Prokaryote vs Eukaryotes

Prokaryote Eukaryote

Nucleus -(nucleoid) +

Organelles - +

Ribosome 70S(30S& 50S) 80S(60S&20S)

Sterols +/- +

Introns -/+ +

1. Prokaryotes no organelles
2. Organelle= structures surrounded by a continuous membrane; all have a double
membrane
a. Mitochondria, chloroplasts & nuclei are organelles
b. ER and golgi body are not organelles
3. Svedberg unit= dependent on rate of movement through a centripetal field; takes
into account mass, density & shape
4. Analogous similar function but have different origin
5. Homologous: same origin but different function
Plasmalemma
1. Bimolecular leaflet composed of glycolipids, glycoproteins, integral proteins &
phospholipids
2. Integral protein is added to the membrane by a secretory vesicle
3. Membrane rigidification
a. Cholesterol: highly hydrophobic;
b. Ergosterol: fungi
c. Variation in fatty acid length: prokaryotes
d. Sterol: Archaebacteria
e. Homeostatic regulation
Aquaporins
1. Unidirectional flow of water (must have one facing each direction)

2. Movement of water without the use of ATP

3. Hydrophilic interior and hydrophobic center

4. Shaped like a crown: circular protein with a central channel

5. Cells have no channels for Ti, so it can be used to determine what is the inside and outside
of cell

6. Cannot regulate water so K+ or glucose must be regulated for osmoregulation

Scanning Atomic Force Microscope

a. Looks at the surface

b. Cantilever- long strip of metal holding out a point that will do the scanning

c. Attached to a transformer which adds voltage and the resistance data is turned into
an image (vibrations)
 d. Non tap: tip really gets close to the sample but it does not touch it→Van der Waals
force

Metal Shadowed Crystal

e. Protein has no electron opacity

f. Metals (heavy nuclei) covers protein to contrast material

g. Need differential covering to see topography of protein

h. Coating with metal must be done at an angle

i. Must be done in vacuum (sample must be dry)

Cell Wall

Plant

1. Cellulose

2. Cell walls set in centripetal fashion (oldest layer outside)

3. Cell wall microfibrils are excreted from cytoplasm

4. Secondary walls made of lignin, which is deposited as monomers and then

polymerized

a. Plants without secondary walls stay upright using turgor pressure

b. Lignin= insoluble

5. Microtubules are related to cell wall deposition

6. Extrusion Mechanism

a. In essence, the extrusion mechanism is found within the cytoskeleton,

which shows that the golgi is connected to nascent extrusion pores (which
are formed in the ER of the cytoplasm). The extrusion pores receive vesicles
from the TGN to form oligmers. The key to the extrusion pore mechanism is
that they are linked by motor proteins (kinesin and dyein) which are attached
to microtubules. Extrusion pores follow the track of microtubules.

b. There may be similar mechanism in fungi and diatoms

c. TGN: trans golgi network

d. viruses use this mechanism to enter cell

Other

1. Fungi

a. Chitin: high protein chitin and aminated carbohydrate

2. Bacteria

a. Murein = peptidoglycan = lipopolysaccharide

 b. Mycolic acid: waxy material full of lipids; acid fast; TB or Hansen’s disease

3. Protist

a. Cellulose: Chlamydomonas (algae)

b. Chitin: protofungi

c. Silica: diatoms; organized in highly ornamented structures; frustle ( built like Petri
dish dishes and each half becomes a part of the daughter cells when they divide)

d. Pellicle: protein cell wall

e. None: amoeboid

Nucleus

1. DNA

a. 5% of DNA encodes for protein

b. 65% of DNA is “junk”

i. Intron: alternate splicing and immunity (mixing of pieces of genes that are
recognized as antigens regulatory role

ii. Non-coding DNA: micro DNA that maybe involved in structural aspects of
chromosomes

iii. Relic genes: no longer have function because organism is no longer exposed
to that environmental stress

iv. Multiple copies of genes (gene dosage) gives organism the ability to
experiment: mutations can occur either creating a new gene or making it
inactive (non-mammalian)

c. Horizontal gene transfer: from viruses and bacteria; between closely associated
organisms

i. Transposon’s – Can improve a gene or break it. Allows for foreign DNA to be
incorporate or utilized, but is also hard to identify.
d. Vertical gene transfer: parents → offspring

e. Epigenetics: chemicals affect DNA and passed on to future generations

2. Nuclear pore

a. 134 different proteins make up the pore complex (function is to comprise the wheel,
spoke, or promote selectivity)

b. 120 nm diameter

c. 25nm working diameter (anything smaller the 25nm can go through pore

d. 9nm- free diffusion

e. Nuclear Envelope Lumen: continuous with lumen of ER (in physical contact); has a
regulatory function

f. Linerize RNA to transport it outside the cell

g. Terms

i. Base energetic molecule of a cell is ATP…but GTP is more important

ii. 3 main regulatory systems in cells: GTP, calcium, or phosphorylation
iii. Nuclear Pore: Passageway by which things are exchanged between
nucleoplasm and cytoplasm
a. Anything under a 100 MW is exchanged by free diffusion
iv. RCC1 – Ran nucleotide exchange factor, now known as GEF (Guanine
Exchange factor)
v. NES – Nuclear import signal; a sequence of amino acids that can be
recognized by the nuclear pore allowing for export for export of certain
materials from the nucleus
a. NES is often found on proteins
b. RNA does not have a NES as it does not have any amino acids
c. Sometimes RNA will bind to a protein in order to be exported
from the nucleus
vi. GAP – GTPase-activating protein; protein involved in changing GTP to GDP,
works by hydrolysis
vii. RNP – ribonucleoprotein
viii. CBC – cap-binding protein
ix. PABP – poly-A binding protein
x. SR proteins – splice (intron/exon) recognition
h. As the molecule is squished through the pore, it will have a NES on the leading end.
Ribosomes wait in the cytoplasm to help reassemble the molecule.

i. Nuclear Pore Import/Export

i. Mechanism is largely the same for either importing or exporting materials in

or out of the nucleus
ii. Import: Start in a cytoplasm with a protein marked with NLS (nuclear
localization signal). This protein will bind to a cargo molecule, which will then
enter into the nucleus. Once in the nucleus, it will be recognized by RAN-GEF
which will associate a GTP with the RAN located on the cargo complex. This
will cause unbinding of the cargo molecule and the localization signal. The
localization signal is then left in the nucleus as the cargo molecule exits the
nucleus.
iii. Export: While exiting the nucleus, the cargo molecule is recognized by RAN-
GAP which hydrolyzes it’s GTP molecule into a GDP.
iv. Importin: Proteins marked with a NLS
v. Exportin: Proteins marked with a NES
vi. RAN-GEF: exchanges one nucleotide phosphate for another, always found in
nucleus, GDP  GTP
j. regulation
i. Ionophore: Molecule that binds to a specific ion and releases it under certain
conditions
ii. NFAT: large group of proteins that are nuclear directed
iii. GFP: Green flouresence protein, Extracted from aequria Victoria
iv. Ran is compartmentalized to control transport direction
a. RAN-GEF is localized in the nucleus and replaces GDP with GTP.
It is also a DNA-bound protein and remains attached to
chromatin near nuclear pores.
 b. RAN-GAP is found within the cytoplasm, and is a hydrolysis
protein that converts GTP to GDP

3. Nuclear translation

a. In the nucleus ribosome associated with proteins that stabilize it structure→

becomes more stable in cytoplasm

b. steps taken to prove that they were observing translation in the nucleus as a
eukaryotic process

i. nucleus one will need tRNA, amino acids (both of which enter the
nucleoplasm by free diffusion through a nuclear pore), ATP/ADP in order for
translation to occur
ii. They injected fluorescent lysine into the nucleus to see where the proteins
are and where translation occurs. They analyzed the cell by confocal laser
spectroscopy (optical thin laser of light illuminates one part of the specimen
at a time).
iii. In order to prove that the translation occuring in the nucleus was not due to
bacteria, they use chloramphenicol which inhibits translation by bacteria
iv. Cycloheximide inhibits eukaryotic translation, which means that there would
be less flouresence
v. Lysine is a critical amino acid involved in protein degradation. Lysine is the
target for ubiquination (ubiquitin attaches to a protein, which signals for it’s
destruction) for transport to proteasomes
4. Nucleolus

a. Disappears during mitosis because during prophase the proteins for making rRNA is
gone

b. rRNA synthesis

Mitochondria

1. DNA

a. Few genes→ most of genes have been transferred to nuclear DNA

b. Lack introns

c. Circular

2. Endosymbiosis

a. Plants and nitrogen fixing bacteria

i. Bacteris amy become a new organelle

ii. Host gaining control over bacteria

b. Paradoxa (red algae)

i. Single cell

ii. Nuclear membranes of five different endosymbiots

3. Cannot arise out of denovo (exception is yeast)

 4. Lipid difference between outer and inner membrane

a. Inner membrane is more prokaryotic than outer membrane

i. Lacks sterols

ii. Rigidity due to variation in fatty acid chain length

b. Outer membrane is more eukaryotic

5. Mitochondria or chloroplast

a. No organism found that has chloroplast but no mitochondria

b. Chloroplasts have more genes than mitochondria→ mitochondria have been

organelles longer so they have lost most of their genes due to nuclear gene transfer

c. Chloroplast can live autonomously for short periods of time and mitochondria
cannot

6. ATPase

a. Can make ATP with high acid concentration

b. Chemiosmosis: use proton gradient to make ATP

c. Components

i. Fo: found in the membrane and is hard to crystallize

ii. F1: can be crystallized and structure is known

d. Inside of cristae membrane

e. Protons build up in inner membrane space

7. Transporter of outer membrane

a. Protein toward matrix

8. Steps of Krebs Cycle learned using pulse chase method

a. Radioactive label substrate of Kreb’s Cycle and after some time unlabeled substrate
is added to keep metabolic activity the same (feedback inhibition can affect)

b. Using chromatograohy to determine which products is the most labeled and this is
the most common pathway

c. If glucose is labeled it will be hard to figure out what material is because wverything
will have a label

Plastids

Chromoplast

1. Developmental outcome of chloroplast due to environment or location in plant

2. Ecological or evolutionary significance

 3. Ex. Fruit

Leucoplast

1. Starch storage

2. Clear or white

3. Found in organs that are found in darkness, like potatoes

Chloroplast

1. Chlamydomonas moewusii

a. Single cell

b. Nucleus is cup shaped

c. Eye spot

a. catornoid containing body

b. photo-tactic (allows organism to detect where light is coming from. So it can

move there to maximize photosynthesis)

d. One chloroplast

e. Acellular: multicellular attribute seen in unicellular organism (ex. Eyespot or anus)

f. Model organism for flagellar development and function and photosynthesis

2. Spirogiro

a. Single helical chloroplast

3. Majority of chloroplast (ex. Corn)

a. 6CO2 + 6H2O + 12NADPH→

b. Membranes

i. Outer

ii. inner

iii. Thylakoid: individual pancake (Granum or fret lamella= stack of thlylaoid )

c. Stroma- rich in enzymes

d. Ribosome

e. Pyrenoid: starch granules (glows under microscope)

f. light reactions take place in the thylakoids

i. determined by freezing granum with liquid N2

 ii. after freezing the light reactions did not take place→must dependent on
enzymes ( biological process)

g. Dark reactions are not affected by freezing→ not under enzymatic control but
dependent upon electron flow

h. Z-scheme

i. Photosystem= A light collection mechanism which shuttles the energy of light

absorbed to one particular component, the PS680/PS700

a. Number=λ at which light is maximally absorbed in red light

b. PS680/PS700 energizes an electron to jump into a higher energy

shell→ picked up by another component (oxidation/reduction
coupling)→loss of energy

c. DCMU= alternate electron reducer which turns from blue to

colorless when it reduces (evidence of electron flow)

ii. Electron carriers include cytochromes containing iron which likes to reduced
or oxidized

iii. Plastoquinone and plastocyanin (water soluble only found in thylakoid lumen)

iv. Lollipop” Proteins decorate the outside of the thylakoid, and are used to
dump ATP into the stroma
a. The pH of the lumen of the thylakoid is more acidic than the pH
of the stroma, as H+ is pumped into the lumen.
i. Radiation is given off as light or heat. Leaves are thin to radiate the heat away more
efficiently.

j. standard measure of light= Einstein= μmol*m-2*s-1

k. Only wavelengths between 450-700 nm are photosynthethically active as that is

visible light

l. Non-Cyclic vs Cyclic

i. Non-cyclic = ATP and NADPH

ii. Cylic= ATP

m. Advantage of two PS

i. Organisms that have one have to use more complex sources if electrons

ii. 2 PS allow the use of water or other compounds with similar redox potentials

n. Chlorophyll

i. Resembles heme except Fe is replaced by Mg

ii. Extremely hydrophobic→ can only be found in granum between two

thylakoids
 iii. 10% of cholorophyll is associated with soluble protein

o. Rubisco= RuBP carboxylase

i. Permiscus enzyme

ii. Substrate is RuBP

iii. CO2 + 5C sugar→unstable intermediate→2 3C sugars (DHAP)

(C3photosynthesis)

iv. Photorespiration

a. Acts as oxygenase

b. O2 + 5C sugar→2C + 3C (2C used like acetone and enters

mitochondria to make ATP)

c. Critical [O2]=21% to make glucose

p. C4 photosynthesis pathways

i. More energy than C3 (C4 plants get more energy because they are exposed
to more sunlight)

a. Plants that are found in hot, dry areas (ex. Corn and sugar cane)

b. CO2 (in the form of HCO3-) + PEP→ oxaloacetate (broken down to

CO2 and 3C sugar in another part of the plant and the rubisco
will not be exposed to O2)

ii. CAM

a. Performed by plants in the crasola genus (found in hot deserts)

b. Stomata remain closed during the day to ensure that water is

not lost

c. Create C4 products (oxaloacetate and malate) at night →C4

products lose CO2 during the day when energy is available

d. Tissues are more acidic at night

iii. Glycoxylic Acid Pathway

q. Calvin Cycle steps learned using pulse chase method

r. Circular DNA

i. 200 genes

ii. Controls pollen viability of a plant

s. Plant development is dependent on light

 i. Chlorophyll development : conversion form Fe→Mg

ii. Genetic control of rubisco

iii. Stems are negatively geotropic (move toward light)

iv. Greening of plants

v. Etiolation

a. When chloroplast doe not fully develop due to lack of light

b. When chloroplast is not exposed to light in 24 hours a etioplast

develops and produces a white or cream color plant

c. Protoplastid has two membranes but no fine details

i. Exposed to light during terminal step→ thylakoid

membrane forms

ii. Not exposed to light during the terminal step→make a

protlamellar body (quasi crystalline array) and the plants
starts to disintegrate

PS I

PS II
Endoplasmic Reticulum

1. Protein synthesis

2. Lipid metabolism

3. Ca2+ storage and regulation (10 -9

M [Ca2+] in cytoplasm)

4. Carbohydrate metabolism

5. Regulation of membrane protein composition

6. Production of exportable protein

a. Soluble proteins made are for outside of the cell

b. Cells that export proteins have more rough ER

i. Brain has low amount of rough ER

ii. Stomach has high amount of rough ER

7. Regulation of the size of opening of nuclear pore (remember that ER is continuous with
nuclear lumen)

Ribosome

1. Self assemble if all proteins are present

2. Ribosomes in cytoplasm make protein for the nucleus

3. Number of Ribosomal associated protein

a. Eukaryotes: 80

b. Prokaryotes: 50

4. L protein

a. L1= core protein; structural unit

b. L2= intermediate

c. L3= functional role; associate with mRNA

Golgi Apparatus

1. Function

a. Shipping and receiving center of the cell

b. Export things from the interior to the exterior of the cell

c. Modification and storage of proteins and lipids from ER

2. Golgi body= stack of flattened membrane bound spaces

 3. All golgi boides in the cell = golgi apparatus

4. Face

a. Proximal or cis: closer to ER (components from cytoplasm and ER and take them
into membrane→modify components→export)

b. Distal or trans: facing away from ER

5. Exported material→vesicles form ER→ golgi apparatus

6. Fenestrated region= interconnected tubular network which composes golgi apparatus

7. Caro and Palade

a. used pulse chase method to elucidate the function of the golgi

b. Incorporated radioactive methionine (Sulfur as the radioactive element) and used

autoradiography
8. Neutra and LaBlond

a. Studied mucus/goblet cells, which are a mixture of polysaccharide and proteins

b. Studied how they are made, where they can be found
c. Used radioactive sugar, amino acids, and sulfur to see where sulfate ends up in
mucus
d. Their research supported all that was known about the Golgi Apparatus
i. everything firm ER goes to golgi
ii. Transport and modification
9. Northcoat and Pickett-Heaps

a. Studied the production of cellulose in plants

b. Incorporation of β ligitures takes place in golgi

c. Concluded that a process like golgi apparatus happens in plant

Cytoskeleton

1. Dynamic structure (ability to transform)

2. Function

a. Support

b. Form

c. Transport

d. Organization

e. Spatial arrangement

3. Microfilaments

a. Architectural role

b. 6nm
 c. Found under the plasma membrane

4. Intermediate filaments

a. Cytoskeleton

b. 6-25 nm (avg 9-12nm)

c. Relaxed fibers

5. Microtubules

a. Scaffolding role

b. 25nm

c. Relaxed fiber

Centrioles

1. Centriole = basal body = polar body

2. Proximal and distal end

3. 9+0 array of triplet microtubules

4. Possible experimental ways to learn if centriole functions in separation of chromosomes

in mitosis

a. Laser beam used to knock out centrioles→ laser can knock out other things, so
result is not definitive

b. Drug that interacts with centrioles, usually tublin→mitosis still works

5. Either all of an organism’s cell have them or none of them have them

6. Does not play a role in mitosis, but the purpose of mitosis to separate centrioles and to
make sure the daughter cell gets a pair of centiroles

7. Where they are found

a. Angiosperms (sycamore) and pine trees do not have centrioles

b. Gingko trees have them

c. Any organism with motile sperm

8. Need other centrioles to create more centrioles

9. Centrioles are always duplicated near the nucleus (duplicated pair and parent pair
found orthogonal to each other)

10. Chaos-chaos

a. Amoeba that goes through haphazard cytokenesis process

b. unlinked cytokenesis and karyokenesis

 c. multiple nuclei to make sure daughter cell get at least two nuclei (similar to
many mitochondria found in human cell)

d. no centrioles

11.May have an origin as a prokaryote, but they have been modified so greatly that
mechanisms of free living organism cannot be seen

a. Spirochetes have almost the same arrangement of tublin

b. 1µ m in width and 1-3 µ m in length→ similar to size of prokaryote

12.Function

a. Origin of flagella

b. Regulator of flagella

Cilia and Flagella

1. Prokaryotic flagella

a. Clockwise rotation of flagella motor results un reverse movement

b. Flagella is passive and the motor does the rotation

c. Made of the protein flagellin

d. Protrudes through the plasma membrane

2. Eukaryotic flagella

a. 9 + 2 arrangement of microtubule

b. Nexin= cross links between doublets

c. Dynein is the motor protein

d. Singlets are not attached to the basal body

e. Dynine flexes on one side and one microtubule crawls up while the other
microtubule doesn’t move

f. Regulation may be done by singlets or ATP flow (GTP may have a role)

g. Flagellum is an internal structure- surrounded by a membrane

h. Axoneme- bundle of microtubules and associated proteins that form the core of cilia
and flagella

i. Sliding tublin mechanism

i. ATP us the mechanism for flagellar movement

ii. Internal rotation different from prokaryote flagellar movement

3. Cilia
 a. Body has more cilia than flagella

b. Cilia are shorter than flagella

c. In eukaryotes the only difference between cilia and flagella is length

Vacuole

1. Plants

a. Static part of development and usually is the biggest part of the cell (90%)

b. Carbohydrates

c. Food reserves

d. Regulate osmotic potential by breaking down starch

e. K+ rich (used to regulate H2O

f. Membrane = tonoplast (fungi and plants)

2. Animal

a. Contractile (found in protists)

b. Not a permanent part in animal cells

c. Vacuoles can fuse

d. Membrane pocket can fill with water and then it releases H2) and collapses

e. Phagosome or food vacuole bring particles in and digest

Lysosome

1. Catabolic enzymes

2. Protein rich

3. 1° lysosome before it fuses with another membrane body

4. 2° lysosome after it has fused with another membrane body (activated)

5. Membrane composed with phospholipids, protein, and cholesterol

a. pH of 8 in lysosome drops to 5.5 to activate enzymes

b. proton pumps used to regulate pH

Peroxisome

1. produced from ER

2. function

a. involved in metabolism in conditions of reduced O2

b. oxidation of long chain fatty acids

 c. synthesis of bile acids

d. detoxification of oxygen radicals

3. contains 85 gene products in humans

4. low O2→ more peroxisome

a. underwater plants

b. roots

c. potatoes and carrots→ thick tissue and as you go further to the center there are
more peroxisomes present