Biochemistry Final: Exam #3 Review Flashcards
What are the three sources of glutamate?
1) Diet (major)
2) Transamination of a-KG
3) Deamination of Glutamine
Transamination
Amino acid + a-KG–> Glutamate + a-ketoacid
- Amine group from amino acid is carried by B6(pyridoxal 5’-phosphate) to a-KG & swapped for carboxyl group
- Makes Glutamate & corresponding a-Ketoacid
Deamination of Glutamine
Glutamine–> Glutamate, via the enzyme “Glutaminase”
Why do we make glutamine?
Glutamine production in peripheral tissues in an important mechanism of ammonium ion removal
How do we make glutamine?
Glutamate–> Glutamine, via the enzyme “Glutamine Synthetase”
- Ammonium ion required (removes toxic substance too!)
- ATP hydrolyzed to ADP + Pi
Where does this glutamine go?
Enters the bloodstream and is absorbed by the:
- Kidneys
- Liver
- Gut
Here, the amide group is hydrolyzed by Glutaminase (Glutamine–> Glutamate), generating Glutamate & NH4+
What do the kidenys and liver do with ammonium ion (NH4) generated by the glutaminase reaction i.e. deamination of glutamate?
- Kidneys excrete NH4 directly
- Liver channels NH4 into the urea cycle
(Gut, NH4 serves as an important nutrient)
PLP
- Active form of pyridoxal phosphate
- Vitamin B6
- Cofactor that is required for aminotransferase reactions
ALT
Alanine + a-KG –> Pyruvate + Glutamate
Pyruvate + Glutamate–> a-KG + Alanine
- Alanine Aminotransferase (ALT)
- Requires Vitamin B6 (PLP)
- Connects muscle & liver metabolism
- Found primarily in the liver
Glucose-Alanine Cycle
- Muscle glycolysis produces pyruvate
- ALT converts pyruvate into alanine that is released into the blood
- Blood carries alanine to the liver
- In liver, ALT converts alanine back into pyruvate
- Pyruvate is used for gluconeogenesis
AST
1) Oxaloacetate + Glutamate –> a-KG + Aspartate
2) Aspartate + ATP + Glutamine–> Asparagine, via the enzyme “Asparagine Synthetase”
Clinical Significance of ALT vs. AST
Serum elevation of ALT is more specific for liver damage
Folate & THF
- Tetrahydrofolate (THF) Serves as an acceptor of 1-carbon groups (methylene)
- Derived from the vitamin, Folate
Most oxidized form of THF
N10-formyl THF
Most reduced from of THF
- N5-methyl THF
- Is NOT readily oxidized back to N10-formyl THF
- Thus, accumulates in the body
Which amino acid is the main donor of 1 carbon groups?
Serine
Serine Hydroxymethyl transferase
Serine + THF–> Glycine + N5, N10-methylene THF + H20
Phenylalanine Hydroxylase
Phenylalanine–> Tyrosine
- Requires oxygen, NADH, & the reduced cofactor tetrahydrobiopterin (THBtn) to oxidize the aromatic ring of phenylalanine
Dihydrobiopterin Reductase
Dihydrobiopterin (DHBtn, oxidized) –>Tetrahydrobiopterin (THBtn, reduced)
Phenylketonuira (PKU)
- Most common inborn error of metabolism
- Accumulation of phenylalanine that causes: severe intellectual disability, recurrent seizures, hypopigmentation, & eczematous skin rashes
- Caused by defect in phenylalanine hydroxylase OR DHBtn Reductase
- Must avoid nutrisweet/ aspartame
The overall rate of amino acid degradation is influenced by the activity of which enzyme? What inhibits this enzyme & what activates this enzyme?
Mitochondrial Glutamate Dehydrogenase
- Inhibited, high energy: GTP, ATP, NADH
- Activated, low energy: GDP, ADP, NAD+
Mitochondrial Glutamate Dehydrogenase
Glutamate + NAD+ + H20 –> a-KG + NADH + NH4+
Which amino acids can be converted into pyruvate? And what is pyruvate eventually used to make?
- Glycine
- Serine
- Cysteine
- Alanine
- OAA
Glycine, through several steps, can eventually be converted into pyruvate. How is glycine also related to the formation of kidney stones?
Glycine–> Serine –> Pyruvate = one possible path
Glycine–> Glyoxalate–> Oxalate= second possible path
- Oxalate is a metabolic end product that is excreted in the urine
- Oxalate also has a high affinity for Ca++, and can precipitate as kidney stones
Besides via pyruvate, two other amino acids can be shunted to make OAA. Which?
- Asparagine
- Aspartate
Asparagine–> Asparate, via enzyme “asparaginase”
Aspartate–> OAA, via AST
Which amino acid can be used to make a-KG?
Glutamine
Glutamine–> Glutamate, via enzyme “Glutaminase”
Glutamate–> a-KG, via Aminotransferases & Glutamate Dehydrogenase
Therefore, amino acids that can make glutamate, can also be used to make a-KG
Which amino acids can make glutamate?
- Proline
- Histidine
- Arginine
Glycine Encephalopathy
- Nonketotic hyperglycemia that presents soon after birth with symptoms of: lethargy, lack of muscle tone, & muscle twitching
- Caused by defects in glycine cleavage system
What amino acids can make propoionyl-CoA?
- Threonine
- Methionine
- Valine
- Isoleucine
What is propionyl-CoA eventually made into, and enzymes & cofactors are needed for that transformation?
Succinyl-CoA
1) Carboxylase= Propionyl-CoA–> D-methylmalonyl-CoA, requires Biotin
2) Racemase= D-methylmalonyl-CoA–> L-methylmalonyl-CoA
3) Mutase= L-methylmalonyl-CoA–> Succinyl-CoA, requires Vitamin B12
What is the clinical significance of defects in Carboxylase/ Biotin, Racemase, or Mutase/ B12?
- Carboxylase/ Biotin= Propionic Acidemia
- Racemase= D-methylmalonyl-CoA Aciduria
- Mutase/ B12= Methylmalonic Aciduria
What is the only direct source of B12?
Bacteria
What protein is needed to absorb B12?
- Intrinsic Factor
- Produced by parietal cells of the stomach
Once in the body, what protein transports B12?
Transcolbalamin
Where do you store B12?
Liver
Pernicious Anemia
- Anemia caused by a lack of intrinsic factor (protein that is needed to absorb B12 from the diet)
- Autoimmune disorder w/ antibodies against parietal cells of the stomach that produce intrinsic factor
Megaloblastic Anemia
- Megaloblastic cells reach a large size because they are unable to complete cell division due to deficient DNA replication
- N5- methyl-THF is the most reduced form of THF
- More oxidized forms of THF are required in the enzymatic reactions that generate purines (A, G) & thymidine for DNA synthesis
- Vitamin B12 is required for the only reaction that converts N5-methyl-THF back to THF
What is the only reaction in mammals that converts N5 methyl-THF back to THF?
Homocytsine–> Methionine, catalyzed by the enzyme “methionine synthase”
How does B12 deficiency lead to mental confusion & loss of sensation?
- Demyelination
- Though that methionine/ methionine synthase reaction (homocytsine–>methionine & requires B12 cofactor) is somehow involved
B12 Deficiency & Atherosclerosis
- Homocysteine builds up in B12 deficiency (methionine synthase reaction impaired)
- Thought that homocysteine damages arteries, oxidizes LDL, & interferes with blood clotting
BCAA Catabolism steps
1) BCAA–> Branched chain a-ketoacid, via “branched chain aminotransferase”
2) Branched chain a-ketoacid–> branched chain acyl-CoA via decarboxylation by BCKDH
3) Remainder proceeds like B-oxidation
BCKDH
Branched chain a-ketoacid dehydrogenase complex
Maple Syrup Urine Disease
- Accumulation of branched chain a-ketoacids in the urine, which gives the urine a characteristic maple syrup odor
- When untreated, can cause: poor feeding, vomiting, slow or irregular breathing, ketoacidosis, hypoglycemia, & neurological dysfunction
- Caused by a defect in BCKDH
- Treatment is a diet low in BCAAs
Tyrosinemia- II
- Rare disorder characterized by keratitism, photophobia, & painful skin lesions on the palms or the hands/ soles of the feet, as well as intellectual disability
- Caused by a tyrosine aminotransferase defect
Alkaptonuria
- Black urine
- Caused by a defect in homogentisate oxidase
- build-up of homogentisate turns black when oxidized by exposure to air
Tyrosinemia- I
- Potentially fatal disease that causes liver failure, kidney dysfunction, & neurological impairment
- Diagnosis is based on succinylacetone in the urine
- Maleylacetoacetate & fumarylacetoacetate accumulate and are eventually converted to succinylacetone
- Succinylacetone inhibits heme synthesis
What is the rate-limiting step of urea synthesis? What is the required allosteric activator of this enzyme?
- Mitochondrial carbamoyl phosphate synthatase I
- N-acetylglutamate
N- acetylglutamate is produced by what enzyme? What activates this enzyme?
N-acetylglutamate Synthetase produces N-acetylglutamate (required cofactor of Mitochondrial carbamoly phosphate synthatase I), which is activated by arginine
What are high levels of arginine indicative of?
High levels of peripheral ammonium
Urea Cycle Mnemonic
- Ordinarily= Ornithine
- Careless= Carbamoyl Phosphate
- Crappers= Citrulline
- Are= Aspartate
- Also= Arginosuccinate
- Frivolous= Fumarate
- About= Arginine
- Urination= Urea
Ornithine Transcarbamylase
- Ornithine + Carbamoyl Phosphate–> Citrulline
- Mitochondria–>Cytoplasm
Arginosuccinate Synthetase
- Citrulline + Aspartate–> Arginosuccinate
- Cytoplasm
Argininosuccinase
- Arginosuccinate–> Fumarate + Arginine
- Cytoplasm
Arginase
- Arginine–> Urea + Ornithine
- Cytoplasm
urea-TCA bicycle
- Fumarate links the urea cycle to the TCA cycle
- Oxaloacetate in the TCA cycle, which is converted to Aspartate completes the bicycle
Where do the two amino groups in urea come from?
1) carbamoyl phosphate
2) aspartate
What is the only organ that can perform the entire urea cycle?
Liver
Hyperammonemia
Caused by defects in the urea cycle
- Early cycle defects are the worst (Carbamoyl Phosphate Synthetase I & Ornithine Transcarbamoylase)
In addition to urea cycle defects, what else can cause hyperammonemia?
- Urea cycle is carried about by the liver
- Liver disease (alcoholic cirrhosis) causes hyperammonemia
- Ammonia is a potent neurotoxin & can cause lethargy (AMS) & convulsions
- Why? causes swelling of astrocytes/ brain
Creatine Kinase
Phosphorylates creatine to creatine phosphate
What is creatine phosphate used for?
- Energy reserve
- Creating phosphate is able to donate high phosphate to ADP, making ATP
A percentage of creatine phosphate spontaneously converts to what? Why is this important?
- Creatinine
- Indication of kidney function
The amount of creatinine excreted per day is proportional to _____?
Muscle mass
What amino acids are the thyroid hormones derived from?
Tyrosine
Thyroid Peroxidase
Iodinates thyroid hormones (T3 & T4)
What amino acid is used to synthesize melanin?
Tyrosine
What enzyme is needed to synthesize melanin from tyrosine?
- Tyrosinase
- Tyrosine–>DOPA–>Dopaquinione
Oculocutaneous Albinism Type I
- Albinism
- Caused by a defect in the TYR gene, which leads to a tyrosinase defect
- Tyrosinase is the enzyme that converts Tyrosine–>DOPA–>Dopaquinone, which is further metabolized to melanin
Melatonin & Serotonin are derived from what amino acid?
Tryptophan
Which amino acid is converted to niacin? What enzyme catalyzes the first step of the reaction?
- Tryptophan
- IDO
Why is IDO important?
- IDO is overexpressed by tumors, which decreases their tryptophan concentration
- This depletion of tryptophan blocks proliferation of T-cells that would normally destroy the tumor
- Thus, IDO has become an anti-cancer drug target
Pellagra
- 4 D’s: Dermatitis, Diarrhea, Dementia, Death
- Caused by a Niacin deficiency OR lack of tryptophan
What amino acid is GABA derived from? What cofactor is required for this reaction?
- Glutamate
- PLP (Vitamin B6)
Histamine is derived from which amino acid?
Histidine
Glutathione
Intracellular reducing agent
What type of bond makes glutathione stable?
Gamma Glutmyl Linkage
Rate determining enzyme of Glycolysis
- Phosphofructokinase- 1
Rate determining enzyme of Gluconeogenesis
- Fructose 1,6-bisphosphatase
Rate determining enzyme of TCA Cycle
- Isocitrate Dehydrogenase
Rate determining enzyme of Glycogenesis
- Glycogen Synthase
Rate determining enzyme of PPP
- Glucose 6-phosphate Dehydrogenase
Rate determining enzyme of de novo pyrimidine synthesis
- Carbamoyl Phosphate Synthetase II
Rate determining enzyme of de novo purine synthesis
- PRPP amidotransferase
Rate determining enzyme of the Urea Cycle
- Carbamoyl Phosphate Synthetase I
Rate determining enzyme of Fatty Acid Synthesis
- Acetyl-CoA Carboxylase
Rate determining enzyme of Fatty Acid Oxidation
- Carnitine Acyltransferase I
Rate determining enzyme of Ketogenesis
- HMG-CoA Synthase
Rate determining enzyme of Cholesterol Synthesis
- HMG-CoA Reductase
Rate determining enzyme of Glycogenolysis
- Glycogen Phosphorylase
Energy Source: Fatty Acid
- Beta-oxidation requires O2; therefore, cannot use for anaerobic activity
- Cannot cross BBB
- Acetyl-CoA cannot be converted to glucose
Energy Source: Glucose
- Can be used for anaerobic activity (Lactate will be produced)
- Can get to the brain
Energy Source: Amino Acids
- Cannot be stored
- Some can be converted to glucose for energy
RBC: fuel preference & special considerations
- Glucose
- produces lactate
Skeletal Muscle: fuel preference & special considerations
- Fat
- Can also use glucose & ketones
- Can store glycogen
- Can break down into amino acids for energy
Heart: fuel preference & special considerations
- Fat
- Cannot function anaerobically
- Stores little energy
Brain: fuel preference & special considerations
- Glucose
- Can use ketones in starvation
Adipose: fuel preference & special considerations
- N/A
- Converts glucose to TAGs for storage
- Breaks down TAGs in times of need
Liver: fuel preference & special considerations
- ALL
- Stores glycogen
- Well-fed, can export fats in lipoproteins
- Fasting, can turn amino acids & FA into glucose & ketones
Well-Fed
- Insulin secretion
- Nutrients must be removed from circulation & put into storage
- Glucose is stored directly in liver & muscles
- Excess glucose is converted to VLDL for storage in adipose tissue
- Amino acids are used for protein synthesis
Early Fast
- Blood glucose concentration falls & alpha cells of the pancreas secrete glucagon
- Objective is to mobilize nutrients stored in the well fed state
- Glucose is released from glycogen stores
- Fatty acids and glycerol are released from adipose tissue
- Ketone bodies are produced from fatty acids by the liver
- Amino acids from protein breakdown are released from muscles
- Urea cycle enzymes are induced to cope with rise in ammonia
Late Fast
- Corticosteroids cause the body to develop an adaptive metabolism
- Basal metabolic rate drops & tissues consume less energy
- CNS begins to increase use of ketone bodies
- Liver glycogen is depleted
- Kidney begins to aid liver in synthesis of ketones
- Breakdown of muscle protein slows down due to the reduced demand for glucose
Refeeding Syndrome: what are the major concerns when refeeding a starved patient?
1) Lack of digestive enzymes–patient will not be able to breakdown dietary carbohydrates & fats, which will lead to diarrhea
2) Intracellular phosphate stores are depleted–& the reintroduction of carbohydrates induces glycolysis, which consumes large amounts of phosphate (ATP)
- leads to life threatening hypophosphatemia
What are the three effects of ineffective glucose removal?
1) No glucose storage–>tissue starvation
2) Damage to blood vessels
3) Osmotic pressure increases–> tissue dehydration & HTN
What are the three chronic morbidities of DM?
1) Retinopathy
2) Nephropathy
3) Neuropathy
Four processes that are regulated by insulin
1) Increase GLUT4 transporters (uptake of glucose)
2) Increase in glucose utilization (glycolysis, glycogen synthesis, FA synthesis, & protein synthesis)
3) Downregulate gluconeogenesis
4) Downregulate FA mobilization
What happens when tissue don’t respond to insulin?
1) Fasting hypoglycemia
2) Hyperlipidemia
3) Uninhibited gluconeogenesis
What are the three causes of tissue damage in DM?
1) Spontaneous glycation
2) Formation of sorbitol (uses NADPH)
3) Loss of antioxidant protection (from NADPH usage)
What enzymes are involved in heme synthesis?
ALA synthase- Succinyl CoA + Glycine–> ALA
PBG Synthase- ALA + ALA –> PBG
UPG Synthase III- PBG x4–> UPG
Ferrochelatase- Insertion of Fe
*begins & ends in the mitochondria
Porphyrias
Diseases of heme synthesis
What is the committed step of heme synthesis?
ALA Synthase
- Inhibited by heme in a classical feedback loop
Why do drugs & alcohol induce heme synthesis?
- Alcohol induces the microsomal ethanol oxidizing system (MEOS), a cytochrome p450 containing enzyme
- Synthesis of cytochrome p450 enzymes consumes heme
- Consuming heme relieves inhibition of ALA synthase
Acute Intermittent Prophyria
- Caused by a deficiency of PBG Deaminase
- Urine turns a dark red color
- Neurological symptoms
Porphyria Cutanea Tarda
- Caused by a deficiency of uroporphyrinogen decarboxylase (UROD)
- Porphyrins absorb UV & visible light, which can lead to generation of ROS & blistering of the skin
- Urine will fluoresce pink under UV light
Which enzymes of heme synthesis are inhibited by lead?
- PBG Synthase
- Ferrochelatase
Causes an accumulation of ALA
What is the breakdown product of heme? How is it excreted?
- Bilibrubin, which is produced by the spleen
1) Binds to albumin to be transported by the circulation to the liver
2) Bilirubin-UDP glucuronyltransferase (UGT) adds glucuronic acid to bilirubin to make it more water soluble (conjugated)
3) Broken down by gut bacteria into urobilins
4) Urobilins are excreted in feces or reabsorbed and excreted in urine
Prehepatic (Hemolytic) Jaundice
- Hemolysis of RBCs overwhelm’s the liver’s capacity to conjugate bilirubin
- Normal amounts in feces & urine
- Unconjugated bilirubin found in other tissues
Hepatocellular Jaundice
- Liver is unable to conjugate bilirubin
- Feces & urine turn pale
- Unconjugated bilirubin is found in other tissues
Cholestatic Jaundice
- Blockage of the bile duct
- Liver is able to conjugate bilirubin, but unable to excrete it into feces
- Conjugated bilirubin is thus excreted via kidneys
- Urine is dark orange color
- Feces are pale
What is the committed step of de novo nucleotide synthesis?
- Conversion of Ribose 5-phosphate to PRPP by PRPP synthase
- PRPP is required for BOTH purines & pyrimidines
What is the committed step of de novo purine synthesis?
PRPP–> PRA, via the enzyme “amidophophoribosyltransferase”
What is the first purine to be produced?
IMP
- Amino acids donate carbon & nitrogen
- CO2 provides carbon & oxygen
- N10-THF is a 1-carbon donor
- ATP is required for several steps
What is IMP the precursor for?
AMP & GMP
What enzyme is necessary to make AMP from IMP?
Adenylosuccinate synthase
- Note that it is inhibited by its product, AMP
What enzyme is necessary for GMP synthesis?
IMP dehydrogenase
- Note that it is inhibited by its product, GMP
- GMP is made via Xanthosine 5’ monophosphate
How do all nucleotides become phosphorylated?
Sequential action of nucleoside 5’-monophosphate kinases & nucleoside 5’ diphosphate kinases
What is the end product of purine metabolism?
Uric acid
- AMP–> Hypoxanthine–> Xanthine
- GMP–> Guanine–> Xanthine
- Xanthine–> Uric acid, via Xanthine Oxidase
What diseases can result from purine breakdown?
1) Hyperuricemia
2) Gout
3) Kidney Stones
How does allopurinol treat gout?
Inhibits xanthine oxidase
- Xanthine–> Uric Acid via Xanthin Oxidase
What enzymes are involved in the production of pyrimidines?
1) CAD
- Carbamoyl phosphate synthetase II (regulated step)
- Aspartate transcarbamoylase
- Dihydrooratase
2) UMP Synthase
Orotic Aciduria
- Caused by a defect in UMP Synthase
How is CTP formed?
CTP Synthase
- Activated by UTP
- Inhibited by CTP
How are deoxyribonucleotides synthesized?
Ribonucleotide Reductase
- In this process Thioredoxin becomes oxidized
- For catalysis to continue, Thioredoxin must be reduced by thioredoxin reductase
- Uses NADPH
SCID
- Adenosine Deaminase Deficiency
- dATP build-up inhibits ribonucleotide reductase
- Immune cell proliferation is inhibited & patient cannot amount appropriate immune response
How is dTMP formed?
dUMP–> dTMP, via the enzyme Thymidylate Synthase
- requires N5, N10 THF
- Need B12
5- Fluorouracil
- Undergoes same pathways as uracil
- Eventually will become FdUMP instead of dUMP
- FdUMP is a irreversible inhibitor of thymidylate synthase i.e. it prevents the formation of dTMP
What enzymes are involved in the salvage of purines?
- HGPRTase
- APRTase
What enzyme is involved in the salvage of pryimadines?
Pyrimidine phosphoribozyltransferase
Which pyrimidine is not salvaged?
Cytosine
Hyponatermia
Overhydration
Hypernatremia
Dehydration
Hypokalemia
Potassium loss
Hyperkalemia
Renal insufficiency
Hypocalcemia
Hormonal problem
Hypercalcemia
Hormonal problem or bone disease
High Phosphate
Bone disease or failed clearance
Low Phosphate
Beware of glucose metabolism (glucose is phosphorylated immediately upon entering the cell)
Albumin
- Carrier protein
- Maintenance of osmotic pressure
- Low, leads to edema
Globulins
Immune system function
C-Reactive Protein
Secreted by the liver in response to acute injury
What enzymes are released from cardiomyocytes in response to MI?
- Myoglobin, very quickly but not heart specific
- Creatine Kinase, quickly
- AST
- Troponins, quickly & most sensitive marker!!!!!
- LDH, days after
How would you distinguish between liver & bone disease in a patient with elevated alkaline phosphatase?
- Check bilirubin levels (Liver)
What is a reactive oxygen species? What radicals are found in human cells?
Reactive intermediates of oxygen metabolism
- Singlet Oxygen- O
- Superoxide anion- O2- (1 electron transfer)
- Hydrogen Peroxide- H2O2 ( 2 electron transfer)
- Hydroxyl Radical- HO ( 3 electron transfer & most reactive!)
Hemochromatosis
- Iron overload
- Accumulation of iron causes cirrhosis of the liver, damage to the pancreas (diabetes), & damage to the heart
What enzymes are protective against ROS?
- Superoxide dismutase (superoxide anion)
- Catalase & Glutathione Peroxidase (hydrogen peroxide)
Which vitamins act as antioxidants?
- Vitamin C
- Vitamin E ( most protective of membranes)
- Vitamin A (singlet oxygen & membranes)
How do ROS damage membranes?
1) HO takes an electron from PUFA & forms a lipid radical
2) Lipid radicals react with O2 to form lipid peroxide
3) Lipid peroxides react with PUFAs & continue the cycle of damage OR reactive with self to form malondialdehyde
Malondialdehyde
Mutagenic reaction with purines
