do they make when they devide

they stick together on different planes making chains, pairs, or clusters

what characteristics do most bacteria have

cell wall, plasma membrane, cytoplasm, vesicles outside of cell, a nucleoid, pili, inclusions, capsule, ribosomes, and flagella

bacteria cell envelope general explaination

plasma membrane (semipermiable bilayer)

what are the jobs of bacteria plasma membrane

photosynthesis/respiration, detects/responds to chemicals in the environment outside the cell

what is lipid bilayer of bacteria made of

phospholipids (fatty acid chains) and also has microdomains with different composition where large proteins are made by flotillins building on eachother

passive diffusion

moving down gradient (no energy needed)

transport proteins

channels (hole in wall) and carriers (waymos that can get thru wall)

facillitated diffusion

transport protein moves substance down gradient (no energy needed)

secondary active transport

ions drive solute uptake. two types:

symporters (two substances in same direction)

antiporters (two dubstances in opposite directions)

active transport

uses energy and carrier proteins to move against gradient (to higher concentration)

group translocation

active transport for organic molecules that are still being modified

bacteria: whats outside the plasma membrne?

cell wall

bacteria: cell wall purpose

shape and protection

bacteria: cell wall made of?

peptidoglycan

bacteria: two types of cell wall

gram-positive: monoderm, purple

gram negative: diderm, with outer membranse containing lipopolysaccharides, pink

bacteria: extracellular vesicles formation

when plasma membrane pinches off and departs from cell

bacteria: more layers outside the cel wall?

capsules, slime, and glycolyces used for protection and movement of the cell

bacteria: what is an S-layer

external most layer for some bacteria and is made of proteins. it has a geometric shape

what is cytoplasm?

the gel in the inside of cell where all the stuff floats around in. its a super concentrated solution of biochemicals

bacteria: what are inclusions

basically like organelles but they are technically just clusters of stuff in the cytoplasm. used for storage, catalyzing reactions, and other stuff

bacteria: ribosome makeup?

proteins and RNA molecules

bacteria: genetic material

located in nucleoid. not enclosed in a membrane. just a closed circle of DNA. there are nucleoid-associated proteins in the cytoplasm that help build the chromosome

bacteria: plasmids

DNA outside the chromosome that is found in some bacteria. episomes = plasmids that are free in the cytoplasm or can be put into the chromosome.

bacteria: short hairs

hair like appendages.

fimbriae work by attatching to surfaces

pili work by twitching

sex pili transfer DNA from one bacteria to another (horizontal gene transfer)

bacteria: long hairs

flagella. they spin to make bacteria move. bacteria have different number and distributions of flagella. every flaggella is made of filament, hook, and basal body

bacteria: movement patterns

most have run and stop/tumble. They dont know where they are going but go in one direction for longer if it is either going towards something good or away from something bad so it eventually goes where it needs to go. 

what is chemotaxis

the reason for moving: away from t=soemthibng bad or towards something good

bacteria: endospores

dormant structures that are very strong and hard to break. they are made by bacteria in response to environmental signals.

what makes eukaryotes different from bacteria and archaea

they are biffer and have more morphological diversity.

membrane bound organelles

eukaryotes: ehy are organelles helpful

they allow cell to do many biochem reactions at once. they also make more surface area for membrane-associated activities like respiration

eukaryotes: envelopes

membranes have lipid rafts. when a cell wall is present its made of polysaccharides (not peptidoglican like bacteria they are much simpler than those)

eukaryotes: cytoplasm made of?

cytosol

eukaryotes: cytoplasm is location of what

organelles and cytoskeleton

eukaryotes: cytoskeleton elements

actin filaments

intermediate filaments

microtubules

(all give cell structure, motility, endocytosis, and cell division

eukaryotes: organelles

endoplasmic reticulum, golgi, mitochondria, chloroplasts

eukaryotes: two categories of organnelles/vesicles

secretory pathways (make materials)

endocytic pathways (uptake materials)

eukaryotes: endoplasmic reticulum made of

tubules and flattened sacs.

rough ER has ribosomes, smooth ER doesnt

eukaryotes: endoplasmic reticulum gives stuff to….

golgi apperatus.

eukaryotes: golgi apperatus made of

stacks of cisternae

eukaryotes: golgi apperatus job

preps and packages cell products for secretion

eukaryotes: lysosomes

gets proteins and enzymes from the golgi. they have enzymes that help with digestion inside the cell

eukaryotes: how are misfolded proteins killed

they are marked for distruction by a polypeptide called ubiquitin and killed by proteasomes

eukaryotes: three types of endocytosis

phagocytosis

clathrin-dependant endocytosis

caveolin-dependant endocytosis

eukaryotes: two types of extracellular vesicles

microvesicles from the plasma membrane

exosomes from endosomes that fuse with plasma membrane

eukaryotes: nucleus

has chromosomes. surrounded by double-membrane envelope with pores for import and export of genetic material made of chromatin

eukaryotes: nucleolus

found in the nucleus and it makes ribosomal RNA and subunits

eukaryotes: where are ribosomes

either free in cytoplasm or bound to endoplasmic reticulum.

eukaryotes: aerobic mitochondria

they have two membranes.

inner membrane is folded into cristae where energy is conserved by respiration

eukaryotes: hydrogenosomes

have double membrane to do fermentation to make hydrogen gas. anaerobic process (no O input)

eukaryotes: chloroplasts

have pigment and do photosynthesis. trap light energy in the thylakoid membranes and CO2 fixation happens in stroma

eukaryotes: motility

Cinlia and flagella. move like whips, celia are shorter and more numerous

define virology

study of viruses and anything acellular

virus: repro

cant repro alone. need living host cell

virus: what do all of them have in structure

Nucleocapsid (made of nucleic acid, either DNA/RNA)

held within a protein capsid made of protein subunits called protomers

virus: two types of nucleocapsid

helical capsids (shape of hallow tube. flexible or rigid)

icosahedral capsids (made of 2 capsomeres. pentons at vertices and hexamers on the edges and faces)

virus: what do large virons have for nucleocapsid type?

binal symmetry = icosahedal heads and helical tails

virus: envelope?

some have a membrane-like envelope around nucleocapsid made of liquid from host cell and proteins coded for by viron itself that look like spikes

virus: metabolism?

no virus has a metabolism. some have enzymes to help with repro.

virus: life cycle discovery

delbruck and ellis’s one-step growth experiment

virus: 5 steps of life cycle

1. virus attatches to host

2. virus enters host cell

3. virus makes nucleic acids and proteins

4. virus puts together nucleocapsids from those ^

5. virus releases from host

virus: life cycle step three info

step 3 = making nucleic acids and proteins

some virsues make it with their own dna and enzymes. others rely on host to make them

virulent viruses

phages and archaeal viruses

go in, make copies, burst host cell open.

called lysic cycle

temperate viruses

can do lysis too.

also can do lysogenic cycle

virus puts its genetic material into host cell’s chromosome and as that cell devides, the virus is passed on with it

what are cytopathic effects (CPEs)

any abnormal changes you can see in an infected cell

virus: lab growth and counting

• must grow it in a living host like tissue, culture, etc

  • phages make plaques (places where cells got killed) which are spots u can count

viroids

infect plants

circular single stranded RNA

dont code for proteins

satellite viruses

code for own capsid proteins

cant replicate without helper virus

nucleic acids (RNA/DNA) are in helper viruses’ proteins, not the satellite.

prions

infectious proteins only (no dna or rna)

come either normal or misfolded (infectious)

misfolded ones convert normal ones to misfolded ones so it snowballs

define refraction

light bending when it goes from air to glass

lense of microscope

focus light at a focal point and magnify images

microscope types

1. bright feild (compound)

2. dark-field

3. phase-contrast

4. differential interference contrast (DIC)

5. flourescence

6. confocal

7. super-resolution

microscope: bright field (compound)

objective lense makes first enlarged image

occular lense (eyepeice) enlargens it again

microscope: dark-field

uses only refracted light so the specimen is bright on black background

microscope: phase-contrast

turns differences in refractive index into differences in brightness so you can see sunstained, live, colorless cells

microscope: differential interference contrast (DIC)

uses two beams of light for high contrast image of live specimen

microscope: fluorescence

specimen is labeled ith a glowing dye called flourochrome and the image comes from the glow

microscope: confocal

for thick complex specimens. only uses light from the plane of focus and blocks light above and below it.

microscope: super resolution

fancier and has way better resulution

what do u do to specimens before bright-feild microscope

fix, then stain