Midterm 2 Flashcards
what are the three primitive functions of metabolism
- generate chemical energy (ATP)
- transport electrons (NADH and NADPH)
- synthesize macromolecules needed for cell growth and survival
what are the two types of metabolism
anabolic, catabolic
anabolism uses
NADPH
FADH2
catabolism uses
NAD
FAD
what is the main idea of glycolysis
take sugar (glucose) and convert it into a form that we can use to create energy
what is the net effect of breathing
SUGAR 6C–> 6 Co2
general map of glycolysis
glucose–> 2 pyrucate –? 2tehanol 2 CO2 OR 2 lactate OR acetly-COA
–> only 2 acetly COA can turn into 4 CO2 + 4 H20
how do we go from glucose to 2 pyruvate
glycolysis (10 successive reactions)
how do we go from 2 pyruvate to 2 ethanol + 2CO@
hypoxis or anaerobic conditions
how do we go from 2 pyruvate to 2 acetyl-CoA
aerobic conditions
how to we go from 2 pyruvate to 2 lactate
anaerobic conditiona
how do we go from 2 Acetly-CoA to 4CO2 and 4H20
citric acid cycle
what are the two overarching phases in glycolysis
investment/preparatory phase
payoff phase
what are the energy curriencies of the cells
ATP and NAD+`
how do we go from oxidized NAD+ to reduced NADH
add an H+ and a 2e- `
write the equation from NAD–> NADH
NAD+. + H+ + 2 e- –> NADH
what is the main idea of the preparatory phase of glycolysis
phosphorylation of glucose and its conversion to glyceraldehyde 3-phosphate
what is the first step of the preparatory phase in glycolysis
glucose phosphorylation
describe glucose phosphorylation(first step of glycolysis)
glucose is phorphorlylated by an enzyme called hexokinase
*** uses 1 atp per glucose molecule
*** IRREVESIBLE
kinase=
enzyme that phosphorylates things
the phosphorylation of glucose does what to its mobility
traps glucose in the cell
glucose is actively brought into cells through
transporters
what is step 2 of glycoslysis preparatory phase
glucose isomerization to fructose
what is isomerization
changing the shape, maintaining the same number of carbons
describe the glucose isomerization to fructose
is a reversible reaction
–> gets the sugar ready for the next step
** pyranose to furanose ring, fructose is less stable than glucose
*** USES PHOSPHOGLUCOSE isomerate ( PG)`
what is step 3 of preparatory phase glycolysis
phosphorylation of fructose-6-P
describe phosphorylation of fructose-6-P
phosphate group added to carbon 1
***carried out by phosphofructokinase
** USES atp
** 2nd IRREVERSIBLE reaction
** highly negative delta G
what is step 4 of preparatory phase glycolysis
cleavage of 6-carbon sugar to two 3-carbon intermediates
describe cleaveage of 6-carbon sugar to two 3-carbon intermediates
** carried out by aldolase
generated do different products , one that cannot that be further oxidized in that form
+ G3P and DHAP
what is step 5 of the preparatory glycolysis phase
isomerization of DHAP to G3P
decribe isomerixation od DHAP to G3P
for DHAP to be oxidized, it is converted to G3P by triose phosphate isomerase
** famous structure TIM barrel
the famous structure Tim barrel is from which step
step 5 of the preparatory phase of glycolysis
what are some key points of the paryoff phase
everything is in double amount bc we have 2x G3P
every intermediate has only 3 carbons in the payoff phase
what is the 6th step of glycolysis payoff phase
oxidation of G3P to 1,3-BPG
describe the oxidation of G3P to 1,3-BPG
inorganic phosphate and NAD+ are used by GAPDH
–> electron transfer
–> stored energy that is used in many other reactions
–> this is why the process is starting to payoff
what is the 6th step of the glycolysis payoff stage
ADP is phosphorylated to ATP using a phosphate from 1,3- BPG
describe the process of ADP is phosphorylated to ATP using a phosphate from 1,3-BPG
mediated by another kinase: phosphoglycerate kinase
unusual that the kinase removes a phosphate, but it can also preform the reverse reaction, which is where it gets its name
what is step 8 of the glycolysis payoff phase
3PG is isomerized to 2 PG
described how 3PG is isomerized to 2PG
mediated by phosphoglycerate mutase
the 3-phosphate is mover to the 2-position
costs no energy, created no energy but needed to prepare for the next step
what is step 9 of the glycolysis payoff phase
2PG is dehydrated to phophoenolpyruvate (PEP)
describe how 2PG is dehydrated to phophoenolpyruvate (PEP)
mediated by enolase
Loss of water dehydration reaction
step 10 of glycolysis payoff phase
PEP is converted to pyruvate
describe how PEP is converted to pyruvate
–> pyruvate kinase takes the phosphate off PEP and phosphorylated ADP to ATP
** LAST IRREVERSIBLE STEP
–> phosphorylation of nucleotide not protein
what are the three irrevesible steps in glycolysis
1) glucose phorphorylation (step 1)
2) phosphorylation of Fructose-6-P ( step 3)
3) PEP is converted to pyruvate (step 10)
pyruvate is NOT…
the end product of metabolism–> will either be further oxidized or fermented
OVERALL what does glycoysis produce
1 glucose makes 2x pyruvate + 2 NADH + 2 ATP
(uses 2 ATP, but generate 4 ATP)
Glycolysis molecules to remember
(in order)
*Glucose, G6P, F6P
* FBP, DHAP, G3P
* BPG, 3PG, 2PG, PEP
* Production of Two pyruvates, two NADHs, and two ATPs
glycolysis enzymes to remember in order
FIRST HALF of glycolysis
*Hexokinase (HK)
* Phosphoglucose (or phosphohexose) isomerase (PG)
* Phosphofructokinase (PFK)
* Aldolase
* Triose phosphate isomerase (TIM, also called TPI)
2nd Half of glycolysis
*Glyceraldehyde-3-phosphate dehydrogenase (GAPDH)
* Phosphoglycerate kinase (PGK)
* Phosphoglycerate mutase (PGM)
* Enolase
* Pyruvate kinase (PK)
all steps of glycolysis using ATP require what?
all steps using ATP require Mg2+ as a cofactor
why is magnesium so important
most enzymes that hydrolyze nucleoside triphosphates require the nucleotide to be in a complex with Mg 2+ or MN2+
what are fun facts about TIM
- DHAP conversion to G3P
- prefers reverse reaction (20:1) but G3P is pulled into the payoff phase
*catalytically perfect or diffusion limited
q
what are the products of glycolysis
2 pyruvate, 2 NADH, 2 ATP
what are the products of aldolase
DHAP and G3P
what are the 5 fates of pyruvate and their products
reduction –> lactate
carboxylation–> oxaloacetate
decarboxylation–> acetaldehyde
transamination –> alanine
decarboxylation –> acetyl-CoA
what is the fate of lactate
transported from cell –> fermentation for eukaryotes and bacteriaw
what is the fate of ocaloacetate
glucose production and gluconegenesis (anabolic )
what is the fate of acetaldehyde
ethanol –> Yeast fermenatation
what is the fate of alanine
protein synthesis anabolic
what is the fate of acetyl-coA
TCA cycle
what are the two major themes of pyruvate catabolism
anerobic
aerobic
what is the difference between anaerobic and aerobic
anearobic = does not require O2
aerobic = requires ocygen
describe anaerobic
- Low energy yield per molecule of glucose
- Also known as fermentation
- Different modes in yeast and other organisms
- Produces lactate or ethanol
describe aerobic
- High energy yield per molecule of glucose
- Requires coupled use of the tricarboxylic acid cycle (TCA) and
oxidative phosphorylation via the electron transport chain - Will be the subject of future lectures
describe yeast fermentation
Pyruvate converted to acetaldehyde via Pyruvate decarboxylase (PDC)
Acetaldehyde converted to ethanol by Alcohol dehydrogenase
how does pyruvate turn into acetaldehyde
pyruvate decarboxylase –> takes a Co2 off
how do we go from acetaldehyde to ethanol
alcohol dehydrogenase
what is the auto-brewery syndrome
eat sugar, make alcohol–> the patient appears drunk
- caused by yeast infection
what is ethanol detoxification
yeast fermentation in reverse
Anaerobic metabolism=
NAD+ regeneration
What is lactic acid fermentation
Pyruvate converted to lactate via Lactate dehydrogenase
lactic acid fermentation occurs mainly in
animal (muscle tissue) and some bacteria ( Lactobacillius)
what is an example of anaerobic metabolism
alligator
lactic acid fermentation is what type of energy
Quick burst of energy–> generate ATP/NAD+ in the muscle quickly without needing O2
what a con of lactic acid fermentation
needs long recovery to clear excess lactate (source of sourness after excersie)
what is the total need of glusoce per day for a human
160 g glucose/day
what is our reserve of glucose
190g
our brains and eyes alone need how much glucose
120g/day
When fasting or conducting extreme endurance exercise we need …
OTHER source of glucose than lactic acid fermentation –> GLUCONEOGENESIS
what are the tissues that synthesize glucose
liver and kidney medulla
what is the definition of gluconerogenesis
synthesis of 6 carbon glucose from 3-4 carbon precursors, normally non-carbohydrate sources
what are sources of precursors for gluconeogenesis
- Lactate: skeletal muscle, erythrocytes
- Amino acids: dietary protein, muscle protein breakdown
- Propionate: derived from fatty acids, amino acids
- Glycerol, and stored fats under starvation conditions
the cori cycle is a type of …
gluconeogenesis
what is the purpose of the cori cycle
turn lactate to glucose then transport it back to muscles
In the cori cycle describe what happens to lactate and glucose after exercise
lactate is transported from muscle to liver
Glucose is transported from live to muscle
Anabolic Glucose metabolism is
pathway known as gluconeogenesis
describe gluconeogenesis in terms of glycolysis
process is strikingly similar to glycolysis with the exception of 4 reactions
Pyruvate cannot be …
directly converted to PEP
*** REQUIRES ATP
Glycolysis happens where
in the cytosol
pyruvate carboxylase is in the
mitochondria
Pyruvate transported to where and converted to what
pyruvate transported to mitochondria and turned into oxaloacetate
Ocaloacetate cannot cross what?
the mitochondria so it is converted to MALATE
malate is transported … to turn into..
malate is transported to cytosol then converted back to OAA
CYTOSOLIC OAA is converted to… by what..
cytosolic OAA is converted to PEP by PEP carboxykinase
*** USED GTP
what is another 2nd diff between glycolysis and gluconeogenesis pathway
fructose biphosphatase used to remove one of the phosphates on the F-16-bP
what is the last difference between glycolysis and gluconeogenesis
glucose 6- phosphatase
** removes the last Pi
** allows glucose to leave the cell
a single molecule of glucose from pyruvate requires …
six equivalents of ATP
** costs 4 ATP and 2 GTP
breaking down a molecule of glucose nets …
2 ATP
how do we keep cells from spending all the energy they make from glycolysis doing gluconeogenesis?
this is known as a futile cycle, pathways running in opposite directions resulting in a loss of energy
compartmentalization is not just about …
oganellar separation of pathways, but TISSUE TOO
not all organs have..
the same metabolic needs
gene expression in different tissues or different cells allows
for the use of one pathway or another
what is a classical example of compartementalization
The cori cycle
descrive gluconeogenesis in general terms
glycolysis in reverse with a few different required steps –> requires 6 energy equivalents to produce 1 molecule of glucose from two of pyruvate
regulatory steps of glycolysis cluster around the
irreversible stepsw
describe feedback inhibition
we have enough products, let’s stop
feed-forward activation
we have enough substrates, let’s go
hexokinase is inhibited by …
its product, classic feedback inhibition
describe the regulation of hexokinase regulation
- 2-Deoxyglucose (2-DG) can be
phosphorylated by hexokinase to
make 2-DG-phosphate (2-DGp) - 2-DGp cannot be converted by
phosphoglucose isomerase,
competitive inhibitor! - Excess 2-DG blocks more
glucose from being
phosphorylated, starving cells
AMP stands for
adenosine monophosphate
at super high levels of ATP ….
dont need more energy –> block glycolysis
if there is an H+ build up –>
too much lactate –> build up of product shuts down mechanisms
What are the things that stop the glycolysis
too much ATP
too much H+
too much Citrate
describe the relationship between Fructose 2-6 bisphosphate and PFK
feed forward activation
strong PFK allosteric activator –> lots of F-6-P leads to production of F-2,6-BP which activates PFK to increase rate
Fructose -2,6- bisphosphate produces another isoform of
PFK called PFK-2
AMP activated protein kinases sense..
high levels of AMP, turns on the kinase activity of PFk-2
PFK-2 then makes F-2,6-BP from F-6-P
* Ramps up glycolysis!
* Protein kinase A (PKA) inactivates PFK-2
kinase and activates PFK-2 phosphatase
function
* F-2,6-BP -> F-1,6-P
* Loss of F-2,6-BP slows glycolysis
acetyl-CoA and alanine are …
downstream products, if they are building up we don’t want to make more
why do we regulate multiple enzymes in glycolysis
glucose is a primary point of entry for carbon at most cells
The carbon is used in almost everything
Glycolysis is common to practically all life on Earth, lots of chances to build in regulatory elements
is glucose easily broken down
YES
plants and animals stroy glucose in more stable …
.POLYMERS
glucose and other sugars on their own are
monosaccharides
sugars are stored as
polysaccharides
what are the types of polysaccharides
starch and cellulose and glycogen
plants make what type of polysaccharide
startch and cellulose
animals make what type of polysaccarhide
glycogen
glycogen is what type of polymer
branching polymer
glycogen is found in what % in the muscle tissues and liver
75% in muscle tissues
25% is in the liver
most tissues cannot create … why??
GLYCOGEN
Glycogen cannot be transported, must be metabolized where it’s made
Muscles never share _____ ____ but the ____ does
muscles never shares liberated glucose but the liver does
in the glycogen synthesis pathway …
Glucose-6-P (G6P) is converted
to Glucose-1-P (G1P) by
phosphoglucomutase (not
phosphoglucose isomerase from
glycolysis)
- G1P is attached to a UDP to
facilitate addition to growing chain - UDP is lost during chain addition
describe the glycogen metabolism breakdown…
glycogen is broken down into glucose 1 phosphate by the enzyme glycogen phosphorylase
glucose 1 phosphate is then made into glucose 6 phosphate through G6Pase and then the glucose 6 phosphate wither goes to the blood or glycolysis
reciprocal control of glycogen metabolism description
reciprocal regulation of glycogen metabolism through phosphorylation and dephosphorylation.
Kinases (activated by glucagon) phosphorylate enzymes, activating glycogen breakdown (phosphorylase) and inhibiting glycogen synthesis (synthase).
Phosphatases (activated by insulin) dephosphorylate enzymes, reversing this effect to promote glycogen storage.
*This ensures that glycogen synthesis and breakdown never occur simultaneously.
Hormone signaling regulates…
GLUCOSE LEVELS
dysregulation drives ….
DISEASE
TYpe 1 diabetes lack of
insulin production drives elevated blood glucose
Insulin malfunction===
high blood sugar ➔ Diabetes
insulin allows glucose to
ENTER THE CELL = exit the bloodstream–> Move glucose from blood to cell:
Blood glucose level goes down
Insulin injection will…
lower blood sugar and increase cell sugar
what can cause too much insulin
stress or exercise
what does too much insulin do to the body
→low blood and cell sugar (hypoglycemia, can cause coma)
pancrease secreats what
glucagon and insulin
glucagon causes what effect on the liver
causes liver to release glucose into the blood
describe the glucagon path way from pancrease to liver
pancrease secreats glucagon which caused the liver to release glucose into the blood
this increase blood glucose levels
high blood glucose levels cause insulin release
describe the insulin pathway from pancreas to liver
pancreas secrets insulin
causes liver to take glucose out of blood and store it as glycogen
low blood glucose levels
caused glucagon release
what regulated PFK-1 and how
AMP increases its activity
ATP decreases its activity
what regulates PFK-2 and how
Insulin increases activity to create more F-2-6–> which keeps PFK1 active
Glucacon decreases activity –> down regulates glycolysis
what are the two types of cyclic nucleotide second messengers
Adenylate cyclase
Guanylate cyclase
what do cyclic nucleotide second messengers do
classic signlaing molecules
–> AMPLIFY initial signals
cyclic nucleotides are produces by ..
produced from ATP and GTP
PKA is activated by ..
cyclic AMP
AMP is activated by …
non-cyclic AMP
low glucose in the end leads tooo
a glycolysis rate decrease
what are the three downstream stages of glucose oxidation
- Acetyl-COA production
- Acetyl-CoA oxidation
- Electron Transport Stage
TCA cycle and electron Transport chain happen in …
the mitochondria
the electron transport chain requires..
OXYGEN to work, hence is aerobic metabolism
what are some sources for electrons other than glucose
fatty acids
amino acids
what activates the pyruvate dehydrogenase complex
formation of pyruvate / glycolysis
what does pyruvate turn into when we add pyruvate dehydrogenase complex to it
acetyl-CoA and CO2 and NaDH
what does pyruvate dehydrogenase complex need to create acetyl-CoA
HAS three subunits ( E1+ E2 +E3)
coenzyme A
Nad+
Tpp
lipoate
FAD
what do we call the process of going from pyruvate to acetyl Co-A
oxidative decarboxylation
what is Coenzyme A
a very long molecule (15A)
**COMPOSED OF ELEMENTS OF ATP
** bulky and trapped in the cell
has vitamin B5, adenine , ribose 3’phosphate`
in pyruvate dehydrogenase what does E1 do
take the CO2 off of the pyruvate
what is the role of E2 subunit isn pyruvate dehydrogenase
generates aceytl-CoA
what does E3 of pyruvate dehydrogenase do?
creates NADH + H+
** recycling cofactors
describe the PDH 3D organization (pyruvate dehydrogenase complex)
an icosahedron complex = 24 E1 + 24 E2+ 12 E3
** E1, E2, E3 each has its own prosthetic group
what are the prosthetic groups for each subunit of PDH
E1: TPP
E2: lipoic acid
E3: FAD
TPP is a product of
Thiamine
Thiamine is what….
Vitamin B1
what can a thiamine deficiency cause
anemia, sometimes lower back pains and canker sores
contrast pyruvate decarboxylase and pyruvate dehydrogenase
Pyruvate decarboxylase -> alcohol (yeast only)
Pyruvate dehydrogenase -> acetyl-CoA -> feeds into TCA cycle
Both catalyze decarboxylation reactions which can be confusing
describe the first step of pyruvate dehydrogenas in depth
Carbanion of TPP + pyruvate + 2H+ creates hydroxyethyl-Tpp and CO2
** Thiazole ring is important for catalysis
lipoic acid is used in what and what is it
lipoic acid is used in the E2 subunit of PDH
** it is an antioxidant and found in cells with lots of mitochondria (red meat, spinach)
describe the hand off from E1 subunit to E2 subunit of PDH
hydroxyethyl-TPP + lipamide = carbonion of TPP and acetyllipoamide
What is the second step of PDH
coenzyme A + acetylippoamide = acetyl CoA + dihydrolipoamide
** handoff from E2 to E3 subunit of PDH
describe the third step of PDH
E3 uses FAD as a cofactor to create FADH2
dihydrolipoamide + FAD –> lipoamide + FADH2 + NADH + H+
large complex allows…
efficient substrate shuttling
lipoic acid helps …
transport the inermediates
what are all the names of TCA
tricarboxylic acid cycle
Krebs Cycle
Citric Acid Cycle
what is the general product and gist of TCA
Uses acetyl-CoA and water to produce NADH and Co2
for every acetyl Co-A entering the cycle–> 3 NADH produced
what did scientists use to follow/understand metabolism
isotope tracing
Compare and Contrast Radioactivity vs Stable isotopes
- Radioactivity is much more
sensitive - You need less incorporation to
see it - Requires lots of extra
certification to use in the lab - Cannot determine different
labeled molecules from each
other without separation
Stable:
Non-radioactive
* No safety concerns
* Can be readily separated by
chromatography and
visualized by mass
spectrometry
* Requires significantly more
incorporation
B1 vitamin is found in
TPP
Lipoic acid is found in
PDH E2
B2 is found in
PDH E3
FAD
B3 is found in
NAD
B5 is found in
Coenzyme A
what is B1
thiamine
what is B2
riboflavin
What is B3
niacinW
What is B5
pantothenic acid
What are the 2 phases of the Citric Acid Cycle
- introduction and lost of 2C
- Regeneration of oxaloacetate
Describe reaction 1 of krebs Cycle
Citrate is formed from acetyl-CoA and oxaloacetate in an aldol condensation. Acetyl-CoA forms the enolate
***IRREVERSIBLE
Citrate is…
PROCHIRAl
–> molecule can be changed from achiral to chiral in a single chemical step
Rxn 2 of the krebs cycle
citrate —> aconitase
Enzyme =aconitase
This is a combined dehydration-hydration reaction, which isomerize the tertiary alcohol citrate to the secondary alcohol isocitrate
what is special about isocitrate
stereospecific reaction produces only one isomer
stereospecific only for one orientation –> ACTS ON THE Z bond
Fluoroacetate (1080) poison
is a suicide substrate for aconitase –> prevents it from doing any other catalysis by covalently bonding to aconitase
reaction 3 of krebs cycle
*** IRREVERSIBLE
isocitrate –> alpha-ketoglutarate
enzyme = isocitrate dehydrogenase
The secondary alcohol in isocitrate is oxidized to give the intermediate oxalosuccinate. wich decarboxylated to give alpha ketoglutarate
** Regulated by substrate availability and product inhibition
Rxn 4 krebs cycle
alpha- ketoglutarate –> succinyl-CoA
enzyme = alpha keto-gluatarate dehydrogenase
Alpha-ketoglutarate undergoes oxidative decaryoxylation, which concerted reaction in which the carboxyl group closest to the carbonyl is lost as CO2 and succinyl-CoA is formed
Rxn 5 Krebs Cycle
succinyl-CoA –> Succinate + HS-CoAn
Enzyme = succinyl-CoA synthetase
this oxidation is substrate level phosphorylation, a reaction that directly generates ATP or GTP
Thioester provides
energy for phosphorylation. Since GPD/ADP are the things getting phosphorylated rather than protein, this is termed substrate
GTP is where
in liver
where is ATP
brain, heart, plant, bacteria
Reaction 6 of krebs cycle
Succinate —> Fumarate
enxyme = succinate dehydrogenase
in this oxidation, electrons from succinate are transferred to FAD to form the trans dioic acid fumarate
FAD gets reduced
why is succinate dehydrogenase different than other enzymes
All the other TCA enzymes are soluble in matrix but
This one is found in the inner mitochondrial membrane (close to ETC)
which is the stronger oxidizer FAD or NAD
FAD
Reaction 7 of krebs cycle
fumarate —> malate
enxyme = fumarase
The alkene moiety of fumarate is hydrated to form the secondary alcohol in malate
fumarase deficiency
autosomal recessive; leads to physical and neurological abnormalities 1:400 million chance in the wild–> increasingly more common in the mormon population especially in utah
Reaction 8 of krebs cycle
malate –> oxaloacetate
enxzyme= malate dehydrogenase
The hydroxyl group of malate is oxidixed to the carbonyl of oxaloacetate. The electrons are harvested to NAD+ in the process. This step is also reversible
which steps have the largest negative overall delta G
irreversible steps
What are the overall products of the TCA cycle and per molecule of glucose
Overall, we have produced:
* 3 NADH
* 1 FADH2
* 1 ATP (or GTP)
* 2 CO2
`
* Per molecule of glucose, TCA
makes:
* 6 NADH
* 2 FADH2
* 2 ATP (or GTP)
TCA cycle is a hub of …
biosynthesis
Molecules that are synthesized out ofthe TCA cycle can often be…
converted
back into TCA intermediates
what are anaplerotic reactions
chemical reactions that replenish the intermediates of the citric acid cycle (TCA cycle)
is it common to have genetic mutations of genes in glycolysis and tCA cyle , if not why
RARE to have genetic mutations of genes in glycolysis and TCA cycle because they are so essential
what is the overall products of TCA cycle
3NADH
1FADH
1ATP or GTP
2Co2
what is the overall product of TCA PER molecule of glucose
6NADH
2FADH
2ATP
4CO2
how many atps do we get per NADH
2.5x ATP per NADH
how many atps do we get per FADH2
1.5x ATP per FADH2
describe ATP equivalence…
basically NADH and FADH2 can be equivalent to ATP BASED
what is glycolysis ATP equivalence
5-7 ATP
what is the ATP equivalence for PDH and TCA
25 ATP
what is the approx number of ATP equivalence for one glucose molecule
32ATP
in the TCA which steps are the most rgulated
IRREVERSIBLE STEPS
Prequel - PDH
TCA- CS, IDH, KGDH
in general what inhibits product formation in TCA
ATP, NADH, intermediates
in general what activates product formation in TCA
energy depletion
AND
Ca2+
why would Ca 2+ activate the TCA cycle
signal for muscle contraction aka I need more energy
what are the two main modes of regulation in PDH
- Product inhibition
- phosphorylation
describe the product inhibition of PDH in more detail
Acety CoA inhibits E2 subunit
High NADH levels inhibit E3 subunit
Fatty Acid also inhibit E2
what can activate the PDH cycle
activated by high levels of CoA-SH and NAD+
describe phosphorylation inhibition/activation in PDH
ATP inhibits E1 and AMP activated it
phorsphorylation= direct covalent modification of the E! subunit
how can we activate the E1 subunit of PDH and why is it inhibited
it has been phosphorylated so we can add Ca2+ to take away the phosphate and stimulated catalysis
Describe what disease can be related to PDH
Mercury Poisoning
Hg2+ binds to the E2 subunit of the PDH inhibiting it
*** happened to karren Wetterhahn (dimethyl mercury) and mad hatter (poisoned by mercury)
describe the first step of the TCA cycle that is regulated
Step 1 = acetyl CoA + oxaloacetate –> citrate
enzyme= citrate synthesis
ATP INHIBITS allosetrically
describe the 2 step of the TCA cycle that is regulated
Step 3 = isocitrate –> alpha ketoglutarate
enzyme= isocitrate dehydrogenase
ATP AND NADH both inhibit allosterically
ADP activates it
phosphorylation also regulated IDH activity
what happens when the isocitrate dehydrogenase is inhibited
concentration of citrate increases causing an increase in acetyl coa and hence FATS
how does phosphorylation inhibition work
basically phosphate attaches to the active site preventing the substate from binding
What is the 3rd step of the TCA that is regulated
alpha ketoglutarate –> succunyl CoA
enzyme = alpha ketoglutarate dehydrogenase
product inhibition:
succinyl coA–> E2
Acetyly CoA–> E2 of PDH
NADH —> E3
Na
why do we need fats
sources of energy, hormones and cell membranes
why fats?
more energy density than other materials
Less water –> six times more energy than glycogen per gram
What are fatty acids
have long hydrophobic tail attached to a carboxylic acid
saturated fatty acids =
no double bonds
packed tightly
unsaturated fatty acids=
double bonds
packed loosely
polyunsaturated fatty acids =
multiple double bonds
describe the Fatty acids naming system
X: Y ^delta Z
x= number of carbons
y= number of unsaturated bonds
z= position of unsaturated bonds
describe fatty acids in two words
Carboxylic Acids
AMPHIPATHIC
True of false:
fatty acids can be detergent cells
TRUE–> dont want these floating around so their transportation and storage is highly regulated
how are fatty acids stored
they are stores as neutral lipids by reacting with a head group such as glycerol
what is the main source of energy storage in the body
Triacylglycerols
what are some types of triacylglycerols
saturated fats
monosaturated fat
polyunsaturated fats
what does cholesterol do in the phospholipid
provides rigidity –> provides important structural support
what are the two types of cholesterol and which is good and bad
LDL- bad cholesterol
HDL- good cholesterol
why is LDL good or bad cholesterol
LDL is BAD cholesterol bc it accumulates plaques on the arterial walls–> causing heart attack
low protein:fat ratio
why is HDL good or bad cholesterol
good cholesterol because it brings cholesterol back to liver
high protein:fat ration
where does fatty acid oxidation occur
happening in the cytoplasm of fat cells
(edit by sydney: i thought it was mitochondria)
what is fatty acid oxidation downregulated and upregulated by
downregulated by insulin
upregulated by glucagon
how are fatty acids transported
by albumin
what enzyme splits fatty acids into glycerol and free fatty acids
Lipases!
describe glycerol oxidation
glycerol –> L-glycerol 3-phosphate–> dihydroxyacetone phosphate –> D-glyceraldehyde 3-phosphate
enzyme: glycerol kinase, glycerol 3-phosphate dehydrogenase , triose phosphate isomerase
the G3P product of the glycerol oxidation goes where
either glycolysis or gluconeogenesis based on what is needed
what are the three stages of fatty acid oxidation
- activation
- transport
- beta oxidation
fatty acids have the highest…
highest yield of energy per gram (9cal) vs protein and carbohydrates (4.5 cal)
what is the net reaction of the activation step in fatty acid oxidatiion
fatty acid + ATP –> acyl-CoA + AMP + PPi
what is the rate controlling step for fatty acid oxidation and why
Step 2 –> Transport
Rate controlling step for fatty acid and oxidation because fatty acyl-CoA cannot go into mitochondrial matrix directly
describe the third step of fatty acid oxidation
Beta Oxidation
Breaks up the acyl-CoA –> two carbons of fat are removed each time attached to CoA as Acetyl-CoA
Last two carbons are just Acetyl-CoA
** includes FAD and formation of a double bond
For a 16C fatty acid how many cycles and acetyl does it makes after beta oxidation
C16 breaks into 8x acetyl-CoA over 7 cycles
the end result of fatty acid oxidation is what and what cycle does it feed into
acetyl-Coa feeds into TCA
electron carriers like FAD go to ETC
What happens when an unsaturated fat enters the Beta oxidation cycle
first undergoes a separate oxidation to remove the double bond costing 1x FADH2
uneven number of carbons will end beta oxidation with
C3 propionyl-CoA not C2 acetyl-CoA which gets turn into succinyl CoA using energy –> which goes for two rounds of TCA cycle
where does the -2 in the fatty acid calculation come from
it comes from the activation stage
what does acetyl-coA carboxylase do
builds malonyl-CoA
-Malonyl-CoA is used by fats
What does fatty acid synthase do?`
Catalyze 7 different reactions
4 are similar to beta oxidation
3 are completely different
builds acetyl-CoA and malonyl-CoA into growing FA chains
describe important details about fatty acid synthase
there are 7 domains, each one catalyzes one reaction
ALL reactions happen while the intermediates are connected to the ACP domain
ACP looks just like…
coenzyme A
what is the difference between coenzyme A and ACP
CoA is derived from ATP
ACP is fused covalently through active site of seriene
CoA is freely diffusable, ACP is always attached to cofactor –>
what are some examples where they are covelently fused to cofactors
lipoic acid –>
Biotin
PPT
How many reactions does it require to undergo a cycle of β oxidation?
4 reactions
2 of which are oxidations, producing 1 NADH and 1 FADH2 (ultimately carrying 4 e-)
1 H2O addition reaction
Where does β oxidation take place? Biosynthesis?
β oxidation: mitochondrion
biosynthesis: cytoplasm
What is the e- carrier in β oxidation? Biosynthesis?
β oxidation: NAD/FAD
biosynthesis: NADP/NADPH
What the acetyl carrier in β oxidation? Biosynthesis?
β oxidation: CoA
Biosynthesis: ACP
What is the acetyl donor in β oxidation? Biosynthesis?
β oxidation: Acetyl CoA (C2)
biosynthesis: malonyl ACP (C3)
What are the cycle enzymes in β oxidation? Biosynthesis (BE GENERAL)
β oxidation: many, separate enzymes
biosynthesis: one protein chain
What are the cycle intermediates of β oxidation? Biosynthesis?
β oxidation: L-OH acyl CoA
biosynthesis: D-OH acyl CAP
What is the metabolic timing for β oxidation? Biosynthesis?
β oxidation: Low EC, starvation
Biosynthesis: High EC, well fed
Malonyl-CoA is built from?
acetyl-CoA
Both _________ and _________ are used in FA biosynthesis.
malonyl-CoA and acetyl-CoA
If we broke down FAs to make acetyl-CoA, it would be a…?
FUTILE CYCLE
The TCA Cycle is also a hub of ______.
bbiosynthesis
What part of the TCA cycle allows for biosynthesis?
inihibition of isocitrate dehydrogenase, allows for buildup of CITRATE
citrase is then broken down into acetyl-CoA using ATP-citrate lyase
citrate –> Acetyl-CoA –> FAs –> lipids
FA biosynthesis and oxidation are __________ __________. When one is activated, the other is _________.
opposing activies
inhibited
FA biosynthesis _______ energy while oxidation _________ energy.
store, produces
FA Metabolism is regulated by?
- citrate and energy state (high/low ATP)
- transporters/compartimentaliztion
- hormones (e.g. insulin and glucagon)
- enzyme phosphorylation state
To activate FA biosynthesis, what must happen?
blood glucose = HIGH
insulin dephosphorylates and stimulates phosphoprotein phosphastases
—> activating ACC (acetyl-CoA carboxylase)
To inhibit FA biosynthesis, what must happen?
blood glucose = LOW
AMP kinase (AMPK) or protein kinase A (PKA) phosphorylate ACC
—> makes ACC inactive/less active
NOTE: PKA is stimulated by epiniphrine and glucagon
What are the activators of ACC?
citrate, ATP, insulin
What are the inhibitors of ACC?
palmitoyl CoA (aka long chain FA-CoA)
AMP
glucagon
What is a regulator of the carnitine shuttle? How does this affect FA oxidation?
malonyl-CoA inhibits
–> inhibits oxidation by blocking FA from entering the mitochondria, allows for biosynthesis
How do you break down triacylglyerides?
using hormone sensitive LIPASES
ADDITION OF H2O
–> broken down into glycerol and FAs
What are the regulators of a hormone sensitive lipase?
activator: glucagon
inhibitor: insulin
**exercise activates lipase
Anaerobic exercise does what?
breakdown sugar (promote glycolysis)
accumulate lactate
(idk if you have to know this):
training: reduce fatigue and increase power burst
Aerobic exercise does what?
mostly burn fat, minor breakdown of sugar, produce CO2
training: reduce fatigue and increase endurance
Aerobic exercise training causes:
- increase in hexokinase rate
- increased gluconeogensis ability
- decrease in total LDH activity (decreases lactate formation)
- increase number and size of mitochondria (enhancing pyruvate DH enzyme rate, Kreb’s cycle enzyme rate, FA oxidation enzyme rate, ETC)
- increased FA availability for OXIDATION due to increased lipase activity (increased FA uptake in skeletal muscle), acyl-CoA synthetase activity (increased activation of FAs for transport into mitochondria), carnitine transporter activity
Anaerobic training causes:
- increases in anaerobic capacity (more muscle cells to use more ATP)
- INCREASED GLYCOLYSIS RATE (raise PFK rate)
- increased gluconeogenesis rate
-increase lactate tolerance in blood and muscle
…BUT HAS LITTLE EFFECT ON:
- OXIDATIVE CAPACITY (e.g. mitochondria #, burning fat, TCA cycle or ET)
- cardiovascular adaptation (heart pumping rate)
What zymogens?
an inactive form of an enzyme that is later activated by something (e.g. another protein, pH change)
What is an example of a zymogen?
pepsinogen (is activated by the low pH of the stomach) –> pepsin (active)
inactive form is meant to prevent digestion of proteins within the cells making them
What are secondary enzymes? Provide an example
other enzymes that activate zymogens
Ex: chymotrypsin is activated by trypsin
Digested ______ _____ enter the blood stream in the intestine.
amino acids
_______ can also be broken down inside _____ then transported into the blood.
proteins, cell
What are some reasons for targeted protein degradation?
- proteins have fulfilled their purpose (or are overperforming) –> ARE RECYCLED
2, proteins are accumulating, aggregating, potentially causing issues –> DESTROYED
_________ proteins are then degraded in the ________.
ubiquinated, proteasome
What is a proteosome? What are its basic mechanics?
a protein degradation machine
polyubiquitin attached to the protein interacts with the proteasome (allows for targeted degradation)
What is polyubiquitinylation?
multiple ubiquitin molecules are attached to a single lysine residue on a target protein
What are some other ubiquitin-like tags?
- SUMO (small ubiquitin-like modifier)
–> traget proteins have altered functions - ISG15 (is antiviral)
–> looks like 2 fused ubiquitin-like domains in one polypeptide chain
What are dietary amino acids used for?
can be used to make proteins, but can also be used to store energy for later
Organisms (do/do not) have a way to store amino acids for energy.
DO NOT
–> they use carbohydrates (glycogen) and lipids (triacylglyerols) for that
Amino acids can be converted to _________, using _______.What is the issue with this?
α-keto acids, using transaminase
AMINE CAN BE LOST AS AMMONIA
The glucose-alanine shuttle shows what processes?
- transamination
- oxidation deamination
Where does excess ammonia go?
UREA CYCLE
Excess ammonia (NH4+) to converted to what first?
carbamoyl phosphate
How do you convert NH4+ to carbamoyl phosphate? Where does this reaction take place?
NH4+ + HCO3- + 2ATP + H2O
—> (USING CARBAMOYL PHOSPHATE SYNTHETASE)
carbamoyl phosphate (1N) + 2ADP + Pi + 2H+
**rxn takes place in the mitochodria
The uera cycle (does/does not) use ATP
DOES
What is the first step of the urea cycle?
carbamoyl phosphate (1N) + omithine (considered the 21st AA) + Pi
—-> (**using omithine transcarbamoylase (OTC))
citrulline (3N)
–> citrulline is then transported form the mitochondrial matrix into the cytosol
What is the second step of the urea cycle?
***IN THE CYTOPLASM
citrulline + ATP + aspartate
—> (**using argiosuccinate synthetase)
arginosuccinate (4N) + AMP + H2O (dehydration)
P-Pi —> (using prophosphatse) 2Pi
What is the third step of the urea cycle?
aginosuccinate
—> (**using arginosuccinase)
aginine + fumarate
What is the fourth step of the urea cycle?
arginine + H2O
—> (**using arginase)
omithine + urea
–> omithine feeds back into the first step
–> urea –> blood –> kidney –> urine
Where does the urea cycle take place?
mitochondrial matrix (for the first step) and the cytoplasm (rest of the steps)
________-________ shunt connect the urea and _______ cycles. How?
Asparate-Arginosuccinate shunt, TCA
–> shunt connects with urea with arginino-succinate
–> shunt connects with TCA with malate and asparate
What is anaplerosis?
the process of “refilling” the TCA cycle with carbon molecules (intermediates) that have been used for other metabolic processes, such as biosynthesis
Anaplerosis: refills for pyruvate
3 carbon skeletons
alanine, cysteine, glycine, serine, threonine, tryptophan
Anaplerosis: refills for acetyl-CoA
2 carbon skeletons
isoleucine, leucine, lysine, threonine
Anaplerosis: refills for acetoacetate (ketone bodies)
2 carbon skeletons
leucine, lysine, phenylalanine, tyrosine
**I DON’T THINK YOU NEED TO KNOW
Anaplerosis: refills for α-ketoglutarate
5 carbon skeletons
arginine, glutamate, glutamine, histidine, proline
Anaplerosis: refills for succinyl-CoA
4 carbon skeletons
isoleucine, methionine, threonine, valine
Anaplerosis: refills for fumarate
4 carbon skeletons
phenylalanine, tyrosine
Anaplerosis: refills for oxaloacetate
4 carbon skeletons
asparagine, aspartate
(TCA –> AA degradation –> Urea) What is the 1st step?
α-ketoglutarate + amino acid
–> (**using amino-tranferase)
α-keto acid + glutamate (1N)
(TCA –> AA degradation –> Urea) What is the 2nd step?
glutamate + ATP + NH4+
–> (**using glutamine synthetase)
glumtamine (2N) + ADP + Pi + H2O
(TCA –> AA degradation –> Urea) What is the 3rd step?
glutamine (blood) —> glutamine (liver)
—> (**using glutaminase)
glutamate + NH4+
–> NH4+ (produced in 3rd and 4th step) is transported to either the liver (urea cycle) or kidney (urine)
(TCA –> AA degradation –> Urea) What is the 4th step?
glutamate
—> (**using glutamate dehydrogenase)
α-ketoglutarate + NH4+
–> NH4+ (produced in 3rd and 4th step) is transported to either the liver (urea cycle) or kidney (urine)
What happens in the glucose-alanine cycle?
(in muscle) glutamate transfers 1N to pyruvate –> alanine
(in liver) α-ketoglutarate gets 1N from alanine –> pyruvate
What’s the differences between the Cori cycle and the glucose-alanine cycle?
Cori cycle: lactate is transported through blood
glucose-alanine cycle: alanine is transported
Which amino acids when oxidized give the same number of carbons as TCA?
alanine, serine
they have 3 carbons
What can defective amino acid oxidation lead to?
- phenylketonuria (PKU): lack ability to degrade phenylalanine
- Albinism: tyrosinase defect
- Maple Syrup urine disease (MSUD): BCKDH defect
–> NOTE: BCKDH is similar to PDH and
Compounds at the beginning of the metabolic pathway (like ___________) are generally _________ ___________ _____________. Compounds at the end of the metabolic pathway (like __________) are generally __________ ___________ _________.
pyruvate, good electron donors
atomic oxygen (1/2 O2), good electron receivers
What is oxidative phosphorylation?
Using all the electrons generated from glycolysis and TCA to make a bunch of ATP through the electron transport chain
What is a key issue when it comes to the ETC? How?
PROBLEM OF COMPARTMENTALIZATION
–> How do you get the electron produced from glycolysis in the cytosol into the mitochondria? (since NADH cannot cross the mitochondrial membrance)
Electrons (are/are not) floating around in cells.
ARE NOT
**they are stored as NADH during glycolysis
NADH (can/cannot) cross the mitochondrial membrane.
CANNOT
ETC: what are the 2 main shuttles used to overcome compartmentalization?
- glycerol phosphate shuttle
- malate-aspartate shuttle (MAS)
What is the glycerol phosphate shuttle?
- (**IN THE CYTOPLASM) DHAP is reduced by NADH to glycerol-3-phosphate
- glycerol-3-phosphate is oxidized back into DHAP by an enzyme located in at the membrane (G3- AND DHAP NEVER ENTER)
–> this step turns FAD –> FADH2 (in the mitochondria) - FADH2 then enters complex II
What is the malate-aspartate shuttle (MAS)?
- aspartate + glutamate –> OAA
- OAA –> malate (NADH –> NAD+) **using malate DH
- malate enters the mitochondrial matrix and is exchanged with α-KG
- malate is converted to OAA in the TCA
- OAA and glutamate undergo a TRANSAMINATION rxn to give aspartate and α-KG
- asparate is exchanged with glutamate
- asprtate and α-KG undergo a TRANSAMINATION to give glutamate and OAA
Malate and aspartate are transported by exchange proteins in a ___:___ ratio.
1:1
For every malate into the mitochondria…?
1α-KG into the cytosol
For every aspartate into the cytosol…?
1 glutamate into the mitochondria
_____ and ______ are used to regenerate OAA and aspartate.
α-KG and glutamate
What are 5 biological e- carriers?
- pyridine linked dehydrogenases (e.g. NAD+ <–> NADH + H+, NADP+ <–> NADPH + H+)
- flavin linked dehydrogenases (e.g. FMN <–> FMNH2, fAD <–> FADH2)
- inorganic FeS centers (No H+, No Heme)
(F3+ <–> Fe2+) - cytochromes (heme; no H+)
(Fe3+ <–> Fe2+, Cu2+ <–> Cu+) - ubiquinone (Coenzyme A)
(e.g. Q –> QH –> QH2)
Details about pyridine linked dehydrogenases?
NAD+ <–> NADH + H+
NADP+ <–> NADPH + H+
free diffusable in the cell
carries 2 e-
Details about flavin linked dehydrogenases?
FMN <–> FMNH2
FAD <–> FADH2
tightly bound enzyme prosthetic groups
carries 2 e-
Details about inorganic FeS centers?
Fe3+ <–> Fe2+
No H+, No Heme
carries 1 e-
Details about cytochromes?
Fe3+ <–> Fe2+
Cu2+ <–> Cu+
Heme; no H+
carries 1 e-
Details about ubiquinone (coenzyme Q)?
Q –> QH –> QH2
membrane restricted, but shuttles e- between different membrane bound complexes
H+ and e- (ONE AT A TIME)
–> QH carries 1e-
—> QH2 carries 2e-
Why is ubiquinone membrane restricted?
due to its prenyl tail (~40 carbons in length)
What are the three redox states of CoA/ubiquinone?
- fully oxidized (ubiquinone)
- semiquinone (semiubiquinone)
- fully reduced (ubiquinol)
Ubiquinone has the capacity for both…?
1e- and 2e- transfer
Ubiquinone is a necessary _______ because…?
cofactor
because part of ETC can only accept 1e- at a time
How many protons does complex I pump out?
4 H+
How many protons does complex II pump out?
0
How many protons does complex III pump out?
4H+
How many protons does complex IV pump out?
2H+
What is the the “complex V”?
ATP SYNTHASE
Which complexes produced the proton gradient?
I, III, IV
buildup of positive charge, will be used by ATP synthetase
Complex V does what?
convert the proton gradient into ATP
What are the 2 key mobile electron carriers?
ubiquinone (coenzyme Q): carries 2 e-
cytochrome c (Cty c): carries 1 e-
Describe the pathway of NADH in ETC. How many protons does NADH pump?
NADH –> I –> Q –> III –> Cyt C –> IV
10H+ pumped
Describe the pathway of FADH2 in ETC. How many protons does FADH2 pump?
FADH2 –> II –> Q –> III –> Cyt C –> IV
6H+ pumped
For every 1 ATP generated…
Explain why.
4 PROTONS PUMPED
4th proton is needed in order to transport Pi, ATP and ADP across the mitochondrial membrane
How much ATP is 1 NADH?
10 protons –> 2.5 ATP
How much ATP is 1 FADH2?
6 protons –> 1.5 ATP
What is the name of complex I?
NAD Dehydrogenase
Describe what happens in complex I.
uses NADH electrons to pump protons into the intermembrane space
–> PUMPS 4H+ AGAINST THE GRADIENT, COSTS ENERGY
uses FMN (flavin mononucleotide)… e- are then transferred to membrane bound ubiquinone (UQ)
What is the name of complex II?
succinate dehydrogenase
Complex II is an enzyme in the…?
TCA CYCLE
Describe the what happens in complex II.
The FADH2 generated from the TCA cycle never left the enzyme
e- are instead transferred to ubiquinone (UQ)
**has Fe-S centers
What is the name of Complex III?
cytochrome c oxidoreductase
Describe what happens in complex III.
harvest the electrons from ubiquinone made in complexes I and II
e- are transfered to a molecule called cytochrome c
energy generated in this reaction pumps more protons across gradient (4H+)
**has Heme group
What is the name of complex IV?
cytochrome oxidase
Describe what happens in complex IV.
harvests the electrons from cytochromc made in complex III
e- are transferred to molecular oxygen –> makes water
energy generated from this reaction pumps more protons across gradient
**has heme group
What complexes give their electrons to ubiquinone?
complex I and II
Complex III transmits ________ to _________, which is a __________, not _________-________ electron carrier.
ubiquinone to cytochrome c, which is a soluble, not membrane-bound electron carrier
Cytochrome c electrons are transferred to ___________, which is the final electron sink.
OXYGEN
MAKES THE WHOLE THING AEROBIC
__________ is the final electron acceptor of aerobic metabolism.
OXYGEN
What is ATP synthase made of? Describe each part.
F0: the anchor (3 main subunits: a, b, c)
F1 (3 copies of each of subunits α and β, and 1 each of subunits γ, δ and ε) –> 5 different TYPES of subunits
Details about F0 of ATP synthase.
is the anchor, embedded into the inner membrane
is the motor (c subunits) that rotates as protons pass through it
Details about F1 of ATP synthase.
mushroom faces the mitochondrial matrix
–> alpha and beta form the mushroom
–> the stem is make of gamma, delta, epsilon
Describe the proton gradient.
HIGH TO LOW
For every turn of ATP synthase, how many ATP is produced?
~3-4 ATP
To produce 1 ATP, the ATP synthase needs to rotate how many degrees?
120
ATP does how many rotations/second? Which how much rpm?
230
~20,000rpm
In mitochondria, what direction does the ATP pump protons? Please also describe the acidity of each side.
matrix (inside): low H+
intermembane space (outside): high H+
ATP synthase pumps from outside (intermembrane space) to inside (matrix)
In chloroplasts, what direction does the ATP pump protons? Please also describe the acidity of each side.
thylakoid lumen (inside): high H+
stroma (outside): low H+
ATP synthase pumps from inside (thylakoid lumen) to outside (stroma)
