function of light microscopes

- bright field

- phast contrAST

-dark field

-florescence

(think eclipse--> bright light the florescents, but eclipse is a phase change to darkness)

- objective lens

- occular lens

enables magnification

1. occular lens
2. objective lens ( 300x, 400x, 20x, 100x)
3. light

-improving contrast results in better final image

- staining with dyes are a possible way

dyes- org cmpd that have different affinities for specific cellular mat

1. methylene blue- stains RNA
2. Crystal violet- cell wall
3. safranin- nucleic acid

(G+) has a thick Peptidoglycan layer compared to( G-). s/p decolorizing with alcohol (G-) loses purple color causing it to be pink, where as G+ w/ thick peptidoglycan remains purple

- also gram neg has outer membrane compared to gram +, which helps to resist interference to cell physcial characteristics such as color

1. stain
2. dry
3. flame heating
4. add crystal biolet
5. add iodine- stabilize
6. add alcohol for 20 mins- 7. look at grams for variation

Be able to draw the different gram bacterias w-

1. outer membrane/ inner membrane/ peptidoglycan

gram -: OM, Peptidoglycan, innermembrane

gram +: large peptidoglycan, inner membrane

Phase contrast Microscopy

- function

-inventor

Fritz Zernike

hint:( nike moves so fast you can only see phases)

1. amplifies diff in refractive index of cell surrounding--> improves contrast w/o staining

2. allows visualization of live samples

Dark field microscopy

-  w/ is its specialized function

- where does light source come from?

- specialized for observing motility

- light source reaches the same from the sides

Fluorescence Microscope

- function

- what is needed

- visualize speciments that fluoresce: some cells nat glow called (autofluorescence)

- dyes are required

acridinc orange- stain DNA, RNA

DAP 1 - strongly binds to DNA

Cofocal scanning laser microscopy (CSLM)

- funciton

- required for usage

Electron microscopes use what for imaging?

what are the 2 kinds of micro scopes that use e-?

electrons

1) TEM (transmission electron microscopy)

2) SEM (scanning electon microscopy)

can look at structures at molecular level (Proteins and nucleic acids)

( bright microscope sees image of .2 micrometer TEM gives you a 1000 more contrast)

scanning electron microscopy (SEM)

-specimens are coated with what?

-function

- coated with heavy metal such as Gold

- an e- beam scans image to produce visual of very large specimens ( but only the surface)

prokaryotic have Nucleoid and no nucleus where Eukaryote cell dooes

Eukaryotics are much more complicated overall with several specialized organelles

1. Eukaryote has nucleus, Pro has nucleotide

2. Eukaryote much larger in size and complexity+ DNA is more then P

3. E has organelles

transcription in Pro in cytosol

1. circular

2. single (haploid)

1. linear

2. diploid

have proteins to help fold b/c so large

25,000

Polycistronic mRNA transcrition

def/ domain***

able to produce several proteins at a time, simultaneous with translation

- Prokaryote

Monocistronic mRNA

def/ domain

mrna transcription for onle ONE protein

-domain: Eukaryote

how can phylogeny be deduced?

what is an excellent molecule for determining phylogeny?

1. isolate DNA from cell

2. DNA underfoes polymerization chain rxn (PCR)

3. amplification of rRNA gene

4. sequence DNA from gene encoding

5. anaylize rRNA gene sequence

6. create a phylogenetic tree

scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands of copies of a particular DNA sequence

(make 1 DNA seq to a thousand)

1. primer- (short DNA frag) + DNA polymerase (taq)

2. DNA polymerase- enzymatically assembles a new DNA sstrand from DNA building blocks, by using single-stranded DNA as a template and DNA oligonucleotides (primer) which are req for initiation of DNA synthesis

1. bacteria

2. archaea

3. eukarya

bacteria + archaea = Prokaryote

eukarya = Eukaryote

Bac + arch are NOT closely related!!!

which of the 3 domains are ancesors of multicellular oganisms?

1. aerobes- extract E with the help of oxygen

2. anaerobes- abscence of Oxygen

Chemolithotroph define.

highly used in what domain

- recieve energy (ATP) through oxidation of inorganic molecules

(prokaryotes- 1. archaea 2. bacteria

define Phototroph.

what are the 2 types of phototrophs

§  ccontains pigments that allow them to use light as an energy source (sun) prokaryotic are both

2.     Oxygenic phototrphs – produces o2 ( all eukaryotes)

3.      Anoxyganic – do not produce o2

(DOES NOT USE CHEMICALS)

organic- sugar acetate etc

inorganic- h2, h2s, Fe, metals etcc...

heterotroph- req one or more organic cmpds as carbon source

Autotroph- uses CO2 as carbon source

chemoorganotrophs are by definition heterotroph

1. euryarchaeota

a. methanogens

b. extreme halphiles

c. thermoacidophies

2. crenarchaeota 

a. methanogens

b. extreme halphiles

c. thermoacidophies

a. methanogens

strict anerobes are unique in that E is conserved  during the production of methane

Importance: anaerobic degradation of organ matter in  nature

crenarchaeota

metabolism

E source

1. algae

2. protozoa

3. fungi

4. mold

" professional swims in algae water and gets funi and mold growing on his toes"

1. lichins

2.fungi and cyanobacteria

3. fungi and algae