Metabolism Flashcards
Metabolism
- the total of ALL chemical reaction in a cell
- 2000 reactions in a cell at any point
Metabolic pathway
- a sequence of chemical reactions
- enzymes in the same metabolic pathway are physically linked
- together or part of cytoskeleton
-cell will couple exergonic and endergonic reactions
Anabolic pathways
- synthesis of more complex compounds
- endergonic (requires energy: +G)
- e.g. amino acids joining via peptide bonds to make a protein
Catabolic
- breaking down of complex molecules
- exergonic (release energy: -G)
- e.g. breakdown of glucose to pyruvate via glycolysis
ATP
- adenosine triphosphate
- energy currency of the cell
- contains:
- an adenine nitrogenous base
- a ribose (5C sugar)
- a triphosphate molecule
Hydrolysis of ATP
ATP + H2O —> ADP + Pi
Delta G = -7.3 kcal/mol
- this energy available for the cell to do work
- each cell uses 1-2billion ATP per day
- why is this exergonic?
1. Charge repulsion (close proximity of neg. charge on PO4-)
2. Resonance stabilization
3. Increased entropy
To make ATP
- to make ATP the cell uses Redox reactions
- transfer of electrons and hydrogen atoms from one compound to another
- OXIDATION is LOSS of elections (and usually H)
- REDUCTION is GAIN of electrons (and usually H)
- ALWAYS COUPLED
- glucose can be oxidized in a highly exergonic reaction which is used to make ATP
Complete oxidation of glucose
C6H12O6 + 6O2 —> 6CO2 + 6H2O + Energy
Delta G = -686 kcal/mol
- cells only 40% efficient at producing ATP
- energy = ATP + heat
Glycolysis
-occurs in the cytoplasm
- starts with 6C: Glucose
- finishes with 2x 3C: 2 pyruvates
- investment of 2ATP at the beginning of glycolysis
- a total of 4 ATP produced (via SUBSTRATE LEVEL PHOSPH.)
- NET GAIN = 2 ATP
-2 NADH are made
NAD+
- nicotinamide adenine dinucleotide
- a non-protein coenzyme
- an electron carrier
- carries 2 ELECTRONS and 1 HYDROGEN
- NAD+ = OXIDIZED form (no e- attached)
- NADH = REDUCED form (e- attached)
Glycolysis products
1 Glucose =
2 Pyruvate
2 ATP (net gain)
2 NADH
Is there oxygen available after glycolysis?
YES —> aerobic respiration (pyruvate go to mitochondria, TCA etc.)
NO —> fermentation/anaerobic (allows for sustained generation of little ATP via glycolysis) Pyruvate is reduced
-we get some ATP from glycolysis but ONLY if NAD+ available
Fermentation
- Regenerates NAD+
- lactic fermentation
- alcoholic fermentation
Lactic fermentation
- after glycolysis, 2 pyruvate molecules REDUCED to 2 lactate molecules
- produces 2 NAD+ (for glycolysis to continue)
- occurs in muscle cells during intense activity
- used to make dairy products
Alcoholic fermentation
- 2 step process
- 2 pyruvate —> 2 acetaldehyde
- 2CO2 as byproduct
- 2 acetaldehyde reduced to 2 ethanol
- 2NAD+ generated
- kombucha = alcoholic fermented tea
- CO2 byproduct makes it fizzy
- acetic acid
- yeast
- all alcohol
Cancer cells
- cancer cells ferment glucose to lactate even in the presence of oxygen
- possibly to make it into a product that still has a carbon skeleton to that it can be used as a precursor for essential molecules for growth
- PET scans use a radioactive glucose analog to find cancer cells
Mitochondria
- where ATP synthesis occurs
- mitochondria are dynamic
- often exist as interconnected structures
- mitochondria fuse and divide
- ER plays important role in fission
Mitochondrial fission
- ER interacts and recruits Drp1
- Drp1 forms helix around mitochondrion
- Mitochondrion splits
Porins
- channels that permit moderately sized molecules to move from the CYSTOL to INTERMEMBRANE SPACE
- in outer mitochondrial membrane
- ATP, pyruvate, NADH can travel through porin
-made of BETA PLEATED SHEETS
Inner mitochondrial membrane
- 3:1 protein:lipid ration (by weight)
- well insulated
- F1 particles (8.5nm)
-cardiolipin
Cardiolipin
- unusual lipid in the inner membrane
- “double” phospholipid
- has 4 fatty acid chains
- called diphosphatidylglycerol
-INSULATES the membrane and makes it IMPERMEABLE
The matrix
- central compartment
- high concentrations of proteins
- site of TCA cycle
- contains ribosomes and circular DNA
- have all the machinery needed to transcribe/translate own proteins but only make about 5% of what they need
- everything else is imported
- endosymbiont theory
Endosymbiont theory
- Lynn Margulis (1960s)
- theory of how mitochondrial double membranes were formed
- small, aerobic prokaryote engulfed by large, anaerobic eukaryote to create double membrane
- explains:
- Why it might have circular DNA
- Presence of ribosomes
- Presence of 2 membrane
Oxidation of pyruvate
- pyruvate moves into the mitochondrion through porins (actively transported into the matrix)
- reaction is catalyzed by pyruvate dehydrogenase
Products of oxidation of pyruvate
-per 1 pyruvate:
- 1 CO2
- 1 acetyl CoA
- 1 NADH
-but there are 2 pyruvate made from glycolysis of one glucose
TCA cycle
-occurs in the matrix of mitochondria
- CoA group leaves Acetyl
- Acetyl attaches to oxaloacetate —> citrate
- 2 CO2 molecules removed
- 3 NADH produced
- 1 FADH2 produced
- 1 GTP/ATP made
- Oxaloacetate regenerated
FADH2
-flavin adenine dinucleotide
- FAD+ = OXIDIZED form
- FADH2 = REDUCED form
- carries 2 electrons and 2 Hydrogens
- electrons have slightly less energy than ones carries by NADH
SO FAR after glycolysis, oxidation of pyruvate, and TCA
-NADH = 10
2 from glycolysis
2 from pyruvate oxidation
6 from TCA
-FASH2 = 2
2 from TCA cycle
-CO2 = 6
2 from pyruvate oxidation
4 from TCA cycle
-ATP = 4
2 from glycolysis
2 from TCA cycle
Oxidative phosphorylation
-production of ATP using energy derived from redox reaction in the ETC
ETC
- electron transport chain
- 4 complexes + ubiquinone + cytochrome C
- occurs in the INNER MEMBRANE of mitochondria
- series of redox reactions
- uses electrons from NADH and FADH2
- each complex has increasing redox potential (ability to acquire electrons
- energy is released every time an electron is passed to the next complex
- ETC is a target for many POISONS
ETC process
- Complex 1: NADH dehydrogenase
- oxidizes NADH —> NAD+ (2e-)
- 4H+ pumped to IMS
- Ubiquinone (CoQ) transports those 2e- to Complex III
- 4H+ pumped to IMS
- hydrophobic: floats inside membrane
- Ctyochrome C transports the 2e- from complex III to Complex IV
- Complex IV: cytochrome C: proton pump, oxidized
- receives e- and they leave to enable formation of water
- Oxygen acts as final e- acceptor (reduced to H2O)
- Complex II: succinate dehydrogenase
- makes FADH2
- feeds e- to Complex III
- succinate —> fumarate
Chemiosmotic Theory
- Peter Mitchel
- Nobel prize 1978
-H+ gradient provides the energy to phosphorylate ADP to synthesize ATP
- proton gradient made up by:
- Concentration difference (pH)
- Charge difference (voltage)
- membrane is IMPERMEABLE to H+ ions
- electrochemical gradient results in PROTON MOTIVE FORCE
ATP Synthase
- contains F1 particles (8.5nm) and F0
- F0 composed of
- 10 c units (which rotate)
- 2 B units (arms for structure)
- 1 a unit (for structure)
- F1 composed of
- 3 alpha units alternating with 3 beta units
- gamma unit (long banana shape that turns… stalk like
Binding change mechanism
- Paul Boyer
- Nobel prize 1997
-H+ enter in one channel, bind to C units, complete one full turn, and exit through a separate channel into the matrix
- in F1 unit, Beta units have important function
- as gamma subunit turns it causes conformational changes in Beta subunits
1. O = Open… ADP + Pi enter
2. L = Loose… ADP and Pi loosely attached
3. T = Tight… ADP + Pi —> ATP spontaneously due to close interaction
- as gamma subunit turns it causes conformational changes in Beta subunits
Ionophores
- allow protons to leak across the membrane and bypass ATP synthase
- hydrophobic weak acids
- move though inner membrane and take H+ to matrix
- uncouplers: uncoupling oxidation of glucose from formation of ATP
- e.g. 2,4-dintrophenol (DNP)
