Biochem Exam #2 Flashcards
Oxygen is required for the degradation of what kind of amino acids?
Aromatic
The liver can carry out ___________ metabolic pathways.
All
The most complicated protein we have discussed thus far:
Nitrogenase FeMo Cluster
PLP-dependent enzymes are usually covalently connected to an amino acid. What amino acid is this and what is the linkage between it and the PLP called?
Lysine, Schiff Base
A Schiff Base
Nitrogen double bonded to carbon
Organ used for fatty acid storage/metabolism
Adipose
glucose/ketone body consumption only
Brain
Urea excretion/gluconeogenesis
Kidneys
Multi-fuel storage / energy converter / gluconeogenesis
Liver
Multi-fuel user / some energy storage
Muscles
Describe the overall mechanism of protein degradation (nutritional)
Proteins from diet are broken down in the stomach by digestive proteases. The proteases use catalytic activity to help break the peptide bonds in the form of hydrolysis of proteins down to amino acids. Allows the amino acids to be reabsorbed and used for other biochemical processes.
What three amino acids usually makeup serine proteases?
Ser-Asp-His
What are the 2 ways proteins are broken down in recycling pathways?
- Lysosomes (non-specific) have their own proteases
- Phagocytosis can capture aggregated proteins that need to be recycled. Chews up proteins with proteases and spits out amino acids where then ribosome will then use those to make new proteins.
Explain the role of protein-structure in Ub-proteasome function.
Ubiquitine is covalently attached through a peptide bond to target cells that are “marked” for degradation. The lysine residue of the target protein will act as a nucleophile and forms a carboxylate of ubitquitin.
REQUIRES ATP TO ACTIVATE CARBOXYLATE.
How may ubiquitine are required for a cell to be deemed to degradation?
more than 4
How many enzymes are present on the ubiquitin proteasome?
3 : E1, E2,E3
What do the 19S caps of the proteasome do?
Regulate access to the core of the proteasome (the 20S) by recognizing “tag” of four carbon units. They then work to unfold the damaged protein (requires ATP to push the protein into the core). It then works to translocate the damaged protein into the proteasome core. Protein is chopped up into amino acid peptides by proteasome
Inside the proteasome core, the damaged protein is degraded into ____ amino acid peptides by the proteasome.
8
Why is energy required to unfold the damage protein before it goes into the proteasome core?
To break hydrogen bonds and to overcome electrostatic interactions. They hydrolyze ATP and use the free energy to drive conformational changes that are necessary to fold the protein so that it can enter the protein core.
What is the overall shape/structure of the 20S proteasome core?
- Barrel shaped with 28 repeating units
- α, β heptamer
- 7α, 7β, 7β, 7α
- Only 3 active proteases: β, β2 and β5
- Hollow spaces in the 20S is to allow proteins to come in.
What are the four potential products of nucleophilic and addition reactions?
1) Phosphate leaving group
2) β-keto (leaves as acetate)
3) Thioester
4) Amine
Describe the role of α-ketoglutarate in amino acid deamination?
- The amino group from an amino acid is transferred to α-ketoglutarate (which is an intermediate of the TCA Cycle)
- Swap out the amino group to make the amino acid an α-keto acid
- Catalyzed by transaminases
During the electron pushing mechanism for the PLP in a transaminase reaction, the _________ is the electrophile and the __________ is the nucleophile.
Carbonyl ; Amine of lysine
PLP cofactors are covalently attached to a protein via the _______ residue.
Lysine
During the PLP transaminase reaction, it is a ________ reaction. ________ is eliminated and ________ is formed.
Addition/elimination ; H2O ; Internal Aldimine
What is the first step of the transaminase reaction?
Conversion of an internal aldimine to an external aldimine by the amino acid substrate.
With lipid metabolism, it occurs in the _______, where we want to generate ______ to go in the ETC.
Mitochondria
What is the redox cofactor for lipid metabolism?
NAD
What is the main thioester used in lipid metabolism?
CoA
What chemistry is done during lipid metabolism?
Oxidation, hydration, oxidation, and break of C-C bond to release C2 unit as Acetyl CoA
Lipid storage/synthesis occurs in ______.
cytoplasm
Redox cofactor of lipid storage/synthesis
NADP
Main thioester used in lipid storage/synthesis.
Acyl-Carrier Protein (ACP)
What chemistry is done during lipid storage/synthesis?
Form C = C to form β-keto, reduce β-keto group, dehydrate, and reduce again.
Why are there so many differences between lipid metabolism and lipid storage/synthesis?
Allows for regulation. Done so that both processes are not occurring at the same time.
Explain how energy from ATP is used to synthesize fatty acids.
ATP is needed to drive the synthesis of the thioester bond.
What is meant by “glucogenic”?
Means the carbon skeleton of amino acids will make an intermediate that will go through gluconeogenesis
What is gluconeogenesis?
The synthesis of glucose from noncarbohyrdate precursors
What is meant by “ketogenic”?
Results in the formation of keto bodies, which is an alternate fuel source in times of need.
What two amino acids are destined to be ketogenic?
Lysine and Leucine
What is meant by “essential” amino acids?
- Can not be synthesized. There is no synthetic pathway to make these.
- We lack the enzymes needed to combine carbon skeletons to make these amino acids.
- Have to obtain these amino acids through our diet
Identify other biomolecules that are made from amino acids.
- Heme cofactors
- Neurotransmitters
Summarize the mechanism of nitrogenase.
-Nitrogenase is the enzyme responsible for reducing N2 to NH3:
N2 + 8(H+) + 16 ATP + 16 H2O –> 2 NH3 + H2 + 16 ADP +16 Pi
What is the purpose of ATP in the nitrogenase mechanism?
The hydrolysis of ATP drives conformational changes.
Nitrogenase is made of two proteins called _______ and ______.
Fe-proteins and MoFe proteins
In the nitrogenase enzyme, where does the ATPase take place?
Fe-protein
What is the flow of electrons between the two proteins of the nitrogenase enzyme?
Electrons come from an electron source to the [4 Fe-4S] complex of the Fe-protein –>The electrons are transferred to the P cluster of the MoFe protein –> Then goes to the FeMo cofactor –> This is where nitrogen reduction takes place.
Describe the P-cluster of the MoFe protein.
- Made of 2 [4Fe-3S] clusters that are attached via a sulfur atom.
- This allows it to function as a single prosthetic group
Describe the FeMo Cofactor of the MoFe protein.
-It is a shell of [4Fe-4S] clusters where they meet and share one atom, the C4- , a carbide atom that has all of its electrons and does not share.
Summarize the major features of fuel metabolism in the brain.
- User of energy reservoirs.
- Uses 20% of oxygen in the body to try to generate ATP.
- Most of the ATP is used to drive Na+/K+ pumps which set the membrane potential for nerves to fire.
- Not much glucose storage, and has to have a constant supply of energy.
- Prefers glucose but can use ketone bodies if needed.
- CAN’T USE ACETYL COA OR FATTY ACIDS!!!
Summarize the major features of fuel metabolism in muscles.
- Some storage for glycogen.
- Use all fuel types
- CAN’T DO GLUCONEOGENESIS! DON’T HAVE THE NECESSARY ENZYMES
- CAN’T BREAKDOWN AMINO ACID PRODUCTS BACK INTO GLUCOSE
- Relies on the liver to convert amino acids to glucose.
Summarize the major features of fuel metabolism in adipose tissue.
- All storage
- Liver is processing center and the adipose tissue is storage
- Can secrete hormones that can drive metabolism in other areas of the body
Summarize the major features of fuel metabolism in the liver.
- Everything metabolic passes through here
- Can do gluconeogenesis
- Main energy storage
- Produces glucose for brain and muscles.
- Only place where ketone body formation takes oplace
- Can do urea cycle
- CAN’T GO FROM ACETYL-COA TO PYRUVATE (MAMMALS ONLY)
- HAS ALL PATHWAYS
2 ways of pathway coordination between organs:
1) Isozymes
2) Cori Cycle
Explain isozymes.
Hexokinase: glucose + ATP ---> glu-6P + ADP - A type of isozyme -ATP is used to phosphorylate glucose. -From brain and muscles. -Completely saturated at 5 mM.
Glucokinase:
- Type of isozyme specific for liver
- For the liver, in the presence of 5 mM, the glucokinase is activated and the cells become more responsive to glucose. Tells that glucose can be brought into the liver to be stored as glycogen.
- Allows brain and muscles to receive glucose before the extra is stored as glycogen.
Describe the Cori Cycle.
-Muscles produce lactate under anaerobic exercise. The muscles can’t break this down so they send it to the liver to be broken down into glucose.
This glucose is then sent back to the muscles when needed.
Summarize the major features of fuel metabolism in kidneys.
-Process urea from the urea cycle of the liver used to break down protein.
-Can do a little bit of gluconeogenesis.
A lot of glutamine from the urea cycle is generated from the urea cycle as the main ammonia carrying molecule. Ammonia is taken off to give α-ketoglutarate that can then be used for glucose. Goes to the brain/muscles to be used or liver for storage.
Describe the metabolic integration pathway of proteins.
1) Proteins are broken down into aa.
2) Amino Acid degradation can lead to the formation of pyruvate (reversible and can be used to make glucose), Acetyl-CoA (irreversible), or oxaloacetate (reversible and can be used to make pyruvate to make glucose)
What are the two “crossroads” molecules of the metabolic pathways?
- Pyruvate
- Acetyl CoA
Pyruvate –> Acetyl CoA is a one way reaction. Irreversible.
Describe the metabolic integration pathway of glycogen.
1) Glycogen becomes glucose-6-phosphate (reversible)
2) Becomes pyruvate and gives off ATP. (reversible)
3) Pyruvate becomes Acetyl-CoA (irreversible)
4) Goes on to the TCA. Gives off oxaloacetate that can go back to pyruvate to make glucose.
Describe the metabolic integration pathway of Triacylglycerols.
1) Broken down into fatty acids.
2) Through beta-oxidation, becomes Acetyl-CoA which can then go on to the TCA or produce ketone bodies.
What are the two products of the TCA cycle?
ATP (with oxidative phosphorylation) and oxaloacetate.
What is required to turn Glucose-6- phosphate into glucose?
ATP
_______ tell when to turn pathways on/off by triggering _______ changes. These come from the _________ glands (pancreas, adrenal glands.
Hormones, cellular ; endocrine
Epinephrine has a ________ receptor.
β-Adrenergic receptor. Energy-store metabolism (triggers them)
Glucose stimulates the release of _______ from _____ in the pancreas.
insulin, β-cells
Type I diabetes is caused by
A virus kills β-cells which means insulin can not be made.
Insulin tells when there is ______ blood sugar. The muscles and adipose tissue are told to _________ with the increase in [glucose]. This inhibits _______ in the liver and __________.
high, uptake glucose ; gluconeogenesis, glycogen mobilization
3 carbon skeleton will produce
pyruvate
4 carbon skeleton will produce
- fumarate
- oxaloacetate
- Succinyl Coa
5 carbon skeleton will produce
alpha ketoglutarate
