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Biochemistry > module 8: Urea cycle > Flashcards

module 8: Urea cycle Flashcards

1
Q

define carbon skeleton

A

structural framework and carbon portion of amino acids

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2
Q

define deamination

A

removal of amine functional group resulting in NH4

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3
Q

what is the process of protein degredation

A

proteins->amino acids-> oxidative deamination->carbon skeleton-> acetyl-CoA->ATP

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4
Q

what happens at the oxidative deamination step in protein degradation

A

amine functional group produces NH4 which results in urea after going through urea cycle

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5
Q

how many steps is the Urea cycle

A

4

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6
Q

What is the first step of the urea cycle

A

carbomyl phosphate + ornithine-> citrulline via ornithine transcarbamoylase

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7
Q

what needs to happen before fully going through urea cycle

A

carbamoyl phosphate synthase 1 converted to cabomyl phosphate

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8
Q

what is second step of urea cycle

A

citrulline becomes arginosuccinate via arginosuccinate synthentase
ATP added and becomes ADP+Pi
Asparatate added to reaction

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9
Q

what is third step of urea cycle

A

arginosuccinate becomes fumerate and arginine via arginosuccinase

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10
Q

what is the 4th step of urea cycle

A

arnginine and fumerate become urea and ornithine via arginase

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11
Q

where does urea cycle happen

A

mitochondria

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12
Q

why does urea have high water soluability

A

hydrogen bonding ability and high concentrations of Nitrogen atoms in the molecule

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13
Q

Define the outer membrane of mitochondria

A

bilayer that has porin proteins that permit flow of ions into intermembrane space

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14
Q

what is the intermembrane space

A

solution between outer and inner membranes

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15
Q

what is the inner membrane of mitochondria

A

highly selective bilayer permitting only select ions and molecules to flow across
contains complexes of electron transport chain

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16
Q

why is selectivity crucial for oxidative phosphorylation and the mitochondrial membrane

A

crucial for maintaining correct concentrations of H+, ATP and other molecules

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17
Q

How many phases are in oxidative phosphorylation

A

3

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18
Q

define matrix

A

innermost space of mitochondria

is where CAC occurs, some sections of FA cycle and urea cycle

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19
Q

what is the first phase of oxidative phosphorylation

A

transfer of electrons from NADH to FADH2

to ETC

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20
Q

what is the reaction of the first phase of oxidative phosphorylation

A

4 H+ + 4e- + O2 → 2H2O

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21
Q

describe the first phase of oxidative phosphorylation

A

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

22
Q

Describe complex 1 of the first phase of oxidative phosphorylation

A

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

23
Q

what is the reaction of complex 1

A

NADH + H+ + CoQ → NAD+ + CoQH2

24
Q

what is the result of complex 1

A

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

25
Q

describe complex 2 of first phase of oxidative phosphorylation

A

transfers electrons and H to CoQ from FADH2

26
Q

what is the reaction of complex 2

A

FADH2 + CoQ → FAD + CoQH2

27
Q

what is significant regarding reaction of complex 2

A

not enough energy to pump ions across the membrane and no pores to allow this to happen
CoQ2 shuttles electrons to complex 3

28
Q

what is the function of complex 3 of first phase oxidative phosphorylation

A

complex 3 receives electrons from CoQ2 then shuttles to cytochrome C

29
Q

how many electrons can cytochrome C accept

A

1 electron- so 4 cytochrome needed

30
Q

Is complex 3 an integral protein

A

yes- 11 polypeptide subunits

31
Q

what is another specific function of complex 3

A

pumps 2 H ions from matrix into intermembrane space

32
Q

Describe complex 4

A

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

33
Q

what is the reaction for complex 4

A

O2 + 4e- + 4H+ → 2H2O

34
Q

what else does the reaction process do in complex 4

A

pumps 4 H from matrix to intermembrane space

35
Q

where does the pumping action come from in reaction 4

A

energy from breaking H bonds

36
Q

How are ATP formed in ETC

A

ATP formed as H+ ions that were pumped out of matrix flow back in through ATP Synthase

37
Q

who developed chemiosmotic theory

A

peter mitchell

38
Q

what does chemiosmotic theory describe

A

explains forming ATP by ATP Synthase

39
Q

What do the parts chemi and osmotic mean

A

chemi: chemical reactions of ETC provide energy
osmotic: create H+ gradient

40
Q

What are some key notes for chemiosmotic theory

A

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

41
Q

what is the pore/channel transmembrane protein that H+ flow through to generate ATP

A

ATP Synthase

42
Q

what happens to H+ as it travels through ATP synthase

A

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

43
Q

what is the reaction of the H+ flow through ATP Synthase

A

ADP + Pi + nHIM+ → ATP + nHM+

44
Q

what are the key componets of ATP Synthase

A
  1. membrane Fo portion
  2. F1 that extends into matrix
  3. axle that joins Fo to F1
  4. Stator that connects Fo to F1
45
Q

what causes the rotation in ATP Sythase

A

rotation due to H+ ions flowing through inner membrane Fo portion of ATP Synthase

46
Q

when do metabolic diseases occur

A

when a chemical reaction is altered due to a mutation in enzyme or protein used in cellular metabolism

47
Q

what does the mutation cause

A

causes the enzyme or protein to stop working

48
Q

what is the name of a metabolic disorder in the mitochondria

A

Myoclonic epilepsy and ragged-red fiber disease

collection of disorders that occur in muscles cells appear deformed with distinct fibers

49
Q

where is the most common mutation found and what is the result

A

in a protein that makes tRNA results in the inability to make ATP correctly

50
Q

what are the symptoms of MERRF

A

muscle twitches, muscle weakness and degeneration of nerve cells

51
Q

what are the nerve conditions with MERRF

A

loss of hearing and loss of eyesight

52
Q

is there a treatment for MERRF

A

currently no- so goal is to manage symptoms

Biochemistry (9 decks)

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