Alexandria University Medical Research Institute Semester: fall Biochemistry Department Academic year: 2019 – 2020 PhD Degree Time allowed: 2 hours Course title: Biochemistry Date: 31 / 12/ 2019 Course code: 1701801 Total marks: 60 Final exam Model answer ______

All questions are to be answered Question I: (30 Marks) A. Multiple Choice Questions (25 Marks, 0.5 mark each) Encircle the correct answer:

1- Receptor-mediated endocytosis is carried out by specific proteins complex of the membrane. They are termed as: a- Membrane Globules. b- Coated vesicles. c- Coated pits. d- Carrier proteins.

2- A membrane- bound enzyme that catalyzes the formation of cAMP from ATP is: a- Adenyl cyclase. b- MAP cyclase. c- Kinase cyclase. d- ATP phosporelase.

3- Which of the following statement is true for the gab junctions? a- Made up of two subunits of connexons. b- Movement of gases takes place freely. c- It is made of connexin protein. d- Allows free movement of large molecules across cells.

4- Pore- like connections between adjacent cells is an example of a- Gap junction. b- Desmosomes. c- Tight junction. d- Cell junction.

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5- Desmosomes is composed of a- Fibers. b- Soft tissue. c- Hard tissue. d- Bones.

6- Junction that prevents two cell compartments from mixing is a- Gap junction. b- Desmosomes. c- Tight junction. d- Cell junction.

7- Gap junction allows exchange of a- Solutions. b- Solutes. c- Solvent. d- Water only.

8- Adherens junctions are specialized cell junctions that form by linking the …………to transmembrane proteins known as …………….. a- Microtubule cytoskeleton; integrins. b- Microtubule cytoskeleton; cadherins. c- Actin cytoskeleton; cadherins. d- Intermediate filament cytoskeleton; integrins.

9- Which of the following statements is NOT TRUE about gap junctions? a- Gap junctions have some functionality of permitting cells to adhere to one another. b- Gap junctions form channels that are comprised of connexin proteins. c- Gap junctions permit the travel of small molecules back and forth between adjacent cells. d- Gap junctions prevent molecules and ions from traveling between cells in the extracellular space.

10- Which of the following proteins forms channels that permit electrical communication between cells across gap junctions? a- Connexin. b- Cadherin. c- Tubulin. d- Ephrin.

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11- What are the two major proteins that comprise tight junctions? a- Claudins and adherins. b- Occludins and connexins. c- Claudins and occludins. d- Claudins and protocadherins.

12- What is the main purpose of gap junctions? a- Prevents cells from separating from one another. b- Allows large molecules to move between cells. c- Prevents water from moving between cells. d- Allows molecules and ions to travel between cells.

13- Which cellular junction will be most useful in preventing the movement of material between cell membranes? a- Hemidesmosomes. b- Desmosomes. c- Gap junctions. d- Tight junctions.

14- Depolarization: a- Is associated with increase in membrane permeability to Na+. b- Is terminated with closure of voltage activated K+ channels. c- Is followed by muscle relaxation. d- Is caused by K+ efflux.

15- Action potential: a- Is a graded potential. b- Is produced by sub threshold stimulus. c- Starts with repolarization caused by outward movement of Cl-. d- Is conducted slower in thin nerve fibers.

16- Myelin sheath: a- Present in the myelinated and unmyelinated nerve fibers. b- Formed of lipoprotein complex and acts as electric insulator. c- It is formed of successive wrappings of the membrane of Schwann cells. d- It is the cause of decreased conduction of nerve impulse.

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17- During depolarization: a- Voltage activated Na+ channels open. b- The membrane becomes impermeable to Na+. c- When membrane potential reaches -55 m.v Na+ and K+ fluxes occur at the same time. d- K+ ions diffuse outside.

18- The resting membrane potential is caused by: a- Diffusion of K+ ions outside the nerve fibers. b- Diffusion of Na+ ions inside the nerve fibers. c- Opening of the chemically activated ion channels. d- Opening of the voltage activated ion channels.

19- Repolarization: a- Occurs at first gradual then becomes fast. b- Results from closure of sodium gates and opening of potassium gates. c- Is represented by the ascending limb of the spike. d- Is followed by appearance of response.

20- Saltatory conduction: a- Occurs in myelinated nerve fibers. b- Occurs by jumping of charges from one node of Ranvier to another. c- Is relatively slow 0.5-2.0 meter / second. d- Occurs in the neuro-muscular junction.

21- ………. send signals away from neurons whereas …….. receive signals from other neurons. a- Axons; synapses b- Synapses; dendrites c- Axons; dendrites d- Dendrites; axons

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22- The point at which the terminal button and another neuron communicate is called ……; communication here is made possible by the release of …………….. a- Synapse; hormones. b- Presynaptic membrane; neurotransmitters. c- Axon hillock; hormones. d- Synapse; neurotransmitters.

23- When the charge across the membrane of a neuron is about …….., the charge is called the ……... This is because there are ……….... a- 60-70 mV; action potential; more negative ions inside the cell. b- 70-100 mV; action potential; more positive ions inside the cell. c- 60-70mV; resting potential; more positive ions inside the cell. d- 60-70mV; resting potential; more negative ions inside the cell.

24- If sodium continues to enter a cell ……... This is called …………... a- The intracellular charge reverses from positive to negative; Repolarization. b- The intracellular charge reverses from positive to negative; Hyperpolarization. c- The intracellular charge reverses from positive to negative; Depolarization. d- The intracellular charge reverses from negative to positive; Hyperpolarisation.

25- If the stimulation of a cell is strong, the strength of the action potential produced would be: a- Stronger than that produced by weak stimulation. b- No different to that produced by weak stimulation. c- Weaker than that produced by weak stimulation. d- Twice that produced by weak stimulation.

26- When depolarisation occurs …………; this allows the release of ……….. into the …………….... a- Potassium channels open; neurotransmitters; synaptic gap. b- Calcium channels open; neurotransmitters; synaptic gap. c- Sodium channels open; neurotransmitters; synaptic gap. d- Calcium channels open; dopamine; cell body.

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27- In a signal transduction where the trimeric G protein with α, ß and γ is involved. Which subuit of the protein will activate the adenylate cyclase enzyme? a- Gamma subunit. b- Beta subunit. c- Alpha subunit. d- All three.

28- Continuous conduction: a- Occurs in myelinated nerve fibers. b- Occurs by jumping of charges from one node of Ranvier to another. c- Is relatively slow 0.5-2.0 meter / second. d- Occurs in the neuro-muscular junction.

29- Saltatory conduction: a- Occurs in unmyelinated nerve fibers. b- May reach up to 120 meter / second. c- Occurs by jumping from one neuron to another. d- Decreases gradually with distance till it disappears.

30- In all or non rule: a- A minimal stimulus produces a maximal response. b- The response in a single nerve fiber increases with increase intensity of stimulus. c- The nerve trunk either respond maximally or not respond at all. d- Minimal stimulus produces minimal response.

31- About growth factors, all the following are correct EXCEPT: a- They are polypeptides. b- All growth factors are specific for a particular cell type. c- They function as growth stimulators. d- They function as growth inhibitor.

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32- Bone homeostasis requires: a- T GF-b and bone morphogenic protein. b- T GF-a and bone morphogenic protein. c- TNF-a. d- Fibroblast growth factors.

33- Immune system is almost paralyzed if: a- Interferons are absent. b- Absence of VEGF. c- T cells are inactivated by AIDS virus. d- B cells growth and differentiation is inactive by AIDS virus.

34- An important cytokine that resists viral replication is: a- Insulin like growth factor. b- Epidermal growth factor. c- Interferon–α. d- Vascular endothelial growth factor.

35- Growth factors induce cellular functions EXCEPT: a- Growth and Survival. b- Differentiation. c- Death. d- Calcium homeostasis.

36- The JAK-STAT system consists of : a- A receptor b- Janus kinase c- Signal transducer and activator of transcription. d- All of the above.

37- For a 70-Kg man, in which one of the periods listed below do ketone bodies supply the major portion of the caloric needs of brain? a- Absorptive state. b- Overnight fast. c- Three-week fast. d- Four-day fast.

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38- Enzymic changes in the absorptive state include: a- Allosteric effectors. b- Covalent modification. c- Induction and repression of enzyme synthesis. d- All of the above.

39- Input from several signaling pathways of growth factors at one time: a- May affect the concentration of common second messenger. b- Enhance the activity of the cell. c- Cause the changes in second messenger to be misinterpreted. d- All of the above.

40- Growth factor that act in a paracrine manner: a- Affect behavior of distant cells. b- Affect behavior of cells that release the growth factors. c- Affect behavior of adjacent cells. d- None of the above.

41- Regarding tumor cells: a- The receptor is activated in absence of a growth factor . b- Secrete growth factors. c- Overexpress its receptors. d- All of the above.

42- ……….. are secreted by target cells and binds to special receptors located on neurons that synapse with target cells: a- Nerve growth factor. b- Vascular endothelial growth factor. c- Fibroblast growth factor. d- Angiogenin.

43- One group of group factors that foster the multiplication and/or development of various types of cells includes: a- Nerve growth factor. b- Insulin like growth factor. c- Epidermal growth factor. d- All of the above.

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44- Growth factor receptor is an example of which type of receptors? a- G-protein coupled receptor. b- tyrosine kinase receptor. c- voltage gated ion channel. d- ligand gated ion channel.

45- Phospholipase C hydrolyses: a- ATP. b- Inositol triphosphate (IP3). c- Phosphatidyl inositol 4,5 biphosphate (PIP2). d- Diacyglycerol.

46- During fasting, resting skeletal muscle

a- Switches from glucose to fatty acids as major fuel source. b- Depends on glucose as major fuel source. c- Catabolizes proteins as major fuel source d- None of the above.

47- Interleukins a- Can induce cells to resist viral replication. b- Produced by fibroblasts. c- Primary action is activation of macrophages. d- None of the above.

48- The following are growth factors are involved in angiogenesis EXCEPT: a- Nerve growth factor. b- Vascular endothelial growth factor. c- Fibroblast growth factor. d- Angiogenin.

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49- In the absorptive period, as regard proteins: a- The body does not store protein. b- Transient increase in the synthesis of the hepatic proteins occurs. c- Replacement of any proteins that may have been degraded. d- All of the above.

50- Members of the CXC chemokines group have: a- Single cysteine near amino terminus. b- Two adjacent cysteine near amino terminus. c- Two adjacent cysteine near the amino terminus are separated by two amino. acids d- Two adjacent cysteine near the amino terminus are separated by a single amino acid. B- Match one numbered item from group A with a lettered item from group B. (2.5 Marks, 0.5 Mark each)

Group A

51- Useful in understanding neurodegenerative diseases E 52- Platelets D 53- Chemokine CXCL8 C 54- Vascular endothelial growth factor F 55- Colony stimulating factor A

Group B

A. Regulate proliferation and maturation of red and white blood cells B. Receptor CCR1,3,5 C. Receptor CXCR1,2 D. Growth factors that causes vascular endothelial cells and vascular Smooth muscle cells to multiply E. Neurotrophins F. angiogenesis G. Interleukins

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C- Mark each of the following as TRUE or FALSE: (2.5 Marks, 0.5 mark each)

56- The cyclin concentration is constant during the cell cycle. F 57- There are 4 main checkpoints that control the cycle in eukaryotes. F 58- In S phase if DNA replication stops at any point on the DNA, the progress through the cell cycle is halted until the problem is solved. T 59- Allosteric changes rarely involves rate-determining reactions. F 60- In the fed state, the brain exclusively uses glucose as a fuel. T

II- Short answrs questions: (30 Marks, 5 marks each) Write short notes on:

1- Carbohydrate metabolism in the liver during absorptive state. (5 marks) Carbohydrate metabolism

Liver is normally a glucose-producing rather than a glucose-using tissue. However, after a meal containing carbohydrate, the liver becomes a net consumer, retaining roughly 60 of every 100 g of glucose presented by the portal system. This increased use reflects increased glucose uptake by the hepatocytes. Their insulin- independent glucose transporter (GLUT-2) has a low affinity (high Km) for glucose and, therefore, takes up glucose only when blood glucose is high. Additional mechanisms by which hepatic glucose metabolism is increased include the following.

1. Increased phosphorylation of glucose: The elevated levels of glucose within the hepatocyte (as a result of elevated extracellular levels) allow glucokinase to phosphorylate glucose to glucose 6-phosphate. (Recall that glucokinase has a high Km for glucose, is not subject to direct product inhibition, and has a sigmoidal reaction curve.

2. Increased glycogenesis: The conversion of glucose 6-phosphate to glycogen is favored by the activation of glycogen synthase, both by dephosphorylation and by increased availability of glucose 6-phosphate, its allosteric effector.

3. Increased activity of the pentose phosphate pathway: The increased availability of glucose 6-phosphate, combined with the active use of nicotinamide adenine dinucleotide phosphate (NADPH) in hepatic lipogenesis, stimulates the

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pentose phosphate pathway ([PPP]. This pathway typically accounts for 5%–10% of the glucose metabolized by the liver.

4. Increased glycolysis: In liver, glycolysis is significant only during the absorptive period following a carbohydrate-rich meal. The conversion of glucose to pyruvate is stimulated by the elevated insulin-to-glucagon ratio that results in increased amounts of the regulated enzymes of glycolysis: glucokinase, PFK-1, and pyruvate kinase ([PK]. Additionally, PFK-1 is allosterically activated by fructose 2,6-bisphosphate generated by the active (dephosphorylated) kinase domain of bifunctional PFK-2. PK is dephosphorylated and active. Pyruvate dehydrogenase (PDH), which converts pyruvate to acetyl CoA, is active (dephosphorylated) because pyruvate inhibits PDH kinase. The acetyl CoA either is used as a substrate for fatty acid (FA) synthesis or is oxidized for energy in the tricarboxylic acid (TCA) cycle.

5. Decreased production of glucose: Although glycolysis and glycogenesis (pathways that promote glucose storage) are stimulated in liver in the absorptive state, gluconeogenesis and glycogenolysis (pathways that generate glucose) are decreased. Pyruvate carboxylase (PC), which catalyzes the first step in gluconeogenesis, is largely inactive due to low levels of acetyl CoA, its allosteric activator. [Note: The acetyl CoA is being used for fatty acid synthesis.] The high insulin-to-glucagon ratio also favors inactivation of other gluconeogenic enzymes such as fructose 1,6-bisphosphatase. Glycogenolysis is inhibited by dephosphorylation of glycogen phosphorylase and phosphorylase kinase.

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2- Classes of tyrosine kinase receptors illustrated by a diagram. (5 marks)

3- G1 check point of the cell cycle. (5 marks)

 This checkpoint is present at the end of the G1 phase and before S phase.  This checkpoint helps in taking the decision of whether the cell should divide, delay division, or enter a resting stage (Go phase). If there are unfavourable conditions for the cell division, then this restriction point restrict the progression to the next phase by passing the cell to Go phase for an extended period of time.This restriction point is mainly controlled by the action of the CKI-p16 (CDK inhibitor p16). The inhibited CDK not bind with cyclin D1, hence there is no cell progression. • Active cyclin D-cdk complexes phosphorylate retinoblastoma protein (pRb) in the nucleus. Page 13 of 18

• Un-phosphorylated pRb acts as an inhibitor of G1 by preventing E2F- mediated transcription. • Once pRb gets phosphorylated, E2F activates the transcription of cyclins

E and A, which then interacts with CDK2 to allow for G1-S phase transition. This brings the cell to the end of the first checkpoint (unphosphorylated Rb inhibits the E2F).

4- a- Action potentials. (2.5 marks) Action potentials occur in two stages: -Depolarization -Repolarization -Depolarization in an action potential When the neuron is excited past its “Threshold” the following events occur: Sodium ions (Na+) rush into the axon. This neutralizes the negative ions inside. -The inside of the axon becomes temporarily (+) while the outside becomes temporarily (-). The reversal of charge is known as “depolarization” Nearby Sodium (Na+) channels open to continue the depolarization. -Repolarization This is the restoring of the (+) charge on the outside of the axon and (-) on the inside. Potassium gates open and potassium floods out.This generates positive charge on the outside of membrane.Sodium Channels Close (no + charges can get inside).The Sodium/Potassium pump rapidly moves Sodium out of the cell. Further creates the (+) charge outside with a (-) charge inside.

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b- Mechanisms of Neurotransmitter Release. (2.5 marks)

. -Docking of Vesicles and Release of Neurotransmitters Neurotransmitters are produced and stored in vesicles at the axon terminal. When the cell is stimulated the intracellular Ca2+ levels increase and stimulate the vesicles to translocate and bind to the plasma membrane via the SNARE proteins. The neurotransmitter is then released via exocytosis. To terminate the signal in a chemical synapse the neurotransmitter must be removed. Then activation of the Postsynaptic Cell occurs.

5- a- Saltatory conduction and refractory period. (2.5 marks) The “jumping” of an impulse between the “Nodes of Ranvier” thus dramatically increasing it’s speed.Only occurs in axons having Myelin. -2m/s  120 m/s.

refractory period:Brief period of time between the triggering of an impulse and when it is available for another.

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b- Synthesis of Collagen fibers. (2.5 marks)

……………………………………………………………………………………… ……………………………………………………………………………………… ……

……………………………………………………………………………………… ……………………………………………………………………………………… ……………………………………………………………………………………… ………………………………………………………………………………………

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6- Mechanism of rhodopsin activation by light and signaling. (5 Marks)

Rhodopsin consists of the protein opsin bound to the visual pigment, 11-cis-retinal. Rhodopsin signaling is initiated when the retinal chromophore absorbs a photon of light. Light absorption causes an electronic rearrangement and isomerization triggering a conformational change in opsin, leading to activation of a bound G protein known as transducin (Gt). All-trans-retinal is released and recycled to 11- cis-retinal which later recombines with opsin. This results in decreased release of neurotransmitter from the cells.

Rhodopsin signaling must be rapidly shut down in order for the eye to detect rapid movement and other changes in objects in our surroundings. The shut down of signaling involves several contributing processes. First, Gt-bound GTP is rapidly hydrolyzed.The hydrolysis of GTP by Gt is stimulated by a dimeric GAP protein (Step 7). Second, Ca2+-sensing proteins that detect a fall in intracellular Ca2+ stimulate the activity of guanylate cyclase, leading to re-opening of ion channels.

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Finally, the ability of activated rhodopsin to stimulate transducin is down-regulated by the phosphorylation of rhodopsin by rhodopsin kinase. Signaling by triphosphorylated rhodopsin is completely blocked by the binding of a protein called arrestin.

GOOD LUCK

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