Board Like Questions 1998 Dennis Livingston

1. Large amounts of ethanol completely overcome the inhibition by ethylene glycol on the enzyme alcohol dehydrogenase. This is most likely an example of: a. allosteric regulation. b. competitive inhibition. c. suicide inhibition. d. noncompetive inhibition. e. transcriptional control.

2. Serum from the two parents of a child with Tay-Sachs disease (deficiency of Gm2 gangliosidase) is tested and each is found to have half the activity of normal person. To make this test: a. the amount of the enzymes substrate should be considerably above the Km value. b. the enzyme should be given a substrate concentration equal to the Km concentration. c. there is no need to measure the protein concentration in the serum. d. the enzyme should be allowed to catalyze the reaction until all the substrate is gone. e. the enzyme must be tested at more than one pH value.

3. A diabetic patient hyperventilates to compensate for the acidosis caused by high levels of serum ketone bodies. Hyperventillation results in:

a. a higher partial CO2 pressure and a higher concentration of bicarbonate. b. a lower partial CO2 pressure but a higher concentration of bicarbonate. c. a higher partial CO2 pressure but a lower concentration of bicarbonate. d. a lower partial CO2 pressure and a lower concentration of bicarbonate. e. no change in either the partial CO2 pressure or in the bicarbonate concentration.

4. A patient is discovered to have cystathionuria. To cure this condition, which of the following vitamins should be given. a. niacin b. riboflavin c. biotin d. pyridoxine (B6) e. folate

5. Pantothenate is a common supplement to food products. This vitamin is important for: a. the conversion of glucose to pyruvate. b. the conversion of lactate to glucose. c. the conversion of glucose to ribose. d. the conversion of glucose to palmitate. e. the conversion of glucose to glycogen.

6. Exercising muscle produces lactic acid. This enhances oxygen release by hemoglobin because: a. muscle cannot carry out anerobic glycolysis. b. lactic acid is an allosteric regulator of hemoglobin. c. oxygen binds less tightly to hemoglobin at lower pH. d. bisphosphglycerate enhances oxygen binding. e. the iron becomes oxidized.

7. A 3 month old child is brought in with a broken arm. After ruling out the likelihood of abuse, you begin to suspect a defect in: a. the beta globin gene. b. the actin gene. c. the tubulin gene. d. the calcitonin gene. e. a collagen gene.

8. One copy of a beta globin gene from a thalassemic patient is subjected to DNA sequencing, and the entire primary sequence is found to be intact. A possible mutation is: a. a frameshift mutation. b. a deletion mutation. c. a nonsense mutation. d. a missense mutation. e. a promoter mutation.

9. Alcoholics have a high serum concentrations of lactate because they: a. cannot metabolize alcohol. b. convert alcohol into lactate. c. cannot convert lactate into pyruvate. d. cannot convert alcohol into fatty acids. e. convert alcohol into glucose.

10. The reason type 1 diabetics have high levels of serum chylomicrons is because insulin is needed to: a. induce high levels of hormone sensitive lipase. b. induce high levels of LDL receptors. c. induce high levels apoCII. d. induce high levels of lipoprotein lipase. e. induce high levels of HDL.

11. After an overnight fast: a. large amounts of ketone bodies circulate in the serum. b. glucagon levels are relatively high. c. serum glucose falls below 3 mM (54 mg/dl). d. the liver is storing glycogen. e. protein kinase A (cyclic A dependent protein kinase) is relatively inactive.

12. The insulin receptor: a. phosphorylates proteins on serine and tyrosine residues. b. makes seven passes throught the membrane. c. is associated with a heterotrimeric G-protein. d. is composed of two alpha and two beta chains. e. binds to DNA.

13. Which of the following genes is induced under gluconeogenic conditions in the liver? The gene enoding: a. phophoenolpyruvate carboxykinase b. phosphofructokinase 1 c. glycogen synthase d. pyruvate kinase e. thiolase

14. Nitric oxide (NO) relaxes smooth muscle. Like hormones: a. it binds to a membrane receptor. b. it is made by an endocrine organ. c. it is made from tyrosine. d. it has a long half-life. e. the target cells amplify its signal.

15. The ammonia used to make carbamoyl-phosphate for urea synthesis is mostly supplied by: a. transamination of pyruvate by glutamate. b. the action of glutamate dehydrogenase on glutamate. c. glutamine synthetase acting on glutamate. d. the action of arginase on arginine. e. spontaneous deamination of cytosine.

Board Like Questions 1998 Dennis Livingston

1. Large amounts of ethanol completely overcome the inhibition by ethylene glycol on the enzyme alcohol dehydrogenase. This is most likely an example of: a. allosteric regulation. b. competitive inhibition. c. suicide inhibition. d. noncompetive inhibition. e. transcriptional control.

2. Serum from the two parents of a child with Tay-Sachs disease (deficiency of Gm2 gangliosidase) is tested and each is found to have half the activity of normal person. To make this test: a. the amount of the enzymes substrate should be considerably above the Km value.

b. the enzyme should be given a substrate concentration equal to the Km concentration. c. there is no need to measure the protein concentration in the serum. d. the enzyme should be allowed to catalyze the reaction until all the substrate is gone. e. the enzyme must be tested at more than one pH value.

3. A diabetic patient hyperventilates to compensate for the acidosis caused by high levels of serum ketone bodies. Hyperventillation results in: a. a higher partial CO2 pressure and a higher concentration of bicarbonate. b. a lower partial CO2 pressure but a higher concentration of bicarbonate. c. a higher partial CO2 pressure but a lower concentration of bicarbonate. d. a lower partial CO2 pressure and a lower concentration of bicarbonate. e. no change in either the partial CO2 pressure or in the bicarbonate concentration.

4. A patient is discovered to have cystathionuria. To cure this condition, which of the following vitamins should be given. a. niacin b. riboflavin c. biotin d. pyridoxine (B6) e. folate

5. Pantothenate is a common supplement to food products. This vitamin is important for:

a. the conversion of glucose to pyruvate. b. the conversion of lactate to glucose. c. the conversion of glucose to ribose. d. the conversion of glucose to palmitate. e. the conversion of glucose to glycogen.

6. Exercising muscle produces lactic acid. This enhances oxygen release by hemoglobin because: a. muscle cannot carry out anerobic glycolysis. b. lactic acid is an allosteric regulator of hemoglobin. c. oxygen binds less tightly to hemoglobin at lower pH. d. bisphosphglycerate enhances oxygen binding. e. the iron becomes oxidized.

7. A 3 month old child is brought in with a broken arm. After ruling out the likelihood of abuse, you begin to suspect a defect in: a. the beta globin gene. b. the actin gene. c. the tubulin gene. d. the calcitonin gene. e. a collagen gene.

8. One copy of a beta globin gene from a thalassemic patient is subjected to DNA sequencing, and the entire primary sequence is found to be intact. A possible mutation is: a. a frameshift mutation. b. a deletion mutation. c. a nonsense mutation. d. a missense mutation. e. a promoter mutation.

9. Alcoholics have a high serum concentrations of lactate because they: a. cannot metabolize alcohol. b. convert alcohol into lactate. c. cannot convert lactate into pyruvate. d. cannot convert alcohol into fatty acids. e. convert alcohol into glucose.

10. The reason type 1 diabetics have high levels of serum chylomicrons is because insulin is needed to: a. induce high levels of hormone sensitive lipase. b. induce high levels of LDL receptors. c. induce high levels apoCII. d. induce high levels of lipoprotein lipase. e. induce high levels of HDL.

11. After an overnight fast: a. large amounts of ketone bodies circulate in the serum. b. glucagon levels are relatively high. c. serum glucose falls below 3 mM (54 mg/dl). d. the liver is storing glycogen. e. protein kinase A (cyclic A dependent protein kinase) is relatively inactive.

12. The insulin receptor: a. phosphorylates proteins on serine and tyrosine residues. b. makes seven passes throught the membrane. c. is associated with a heterotrimeric G-protein. d. is composed of two alpha and two beta chains. e. binds to DNA.

13. Which of the following genes is induced under gluconeogenic conditions in the liver? The gene enoding: a. phophoenolpyruvate carboxykinase b. phosphofructokinase 1 c. glycogen synthase d. pyruvate kinase e. thiolase

14. Nitric oxide (NO) relaxes smooth muscle. Like hormones: a. it binds to a membrane receptor. b. it is made by an endocrine organ. c. it is made from tyrosine. d. it has a long half-life. e. the target cells amplify its signal.

15. The ammonia used to make carbamoyl-phosphate for urea synthesis is mostly supplied by: a. transamination of pyruvate by glutamate. b. the action of glutamate dehydrogenase on glutamate. c. glutamine synthetase acting on glutamate. d. the action of arginase on arginine. e. spontaneous deamination of cytosine.

Answers to 1998 board like questions: 1. b 2. a 3. d 4. d 5. d

6. c 7. e 8. e 9. c 10. d 11. b 12. d 13. a 14. e 15. b

Dennis Livingston 1999 Please help by filling in the differential diagnosis. Biochemical Board Diseases

Disease

Enzyme/Protein/Vitamin Differential Diagnosis

sickle cell anemia

beta globin

beta thalassemia

beta globin

osteogenesis imperfecta

collagen

Ehlers-Danlos Type IV

collagen

alpha-1-antitrypsin deficiency

alpha-1-antitrypsin

phenylketonuria

phenylalanine hydroxylase

alcaptonuria

homogentisate oxidase

maple syrup urine disease

alpha-keto acid dehydrogenase

gout

xanthine oxidase

ornithine transcarbamylase deficiency

ornithine transcarbamylase

albinism

tyrosinase

porphyrias

heme biosynthesis

light sensitive skin; funny colored urine

Fabry's

alpha-galactosidase

Hunter

iduronate sulfatase

Hurler+Scheie

alpha-L-iduronidase

Tay-Sachs

hexosaminidase A

Gaucher's

beta-glucosidase

Niemann-Pick

sphingomylinase

familial LDL receptor hypercholesterolemia

severe combined immunodeficiency syndrom (SCIDS)

adenosine deaminase

hemophilia A

Factor VIII

pernicious anemia

vitamin B12 binding protein (intrinsic factor)

Cushing's disease

ACTH

McArdle's

muscle glycogen phosphorylase

Von Gierke's

glucose-6-phosphatase

fructoseuria

aldolase B

G6PD deficiency

glucose-6-phosphate dehydrogenase

MCAD deficiency

medium-chain acyl dehydrogenase

Lesch-Nyhan

hypoxanthine-guanine phosphoribosyl transferase

Zellweger's

no peroxisomes

xeroderma pigmentosum

nucleotide excision repair enzymes

hereditary nonpolyposis colerectal cancer

mismatch repair enzymes

beriberi

thamine (B1)

pellagra niacin

niacin

scurvy

vitamin C

rickets

vitamin D

Biochemistry Board Review 1999 Dennis Livingston

I. Proteins and Enzymes A. The twenty amino acids specified by the genetic code impart different properties to proteins depending on their side group. 1. acids and bases: glutamic acid, aspartic acid, histidine, cysteine, lysine, tyrosine, arginine 2. hydrogen bond formers: all the above plus asparagine, glutamine, serine, threonine, nitrogen on tryptophan, sulfur on methionine 3. nonpolar: alanine, leucine, isoleucine, valine, proline, methionine, tryptophan ring, phenylalanine 4. sulfur containing: cysteine and methionine 5. almost anywhere: glycine

B. Proteins fold into specific three dimensional shapes. These shapes are called conformations. C. Substructures/domains (secondary structures) made of repetitive arrangements of amino acids are common elements of conformation. 1. alpha helix 2. beta sheet (prion proteins) 3. collagen triple helix (see below) D. Some proteins assume more than one conformational state, i.e., undergo allosteric changes. E. Hemoglobin 1. composed of two alpha and two beta chains 2. mostly alpha helix, no beta sheet 3. heme holds ferrous (+2) iron that holds oxygen 4. four oxygens per tetramer 5. oxygen binding curve/oxygens bind cooperatively because of allosteric changes 6. protons push oxygen off (Bohr effect) 7. BPG (bisphosphoglycerate) inhibits oxygen binding to shift curve to physiological range F. Collagen 1. Most of protein has repeating structure of gly pro X where X is usually pro or posttranslationally modified hydroxylated pro. 2. Hydroxylation requires vitamin C. Lack of vitamin C, scurvy, causes weak triple helices and faltering connective tissue. 3. We have many (about a dozen) different types of collagen, i.e., about that number of collagen genes.

4. Mutations in gene family members leads to different inherited disorders (EhlersDanlos syndrome, osteogenesis imperfecta, epidermolysis bullosa). The disorders are distinct because different collagens are used in different connective tissues, e.g., bone, skin, cornea. In some cases the mutations are not in the collagen gene but in genes encoding enzymes that are needed to process precursor forms of collagen or posttranslationally modify it, e.g., deficiency of lysyl oxidase needed for collagen crosslinking giving rise to a form of Ehlers-Danlos. G. Enzymes catalyze chemical reactions. 1. A plot of reaction velocity, v, versus substrate concentration, [S], yields a curve that saturates. Reciprocal plots of 1/v versus 1/[S] sometimes give an easier method of determining important kinetic values. 2. Some enzymes don't yield a simple hyperbolic plot but rather a sigmoidal plot. This indicates coopertivity between catalytic sites that can only occur with a protein containing multiple catalytic subunits. 3. Km is a measure of affinity for the substrates, i.e., the lower the Km the tighter the affinity. (cf. hexokinase versus glucokinase) 4. Vmax is the fastest an enzyme can go. It is the product of two terms, k2, the turnover number for a mole of enzyme molecules, and the enzyme concentration. H. Enzyme activities can be altered by pharmacological or by physiological molecules. 1. Competitive inhibitors compete for the same binding site as the enzyme substrate. They make the enzyme appear to bind substrate less well, appear to increase Km, without altering the Vmax. This is because adding large amount of substrate swamps out the inhibitor. 2. Noncompetitive inhibitors don't alter substrate binding but prevent catalysis. They are recognized by their decrease of Vmax without an effect on Km. 3. Physiological inhibitors are normally of the allosteric type. This is because nature has evolved the enzymes to contain binding sites for regulatory molecules. Allosteric inhibition is normally hard to place into the competitive/noncompetitive categories. 4. Really good pharmacological agents either mimic the transition state of the normal substrate of the enzyme, e.g., statins like pravostatin that inhibit HMG-CoA reductase,

or, even better, form covalent adducts to the enzyme to kill them, e.g., fluorouracil action on thymidylate synthase. I. Proteolysis is important. 1. activation of digestion proteases 2. regulation of protein turnover 3. activation of the blood clotting cascade 4. apoptotic signals J. The pH of cells and serum is maintained by buffering. 1. Amino acid side chains that are weak acids and bases (glutamate, aspartate, histidine, cysteine, lysine, tyrosine and arganine) contribute to buffering. 2. The histidine imidazole side chain has a pKa near 7. 3. Bicarbonate is the major buffer in serum. 4. pH = pKa + log[base]/[acid]. 5. Translated to blood chemistry, pH = 6.1 + log[HCO3-]/(.03 X PCO2). 6. When pH = pKa, there is an equal concentration of base and acid.

II. Molecular Biology A. Genes 1. We have 50,000 to 100,000 of them. 2. They are ordered along chromosomes. The purpose of the genome sequencing project is to identify all genes. 3. Each gene encodes a protein (or a RNA like tRNA or rRNA).

4. Each gene has a promoter that regulates transcripton plus exons and introns. The introns are intervening sequences between the exons. Most (but not all) exons hold coding information for amino acids. 5. Most (>80%) of our DNA is composed of introns, spacer regions between genes, repetitive sequences or foreign elements that jump around our genome. 6. Our DNA is highly condensed in the nucleus. The primary packaging is done by histone proteins. These are small basic proteins that are probably the most conserved proteins in evolution. B. Mutations disrupt gene function either by disrupting transcription, splicing and translation or by changing the amino acid sequence in the encoded protein. 1. Missense mutations alter the amino acid sequence. The best known missense mutation is the one the gives rise to sickle cell anemia. It is a single base change in the sixth codon of the beta globin gene that changes a glutamate to a valine. 2. Frameshift mutations alter the reading frame by inserting or deleting any number of bases that are not divisible by three. 3. Nonsense mutations change an amino acid coding codon to become a stop codon. 4. Promoter defects alter the signals that control the translation of a gene. 5. Splicing defects can be caused by altering the recognition signal for 5'- (donor) or 3'- (acceptor) splice junctions. 6. Deficiencies (deletions) remove large portions of a gene. 7. Insertion mutations in the human genome often occur when transposable elements like Alu and LINE sequences insert into genes. 8. Silent mutations are changes in DNA sequence that have no phenotypic consequence. We have lots of these types of changes, often referred to as polymorphisms. They are good for forensic purposes to distinguish among us. 9. Missense in the beta globin gene are called hemoglobinopathies. The best example being sickle cell. 10. Frameshift, nonsense, promoter, splicing and deficiency mutations have been discovered in the beta globin gene and are classified as thalassemias.

C. A bunch of techniques can be used to clinically determine whether people carry mutations. 1. Southern blotting can look at large changes like deficiencies or changes that fortuitously change restriction enzyme recognition sites in genes. 2. PCR (polymerase chain reaction) is a means of making many copies of a gene. The technique can easily distinguish alterations that change the size of a gene. It can also be used to detect single base changes because it depends on primers that recognize specific sequences. 3. If all else fails, PCR products can be sequenced. 4. All techniques have been made possible because genes can be cloned. a. Gene cloning means isolating DNA and combining with a vector (plasmid) so that a host (like the bacteria E. coli) can make a lot of the DNA. b. Genomic clones contain pieces of chromosomal DNA. c. cDNA clones contain mRNA molecules that have been reverse transcribed into DNA form. (cDNAs obviously lack introns as well as regulatory sequences.) D. Many of our genes are members of families, i.e., genes or proteins that have similar function or are evolutionarily related. A good example is the beta globin cluster that includes embryonic, fetal and adult forms of hemoglobin. In this case the genes are close together and are ordered in sequence with our development. Gene families may be dispersed. The alpha globin genes are on a different chromosome from the beta globin cluster. Similarly, most members of the collagen gene family are dispersed. E. Replication 1. Replication starts at a unique site called the origin of replication. Replication proceeds bidirectionally, i.e., in both directions, meaning there are two forks. 2. The fork is composed of the leading and lagging strands. 3. DNA polymerases attach dNTP to primers using base complementarity. 4. The lagging strand is replicated by Okazaki fragment formation requiring a primase to prime DNA polymerase and ribonuclease H and DNA ligase to join fragments.

5. DNA repair systems are present to recognize, remove and replace DNA damaged by chemical changes including UV irradiation. UV light causes adjacent thymine residues to covalently attach to each other. 6. Reverse transcriptase is a DNA polymerase that uses RNA as a template. 7. dAZT has a -N3 group instead of an -OH on a thymidine and blocks chain elongation for reverse transcriptase. F. Transcription 1. RNA polymerase is to transcription what DNA polymerase is to replication except it does not require a primer. 2. Signals in front of genes tells RNA polymerase where and when to start. All together the signals are called promoters. Promoters usually have multiple parts including enhancers and response elements plus basal transcription signals like TATAA boxes. 3. Transcription factors bind to specific signals, i.e., specific DNA sequences, to promote or to hinder RNA polymerase. The best known transcription factors are the steroid hormone receptors that bind to response elements in front of regulated genes when bound with the hormone. 4. The product of transcription is a primary transcript. In eukaryotes the primary transcript must be capped, spliced and polyadenylated. 5. Splicing is the removal of introns to leave all the exons fused as a mature mRNA. G. Posttranscriptional modifications transform precursor messenger RNAs to mature mRNAs in the nucleus. 1. Splicing the is the process of removal intron sequences from the primary transcript. Splicing takes place on spliceosomes containing snurps composed of snRNAs and spliceosome proteins. Spliceosome proteins were recognized long ago because lupus patients make antibodies that react against them. a. Splicing is carried out by a ribonuclear protein complex (snRNAs + proteins) called snurps. b. Snurps recognize the exon-intron junction.

c. Snurps attach 5'-splice junction (donor site) to the internal accepting sequence before cleaving the 3'-splice junction (acceptor site) and fusing the exons. The intron RNA is released as a lariat. 2. Alternate splicing, skipping exons, particularly near the beginning and end of genes, is common for genes expressed in more than one tissue. (For example, the calcitonin gene is alternatively spliced in thyroid and brain to yield the proteins calcitonin and calcitonin-gene related protein, respectively.) 3. Eukaryotic messages contain a cap of methylated G. This is thought to protect the message. 4. Eukaryotic messages contain a tail of poly A. a. A string of A's is put on by a polymerase that doesn't need a template. b. The sequence AAUAAA in the 3'-untranslated region is the signal for the polymerase. c. Polyadenylation probably stabilizes the mRNA and makes it more transportable from nucleus to cytoplasm. H. Translation 1. Translation is the process of making the primary sequence of proteins from the amino acids. 2. The translation apparatus consists of tRNAs and ribosomes. 3. tRNAs covalently hold amino acids. 4. Amino acyl tRNAs place the correct amino acid into the growing polypeptide by codon-anticodon base pairing. The codon is the three base sequence copied into the RNA from the DNA code during transcription, while the anticodon is in the anticodon loop of the tRNA. 5. Translation begins at the first AUG after the cap and establishes a reading frame. Disruption of the reading frame creates a frameshift mutation. 6. Translation ends at stop codons (of which there are three: UAA, UAG and UGA).

III Intermediary Metabolism A. Our major energy sources are carbohydrates, fats and proteins. 1. We oxidize the carbon atoms of these compounds to carbon dioxide. In turn we reduce cofactors such as NAD+ (made from the vitamin niacin) and FAD (made from the vitamin riboflavin). 2. The reduced NADH and FADH2, in turn, reduce components of the electron transport chain found embedded in the inner mitochondrial membrane. Ultimately, molecular oxygen (that we breath) is reduced to water. 3. During reduction/oxidation in the electron transport chain, protons are pumped out of the mitochondria. The return of protons into the mitochondria is coupled to ATP production by ATP synthase, the lollipop looking knobs on the membrane. 4. ATP is used for lots of things including the transport of molecules across membranes and muscle contraction. B. Glucose is central to carbohydrate metabolism. 1. Carbohydrates are taken in as starch (chains of glucose with alpha 1-4 linkages with branches of alpha 1-6 linkages) or disaccharides such as sucrose and lactose. 2. We store glucose in liver and muscle as glycogen (structure similar to starch). 3. Glucose is partially oxidized to pyruvate in the cytoplasm by the glycolytic pathway. This does not use oxygen and does not make a lot of ATP. The pyruvate enters the mitochondria where it is converted to acetyl-CoA by pyruvate dehydrogenase. a. Coenzyme A (CoA) is derived from the vitamin pantothenate. b. The acetyl-CoA goes around the citric acid cycle. 4. Some glucose goes through the pentose phosphate shunt. a. The shunt makes NADPH for biosynthesis. b. The shunt makes all sorts of sugars, like ribose for RNA.

5. Glucose is made from gluconeogenic sources such as amino acids (but not fats). a. The Cori cycle is the recycling of lactate from muscle or red blood cells into glucose by the liver. b. Alanine from protein degradation is made into pyruvate which is also a gluconeogenic source. c. To make glucose, lactate and pyruvate need to be made in phosphoenolpyruvate. This is done by making pyruvate into oxaloacetate (pyruvate carboxylase requires biotin). Oxaloacetate is made into PEP by PEP carboxykinase (PEPCK), the rate limiting step of gluconeogenesis. 6. Glycogen is made from UDP glucose by glycogen synthase and degraded into glucose by glycogen phosphorylase. 7. Glycogen storage diseases are those where people either don't make or cannot degrade glycogen. They give rise to muscle cramps and liver problems, i.e., problems in the organs where glycogen is made and degraded. They may also result in hypoglycemia even during fasting. God forbid if you're asked to distinguish between Von Gierke's (glucose-6-phosphatase) and McArdle's (muscle glycogen phosphorylase)! 8. Glucose is kept at 4.5 to 5.0 mM (100 mg/dl) by the liver. a. Glucagon signals the need to supply glucose to peripheral tissues. b. Glucagon acts by activating adenylyl cyclase that makes cAMP. This activates protein kinase A (cyclic A dependent protein kinase.) c. Protein kinase A phosphorylates glycogen synthase, phosphorylase (by first phosphorylating phosphorylase kinase) and the bifunctional enzyme phosphofructokinase-2/2,6-bisphosphatase. Because glucagon is signaling the need for the export of glucose, this must mean that phosphorylated glycogen synthase is inactive, phosphorylated phosphorylase is active, and the bifunctional enzyme is tilted towards the phosphatase. (Activation of the fructose-2,6-bisphosphatase destroys the secondary metabolite fructose-2,6-bisphosphate. This metabolite stimulates glycolysis by activating phosphofructokinase-1. Thus, by destroying the activator of glycolysis, gluconeogenesis is stimulated.)

d. Glucose-6-phosphate made from glycogen (via glucose-1-phosphate) or by gluconeogenesis is released into the serum as free glucose thanks to the enzyme glucose-6-phosphatase, an enzyme peculiar to the liver. e. Insulin signals the fed state by working to activate a protein phosphatase that removes phosphates from all the enzymes. f. Type 1 diabetics feel starved, because of high glucagon, and put out glucose in quantity from the liver leading to hyperglycemia. C. Fats are the major storage form of energy. 1. Fats are triglycerides composed of glycerol (a gluconeogenic source) and three fatty acids. 2. Unsaturated fatty acids (containing double bonds) are good for us because triglycerides that contain these fatty acids have lower melting temperatures meaning that fat incorporated into our membranes and deposited on our blood vessels are more flexible and are less likely to crack giving rise to thrombosis. 3. Some fatty acids, e.g., those having multiple double bonds, are essential to our diet because we make the signaling molecules eicosinoids from them. 4. Triglycerides are stored in adipocytes. a. Glycogen signals the release of fatty acids from the adipocytes by activating (through PKA) hormone sensitive lipase. b. Fatty acids are put out in the serum complexed to serum albumin. 5. Ingested triglycerides are carried by chylomicrons and are taken up by muscle and adipose tissue by the capillary enzyme lipoprotein lipase, an enzyme whose level on the capillary surface is controlled by insulin. D. Fats are oxidized in the mitochondria and peroxisomes of cells. 1. Fatty acids are brought into the mitochondrial matrix using carnitine as a carrier. (Carnitine is not a vitamin.) 2. Mitochondrial oxidation is called beta oxidation because it removes two carbon units as acetyl-CoA. 3. NAD+ and FAD are reduced while the fatty acid is oxidized to acetyl-CoA.

E. Fatty acids are made in the cytoplasm on a large enzyme complex called fatty acid synthetase. 1. Acetyl-CoA must be made into malonyl-CoA by acetyl-CoA carboxylase. a. The enzyme uses the vitamin biotin (for the carboxylation). b. The enzyme is allosterically controlled by citrate (activation) and by palmitoyl-CoA (inhibition). This says that a cell with lots of energy, i.e., high citrate, will make fats, while a cell with a lot of fat, i.e., palmitoyl-CoA, will not. c. Malonyl-CoA is an inhibitor of carnitine transferase. This means that a cell making fats will not be taking fats into the mitochondria for oxidation. d. The very first step of synthesis joins a malonyl-CoA to a acetyl-CoA eliminating the carbon dioxide just added by acetyl-CoA carboxylase. e. The fatty acid synthase uses the vitamin pantothenate attached to a protein (acyl carrier protein ACP) to hold growing fatty acids. 2. Acetyl-CoA is derived from glucose via pyruvate dehydrogenase. It is brought out of the mitochondria in the form of citrate and cleaved into acetyl-CoA and oxaloacetate (the reverse of what happens in the citric acid cycle.) 3. The oxaloacetate is made into malate that is then converted by the malic enzyme into pyruvate, in turn producing NADPH for the reduction of acetyl-CoA (malonylCoA) in fatty acids. 4. The other half of the NADPH needed for fatty acid synthesis is derived from the pentose phosphate shunt. F. Some tissues, like the brain, utilize glucose over fatty acids, because of peculiarities of their metabolism. Other tissues, like red blood cells, utilize glucose because they lack mitochondria and cannot oxidize fats. Still other tissues, muscle, in particular, are fairly happy to use fatty acids as long as oxygen is available. Although muscle carries out anaerobic glycolysis for short times, sustained action requires aerobic utilization of fats. G. In times of starvation (or in hyperglycemic diabetics) ketone bodies are formed from fatty acids. 1. The major ketone bodies are acetoacetate and beta-hydroxybutyrate.

2. These are made in the liver from acetyl-CoA (derived from the breakdown of fatty acids). 3. Brain and heart muscle use the enzyme thiolase to make the ketone bodies back into acetyl-CoA for energy production from the citric acid cycle. 4. The ketone acids are the reason diabetics go into ketoacidosis. H. Cholesterol is important for human health. 1. We make most of the cholesterol we need but worry about the cholesterol we eat. 2. Cholesterol is needed for membrane synthesis, for bile acid synthesis and for the production of steroid hormones. 3. Cholesterol is taken up in the intestines into the lipoprotein complexes chylomicrons. 4. Cholesterol made in the liver (or deposited there by the chylomicron remnants) is elaborated in the serum as VLDL particles. 5. VLDL particles give up their fats and cholesterol and return to the liver as LDL particles. 6. The LDL receptor is needed to remove LDL so that excess cholesterol does not surge through the blood vessels. People who inherit a mutation in the gene for the LDL receptor have familial hypercholesterolemia and usually have heart attacks at an early age because of the atherosclerotic plaques (containing cholesterol) that build up in the vessels. 7. HDL is the good cholesterol because it scavenges excess cholesterol from vessels. It esterifies the single hydroxyl on cholesterol with a fatty acid to make cholesterol esters that are less toxic and more likely to be excreted. 8. The lipoprotein particles contain apolipoproteins as baggage tags. a. CII is associated with chylomicrons and VLDL particles. It acts as a baggage tag for lipoprotein lipase on the capillary wall to know what particles to nibble fats off of. CII on VLDL may be placed there by HDL. b. B100 is associated with VLDL and LDL. The LDL receptor recognizes B100. I. The citric acid cycle oxidizes acetyl-CoA to carbon dioxide.

1. Acetyl-CoA is combined with oxaloacetate (four carbons) to make citrate (six carbons). The citrate is oxidized by the steps to make oxaloacetate and carbon dioxide. This creates a lot of NADH that is used in the electron transport chain to make ATP. 2. Other metabolites feed into the cycle. For example, glutamate enters as alpha ketoglutarate. 3. A bigger problem is that intermediates in the cycle are drawn off to make other cellular components. For example, citrate is drawn off to make fatty acids and oxaloacetate is drawn off to make aspartate. 4. Anaplerotic reactions are needed to replenish oxaloacetate (or any other component of the cycle that can be made into oxaloacetate). Probably the reaction that should be learned is the pyruvate carboxylase reaction that makes pyruvate into oxaloacetate. You see this reaction used in gluconeogenesis and also as the step after the malic enzyme step in the production of NADPH for fatty acid synthesis. 5. The cycle can be stopped by the lack of NAD+. This is a problem for alcoholics because alcohol is like a little fatty acid yielding a lot of NADH with no place to dissipate it. 6. Not much has been said about pyruvate dehydrogenase that converts the pyruvate from glycolysis into acetyl-CoA. This is an important enzyme in making sure that cells preferentially oxidize fats over glucose. (It is inhibited by acetyl-CoA.) J. The electron transport chain converts the energy of oxidation into ATP energy. 1. Electrons removed from the oxidation of carbon atoms are passed to NADH and FADH2. 2. NADH and FADH2 are oxidized by complex I and complex II in the mitochondrial membrane. 3. Electrons are passed from complex I to complex II to complex III to complex IV (a.k.a. cytochrome oxidase) and onto oxygen to make water. 4. Protons are pumped out of the mitochondria. 5. Protons reentering the mitochondria go through the ATP synthase, the lollipop structures on the inner mitochondrial membrane. This enzyme uses the returning protons like water in a hydroelectric plant to make energy by combining ADP to Pi.

6. Cyanide kills us by preventing oxygen binding to cytochrome oxidase, the enzyme that will reduce molecular oxygen. Uncouplers, like valinomycin, work by letting protons (or other ions) back into the mitochondria without going through ATP synthase. K. The inner mitochondrial membrane is very impermeable. Getting molecules in and out requires symporters and antiporters. In particular NADH cannot pass through the membrane so that the electrons of cytoplasmic NADH must be brought into the mitochondria as reduced carbon, either as glycerol phosphate (the reduced form of dihydroxyacetone phosphate) or malate (the reduced form of oxaloacetate). L. Amino acids serve as an energy source, a source of nitrogen, a source of essential components and a source of sulfur. 1. The nonessential amino acids are the ones we can make. a. Alanine, aspartate and glutamate are made directly by transamination of pyruvate, oxaloacetate and alpha ketoglutarate. b. Proline and glutamine are derivatives of glutamate and asparagine is a derivative of aspartate. c. Serine and glycine come in during one carbon metabolism (see below). d. Tyrosine and cysteine are made from the essential amino acids phenylalanine and methionine. e. Arginine is a special case. It is made in the urea cycle. Growing children need arginine. 2. The essential amino acids are leucine, valine, isoleucine, histidine, lysine, phenylalanine, methionine, threonine, and tryptophan. (Personally, I remember these by subtraction. I know all twenty and know the metabolism of the ones we make. I then subtract these from the twenty to get the essential ones.) 3. Amino acids can be oxidized for energy. They are either glucogenic or ketogenic. a. Glucogenic means the carbons can be made into pyruvate or a citric acid cycle intermediate that can travel back to glucose. (Note that the body does not necessarily make these into glucose unless you are fasted or starved and the brain needs glucose.)

b. Ketogenic means the carbons go into acetyl-CoA or acetoacetyl-CoA, meaning they cannot be made into glucose. c. Some amino acids are purely glucogenic (alanine, glutamate), some are both and only two are purely ketogenic (leucine and lysine). 4. Getting rid of certain amino acids is a problem. a. In phenylketonuria, phenylalanine cannot be converted to tyrosine. This is tested at birth by a chemical reaction on a drop of blood. b. Maple syrup urine disease is caused by the inability to oxidize the carbon skeleton of valine, isoleucine and leucine that is carried out by a single enzyme that resembles alpha keto glutarate dehydrogenase. N. The metabolism of the amino acids glycine, serine, cysteine and methionine involve "one-carbon" metabolism. One carbon metabolism is synonymous with the vitamin folate and also peripherally with vitamin B12. 1. Folate hold one carbon units in various oxidation states (N5-methyl, N5,N10methylene, etc. FH4). 2. The carbons come in through the conversion of serine to glycine (or in the oxidation of glycine). 3. The carbons leave to make compounds such as the methyl group of thymine, some of the carbons of the purine ring and many other exciting reactions. 4. Methyl folate donates a methyl group to vitamin B12. Methyl vitamin B12 contributes the methyl group to homocysteine to convert it to methionine. Methionine is made into S-adenosyl methionine that is a source of methyl groups. 5. Without vitamin B12 to dissipate the methyl groups, much of the folate gets hung up as methyl folate. Thus, a B12 deficiency can cause a folate deficiency as well. 6. Homocysteine, derived from methionine that has given up its methyl group during a SAM mediated reaction, is needed to make cysteine through the joining of homocysteine with serine. 7. High levels of serum homocysteine are associated with an increased risk for heart attacks (for reasons that are not clear). People take high doses of folate to enhance the

vitamin B12 conversion of homocysteine into methionine. Some also take vitamin B6 (PLP) presumably to enhance production of cystathionine. O. Nitrogen in the form of ammonia is a neurotoxic compound and must be kept in a nontoxic form. 1. Excess ammonia is carried in the serum as the gamma amino group of glutamine and as the alpha amino group of other amino acids. 2. Ammonia groups can be taken up by the enzyme glutamate dehydrogenase (GDH) to convert alpha ketoglutarate into glutamate. Thus, this enzyme is central to detoxifying ammonia and brokering the nitrogen in the body. 3. Glutamate can contribute the alpha amino group to alpha keto acids like pyruvate and oxaloacetate to make alanine and aspartate, respectively. (It can also transaminate alpha keto acids that form the other amino acids.) 4. Transamination requires the vitamin B6 derivative, pyridoxal phosphate. A good bet is that if a vitamin is needed in a reaction involving amino acid metabolism, it will be B6. N. The urea cycle is need to excrete excess nitrogen. 1. The reactions take place only in the liver, partially in the cytoplasm and partially in the mitochondria. 2. Urea has two nitrogens plus one carbon. a. One nitrogen enters as ammonia liberated by GDH (running in the reverse direction) or glutaminase that converts glutamine into glutamate. b. The other nitrogen enters as aspartate, the transamination product of oxaloacetate. c. The carbon is carbon dioxide (carbonate). 3. Carbamoyl phosphate synthetase I makes carbamoyl phosphate from ATP, ammonia and carbonate. 4. Carbamoyl phosphate combines with ornithine to make citrulline. 5. Aspartate comes in. 6. Arginine is made. Cleavage of arginine by arginase makes urea plus ornithine.

7. Arginine can be drawn off for use without getting rid of urea. In kids this reaction is not sufficient to keep up with demand so that arginine is essential to growing children but not adults. 8. Thus, ornithine is to oxaloacetate as carbamoyl phosphate is to acetyl CoA. O. The metabolism of the nitrogenous bases found in RNA and DNA involves amino acids as donors of carbon and nitrogen atoms. 1. Purine bases are made on the scaffold of ribose-phosphate with carbons and nitrogens donated from one carbon sources, i.e., folate derivatives, and amino acids. Consequently they end up as nucleotides (sugar + base + phosphate). 2. Pyrimidines are made in one quick step by combining carbamoyl phosphate with aspartate to produce orotic acid that is then combined with ribose. 3. The deoxyribose form of the bases are made by the enzyme ribonucleotide reductase that can be inhibited by the chemotherapeutic agent hydroxyurea. 4. The DNA base thymine is made from UMP by thymidylate synthase that takes the methyl group from tetrahydrofolate. a. Thymidylate synthase is inhibited by fluorouracil. b. Methotrexate, which looks like folate, inhibits the reconversion of dihydrofolate into tetrahydrofolate. 5. Problems in human health are caused by not being able to get rid of excess bases. We cannot use them for energy production. a. Gout is the inability to convert purines into uric acid. Uric acid precipitates in our joints and causes the pain of gout. The drug allopurinal is a competitive inhibitor of xanthine oxidase that converts xanthine into uric acid. By inhibiting the enzyme it leaves the purines in the form of xanthine that is more soluble and can be excreted. b. Biochemistry textbooks like to dwell on the enzyme that scavenges excess purines (hypoxanthine-guanine phosphoribosyl transferase {base + phophoribosylpyrophosphate PRPP}) because its loss gives rise to Lesch-Nyhan. P. Phospholipids based on glycerol and sphingosine are needed to form the lipid bilayer of membanes.

1. Membrane phospholipids contain glycerol with two fatty acids, the second often unsaturated. 2. A polar had group attaches to the third position via phosphate. a. Inositol is an acidic head group. b. Ethanolamine and choline are basic head groups. 3. Sphingolipids, such as sphingomyelin and cerebrosides, are found in neuronal tissues. 4. Acidic groups are added to CDP-diacylglycerol while basic groups are added as CDP derivates, e.g., CDP-choline, to phosphatidic acid (diacylglycerol phosphate)

IV. Nutrition A. A calorie on a package label is a kilocalorie. B. We derive 4 kcal/g of energy from carbohydrates, 9 kcal/g from fats, 4 kcal/g from amino acids and 7 kcal/g from alcohol (because it is halfway between a fat and a sugar). C. Indirect calorimetry measures our respiratory quotient (CO2 expelled to oxygen consumed) that tells us whether the body is burning fats or carbohydrates. A respiratory quotient of 1.0 indicates the burning of carbohydrates, while a value closer to .7 indicates a burning of fat during aerobic exertion. D. Basal metabolic rate (BMR) is the amount of energy needed at rest. It constitutes approximately three-quarters of our daily need (unless we do physical labor or exercise vigorously). It varies with age, sex, mass and height. E. We store most of our energy in the form of fat in our adipocytes that live under our skin and around our organs. F. We store very little energy as glycogen in our livers and muscles. G. Muscle tissue only serves as an energy store during fasting and starvation when amino acids are needed to make glucose.

1. A means of assessing whether proteins are being degraded for gluconeogenesis is to assess whether there is a negative nitrogen balance (more excreted than eaten). 2. Surgical patients need proteins/amino acids because their body is in a catabolic state where they need new protein for wound repair. 3. Growing children are not much different in their need for protein. H. We are told to take in only 30% of our calories as fats. This is probably good advice because: 1. This may keep us from taking in more calories than we need so that we do not get obese. 2. This may keep us from taking in a lot of animal fat that contains saturated fatty acids. Because these have a higher melting temperature than unsaturated fatty acids, they tend to contribute to the rigidity of atherosclerotic plaque. 3. This may keep us from taking in a lot of animal fat that contains cholesterol that is known to accumulate in atherosclerotic plaque. 4. This may mean that we take in more plant fats that contain unsaturated fats, particularly monounsaturated fatty acids, that play a role in esterifying cholesterol for disposal. I. High serum cholesterol is well correlated with heart attacks. LDL is bad; HDL is good. J. Micronutrients (vitamins and minerals) are also needed. 1. Vitamin deficiencies are rare in this country because we are well fed and our food (bread and milk) is supplemented. 2. RDAs (recommended dietary allowances) are a good guess by educated scientists about how much we need based on people with experimental dietary deficiencies or on studies examining excretion of fed vitamins. 3. Vitamin B12 deficiency leads to pernicious anemia. As people age they lose the protein, named intrinsic factor, that is needed for B12 uptake. 4. The current vitamin of interest is folate. Folate deficiencies can lead to neural tube defects in pregnancy.

5. Some polyunsaturated fats are essential for making eicosinoids.

V. Hormonal Signaling A. Signaling molecules come in different varieties but have a common biochemical mechanism of interacting with receptors to signal target cells. 1. Neruonal signaling is not dissimilar to hormonal signaling in that it involves the release of a signaling molecule, in this case a neurotransmitter, that acts on a target cell. The target cell has a receptor at the synapse for transmitter uptake. Because the transmitter needs to work locally at a synapse and at a very fast rate, it is released in higher concentrations than most endocrine hormones. 2. Paracrine signaling involves signaling between adjacent cells rather than between cells of one tissue acting on target tissues at great distances, as is the case in hormonal signaling. 3. Hormonal signaling takes place between different tissues, often between different organs, at great distances. Hormones act is small quantities and are usually carried in the serum. B. Without being too rigid, there are basically three mechanisms by which hormones signal. 1. Some hormones directly effect gene expression (mostly through transcriptional regulation). The classic are the sex hormones, most of which are based on cholesterol. 2. Some hormones alter the cellular concentration of second messenger molecules, the classics being cyclic AMP (cAMP), phosphatidyl inositol (PIP2) and Ca+2. Second messengers are allosteric effectors of metabolic enzymes, or more commonly, of protein kinases that phosphorylate metabolic enzymes. These are mostly peptide hormones, such as glucagon, or compounds made from tyrosine, such as epinephrine (an adrenergic hormone.) 3. Some hormones effect the phosphorylation/dephosphorylation of a network of proteins that alter both metabolism and gene activity. In this case the hormone receptors are either themselves enzymes capable of protein phosphorylation or directly associated with such protein kinases. The action of these hormones is so

complex that their means of signaling is only now being worked out. The classic example is insulin, a peptide hormone. C. Each of the three signaling mechanisms includes amplification steps. 1. For hormones effecting gene expression, the binding of receptor to a promoter results in the passage of many RNA polymerase molecules (or the prevention in the case of negative regulation). 2. The second message systems are synonymous with amplification in that the binding of small amounts of hormone increase the concentration of these molecules out of proportion. 3. The hormones that are enzymes also amplify their signal by phosphorylating many proteins before their action is extinguished by downregulation. D. Some hormones cross the target cell membrane and bind to an intracellular receptor. 1. Most of these hormones are steroid hormones or honorary ones like thyroid hormone and vitamin D (that is really not a vitamin). 2. The vast majority of intracellular receptors are transcription factors that alter the expression of genes because these responsive genes have response elements that bind receptor. 3. Not all responses increase expression (transcription). Receptors may turn off (decrease transcription of) particular genes. 4. Sometimes there is both a primary response, i.e., genes directly turned on or turned off by the hormone receptor, and a secondary response, i.e., gene products (protein transcription factors) from the primary response that turn on another set of genes. In this case hormone action is indirect. E. G-protein coupled receptors work with the signaling ligand, e.g., adrenaline, glucagon, etc., binding to a receptor on the cell surface. 1. Different tissues have different constellations of hormone receptors. In addition, the hormone receptor for a particular hormone may be an isoform of the receptor found on another tissue. The classics in this case are the adrenergic receptors, many of which bind epinephrine, but are tissue specific.

2. G-protein coupled receptors are intramembrane proteins with seven transmembrane alpha helices. 3. Heterotrimeric G-proteins are a class of proteins. They are often distinguished by a subscript, like Gs, for G stimulatory, Gi or G inhibitory or Gq, for the one that effects PIP2. The expression of the various members of this class of proteins is tissue specific. 4. The tissue specificity of a hormone receptor and its coupled G-protein means that a hormone can have different effects on different tissues. Again, the classic is epinephrine, that acts on beta adrenergic receptors in muscle to increase glycogenolysis, and acts on alpha adrenergic receptors to constrict blood vessels. 5. In all cases, the bound receptor binds to a trimeric G-protein (alpha, beta, gamma). 6. In all cases, GDP on the alpha subunit is exchanged for GTP. 7. At this point there are two major types of responses depending the flavor of the coupled G-protein. 8. The adenylyl cyclase response results in either an increase or a decrease in cAMP. a. Whether cAMP goes up or down depends on whether the alpha protein of the trimeric G-protein is a Gs or a Gi. b. Adenylyl cyclase is a membrane protein that directly interacts with the alpha subunit of the G-protein. c. cAMP activates cAMP dependent protein kinase (protein kinase A, a.k.a. PKA). PKA is a tetramer of two regulatory, i.e., cAMP binding, subunits and two catalytic subunits. The regulatory subunits inhibit the catalytic subunits. cAMP binding releases the catalytic subunits to activate them. d. Protein kinase A phosphorylates enzymes like glycogen synthase and phosphorylase kinase. e. Eventually the alpha subunit hydrolyzes the GTP to GDP and is no longer stimulatory/inhibitory. f. Cholera toxin gets us by adding ADP to the alpha subunit of Gs. This prevents GTP hydrolysis so that adenylyl cyclase is always activated.

g. Pertussis toxin gets us by adding ADP to the Gi. This prevents Gi from interacting with the receptor, keeping GDP bound to the alpha subunit. Adenylyl cyclase is never turned off, just as with the action of Cholera toxin on Gs. 9. The phosphatidyl inositol response results in the cleavage of phosphatidyl inositol bisphosphate (PIP2) into diacylglycerol (DAG) and inositol trisphosphate (IP3). a. Binding of Gq to phospholipase C-beta results in activating the enzyme to cleave PIP2 into DAG plus IP3. b. Phospholipase C-beta, PIP2 and DAG are all in the membrane. c. IP3 diffuses to the endoplasmic reticulum, releasing Ca+2. d. DAG (and probably Ca+2) activate protein kinase C, a membrane protein. e. Unlike the known action of protein kinase A, the exact targets of protein kinase C are not well understood. One of its actions is to activate NF-kappa B to increase transcription. It also has actions at the metabolic level. f. Ca+2 also acts by stimulating a protein kinase called the calmodulin-dependent protein kinase (CaM-kinase). Calmodulin is a small calcium binding protein. Most proteins that are stimulated by calcium actually bind calcium bound calmodulin rather than free calcium. F. Nitric oxide is sexy, fun and is sort of an exception to the rules. (I will bet that there will be at least one question on the boards about it!) 1. It is a short lived gas, combining rapidly with oxygen to form harmless nitrate. 2. It is made from arginine by NO synthase. 3. It reacts with Fe in guananyl cyclase to stimulate production of the second messenger cGMP. This means that it really doesn't have a receptor like most other hormones. 4. Autonomic nerves release acetylcholine that in turn stimulate endothelial cells to make NO. NO makes smooth muscle cells relax. 5. Nitroglycerin works because it is converted to NO, dilating blood vessels to increase blood flow.

G. The enzyme linked receptors are also currently in vogue because their action is a major area of research and because the signaling cascades in which they participate are often tied to cancer. 1. Most of the receptors are single pass membrane proteins, i.e., unlike the G-protein receptors that have seven membrane spanning domains, these receptors have one spanning domain per polypeptide. 2. Most bind peptide hormones. 3. Most are called tyrosine or serine/threonine kinases because they phosphorylate tyrosine or serine and threonine on their (not well known) target proteins. 4. Some tyrosine kinase receptors self stimulate by phosphorylating themselves on tyrosines. 5. This results in their recognition by mediators that contain a folding domain called the SH2 (where S stands for src, an oncogene) domain. This serves as a signal to propagate the message into the cytoplasm and nucleus. Often the mediators that recognize the phosphorylated tyrosine residue on the receptor through the SH2 domain also contain a domain called SH3 that mediates binding to yet other members of the signaling cascade. 6. One important downstream signaling protein is Ras. a. Ras, like a G alpha protein, binds and hydrolyzes GTP. It is active when GTP is bound, and inactive when GDP is bound. b. Mutations that keep Ras in its activated state lead to colon, as well as other, tumors. c. One of Ras' downstream actions is to activate the MAP kinase cascade. 7. MAP kinase stands for mitogen activated protein kinase. a. These are a series of serine/threonine kinases that mediate the response of external agents, including hormones, with the cells growth and division decision making system. b. The cascade is pleasurably named MAP-kinase, MAP-kinase-kinase and MAPkinase-kinase-kinase. c. One interest in this cascade is that it activates the oncoproteins jun and fos that are transcriptional regulators.

8. Be aware that some receptors do not contain a kinase themselves but instead are intimately coupled to a membrane enzyme that is a kinase. The classic example is the growth hormone receptor. 9. Be aware that there are receptor phosphoprotein phosphatases, e.g., CD45 found in B and T cells. 10. Be aware that an important class of serine/threonine kinase receptors are the TGFbeta family (for transforming growth factor) needed for growth such as in bone. H. The insulin receptor falls into the tyrosine receptor kinase class of hormone receptors. a. It consists of four polypeptide chains, two each of alpha and beta. The beta subunits make a single pass through the membrane b. What the insulin receptor phosphorylates and what cascades it signals through is not completely understood. One pathway it activates is the Ras/MAP-kinase pathway. c. Insulin's effects are both on metabolism (some through activation phosphoprotein phosphatase-1) and some at the genetic level (upregulation of the PEPCK gene). Board Like Questions 1999 Dennis Livingston 1. In order to bind to DNA, the primary sequence of the histone proteins contain many residues of: a. tyrosine and phenylalanine. b. cysteine and methionine. c. leucine and isoleucine. d. glutamate and aspartate. e. lysine and arginine. 2. The amyloid plaques found in the brain cells of Alzheimer patients contain proteins with conformations composed almost entirely of: a. alpha helices. b. beta pleated sheets.

c. random coils. d. beta turns. e. leucine zippers. 3. The property of hemoglobin that causes oxygen saturation in the lungs and nearly complete oxygen release in the tissues is: a. the coopertivity among its four subunits. b. the avidity with which myoglobin picks up oxygen in the tissues. c. high concentrations of diphosphoglycerate in the lungs. d. low concentrations of acid in the tissues. e. its hyperbolic saturation curve for oxygen. 4. Lactate produced in exercising muscle has the beneficial effect of: a. being converted back into glucose in the muscle. b. slowing the release of calcium from the sarcoplasm reticulum. c. causing an acidic environment that unloads oxygen from hemoglobin. d. being an anerobic source of energy. e. being the precursor of creatinine phosphate. 5. Collagen is the most abundant protein in the body. It is composed of: a. a triple helical structure. b. a single amino acid chain of alpha helix. c. a double chain of amino acids in an alpha helix. d. beta pleated sheet. e. a repeating sequence of four amino acids.

6. Because the Km of liver hexokinase is higher than brain glucokinase: a. glucose is converted preferentially to glucose-6-phosphate at lower serum concentrations in brain than in muscle. b. the Vmax of liver hexokinase has to be higher than the Vmax of brain glucokinase. c. the Vmax of liver hexokinase has to be the same as the Vmax of brain glucokinase. d. the Vmax of liver hexokinase has to be less than the Vmax of brain glucokinase. e. most glycolytic enzymes are missing from the liver. 7. The statins, e.g, mevacor, bind noncovalently to the enzyme HMG-CoA reductase because they mimic the transition state of the enzyme. This means they: a. are irreversible in their action. b. compete with the substrate HMG-CoA for binding to the active site. c. are considered suicide (mechanism based) inhibitors. d. bind to the allosteric site of the enzyme. e. make the binding of the substrate appear to be tighter, i.e., appear to make the Km of the enzyme lower. 8. RNA polymerase II: a. transcribes the genes encoding ribosomal RNA. b. makes polyA tails. c. adds 5-guanyl caps. d. begins at a strat codons. e. transcribes the beta hemoglobin gene. 9. Stop codons: a. tell RNA polymerase where to stop.

b. tell DNA polymerase where to stop. c. effect the release of the protein from the tRNA holding the final amino acid. d. appear in every exon. e. are six bases long. 10. The most common mutation found in cystic fibrosis is the removal of a three base pair sequence in an exon of the CFTR gene. This gives rise to a: a. frameshift mutation. b. nonsense mutation. c. inversion mutation. d. silent mutation. e. deletion mutation. 11. The hemoglobin genes are expressed only in hemopoetic cells. This is likely the result of the specificity of the: a. stop codons. b. start codons. c. TATAA boxes. d. enhancer and response elements. e. splice sites. 12. Replication of the DNA in the chromosomes: a. begins at transcriptional promoters. b. occurs throughout the cell division cycle. c. requires RNA polymerase II. d. begins at multiple origins of replication.

e. proceeds in one direction along each chromosome. 13. The drug AZT inhibits DNA polymerization by: a. inhibiting primase. b. preventing helicase from unwinding the nucleic acid strands. c. blocking the addition of nucleotides to an AZT terminated primer. d. intercalating into the template strand. e. preventing proofreading. 14. AZT is an inhibitor of the enzyme: a. DNA ligase. b. DNA helicase. c. DNA topoisomerase I. d. DNA topoisomerase II. e. viral encoded reverse transcriptase. 15. The enzyme peculiar to the liver that permits it to secrete glucose into the serum is: a. phosphofructokinase-1. b. fructose-6-phosphatase. c. glucose-6-phosphatase. d. glycogen phosphorylase. e. PEP carboxykinase. 16. The gluconeogenic conversion of lactate or alanine into glucose by the liver requires: a. phosphoenolpyruvate (PEP) carboxykinase.

b. pyruvate dehydrogenase. c. pyruvate kinase. d. acetyl-CoA carboxylase. e. glycogen synthase. 17. Dietary cholesterol and lipids are brought to tissues by: a. chylomicrons. b. LDL. c. HDL. d. albumin. e. transferrin. 18. In the postprandial state: a. liver phosphofructokinase-1 is inactivated. b. adipocyte hormone sensitive lipase is activated. c. liver glycogen phosphorylase is activated. d. liver glycogen synthase is activated. e. GLUT 4 (skeletal muscle glucose transporter) is reduced in quantity. 19. Liver phosphofructokinase-1 is activated: a. by high levels of serum glucagon. b. by high intracellular concentrations of fructose-2,6-bisphosphate. c. by high intracellular concentrations of ATP. d. by high intracellular concentrations of cAMP, e. during gluconeogenesis.

20. During pregnancy the placenta secretes hormones that increase lipolysis in maternal adipocytes and create maternal resistance to insulin. The net effect is to: a. prevent hypoglycemia in the mother. b. increase glycolysis and prevent lipolysis in the mother. c. increase both glycolysis and lipolysis in the mother. d. decrease the secretion of glucagon. e. spare maternal glucose for fetal metabolism. 21. One problem with cirrhosis of the liver is high serum concentrations of: a. glucose. b. chylomicrons. c. urea. d. ammonia. e. ketone bodies. 22. The vitamin niacin is needed for the conversion of: a. alanine into pyruvate. b. glucose into glucose-6-phosphate. c. glycerol plus fatty acids into triglycerides. d. malate into oxaloacetate. e. acetylCoA plus CO2 into malonylCoA. 23. Trimeric G-proteins: a. have a receptor protein that passes through the membrane once. b. phosphorylate adenyl cyclase.

c. are active when bound with GTP. d. transport hormones into cells. e. always increase the intracellular level of cAMP. 24. The insulin receptor: a. binds to DNA. b. activates adenyl cylase. c. is an integral membrane protein. d. transports insulin into the cytoplasm e. is a phosphatase. 25. The insulin receptor: a. is a nuclear receptor. b. is a G protein. c. possesses tyrosine kinase activity. d. is inhibited by cholera toxin. e. has a single amino acid chain. 26. The estrogen receptor: a. is a tyrosine kinase. b. binds to a specific sequence of DNA c. activates adenylate cyclase. d. activates map kinase. e. is located in the plasma membrane. 27. Intracellular signalling proteins that interact with the insulin receptor possess:

a. leucine zippers. b. homeoboxes. c. helix loop helix motifs d. SH2 domains. e. zinc findegers. Answers to Board Like Questions 1999 Dennis Livingston 1. e 2. b 3. a 4. c 5. a 6. a 7. b 8. e 9. c 10. e 11. d 12. d 13. c 14. e 15. c 16. a

17. a 18. d 19. b 20. e 21. d 22. d 23. c 24. c 25. c 26. b 27. d