Ординатура / Офтальмология / Английские материалы / Biochemistry of the Eye 2nd edition_Whikehart_2003

Glossary • 299

Phospholipid — A lipid in which two fatty acids and a polar head group are esterified to glycerol. Phospholipids are important membrane components.

Phosphorylation — The process of adding a phosphate group (PO4–3) to a compound or metabolic intermediate. In the generation of high energy ATP (see text) phosphorylation can be either simple (substrate level) or complex (oxidative). In the latter case, electron and proton transports are involved.

PITX genes — pituitary homeobox genes. These genes make transcription factors for RNA associated with eye and other organ development.

Pl — Isoelectric point. The pH at which all of the positive and negative charges on a protein or other compound are equal.

Plasma cells — B cells that are actively producing antibodies.

Platelet activating factor — A phospholipid plasmologen having a vinyl ether linkage on one fatty acid (glycerol–CH2–O–CH=CH–R1). This compound causes blood pressure lowering, blood clotting, and other effects.

Polar interactions — See Hydrogen bonding.

Polar nature — The property or ability of a molecule to possess displaced electrons causing partial charges to exist in the molecule.

Polymerase — An enzyme that synthesizes nucleic acids. There are several types, a DNA directed DNA polymerase makes DNA from a DNA template. DNA-directed RNA polymerases make RNA from a DNA template. Viruses use other types as well.

Polymorphonuclear lymphocytes — PMNs. White blood cells having polylobulated nuclei.

Polyols — Polyhydroxy intermediates formed in the polyol pathway that are a source of osmotic stress for cells, especially those of the lens.

Polysaccharide — A polysaccharide consisting of 10 or more sugar units branched or unbranched. Glycogen is an example.

Postsynaptic inhibition — The process in which nervous transmission is prevented in the postsynaptic nerve or muscle cell. This may take the form of an increased hyperpolarization of that cell. The term inhibitory postsynaptic potential (IPSP) is also used. An IPSP may be caused by an inhibitory neurotransmitter or by a decrease in the amount of neurotransmitters released across the cleft (as occurs with cone photoreceptors).

Postsynaptic stimulation — The process in which nervous transmission or depolarization is continued in the postsynaptic nerve or muscle cell. The term excitatory postsynaptic potential

(EPSP) is also use. However, note that in photoreceptor cells that an EPSP is caused by a presynaptic hyperpolarization that stops the release of neurotransmitters.

Post-translational modification — The biochemical alteration of a protein after the synthesis of its polypeptide chain.

Potential difference — A charged force, usually given in mV, that exists across a cell membrane. Strictly defined, it is the work that must be accomplished to move a charge over a defined distance.

300 • Biochemistry of the Eye

Promoter site (region) — Location on a DNA strand where the synthesis of new RNA is controlled. It is also called a promoter element.

Prostaglandin synthase — Also known as cyclooxygenase or COX, is a multifunctional enzyme that converts arachidonic and other long-chain fatty acids into an initial prostaglandin product. The synthase has both cyclooxygenase and peroxidase activities.

Prosthetic group — A nonprotein portion of a complete or holo-protein.

Protein — Polymer of amino acids linked by peptide bonds usually with a molecular weight of 10,000 daltons or greater.

Protein kinase C (PKC) — An enzyme that is involved in hormonal signal transduction by catalytic phosphorylation. It is calcium dependent. In the diabetic state, PKC induces the synthesis of endothelin-1, a protein responsible for pathological changes to blood vessels. PKC itself is stimulated by a metabolite of glucose (i.e., diacylglyerol) derived indirectly from the E-M pathway.

Protein structure — There are several divisions of this term. Primary: the amino acid sequence; Secondary: the unique shapes of part of the sequence (α-helices, β-pleated sheets, β-turns, and random coils); Tertiary: conformation of a single polypeptide; Quaternary: conformation of two or more polypeptides that comprise one protein. A domain is an intermediary form between secondary and tertiary structure.

Proteoglycan — The complex that results from the binding of a GAG to a protein.

Pseudo V genes — Pseudogenes are normally nonfunctional genes present in the cell’s genome. It has been proposed that pseudogenes for the V domain of antibodies might become activated as an extension of the antibody diversity hypothesis.

Pulverulent cataract — A congenital cataract of the nucleus consisting of fine, “powder like” diffused opacities. The cataract has been linked to a defect in chromosome 1.

Pyran — A six-membered carbon ring in which one member of the ring is oxygen. Six-membered carbohydrate rings are based on the structure of this compound.

Pyrimidine dimers — Two adjacent pyrimidine bases on the same

DNA chain having a common bond.

Pyruvate dehydrogenase complex — A molecular complex inside of the mitochondrial matrix that is composed of three different enzymes and five co-enzymes. The complex catalyzes the formation of acetyl co-enzyme A from pyruvate.

q arm — The longer arm of a chromosome extending out from its centromere. The other arm is referred to as a p arm.

Rate limiting enzyme — An enzyme that governs the formation of products in one direction. Its rate of catalysis is usually slower than other enzymes in a pathway.

Rb — Retinoblastoma protein. A cell cycle control protein often bound to the E2F protein to inhibit the cell cycle at G1. Like E2F, Rb is a transcription factor that promotes the S phase when

Glossary • 301

phosphorylated to separate it from E2F. The Rb gene (or Rb1) is defective (nonfunctional) in retinoblastoma and does not make Rb protein. This allows uncontrolled cell division to take place.

Recoverin — Protein, also known as S-modulin, that binds to Ca+2 ions. It has been proposed to inhibit rhodopsin kinase.

Reducing carbon — Carbon number one on an aldose (i.e., aldehyde carbohydrate) that is able to transfer electrons to a number of other compounds (i.e., it reduces them).

Refractory period — The time during which a nerve cannot depolarize again due to an overshoot in hyperpolarization.

Releasing factors — Peptide hormones of the first order that are released by the hypothalamus. (See Figure 6–3 for an example.)

Replication — The process of making new DNA.

Replication fork — DNA location at which replication commences.

Reporter genes — A gene that synthesizes a protein whose presence can be readily detected (e.g., by chemical assay). Reporter genes can be used to determine whether a transfection is successful.

Respiratory burst — The process of generating large quantities of superoxide and other radicals for the purpose of destroying antigens by leucocytes.

Retinal — Vitamin A aldehyde. It is the prosthetic group bound to opsin to form rhodopsin.

Retinitis pigmentosa — A primary degeneration of the neuroepithelium of the retina, its pigment, and its blood vessels. Main symptoms are night blindness with progressive loss of the visual field. Its cause is unknown.

Retinoblastoma — A carcinoma (cancer) of the retina in which neural precursor cells grow as multiple tumors. See text.

Rhodopsin — Rod pigment protein that contains 11-cis retinal and is involved in the initial phase of phototransduction.

Ribonucleic acid (RNA) — A genetic molecule that is involved in supplying the code for protein synthesis. It is similar to DNA but substitutes uracil for thymine and ribose for deoxyribose. See text for types.

Ribosome — A complex molecular assembly of proteins and RNA that is used to house the machinery for the formation of polypeptides and proteins.

RNA primase and RNA primer — The primase enzyme catalyzes the formation of RNA primer from RNA. RNA primer is a short strand of RNA required to initiate Okazaki fragment formation.

S chain — A polypeptide that surrounds an immunoglobulin to protect it from enzyme degradation (found in secretory IgA). S stands for “secretory.”

Saccharide — Alternate name for a carbohydrate or sugar.

Saponification — Hydrolysis of an ester, such as a membrane ester, in a base, such as sodium hydroxide.

Schiff base — R1–CH=NH+–R2, the bond that exists between retinal and opsin. The bond is protonated in rhodopsin and is comparatively weak for a covalent bond.

302 • Biochemistry of the Eye

Shirmer Lysoplate Assay — See Micrococcus Agar Diffusion Assay.

Second messenger — An internal cell hormone: cAMP, cGMP, Ca+2, or a phosphoinositide.

Sickle cell anemia — A hereditary disease in which the red blood cells of the patient form a sickle shape impeding normal blood flow and causing early destruction of the red blood cells. It is due to the substitution of Val for Glu on β-subunits of hemoglobin. The disease is prevalent among native Africans and in some parts of Asia.

SIX genes — sine oculis (Latin: without eyes) optix and similar genes involved in ocular development.

Solubility — The ability of a molecule to be (and remain) equally distributed in a liquid.

Spectral shifting — The process in which the sensitivity of light of a given wavelength is altered (in visual transduction) by changing the amino acid composition of rhodopsin.

Spherule — The terminal structure of a rod photoreceptor that usually is a single synaptic complex. The synaptic complex, termed a triad, contains one bipolar and usually two horizontal cell processes.

Sphingomyelin — The compound formed when a phosphocholine is esterified to ceramide (see Figure 4–12).

Sphingosine — A long-chain dihydroxy amino alcohol used to form glycolipids (see Figure 4–11).

Starch — The polymer storage form of sugar in plants. There is less branching of the main chain compared to glycogen.

Stargardt’s disease — A degeneration of the macula lutea.

Steroids — Any chemical substance with four fused rings that is derived from cholesterol. Many of these substances are hormones such as cortisol.

Substrate — Substance or metabolite that is converted to a product by an enzyme.

Substrate-level phosphorylation — In the formation of ATP, the substrate is the immediate source of phosphate. (See Adenosine triphosphate and Oxidative phosphorylation.)

Sulfoxide bond — A bond formed between sulfur and oxygen in the amino acid methionine found in proteins (see Figure 1–13). It accompanies disulfide bond formation in crystallins.

Svedberg unit (S) — A sedimentation coefficient used in high speed or ultracentrifugation. The unit is roughly proportional to particle mass and it is used when the molecular weight of the particle is unknown. S = the specific volume (mL/g) of the particle divided by the product of the angular velocity per sec times the revolutions per min.

Symport — Transport of substances in the same direction.

Synaptic cleft — A closed compartment between the presynaptic and postsynaptic membranes across which a neurotransmitter diffuses.

Synaptic ribbon — A molecular complex found in the presynapse of photoreceptors and a few other specialized cells that cause a high continuous release of neurotransmitters when the cell is not stimulated.

Glossary • 303

Target tissues (cells) — Tissues whose cells have receptor proteins either at their plasma membranes or in their cytoplasm for specific endocrine or paracrine hormones.

Tay-Sachs disease — A disease in which there is a deficiency of hexosaminidase A leading to an accumulation of Tay-Saches ganglioside. It is a glycolipid storage disease. (See text.)

Telomeres — Noncoding sequences of DNA located at the ends of chromosomes. One of their functions is to act as a mitotic clock in cell aging.

Thromboxanes — Eicosanoids formed by thromboxane synthase from a prostaglandin precursor. Their role in ocular function has not been well investigated.

Thyroglobulin — Thyroid gland protein at which the precursors to the thyroid hormones T4 and T3 are synthesized.

Thyroid peroxidase — Enzyme that incorporate iodinium ions (I+1) into Tyr amino acids in thyroglobulin.

Thyroid-stimulating immunoglobulins (TSI) — Immunoglobulins that are able to bind to the same receptor as that for the thyroid stimulating hormone.

Thyroxine (T4) — Tetraiodothyronine, along with triiodothyronine (T3), are hormones released by the thyroid gland.

Transcription — The process of making RNA from DNA. Reversed transcription is forming DNA from RNA as occurs in some viruses and with telomere formation.

Transducin (Gt) — The G protein of photoreceptors that is stimulated by rhodopsin. (See Chapter 6.)

Transduction — Process in which a substance or energy is altered from one form to another (e.g., light may be altered initially to a chemical signal during visual transduction).

Transfection — The process of introducing DNA into a cell by making the cell plasma membrane temporarily permeable to the DNA.

Translation — The process of polypeptide (protein) synthesis from RNA.

Triacylglyerol — A lipid storage form composed of three fatty acids esterified to glycerol.

Triphosphoinositide — Component derived from membrane phosphotidyl inositol-4,5-bisphosphate that acts as a second messenger hormone. It causes the release of Ca+2 ions that also act as second messengers.

Tropocollagen — The essential triple helical unit of collagen.

Tumor necrosis factor-α (TNF-α) — A protein secreted by fat cells that inhibits insulin receptor function. Increased secretion of TNF-α is associated with type 2 diabetes.

Type 1 diabetes — Diabetes caused by an insufficient amount of circulating insulin.

Type 2 diabetes — Diabetes caused by a defect in the insulin receptors or the insulin receptor mechanism of insulin dependent cells.

Tyrosine kinase receptor — Hormone receptor for insulin and similar hormones. It ultimately causes the uptake of glucose by activation of tyrosine kinase through a cascade mechanism.

304 • Biochemistry of the Eye

Unsaturation (or saturation) — The amount of double bonds present in a compound. A completely saturated compound has no double bonds.

Upstream promoter (element) — A region of DNA on the 3’ side of one or more genes that controls transcription of that gene by DNA-directed RNA polymerase.

Variable domain — A domain of an Ig that participates in binding to an antigen. It has both hypervariable and conserved sequences.

Velocity (V) — Velocity of a reaction is usually given as moles of substrate used or product formed per unit time. For MichaelisMenten kinetics, the velocity equation (2–4) is derived as follows:

by rearrangement

[Eo][S] = [ES] Km + [S]

Since the velocity of a reaction is also

v = k3[ES] By substitution

v = k3 [Eo] Km + [S]

The maximal velocity of the reaction

Vmax = k3[Eo]

Therefore, the Michaelis-Menten velocity of a reaction is

v = Vmax[S]

Km + [S]

Versican — A chondroitin sulfate proteoglycan found in the vitreous that also binds to hyaluron.

Virus — A genetic entity, minimally composed of nucleic acids and a capsid, which enters a cell to reproduce itself. In the process, it eventually kills the host cell by manipulating its genetic machinery.

Viscoelasticity — The property of a gel (e.g., that of the vitreous) in which the gel can reform its original shape after sudden deformation and yet still be able to flow as a liquid.

Vitamin — A substance that is essential for biological metabolism in highter organisms, but one that the organisms cannot make. There are two classes, lipid-soluble and water-soluble vitamins.

Glossary • 305

Vitreous — Usually refers to the secondary vitreous, the gel existing in the eye from the back of the lens/ciliary body to the retina.

Vitreous detachment — Usually posterior, it is the collapse of the vitreous away from the remaining vitreous gel.

Vitrosin — Collagen found in the vitreous. It is type II collagen to which are attached types IX and V/XI.

Vmax — Maximum velocity of an enzyme catalyzed reaction.

Voltage gated ion channel protein — A membrane bound protein that transports a specific ion when induced by a voltage change in the membrane.

Warburg effect — The production of more ATP than can be explained by aerobic metabolism alone. It was first observed by Otto Warburg in cancer cells in 1926 and commonly occurs in highly metabolizing photoreceptor cells.

Wax — Ester made up of a fatty acid and a long-chain alcohol.

Zonules — Suspensory proteinaceous ligaments that support the lens whose tension normally supports far focus. It is also known as the tertiary vitreous.

Answers • 307

2.QBA is a bridge compound between crystallin molecules formed by the oxidation of hydroxykynurenine, itself an oxidized form of the amino acid tryptophan. QBA stands for quinilinobenzoxamine. It has been identified as the complex that bonds between crystallins and forms a yellow to brown color in nuclear cataracts.

3.A deficiency in lysyl hydroxylase would inhibit the formation of hydroxylysine in collagen. This hydroxylated amino acid is important for crosslinking formation in collagen microfibrils. The crosslinking adds marked strength to the fibers. Therefore, the collagen tissues would be considerably weakened without the activity of this enzyme. A deficiency of procollagen peptidase would prevent the formation of tropocollagen units, the building blocks of collagen fibers. Accordingly, fiber formation itself would be impeded in collagen tissues.

4.The protein has a quarternary structure composed of one tertiary polypeptide of 34,000 D and two tertiary polypeptides of 25,000 D. In the second electrophoresis, mercaptoethanol separated the polypeptides by breaking the bonds between the Cys groups. The darker 25,000-D band confirmed that twice as much of that polypeptide was present as the 34,000-D polypeptide.

5.Chaperone activity is the ability of a protein molecule to maintain the normal structure/function of another protein molecule. That is, it prevents the protein from being denatured. Chaperone activity is probably important in lens fiber cells since these cells soon lose the ability to bring about protein synthesis. It would, therefore, be important for these cells to retain as many functioning proteins as possible (i.e., crystallins) in order to retain their shape and ability to refract light.

Chapter 3

1.The Km is a measure of the affinity of a substrate for an enzyme. However, as mathematically formulated, a Km actually represents a dissociation constant. So it is opposite in meaning. Therefore, the

higher the Km value, the more an enzyme and substrate will dissociate rather than associate. Good substrates have low Km values.

2.First, obtain reciprocal values for all of the data in order to construct the plot. Extend the line drawn through the points to a negative intercept on the x-axis. The interception point should be approximately –2.5/mM. Solving for the intercept as a reciprocal value should give

a Km = 0.40 mM. Note that the negative values of –x and –2.5/mM cancel out.

3.The Vmax/2 is by definition one-half of the maximal velocity of the enzyme. However, the concentration of substrate at which Vmax is one-half is also influenced by the binding of activator and inhibitor substances.

4.The y-intercept (for noncompetitive inhibition) = (1 + [I]/Ki) divided by Vmax. Using the information given then, 0.02/mmoles/sec = (1 +

0.5mM/Ki) divided by 70 mmoles/sec. When solved, this =

1.25mM.

308 • Biochemistry of the Eye

5.At Vmax/2, the concentration of the inhibitor is equal to the Ki of the inhibitor or 0.6 mM. This may be verified by solving the equation

of y at Vmax/2 (or 0.0625/moles/sec) = (1+[I]/0.6 mM) divided by 32 mmoles/sec.

Chapter 4

1.The E–M pathway is driven by both the available glucose and the cell’s need for energy. Under relatively anaerobic conditions, the cell

may run the anaerobic exit of the E–M pathway at 18 to 19 times the normal rate to obtain 36 to 38 molecules of ATP (2 ATPs × 18 or 19 molecules of glucose). It should be evident that the cost for this is a higher consumption of glucose.

2.Since electron flow is completely blocked, no protons can be transported to the intermembrane space. The resulting lack of protons will inhibit ATP synthase and the production of ATP. Death follows quickly!

3.Type 2 diabetes. One would place the patient on a weight reduction and exercise program. Fat cells produce tumor necrosis factor-α which, in turn, may inhibit insulin receptor autophosphorylation— part of the activation process for the receptor.

4.Several contributing biochemical factors bring about the degeneration of ocular blood vessels and lead to blindness. Both protein kinase C and MAP kinase may cause the synthesis of endothelin-1, a protein that increases blood vessel leakiness and its thickness. PKC is activated by a glucose metabolite when it is high in concentration. Glycation is another factor that produces denatured AGE proteins. These proteins cause similar pathological effects to the blood vessels.

5.These diseases develop due to an inherited enzyme defect that brings about the accumulation of incompletely catabolized GAGs. The accumulation occurs in both ocular and nonocular tissue. The accumulated GAGs hinder vital body functions and can cause eventual death.

Chapter 5

1.Approximately 0oC. Hexadecenoic acid is a 16-carbon fatty acid with one double bond.

2.The concentration of cholesterol in these membranes would be minimal to maintain the high degree of fluidity necessary for visual transduction.

3.Rhodopsin is an intrinsic or integral membrane protein requiring detergents to displace it from its surrounding lipids. This protein would be expected to penetrate the bilipid layer of its membrane.

4.A diester. That is, it is a lipid containing two ester bonds.