module 8: Urea cycle Flashcards
define carbon skeleton
structural framework and carbon portion of amino acids
define deamination
removal of amine functional group resulting in NH4
what is the process of protein degredation
proteins->amino acids-> oxidative deamination->carbon skeleton-> acetyl-CoA->ATP
what happens at the oxidative deamination step in protein degradation
amine functional group produces NH4 which results in urea after going through urea cycle
how many steps is the Urea cycle
4
What is the first step of the urea cycle
carbomyl phosphate + ornithine-> citrulline via ornithine transcarbamoylase
what needs to happen before fully going through urea cycle
carbamoyl phosphate synthase 1 converted to cabomyl phosphate
what is second step of urea cycle
citrulline becomes arginosuccinate via arginosuccinate synthentase
ATP added and becomes ADP+Pi
Asparatate added to reaction
what is third step of urea cycle
arginosuccinate becomes fumerate and arginine via arginosuccinase
what is the 4th step of urea cycle
arnginine and fumerate become urea and ornithine via arginase
where does urea cycle happen
mitochondria
why does urea have high water soluability
hydrogen bonding ability and high concentrations of Nitrogen atoms in the molecule
Define the outer membrane of mitochondria
bilayer that has porin proteins that permit flow of ions into intermembrane space
what is the intermembrane space
solution between outer and inner membranes
what is the inner membrane of mitochondria
highly selective bilayer permitting only select ions and molecules to flow across
contains complexes of electron transport chain
why is selectivity crucial for oxidative phosphorylation and the mitochondrial membrane
crucial for maintaining correct concentrations of H+, ATP and other molecules
How many phases are in oxidative phosphorylation
3
define matrix
innermost space of mitochondria
is where CAC occurs, some sections of FA cycle and urea cycle
what is the first phase of oxidative phosphorylation
transfer of electrons from NADH to FADH2
to ETC
what is the reaction of the first phase of oxidative phosphorylation
4 H+ + 4e- + O2 → 2H2O
describe the first phase of oxidative phosphorylation
oxygen is breathed in, electron come from NADH and FADH2, and H from matrix
occurs in stages at large protein complexes
electrons flow spontaneously through ETC
Describe complex 1 of the first phase of oxidative phosphorylation
transfer electrons from NADH and FADH2 to complex 1
large integral protein- 40 peptides and contain flavin and CoQ
oxidizes NADH to NAD and uptake H from matrix
think water being pumped upward into a tank
what is the reaction of complex 1
NADH + H+ + CoQ → NAD+ + CoQH2
what is the result of complex 1
4 H ions are pumped across matrix to intermembrane space
pumped H ion will be used to make ATP later
CoQH2 will shuttle electron and H to complex 3
describe complex 2 of first phase of oxidative phosphorylation
transfers electrons and H to CoQ from FADH2
what is the reaction of complex 2
FADH2 + CoQ → FAD + CoQH2
what is significant regarding reaction of complex 2
not enough energy to pump ions across the membrane and no pores to allow this to happen
CoQ2 shuttles electrons to complex 3
what is the function of complex 3 of first phase oxidative phosphorylation
complex 3 receives electrons from CoQ2 then shuttles to cytochrome C
how many electrons can cytochrome C accept
1 electron- so 4 cytochrome needed
Is complex 3 an integral protein
yes- 11 polypeptide subunits
what is another specific function of complex 3
pumps 2 H ions from matrix into intermembrane space
Describe complex 4
4 proteins of cytochrome C each deliver an electron to complex four calling it cytochrome oxidase
4 electrons flow through to complex 4 to an O2 molecule that reacts with 2 H to create water
what is the reaction for complex 4
O2 + 4e- + 4H+ → 2H2O
what else does the reaction process do in complex 4
pumps 4 H from matrix to intermembrane space
where does the pumping action come from in reaction 4
energy from breaking H bonds
How are ATP formed in ETC
ATP formed as H+ ions that were pumped out of matrix flow back in through ATP Synthase
who developed chemiosmotic theory
peter mitchell
what does chemiosmotic theory describe
explains forming ATP by ATP Synthase
What do the parts chemi and osmotic mean
chemi: chemical reactions of ETC provide energy
osmotic: create H+ gradient
What are some key notes for chemiosmotic theory
Intermembrane space has higher concentration of H+ ions makes space more positive than matrix
H+ ions will spontaneously flow back into matrix as it goes toward the negative and away from the positive
what is the pore/channel transmembrane protein that H+ flow through to generate ATP
ATP Synthase
what happens to H+ as it travels through ATP synthase
H+ attacted by negatvie matrix
as H+ goes through ATP synthase causes synthase to catalyze ADP to ATP
H+ flow moves like a propeller as it rotates and continues as long as H+ ions flow
what is the reaction of the H+ flow through ATP Synthase
ADP + Pi + nHIM+ → ATP + nHM+
what are the key componets of ATP Synthase
- membrane Fo portion
- F1 that extends into matrix
- axle that joins Fo to F1
- Stator that connects Fo to F1
what causes the rotation in ATP Sythase
rotation due to H+ ions flowing through inner membrane Fo portion of ATP Synthase
when do metabolic diseases occur
when a chemical reaction is altered due to a mutation in enzyme or protein used in cellular metabolism
what does the mutation cause
causes the enzyme or protein to stop working
what is the name of a metabolic disorder in the mitochondria
Myoclonic epilepsy and ragged-red fiber disease
collection of disorders that occur in muscles cells appear deformed with distinct fibers
where is the most common mutation found and what is the result
in a protein that makes tRNA results in the inability to make ATP correctly
what are the symptoms of MERRF
muscle twitches, muscle weakness and degeneration of nerve cells
what are the nerve conditions with MERRF
loss of hearing and loss of eyesight
is there a treatment for MERRF
currently no- so goal is to manage symptoms
