CELL BIO UNIT 2 NOTES

Oxidative phosphorylation

Oxidative phosphorylation

ADP+PI → ATP INNER MEMBRANE

Electron transport equation-

• NADH + ½ O2+H+->NAD+ +H2O  NET OF INNER TRANSPORT

Biological oxidation is important

so humans don’t combust spontaneously and the energy in the bonds are in small dosages

_____is important for biological oxidation so there is a place for

O2

What cycle feeds into complex one in the mitochondria

Citric Acid Cycle

Write the mitocondria energy diagram on the board

A molecule must first be_________ in order to be _______.

Reduced, oxidized

Redox is measured in - and free energy in -

mV, KJ/mole

Redox potential can be influences by

Redox concentration

The heme group is attached to what complex

Cytochrome C

The copper complex is attach to what complex

Complex 4, cytochrome C oxidase

The iron sulfur complex is found where

Cyctocrome C oxidase/reductase and Q

The matrix arm of the NADH dehydrogenase

Electron transport

The membrane arm is associated with

Proton pumping

Pros and cons of proton highways

40x faster but it’s non selective hypothesized to be unidirectional

Draw when 2H+ joins Q

 

Cytocrome C can indicate

Cell death

Describe the glycolysis equation

1 glucose > 2 pyruvate+2NADH(1.5ATP)+2ATP

Pyruvate dehydrogenase

2pyruvate>2acetyl coA+2NADH(2.5 ATP per)

CAC equation

2acetyl CoA>6NADH+2FADH2+2GTP

Net mirocondria equation

2pyruvate > 8NADH+2FADH2 (1.5 ATP)+2GTP

Net fatty acid oxidation

1 palmitoyl CoA-> 8Acetyl CoA +7NADH +7 FADH2

Net Acetyl CAC equation

8 Acetyl CoA.>24 NADH + 8 FADH2 +8 GTP

Net result mitocondria equation palymitoyl

1 palmitoyl CoA >31 NADH +15FADH2 +8 GTP

Why does NADH have 2 values because the

Location changes

What is the free energy value of ATP hydrolysis

-30.5 kJ/mole

What is the free energy value of 1 ATP

-54 kJ/mole

What kind of reaction is NADH to O2

A spontaneous one

How many protons run through the ETC

14

What percentage of energy reaches the next complex

61.4%

Delta G is coupled with positive , what examples

NADH oxidation and creation of the proton gradient

Diffusion of the proton gradient and generation of atp synthase

Rotor stalk is used for what

To anchor the F1 subunit to drive atp synthase

Describe the protons being moved through the atp synthase

As the protons move they loose their negative and is pushed into the matrix

Each hairpin is depicted as a bump, how many protons do you need for 20 hairpins

20 protons

What drives the rotor around

The charge differential and sink

What is the function of dimers

They stabilize the atp synthase

How many revolutions per minute and per turn

8000 , 3

The inner membranes space is the more

Positive side

What makes bacteria different in terms of ETC

They use a pump nutrients into the cell and in anaerobic bacteria atp pumps and na but no gradient is established

What is the equivalent of the mitocondria matrix in chloroplast

Stroma

What is the equivalent of cristae in chloroplasts

Thylakoids

Where is ATP produced in chloroplasts? And consumed?

Stroma

High level electrons are excited by what and what molecule replaces those electrons

Light, water is split by p680

Carboxylation equation

5C +1C=6C/2=3C

What does Rubisco do

Fixes the carbon

What is reduction

is gain of electrons and remodeling of bonds 6 3 Carbon molecules NADPH is in the bond energy , 5 continue because we keep one to break down 

Regeneration equation

5 * 3C +ATP from light

carbon cycle net equation

CO2+ribulose 1,biphosphate>w/rubisco intermediate +H2O2 molecules of 3-phosphoglycerate

Make sure you know how to draw this diagram

What does Mn cluster do

Water for electrons to be excited into the z scheme

Photosystem 2 has

One rapid pathway photosystem 1 has multiple

What is the alpha rotor made of

has 12 subunits=12 - charged residues

What happens every time a proton enters the alpha rotor

Every time a proton enters the hairpin is moved one over

How many protons are needed for 3 ATP

12

What is ancient orgin ATP synthase function

(used originally for protons not ATP) first then ETC and then they’d are combined 

What did atp synthase start from

ancestral fermenting minimal atp and H2S synthesis’s 

Describe the purpose of purple non sulfur bacteria

Purple non sulfur bacteria used something like cytochrome c but it wasn’t 

The cytoskeleton is akin to

Freeway system made out of ants

What is the purpose of the cytoskeleton

maintains org,cell structure , cell shape  changes,cell movement, and intracellular trafficking of vesicles/organelles, cell division 

Cytoskeleton react in response to a lot of signals and as a result can

Depolarize and rebuild the cell skeleton to move better

What filaments are dynamic to reformation

Actin and microtubules

All filaments need ___________

1000 monomeric subunits and even though they are simple prokaryotes have different derivatives for this

Wht filament has + and - ends

Microtubules

In what circumstances would microtubules not be polar

Intermediate filaments are made of a-helical region its coiled together until dimer becomes a Teramer and it is no longer polar

Microtubules are normally made out of

32 IFs and it is used for mesenchymal cell muscle and keratin

What does nuclear lamins do

give tremendous structural support unless it’s phosphorylated and it falls apart

What are epidermal ifs used for

keratin filaments connect through desmosomes or hemidesmosomes

What is EBS

rapid blistering and lack of pressure resistance a problem with the epediermal IF

What are actin filaments

most abundant proteins in animals, all cells need it, 7nm , used as a reference control in everything and thin mesh work, relatively short lived and creates striated muscles

How do you make a cell move really quickly

Dynamic bursts of polymerazation

What is G-Actin

is a mono subunit, it is a spherical protien with a + and - end and had ATP embedded inside the g-actin so it can polymerize and fix in place in f-actin

F-actin

there is a + and - end,Suitable pool of charged g-actin ATP,Add more readily to the + end You cannot depolymerize from the middle Polymerization happens in one configuration

Myosin’s effect on f-actin

creates a barb and the plus end is more barbed 

Describe the process of polymerizing

1.lag phase2.growth phase3.equilibrium phase lots of gactin to factin ,Lag phase - nucleation it’s rryl long,The growth phase occurs as a monomer add to the exposed ends of the growing filaments, causing filament elongation,If a gactin needs to be added then it needs to be removed, balanced, We run out of free subunits and it hits an equilibrium, Disassembly is more favorable at the - end ,Once they are in the polymer there is no difference in the - and + surface

Why is the plus end more stable

because they ATP binds initially (glue) that does not happen to the negative end 

Critical concentration

is higher for the ATP bound + side then the ADP bound - side, Hydrolysis is not necessary

What is treadmilling

when the actin filaments results when assembly at the plus end is concomitant with depolymerization at the minus end

Memorize this drug table

Image

Arp2 and Arp3 filaments are related heavily to what

Actin

Arp 3/2 binds to what

NPF and clicks both into a active state so it can bind to a uncleared actin filament (ON MINUS END

ARPS Actin

ARPS kind of glue onto the edge (70° angle) these make branched formations 

What is profilin opposed by

Thyomisin

Profilin

Forms clamp the actin and myosin to the membrane (associated with the plus end)

What are the mechanisms of muscle fibers

Uniform Z disks lead to striating ,Tropomodilin and CapZ prevent polymerization and depolarizing 

What does cofilin do

to break off actin filament ends(induces severe twisting) and creates new ends to deassemble more rapidly

Filamin

Is a gel forming protien that the brain relies on

Make sure to memorize these protiens

Image

What does cadaherins respond to

protiens respond to adherin junctions 

What conditions are best for cadaherins

High calcium is needed for cadaherims to link and then anchor to the cytoskeleton

Under tension what happens to protiens

are extended to reduce stress on the molecule 

Adherin junction properties

cell connections, important and weak, useless without junction can generate force and bend and pull tubes out 

What are desmosomes

Cell to cell anchoring junctions they are embedded within the plasma membrane microtubules are strewn within

Make sure you understand embedment of cadeherims in desmosomes

Image

What are integrins

is like cadaherins but it binds to the extracellular material

What are tight junctions

elaborate array of protien, function is to seperate spaces that are created by a layer of cells, separates interstitial and blood stream(Tupperware lid) creates a seal

Clodins and aculin

Series of protiens stitched together with lateral attachments across

What are the limitations of gap junctions

connects cytosol , chemical synapses, only 1000 daltons can pass small ions and molecules can pass

Gap junctions that are small

Stack together

What is the ECM like

is diverse and complicated mixture, its secreted and it can be structural or space filling,

Make sure to memorize this

These make you durable and promotes compression resistance, fibrous protiens provide tensile resistance