Biochemistry Flashcards
What amino acids are histones rich in?
Where are the different histones?
Arginine and lysine (HAL)
H1 is outside the core and is responsible for further condensing the DNA
H2A, H2B, H3 and H4 are in the core
Effect of DNA methylation
Example?
occurs at cytosine-guanine dinucleotide repeats (CpGs) in thee promoter region of genes – silencing transcription
(CpG Methylation Makes DNA Mute)
Fragile X syndrome
Effect of histone methylation
Usually reversibly represses DNA transcription but can activate it in some case depending on methylation location
(Histone Methylation Mostly Makes DNA Mute)
Effect of histone acetylation
Example disorder?
relaxes DNA coiling and allows for transcription (Histone Acetylation makes DNA Active)
o Huntington’s disease causes increased deacteylation of histones and silences genes necessary for histone survival
Which amino acids are necessary for purine synthesis? For pyrimidine synthesis?
Purine: (GAG) Glycine, Aspartate, Glutamine
Pyrimidine: Glutamine and aspartate
Role of exonuclease in DNA replication?
Proofreading each added nucleotide in a 3’ to 5’ direction
Role of DNA pol III vs DNA pol I
DNA pol III adds DNA from the RNA primer
DNA pol I removes the RNA primers and replaces them with DNA
Missense mutation: mechanism and example
nucleotide substitution that results in a changed amino acid
Ex. Sickle Cell Anemia (Val replaces Glu)
Nonsense mutation
nucleotide substitution results in a stop codon and results in a nonfunctional protein
(Stop the nonsense)
What type of a mutation is seen in Duchenne muscular dystrophy?
Frameshift mutation: deletion or insertion resulting in misreading all downstream nucleotides
Where is the mutation in B thalassemia?
mutation at a splice site causes a retained intron in mRNA
Lac operon
genetic response to an environmental change
Glucose is the preferred metabolic substrate of E coli, but when it is absent, the lac operon switches on and can use lactose for metabolism – lactose binds to the repressor and prevents it from binding to the Operon – allows for the transcription and translation of B galactosidase and permease
One mRNA codes for multiple proteins (“polycistronic”)
Mutation in sickle cell anemia
Point mutation: missense mutation (Val for Glu)
Nucleotide excision repair: mechanism and example disorder
involves the removal of a group of nucleotides from a DNA strand using Endonuclease. DNA polymerase and ligase fill and reseal the gap.
Defective in xeroderma pigmentosum
Mismatch repair: mechanism and example disorder
the removal of mismatched nucleotides from a newly synthesized strand by exonuclease
Defective in Lynch syndrome
Base excision repair: mechanism
base-specific glycoslyase removes the damaged base and creates an AP site (apurinic or apyrimidinic site). AP endonuclease removes the 5’ site and lyase removes the 3’ site. DNA polymerase and ligase fill and reseal the gap.
What type of mutation is seen in ataxia telangiectasia?
Nonhomologous end joining repair: brings together 2 ends of DNA fragments to repair double stranded breaks (this is defective in ataxia telangiectasia)
RNA polymerase I
RNA polymerase II
RNA polymerase III
I –> makes rRNA
II –> makes mRNA
III –> makes tRNA
These are found in eukaryotes, in prokaryotes there is one RNA polymerase for all three functions
What happens when you ingest deathcap mushrooms?
a-amanitin found in death cap muschrooms inhibits RNA pol II and prevents synthesis of mRNA
mRNA = mushroom
Heterochromatin vs Euchromatin
Heterochromatin: condensed, transcriptionally inactive, usually found in periphery of nucleus (ie Barr body)
Euchromatin: less condensed, transcriptionally active
tRNA structure: what part attaches to the amino acid?
the 3’ end which is always CAA
Can Carry Amino acids
Smooth ER: function and example of cells with well developed organelle
site of steroid synthesis and detoxification of drugs and poisons
Liver hepatocytes and steroid-hormone producing cells have well developed sER
Rough ER: function and example of cells with well developed organelles
Site of synthesis of secretory proteins
Mucus-secreting goblet cells of the small intestine and antibody secreting plasma cells are rich in rER
Peroxisomes: function and consequences of defect
involved in catabolism of very long chain fatty acids (via B-oxidation), branched chain fatty acids (via a-oxidation), amino acids, and ethanol
When peroxisomes are absent or nonfunctional, these substances accumulate within tissues → commonly leads to neurologic defects from improper CNS myelination
Proteasomes: function and consequences of defect
protein complex that degrades damaged or ubiquitin-tagged proteins.
Defects in the ubiquitin-proteasome system have been implicated in some cases of Parkinson disease
Patient presents with bleeding gums, gingivitis, coiled hairs, petechiae and impaired wound healing. They admit to a poor diet without fruits or veggies.
Scurvy- Vitamin C Deficiency
Impairment of hydroxylation of proline and lysine in collagen synthesis (requires vitamin C)
Functions of vitamin C (ascorbic acid)
- Collagen hydroxylation
2. Conversion of dopamine to norepinephrine (cofactor for dopamine hydroxylase)
Steps of collagen synthesis
- Pro a-chain backbone made up of Gly-X-Y
- Hydroxylation of proline and lysine residues (requires vitamin C)
- Glycosylation (add sugar to backbone)
- Triple helix formation (procollagen)
- Exocytosis
- Cleavage of procollagen C and N terminals (tropocollagen)
- Formation of lysine-hydroxylysine cross links to make collagen fiber
What causes wrinkles of aging?
Due to dec collagen and elastin production
Variable expressivity
phenotype varies among individuals with the same genotype (ex. Neurofibromatosis type I)
Incomplete penetrance
not all individuals with the mutant genotype show the mutant phenotype (ex, BRCA1 gene mutation)
Pleiotropy
one gene contributes to multiple phenotypic effects (ex. PKU manifests with light skin, intellectual disability, and musty body odor)
Anticipation
increased severity or earlier onet of disease in succeeding generations (ex. Huntington’s)
Mosaicism
presence of genetically distinct cell lines in the same individual (Ex. McCune Albright Syndrome, some forms of Down Syndrome)
Locus heterogeneity:
mutations at different loci can produce a similar phenotype (ex. Albinism)
Allelic heterogeneity:
different mutations at the same locus can produce the same phenotype (ex. B Thalassemia)
Heteroplasmy
presence of both normal and mutated mitochrondial DNA, resulting in variable expression in mitochrondrially inherited disease
Uniparental disomy
offspring receives 2 copies of a chromosome from one parent and no copies from the other parent
(consider this when there is an individual manifesting a recessive disorder when only one parent is a carrier)
Imprinting
when only one allele is active and the other is inactive due to methylation – with one allele inactivated, deletion of the active allele leads to disease
Prader-Willi syndrome
maternal imprinting – gene from mom is silent and paternal gene is deleted/mutated.
Results in hyperphagia, obesity, intellectual disability, hypogonadism, and hypotonia
Angelman syndrome
paternal imprinting – gene from dad is silent and maternal gene is deleted/mutated
Results in inappropriate laughter (“happy puppet”), seizures, ataxia, and severe intellectual disability
Vitamin deficiency: swollen gums, anemia, poor wound healing, perifollicular hemorrhages, corkscrew hair
Vitamin C
Vitamin deficiency: night blindness and dry skin, corneal degeneration, bito spots on conjunctiva
Vitamin A
Vitamin deficiency: neurologic problems (ataxia, dysathria, lower limb arreflexia, peripheral neuropathy) as well as hemolytic anemia
Vitamin E – neurologic problems are due to posterior column and spinocerebellar tract demyelination
Closely resembles Friedrich Ataxia
Appears similar to B12 deficiency but has no megaloblastic anemia
Which vitamins are produced by enteric bacteria?
Vitamine K and folate
What does a beefy red tongue suggest?
Vitamin B12 (cobalamin) deficiency, folate deficiency or iron deficiency
Patient presents with vomiting, rice water stool, and garlic breath. What do you suspect? What is the antidote?
Arsenic poisoning
- Arsenic inhibits lipoic acid (part of pyruvate dehydrogenase)
Treat with Dimercaprol (chelating agent)
Kwashiokor vs Marasmus
Kwashiorkor = protein malnutrition
Marasmus = total calorie malnutrition
What causes the neurologic problems in vitamin B12 deficiency?
Degeneration of the dorsal spinal colums, spinocerebellar tract, and lateral corticospinal tract
Associated with inc methylmalonic acid and inc homocysteine levels
Pellagra
due to niacin (B3) deficiency and is characterized by the 3 D’s: dermatitis, diarrhea, and dementia (can also see ataxia)
Niacin can be obtained through dietary intake or synthesized endogenously from tryptophan
Tryptophan is an essential amino acid and a precursor for NAD+, nicotonic acid, serotonin, and melatonin
Hartnup disease
(AR) deficiency of amino acid transporters in the PCT of the kidney and on enterocytes causes deficiency of tryptophan (due to inc excretion).
Dec tryphophan availability for conversion to niacin causes pellagra like symptoms (Diarrhea, dermatitis, dementia)
Functions of pyridoxine (B6)?
Cofactor for Dopa decarboxylase for the formation of dopamine, NE, and epinephrine
Cofactor for cystathionine B synthase for production of cystathionine
Synthesis of heme (ALA synthase)
Transaminase (a ketoglutarate –> glutamate)
Functions of biotin (B7), What can cause deficiency?
pyruvate carboxylase (gluconeogenesis)
acetyl CoA carboxylase (fatty acid synthesis)
propionyl CoA carboxylase (formation of succinyl-CoA)
Deficiency can be caused by excessive consumption of egg whites
Enzymes involved in ethanol metabolism?
Drugs that target them?
Alcohol dehydrogenase (Fomepizole)
Acetaldehyde dehydrogenase (disulfiram)
Fomepizole
Inhibits ADH
Used for methanol or ethylene glycol poisoning
Disulfiram
Inhibits ALDH – causes buildup of acetaldehyde which causes nausea, vomiting – used as aversive alcohol treatment
Ethanol effects on the TCA cycle
Inc NADH/NAD+ ratio disfavors TCA cycle production of more NADH
Acetyl-CoA is instead used for ketogenesis (ketoacidosis) and for lipogenesis (hepatosteatosis)
Consequences of ethanol use
- Inc pyruvate → lactate (lactic acidosis)
- Inc triglyceride formation → hepatosteatosis
- Converts Oxaloacetate → malate (prevents gluconeogenesis and causes hypoglycemia)
- Dec TCA cycle activity – acetyl CoA is instead used for ketogenesis (ketoacidosis) and lipogenesis (hepatosteatosis)
What promotes the formation of ketone bodies?
When there is an accumulation of Acetyl-CoA (from ethanol metabolism or B oxidation of excess fatty acids usually due to lack of insulin)
What are the ketone bodies?
Acetoacetate and B hydroxybutyrate
Which tissues can use ketone bodies and which can’t?
Liver and RBC can’t
Muscle and kidney can use it for generation of ATP
Brain uses ketones during times of starvation
What gives patients with DKA their fruity breath?
Formation of acetone from ketone bodies (acetoacetone) – expired from lung
How does diabetes lead to ketone production?
Lack of insulin allows lipolysis to proceed unchecked –> inc Acetyl CoA that is then used for the production of ketones
Glucokinase vs Hexokinase
Location
Km
Vmax
First committed step of glycolysis (and glycogenesis)
Glucokinase is in the liver and B cells of the pancreas
High Km (low affinity)
High Vmax (high capacity)
**Stores glucose in the liver when glucose levels are high
Hexokinase is in all other tissues
Low Km (high affinity)
Low Vmax (low capacity)
**Stores glucose in the tissues when glucose levels are lower
What induces glucokinase (glycolysis) activity? What happens when there is a mutation in glucokinase?
After a meal – high levels of glucose and inc levels of insulin
Mutation leads to maturity-onset diabetes of the young
What is metabolized fastest through glycolysis and why? Fructose, Mannose, Galactose, or Glucose?
Fructose – bypasses PFK-1 which is the rate limiting step of glycolysis
I cell disease
a lysosomal storage disorder in which the Golgi fails to phosphorylate mannose residues on glycoproteins
Proteins are secreted extracellularly instead of being delivered to lysosome
Results in coarse facial features, clouded corneas, restricted joint movement, and high plasma levels of lysosomal enzymes
Usually fatal in childhood
Effects of fructose 2,6 bisphosphate on glycolysis and gluconeogenesis? How is F26BP made and broken down?
F26BP induces glycolysis
F26BP inhibits gluconeogenesis
Insulin stimulates PFK-2 to produce F26BP (promotes glycolysis and blocks gluconeogenesis)
Glucagon stimulates FBPase2 to break down F26BP to promote gluconeogenesis
Function of and cofactors for pyruvate dehydrogenase
Pyruvate kinase links glycolysis and the TCA cycle Pyruvate → acetyl CoA)
Cofactors = "TLC For Nancy" Thiamin (B1) Lipoic acid CoA (B5) FAD (B2, riboflavin) NAD (Niacin, B3)
Consequences of pyruvate dehydrogenase complex deficiency?
Causes a buildup of pyruvate that gets shunted to lactate (via lactate dehydrogenase) or to alanine (via ALT)
Leads to neurologic defects and lactic acidosis and inc serum alanine in infancy
**X linked disorder
How can you treat a person with pyruvate dehydrogenase complex deficiency and make sure they produce ATP?
Give them lysine and leucine (purely ketogenic amino acids) or high fat diet (promote ketone formation)
Allows them to make ATP via ketogenesis
Which organs carry out gluconeogenesis?
The liver and the kidney
Muscle cannot because it lacks glucose 6 phosphatase
Role of the HMP shunt (pentose phosphate pathway)? Where in the cell does it take place?
responsible for producing NADPH from glucose metabolism and for the production of ribose 5 phosphate needed for the synthesis of nucleotides
Reactions take place in the cytoplasm
Oxidative vs Non oxidative reactions of the HMP shunt
Oxidative reactions = formation of NADPH (G6P dehydrogenase)
Non-oxidative reactions = formation of ribose 5 phosphate (transaldolase and transketolase)
Mechanism of uncoupling agents
Examples?
lead to increase permeability of the mitochondrial membrane and decrease the proton gradient – uncouples electron transport and phosphorylation
ATP synthesis stops but O2 is still used up – energy released by the electron transport chain produces heat
- Brown fat in neonates: responsible for heat production.
- Aspirin: fevers can occur after overdose, Reye syndrome
- 2,4 Dinitrophenol: used elicitly for weight loss
Cyanide and Carbon Monoxide poisoning
blocks complex 4 of the electron transport chain (CO/CN = 4)
Decreases ATP synthesis
Glucose 6 Phosphate Dehydrogenase
Used to make NADPH –
NADPH is necessary for keeping glutathione reduced so it can detoxify free radicals and peroxides
NADPH is also used for cholesterol synthesis and fatty acid synthesis
Glucose 6 Phosphate Dehydrogenase Deficiency
Leads to hemolytic anemia (bite cells and Heinz bodies)
RBCs are unable to defend themselves against oxidizing agents (fava beans, infection, sulfonamides, primaquine, anti TB drugs)
Which of the following is more severe and why? Essential fructosuria or Fructose Intolerance?
Fructose Intolerance is worse: inhibition of Aldolase B causes a buildup of Fructose 1 P in the cell, which traps a large amount of phosphates and makes it unavailable for ATP formation – inhibits glycogenolysis and gluconeogenesis
Essential fructosuria is caused by a defect in fructokinase. Fructose builds up and is excreted in the urine or it is converted to Fructose 6 phosphate by hexokinase and enters glycolysis
Which of the following is worse and why? Galactokinase deficiency or Classic Galactosemia?
Classic Galactosemia (most common): defect in galactose 1 P uridyltransferase. Causes accumulation of toxic substances (Galactitol → cataracts)
Phosphate is trapped as galactose 1 P which causes dec ATP and dec gluconeogenesis and glycogenolysis – failure to thrive, mental retardation, can lead to E coli neonatal sepsis
Pathophysiology of cataracts and peripheral neuropathy in diabetes:
Osmotic damage:
during hyperglycemia, excess plasma glucose is converted to sorbitol by aldose reductase. Sorbitol accumulates in some cells (eye lens and schwann cells) and attracts water into these tissues leading to osmotic cellular injury.
Treatment for essential fructosuria and fructose intolerance
Avoid fructose and sucrose (fructose + glucose) in diet
Treatment for galactokinase deficiency and classic galactosemia
Avoid galactose and lactose (galactose + glucose) in diet
Which amino acid plays an important role in the urea cycle?
Aspartate – gives the NH2 for formation of urea
Defects/deficiencies in which enzymes can cause hyperammonemia? Which one is more common and how can you differentiate between them?
1) Carbomoyl phosphate synthetase I (or cofactor N-acetylglutamate)
2) ornithine transcarbamoylase (most common)
Differentiate by presence of orotic acid – in ornithine transcarbamoylase defect, the excess carbamoyl phosphate accumulates in the mitochondria until it leaks into the cytoplasm → inc rate of pyrimidine synthesis and inc orotic acid
What causes inc orotic acid but normal ammonia levels? How can you treat this?
Deficiency in UMP synthase (pyrimidine synthesis pathway)
Supplement with uridine
How can you differentiate between Carbomoyl phosphate synthetase I defect or ornithine transcarbamoylase defect causing hyperammonemia?
Differentiate by presence of orotic acid
In ornithine transcarbamoylase defect, the excess carbamoyl phosphate accumulates in the mitochondria until it leaks into the cytoplasm → inc rate of pyrimidine synthesis and inc orotic acid
Patient presents with asterixis, slurred speech, somnolence, vomiting, and blurred vision. Has a history of liver disease. What is going on?
The patient has hyperammonemia due to defective liver function.
The accumulation of NH3 leads to a depletion of a-ketoglurate, which leads to inhibition of the TCA cycle
What are the derivatives of phenyalanine
Thyroxine (thyroid hormone) Melanin Dopamine NE Epinephrine
What are the derivatives of tryptophan?
Niacin –> NAD
Serotonin –> Melatonin
What are the derivatives of histadine?
Histamine
What are the derivatives of Glycine?
Porphyrin –> Heme
*Heme is also synthesized from Succinyl CoA
What are the derivatives of glutamate?
GABA
Glutathione
What are the derivatives of arginine?
Urea
Nitric Oxide
Creatine
Cystinuria
AR) defect in cysteine-reabsorbing PCT transporter causing cystinuria → also leads to poor absorption of Ornithine, Lysine, and Arginine (COLA)
o Hexagonal cysteine stones in urine
o Treat with alkalinization of urine
Inherited homocysteinuria
Autosomal recessive
o Cystathionine synthase deficiency
o Dec affinity of cystathionine synthase for vitamin B6 (pyridoxal phosphate)
o Methionine synthase deficiency
o S/S: marfanoid body habitus, inc homocysteine in urine, intellectual disability, lens subluxation, atherosclerosis (MI/stroke)
Role of epinephrine and glucagon in glycogen processing
Promote glycogenolysis: mobilization of glucose stores
Both act on adenylate cyclase to inc cAMP and activate protein kinase A which activates glycogen phosphorylase kinase and activates glycogen phosphorylase
Role of insulin in glycogen processing
Promotes glycogenesis: storage of glucose
Acts on tyrosine kinase receptor which activates protein phosphatase, which activates glycogen synthase and inhibits glycogen phosphorylase
Patient with a glycogen storage disease presents with gout, lactic acidemia hyperlipidemia, and inc glycogen levels. What is the glycogen storage disease and what enzyme is effected?
Von Gierke disease (type I)
Defect in glucose 6 phosphatase
Impaired gluconeogenesis and glycogenolysis
Cori disease (GSD Type III)
Defect in debranching enzyme
(impaired glycogenolysis, normal gluconeogenesis)
Accumulation of dextrin-like structures in cytosol
Patient presents with painful muscle cramps and red urine after working out. What is the glycogen storage disease and what enzyme is effected?
McArdle Disease (Type IV)
Defect in skeletal muscle glycogen phosphorylase
(normal blood glucose levels because liver glycogen phosphorylase is normal)
McArdle = Muscle
Child is brought in with hypotonia and hepatosplenomegaly. CXR shows cardiomegaly. Echo shows evidence of hypertrophic cardiomyopathy. What glycogen storage disease is this and what is the enzyme defect?
Pompe Disease (type II) defect in lysosomal a-glucosidase (acid maltase) (normal glucose levels). Accumulation of glycogen in lysosomes effects cardiac and skeletal muscle
Patient presents with bone crises, aseptic necrosis of the femur (with Erlenmeyer flask deformity), hepatosplenomegaly and pancytopenia. Histo shows lipid laden macrophages (that look like crumpled tissue paper)
Gaucher disease
Defect in glucocerebrosidase
Patient has peripheral neuropathy and optic neuropathy with globoid cells
Krabbe disease
Defect in galactocerebrosidase
Inc in psychosine
Lysosomes with onion skin appearance
Tay Sachs disease
Defect in hexosaminidase A
Accumulation of GM2 ganglioside
Patient presents with triad of peripheral neuropathy, angiokeratomas, and hypohidrosis.
Fabry disease
Defect in a galactosidase A
Accumulation of ceremide trihexoside
Can lead to cardiovascular disease and renal failure
Fatty Acid Metabolism:
Carnitine vs Citrate
Carnitine: brings fatty acids into the mitochondria for B oxidation –> form Acetyl CoA
• Carnitine = fatty acid carnage
• Inhibited by Malonyl-CoA
Citrate: brings citrate (made from Acetyl-CoA) into cytoplasm for fatty acid synthesis
• Citrate = “Cynthesis” of fatty acids
What vitamin is necessary for fatty acid synthesis?
Biotin (B7)
Carnitine deficiency
Defect in transport of long chain fatty acids into mitochondria causes toxic accumulation – weakness, hypotonia, and hypoketotic hypoglycemia
What stimulates lipolysis and what inhibits lipolysis?
Stimulated by epinephrine and glucagon (catabolic)
• glucAgon activates Adenylyl cyclase → increases cAMP → activates protein kinase A → activates Hormone Sensitive Lipase → releases fatty acids from triacylglycerides
Inhibited by insulin (anabolic)
• Insulin activates phosphodiesterase (inc cAMP → AMP)
• Insulin activates protein phosphatase which inactivates Hormone Sensitive lipase
Ubiquitin
Ubiquitin is a protein that undergoes ATP-dependent attachment to other proteins, labeling them for degradation by proteasomes
Defects in the ubiquitin-proteasome system have been implicated in some cases of Parkinson disease and Alzheimer’s
Patient presents to the ER after being lost in the forest and labs show low ketones and low glucose levels. What enzyme is likely deficient?
Hypoketotic hypoglycemia after a period of fasting indicates a defect in fatty acid B oxidation in the mitochondria (most common defect is in acyl-CoA dehydrogenase)
• Affected patients may remain asymptomatic for long periods until they experience a significant fast
Which vitamin overdoes can cause pseudotumor cerebri, dry skin, and allopecia?
Vitamin A overdose
Hunter syndrome
(X linked recessive) defect in iduronate sulfatase leading to accumulation of heparin sulfate and dermatan sulfate
o Present as a milder version of Hurler syndrome plus aggressive behavior, but no corneal clouding.
“Hunters see clearly and aim for the X!”
Hurler syndrome
(AR) defect in a-L-iduronidase leading to accumulation of heparin sulfate and dermatan sulfate
o Present with developmental delay, gargoylism, corneal clouding and hepatosplenomegaly
Role of proteasomes in apoptosis
Proteasomes regulate the balance of pro- and anti-apoptotic proteins, and their inhibition leads to an excess of proapoptotic proteins
What do homeobox (HOX) genes code for?
Transcription factors
highly conserved DNA sequences of about 180 nucleotides that typically code for transcription factors that bind to regulatory regions on DNA, altering the expression of genes involved in the segmental organization of the embryo
What happens to pyruvate dehydrogenase during hypoxic conditions? Why?
What is the consequence of this?
Pyruvate dehydrogenase is inhibited under hypoxic conditions due to a build up of NADH (there is no O2 to act as the final electron receptor in the oxidative phosphorylation pathway so NADH builds up)
o Causes lactic acidosis
HOX genes
Highly conserved DNA sequences of about 180 nucleotides that typically code for transcription factors that bind to regulatory regions on DNA, altering the expression of genes involved in the segmental organization of the embryo
Homeobox mutations interrupt the developmental process and often result in severe abnormalities such as skeletal malformations and improperly positioned limbs and appendages
