Week 2 Biochem Flashcards
The Pentose phosphate pathway creates ______ to use for ________ in anabolism.
- NADPH
2. Reducing Power
After becoming G-6-P in the cells, glucose undergoes ________ to yield ______. In anaerobic cells, this is then converted into ______. In aerobic cells, it then enters the _______, is utilized in ________, and yields ______.
- Glycolysis
- TWO Pyruvate
- Lactate
- Mitochondria
- The electron transport chain
- ATP
The GLUT-2 transporter is found in _______, and is characterized as _______.
- The Liver
2. Insulin-Independent
The GLUT-4 transporter is found in _______, and is characterized as _______.
- Skeletal muscle and adipose tissue
2. Insulin-Dependent
_______ is the only metabolic process that is able to produce ATP anaerobically. It is also said to be ________, because regulation of it may be different between species/life forms.
- Glycolysis
2. Ubiquitous
Glucose is structurally considered an ___________, meaning that it has: _______
- Aldo-hexose
2. An aldehyde on the end of its 6-carbon chain
Pyruvate is structurally considered an _______.
Alpha keto acid
Glycolysis inputs: (which is oxidizer/reducer)
Glycolysis outputs:
- Inputs:
- 2 ATP = oxidizer
- 2 NAD+ = reducer
- Outputs:
- 2 NADH (reduced)
- 4 ATP (oxidized)
Glycolysis is broken into 2 Stages:
The first stage involves ________ and is referred to as the ________. The second stage involves ______ and is referred to as the _________.
- Input of 2 ATP
- Priming stage
- Oxidation of ATP to yield a net of 2 ATP
- Payoff Stage
Describe how one might also split glycolysis into 3 phases:
Stage 1: Activation= 2 ATP consumed
Stage 2: Isomerization= Splitting of hexose-bisphos.
Stage 3: Oxidation: Of Glyceral-3-P to form ATP/NADH
What are the 3 types of rxns involved in glycolysis?
- Breakdown of carbon skeleton
- Phos. of ADP
- Formation of reduced coenzyme - NADH
The first step of glycolysis consumes a molecule of ATP and is therefore considered to be _______.
Exergonic
What is the most important regulatory enzyme of glycolysis? Why? Also, What type of enzyme is this?
- Phosphofructokinase-1 (PFK-1)
- After it conducts its catalytic activity, the molecule MUST continue through glycolysis to yield pyruvate.
- Allosteric Enzyme
The glycolytic pathway is OVERALL considered to be ______.
Exergonic
Why is the 4th step of glycolysis driven toward a net breakdown of G-6-P?
Because the products of that reaction are taken away, creating a need for more to be made.
ALL reactions of the glycolytic pathway occur in _______.
The Cytoplasm
What are the 4 major fates of Pyruvate after being formed from glycolysis?
- Acetyl CoA: For mitochondrial ATP production
- Ethanol: In yeasts/bacteria to produce NAD+ and continue glycolysis anaerobically
- Lactate: Same as ethanol, but in eukaryotes
- Oxaloacetate: 1st step of gluconeogenesis
Why must the cell maintain separate pools of NAD+/NADH?
The NADH molecule signals that the cell is in a high energy state and is therefore regulatory in nature. Since reactions are occurring separately in the cytoplasm and mitochondria, they must each have their own pool as a regulator.
Which enzyme catalyzes the conversion of pyruvate to L-Lactate in anaerobic metabolism
Lactate Dehydrogenase
When does the reverse reaction (L-Lactate becomes Pyruvate) occur?
Under Aerobic Conditions
Red blood cells have no ______, and therefore they can only use ______ to generate ______. This means they are constantly undergoing ______.
- Mitochondria
- The Glycolytic Pathway
- ATP
- Lactic Acid Fermentation (Lactate–>Pyruvate)
What is the main point of alcoholic fermentation of pyruvate to ethanol in yeasts?
To produce NAD+ for the glycolytic pathway to continue
In the presence of oxygen, newly formed pyruvate will then ________ in order to ______.
- Enter the mitochondria
2. Complete Oxidation
In order to enter the mitochondria, pyruvate must be ______ to form the ______.
- De-carboxylated (by Pyr. De-H-ase)
2. Pyruvate Dehydrogenase Complex
Pyruvate entering the mitochondria will ultimately form _____ which will go on to be used in ______.
- Acetyl CoA
2. The T.C.A. cycle
What is the function of Insulin?
To move GLUT-4 transporters from the cytoplasm (basal state) to the cell surface to allow uptake of glucose in response to glucose intake
Why is Glucokinase not regulated? How IS Hexokinase regulated?
- Because in the liver, Glucose uptake is constantly possible due to GLUT-2 transporters
- By Glucose-6-Phosphate formation. A buildup will signal these cells that Glycolysis can be inhibited (feedback inhibition).
How is PFK-1 DOWN regulated? (2)
- An abundance of ATP will signal that the cell is in a high energy state and exhibit feedback inhibition on PFK-1
- An abundance of Citrate from the C.A.C.
How is PFK-1 UP regulated? (2)
- Abundant AMP signals a low energy state.
2. Fructose-2,6-Bisphosphate affects substrate affinity
Insulin from Beta Cells ________ glycolysis.
Glucagon from Alpha Cells ______ glycolysis.
Both are able to determine levels of ______ in the ______.
- Stimulates
- Decreases
- Fructose-2,6-Bisphosphate
- Liver
The insulin receptor activates a ________ and almost always ultimately regulates metabolic pathways by activating _______.
- Receptor Tyrosine Kinase
2. Phosphatases
What is the function of PFK-2? What enzyme reverses this action?
- To convert Fructose-6-Phosphate into Fructose-2,6-Bisphosphate.
- Fructose-2,6-Bisphosphatase
What effect does Insulin have by activating phosphatases in liver cells?
Those phosphatases DEphosphorylate PFK-2 in order to INCREASE its sugar KINASE activity of converting Fructose-1,6-BP into Fructose-2,6-BP, but also DECREASE its sugar PHOSPHATASE activity.
*Ultimately= INCREASE Fructose-2,6-BP to be converted into Fructose-1,6-BP
What enzyme converts Fructose-2,6-BP into Fructose 1,6-BP? Under what conditions does this reaction occur?
- PFK-1
- High blood sugar: Since the liver is freely taking up glucose, this is when Insulin can signal the liver to speed up glycolysis (due to an abundance of glucose).
What happens when Glucagon binds its glucagon receptor?
The GPCR pathway activates PKA, which phosphorylates PFK-2. This INHIBITS its sugar kinase and ACTIVATES its sugar phosphatase, REDUCING the amount of Fructose-2,6-BP in the liver cells, and slowing glycolysis.
Why does an increase in Fructose-2,6-BP speed up glycolysis?
It INCREASES the affinity of PFK-1 for its substrate, Fructose-6-Phosphate (lowers its Km).
Pyruvate Kinase is inhibited by ____ and ____. It is activated by _____ and ______.
- ATP (high energy intermediate)
- Acetyl CoA (fuel from FA oxidation)
- AMP abundance (low energy intermediate)
- Fructose-1,6-BP (feed-forward mechanism because it has been committed)
How does Glucagon in the LIVER regulate Pyruvate Kinase activity?
The end result of Glucagon binding its receptor in the liver is activation of a KINASE, which phosphorylates Pyruvate Kinase to deactivate it and inhibit glycolysis.
In the Liver, Fructose can enter Glycolysis at the ______ stage.
3-Carbon (as DHAP and G-3-P)
Fructose is structurally considered a _______.
Keto-Hexose
What is the first step of Fructose metabolism (in the liver) for use in glycolysis?
Fructokinase converts it into F-1-P
What is the second step in Fructose metabolism (in the liver) for use in glycolysis?
Aldolase B converts F-1-P into DHAP and glyceraldehyde
Why is deficiency of Fructokinase considered benign but deficiency of Aldolase B is potential lethal?
Because Fructose can be readily metabolized and excreted in the urine, whereas a build up of F-1-P will lead to liver problems since there will be a loss of hepatic phosphate (decreased hepatic ATP) since the phosphate is tied up in F-1-P.
What is the 1st step in Fructose metabolism in the muscle for use in glycolysis?
Phosphorylation by Hexokinase, converting it into F-6-P which enters directly into glycolysis
If a person has Aldolase B deficiency, what dietary restrictions must they implore and why? If a person has a deficiency in ANY of the 3 Galactose metabolizing enzymes, what dietary restrictions must they implore and why?
- Fructose avoidance (i.e. Sucrose, Fructose, honey, etc.) because the buildup of F-1-P will occupy all liver phosphate.
- Lactose avoidance because it can form galactose and cause buildup in the liver.
What are the 3 counter-regulatory hormones of Insulin?
- Glucagon
- Epinephrine
- Cortisol
In the absence of cAMP, PKA exists as _______. This form consists of _________.
- An inactive tetramer
2. TWO regulatory and TWO catalytic subunits
What specifically does binding of cAMP to PKA cause?
Dissociation of the catalytic subunits that act as protein kinases
List the 3 common catabolic pathways:
- TCA Cycle
- Electron Transport Chain
- ATP synthesis (Cellular Respiration)
What is the link between glycolysis and the TCA cycle for the complete oxidation of glucose?
The Pyruvate Dehydrogenase Complex
What are the 3 soluble substrates for the PDH complex?
- Pyruvate
- Coenzyme A
- NAD+ (electron acceptor)
What are the 3 enzyme-bound CoFactors of the PDH complex?
- Thiamine-Pyrophosphate (Vitamin B1)
- Lipoic Acid
- FAD+/FADH2 (electron acceptor)
What makes the PDH so efficient?
Each reaction is coupled to the next through channels within the enormous enzyme complex
At the end of one cycle of AcetylCoA formation (by the Pyruvate Dehydrogenase complex), what are we left with and how does it re-enter the cycle?
- NADH
2. It enters the electron transport chain to be converted back into NAD+.
What kind of feedback inhibition does the PDH complex exhibit?
- Buildup of NADH and AcetylCoA inhibit the PDH complex from making more of them.
- Buildup at ATP will inhibit allosterically , while ADP buildup will stimulate allosterically.
How do kinases and phosphatases play a role in regulation of the PDH complex?
- Phosphorylation by PDH complex kinase will DECREASE activity of it.
- Dephosphorylation by the PDH complex phosphatase will INCREASE activity of it.
What factors increase the PDH activity? (2)
Insulin and Ca2+
What enzyme converts pyruvate into oxaloacetate?
Pyruvate carboxylase
What does “TCA Cycle” stand for?
Tricarboxylic Acid Cycle
What does the TCA cycle facilitate?
Complete oxidation of AcetylCoA to CO2
Name the Tricarboxylic Acid referred to in the TCA Cycle:
Citrate (Citric Acid)
Where does the TCA cycle occur?
In the Mitochondrial Matrix
In the TCA cycle, electron are accepted by _______ to form the reduced coenzymes _______.
- NAD+ and FAD
2. NADH and FADH2
How is the TCA cycle amphibolic?
Its ultimate goal is to form energy molecules, NADH and FADH2, but many of its intermediates, like Citrate, can be used to form fatty acids and steroids for example.
How is the TCA cycle anaplerotic?
May intermediates of the cycle can be put back into the cycle to continue along in it and produce energy.
What happens to the oxaloacetate used in the 1st step of the TCA cycle? Why is this important?
It is eventually reformed during the cycle. This shows that there is no net change in the amount of inputs used in the cycle.
Which is the only enzyme involved in the TCA that is actually embedded in the mitochondrial membrane?
The Succinate Dehydrogenase Complex
Activators and Inhibitors of Citrate Synthase:
Activators: -Ca2+ -ADP Inhibitors: -ATP -NADH -Succinyl-CoA (feedback from committed steps)
Why is calcium an activator of several metabolic enzymes in the TCA cycle and other pathways?
It is a signal from muscle cells that there is a high energy demand due to muscle contraction.
Activators and Inhibitors of Isocitrate De-H-ase:
Activators: -Ca2+ -ADP -NAD+ Inhibitors: -ATP -NADH
Activators and Inhibitors of Alpha-Ketogluturate De-H-ase complex:
Activators: -Ca2+ -AMP Inhibitors: -ATP -GTP -NADH -Succinyl CoA
What is the most important regulator of the TCA Cycle and why?
- AMP
- Because it’s change in concentration from a rest to exercise state exhibits an almost 1000 fold increase, which is much more obvious than the same relative change in ADP or ATP.
Define Anapleresis:
“Filling Up”, which implies that reactants in these reactions exhibit no net change in amount in any one cycle, and have a duel nature to create energy molecules as well as materials for biosynthesis of other biomolecules.
i.e. The intermediates are replenished
What are 3 other ways that intermediates can enter the TCA Cycle?
- Pyruvate —> Oxaloacetate
- Aspartate —> Oxaloacetate
- Glutamate —> Alpha-KG
Define Transamination:
Transferring an Amine group from an Amino Acid to an alpha-keto acid to form a NEW Amino Acid and a NEW alpha-keto acid.
Describe the reaction that Aspartate undergoes to enter the TCA cycle: (Give the type of Reaction and Enzyme responsible as well)
- Transamination
- Aspartate Transaminase (and Vitamin B6)
- Aspartate in abundance donates an amino group to alpha-KG to form Glutamate, while accepting Aspartate itself becomes Oxaloacetate.
Describe the reaction that Glutamate undergoes to enter the TCA cycle: (Give the Enzyme responsible as well)
- Glutamate De-H-ase
2. Glutamate gets rid of ammonia (NH3) to become alpha-KG, but can also work in reverse.
The ETC essentially functions to move electrons directly into ________ in order to power ________. This creates ________ which is used for ______.
- The mitochondrial inner membrane
- The pumping of protons into the inter-membrane space
- A pH gradient
- The formation of ATP
Define Cristae:
Highly convoluted folds of the inner mitochondrial membrane
While the outer mitochondrial membrane is ______ (and contains lots of ______ to give it rigidity, the inner membrane is actually ______ does not contain this substance.
- Not very selective (highly permeable)
- Cholesterol
- VERY selective
What is meant by Oxidative Phosphorylation?
ADP + Pi —> ATP
List the 5 components of the ETC:
- Flavoproteins
- Copper-Containing Proteins
- Iron-Sulfur Proteins
- Ubiquinone
- Cytochromes
Flavin structure has ______, making it very ______. This is important because ______.
- THREE Rings
- HYDROPHOBIC
- When it transfers electrons it releases them AS hydrogen atoms.
Ubiquinone possesses a ___________, making it very _______.
- 30-50 Carbon tail
2. Hydrophobic
Cytochrome molecules contain __________, which consists of _______. They are involved in ______.
- A heme group
- A porphyrin ring and an Iron atom
- 1 electron transfer
How do Iron-Sulfur proteins differ from Cytochromes? How are they similar?
- (Differ) Their Iron atom is attached to Cysteine or FREE sulfur inside of a protein, but NOT heme.
- (Similar) They are both involved in 1 electron transfer.
Copper-bound ions are involved in ______.
1-electron transfer
Which is the only 1 of the 5 components involved in ETC complexes that is associated with MORE than 1 electron transfer?
Flavoproteins (Flavin)
Of the 5 ETC complexes, which are involved in electron transfer? What is the goal of the other complexes?
- Complexes 1-4 are involved with electron transfer
2. Complex 5 is the ATP synthase that functions in assembly of ATP
Ubiquinone is also called ______.
Coenzyme Q
What is the chemiosmotic hypothesis?
ATP synthase is driven by the electrochemical gradient created by the pumping of protons from the mitochondrial matrix to the inter-membrane space.
The electrochemical gradient favors ________.
The movement of H+ back into the mitochondrial matrix
Protons pass through a ________ located in _______. ATP synthase then catalyzes _______.
- H+ channel (back into the matrix)
- The base of ATP synthase
- The phosphorylation of ADP
Describe the 2 components of ATP synthase:
- F-0:
- Integral to the membrane
- Hydrophobic
- IS the transmembrane channel for H+ movement
- F-1:
- Catalyzes ATP synthesis
- Coupled to rotation unit (gamma subunit)
- TURNS as protons pass through F-0
How SPECIFICALLY is the proton gradient harnessed for ATP synthesis?
The passing of H+ through the F-0 channel POWERS the rotation of the gamma subunit that moves the catalytic F-1 subunit
How does ADP get back into the mitochondrial matrix? (And vice versa, how does ATP leave the matrix?)
The ADP/ATP Translocase exchanges them through both membranes and is powered BY the same proton gradient.
What is Atractyloside?
A plant toxin that can inhibit the ADP/ATP Translocase by blocking ADP entry into the matrix
What is the difference between primary and secondary active transport?
Primary: Relies on ATP hydrolysis to power activity
Secondary: Relies on concentration gradient of some other source for power
What is the MAIN control of ATP synthesis?
The availability of ADP in the matrix controls oxygen consumption for ATP synthesis
How many ATP equivalents can be produced from 1 molecule of:
- NADH: ____
- FADH2: ____
- NADH = 2.5
2. FADH2 = 1.5
What 3 processes must be considered in tallying the total number of ATP molecules that can be produced from ONE substrate level phosphorylation and the oxidation of NADH and FADH2?
- Glycolysis
- PDH Complex
- TCA Cycle
Why do early models of maximal ATP production per substrate level phosphorylation exhibit OVER-estimation of total ATP production?
Because they don’t take into account that we lose some of the proton gradient due to the Phosphate-Hydrogen symporter and also to the ADP/ATP-Translocase.
