Chemiosmosis And Tca

Front 1

What is the main purpose of TCA cycle? Other purposes?

Back 1

main: capture high energy electrons via redox of carbon compounds and transfer to FADH2 and NADH

other: some ATP made, lipids from acetyl-CoA

Front 2

where in the body is there a lot of mitochondria? why? where not so much?

Back 2

A lot in the heart, because needs a lot of energy to pump

not many in liver because not an actively proliferating tissue

Front 3

what is located in the inner mitochondrial membrane?

Back 3

oxphos proteins and enzymes for ETC

Front 4

what is in the matrix?

Back 4

TCA cycle

Front 5

what is in the cristae?

Back 5

cofactors/proteins involved in TCA and ETC

Front 6

PDH links....

Back 6

glycolysis to TCA

Front 7

how does pyruvate enter mitochondria? what happens if it does or doesnt?

Back 7

enters via active transport to become acetyl-CoA or OAA

if doesn't enter becomes lactate

Front 8

which step in PDH mechanism would be good for pharmacological intervention?

Back 8

the regeneration of lipoamide because it is a key reaction necessary to allow the pathway to continue

Front 9

how is the entry of pyruvate into TCA regulated (list)

Back 9

- energy need

- covalent modifications of PDH

- enzymatic activity (transcription, translation)

Front 10

high energy charge regulates PDH via..

Back 10

products (ATP, Acetyl CoA, NADH) turn down activity of PDH

Front 11

low energy charge

Back 11

ADP and pyruvate stimulate PDH activity

Front 12

how does structural changes in citrate synthetase allow its reaction to occur correctly?

Back 12

OAA binds first to 2 binding sites on CS, then acetyl coA can bind

confirmation closes and condensation to citrate occurs, avoids indiscriminate hydrolysis of acetyl-coA

Front 13

which citric acid cycle intermediate may be used as biosynthetic precursors?

Back 13

citrate is the main one exported, in the cytosol an enzyme changes it back to Acetyl-CoA to make lipids

Front 14

in a rapidly proliferating cell, how is the slowdown of TCA prevented when citrate is being used to make lipids?

Back 14

Glutamine-->glutamate-->a-KG which enters TCA

Front 15

Mutant vs wt IDH

Back 15

wt: citrate-->a-KG

mutated: a-KG--> D-2-HG which isnt normally found in the body (biomarker)

Front 16

NADP+--> NADPH in mutant vs wt IDH

Back 16

wt: IDH creates lots of NADPH

mutant: almost no NADPH present because it's being used to produce NADP+ and is consuming a lot

Front 17

how does mutated IDH affect transcription?

Back 17

When genes are not being transcribed are methylated at glycine residues

2-HG blocks enzymes that strip glycines off (using a-KG) from transcribing genes at that loci

Front 18

what is an inhibitor of aconitase and how does it work?

Back 18

fluoroacetate-->fluoroacetyl-Coa + citrate--> fluorocitrate which is an ireversible inhibitor of aconitase that reduces TCA and respiration

Front 19

why must biosynthetic precursors like lipids be made de novo?

Back 19

have specifications that must be met depending on where they are in the cell

Front 20

which of the TCA enzymes are in the inner mitochondrial membrane rather than the matrix?

Back 20

SDH (forms complex with FADH2)

Front 21

how is malate-->OAA driven forwards despite not having favourable free energy?

Back 21

by products (OAA, NADH)

Front 22

how do tumors rely on glycolysis when they shut off PDH?

Back 22

when oxygen decreases in the tumor, transcription factor HIF-1 gets PDK-1 to hydrolyze ATP and adds Pi to PDH to turn it off

use Glycolysis for ATP

do pathway in cytosol (glutamine--> glutamate--> a-KG--> isocitrate cleaved by ACL-->citrate--> AcCoA and some OAA)

Front 23

why must TCA and ETC occur in certain locations

Back 23

- build gradient

- keeps everything together to react correctly in right order

Front 24

why not have all ETC energy released at once?

Back 24

less control, which you want so the energy is used specifically to make ATP

Front 25

experiment: measure electron transfer potential

Back 25

set up two half reactions with the reference reaction having an electron transport potential of zero

the reduction potential of sample is observed voltage at the start of the experiment

Front 26

how are ROS formed?

Back 26

incomplete reduction of O2

Front 27

ROS are good for...?

Back 27

Pathogen clearance (anti-viral response) Activation of T cells proliferation

ROS can kill cells (radiotherapy)

Inactivates Fe-S clusters (i.e. aconitase

Front 28

ROS are bad for..?

Back 28

Oxidative damage: lipids DNA proteins

Aging, cancer (mutations)

Front 29

ROS detox

Back 29

superoxide dismutase: converts ROS to O2 and peroxide

peroxide is still reactive though so catalase breaks it down to water and oxygen

Front 30

how does cytochrome C link bioenergetics to cell fate?

Back 30

usually found only in mitochondria but leaks out when apoptosis signals received

form apoptosome complex to initiate caspases which initiate cascade towards apoptosis

Front 31

What happens when you take away a cell's mitochondrial DNA?

Back 31

Rho0 cells formed that have no functional respiratory chain

don't die and can proliferate

make fatty acids through other pathways in cytosol

Front 32

what are the two main components of ATP synthase? where are they located? which does catalysis?

Back 32

F1: matrix (catalysis)

F0: mitochondial membrane

Front 33

structure of ATP synthase : F1

Back 33

5 different polypeptide chains, alpha and beta chains in a hexameric ring

stalk contains gamma and epsilon proteins in chains

Front 34

structure of ATP synthase : F0

Back 34

beta parts can have open, loose, or tight states each allowing whether nucleotides can go in or out or whether they're converted to ATP

Front 35

open state

Back 35

binds and releases nucleotides

Front 36

loose state

Back 36

binds ADP and Pi but not release them

Front 37

tight state

Back 37

binds ATP and can convert ADP + Pi to ATP, but can't release the ATP that's formed

Front 38

binding and transformation of ADP+ Pi to ATP can occur....

Back 38

in the absence of proton motor force

Front 39

what powers ATP synthesis? how?

Back 39

- proton flow through F0 C-ring

- has two half channels, one in cytosol and one in matrix

-Aspartic residue captures proton as gradient builds up and H+ enters cytoplasmic half

- ring rotates in a clockwise direction and proton is shifted to the matrix channel where it's released

Front 40

rotation of c ring is coupled to

Back 40

ATP synthesis

Front 41

Why must there be mechanisms to interchange NAD+ and NADH in the cell?

Back 41

not directly interchangeable

Front 42

how many ATP from one Glc?

Back 42

about 30

Front 43

how are defects in mitochondria measured?

Back 43

oxygen levels

Front 44

how does FCCP affect mitochondria?

Back 44

proton ionophore that causes protons to leak into matrix (collapses proton gradient)

Front 45

how does oligomycin affect mitochondria?

Back 45

blocks ATP synthase (dramatic O2 conjucation decrease)

Front 46

Rot/Myx vs oligo vs FCCP effect on ETC graph

Back 46

Oligo mycin decrease O2 conjugatoin, then FCC collapses gradient so conj. goes back up to re-establish gradient, Rot/Myx decreases again

Front 47

what do uncoupling proteins do? where are they?

Back 47

dissipate proton gradient, stop ATP production

found on the membrane, especially in fatty acid tissues

Front 48

why do proliferating cells prefer glycolysis over oxphos?

Back 48

make more than you need

Front 49

what can be made from glucose from oxphos

Back 49

36 ATP