1040 Bichemistry

Topic 1: Metabolism in General

• Metabolism involves movement of electrons directly or via electron carriers (coenzymes) undergoing reversible REDOX reactions such as NAD, NADP, FAD, and FMN.

• The coenzyme Biocytin uses Biotin as a precursor and transfers CO2

• Coenzyme A uses Pantholenic acid as a precursor and transfers Acyl groups

• FAD uses Riboflavin as a precursor and transfers Electrons

• Co-B12 uses Vitamin B12 as a precursor and transfers H+, alkyl groups

• Lipolate uses None as a precursor and transfers Electrons, acyl groups

• NAD uses Niacin as a precursor and transfers Hydride ions

• Tetrahydrofolate uses Folic acid as a precursor and transfers 1-carbon groups

• PLP uses Vitamin B6 as a precursor and transfers Amino groups

• TPP (Thiamine pyrophosphate) uses Vitamin B1 as a precursor and transfers Aldehydes

• Enzymes increase the rate of reaction without being consumed, decreasing activation energy.

• The rate of reaction is determined by reactant concentration, catalyst presence, effectors (allosteric, competitive, ions/pH), and temperature.

• ΔG signifies the energy available to perform work

• ΔG is additive in a pathway

• A negative ΔG indicates an exergonic reaction, while a positive ΔG indicates an endergonic reaction.

• Metabolism is the sum of chemical/molecular reactions in all organs and cells, extracting energy, storing fuels, synthesizing building blocks, and eliminating waste.

• Metabolic pathways consist of related reactions, are highly conserved, and interconnected.

• Catabolism is a convergent process releasing energy through molecule degradation, such as glucose oxidation.

• Anabolism is a divergent process absorbing energy to synthesize simple molecules.

Regulation of Catabolism/Anabolism

• Pathways differ by at least one enzyme
• Pathways are differentiated through compartmentalization
• Compartmentalization means the separation of cofactors, enzymes, coenzymes and substrate availability
• Irreversible reactions that are thermodynamically unfavourable also create differentiation points
• Feedback inhibition involves allosteric regulation where molecules bind non-covalently to a site other than the active site.
• Feedback inhibition acts to regulate the enzyme positively or negatively
• Regulation of enzyme production involves extracellular signals, gene transcription, mRNA degradation, and mRNA translation
• Protein degradation means that enzymes are taken into organelles, bind to substrates/ligands, become phosphorylated/dephosphorylated, or combine with regulatory proteins

Appetite and Hunger

• Leptin causes satiety and decreases fat storage, released by adipocytes and enterocytes

• Ghrelin increases hunger/appetite, food intake, and fat storage

Topic 2: Carbohydrates

• Glycosidic bonds are broken down by glycogen hydrolases (glucosidases)

• α-amylase breaks non-specific α(1-4) bonds

• Specific bond hydrolases:

• Isomaltase: α(1-6) bonds

• Maltase: α(1-4) bonds

• Sucrase: α(1-2) bonds

• Trehalase: α(1-1) bonds

• Lactase: β(1-4) bonds

• Glycogen is a branched polymer of glucose, while cellulose is an unbranched polymer with β(1-4) bonds.

• Inherited deficiencies in disaccharide enzymes lead to disaccharide intolerance, causing malnutrition, malabsorption, osmotic diarrhea, boating, and abdominal pain

• Lactose intolerance is an example that can be mitigated by consuming live yogurt/cheese with lactic acid bacteria (LAB) strains or taking lactase pills.

• Sodium-dependent glucose transporters (SGLT) require energy and cotransport with Na+

• SGLT1/SGLT2 are found in the intestine, heart, and kidney

• SGLT3 is located in the intestine, spleen, liver, kidney, and muscle

• SGLT4/SGLT6 are multivitamin transporters

• SGLT5 transports thyroid iodide

• GLUT1 is present in erythrocytes and the blood-brain barrier.

• GLUT2 is found in the liver, kidneys, and pancreatic β-cells (regulating glucose release and uptake).

• GLUT3 is located in neurons.

• GLUT4 is present in muscles and adipose tissue and is insulin sensitive.

• GLUT5 is a fructose transporter in the intestine and testes.

• Glycosuria indicates diabetes

• In healthy individuals, 98% of glucose is reabsorbed into the blood via SGLT2; inhibiting this is a target for lowering blood glucose levels

Diabetes Mellitus

• Type I shows Impaired insulin secretion: glucose is not taken up into cells, accessing adipose tissue and causing fatty acids production, ketogenesis, and an increase in glucose

• Impaired insulin secretion results in ketoacidosis, potentially leading to diabetic coma

• Can also trigger gluconeogenesis, resulting in hyperglycemia

• This can lead to lactic acidosis

• Insulin administration is required for treatment

• Autoimmune destruction of pancreatic β-cells

• GLUT4 is not brought to the membrane efficiently without insulin

• Glycosuria is a common symptom because of hyperglycemia

Type II Diabetes Mellitus

• Overactivation of receptors, resulting in malfunction
• Usually manifesting later in life due to diet; is associated with Hyperinsulinemia
• Therapy involves drastic lifestyle changes with reduced caloric intake

Metformin and Diabetes

• Metformin inhibits complex 1 affecting NADH/NAD+ ratio
• Metformin inhibits mitochondrial glycerophosphate dehydrogenase
• This alters DHAP levels
• Metformin targets glucagon by inhibiting gluconeogenesis
• Finally Metformin inhibits SGLT2 which promotes glucose excretion in urine

Glucose Fates

• Glucose can play a key role in creating structural matrix, produce glycogen, or create extracellular matrix
• Glycolysis is a path for energy intermediates
• The pentose phosphate shunt can also provide energy

Fates of Pyruvate

• Alanine is created from Pyruvate via Alanine transaminase
• Oxaloacetate is created from Pyruvate via Pyruvate carboxylase
• This created Citrate by way of Citrate Synthase
• Acetyl-CoA produced from oxidation of Pyruvate via Pyruvate dehydrogenase
• This created Citrate through way of Citrate Synthase
• Lactate production from Pyruvate via Lactate Dehydrogenase

Regulation of Glycolysis

• Extrahepatic
• Glucose to G-6-P via hexokinase, G-6-P to Fructose-1,6-bisphosphate via phosphofructokinase-1, and lastly PEP to Pyruvate via Pyruvate Kinase
• P-i is an activator while G-60P acts as an inhibitor with respect to Hexokinase
• AMP and ADP are activators while ATP and Citrate acts as inhibitors with respect to Phosphofructokinase-1
• ADP is an activator while ATP and NADH acts as inhibitors with respect to Pyruvate kinase

Hepatic Regulation and Glycolysis

• Liver hepatocytes control glycolysis with a regulating protein

• Glucose upregulates glycolysis, stimulating the release of GK from GKPR in the nucleus/cytosol

• Binds Glucokinase competitively

• Fructose-6-P downregulates glycolysis through increased GK-GKPR binding

• Therefore, glucose-6-P will indirectly inhibits glycolysis

Hormonal Effects on Regulation of Glycolysis

• Insulin activates Glucokinase, phosphofructokinase-1, and Pyruvate Kinase

• Glucagon inhibits glucose metabolism

Glycogen Storage Disease

• Enzymes and deficiency symptoms due to their loss

Glucose Homeostasis

• Ideal: Glucose concentration (↑) = Beta-cells release insulin to have the Glucose absorbed = ↓ Glucose
• Ideal: Glucose concentration (↓) = Beta-cells release Glucagon to have it release = ↑ Glucose
• Insulin increases glucose uptake in the liver and in the body
• Glucagon stimulates breakdown of glycogen

Cancers and anaerobic metabolism

• Warburg effect causes increased anaerobic metabolism
• Increased hexokinase is the target to reducing cancer cell growth
• Increased GLUT1 and GLUT3 are created under induced hypoxia by HIF-a
• p53 mutations inhibit aerobic respiration

Impaired mitochondrial DNA and cancer

• Decreased ATP synthesis: leading to lactic acidosis and reactive oxygen species production
• tRNA defects:
• Leucine defects lead to lactic acidosis
• Lysine defects can affect Cytochrome C activity
• Leber hereditary neuropathy: blindness via mutation in NAD 1,4 and 6
• MOMP
• Enzymes here may act as tumor suppressors
• Mutations may cause build up in succinate of fumarate -> pseudo hypoxia
  • This can lead to more cancerous tumors

The Cori Cycle explained

• Lactate is transported from muscle to liver to regenerate glucose
• Alanine in muscle comes from pyruvate accepting Ammonia from Glutamate
• Alanine is converted back to pyruvate in Liver

The Folate Cycle

• 7,8 - dihydrofolate is converted into 5,6,7,8- Tetrahydrofolic acid
• The donor in this process is NADPH while dyhydrofolate reductase (DHFR) is the enzyme
• FH4 to 5,10 methylene FH4 the donor is Serine and enzyme is Serine hydromethytransferase
• There is feedback inhibition from Thymidylate synthase
• THF is converted to Carbon Dioxide and releases methyl groups
• Vitamin B12 deficiency can stall reaction

Topic on Glycolysis and Anaerobic Metabolism

• All cells need energy at a constant rate
• This needs Glucose constantly regardless of Oxygen availability
• Exercise removes ATP faster than Oxidative Phosphorylation provides
• There is a need for ATP regardless of blood supply
• There is a tradeoff in speed vs efficiency for cellular respiration
• Aerobic oxidation produces high energy for low speed
• Anaerobic does it at a constant rate

###Topic 3: Amino Acid Metabolism

• Amino acids are linked to the common COO- with H+3N, a Carbon and R structure

Glucogenic & Ketogenic

• Ketogenic Aas are converted to ketones

  • This uses Isoleucine, Leucine, Tryptophan and Threonine

• Glucogenic is converted to Glycolysis

  • This uses Alanine, Cysteine, Glycine, Serine, Threonine and Tryptophan

• Ketogenic can feed to ketones while the rest enter Glycolysis

Dietary intake

• There is a 1 to 2G loss of Nitrogen through feces
• AA are proteins that become di and tri peptides
• No net is lost unless there is starvation = Muscle proteins are broken down

AA Catabolism

- AA gets oxidized to go to ATP
- Surpluses = oxidized to go to ATP
- Or there is uncontrolled glucose/carbohdyrate loss = oxidation

Process

• Proteases are used for AA absorption
• proenzymes/zymogens are inactive
• Pepsinogen in the Stomach can be released for cutting proteins inpeptides
• The Pancreas controls the process and uses Cholecystokinin + secretin to release products
  • Trypsin/chymotrypsin come in and cut into pieces
  • Ends are marked by exopeptidases in A/B

Diet and uptake system

• endo, amino + di peptidase comes in
• Brush is borderned for duodenal entry
• A/B is used for pancreatic breakdown- uptake is moved to the muscle
• To do so, this needs an AC or the gradient

Conditions/Diseases involving Dietary Protein

• Hartnup disease
  • recesive disorder with improper gut AA balance
  • Tryptophan isn't used with Nicotinammide and NAD+ needs it most
    • Red scale with sun exposire
  • Check by measuring high levels
• Gluten intollerance: gluten cant be degraded
  • the PQ is toxic to mucosa causing immune response
• Cystinuria comes from a small intake of AC
  • stones appear if its not uptaken

Sorting and protien breakdown

• MRNA goes through the reticulum
• PEST is a promoter of break down
• Enzymes and AA degradation are not free
• Two patheways for breakdown
  • ATP Independent
  • ATP Dependent
• ATP needs: membrane, EC AA and long 1/2 life AA
  • this needs 4 digesive processes mediated by enzymes
  • endo/pino/phogo/au tophases

ATP dependent

• defective and short lives must be tagged
• they then covelently bind to Lysine
• must be mono and mulit ply ubuntianited
• min requires 4 for the enzyme to recognize

AA Defects

• Liddles can cause too much Na+ and sever hypertension
• HPV is the use of p53 with E3

AA degradation

• first sepoerates the AA by a-skeleton
  • the carbon gets shjunted and turns to amonia
  • the transfers happen as a group within the liver

Glutmate in liver

• Collects after diet
• Collects to amone in tissue
• are converted to TCA intermediates

Enzymes for AA metabolism

• Aspartate comes in and uses low serum
• these are all damaged by the enzymes

P-L-P

• they all bind
• either reversibly or non reversivly
• with schiff bases
• one substate will bind while others leave

Deamination

• AA oxidase
• uses a-keto acids with amonia
• Glutmate does it

Urea and Liver Process

• for serine + ethionine u can dehyde
• the Ammonia gets added to create the Urea
• this happens though G synth
• its found in the liver
• controlled through feed back from glyc and alanine intake

Skeletal System

• under anarobic respiration glucose is needed and must be removed to allow pyruvate
• glutatamete and alanin transfferease needs to add these
• all gets transferred to the liver but away from the muscle

90% of all AA

• Most waste excretion uses Amonia, O2 and CO2
• Transpoerting it goes through blood and the kidnes before going
• It will then feed back to the cycle

Key Enzymes

• Synthase controls the cycel
• this must contain a Arginine in high amounts
• The synthatse also must use argenic concentrations
• Cycilcioc is another to

Cycle

• to do this must be 4 atp and other bases

Transports into Cycle

• These will allow an increaes in CO 2 and CO2
• there will also be a change in lysene

Treatments

• to keep it moving you can try
• Organ implants
• Blood transfer
• Stem cell implants