module 8: Urea cycle

Question 1

define carbon skeleton

Answer 1

structural framework and carbon portion of amino acids

Question 2

define deamination

Answer 2

removal of amine functional group resulting in NH4

Question 3

what is the process of protein degredation

Answer 3

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

Question 4

what happens at the oxidative deamination step in protein degradation

Answer 4

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

Question 5

how many steps is the Urea cycle

Answer 5

4

Question 6

What is the first step of the urea cycle

Answer 6

carbomyl phosphate + ornithine-> citrulline via ornithine transcarbamoylase

Question 7

what needs to happen before fully going through urea cycle

Answer 7

carbamoyl phosphate synthase 1 converted to cabomyl phosphate

Question 8

what is second step of urea cycle

Answer 8

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

Question 9

what is third step of urea cycle

Answer 9

arginosuccinate becomes fumerate and arginine via arginosuccinase

Question 10

what is the 4th step of urea cycle

Answer 10

arnginine and fumerate become urea and ornithine via arginase

Question 11

where does urea cycle happen

Answer 11

mitochondria

Question 12

why does urea have high water soluability

Answer 12

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

Question 13

Define the outer membrane of mitochondria

Answer 13

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

Question 14

what is the intermembrane space

Answer 14

solution between outer and inner membranes

Question 15

what is the inner membrane of mitochondria

Answer 15

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

Question 16

why is selectivity crucial for oxidative phosphorylation and the mitochondrial membrane

Answer 16

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

Question 17

How many phases are in oxidative phosphorylation

Answer 17

3

Question 18

define matrix

Answer 18

innermost space of mitochondria

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

Question 19

what is the first phase of oxidative phosphorylation

Answer 19

transfer of electrons from NADH to FADH2

to ETC

Question 20

what is the reaction of the first phase of oxidative phosphorylation

Answer 20

4 H+ + 4e- + O2 → 2H2O

Question 21

describe the first phase of oxidative phosphorylation

Answer 21

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

Question 22

Describe complex 1 of the first phase of oxidative phosphorylation

Answer 22

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

Question 23

what is the reaction of complex 1

Answer 23

NADH + H+ + CoQ → NAD+ + CoQH2

Question 24

what is the result of complex 1

Answer 24

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

Question 25

describe complex 2 of first phase of oxidative phosphorylation

Answer 25

transfers electrons and H to CoQ from FADH2

Question 26

what is the reaction of complex 2

Answer 26

FADH2 + CoQ → FAD + CoQH2

Question 27

what is significant regarding reaction of complex 2

Answer 27

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

Question 28

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

Answer 28

complex 3 receives electrons from CoQ2 then shuttles to cytochrome C

Question 29

how many electrons can cytochrome C accept

Answer 29

1 electron- so 4 cytochrome needed

Question 30

Is complex 3 an integral protein

Answer 30

yes- 11 polypeptide subunits

Question 31

what is another specific function of complex 3

Answer 31

pumps 2 H ions from matrix into intermembrane space

Question 32

Describe complex 4

Answer 32

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

Question 33

what is the reaction for complex 4

Answer 33

O2 + 4e- + 4H+ → 2H2O

Question 34

what else does the reaction process do in complex 4

Answer 34

pumps 4 H from matrix to intermembrane space

Question 35

where does the pumping action come from in reaction 4

Answer 35

energy from breaking H bonds

Question 36

How are ATP formed in ETC

Answer 36

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

Question 37

who developed chemiosmotic theory

Answer 37

peter mitchell

Question 38

what does chemiosmotic theory describe

Answer 38

explains forming ATP by ATP Synthase

Question 39

What do the parts chemi and osmotic mean

Answer 39

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

Question 40

What are some key notes for chemiosmotic theory

Answer 40

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

Question 41

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

Answer 41

ATP Synthase

Question 42

what happens to H+ as it travels through ATP synthase

Answer 42

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

Question 43

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

Answer 43

ADP + Pi + nHIM+ → ATP + nHM+

Question 44

what are the key componets of ATP Synthase

Answer 44

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

Question 45

what causes the rotation in ATP Sythase

Answer 45

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

Question 46

when do metabolic diseases occur

Answer 46

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

Question 47

what does the mutation cause

Answer 47

causes the enzyme or protein to stop working

Question 48

what is the name of a metabolic disorder in the mitochondria

Answer 48

Myoclonic epilepsy and ragged-red fiber disease | collection of disorders that occur in muscles cells appear deformed with distinct fibers

Question 49

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

Answer 49

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

Question 50

what are the symptoms of MERRF

Answer 50

muscle twitches, muscle weakness and degeneration of nerve cells

Question 51

what are the nerve conditions with MERRF

Answer 51

loss of hearing and loss of eyesight

Question 52

is there a treatment for MERRF

Answer 52

currently no- so goal is to manage symptoms