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422 Cards in this Set

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What is a nucelosome?

Histone core + linker DNA

Which bacterial DNA polymerase has 5´to 3´exonuclease activity? And why is it important?

Polymerase I


Primer removal and DNA repair

Which DNA polymerase has 3´to 5´exonuclease activity? And why is it important?

Polymerase I, II and III


Proofreading and error correction of the newly synthesized DNA strand.



What does it mean that replication is semiconservative?

Each DNA strand serve as a template for the synthesis of a new DNA strand producing 2 new DNA molecules, each with 1 old and 1 new DNA strand.

In which direction does DNA synthesis happen?

DNA synthesis is allways in a 5 ́to 3 ́direction.

What is the role of Dam methylase?

Methylates the newly synthesized DNA strand.


The two strands can no longer be distinguished.

Methyl directed mismatch repair (the enzymes and their function)

MutS, MutL, MutH: winds up the DNA molecule




MutH: cleaves the unmethylated strand at methylated site




DNA helicase: unwinds the DNA strand




Exonuclease I: removes the newly synthesized fragment from the MutH cleavage site to just beyond the mismatch




DNA polymerase III: makes the new strand

Base-excision repair pathway (the enzymes and their function)

DNA glycosylase: recognize common DNA lesions and remove the affected base (AP site is formed)




AP endonuclease: cut the DNA strand containing the AP site. A segment of DNA including the AP site is removed.




DNA polymerase I: replaces the removed DNA




DNA ligase: seals the remaining nick

Nucleotide excision repair (the enzymes and their function)

DNA lesion is detected.




Exinuclease: cleaves the DNA on each side of the damage.




DNA helicase: removes the DNA segment.




DNA polymerase (I in Ecoli, ε in human): fills the gap




DNA ligase: seals the nick

What are the different types of direct repair of DNA molecules?

1. Repair of pyrimidine dimers with photolyase




2. Direct repair of O^6-Methylguanine by O^6-Methylguanine-DNA methyltransferase


- Transfers the methyl group onto its own Cys-residue




3. Direct repair of alkylated bases by AlkB


- α-ketoglutarate donates a hydroxyl group to the alkylated base and in next step the methyl group is removed in the form of an aldehyde group.

What are the different types of short RNAs?

miRNA, siRNA, saRNA, snRNA, snoRNA, rasiRNA piRNA, qiRNA, tmRNA, gRNA

What are the different types of RNA molecules and their function?

mRNA: Encode the amino acid sequence of one or more polypeptides specified by a gene or a set of genes.




tRNA: Read the information encoded in the mRNA and transfer an amino acid to the growing polypeptide chain in protein synthesis.




rRNA: Are constituents of ribosome.

Examples of ribozymes

Ribozymes = ribonucleic acid enzymes. They increase the speed of reaction.




Group I introns


Rnase P


rRNA


Spliceosomes


Hammerhead ribozyme

What is the role of Sigma factor?

Sigma factor is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. It controls promoter recognition and specificity.

What is the function of the Rho factor?

Prokaryotic protein involved in the termination of transcription.

What inhibits transcription in bacteria? (name and function)

Tetracycline: blocks binding of aminoacyl-tRNA to A-site of ribosome.




Streptomycin: prevents the transition from initiation complex to chain-elongating ribosome and also causes miscoding




Chloramphe-nicol: blocks the peptidyl transferase reaction on ribosomes




Erythromycin: blocks the translocation reaction on ribosomes




Rifampicin: blocks initiation of RNA chains by binding to RNA polymerase (prevents RNA synthesis)

What inhibits transcription in both bacteria and eucaryotes? (name and function)

Puromycin: causes the premature release of nascent polypeptide chains by its addition to growing chain end.




Actinomycin D: binds to DNA and blocks the movement ofRNA polymerase (prevents RNA synthesis)

What inhibits transcription only in eukaryotes? (name and function)

Cycloheximide: blocks the translocation reaction on ribosomes




Anisomycin: blocks the peptidyl transferase reaction on ribosomes




α-Amanitin: blocks mRNA synthesis by binding to RNA polymerase.

What is the function of 5´cap?

- Protect mRNA and prevent degradation by endonucleases.


- Promotion of ribosome binding and translation


- Regulates nuclear export

What is the function of poly (A)?

- Protection


- Transport


- Translational enhancement

What is the difference between virus and retrovirus?

Virus contain both DNA and RNA, retrovirus contain only RNA.


Viruses have transcription process, whereas retroviruses have reverse transcription process. It needs to convert their RNA into DNA before it can insert it into the host genome.

What is transposon/retrotransposon?

DNA sequence that can change its position within the genome, sometimes causing mutations and altering the genome size.

What is the function of molecular chaperones? And what are the members of the chaperone family?

Molecular chaperones: proteins assisting folding of nascent polypeptides, by preventing wrong folding.Molecular chaperones catalyze the formation of correctly folded, functionally active, native proteins, but they are not part of the product.




Chaperone family:


- Nucleoplasmins


- Chaperonins


- Heat Shock proteins 70 (HSP 70)


- Heat Shock proteins 90 (HSP 90)



What is heat shock proteins?

Expression of many chaperones is induced by stress, such as by heat,because during heat-stress the probability of wrong folding is higher, therefore cells need more protection.These chaperons are called heat shock proteins (HSP’s).

Examples of diseases due to misfolding of proteins

Cystic fibrosis mutant


Parkinson’s disease


Alzheimer’s disease


Huntington’s disease

Hoe does protein degradation happens in eukaryotes and bacteria respectively?

Eukaryotes: Ubiquitination (signal of death for proteins) and proteasome (enzyme where proteins are degraded)




Bacteria: Lon (an ATP dependent protease) and other proteases




Proteins are degraded into short peptides, and not amino acid. This is important for immune surveillance.

What are the 7 processes that can affect the steady-state concentration of a protein?

1. Transcription


2. Posttranscriptional processing


3. mRNA degradation


4. Translation


5. Posttranslational processing


6. Protein degradation


7. Protein trageting and transoprt

Gene regulatory mechanisms

1. Transcriptinal mechanims (promoter and RNA polymerases)




2. RNA porcessing (5´capping, 3´poly-adenylation, splicing and alternative splicing)




3. Translational mechanisms (miRNA inhibit translation and degrade mRNA, silencer RNAs degrading mRNA)




3. Epigenetic mechanisms (DNA methylation, histone modification, chromatin remodeling)

What are enhancers elements?

DNA sequence with no promoter activity of their own, but they that increase the activities of many promoters in eucaryotes. Enhancers function by serving as binding sites for specific regulatory proteins.




It increase the rate of transcription.

What are the 3 transmit messages between cells?

1. Neurotransmitters - nervous system


2. Hormones - Endocrine system


3. Cytokines - immune system

Peptide hormones

Insulin, glucagon, somatostatin, hypothalamic (releasing) hormones, pituitary hormones




Synthesis: proteolytic cleavage of the precursor proteins




Mode of action: bind to receptors in the plasma membrane

Catecholamine hormones

Epinephrine and norepinephrine




Synthesis: brain, adrenal glands




Mode of action: act through plasmamembrane receptors




Effects: increased heart rate and blood pressure (increased delivery of O2 to tissues). Increased glucose and ATP production, fatty acid mobilization. Increased glucagon secretion and decreased insulin secretion.

Eicosanoids (fatty acid derivatives)

Derived from polyunsaturated fats and produced only when needed. They are paracrine hormones.




Prostaglandins, thromboxanes and leukotrienes




Mode of action: act through plasma membrane receptors.




They are involved in inflammation, fever and painassociated with injury or disease, in the formationof blood clots and the regulation of bloodpressure.

What is the role of phospholipase A2?

- Arachidonate --> leukotrienes by lipoxygenase.


- Arachidonate --> prostaglandins and thromboxjnes by cyclooxygenase.

- Phospholiase A convert phospholipids to arachidonate.




- Arachidonate --> leukotrienes by lipoxygenase.




- Arachidonate --> prostaglandins and thromboxanes by cyclooxygenase.

Steroids

Steroid hormones are endocrine hormones.


Derived form cholesterol: Cortisol, progesterone, testosteron.





What is the mode of action of steroid hormones?

Vitamin D

Mode of action: acts through nuclear receptors (intestinal Ca2+-binding protein) --> uptake of dietary Ca2+




Effects: works in Ca2+ homeostasis,regulating balance between Ca2+ deposition and Ca2+ mobilization from bone.

Retionic acid hormones

Regulation of gene expression


Biosynthesis: In liver from vitamine-A




Mode of action: Nuclear receptors




Effects: regulate the growth, survival,and differentiation of cells.

Thyroid hormones

Thyroglobulin-Tyr ---> Thyroglobulin-Tyr-I (iodinated Tyr residues) ---> Thyroxine (T4) and triiodothyronine (T3)




Mode of action: through nuclear receptors




Effects: stimulate energymetabolism in the liver and muscle



Describe the desensitization of the beta-adrenergic receptor by epinephrine.

The genes which expression are supressed by insulin.

- PEP carboxykinase (gluconeogenesis)


- Glucose-6-phosphatase (release glucose to blood)



The genes which expression are increased by insulin.

Glycolysis: Hexokinase 2, Hexokinase 4, phosphofructokinase-1, pyruvate kinase




Regulation of glycolysis/gluconeogenesis: PFK-2/FBPase-2




Pentose phosphate pathway: glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase




Fatty acid synthesis: pyruvate dehydrogenase, acetyl-CoA carboxylase, malice enzyme, ATP-citrate lyase, fatty acid synthase complex



What enzymes are regulated by PKA?

Increase:


- Phosphorylase b kinase (glycogen breakdown)


- Fructose-2,6-bisphospatase-2 (gluconeogenesis)


- Hormone-sensitive lipase (triacylglycerol mobilization and fatty acid oxidation)




Decrease:


- Glycogen synthase (glycogen synthesis)


- Pyruvate kinase (glycolysis)


- Pyruvate dehydrogenase complex (pyruvate to acetyl-CoA)


- Phosphofructokinase-2 (glycolysis)



What are the metabolic functions of PKB?

- Translation initiation


- Translation elongation


- Increase glucose uptake (by stimulating GLUT4 transporter)


- Stimulate glycolysis (by increase prod. of PFK2)


- Increase glycogen synthesis (by inhibiting GSK-3)

What is AMPK stimulated by and what does it stumulates?

It is stimulated by stress, exercise, fasting ( increased [AMP])




It stimulates glucose uptake and transport, glycolysis, fatty acid uptake, beta-oxidation

What does AMPK inhibit?

- HMG-CoA reductase (cholesterol synthesis)


- Fatty acid synthesis (ACC - acetyl-CoA carboxylase)


- Insulin secretion


- Transcription

What happens if there is hypoxia (low pO2)?

1. Increased transcription of HIF-1α. HIF-1 regulates gene expression to reduce ROS formation


2. HIF-1α is phosphorylated


3. HIF-1α increases transcription of other enzymes and proteins (glucose transporter, glycolytic enzymes, lactate dehycrognease, protease)


4. --> ATP production by glycolysis increases and complex IV properties are adapted to low pO2.



How is the cholesterol synthesis regulated?

Intracellular cholesterol concentration: High intracellular concentrations has a negative feedback and stimulate proteolysis of HMG-CoA reductase. It activate ACAT, which increase esterification of cholesterol for storage. A high cellular cholesterol level also diminishes transcription of the gene that encodes the LDL receptor, reducing production of the receptor and thus the uptake of cholesterol from the blood.




Hormonal regulation: stimulated by insulin and inhibited by glucagon. Covalent modification of HMG-CoA reductase. Glucagon stimulates phosphorylation which inactivates the enzyme, while insulin promotes dephosphorylation, activating the enzyme.




Transcriptional regulation:


SREBP activates HMG-COA reductase as a transcription factor.


SCAP (cleavage-activating protein) prevents release of SREBP.

Which enzymes uses TPP (thiamin diphosphate) as a cofactor?

Catalyze oxidative decarboxylation:


- Pyruvate dehydrognease


- a-ketoglutarate dehydrogenase complex


- Branched-chain keto-acid dehydrogenase


- Pyruvate decarboxylase (in bacteria)




Also a coenzyme for transketolase in pentose phosphate pathway.

Which enzyme are vitamin B12 dependent enzymes?

- Methymalonyl CoA mutase


- Methionine synthase


- Leucine aminomutase

Which enzymes uses biotin as a coenzyme?

- Acetyl-CoA carboxylase


- Pyruvate carboxylase


- Propionyl-CoA carboxylase


- Methylcrotonyl-CoA carboxylase

What function has riboflavin (B2)?

Water-soluble vitamin


Coenzyme in oxidation and reduction reactions (FAD)


Prosthetic group of flavoproteins

What function has nicotinic acid/nicotinamide (niacin)?

Coenzyme in oxidation and reduction reactions, functional part of NAD and NADP.

Lipid-soluble vitamins

Hydrophobic compounds. Can be absorbed efficiently only whenthere is normal fatabsorption Are transported in theblood in lipoproteins or attached to specificbinding proteins.




D - Calciferol


E - Tocopherols, tocotrienols


K - Phylloquinone: menaquinones


A - Retinol, b-Carotene

Water-soluble vitamins

Hydrophilic compounds. Function mainly as enzyme co-factors.




B1 - Thyamin (TPP)


B2 - Riboflavin (FAD)


B3 - Niacin (NAD/NADP)


B5 - Panthotenic Acid (part of CoA and ACP)


B6 - Pyridoxin (PLP)


B7 - Biotin


B9 - Folic acid


B12 - Cobalamin


C - Ascorbic Acid

What are the different types of glucose transporters and their function?

GLUT-1


- RBC, brain


- Transport across blood-brain barrier




GLUT-2


- Liver, kidney, pancreas


- Regulation on insulin release




GLUT-3


- Brain, placenta, others


- Uptake into neurons




GLUT-4


- Muscle, adipose tissue


- Insulin-mediated transport




GLUT-5


- Kidney and gut


- Absorption of fructose

What is the difference between hexokinase II and IV?

Hexokinase II is in muscle cells, have high affinity for glucose and is inhibited allosterically by its product glucose-6-phosphate.




Hexokinase IV (glucokinase) is in liver cells, have low affinity for glucose and is inhibited by a regulatory protein (not G6P). It is activated by glucose or fructose-6-phosphate.

How is phosphofructokinase-1 (PFK1) regulated?

Allosteric regulation.




Activated by ADP, AMP and fructose-2,6-bisphosphate (F2,6BP).




Inhibited by ATP and citrate.




(Citrate serves as an intracellular signal that the cell is meeting its current needs for energy-yielding metabolism by the oxidation of fats and protein)

What is the role of fructose-2,6-bisphosphate in regulation of glycolysis and gluconeogenesis?

 F2,6P is formed by phosphofructokinase 2 (PFK2). PFK2 is activated by insulin and inhibited by glucagon (↑ [cAMP])

F2,6P is formed by phosphofructokinase 2 (PFK2). It is an allosteric regulator of PFK-1 and FBPase-1. They are regulated reciprocal. PFK2 is activated by insulin and inhibited by glucagon (↑ [cAMP]).




Increased F26BP stimulates glycolysis and inhibits gluconeogenesis. Decreased F26BP inhibits glycolysis and stimulates gluconeogenesis.

How is pyruvate kinase regulated?

In all glycolytic tissues: (M pyruvate kinase)


Activated by fructose 1,6-bisphosphate


Inhibited by ATP, alanine, acetyl CoA, long chain fatty acids.




Only in the liver: (L pyruvate kinase)


Low blood glucose --> glucagon release --> cAMP-dependent protein kinases phosphorylates the L (liver) isozyme of pyruvate kinase via PKA. This inactivates the enzyme.

What are the 3 possible catabolic fates of the pyruvate formed in glycolysis?

Gluocose --> 2 pyruvate


1. 2 lactate


- Under anaerobic conditions


- Lactate dehydrogenase




2. 2 acetyl- CoA


- Enter citric acid cycle)


- Under aerobic conditions


- Pyruvate dehydrogenase complex




3. 2 ethanol + 2 CO2


- Only in bacteria!


- Pyruvate decarboxylase + alcohol dehydrogenase



One reaction which acetyl-CoA inhibit and one reaction which acetyl-CoA stimulate.

Inhibit: pyruvate kinase, pyruvate dehydrogenase complex




Stimulate: pyruvate carboxylase



How is pyruvate dehydrogenase complex (PDC) regulated?

Inhibited by ATP, acetyl-CoA, NADH and fatty acids.


Activated by AMP, CoA, NAD+, Ca2+.




Pyruvate dehydrogenase kinase (PDK) phosphorylates PDC --> INACTIVE


Pyruvate dehydrogenase phosphatase (PDP), dephosphorylates PDC ---> ACTIVE




PDK is stimulated by NADH and acetyl-CoA, and inhibited by CoA-SH, NAD+, ADP, pyruvate.




PDP is stimulated by Ca2+, Mg2+, insulin

How is citrate synthase regulated?

Inhibited by NADH, succinyl- CoA, citrate, ATP


Activated by ADP.

How is the gluconeogenesis regulated hormonally?

Insulin: inhibit


Glucagon: stimulate


Epinephrine, norepinephrine: stimulate


Glucocorticoids: stimulate

How is the glycogen synthase regulated?

Glycogen synthase has two forms, a (active) and b (inactive).




GSK3 = glycogen synthase kinase 3. Casein kinase (CKII) phosphorylates GSK3 for activation. GSK3 phosphorylates the glycogen synthase , form glycogen synthase b and inhibits glycogen synthesis. It is inhibited by insulin. Insulin will trigger activation of glycogen synthase a by blocking the activity of GSK3, and activating PP1 in muscles.




PP1 dephosphorylates glycogen synthase b forming glycogen synthase a. This promotes glycogen synthesis. PP1 is activated by insulin, glc-6-P and glc, and inhibited by glucagon and epinephrine.

What are the different enzymes that regulates different processes in lipid metabolism?




(biosynthesis of FA, β-oxidation, cholesterol biosynthesis, ketonebodies, signal transduction)

- Regulation of biosynthesis of FA: ACC


- Regulation of β-oxidation: CAT


- Regulation of cholesterol biosynthesis: HMG-CoA-reductase, transcriptional regulation


- Regulation of ketonebodies: succinyl-CoA


- Regulation of lipid metabolism by signal transduction (AMPK, PPAR)

What are the hormones that regulates lipid metabolism?

Insulin, glucagon, glucocorticoids, epinephrine

In which intracellular compartments does the different lipid metabolism processes happen?

Cytosol: Fatty acid synthesis (up to C16), cholesterol synthesis




ER: phospholipid synthesis, fatty acid elongation, fatty acid desaturation




Mitochondria: fatty acid oxidation, acetyl-CoA production, ketone body synthesis, fatty acid elongation

How is Acetyl-CoA carboxylase (ACC) regulated?

Inactivated by when phosphorylated by AMP-activated protein kinase. Glucagon, adrenaline, AMP, palmitoyl-CoA --> phosphorylation of ACC.




Protein phosphatase 2A dephosphorylates ACC and activating it. Glucagon inhibits protein phosphatase A2. It is activated by insulin and citrate.

How is the formation of ketone bodies regulated?

Regulation of ketone body synthesis happens via mitochondrial HMG-CoA synthase.




Stimulated by acetyl CoA.


Inhibited covalently by succinyl-CoA

Write with structures the reaction that is defective in phenylketonuria (PKU).

Defect phenylalanine hydroxylase.

Defect phenylalanine hydroxylase.

Write with structures the reaction that is defective in Maple syrup urine disease.

Defect branched-chain alfa-kets acid dehydrogenase complex.

Defect branched-chain alfa-keto acid dehydrogenase complex.

Write with structures the reaction that is defective in Tyrosinemia I.

Defect fumarylacetoacetase.

Defect fumarylacetoacetase.

Write with structures the reaction that is defective in Tyrosinemia II.

Defect tyrosine aminotransferase.

Defect tyrosine aminotransferase.

Write with structures the reaction that is defective in Tyrosinemia III.

Defect p-hydroxyphenylpyruvtae dioxygenase.

Defect p-hydroxyphenylpyruvtae dioxygenase.

Write with structures the reaction that is defective in Citrullinemia type I.

Argininosuccintae synthetase deficiency.

Argininosuccintae synthetase deficiency.

Write with structures the reaction that is defective in argininocsuccinate aciduria.

Argininosuccinase deficiency

Argininosuccinase deficiency

Write with structures the reaction that is defective in homocystinuria I.

Cystathionine ß synthase deficiency.

Cystathionine ß synthase deficiency.

Write with structures the reaction that is defective in argininemia.

Argininase deficiency.

Argininase deficiency.

Write with structures the reaction that is defective in alkaptonuria.

Homogentisate-1,2-dioxygenase deficiency.

Homogentisate-1,2-dioxygenase deficiency.

Write with structures the reaction that is defective in methylmalonic aciduria.

Methylmalonyl-CoA mutase deficiency.

Methylmalonyl-CoA mutase deficiency.

What is the function of intestinal lipase?

Degradation of triglycerols to diacylglyderides and monoacylgylcerols in the intestines.

What is the function of apoprotein?

- Structural role in lipoproteins


- Regulation of enzymes


- Targeting the lipoproteins: Lipid-binding protein in blood, transport phospholipids, cholesterol and cholesterol esters between organs.

What is the function of lipoprotein lipase?

Converts triacylglycerols in lipoproteins to fatty acids and glycerol.

What is the function of hormone-sensitive lipase?

Mobilization of stored triacylglycerols in adipocytes.




Stimulated by glucagon/adrenaline


-- > PKA activates hormone-sensitive lipase through phosporylation --> triacylglycerols are hydrolyzed --> free fatty acids are released into the blood.

What is the function of serum albumin in lipid metabolism?

Binds fatty acids and transports them through the blood.

What is the CORI cycle

When lactate is formed by active skeletal muscles (or RBC), it can be recycled. It is carried to the liver by the blood, and in the liver it is first converted to pyruvate, and then to glucose by gluconeogenesis. The glucose then returns to muscl...

When lactate is formed by active skeletal muscles (or RBC), it can be recycled. It is carried to the liver by the blood, and in the liver it is first converted to pyruvate, and then to glucose by gluconeogenesis. The glucose then returns to muscle through the blood and is again used for energy.

Galactosemia

Defect in either galactokinase, galactose-1-phosphate uridylyltransferase or UDP-glucose-4-epimerase.

What are the inhibitors of complex I, III and IV in the respiratory chain and the ATP synthase?

Complex I: rotenone, amytal, piercidin A




Complex III: antimycin A, myoxothiazol




Complex IV: CN- (cyanide) and CO




ATP synthase: oligomycin, venturicidin



What are the most common uncoupling agents in the ATP synthesis?

DNP (2,4-dinitrophenol


FCCP




Causing the oxidation to continue even if ATP synthesis is blocked.

What is the function and location of the malate-aspartate shuttle?

System that transport the NADH generated by glycolysis in the cytosol into the mitochondrial matrix. The mitochondrial membrane is not permeable to NADH.

Functions in liver, kidney, and heart mitochondria.

System that transport the NADH generated by glycolysis in the cytosol into the mitochondrial matrix. The mitochondrial membrane is not permeable to NADH.




Functions in liver, kidney, and heart mitochondria.

Glycerol-3-phosphate shuttle (function and location)

NADH shuttle used in skeletal muscle and brain. 

NADH in cytosol is converted to FADH2 in the mitochondrial matrix
Electrons are transported to complex II.

NADH shuttle used in skeletal muscle and brain.




NADH in cytosol is converted to FADH2 in the mitochondrial matrix


Electrons are transported to complex II.

What are the sources of reactive oxygen species (ROS)?

- CoQ of the respiratory chain


- Production of ROS in the peroxisome


- Cytochrome P450 monoxygenases

What is the function of antioxidants and name some examples?

Enzymes and other molecules that help protect the cell from harmfull effects of ROS.




Superoxide dismutase


Catalase


Glutathione: oxidized to donate reducing equivalents to regenerate oxidized cellular molecules

Where does the gluconeogenesis takes place and what is its function?

Takes place in the liver.


Function is to maintain the blood glucose levels during fasting.

How is the gluconeogenesis regulated?

Activators: Acetyl Coa, glucagon, epinephrine, norepinephrine, glucocorticoids




Activators of glycolysis (inhibitors of gluconeogensis): ADP, AMP, citrate, fructose-2,6-bisphosphate, insulin.

What is the function of the pentose phosphate pathway and in which cells is it present?

Location: rapidly dividing cells, such as those of the bone marrow, skin and intestinal mucosa.




Function: uses ribose-5-phosphate to produce NADH, RNA, DNA, ATP, FADH2 and CoA.




In other tissues, the essential product of the pen-tose phosphate pathway is not the pentoses but theelectron donor NADPH, needed for reductive biosynthesis or to counter the damaging effects of oxygen radicals.



Which pathways requires NADPH created by the pentose phosphate pathway?

Synthesis:


- fatty acid biosynthesis


- cholesterol biosynthesis


- neurotransmitter biosynthesis


- nucleotide biosynthesis




Detoxification:


- reduction of oxidized glutathione


- cytochrome P450 monooxygenases

What does glucose-6-phosphate dehydrogenase deficiency lead to?

Glucose-6-phosphate dehydrogenase deficency lead to NADPH deficiency.

NADPH maintains the supply of reduced glutathione in the cells that is used to remove free radicals that cause oxidative damage. 
Gluthahtione peroxidase: 2GSH + H2O2 ---> GSSG...

Glucose-6-phosphate dehydrogenase deficency lead to NADPH deficiency.




NADPH maintains the supply of reduced glutathione in the cells that is used to remove free radicals that cause oxidative damage.


Gluthahtione peroxidase: 2GSH + H2O2 ---> GSSG + 2H2O.




The G6PD/NADPH pathway is the only source of reduced glutathione in red blood cells (erythrocytes). If there is not enough reduced glutathione in the cells the free radicals produce Heinz bodies in the RBC, which is denatured hemoglobin caused by oxidative stress.



What is the Wernicke-korsakoff syndrome?

Mutation in transketolase gene, affinity to TPP is decreased --> thiamine deficiency (vitamin B1) --> entire pentose phosphate pathway slows down




Symptoms: severe memory loss, mental confusion and partial paralysis.

Where is glycogen stored and what is the function?

Glycogen is stored in liver and skeletal muscle.




Liver glycogen is used to maintain blood glucose levels.




Muscle glycogen is used to generate ATP for muscle contraction when is needed.

Which enzymes are needed for glycogen synthesis?

- Hexokinase/glucokinase


- Phosphoglucomutase


- UDP-glucose pyrophosphorylase


- Glycogen synthase


- Glycogen branching enzyme

What is the function of glucogenin?

Primer for glycogen synthesis.




Glycogenin catalyzes the addition of glucose to itself (autocatalysis) by firstbinding glucose from UDP-glucose to the hydroxyl group of Tyr-194. Seven moreglucoses can be added, each derived from UDP-glucose, by glycogenin'sglucosyltransferase activity. Once sufficient residues have been added, glycogensynthase takes over extending the chain. Glycogenin remains covalently attached tothe reducing end of the glycogen molecule.

Which enzymes are needed for glycogen degradation (glycogenolysis)?

- Glycogen phosporylase


- Debranching enzyme


- Phosphoglucomutase


- Glucose-6-phosphatase

How is glycogen phosphorylase regulated?

PP1 is activated by insulin (glucose in the liver).

Glycogen phosphorylase has 2 forms, glycogen phosphorylase a (more active) and glycogen phosphorylase b (less active)




Glycogen phosphorylase a is activated by phosphorylase b kinase by phosphorylation. Epinephrine, Ca2+, AMP will activate the kinase in muscle, while glucagon will activate it in liver. Will activate via cAMP --> PKA. PKA phosphorylates and activates phosphorylase kinase.




Glycogen phosphorylase is dephosphorylated by PP1 which makes it less active.




Glycogen phosphorylase in liver has glucose sensor. Glucose will bind to an allosteric site of phosphorylase a (PP1), and this causes a change in conformation which exposes it's phosphorylated groups. The PP1 will convert it to phosphorylase b. Reducing the activity, and slowing glycogen breakdown. Also stimulated by insulin indirectly.

How many citrate molecules are needed frommitochondria to cytosol to synthesize palmitate?

8 (Synthesis of palmitate need 8 acetyl-CoA = 8 citrate)




Acetyl CoA from pyruvate cannot be transported through the mitochondrial membrane to the cytosol, so it forms citrate together with oxaloactetate, which is transported out through a citrate transporter.




In the cytosol, citrate is reconverted to acetyl-CoA and oxaloacetate, and acetyl CoA process to fatty acid synthesis in the cytosol. Oxaloacetate is reduced to malte and is transported back into the mitochondria.

What is special with the desaturation of fatty acids in animals?

Animals can only put double bonds before the 10th carbon.




Therefore it is essential for animals to have fatty acids with double bonds >10 in their diet, like inolenate and alfa-linolenate which are essential fatty acids for mammals




These can be made into arachidonate, which can turn into prostaglandins, thromboxanes and leukotrienes.

What inhibit the production of prostaglandins, thromboxanes, leukotrienes?

Steroids inhibit the synthesis of arachidonate from phospholipids ---> no prostaglandins, thromboxanes or leukotrienes.




Non-steroids (aspirin, ibuprofen) inhibit COX (cyclooxygenase) ---> prostaglandins or thromboxanes.



What is the common precursor for both ketone bodies and cholesterol, and what is the enzymes for the different synthesis reactions?

HMG-CoA (beta-hydroxy-beta-methylglutaryl CoA)




Synthesized from acetyl-CoA and acetoacetyl-COA by HMG-CoA synthase-




Mitochondria:


HMG-CoA lyase --> acetoacetate (ketone body) + acetyl CoA




Acetoacetate --> acetone (acetoacetate decarboxylase) and D-beta-hydroxybutyrate (hydroxybutyrate dehydrogenase)




Cytosol:


HMG-CoA reductase --> mevalonate (cholesterol synthesis)

What is the different lipoproteins?

Chylomicrons


VLDL


LDL


HDL

What regulates the cholesterol synthesis?

Activators: insulin




Inhibitors: glucagon, cholesterol, metabolites

What are the fates of cholesterol?

Propionemia (propionic acidemia)

Deficiency in the enzyme propionyl-CoA carboxylase, inhibiting the conversion of propionyl-CoA to D-methylmalonyl CoA.

Methylmalonyl-uria

Deficiency of the enzyme methylmalonyl-CoA epimerase, inhibiting D-methylmalonyl CoA to L-methylmalonyl CoA.

What are the fates for the amino group and the carbon skeleton of an amino acid?

Amino group (NH4+): biosynthesis of amino acids and nucleotides, urea cycle




Carbon skeleton: citric acid cycle

What are the transporters of NH4+ from amin-acids to urea cycle?

Glutamate and glutamine




The amino group is transferred through transamination.

How is the transamination reactions?

alfa-ketogluatarate + NH4+ --> glutamate.

Glutamate + NH4+ --> glutamine.

An amino acid without NH4+ = alfa-keto acid.

Alfa-ketogluatarate + NH4+ --> glutamate.




Glutamate + NH4+ --> glutamine.




An amino acid without NH4+ = alfa-keto acid.




The enzyme for the reaction is aminotransferase which requires PLP as a cofactor.




Examples: alanine aminotransferase (ALAT) and aspartate aminotransferase (ASAT).





What is oxidative deamination?

The release of NH4+ from glutamate, forming alfa-ketoglutarate. The enzyme for this reaction is glutamate dehydrogenase, which is the only enzyme that use either NAD+/NADP+.




Glutamate dehydrogenase is stimulated by ADP (GDP) and inhibited by GTP (ATP).

What is transdeamination?

Transamination + oxidative deamination = transdeamination

Transamination + oxidative deamination = transdeamination

What are the sources of NH4+ in the liver?

- Amino acids from ingested proteins


- Alanine from muscle (glucose alanine cycle)


- Glutamine from muscle and other tissues (brain)

What are the sources of ammonia NH3 in the urea cycle?

- Amino acid degradation in every organ (especially in the liver and muscle)


- Ammonia secretion in kidney tubule from glutamine


- Nucleotide degradation (pyrimidine)


- Intestinal bacteria produce it from amino acids and urea





What is the problem with ammonia?

Ammonia is very toxic. It is quickly protonated to NH4+ in mitochondrial matrix and converted to urea, which is excreted in the kidney.




If the blood ammonium level increase it can cause cerebral edema and increased cranial pressure.

Which enzymes of the urea cycle is located in mitochondria and which is located in the cytosol?

Mitochondria: Carbamoyl phosphate synthetase I and ornithine transcarbamoylase




Cytosol: argininosuccinate synthetase, argininosuccinase (argininosuccinate lysase and arginase.

Which metabolic intermediates are common between citric acid cycle and urea cycle?

Aspartate, fumarate and malate.

How is the urea cycle regulated? (short term and long term)

Long term: Regulation of the rates of the synthesis (transcriptional regulation) of the 4 urea cycle enzymes and carbamoyl phosphate synthetase I.




Short term: Allosterically activation. Arginine stimulates the synthesis of N-acetylglutamate by N-acetylglutamate synthase. N-acetylglutamate stimulates the formation of carbamoyl phosphate by carbamoyl phosphate synthetase I.



What are the difference between ketogenic and glycogenic amino acids?

Ketogenic: produce ketone bodies in the liver




Glucogenic: produce glucose and glycogen




Mixed: both ketogenic and glucogenic

Which amino acids are glucogenic?

Aspargine


Aspartate


Methionine


Valine


Arginine


Glutamine


Glutmate


Hisitidine


Proline




They can become either pyruvate or oxaloacetate --> glucose

What are the purely ketogenic amino acids?

Leucine and lysine




--> Acetyl-Coa --> ketone bodies or citrate

How is the enzyme glutamine synthetase regulated? (allosteric and covalent)

Allosteric regulation: Each inhibitor produce partial inhibition, all 8 inhibitors together shut down the enzyme.


1. Glycine


2. Alanine


3. Glucosamine-6-phosphate


4. Histidine


5. CTP


6. Carbamoyl phosphate


7. Tryptophan


8. AMP




Covalent regulation: adenylation --> inactive


- Adenylation = (AMP) molecule is covalently attached to a protein side chain


- Adenylation stimulated by: glutamine, Pi


- Deadenylation stimulated by: ATP, alfa-ketoglutarate

What is the most important antioxidant in RBC and what is the active amino acid making the anti oxidation effect?

Gluthathione


Antioxidation effect: cysteine




It protects proteins for oxidation in erythrocytes. Removes toxic peroxide formed during growth and aerobic metabolism: glutathione peroxidase reaction.




Produced form glutamate, glycine and cysteine.

What neurotransmitters is produced from the amino acids tyrosine, glutamate, histidine, tryptophan, methionine, arginine respectively?

Tyrosine: dopa, dopamine, norepinephrine, epinephrine.




Glutamate: GABA (inhibitory neurotransmitter)




Histidine: histamine (vasodilator, released in allergic response, stimulates acid secretion in the stomach)




Tryptophan: serotonin




Methionine: spermine, spermidine (involved in DNA packaging)




Arginine: NO (important in neurotransmission, blood clotting and blood pressure control = vasodilator)

The glucose-alanine cycle

In the muscle, muscle protein is degraded to amino acids which inturn gives NH4+. 

In the alanine cycle we can transport both NH4 and pyruvate to the liver by alanine aminotransferase, which transfer the amino group to pyruvate and form alanine...

In the muscle, muscle protein is degraded to amino acids which inturn gives NH4+.




In the alanine cycle we can transport both NH4 and pyruvate to the liver by alanine aminotransferase, which transfer the amino group to pyruvate and form alanine. Alanine is transported in the blood. NH4 enters urea cycle, and pyruvate enters gluconeogenesis.

Why is the overall energetic cost of urea synthesis is reduced?

Because 1 NADH is formed in the malate dehydrogenase reaction (aspartate-argininisuccinate shunt).

What is common between activation of fatty acids and activation of amino acids?

Both need energy. They uses ATP which are converted to AMP + PPi.

4 possible fates of fatty acids in the liver

1. Free fatty acids


2. Beta-oxidation --> Acetyl CoA




Acetyl-CoA:


3. Cholesterol synthesis


4. Ketone body synthesis


5. Citric acid cycle




6. Storage as lipids


7. lipoproteins

How many CO2 molecules are produced form one glucose molecule, what are the reactions producing those CO2?

6 CO2 molecules




- Pyryvate dehydrogenase complex reaction


- Isocitrate dehydrogenase reaction


- Alfa-ketoglutarate dehydrogenase complex reaction



What is the biological role of creatine and carnitine, ans what enzymes catalyzes them?

Creatine: phosphocreatine is an energy reservoir in skeletal muscle during light activity or rest. Can rapidly regenerate ATP from ADP


Enzyme: Creatine kinase


Creatine + ATP <––> phospocreatine + ADP




Carnitine: transport long-chain fatty acids into the mitochondrion and regulate the intramitochondrial ratio of Acyl-CoA to free CoA.


Carnitine acyltransferase: carnitine + acyl-CoA <--> Acyl-carnitine

What is the role of DNA-dependent RNA polymerase?

An enzyme that produces primary transcript RNA. RNA polymerase is necessary for constructing RNA chains using DNA genes as templates, a process called transcription.

What is the role of RNA-dependent RNA polymerase?

RNA-dependent RNA polymerase or RNA replicase, is an enzyme that catalyzes the replication of RNA from an RNA template.

Name the substrates and the products of the light reaction of photosynthesis

2H2O + 2NADP+ ---> O2 2NADPH + 2H+

Write with structures the reaction where an inhibitory neurotransmitter is produced from anamino acid directly.

Glutamate decarboxylase reaction.

Glutamate decarboxylase reaction.

What are the small RNAs other than microRNA that have a role in splicing and rRNA maturation respectively?

Splicing: snRNA (small nuclear) - part of the spliceosome.




Maturation of rRNA: snoRNA (small nucleolar)

What is called the secondary genetic code?

= proofreading activity


Amino acid tRNA synthetase and tRNA interaction will recognize the tRNA that belongs to which amino acid. Get right anticodon for the right amino acid.

Namea cell type that does not express MHC I on its surface.

RBC and neurons only

What can happen to glucose-6-phosphate in the liver?

1. Glycolysis: glucophospho isomerase (energy production)




2. Gluconeogenesis: glucose 6-phosphatase (remove P toincrease blood sugar concentration)





3. Pentosephosphate pathway: Glucose 6-phosphatedehydrogenase (Ribose and NADPH production)




4. Glycogen synthesis: phosphoglucomutase (glycogen storage)

Which transcription factor is the most important regulator in the expression of erythropoietin?

HIF1 α (Hypoxia-inducible factor 1, α unit) --> Erythropoietin --> RBC production (since oxygen levelaccommodate to it)

How to calculate the maximum amount of ATP produced from fatty acid degradation to CO2 and H2O?

1. Number of Carbons/2 = Number of Acetyl CoA formed




2. Number of rounds in the Beta-oxidation necessary for converting the whole fatty acid to Acetyl Co A units = Number of Acetyl CoA - 1 = NADH and FADH2




3. NADH yields 2.5 ATP and each FADH2 yields 1.5 ATP. Multiply the number of rounds with 4.




4. Multiply the number of Acetyl CoA times 10 (10 ATP in each round of citric acid cycle)




5. Minus two ATP that were used for the activation of the fatty Acid.

Why is it advantageous for the long fasting man that his brain is able to utilize ketone bodies (produced by the liver) as a fuel?

Ketone bodies are produced from fat, converted to acetyl-CoA and then transported to the brain where it is used for energy. This prevent amino acid degradation, ketone bodies is used instead.

4 factors/accommodations for transport ofGlc-6-P out of cell as free glucose

1. High glucagon levels = low glucose levels in the blood


2. Glucose-6-phosphatase enzyme (only in the liver) - covert glc-6-P --> glucose


3. GLUT7 transporter (transport glucose from ER to cytosol


4. GLUT2 transporter (release glucose to the bloodstream)

4 enzymes that release ammonia (NH3) directly

Glutamate dehydrogenase


Glutaminase


Serine dehydratase


Adenosine deaminase

Which immunoglobulin participate in the fetus passive immune system. Why?

Passive immunity = when maternal antibodies are transferred to the fetus through the placenta.




IgG is the only immunoglobulin that can pass through the placenta. It protect against bacterial and viral infections in fetuses.

Name 3 reactions in the animal tissue as possible sources of NADPH.

Malic enzyme: malate <--> pyruvate




Glucose-6-phosphate dehydrogenase: glc-6-P <--> 6-phosphoglucono lactone




6-phosphogluconate dehydrogenase: 6-phosphogluconate --> ribulose-5-P

Which mitochondrial enzymes are required during conversion of glucose to fatty acid?

Pyruvat-Dehydrogenase-complex


Citrat-Synthase

What does processivity mean, in relation to polymerases?

Nucleotides added before the polymerase dissociates.




Polymerase I: 3-200


Polymerase II: 1500


Polymerase III: > 500 000



What is the Shine-Dalgarno sequence and what is its biological role?

Ribosomal binding site in the mRNA, generally located 8 basepairs upstreams for the AUG start codon.

List hormone-familiesthat have nuclear receptors.

Retinoic acid


Vitamin D


Thyroid


Steriod

Which catalytic function is missing in retroviral reverse-transcriptase compared to human and E-coli DNA polymerase?

Proofreading action. It is not able to do repair on the template, and mutations are very common (may cause immunity against drugs).

Name two metabolic pathwayswhich take place partially in the mitochondria and partially in the cytosol.

Gluconeogenesis


Urea cycle



Possible Fates of amino acids in the liver

1. Liver proteins


2. Nucleotides


3. Hormones


4. Porphorins


5. Urea Cycle


6. Gluconeogenesis


7. Acetyl-CoA:


TCA cycle


Fatty Acids

By what mechanism can a G protein coupled hormone receptor regulate gene expression?

G protein --> Adenylate Cyclase --> cAMP --> PKA

What are the modifications on individual amino acids in posttranslational modification?

Phosphorylation, carboxylation, methylation, sulfation, hydroxylation on the side chains.

What are the different posttranslational modifications in protein synthesis?

1. Modifications on both terminal ends


2. Loss of singal sequences


3. Modifications of individual amino acids


4. Glycosylation: attachment of carbohydrate side chains


5. Acylation: prenylation and farnesylation or


acetylation/deacetylation


6. Addition of prosthetic groups


7. Proteolytic processing


8. Disulfide crosslink formation

What is the function of dolichol in post translational modification of proteins?

It has an isoprene structure that is important in the glycosylation of proteins.

Put in order of highest protein content of lipoproteins.

HDL > LDL > IDL > VLDL > chylomicron

Put in order of highest cholesterol content of lipoproteins.

LDL > HDL > IDL > VLDL >chylomicrons

What is the biological role of the reaction catalyzed by cytochrome P450?

It detoxifies the body of drugs and toxins by hydroxylation.

Name 5 types of antibodies/immunoglobulins found in humans.

IgM, A, D, G,E.




Secreted form B cells in bone marrow.


Bind bacteria, viruses or large foreign molecules.

Which antibody is mainly involved in allergic reactions?

IgE

List 3 differences between DNA and RNA polymerases.

1. RNA polymerase does not need a primer


2. RNA polymerase has no 3’->5’ exonuclease activity


3. No proofreading

What distinguishes the newly synthesized DNA strand from thetemplate?

The template ismethylated.

What is the role MutH/MutS/MutL?

They are the main components of methyl directed mismatch repair. They winds up the DNA molecule.

Name the factors responsible for promotor recognition inprokaryotes and eukaryotes.

Prokaryotes:Sigma Factor


Eukaryotes:TATA binding protein

What are the heme containing complexes of the respiratory chain?

Complex IV


Cytochrome C


Complex III

What is an allosteric inhibitor of carnitine acyl transferase?

Malonyl-CoA

In which glycolytic reaction is a C-C bond broken?

Aldolase reaction




Fructose-1,6-bisphosphate <--> dihydroxyacetonephosphate + glyceraldehydphosphate

Which enzyme enables yeast to synthesize glucose from acetyl-CoA

Isocitrate lyase


Malate synthase




Glyoxylate cycle



Name the 4 vitamins that givecofactors participating in alpha-ketoglutarate dehydrogenase reaction.

TPP (B1) -> Thiamine


FAD (B2) -> Riboflavin


NAD (B3) -> Niacin


CoA-SH (B5) -> Pantothenic acid

The enzyme in the oxidative phase of the pentose phosphate pathway

Glucose-6-phosphate dehydrogenase


Lactonase


6-phosphogluconate dehydrogenase


Phosphopentose isomerase

When is the non-oxidative phase in the pentose phosphate pathway active?

In tissues which primarily require NADPH, pentose phosphates will be recycled back into glucose-6-phosphate in a series of rearrangements of the carbonskeletons .




Enzymes: Transketolase and transaldolase

What are 4 fates of glucose-6-phosphate in the pentose phosphate pathway?

1. Ribose-5-phosphate is needed:


Glc-6-P --> Frc-6-P --> ribose-5-p


Glyceraldehyde-3-P --> ribose-5-P




2. Ribose-5-phosphate and NADPH is needed:


Glc-6-P --> Ribulose-5-P + 2NADPH --> Ribose-5-P




3. NADPH needed:


Ribulose-5-P produced from Glc-6-P, but recycled. Prod NADPH.




4. NADPH and ATP needed:


Ribulose-5-P + NADPH is first made, then ribose-5-P is sent into glycolysis via fructose-6-p and glyceraldehyde-3-p, where ATP is produced.

What are the enzyme reactions in the gluconeogenesis which are irreversible and different from the glycolysis?

Pyruvate carboxylase


PEP carboxykinase


Fructose 1,6biphosphatase


Glucose 6 phosphatase

What is the enzyme in the gluconeogenesis, found in both mitochondria and cytosol, and why is this enzyme important?

Mitochondrial malate dehydrogenase and cytosolic malate dehydrogenase.




Pyruvate is converted to oxaloacetate by pyruvate carboxylase. Oxaloacetate can't pass the mitochondrial membrane, and is therefore converted to malate by mitochondrial malate dehydrogenase. Malate is transported into cytosol where it is converted back to oxaloacetate by cytosolic malate dehydrogenase

What are the different transcriptional regulations of gluconeogenesis and glycolysis?

SREBP-1 (sterol regulatory element binding proteins)




CREB (cAMP response element binding protein)




FOXO1 (forkhead box other)




ChREBP (carbohydrate response element binding protein)

How does SREBP-1c regulate gluconeogenesis and glycolysis?

SREBP-1c = sterol regulatory element binding proteins




Synthesis is increased by insulin and decreased by glucagon.




SREBP-1c will increase synthesis of: Hexokinase IV, pyruvate kinase, lipoprotein lipase, acetyl-CoA carboxylase, fatty acid synthase complex.




SREBP-1c will suppress synthesis of: PEP carboxykinase, FBPase-1, glucose 6-phosphatase (gluconeogenesis).



How does CREB regulate gluconeogenesis and glycolysis?

CREB = cAMP response element binding protein




Synthesis is increased by glucagon via cAMP.


Increases synthesis of PEP carboxykinase and glucose-6-phosphatase (stimulates gluconeogenesis)

How does FOXO1 regulate gluconeogenesis and glycolysis?

Insulin will have the effect of turning off expression of the genes. Insulin will activate a signalling cascade, which leads to activation of PKB. PKB will phosphorylate FOXO1 in cytosol. FOXO1 will be attached t ubiquitin, which will mark it for destruction via proteasome. FOXO1 which remains dephorphorylated can enter the nucleus and attach to DNA to trigger transcription of it's associated genes.




It increases synthesis of gluconeogenetic enzymes.


It supresses synthesis of glycolytic enzymes, pentose phosphate pathway enzymes and triacylglycerol synthetic enzymes.

How does chREBP regulate gluconeogenesis and glycolysis?

ChREBP = carbohydrate response element binding protein




ChREBP is inactive located in the cytosol when it is phosphorylated (2x), and cant move into nucleus. PP2A dephosphorylates it, allowing it to enter nucleus. In nucleus a second dephosphorylation by PP2A. This allows it to be associated with mix. ChREBP-Mix complex will bind to a carbohydrate response element, and stimulate transcription.




PP2A is allosterically activated by xylulose-5-phosphate. Xylulose-5-phosphate is a signal that other pathways which utilize glucose, has enough substrate.




ChREBP will therefore turn on synthesis of several enzymes: Pyruvate kinase, fatty acid synthase and acetyl-CoA carboxylase

How is GSK-3 regulated?

GSK-3 phosphorylates glycogen synthase b --> inhibiting glycogen synthesis. It is Inhibited by insulin.




GSK-3 requires prior phosphorylation or priming from casein kinase II.




Insulin will trigger activation of glycogen synthase a by blocking the activity of GSK3, and activating PP1 in muscles. Insulin will phosphorylate GSK3 via PKB/PKA.

What enzyme can remove phosphoryl groups from all three of the enzymes phosphorylated in response to glucagon in liver and epinephrine in muscle/liver? How is it regulated?

PP1 can remove phosphate groups from phosphorylase kinase, glycogen phosphorylase and glycogen synthase.




PP1 is not found in free form, but tightly bound to its traget protein by glycogen-targeting proteins.




Bind glycogen, each of the three enzymesRegulated- Positive allosteric regulation by glucose-6-phosphate- Negative covalent phosphorylation by PKA

What are the possible pathways in enzyme regulation and degradation? (10)

1. Extracellular signal


- Hormonal- neural- growth factors




2. Transcription of specific gene(s)




3. mRNA degradation




4. mRNA translation on ribosome




5. Protein degradation


- Tagged by ubiquitin for degradation by proeasomes




6. Enzyme sequestered in subcellular organelle




7. Enzyme binding substrate




8. Enzyme binds ligand (allosteric effect)




9. Enzyme undergoes phosphorylation/dephosphorylation




10. Enzymes combines with regulatory protein

What are the steps of fatty acid synthesis, which enzymes, cofactors and products do we find?

Before fatty acid synthesis we must activate Acetyl-CoA + ATP + HCO3- --> malonyl-CoA




Step 1 - Condensation


- Ketoacyl synthase


- Condensates the substrates, creating acetoacetyl-ACP


- CO2 is released




Step 2 - Reduction


- Ketoacyl reductase reduces NADPH + H --> NADP+


- D-B-hydroxybutyryl-ACP is formed




Step 3 - Dehydration


- Hydroxyoacyl dehydratase removes water from the substrate




Step 4 - Reduction


- Enoyl reductase reduces NADPH+H -> NADP+


- Double bond is saturated


-Saturated acyl group is formed, lengthened by two carbons

What are the enzyme components of fatty acid synthase?

8 enzymes in a complex


4 basic enzymes:


- Ketoacyl synthase


- Ketoacyl reductase


- Hydroxyacyl dehydratase


- Enoyl reductase




4 other:


- Acetyl carrier protein (ACP)


- Acetyl-CoA-ACP acyltransferase (AT)


- Malonyl-CoA-ACP acyltransferase (MT)


- Palmitate deacylase (PD)

What is mechanism of fatty acid elongation in animal cells?

Takes place in ER and mitochondria.




Palmitate is the precursor for most longer fatty acids. Similar mechanism as fatty acid synthesis, but with other enzymes, and using CoA instead of ACP.




Fatty acids are elongated on the head.




Elongation starts with donation of carbons by malonyl-CoA, thhen reduction, dehydration and reduction

What is the mechanism of desaturation in vertebrates?

Happens in smooth ER.




Fatty acid desaturation is needed for cell membrane fluidity in different temperatures. Double bond introduced via an oxidative reaction by fatty acyl-CoA desaturase.




During this process 2 different substrates will at the same time undergo electron oxidations.


- Electrons will flow via cytochrome and cytochrome reductas.


1. NADPH will give its electrons to cytochrome reductase - FAD --> FADH2


2. Cytochrome reductase (FADH2) will give it's electrons to cytochrome - Fe3+ -> Fe 2+


3. Cytochrome (Fe2+) will give them on to the fatty acid

How can glycerol-3-phosphate be synthesized in liver and adipose tissue?

In liver:


- Glycerol kinase


- Glycerol-3-phosphate dehydrogenase




In adipocytes:


- Glycerol-3-phosphate dehydrogenase

What are the different head groups for phosphatidic acid? what else can phosphatic acid produce?

Head groups can be ethanolamine, serine, inostiol, choline.




Triacylglycerol can be produced from phosphatidic acid


- Phosphatidic acid phosphatase (--> 1,2-Diacylglycerol)


- Acyl transferase (--> triacylglycerol)

How is lipid synthesis regulated?

Insulin




Favors synthesis of both acetyl-CoA (--> ketone bodies) and fatty acids (--> triacylglycerol synthesis)

Synthesis of triacylglyceride

1. Production of glycerol-phosphate


- Either via glycerol-3-phosphate (liver and fat) or glycerol kinase (liver)




2. Production of phosphatidic acid


- Acyl transferase twice




3. Production triacylglycerols and glycerophospholipids


- Phosphatidic acid phosphatase + acyl transferase --> triacylglycerol


Attachment of head group -> glycerophospholipids

What is steps in the glyceroneogenesis?

A shortened version of gluconeogenesis 
1. Pyruvate
 - Pyruvate carboxylase

 2. Oxaloacetate 
- PEP carboxykinase 

3. Phosphoenolpyruvate 
- Multistep 

4. Dihydroxyacetone phosphate 
- Glycerol-3-phosphate dehydrogenase 

5. Glycerol-...

A shortened version of gluconeogenesis


1. Pyruvate


- Pyruvate carboxylase




2. Oxaloacetate


- PEP carboxykinase




3. Phosphoenolpyruvate


- Multistep




4. Dihydroxyacetone phosphate


- Glycerol-3-phosphate dehydrogenase




5. Glycerol-3-phosphate




6. Triacylglycerol synthesis

What is the role of glyceroneogenesis?

Adipose tissue is coupled with reesterification of free fatty acids to control the rate of fatty acid release in blood.




In fasting humans, it supports the synthesis of glycerol-3-P enough to account for 65% of fatty acid reesterification to triacylglycerol.

How is the glyceroneogenesis regulated?

Glucocorticoid hormone


- Stimulates glycerneogenesis in liver


- Inhibits glycerneogenesis in adipocytes




Thialozolidine


- Increases glyceroneogenesis --> increasing resynthesis of triacylglycerol in adipose tissue --> reduced amount of free fatty acid in blood


- Treats type II diabetes

What are the two strategies for synthesizing complex lipids?

Strategy 1:


Diacylglycerol activated with CDP and then add head group


- Remove CMP




Strategy 2:


Diacylglycerol + head group activated with CDP


- Remove CMP

Which complex lipids use CDP-Diacylglycerol as precursors?

Phosphatidylglycerol


- CDP-diacylglycerol + glycerol




Cardiolipin


- CDP-Diacylglycerol + phosohatidylglycerol




Phosphatidylinositol


- CDP-diacylglycerol + inostiol

How do inositol phosphates function as intracellular signaling molecules?

Splitting by phospholipase C


-Diacylglycerol --> DAG


- Inositol-1,4,5-triphosphate -> IP3




Splitting by phophatidyl-inositol 3 kinase (PI3K)


- Phosphatidyl-inositol 3,4,5 triphosphate or PIP3

What are the roles of IP3 and DAG?

IP3 and DAG both contribute to activation of protein kinase C (PKC), by raising cytosolic Ca2+ concentration and IP3 also activates Ca2+ dependent enzymes.




1. Hormone binding


2. GDP-GTP exchange on G protein


3. Activation of PLC by GTP-G


4. Cleavage of PIP2 to IP3 and DAG


5. Binding of IP3 to ER IP3 -receptor evoking Ca2+ release


6. DAG and Ca2+ activate PKC


7. PKC phosphorylates target proteins triggering hormone response

How is acetoacetate activated for metabolism?

Done by B-ketoacyl-Coa transferase


Succinate-CoA --> Succinate


Acetoacetate --> Acetoacetyl-CoA

What are the steps of cholesterol synthesis?What is the rate determining step?

1. Synthesis of mevalonate from HMG-CoA


- HMG-CoA reductase


- Rate determining step




2. Mevalonate is converted into a chain of activated isoprenes.


- ATP is utilized to attach phosphate groups activating isoprenes


- Geranyl pyrophosphate = 10 Carbons




3. After several steps squalene is formed = 30 carbons


- Precursor is farnesyl-pp = 15C




4. Cholesterol is formed from squalene after a sequence of reactions


- Cholesterol = 27 C


- One of the enzymes is cyclase

The reactions of prenyl transferase

Dimethylallyl-pp + isopenthenyl-pp --> geranyl-pp




Geranyl-pp + isopenthenyl-pp --> farnesyl-pp




Both reactions are head to tail condensations.

What is the head to head reaction in cholesterol synthesis?

2 farnesyl-pp --> squalene

Esterification of cholesterol

Cholesterol esters are formed in the liver by acyl-CoA-cholesterol acyl transferase (ACAT): Cholesterol + fatty acyl-CoA --> Cholesteryl ester + CoA




Cholesterol esters can also be formed from lecithin-cholesterol acyl transferase (LCAT): Cholesterol + Lecithine (phosphatidylcholine) --> Cholesteryl ester + Lysolecithine

What is PPAR? What are the different types of PPARs and what are their function in lipid metabolism?

PPAR - Peroxisome proliferator-activated receptors


- Nuclear receptors


- Transcription factor, regulating expression of genes


- Effect on lipid transport




PPARα:


- In liver, heart, muscle and kidney


- Regulates FA metabolism, transports HDL-cholesterol into the liver




PPARβ:


- In ubiquitous


- Keratinocyte differentiation, wound healing, mediating VLDL signaling of the macrophage




PPARγ:


- In adipocytes and macrophages


- Adipocyte differentiation, lipid storage, glucose homeostasis




What are the 3 most common fates of cholesterol?

Biliary cholesterol, bile acids and cholesterol esters.




All growing animal tissues need cholesterol for membrane synthesis, some organs (adrenal gland, gonads) use cholesterol as precursors for steroid hormone production.

What are the 3 enzymes of the ATP-dependent pathway of protein degradation?

E1: ubiquitin-activating enzyme


E2: ubiquitin-conjugating enzyme


E3: ubiquitin-protein ligase

What is the role of PLP and what enzymes requires PLP?

PLP is an intermediate amino group carrier - accepts and donates amino groups.


1. Transamination (aminotransferase)


2. Decarboxylation (decarboxylase)


3. Side chain cleavage (aldolase)




- Glycogen phosphorylase


- Aminotransferases (ALAT, ASAT)


- Cystathionine β-synthase


- Serine dehydratase


- Glutamate decarboxylase


- Histidine decarboxylase

Where does the glutamine reaction take place?

Liver, kidney, intestine


Mitochondria

What are the mixed amino acids?

Tryptophan


Phenylalanine


Tyrosine


Threonine


Isoleucine


Alanine


Cysteine


Glycine


Serine

Which reaction can incorporate ammonia into organic compounds?

1. Glutamine synthetase reaction:
- In all organisms
- Important regulatory point 

2. Glutamate synthase reaction 
- Only in plants and bacteria

					
				
			
		
	


Net ammonia incorporation is the result of the 2 reactions.

1. Glutamine synthetase reaction:


- In all organisms


- Important regulatory point




2. Glutamate synthase reaction


- Only in plants and bacteria




Net ammonia incorporation is the result of the 2 reactions.

What is nitrogen fixation?

Reduction of N2 gas to ammonia:


N2 + 3 H2 ---> 2 NH3


The N-N triple bond is very stable. Therefore the activation energy of N-fixation is extremely high.




Nitrogen fixation is carried out by a highly conserved complex of proteins called the nitrogenase complex.




Hydrolysis of 16 ATP.




Overall equation:


N2 + 10H+ + 8e– + 16ATP --> 2NH4+ + 16ADP + 16Pi + H2




Hyperammonia

A typical result of urea cycle defects (UCDs) ishyperammonemia and/or the build-up of one or more ureacycle intermediates (depending on the missing enzyme).




Permanent activation of glutamate dehydrogenase also causeshyperammonemia (hyperinsulinism-hyperammonemiasyndrome).

Hyperglycinemia



	
		
		
	
	
		
			
				
					
						Defect of the glycine cleavage enzyme.

Defect of the glycine cleavage enzyme.

Write with structures the reaction that is defective in albinism.

Defect of tyrosinase - melamine synthesis form trypsin --> lack of pigmentation: white hair and pink skin.

Defect of tyrosinase - melamine synthesis form trypsin --> lack of pigmentation: white hair and pink skin.

What are the steps in the biosynthesis of heme?Where does the biosynthesis of heme in mammals take place and how is it regulated?

1. Synthesis of δ-aminolevulinate


- From succinylCoA and glycine by δ-aminolevulinate synthase




2. Synthesis of porphyrins


- Chain of different reactions --> protoporphyrin




3. Synthesis of heme


- Protoporphyrin --> heme by ferrochelatase




Takes place in mitochondria and in the cytosol.


Heme is a feedback inhibitor.

Degradation of heme

Heme degradation protects cell from oxidative damage.




Heme oxygenase reaction:


Heme + 2O2 + NADPH + H+ --> Biliverdin + Fe2+ + CO + H2O + NADP+




- Fe2+ binds to ferritin


- CO binds to hemoglobin - toxic at high conc. and vasodilator at low conc.


- Biliverdin reductase reaction --> bilirubin, which binds to serum albumin. Important antioxidant in the blood.









Aspartate-agininosuccinate shunt

Argininosuccinate will form arginine and fumarate via the enzyme argininosuccinase. This fumarate can be converted to malate and enter the citric acid cycle. This connection is the aspartate-argininosuccinate shunt of citric acid cycle.

Argininosuccinate will form arginine and fumarate via the enzyme argininosuccinase. This fumarate can be converted to malate and enter the citric acid cycle. This connection is the aspartate-argininosuccinate shunt of citric acid cycle.




Oxaloacetate from citric acid cycle reacts with glutamate and form aspartate and alfa-ketoglutarate. Aspartate enter urea cycle and reacts with citrulline.

What are the ATP dependent reactions of the urea cycle, and where do they happens?

Carbamoyl phosphate synthase I


- Requires 2ATP


- NH3 reacts with bicarbonate to form carbamoyl phosphate which enters cycle


- Reaction takes place in the mitochondria




Argininosuccinate synthetase


- Requires ATP --> AMP


- Takes place in cytosol


- Aspartate enter the urea cycle from the citric acid cycle

What are the two pathways to protein degradation?

1. ATP-dependet pathway used for degradation of defective proteins, and those with short half-lives


- Involves ubiquitin, which becomes covalently linked to proeins slated for destruction via an ATP-dependent pathway


- Involves E1, E2, E3


- Ubiquinated proteins are degraded by proteasome




2. A second system is found in lysosomes. This recycles the amino acids of membrane proteins, extracellular proteins and those with longer half-lives.

What is the effect of cholesterol entering the cell on cholesterol synthesis?

1. Down regulation of receptor mediated endocytosis


2. Inhibition of cholesterol synthesis


3. Promotion of cholesteryl esters


4. Inhibition of endocytotic receptor synthesis

What are some substrate-level phosphorylations?

Glycolysis:


- Phosphoglycerate kinase


- Pyruvate kinase




Citric acid cycle:


- Succinyl-CoA synthetase

What are the roles of nucelotides in cells?

1. DNA and RNA precursors


2. Carrier of chemical energy (ATP and GTP)


3. Co-factor components (NAD, FAD, coenzyme A, S-adenosylmethionine)


4. Activated intermediates (UDP-glucose, CDP-diacylglycerol)


5. Cellular second messenger (cAMP, cGMP)

What are the two ways of nucleotide synthesis?

1. Salvage pathway


- Activated ribose (PRPP) + base --> nucleotide


- Recycles free bases and nucleotides released during nucleic acid breakdown


- Adenine + PRPP --> AMP + PPi


- Hypoxanthine + PRPP --> IMP + PPi


- Guanine + PRPP --> GMP + PPi




2. De novo pathway


- Activated ribose (PRPP) + amino acids + ATP + CO2 + NH3 --> Nucleotide

What are the common motives of purine and pyrimidine synthesis?

1. Uses 5- phosphoribosyl-1- pyrophosphate (PPRP)




2. Uses amino acids-


- Glycine --> purine


- Aspartate --> - pyrmidine




3. N donor: glutamine (aspartate - purine)

Why can nucleotide synthesis limit rate of DNA replication and transcription?

Cellular pool of nucleotides i 1% or less of the amounts required to synthesize the cell's DNA.

How is purine nucleotide biosynthesis regulated?

It's regulated by feedback inhibition.It is regulated in 4 steps by the end-products.




1. AMP, GMP and IMP will inhibit the first reaction- Glutamine-PRPP amidotransferase: PRPP --> 5-phosphoribosylamine




2. The end-products will inhibit their own synthesis from IMP.


- AMP will inhibit adenylosuccinate synthetase


- GMP will inhibit IMP dehydrogenase




3. Reciprocal regulation


- Balance between AMP and GMP




4. AMP from end-product will be phosphorylated to ADP, and ADP will inhibit ribose phosphate pyrophosphokinase (PRPP synthetase): ribose-5-phosphate --> PRPP

What are the different types of purines and pyrimidines?

Purines: 2 rings


- Adenine and guanine




Pyrimidine: 1 ring


- Cytosine, Thymine (DNA), Uracil (RNA)

What type of enzymes are used in the nucleotide synthesis?

Large, multienzyme complex in the cell

What are pyrimidine nucleotides made from?

Made from aspartate, carbamoyl phosphate and PRPP.

What are purine nucleotides made from?

Made from CO2, glycine, formate, glutamine and aspartate. 

Made from CO2, glycine, formate, glutamine and aspartate.

How is pyrimidine biosynthesis regulated?

Regulated by feedback inhibition (negative feedback) of the end-product.




- Cytidine-5-triphosphate (CTP) inhibits aspartate transcarbamoylase allosterically.




- ATP is a positive modulator of the same enzyme. It prevents change induced by CTP.

What does degradation of purines and pyrimidines give?

Purine --> uric acid


Pyrimidine --> urea

Adenosine deaminase deficiency

Causes immunodeficiency


- T and B wont properly develop

Lesch-Nyhan syndrome

Brain highly depends on salvage pathways.


Without salvage pathway, PRPP levels rise.




This syndrome prevents salvage pathway of guanine.




Causes:


- Purine overproduction


- High levels of uric acid


- Brain damage

What are the different types of histones?

H1, H2A, H2B, H3, H4

What is the function of chromatin remodelling complex SWI/SNF?

Dissociates DNA from the surface of nucleosomes, decondensing thechromatin and making the DNA more accessible to transcriptionfactors.

What is the function of chromatin remodelling complex NURF?

Activates RNA polymerase II thus participating in transcriptional activation.

What is the function of chromatin remodelling complex INO80?

Transcriptional activation, DNA repair, telomereregulation, chromosome segregation and DNA replication.

What is the function of microRNA (miRNA)?

Post-transcriptional regulators, silencing of many genes




22 nucleotide long RNA sequence

What is a holoenzyme?

A catalytically active enzyme together with its boundcoenzyme and/or metal ions

What inhibits RNA polymerases in prokaryotes and eukaryotes respectively?

- Actinomycin D: both pro- and eukaryoticRNA polymerase


- Rifampicin: prokaryotic RNA polymerase


- α-amanitin: eukaryotic RNA polymerase (Pol II, Pol III)

Describe breifly mRNA processing

1. Start with DNA strand


2. Transcription and 5´capping --> Primary mRNA transcript (contains 5´cap, exons and introns)


3. Spilcing, cleavage and polyadenylation --> mature mRNA (contains 5´cap and exons, no introns)

What is the function of siRNA (small interfering)?

Binds to the mRNA and silence it.

What is the function of saRNA (small activating)?

Induce gene activation (long lasting)

What is the function of snRNA (small nuclear)?

Processing of pre-mRNA in the nucleus.


Part of the spliceosome.

What is the function of snoRNA (small nucleolar)?

Guide chemical modifications of other RNAs (methylation or pseudouridylylation).

What is the function of piRNA (piwi-interacting)?

- Largest class of small RNAsin animal cells.


- Transcriptional gene silencing of retrotransposons in germline cells.

What is the function of rasiRNA (repeat associated small interfering RNA)?

- Establishes and maintaining heterochromatin structure.


- Control transcripts that emerge from repeat sequences


- Silencing transposons and retrotransposons.

What is the function of tmRNA?

- Rescues ribosomes (mRNA without stop codon).


- Recycles the stalled ribosome


- Facilitates degradation of non-normal mRNA.

What is the function of qiRNA?

- DNA damage induces its expression


- Role in DNA damage response: inhibiting protein translation

What are the regulation factors of the ribosomal section of translation?

eIF2, eIF4E, mTOR, antibiotics

What is interferon control?

Virally infected cells turn off translation to prevent spread of viruses.This is achieved using interferons (a cytokine). They induce RNA dependent protein kinase (PKR) that phosphorylates eIF-2 (inactivation), which reduce translation. PKR also indirectly induce RNase L (and thus mRNA degradation.



What are the protein factor required for initiation of translation in bacteria and eukaryotes respectively?

Bacteria: IF-1, IF-2, IF-3




Eukaryotes: elF2, elF2B, elF3, elF4A, elF4B, elF4E, elF4G, elF5, elF6



What is special with mitochondria replication, transcription and synthesis?

- Happens in the matrix


- Replication not limited to S-phase


- Individual mtDNAs replicate randomly (some more than others)


- Double stranded ring, nucleoid


- No histones, no introns, polycistronic transcription (many genes)


- Only 22 tRNA for protein synthesis


- Reduced accuracy: 10x greater rate of nucleotide substitution


- Mitochondrial mRNA: no 5 ́cap, but a poly-A at 3 ́end added post-transcriptionally


- mtDNA is inherited maternally, non-mendelian

What are the effects of insulin on blood glucose, uptake of glucose and storage ad triacylglycerols and glycogen?

Increase:


- Glucose uptake (in muscle, adipose tissue and liver)


- Glycogen synthesis (liver and muscle)


- Glycolysis, acetyl- CoA production (liver and muscle)


- Fatty acid synthesis (liver)


- Triacylglycerol synthesis (adipose tissue)




Decrease:


- Glycogen breakdown (liver and muscle)

What are the effects of glucagon on blood glucose, production and release of glucose by the liver?

Increase:


- Glycogen breakdown


- Gluconeogenesis


- Fatty acid mobilization


- Ketogenesis




Decrease:


- Glycogen synthesis


- Glycolysis

What does the theory of glucose fatty acid cycle state?

If plasma glucose is decreased, fatty acids are mobilized from adipose tissues (fasting, effect of glucagon) and the increased fatty acid level will decrease glucose utilization, restoring glucose level and maintaining homeostasis.

Arsenate poisining, and what is a reaction which can use arsenate?

Arsenate (AsO4), is structurally and chemically similar to inorganic phosphate (Pi). This allows many enzymes, which require phosphate to use arsenate instead, making it very dangerous. Arsenate is very toxic to most organisms,




Glyceraldehyde-3-phosphate dehydrogenase. Will create 1-arseno-3-phosphoglycerate instead of 1,3-bisphosphoglycerate. No TCA and respiratory chain --> no ATP is produced --> no ATP is produced --> fatal

How is isocitrate dehydrogenase regulated?

Inhibited by ATP.


Activated by Ca2+ and ADP.

How is a-ketoglutarate dehydrogenase complex regulated?

Inhibited by succinyl-CoA (product), NADH


Activated by Ca2+

How is glycogen-targeting protein, Gm regulated?

Gm binds glycogen to enzymes, like PP1.
Gm can be phosphorylated at 2 different sites, which give different effects
 -  In response to epinephrine and insulin.

1. Insulin stimulated phosphorylation 
- Phosphorylation at site 1 
- Activates P...

Gm binds glycogen to enzymes, like PP1.


Gm can be phosphorylated at 2 different sites, which give different effects


- In response to epinephrine and insulin.




1. Insulin stimulated phosphorylation


- Phosphorylation at site 1


- Activates PP1, which dephosphorylates phosphorylase kinase, glycogen phosphorylase and glycogen synthase


- Insulin inhibit glycogen breakdown, and stimulate glycogen synthesis




2. Epinephrine stimulated phosphorylation


- Phosphorylation at site 2


- Dissociation from PP1, inactivating it


- Preventing access of PP1 to glycogen phosphorylase and synthase


- PP1 is also connected to phosphorylated inhibitor 1, inactivating it


- Epinephrine or glucagon will stimulate glycogen breakdown, and inhibit glycogen synthesis

What are the names of the different complexes in the respiratory chain?

Complex I = NADH dehydrogenase


Complex II = Succinate-dehydrogenase


Complex III = Ubiquinone-cytochrom-c- oxidoreductase


Complex IV = Cytochrome-oxidase

4 fates of pyruvate in the liver

1. Acetyl-CoA --> citric acid cycle = pyruvate dehydrogenase complex


2. Lactate (anaerobic conditions) = lactate dehydrogenase


3. Oxaloacetate (gluconeogenesis) = pyruvate carboxylase


4. Malate = malic enzyme

Which amino acid and vitamin make up collagen?

Glycine


Vitamin C

What is the function of beta-arrestin?

Acts as a cofactor in the beta-adrenergic receptor kinase (BARK) mediated desensitization of beta-adrenergic receptors.




Also function as a scaffold protein.

Through which molecule is PKA, PKB, PKC and AMPK activated in each case?

- epinephrine/glucagon --> cAMP --> PKA


- PDK-1 --> PKB


- DAG and IP3 --> increased cytosolic Ca2+ --> PKC


- High concentrations of AMP (stress, exercise), leptin (fasting) --> AMPK

Name four basic mechanisms and molecular processes that guarantee the accuracy of translation.

- Secondary genetic code


- Wobble formation (first two bases in codon has strong base pairing)


- Proofreading


- Ribosomal with aminoacyl t-RNA synthase

What is replisome and what are the structure?

The entire complexresponsible for coordinated DNA synthesis at a replication fork. The replisome promotes rapid DNA synthesis.




SSB - binds to single stranded DNA and prevent it from re-forming a double stranded structure.


Helicase - used to separate strands of double stranded DNA molecule


Primase - catalyze synthesis of primer


DNA polymerase - synthesize DNA


DNA ligase - facilitates the joining of DNA strands together


DNA gyrase (topoisomerase II) - prevent supercoiling ahead of replication fork

Give 3 hormones that are phosphorylated by glucagon indirectly via cAMP?

- Phosphofructokinas


- Pyruvate dehydrogenase complex


- Glycogen phosphorylase kinase

Function of mTOR, how it enables translation and moleculesinvolved. Function of elF4E.

mTOR functions as a serine/threonine protein kinase that regulates cell growth, cell proliferation, cell motility, cell survival, protein synthesis, autophagy, and transcription.




- mTOR is a protein kinase activated by Akt/PKB.


- It phosphorylates a protein (4E-BP) that block elF-4E, thus suppressing the formation of the complete initiation complex.


- When the block comes off --> elF4E can bind to 5 ́Cap of mRNA --> initiation of translation.


- Too high eIF-4E activity can lead to tumorigenesis.

What makes elF4E so important in regulation of gene expression?

Since eIF-4E has the lowest cellular level of all eIFs, it is an efficient regulation pointfor the whole translation process.

How is elF-4E regulated?

Transcription


Phosphorylation


Inhibited by interactions with binding proteins

Protein targeting

Directs the structures to specific destinations by synthesizing a signal sequence of amino acids on the end.




Signal recognition particle binds to ribosome, and direct it to SRP receptor on ER.


- Binds GTP




Ribosome receptor and SRP receptor are found on the outside of ER.




On the inside peptide translocase complex is found.




The product is guided into the ER, and signal peptidase will cleave off the signal sequence.

Definition of lipoproteins
Large aggregates with non–covalent interactions between lipids and proteins.
What is the general function of lipoproteins?
Carry and transfer different types of lipids between organs and tissues.
What is the structure of lipoprotiens?
Core: Triacylglycerols, cholesteryl esters



Shell: Phospholipids, cholesterol, apo(lipo)proteins

The content and ratio between the different molecules varies in different types of lipoproteins.

The size differs betweeen the different types of lipoproteins.

Put in order of highest triacylglycerol of lipoproteins.
Chylomicron > VLDL > LDL > HDL
Density of lipoproteins
The density increases as the size decreases.
HDL > LDL > VLDL > Chylomicrons
Apoproteins in the different lipoproteins
IDL, LDL, VLDL: Apo B100
Chylomicrons: Apo B48
HDL: Apo A-I, A-II
Transport of lipids
Lipases cleave triacylglycerols to fatty acids and monoacylglycerols in the lumen, which are transported through the membrane. Then they are converted back to triacylglycerols in the mucosal cells. Then the triacylglycerols form chylomicrons toget...
Lipases cleave triacylglycerols to fatty acids and monoacylglycerols in the lumen, which are transported through the membrane. Then they are converted back to triacylglycerols in the mucosal cells. Then the triacylglycerols form chylomicrons together with other lipids and proteins. The chylomicrons are transported to the lymph system.
Transport and properties of plasma lipoproteins
- Chylomicron: hydrolysis by lipoprotein lipase.
- Chylomicron remnant: Receptor-mediated endocytosis by liver.

- VLDL: Hydrolysis by lipoprotein lipase.

- IDL (VLDL remnants): Receptor-mediated endocytosis by liver and conversion into LDL.

- ...
- Chylomicron: hydrolysis by lipoprotein lipase.



- Chylomicron remnant: Receptor-mediated endocytosis by liver.




- VLDL: Hydrolysis by lipoprotein lipase.




- IDL (VLDL remnants): Receptor-mediated endocytosis by liver and conversion into LDL.




- LDL: Receptor-mediated endocytosis by liver and other tissues.




- HDL: Transfer of cholesterol esters to IDL and LDL.

Energy sources for muscle contraction
Light activity or rest: Fatty acids, ketone bodies, blood glucose


Heavy activity: muscle glycogen, phosphocreatine
Light activity or rest: Fatty acids, ketone bodies, blood glucose


Heavy activity: muscle glycogen, phosphocreatine
Energy sources for the brain
Starvation: ketone bodies

Normal diet: glucose

NB: No glycogen storage in the brain!

When there is enough glucose in the blood the brain will only use glucose as an energy source.

The brain operates more efficiently during starvation, when the energy source is ketone bodies and not glucose.
What is the normal range of blood glucose in human?
60–90 mg/100 mL
Hypothalamic regulation of food intake
Hypothalamus secrete norepinephrine which is a signal for adipose tissue to secrete leptin into the blood. Leptin is a "satiety hormone" that regulates food intake.
Hypothalamus secrete norepinephrine which is a signal for adipose tissue to secrete leptin into the blood. Leptin is a "satiety hormone" that regulates food intake.
How is the short–term eating behavior regulated?
Ghrelin
Effects of adiponectin
Stimulates AMPKMuscle: Increase fatty acid uptake, beta oxidation and glucose uptakeLiver:Increase glycolysis, decrease gluconeogenesis and fatty acid synthesis.
Stimulates AMPK

Muscle:
Increase fatty acid uptake, beta oxidation and glucose uptake

Liver:
Increase glycolysis, decrease gluconeogenesis and fatty acid synthesis.
What are the main functions of the liver?
- Synthesis (plasma proteins, sugars, clotting factors, urea, lipids, bile)

- Detoxification


- Excretion


- Storage (Glycogen, vitamins, Cu)

What are the toxic compounds which need biotransformation (detoxification)?
Compounds poorly soluble in water, biologically active and some toxic.
What can failure of the detoxification system lead to?
– Inflammatory conditions
– Rheumatoid Arthritis
– Parkinson’s
– Alzheimer’s
– Cancer
– ME
What are the organs which process and eliminate waste?
– Liver (most intensive site of detoxification)
– Intestines (second most intensive site)
– Kidneys
– Blood and bile
– Lungs
Definition of biotransformation
Biotransformation of drug is defined as the conversion from onechemical form to another. The term is used synonymously with metabolism.



E.g. Active drug (salicylic acid) --> inactive drug (salicyluric acid)

What are the parts (phases) of biotransformation?
- Phase 1: Oxidation (P450), reduction or hydrolysis

- Phase 2:  Conjugation
(Glucuronidation, sulfation, glutathionconjugation, methylation)
Adds molecules to increase the solubility of the compound.
What are the difference between microsomal and non–microsomal enzymes?

What does the cytochrome P450 enzyme system contain?
Monooxigenase
650 isoenzyme
Electron donor: NADPH
P450 gene family
CYP1, CYP2, CYP3, CYP4


Individual distribution of the different types.
What are the causes of alcohol consumption?
– Primary cause of liver disease
– Can be toxic to brain, GI tract, and pancreas
– Abuse leads to nutrient deficiencies
Pathway of alchohol
1. Mouth and esophagus: alcohol is diluted by saliva before being swallowed. Some is immediately absorbed.

2. Stomach: more alcohol is absorbed here, irritating the lining of the stomach and increasing the acidity. Men have alcohol dehydrogenase in the stomach which lead to start of alcohol metabolism, but women does not have this enzyme in the stomach.

3. Small Intestine: any remaining alcohol is passed here and is the site of most alcohol absorption.

4. Bloodstream: a
lcohol quickly diffuses through the body, affecting almost all cells.

5. Brain: these cells are more susceptible because they are usually protected from toxic by blood-brain barrier.



6. Liver: blood alcohol is metabolized in two stages and then respired into CO2, H2O and fatty acids.




7. Excretion via urine, the lungs and sweat.

What is special with the alcohol metabolism?
There is no hormonal regulation of alcohol metabolism. What we consume will be absorbed.




How is the alcohol processed in the liver?
Alcohol is processed by the liver as it arrives from the bloodstream.

The liver produces enzymes called alcohol dehydrogenase (ADH).



ADH: ethanol + NAD+ <--> Acetaldehyde + NADH + H+




Acetaldehyde is more toxic than alcohol itself (can cause inflammation). Acetaldehyde is then converted into acetate by ALDH in the mitochondria.




ALDH: acetaldehyde + NAD+ --> acetate + NADH + H+




Acetate is digested into fatty acid, CO2 and H2O.




Fatty acids, when digested, create 7 calories per g alcohol.

What are the three alcohol enzymes?
The three enzymes which can convert alcohol to acetaldehyde are:
Alcohol dehydrogenase (ADH) – cytosol
Cytochrome P450 (CYP2E1) – microsomes
Catalase – peroxisomes

These three enzymes are each found in different parts of the body and each of them handles the hydrogen atoms which are stripped off from the alcohol molecule in a different way.
What are the metabolic consequences of increased NADH/NAD ratio?
– Decreased gluconeogenesis (hypoglycemia)
– Increased lactate
– Decreased TCA cycle
– Inhibition of most oxidations that use liver NAD (inhibition of some drug and hormone metabolism)
– Decreased fatty acid oxidation
– Increased fatty acid synthesis
Microsmal (cytochrome P450) oxidation of ethanol
CH3CH2OH + O2 + NADPH + H––> NADP+ + CH3CHO + 2H2O
Catalase–Dependent Oxidationof Ethanol
CH3CH2OH + H2O2 ––> CH3CHO + 2H2O

Catalase, a heme enzyme, is found in the peroxisomal fraction of the cell. This is an important antioxidant enzymesince it normally catalyzes the removal of H2O2.
H2O2 + H2O2 ––> 2H2O + O2

The primary catalytic enzyme in the brain cells.
What are the long term effects of excess alcohol consumption?
- Tissue damage

- Liver damage


- Brain damage


- Weight gain


- Skin damage

What are the most important trace elements in the body?
Fe, Mn, Co, Cu, Zn, Mo, V, Cr, Ni, F, Si, Se, As

<0,01 % of the body weight
What is the requirement and the minimum intake of iron per day? What is the body iron content
Requirement: ~ 1–3 mg/day
Minimum intake: 5–20 mg/day

Body iron content: 3-4 g

What are the iron containing proteins in humans?
75% heme iron (hemoglobin, myoglobin, cytochromes, catalase, peroxidase, PG–synthase,NO synthase)

25 % non–heme iron (transferrin, ferritin, Fe–S proteins)
How is the copper transported in the blood.
Transported in blood by ceruloplasmin, albumin.
Copper containing enzymes
– Redoxenzymes
– Cytochrome oxidase (complex IV)
– Superoxide dismutase
– Hydroxylases (e.g dopamine–beta–hydroxylase)
Which diseases do copper deficiency lead to?
Wilson´s disease: Intracellular Cu deposition (liver, brain and kidney), low serum Cu and high urinary Cu, low ceruloplasmin. Cannot be cured, only treated by removal by complex formation (penicillamin).

Menke´s syndrome: disorder of cellular Cu uptake (deficiency of ATP7A membrane transporter).
Which enzymes/molecules contains zinc?
– DNA–RNA polymerase
– Zn–finger (DNA–binding domain of certain transcription factors)
– Alcohol dehydrogenase
– Proteases
– Carbonic anhydrase
Where is manganese present?
Cofactor: oxidoreductases (e.g.. Xanthine oxidase), transferases, hydroxylases, lyases, isomerases, ligases, pyruvate carboxylase, arginase



- Retroviruses: HIV


- Glycogenin


- Photosynthesis

What structures does RBC´s lack?
Nucleus (DNA)
Mitochondira
ER, golgi, ribosomes
What is the function of RBCs?
Transport O2 and CO2, NO
2,3–biphospho–glycerate
Decrease the affinity of oxygen of hemoglobin (right shift).
Structure of hemoglobin
2 parts : heme +globin

Globin: four chains There are four types of chains; α, β, γ and δ. 2 alfa (chromosome 16) and 2 beta (11 chromosome) chains is the normal structure.

Heme: porphyrin ring with central iron. Iron is the site of attachment with O2.
Adult hemoglobin vs fetus hemoglobin
Adult (HbA): 2 alfa chains and 2 beta chains
Fetus (HbF): 2 alfa chains and 2 gamma chains
Sickle cell disease
– Homozygous for the abnormal gene that codes for Hb S.
– Hb S results from a substitution of valine for glutamic acid at the sixth position from the NH2 terminal end of the β chain.



Hb S: 2 alfa 2beta, 6Glu ––> Val




Cause the red cell to deform into the sickle shapeand reduce the cells ability to circulate. This leads to hypoxia,pain and infarction of organs.



Hemoglobin C
Found almost exclusively in Negro populations.



Hb C differs from normal Hb A by the single aminoacid substitution of lysine for glutamic acid in the sixthposition from the NH2 terminal end of the β chain.





Hb C: 2 alfa 2beta, 6Glu ––> Lys




Causes mild chronic haemolytic anaemia withassociated splenomegaly and abdominal discomfort.

Functions of blood
– Substance distribution
– Regulation of blood levels of particular

- Body protection

What does blood transport?
- Oxygen from the lungs and nutrients from the digestive tract

– Metabolic wastes from cells to the lungs andkidneys for elimination


- Hormones from endocrine glands to targetorgans

Blood maintains
- Appropriate body temperature by absorbing and distributing heat to other parts of the body

– Normal pH in body tissues using buffer systems


- Adequate fluid volume in the circulatorysystem

What does blood prevent?
Blood prevents blood loss by:
– Activating plasma proteins and platelets
– Initiating clot formation when a vessel is broken

Blood prevents infection by:
– Synthesizing and utilizing antibodies
– Activating complement proteins
– Activating WBCs to defend the body againstforeign invaders
Average blood volume
5–6 L for males
4–5 L for females (normovolemia)

Hypovolemia: low blood volume
Hypervolemia: high blood volume
Viscosity, pH and osmolarity and salinity of blood
– Viscosity (thickness): 4 – 5 (where water = 1)

– pH of blood is 7.35–7.45; x = 7.4

– Osmolarity = 300 mOsm or 0.3 Osm
This value reflects the concentration of solutes in the plasma.

– Salinity = 0.85%
Reflects the concentration of NaCl in the blood
Blood plasma components
Water = 90–92%

Proteins = 6–8%
– Albumins: maintain osmotic pressure of the blood
– Globulins: Alpha and beta globulins are used for transport purposes. Gamma globulins are the immunoglobulins (IgG, IgA, IgM, IgE, IgD)

- Fibronogen: clotting protein




– Organic nutrients: glucose, carbohydrates, amino acids


- Electrolytes: sodium, potassium, calcium, chloride, bicarbonate.


- Nonprotein nitrogenous substances: lactic acid, urea, creatinine.


- Respiratory gases: oxygen and carbon dioxide

Prealbumin
Prealbumin migrates faster than albumin in the classicelectrophoresis.

It is the transport protein for:
– Thyroid hormones
– Retinol (vitamin A)
In which diseases are prealbumin decreased?
Prealbumin is decreased in:
– Liver disease
– Nephrotic syndrome
– Acute phase inflammatory response
– Malnutrition
Albuminuria
When albumin is detected in urine. This is due to physiological or pathological conditions.
What is the functions of albumin?
1. Oncotic pressure:Albumin is responsible for ~80% of the plasma oncotic pressure.It is a major determinant of the distribution of fluids betweenintravascular and extravascular compartments.Hypoalbuminemia leads to edema.



2. Buffering




3. Transport:Many substances are transported in the blood bound to albumin.


Lipid-soluble substances; hormones (thyroid hormones and steroid hormones), calcium, drugs, free fatty acids (FFA) and bilirubin.

alfa1–Antitrypsin
Synthesized by the liver and macrophages

It is acute–phase protein in order to inhibit proteases.

Proteases arise from:
– Endogenous production : by digestive enzymes such as trypsin& chymotrypsin.
– Infection: protease release from bacteria and from leukocytes(inflammatory response)
Acute Phase Proteins
Produced after stress reactions, infection, inflammation , malignancy, trauma or major surgery. They are produced in response to humoral mediators which are produced by tissue macrophages, monocytes and endothelial cells in inflammation

– a1–Antitypsin
– Haptoglobin
– Ceruloplasmin
– Fibrinogen
– C–reactive protein
Ceruloplasmin
– Synthesized by the liver
– Contains over 90% of serum copper.
– It is important in acute phase response as it is able to inactivate reactive oxygen species (ROS) that produce tissue damage.
Fibronogen
– Synthesized in the liver.
– Its function is to form a fibrin clot (when activated by thrombin). Fibrinogen is removed in the clotting process and is not seen in serum.
What does an increase in ECF lead to?
Increase in extracellular fluid results in increased blood volume and arterial pressure.

Normal body response: kidneys excrete excess extracellular fluid and returns the pressure to normal.

Mechanism reverses if reduced blood volume.
Renin–Angiotensin system
Renin is a  hormone that acts as an enzyme. It is released when arterial pressure drops. Renin converts angiotensinogen to angiotensin I. ACE in the lungs coverts angiotensin I to angiotensin II.
Angiotensin II cause Na+ and water retention in the...
Renin is a hormone that acts as an enzyme. It is released when arterial pressure drops.

Renin converts angiotensinogen to angiotensin I. ACE in the lungs coverts angiotensin I to angiotensin II.



Angiotensin II cause Na+ and water retention in the kidneys and vasocontriction, which increase arterial pressure.

Receptors of renin–angiotensin system
(P)RR protein receptor
AT1 and AT2 angiotensin receptors
Mas receptor
MR – mineralocorticoid receptor
Role of ROS in contraction induced by angiotensin II in vascular smooth muscle cells
Red lines show inhibitory effectsand blue lines depict activation. ROS (reactive oxygen species)AT1R (angiotensin II receptortype 1)PLC (phospholipase C)PIP2 (phosphoinositol biphosphate)IP3 (inositol 1,4,5 triphosphate) IP3R (inositol 1,4,5 triph...
Red lines show inhibitory effectsand blue lines depict activation.

ROS (reactive oxygen species)
AT1R (angiotensin II receptortype 1)
PLC (phospholipase C)
PIP2 (phosphoinositol biphosphate)
IP3 (inositol 1,4,5 triphosphate)
IP3R (inositol 1,4,5 triphosphatereceptor)
SERCA (sarco/endo–plasmicreticulum Ca2+–ATPase)
GEF (guanine nucleotideexchange factor)
GTP (guanosin triphosphate)
ROCK (Rho–associate kinase)
MLC (myosin light chain).
cGMP–PKG
Decreases intracellular Ca2+ levelsand promotes the relaxation of smooth muscle
Anti–hypertensive
Used to antagonize the actions of factors that increase blood pressure.

Used to ‘potentiate’ the actions of factors that decrease blood pressure.
Functions of diuretics
Diuretics act on your kidneys to help your body eliminate sodium and water, reducing blood volume. The long–term effect is vasodilation and decreased vascular resistance.
Beta–adrenergic receptor blockers
Reduce the workload on your heart and open your blood vessels, causing your heart to beat slower and with less force.
Angiotensin–converting enzyme (ACE) inhibitors

Inhibits angiotensin-converting enzyme and prevent the conversion ofangiotensin I to angiotensin II.


Captopril, Enalapril
Angiotensin II receptor blockers (ARBs)
Losartan, Valsartan

Inhibit actions of angiotensin II by blocking angiotensin type–1 receptors.


Reduce vascular resistance without reducing cardiac output. Renal blood flow is maintained.

These medications are as effective in lowering blood pressure asthe ACE inhibitors.

Mechanism of action of beta–adrenergic receptor blockers
Lower blood pressure by decreasing cardiac output, inhibiting the release of renin, possibly reducing norepinephrine release from sympathetic neurons, and decreasing central vasomotor activity.
Factors affecting neuronal survival and differentiation
– Matrix
– Target derived neurotrophic factors (NGF, BDNF, CNTF, GDNF, NT–3)
– Contact (neighbours)
– Developmental window
– Spatial localization

- Activity

Irreversible dementia
Alzheimer’s
Huntington’s
Parkinson’s
Pick’s
Balo’s
Multi–infarct state
AIDS–related
Reversible dementia
Chronic drug intoxication
Vitamin deficiencies (B–12 and folate)
Subdural hematoma(s)
Major depression (causing forgetfulness)

Hypothyroidism

Mutations leading to Alzheimer disease
APP = amyloid precursor protein (Chr 21)
Monogenetic causes of Parkinsons´s disease
alfa–Synuclein (membrane associated protein)
Parkin (ubiquitinylation)
PINK–1 (mitochondrial kinase)
Cause of Huntington´s disease
Excessive sequence of CAG repeats in the IT15 gene on arm 4p (mutanthuntingtin)


GABA is low inbasal ganglia
Mechanisms involved in Huntington chorea
1. Excitotoxicity

2. Oxidative stress


3. Impaired energy metabolism


4. Apoptosis

Cause of Friedreich’s ataxia
Chromosome 9, frataxin gene is deficient in the 1st intron.

GAA repeat expansion from ~15 to >100 cause gene silencing
Normal pH value of the blood plasma
7.35 – 7.45



Below 7.35 = acidosis


Above 7.45 = alkalosis

pH range in blood plasma compatible with life
7.0–7.9
The acid–base equilibrium
Acid production:
– CO2 (volatile acid)
– Lactic acid
– Ketone bodies
– Other organic acids (from food)

Acid excretion/removal:
– Respiration/lungs (CO2)
– Acid excretion in kidneys
– Metabolism: in cori cycle or as fuels (temporarily)

Base production:
– Amino acid degradation (in balance)
– 2 Glutamine + 3O2 + 6H20 ––> Glucose + 4HCO3– + 4NH4+ (within kidneys)

Base excretion:
– HCO3 – + NH4+ ––> urea (excreted in urine)

*In acidosis increases


* In alkalosis decreases


– HCO3– ––> neutralizes acids in blood
– NH4+ ––> excreted in the kidney

The source of CO2
Fuel degradation (oxidative decarboxylation of alfa–ketoacids):
– Pyruvate dehydrogenase complex
– Isocitrate dehydrogenase dehydrogenase
– alfa–ketoglutarate dehydrogenase complex
– Degradation of certain amino acids

Spontaneous decarboxylation of beta–keto acids:
– Pentose phosphate pathway
– Acetone formation
– Porphyrin synthesis
The fate of CO2
Carbonic anhydrase

Carboxylation reactions (not blood CO2 but uses mitochondrial CO2):
– Pyruvate carboxylase
– CPS
– ACC
– Propionyl–CoA carboxylase
The control of CO2/HCO3– equilibrium
Respiratory control: the chemoreceptor cells

Excretion and reabsorption of bicarbonate in the kidney.
The source and fate of lactate
Source:
Anaerobic conditions: (absent mitochondria (e.g RBC) or hypoxia). Glycolysis produces pyruvate and pyruvate is converted to lactate by lactate dehydrogenase.

Aerobic conditions: in the presence of PFK1–F isozyme, glycolysis is „faster” than pyruvate uptake of mitochondria.



Fate:


- Gluconeogenesis in liver (cori cycle) in hunger


- Energy production in red muscle fibers and in liver in well-fed state



Cause of lactic acidosis
1. Overproduction of lactate

- intense muscle work


- Oxygen supply problems (anemia etc.)



2. Decreased lactate removal
– Liver insufficiency (alcohol; drug, certain enzyme defects)
– Fructose ingestion ––> pyruvate overproduction

3. Decreased activity of pyruvate dehydrogenase (15–30 % activity)


- Thiamine deficiency and acetyl-coe accumulation

4. Decreased activity of pyruvate carboxylase

Examples of free radicals
Hydrogen atom
Superoxide
Hydroxyl
Peroxyl, alkoxyl
Oxides of nitrogen
Enzymes that generate the superoxide radical
Peroxidases
NO synthase
Xhantihine oxidase
Definition of inflammation
The complex biological response of vascular tissues to harmfulstimuli, such as pathogens, damaged cells, or irritants.
5 signs of inflammation
Heat
Redness
Swelling
Pain
Loss of function
Mechanism of inflammation
1. Vasodilation
2. Exudation – edema
3. Emigration of cells
4. Chemotaxis
5. Phagocytosis
Comparison between acute and chronic inflammation

Systemic inflammatory response syndrome (SIRS)
At least 2 symptoms:
– Temperature > 38 or < 36 degrees
– Heart frequency > 90
– Respiratory ratio > 20 or PaCO2 < 32 torr (< 4,3 kPa)
– Number of leukocytes > 12 000 cells/mm^3 or <4000 cell/mm^3 or 10% immature (band) cells
Sepsis definition
SIRS in response to documented infection.
Septic shock
– Systemic vasodilation and hyptotension
– Tachycardia
– Blood vessel/endothel damage and edema; hypovolemia
– Insufficient blood flow to organs
– Intravascular coagulation
– Abnormal blood gases and acidosis
– Respiratory changes and multiple organ failure
Infammatory pathway
Pathogen ––> pathogen associated molecular patterns (PAMP) ––> pattern recognition receptor (PRR) ––> response

Activation of pancreatic protein and lipid digestion enzymes

Digestion and absorption of proteins

Digestion and absorption of carbohydrates

Digestion and absorption of lipids

What are the results of degradation of ethanol?

1. Acetaldehyde formation


2. Increase ROS formation


3. Increase NADH:NAD+ ratio

Where is selenium present?

Selenocysteine is present in:


- Glutathione peroxidase: 2GSH+ H2O2 → GSSG + 2H2O




- Deiodinase: T4 --> T3




- Thioredoxin reductase



Iron absorption

- Iron is kept soluble and in ferrous state by gastric acid.
- Absorbed mainly in duodenum.
- Quantity absorbed regulated by enterocyte.
- Ascorbic acid (vitamin C) enhances absorption of non-animal sources of iron. 
- Fe2+ better absorbed than F...

- Iron is kept soluble and in ferrous state by gastric acid.


- Absorbed mainly in duodenum.


- Quantity absorbed regulated by enterocyte.


- Ascorbic acid (vitamin C) enhances absorption of non-animal sources of iron.


- Fe2+ better absorbed than Fe3+.


- DMT-1 = divalent metal transporter 1

What is the function of hephaestin?

Converts Fe2+ to Fe3+ before the iron enter the circulation.

What is the function of ferritin?

Iron-storage protein

Iron regulation

Iron regulates the synthesis of its
own key
transport and storage proteins.
-  Iron responsive elements (IREs)
- Iron responsive element binding proteins (IRPs)

Iron regulates the synthesis of its _own keytransport and storage proteins.


- Iron responsive elements (IREs)


- Iron responsive element binding proteins (IRPs)

Hepcidine regulation by iron

Hepcidine is synthesized by hepatocytes in the liver.
- Production stimulated with increased  pasm iron levels and tissue stores.
- Downregulated in hypoxia, anemia, oxidative stress and ineffective erythropoiesis.

- Negative feedback - hepcidin...

Hepcidine is synthesized by hepatocytes in the liver.


- Production stimulated with increased pasm iron levels and tissue stores.


- Downregulated in hypoxia, anemia, oxidative stress and ineffective erythropoiesis.




- Negative feedback - hepcidin decreases release of ironinto plasma (from macrophages and enterocytes).


- It binds ferroportin, complex internalised and degraded.

Different stages of iron deficiency and anemia

Toxicity of acetaldehyde

- Deactivation of proteins


- Increased collagen production (fibrosis)


- Inhibited DNA repair


- Impaired mitochondrial electron transport chain

What type of enzyme activity produces the neurotransmitters dopamine,serotonin and GABA?

Decarboxylase

Excitation and recovery in the rods (vision)



Molecular events of olfaction

Transduction mechanism for taste (sweet)

List types of sensing that are mediated by 7TMreceptors.

7TM receptors = 7-Transmembrane receptors, also known as G-protein-coupled receptors, or GPCRs.




Vision, olfaction, taste: bitter, umami, sweet

List the proteins involved in mediating sweet taste (upto generation of action potential).

Gustducin (G protein), adenylate cyclase, PKA, K+-channel

List the proteins involved in regeneration of rhodopsin.

Rhodopsin kinase, recoverin, arrestin

Function of voltage sensitive K+ channels

Regulates resting potential


Affects excitability of electrically active cells

GLP-1

Glucagon-like peptide-1




GLP-1 acts on pancreatic α-cells to inhibit glucagonsecretion and thereby reducehepatic glucose production.

Local and systemic effects of cytokines produced by activated macrophages

Definition of apoptosis

Programmed cell death (PCD).




Physiological process by which unwanted or useless cellsare eliminated during development and other biologicalprocesses, and ATP level remains close to normal level.




For normal development, maintenance ofcellular homeostasis.

Definition of necrosis

Cell death is the pathological process which occurs whencells are exposed to a serious physical or chemical insult,and ATP level collapse

Phases of apoptosis (3)

1. Initiation


2. Effectorphase


3. Degradation phase

What can defect of apoptosis cause?

- Autoimmune-disorders


- Cancer


- AIDS

Phases of cell cycle


Proto-oncogne

Encodes a normal (wild type) protein involved in:


- Promoting cell proliferation


- Inhibiting cell death (apoptosis)




Upon a gain-of-function (single allele) mutation become oncogens.

Oncogene

A dominant rare mutant allele of a proto-oncogene.




Results in gain-of-function phenotype


- Constitutive activation of celldivision


- Constitutive inactivation ofapoptosis

Tumor supressor gene

Encodes a normal (wild type) protein involved in:


- Inhibition of cell proliferation


- Promotion of apoptosis


- DNA repair




Recessive, loss-of-function mutations (in both alleles): the cell can not


- Suppress cell division


- Carry out apoptosis


- Repair damaged DNA

Cancer development

- Accumulation of genetic changes


- Activation of oncogenes


- Inactivation of tumor suppressor genes


- Five or six independent mutational events

Classes of protooncogens

1. Growth factors: FGF, PDGF




2. Growth factor receptors: EGF receptor




3. Signal transducing proteins:


- Ras (most commonly mutated oncogene)


- Akt (promotes cell survival)


- Abl and Src (non receptor tyrosine kinases)




4. Nuclear transcription proteins: - myc (production of proteins that allow cellsto advance through the cell cycle)


- NFkB (promotes cell survival)




5. Cell cycle regulators


- CyclinD


- CDK4




6. Antiapoptotic proteins: Bcl-2, Bcl-XL

Classes of tumor suppressor genes

1. Cell surface molecules: TGF-beta receptor (stimulates production of CDL inhibitors)




2. Regulators of signal transduction: NF-1, APC




3. Nuclear transcription proteins


- RB (inhibits entrance into S phase)


- p53 ( regulates cell cycle + apoptosis - mots common molecular alternation in cancer)



4. Cell cycle regulators: CDK inhibitors (p16, p21, p17)




5. Proapoptopic protiens: Ba, Bad, Bak

Beta-adrenergic pathway (GPCR signaling)

Regulation of:


PFK-1


FBpase-1


Glycogen phosphorylase


Pyruvate dehydrogenase complex


Carbamoyl phosphate synthase


Glycogen synthase


Isocitrate dehydrogenase


Citrate synthase


Alfa-ketoglutarate dehydrogenase


Acetyl-CoA carbocylase (ACC)


HMG-coA reductase


Pyruvate kinase (muscle + liver)











What does HbA1c consist of? What does its concentration in blood refer to?

HbA1c is glycated hemoglobin. Consist of glucose and hemoglobin.




It's concentration is used to identify the long term (3-month) average plasma glucose concentration.

How galactose enter glycolysis?

Galactose --> Galactose-1-p --> UDP-galactose --> UDP-glucose --> Glucose-1-phosphate --> Glucose-6-phosphate



Galactokinase --> Gal-1-P


UDP-glucose: Galactose-1-phosphate uridyltransferase --> UDP-Gal


UDP-glucose 4-epimerase --> UDP-Glc


UDP-glucose: Galactose-1-phosphate uridyltransferase --> Gal-1-p


Phosphoglucomutase --> Gal-1-p

How fructose enter glycolysis?

Fructose --> hexokinase


Enters at fructose-6-phosphate in step 3

How mannose enter glycolysis?

Mannose --> mannose-6-P


(Hexokinase)




Mannose-6-p --> fructose-6-p


(Phosphomannose isomerase)

How fructose-1-P enter glycolysis?

F-1-P --> glyceraldehyde + dihydroxyacetonephosphate (F-1-p aldolase)




Glyceraldehyde --> glyceraldehyde-3-p


(Triose kinase)




Dihydroxyacetone phosphate --> glyceraldehyde -3-p-


(triose phosphate isomerase)




Enters at 6 stage of glycolysis

Which nuclear receptor enhances glucose uptake?

PPAR gamma