Exam 3 Study Questions Flashcards
What is a carbohydrate?
Carbohydrates are built from monosaccharides
Monosaccharides consist of three to nine carbon atoms w/ the empirical formula of (C-H2O)n
“Carbon Hydrate”
What is the difference between monosaccharide, disaccharide and polysaccharide?
Monosaccharide are aldehydes or ketones with multiple hydroxyl groups
Disaccharides are 2 monosaccharide (Ex:Sucrose, lactose, and maltose)
Polysaccharideslong are chains of monosaccharide units bound together by glycosidic linkages (Ex: glycogen)
How are sugars bound together?
glycosidic bonds
What’s the differene between glycogen, starch & cellulose?
Glycogen is a storage polyksaccharide. It consist of repeating glucose subunit held together by glygocidic bonds. It also contains branches of glucose polymers.
Starch is a storage polysaccharide. Unbranched starch is called amylose. Branched starch is called amylopectin.
Cellulose is a structural polysaccharide. It consist of polymers of glucose also connected by glycosidic bonds. Forms long chains b/c of beta configuration. Human don’t express cellulase and can’t break it down. (Linear)
What is dietery fiber?
Dietary fiber consist of insoluble and soluble fiber.
Cellulose can’t be broken down and is considered insoluble fiber. It speeds up the rate that digestive products travel through the intestines.
Pectin (polygalacturonic acid) is soluble fiber. It slows the movement of food through the digestive track to allow for better uptake of nutrients.
What are glycosaminoglycans?
They are polysaccharide chains made of repeating disaccharide units.
Typically contain disaccharide repeats of amino sugars
What are proteoglycans?
Proteoglycans are proteins attached to glycosaminoglycans. 95% of biomolecule is polysaccharide. Most of the weight come from carbohydrate.
The majority is carbohydrate with a little bit of protein. The carbohydrates allow this tissue to be spongy. Carbohydrates are very polar, water loving. Needed for cushion on th knees and elbows. Function as lubricants.
Structural component of the connective tissue that adheres cells to the extracellular matrix
It’s the glycosaminoglycans that are attached to this protein making it a proteoglycan.
What is EPO?
A glycoprotein hormone erythropoietin (EPO) secreted by the kidneys and stimulates the production of red blood cells.
It is also a performance enhancing drug that enhances red blood cells production. This means you can carry more oxygen to your tissues and perform better.
It’s glycosylated.
The mature EPO is 40% carbohydrate by weight, and glycosylation enhances the stability of the protein in the blood.
How is ABO blood type defined?
It’s the difference in a specifc carbohydrate that is on the surface of protein (red blood cells).
Glycosyltransferases are repsonsible for generating the ABO blood groups.
Where does protein glycosylation occur and what is it?
In the lumen of the ER & Golgi complex
It’s adding a sugar to a protein.
What are lectins?
Lectins are specific carbohydrate binding proteins.
These are glycan-binding proteins that bind specific carbohydrate structures on neighboring cell surfaces.
Lectins contain two or more binding sites for carbohydrate units.
Mediate cell-cell contact in animal cells. Lectin on one cell interacts w/ specific carbohydrate on another cell.
Lectin normally found in plants & selectin normally found in animals. Selectins are normally membrane bound. They are important to getting the white blood cells to the wound site.
What is H1N1 and how does it contribute to viral infection?
H1N1 indicates the proteins present on the viral surface.
- Hemagglutinin on virus binds to sialic acid on proteins embedded in host cell membrane
- Neuraminidase cleaves glycosidic bonds of sialic acid to allow the virus to infect the cell
We have evolved to protect ourselves and on the surface of all of our cells is sialic acid. It’s moist and sticky. It prevents bacteria from binding to the surface of our cells and doing bad things to our cells. Influenza has figured out a way to use sialic acid to infect us. Influenza has a lipid bilayer and embedded in that bilayer (hemagglutinin - a lectin) & (neuraminidase). Hemagglutinin binds to and recognizes sialic acid, (it’s a lectin that recognizes sialic acid). It binds to the to the surface of the cells and it’s now attached to your cells. Neuraminidase has the ability to cleave neuraminate and cut sialic acid off the surface of your cells allowing it to penetrate the plasma membrane and being able to inject its genetic info into your cells.
What is catabolism?
Metabolic reactions that transform fuels into cellular energy are called catabolic reactions or, more generally, catabolism.
Fuel (carbohydrates, fats) → CO2 + H2O + useful energy
The break things down, converting enery in the bonds into biological useful froms (ATP). Energy is being released.
What is anabolism?
Those reactions that require energy—such as the synthesis of glucose, fats, or DNA—are called anabolic reactions or anabolism.
Useful energy + simple precursors → complex molecules
Anabolic build up, need ATP for things to happen. An input of energy is needed.
What is amphibolic?
Either anabolic or catabolic depending on the energy conditions of the cell.
Why is ATP so useful & efficient in terms of being a phosphoryl group donor?
ATP is an effeicient phosphoryl-group donor because of:
- Resonance stabilization
- Electrostatic reupulsion
- Stabilization due to hydration
When there is a free inorganic phosphate, there are more choices for the electrons. There are also 3 phosphoryl groups in a row all with negative charges. The last guy doesn’t want to be there. Like charges repel. More water can surround ADP than ATP.
This intermediate position enables ATP to function efficiently as a carrier of phosphoryl groups. ATP falls right in the middle.
Why is ATP hydrolysis so effecient?
Because ATP hydrolysis is exergonic. Large amounts of free energy is liberated when ATP is hydrolysized.
Delta G° = -7.3 kcal/mol
How are metabolic processes regulated?
- Controlling the amount of enzyme
- synthesis and degradation
- Controlling catalytic activity
- Reversible allosteric control or reversible covalent modification controlled by hormones or energy
- Conrolling the acceibility of substrates
- Compartmentalization of eukaryotic cells segregates opposed reactions
How does energy charge regulate metabolism inside a cell?
- ATP-generating pathways are inhibited by high energy charge (catabolic)
- ATP-utilizing pathways are stimulated by high energy chage (anabolic - building something b/c you broke down ATP)
When you need to make ATP you’re doing catabolic pathways b/c your breaking down molecules to generate ATP
At high energy charge you have a lot of ATP so you’re going to use it so there’s going to be biosynthesis happening
Low energy charge it means there is not much ATP and you have to make it. You have to pull out the glucose reserves and break it down so you can generate ATP, pull out the fat reserves from breaking it down, from the oxidation of these molecules
What is glycolysis?
Glycolysis is the sequence of reactions that metabolizes one molecule of glucose to two molecules of pyruvate with the concomitant net production of two molecules of ATP.
This process is anaerobic (i.e., it does not require O2).
Where does glycolysis happen?
In the cytoplasm
Is oxygen necessary for glycolsyis?
No
What are the products of glycolysis?
2 net ATP & 2 net NADH
What is hexokinase?
It’s an enzyme that traps glucose in the cell and begins glycolysis.
It phosphorylates glucose on the 6th carbon. This is important because there are no transporters for phosphorylated glucose inside the cell so it can’t leave. ATP (a kinase) is the source of phosphate.
The addition of the phosphoryl group acts to destabilize glucose, thus facilitating its further metabolism.
What is glucose 6-phosphate and what happens to it?
It’s phosphorylated glucose and it gets isomerized to fructose 6-phosphate.
(changes from cicurlar to linear)
What happens to fructose 6-phosphate?
Fructose 6-phosphate gets phosphorylated by phosphofurctokinase (PFK) to fructose 1,6-biphosphate.
It’s phosphorylating fructose that has already been phosphorylated.
How is glycolysis regulated in muscle?
It is regulated by PFK, Hexokianse & Pyruvate kinase.
How is PFK regulated in the muslce?
At high energy charge, ATP turns PFK off and AMP turns PFK on.
It’s allosterically inhibited by ATP (lower affinity for furctose 6-phosphate)
AMP reverses inhibitory effect of ATP
At high energy charge ATP allosterically regulates PFK in a negative way. There is a negative effect of ATP onto PFK.
You have enough ATP, you don’t need to do the pathway that will generate ATP, it slows down the enzymes.
How is hexokinase inhibited?
Once PFK is slowed down, you have a build up of fructose 6-phosphate which leads to a build up of glucose 6-phosphate which will negatively inhibit hexokinase, when there is a lot of glucose 6-phosphate is present then hexokinase is inhibited, it’s not directly inhibited by energy charge, it’s an indirect effect. The glucose 6-phosphate gets pushed into another pathway to generate glycogen
It’s inhibited by glucose 6-phosphate when PFK is inhibited
What happens with glycolysis when you have low energy charge in your muslces?
Glycolysis is stimulated.
When you decide to exercise in sec you use up all of your available ATP in your muscles, you have to make more by high AMP, you have low energy charge, it positively regulates PFK, also have a positive regulation of pyruvate kinase. Hexokinase doesn’t do anything b/c there isn’t any build up anymore.
Hexokinase is inhibited by a feedback mechanism when PFK slows down.
How is pyruvate kinase inhibited in muslce during glycolysis?
Allosteric inhibition by ATP and alanine
Activted by furctose 1,6-phisphoshate
ATP turns it off
Why does phosphoenolpyruvate (PEP) have high phosphoryl-transfer potential?
Because PEP is a very unstable intermediate, thermodynamically it doesn’t want to exisist. There are two negatie charges right next to each other and a double bond.
It’s good b/c it generates enough energy to generate a pyruvate and an ATP in the process.
Phosphate leaes 1st & left w/ pyruvate in a enol-keto conversion
The high phosphoryl-transfer potential of phosphoenolpyruvate (PEP) arises primarily from the large driving force of the subsequent enol–ketone conversion.
•Hydrolysis of 2-phosphoglycerate has Delta G = -3 kcal/mol •Hydrolysis of PEP has Delta G = -15 kcal/mol
How does the liver maintain blood-glucose levels?
–Stores glucose as glycogen when glucose is plentiful
–Releases glucose when supplies are low
What regulates PFK in the liver?
How is it regulated?
Fructose 2,6-biphosphate
•Fructose 6-phosphate rises when blood glucose concentration is high
–Accelerates synthesis of fructose 2,6-bisphosphate
–F-2,6-BP stimulates PFK in feedforward stimulation
When there is a build up, of fructose 6-phosphate, what your going to do is shuttle some of it off into fructose 2,6 BP, which tells PFK to hurry up and make more F-1,6-BP.
What you’re doing is generating a molecule that allosterically activates PFK. B/C PFK doesn’t care about energy charge when it’s in the liver.
The presence of F-2,6-BP in the liver tells PFK 1 you better get going, we need more ATP
How is pyruvate kinase in the liver regulated?
It’s regulated two ways.
(1) Its regulated allosterically by ATP
(2) It is also regulated in a covalent kind of fashion, it is phosphorylated in the presence of low glucose so that it becomes and remains less active. And then when glucose levels are high, it can get dephosphorylated and regain it’s activity.
Showing that both (L&M) are still allosterically controlled by energy charge. So high levels of ATP turn down pyruvate kinase.
The L form has the ability to be phosphorylated. So pyruvate kinase is phosphorylated when there is low blood glucose. So it more permanently turns it off than just the allosteric control of ATP.
So blood glucose is low, no need to worry about any pyruvate kinase activity in the liver b/c all of the glucose that’s available needs to go to the brain. So, this is phosphorylated, remains in a less active state, until blood glucose levels are high enough. It gets dephosphorylated and back into a more active state.
What is gluconeogenesis?
What do you start and end with?
Gluconeogensis converts pyruvate into glucoes. Examples of pyruvate include lactate, amino acids & glycerol.
How is pyruvate kinase overcome in gluconeogenesis?
Conversion of pyruvate into PEP goes through oxaloacetate.
How does glucose 6-phosphatase work?
It’s an integral membrane protein of the ER
There is a transporter that brings this in, the enzyme is embedded in the membrane and the active site is open to the lumen, then glucose 6-phosphate comes it, gets diphosphorylated, and each will go out through it’s own transporter and you now have glucose in the cytoplasm of the liver cell that can now be released out into the body if the rest of the body needs glucose
How does energy charge determine whether glycolysis or gluconeogensis is most active?
If you have a lot of ATP, Citrate, H+, there is positive energy charge and it will inhibit PFK1. At the same time it will stimulate fructose 1,6-biphosphatase.
If you have low energy charge (a lot of AMP) it will stimulate PFK1 and inhibit fructose 1,6-bisphosphatase.
How is balance regulated between glycolysis and gluconeogenesis in the liver?
Balance is regulated by a bifunctional enzyme.
•Fructose 2,6-bisphosphatase and PFK2 are on the same polypeptide
–Regulatory domain
–Kinase domain
•P loop NTPase domain
–Phosphatase domain
•Activity controlled by reversible phosphorylation of a serine residue
How does the bifunctional enzyme balance glycolysis and gylconeogensis?
A low blood-glucose level as signaled by glucagon leads to the phosphorylation of the bifunctional enzyme and hence to a lower level of fructose 2,6-bisphosphate, slowing glycolysis. High levels of fructose 6-phosphate accelerate the formation of fructose 2,6-bisphosphate by facilitating the dephosphorylation of the bifunctional enzyme.
Explain The Cori Cycle of lactate metabolism.
showing the relationship b/w the liver and the muscle
muscle is taking glucose out of the blood, it’s doing glycolysis, the pyruvate is going to lactate, it’s out pacing aerobic respiration, it doesn’t care, lactate goes into the blood stream, the lactate is picked up by the liver, goes back to pyruvate, pyruvate goes through gluconeogenesis, to generate glucose, that goes out into the blood stream, and should be used by the brain, but it is used by the muscle
Explain pathway intergration.
Pathways cooperate during a sprint
Muscle cell is using the glucose. It also uses some of it’s glycogen stores. We go through glycolysis getting to pyruvate. Some of the muscle will be able to fully oxidize this. But it has a lot of pyruvate, so it’s going to go to lactate. It made a enough NAD+ so it can keep using up glucose. But it gets rid of the lactate. The lactate will go the the cardiac muscle cells, it goes in as lactate and then oxidized back to pyruvate. The blood glucose is also powering your heart. The heart will also take some glucose away from glycogen stores. The over all point of the heart is to beat, absolutely need ATP for contraction. That’s all the heart worries about. So nothing is coming out of the cardiac cell.
The lactate can also go into the liver. The liver can generate some ATP for its own purposes. It can also take the pyruvate and break down protein or fat. We can get gluconeogenesis going.
What is the overall point of he citric acid cycle?
The citric acid cycle oxidizes two-carbon units, producing two molecules of CO2, one molecule of ATP, and high-energy electrons in the form of NADH and FADH2.
To make high energy electron carriers from carbon fuels.
What are the two states of cellular respiration?
*the enzyems for the citric acid cycle are found in the matrix of the mitochondria.
What are three steps that catalyze the pyruvate dehydrogenase complex?
- Decarboxylation
- Oxidation
- Formation of acetly CoA
What is pyruvate dehydrogenase?
•Enzyme complex consists of three enzymes and five coenzymes
–Enzymes include pyruvate dehydrogenase component, dihydrolipoyl transacetylase, and dihydrolipoyl dehydrogenase
–Coenzymes include catalytic cofactors thiamine pyrophosphate (TPP), lipoic acid, and FAD; and stoichiometric cofactors CoA and NAD+
In regards to the pyruvate dehydrogenase enzyme complex, which component catalyze the decarboxylation?
Pyruvate dehydrogenase catalyzes
Pyruvate combines with TPP and becomes decarboxylated
In regards to the pyruvate dehydrogenase enzyme complex, which component catalyze the oxidation?
Pyruvate dehydrogenase component catalyzes the oxidation
•Hydroxyethyl group on TPP is oxidized to form an acetyl group while simultaneously transferred to lipoamide
–Produces an energy-rich thioester bond
In regards to the pyruvate dehydrogenase enzyme complex, which component catalyzes acetyl CoA formation?
Dihydrolipoyl transacetylase catalyzes acetyl CoA formation
This enzymes moves the acetyl gorup onto Coezyme A
What does dihydrolipyl dehydrogenase do?
It regenerates the lipoamide
How is pyruvate dehydrogenase complex regulated?
There is an allosteric component & covalent modification component
•Acetyl CoA formation is an irreversible step. Therefore regulation of the pyruvate dehydrogenase complex is tightly controlled
–Allosteric regulation
- Acetyl CoA inhibits the dihydrolipoyl transacetylase
- NADH inhibits the dihydrolipoyl dehydrogenase
–Covalent modification
- Phosphorylation inhibits enzyme activity when energy charge is high
- NADH, Acetyl CoA, and ATP activate kinase activity to inactivate the PDH complex
- ADP and pyruvate inhibit the kinase to activate the PDH complex
- Ca+2 also activates the phosphatase to activate the PDH complex
How does energy charge regulate pyruvate dehydrogenase (PDH) complex?
Phosphorylation inhibits enzyme activity when energy charge is high.
Things that are high energy charge:
ATP, Acetyl CoA, NADH negatively effects
ADP & pyruvate positively effects this
In the citric acid cycle regulated there are two specific enzymes that are regulated by energy charge. What are they and ow does this happen?
It’s controlled at several points.
•Isocitrate dehydrogenase
–Allosteric stimulation by ADP
–ATP is inhibitory (high energy charge)
(low energy charge means you need to make more ATP)
–NADH displaces NAD+ which inhibits the enzyme
•a-ketoglutarate dehydrogenase
–Inhibition by succinyl CoA and NADH
–Inhibited by high energy charge
If you deplete oxaloacetate from the citric acid cycle, how can you make more?
You can through the 1st step of gluconeogenesis
The citric acid cycle is catabolic, it’s breaking down citric acid.
If you have a build up of citric acid, you can store it in the form of fatty accids, sterols… etc
What does pathway intergration allow you to do?
It allows oxaloacetate and acetyl CoA to be replinished.
What do mitochondria look like & where come from?
Mitochondria are the sites of oxidative phosphorylation in eukaryotes
•Mitochondria contain four separate compartments
–Outer membrane
–Inner membrane
–Intermembrane space
–Matrix
Mitochondria are thought to have originated by endosymbiosis
Where do electrons go when they leave Complex I?
They go to coenzyme Q (CoQ)
Where do electons go when the leave CoQ?
Electrons from CoQ flow to cytochrome C
•Complex III is Q-cytochrome c oxidoreductase
–Moves electrons from QH2 to cytochrome c
–Pumps protons out of matrix
–Contains two heme-containing cytochromes and Fe-S center
Explain the Q cycle and where does it happen?
In complex III.
- Proton gradient is formed
- Efficient funneling of electrons from a two-electron carrier (QH2) to a one-electron carrier (cytochrome c)
QH2 has 2 e- but can only pass 1 to cytochrome c. One electron goes to
Cyt C and the other goes to a resident Q of the complex III. It takes theother e- and it makes the intermediate semiquinone. It doesn’t go anywhere. The original Q is void of all it’s e- and goes back to the Q poolto get more e-. In step two, another QH2 comes & and gives an electronto Cyt C that moves along and the 2nd e- goes to the semiquinone, makingit fully reduced. Now it has the ability to leave complex III. It now can can contribute to Q pool and donate electrons. When the reduced Q leavesa new oxidized Q comes in to replace it.
Qs are mobile. They can go where ever they want. Their job is to shuttle electrons b/w the non mobile parts.
The Qs go b/w complex 1 & 3 and b/w complex 2 & 3 or 3 to 3
Summerize the electron transport chain
The electrons are leaving complex 1 and going to Q, they came from NADH. NADH gives it’s electrons to complex I. Complex I gives it’s electrons to Q. Q gives its electrons to complex III, III gives its electrons to cytochrome c, cytochrome c gives its electrons to IV, and IV gives the electrons to oxygen to make water.
FADH is generated as part of the citric acid cycle, which is part of II, the electrons move through those centers and go from II to Q. Q gives its electrons to III, III gives electrons to Cyt C, Cyt C gives electrons to IV, IV gives it to oxygen
We are moving protons against the gradient, they are being PUMPED, this is active transport, pulling the out of the matrix and putting them into the intermembrane space.
There needs to be an input of energy, the input of energy is coming from the flow of electrons.
Reduction potential gives us a delta G thats the energy required to pump protons against their gradient
What is the driving force for ATP synthase?
Movement of electrons which allow a proton gradient to be setup.
In terms of ATP synthesis, what does F0 portion do?
F1 has a gamma stalk that goes up into the C ring, cant see it here but it sits inside there. That’s the part that does spin. As it spins, it changes the conformation of the subunits that are attached.
In terms of ATP synthase, how does the F0 channel work?
The a polypeptide and c polypeptides move protons through the F0 subunit
How is ATP synthesis powered?
Proton flow around the c ring powers ATP synthesis
The proton comes down the half channel and attach to the aspartic acid. Then the c subunit moves in a circle. So then the proton is moved over by the turning and then there is another open aspartic acid. So then a new proton can come in and ride the C ring. The protons keep going around until they get to the other half channel. There is a very low concentration of protons in the matrix b/c we’ve been pumping them out from the ETC. So there is an affinity for those protons to get off the aspartic acid and go into the matrix.
How do beta subunits of the F1 portion generate ATP?
When the gamma stalk turns, it changes it’s interaction w/ each of the beta subunits. It causes each of those subunits to change confirmation, as the gamma subunit turns.
As it turns the beta changes from open –> lose –> tight
What are he diffrent configurations of the beta subunits of the F1 subunit?
Open, loose, tight (where it’s squished)
