NBDE

Biochemistry and Physiology

requires glucantransferase and amylo-alpha-1,6 glucosidase Glycogen storage diseases:

Von Gierke disease (type I glycogenosis) – autosomal recessive G6Pase deficiency that causes hepatomegaly, renomegaly, platelet disfunction, stunted growth

Pompe disease (type II glycogenosis) – autosomal recessive lysosomal glucosidase deficiency that causes hepatomegaly, cardiomegaly, muscle hypotonia

McArdle syndrome (type V glycogenosis) – autosomal recessive muscle glycogen phosphorylase deficiency that causes muscle crapping and myoglobinuria

Inulin – fructose polymer, highly water soluble, determines GFR

Glycosaminoglycans (GAGs) AKA mucopolysaccharides – heteropolymer, unbranched chains of repeating disaccharide units of an amino sugar (hexosamine) or an uronic acid; they are the major structural

polysaccharides of ECM, CT and outer cell membranes. They are highly negatively charged and easily attract water. Accumulation of GAG’s can cause disease.

Their high viscosity imparts low compressibility, making them ideal for lubricating joints. However, their rigidity provides structural integrity to the cells and provides passageways between cells allowing for cell migration. They act as a “molecular sponge”

The disaccharide units contain either of 2 modified sugars: GalNAc or GlcNAc an da uronic acid such as glucoronate or iduronate

Chondroitin sulfate – most abundant GAG; found in cartilage, bone, tendon and ligaments, heart valves

o N-acetylgalactosamine + D-gluconuric acid

o Acts as a building block for proteoglycan molecules and has anti-inflammatory properties Hyaluronic acid – doesn’t form proteoglycan and doesn’t contain sulfur; found in ECM, synovial fluid, vitreous humor

o N-acetylglucosamine + D-glucoronic acid

o Known as the “cement substance” of tissues; they are large, shock-absorbing polymers o Hyaluronidase promotes depolymerization of the extracellular matrix GS. It slits hyaluronic

acid, lowering its viscosity and increasing the permeability of CT to absorption of fluids. Heparan sulfate – basement membranes; formed by N-acetylglucosamine + glucoronic acid (or L-iduronic)

o Contains higher acetylated glucosamine than heparin

Heparin – found in mast cell granules; made of same components as heparin sulfate but more sulfated o Serves as an anticoagulant

Dermatan sulfate – skin and vasculature; N-acetylgalactosamine + L-iduronic acid

Keratan sulfate – cornea, cartilage, bone; contains N-acetylglucosamine + galactose (this is the most heterogeneous GAG)

Mucopolysaccharide Disorders

Hurler’s syndrome – deficiency of α-L-iduronidase  accumulation of heparin sulfate and dermatan sulfate

o Mental retardation, corneal clouding, gargoylism o Autosomal recessive

Hunter’s syndrome – deficiency of L-iduronate sulfatase  accumulation of heparin sulfate and dermatan sulfate

o Mental retardation, gargoylism (no corneal clouding) o X-linked recessive

Proteoglycans – linkage of GAG’s to core protein involves a specific trisaccharide composed of 2 galactose and 1 xylose residue. The protein cores are rich in serine and threonine residues, allowing multiple GAG attachments. Proteoglycans lubricate, form ECM, and act as a molecular sieve.

Cellulose – homopolymer of β-D-glucopyranose linked by β-1,4 bonds Chitin – homopolymer of N-acetyl-D-glucosamine linked by β-1,4 bonds

Bacterial Polysaccharides

Dextran – homopolymer of glucose (α1,6 with some α1,3 branches) formed by hydrolysis of sucrose;

made by Strep mutans

o Produced outside of the cell by dextran sucrase (glycosyl transferase), which splits sucrose into glucose and fructose then links the glucose molecules into dextran, which is deposited as a thick glycocalyx around the cell

o It is essential for cariogenicity of Strep mutans

Levan – homopolymer of fructose formed by hydrolysis of sucrose by the enzyme levan sucrase

o Also increase the adhesion of bacteria to teeth, and promote formation of dental plaque o They are considered to be reserve nutrients for bacteria

The bacterial cell wall contains heteropolysaccharide made up of alternating acetylglucosamine and N-acetylmuramic acid units.

Glycoproteins – structural components, transport molecules, enzymes, receptors, hormones, cell-to-cell interactions; they include collagens, proteoglycans, immunoglobulins, selectins, fibronectin, laminin, TSH, alkaline phosphatase

The carbohydrate portion of glycoproteins differes from proteoglycans in that it is shorter and branched.

Glycolipids – sphingolipids with attached carbohydrates; found on outer cell membranes especially of the brain and NS

Derived from the lipid ceramide

Gangliosides, galactosylceramide, glucosylceramide

**Sugars that contain aldehyde groups that are oxidized to carboxylic acids are called reducing sugars. Examples include: lactose, maltose, glucose, galactose, and fructose. Reducing sugars have a free anomeric carbon (the oxygen on C1 is available for redox) that can be oxidized. If the oxygen on the anomeric carbon (the carbonyl group) isn’t attached to any other structure, then the sugar is a reducing sugar. A reducing sugar can reduce other substances as the anomeric carbon itself becomes oxidized.

This used to be the basis for reducing-sugar tests for things like diabetes, but now most blood glucose tests use glucose oxidase reactions.

Sucrose is not a reducing sugar because both anomeric carbons are involved in the bond.

Common test reagents are: Benedict’s reagent (CuSO4/citrate) and Fehlings reagent

(CuSO4/tartrate); they are reducing sugars because they reduce Cu2+ to Cu+ which forms a red

precipitate—copper (I) oxide.

SALIVA – hypotonic fluid with pH ranging from 6-7 and containing mostly water, electrolytes, and organic factors

Functions of saliva Antimicrobial:

o Secretory IgA – opsonization

o Lysozyme – hydrolyzes bacterial cell walls

o Lactoperoxidase – inhibits lysine/glutamic acid accumulation

Dental integrity – calcium and phosphate for mineralization, glycoproteins for pellicle formation Also cleansing, digesting (alpha-amylase), buffering (HCO3-) and lubricating

- High K+ and HCO3- concentrations, low NaCl concentrations, production inhibited by vagotomy, hypotonic solution.

- Main organic components are lingual lipase, mucopolysaccharides, proline-rich glycoproteins; also IgA (only Ig in saliva), lysozyme, lactoferrin, albumin, urea and glucose

Parasympathetics  serous secretions Sympathetics  mucous secretions PROTEINS

All amino acids in protein are L configuration; D-amino acids are found in some antibiotics and bacterial cell walls

Polar, uncharged (hydrophilic) Nonpolar, alipathic (hydrophobic) Acidic (negatively charged) Basic (positively charged) Aromatic Thiol Asparagine Cysteine Glutamine Serine Methionine Threonine Alanine Glycine Proline Valine Leucine* Isoleucine* Aspartate Glutamate Arginine Histidine Lysine* Tyrosine* Phenylalanine* Tryptophan* Generally non-polar Cysteine Methionine

**The nine amino acids in bold are ESSENTIAL amino acids.

**Hydrophobic amino acids have side chains that contain alipathic groups (Val, Leu, Iso) or aromatic groups (Phe, Tyr, Trp)

**Non-essential amino acids are synthesized from glucose, except for tyrosine. Tyrosine is made from the essential amino acid phenylalanine

Important: nonessential amino acids can be made from corresponding keto acids, an alpha-amino acid, a specific transaminase enzyme, and the coenzyme pyridoxal phosphate (Vitamin B6). These amino acids include alanine, aspartate, and glutamate.

Dopamine, the thyroid hormones, melanin, NE and Epi are all made from tyrosine.

The other nonessential amino acids are synthesized by amidation (glutamine and asparagines). Note: cysteine, although it’s carbon skeleton can be formed from carbohydrates, requires methionine (essential amino acid) to supply the sulfhydryl group

Amino acids can be categorized by their metabolic end products, also. They are either

*Ketogenic (producing ketone bodies and acetyl-CoA) Glucogenic (producing glucose, and thus pyruvate) *Some amino acids produce both

Cysteine and methionine both have sulfur-containing side groups.

Peptide bonds – short, polar, allow alpha-carbon to rotate freely, generally trans, proteolytic enzymes required to break them

Has partial double-bond character due to the carbonyl group

Peptide bonds are NOT cleaved by denaturing agents, stable to heating in strong acids The peptide bond does not accept or give off protons, so it is not ionized at physiologic pH Uncharged, but polar bond

Proline restricts the rotation around the alpha-carbon in the peptide bond

Note: disulfide bonds are formed from sulfhydryl groups of 2 cysteine residues, forming a cystine residue; these help protect proteins from denaturation in the extracellular environment (insulin and Ig’s are examples)

Amino Acid derivatives:

Phosphoenol pyruvate  tryptophan and tyrosine

Erythrose-4-P  phenylalanine  tyrosine  Dopa, etc…

Tryptophan  serotonin, melatonin, niacin, NAD and NADP

o Serotonin, released from platelets upon vessel damage, is a potent vasoconstrictor and increases vascular resistance; in gastric mucosa it is secreted by enteroendocrine cells to cause smooth muscle contraction; in brain it is a NT

Histidine  Histamine

 Histamine is released by basophils and mast cells, causing vasodilation and bronchoconstriction

 H1 receptors mediate Type I hypersensitivity, H2 receptors mediate gastric acid and pepsin secretion

Arginine  NO; nitric oxide is released largely by vascular endothelium, causing vasodilation Glycine  porphyrin  heme

Synthesis of other amino acids:

Alpha-KG + ammonia  Glutamate  Glutamine, proline or arginine 3-phosphoglycerate  serine  glycine or cysteine

Oxaloacetate  aspartate  asparagines, methionine, threonine, or lysine Pyruvate  alanine, valine, leucine, isoleucine (Isoleucine can also be formed from threonine)

Phosphoenolpyruvate + erythrose-4-P  shikimate  chorismate  Tryptophan, tyrosine, phenyalanine (in humans tyrosine is made from phenylalanine)

Ribose-5-P  histidine Transamination Reactions

Involve the transfer of an amino group from one amino acid to an alpha-keto acid (often glutamate and alpha-KG)

Transaminases or aminotransferases catalyze the reactions

Pyridoxal phosphate, derived from vitamin B, serves as the cofactor for these reactions; it functions as a carrier of amino groups because it undergoes reversible transformation between its aldehyde form (PLP) and aminated form (PMP)

Lysine, serine and threonine are not transaminated

Oxidative Deamination Reactions - result in the liberation of the amino group as free ammonia (NH3); these reactions occur in the liver and kidney to provide ketoacids and ammonia; enzymes involved in deamination include:

o Glutamate DH – an oxidoreductase that catalyzes the oxidative deamination of glutamate; unusual enzyme because it can use either NAD or NADP as a coenzyme [only amino acid undergoing rapid oxidative deamination]

o Histidase – creates ammonia and urocanate from histidine

o Serine dehydratase -- converts serine  pyruvate and also threonine  alpha-ketobutyrate o Asparaginase – deaminates asparagines to aspartate

Defects of amino acid metabolism

Phenylketonuria – deficiency of phenylalanine hydroxylases  severe mental retardation, ↓skin/hair pigmentation

Albinism – deficiency of tyrosinase  lack of melanin pigmentation

o Albinos do not have deficiency of NE or Epi because a different enzyme is used in melanocytes for DOPA synthesis

Alkaptonuria – deficiency of homogentisic acid oxidase (helps degrade tyrosine)  excessive excretion of homogentisic acid, a tyrosine degradative byproduct, causing black urine

Cystinuria – impaired renal reabsorption of cysteine  excessive urinary excretion of cysteine Collagen

3 polypeptide alpha-chains wound around one another to form a triple helix with high tensile strength Collagen is produced by fibroblasts, epithelial cells, odontoblasts, osteoblasts, and chondrocytes Collagen is 35% glycine, 21% proline and 11% alanine; hydroxyproline and hydroxylysine are also present

Synthesis: three preprocollagen peptide chains (alpha chains) are made at the RER; their sequence is Glycine-X-Y

o Hydroxylation of proline and lysine (Vit C dependent) occurs in the RER lumen

o Glycosylation of alpha chains occurs in the Golgi and the procollagen triple helix (with N- and C-terminal propeptides) is formed

o Outside of the cell, endopeptidases cleave the N and C terminal propeptides from procollagen (procollagen peptidase), forming tropocollagen; tropocollagen molecules aggregate at specific intervals to form collagen fibrils

o Multiple fibrils form fibers and collagen is attached to cell membranes via fibronectin and integrin.

Tropocollagen is the longest known protein; it is also present in reticulin, a component of reticular fibers.

Mature collagen lacks aromatic and sulfur-containing amino acids **Vitamin C deficiency stops collagen synthesis at hydroxylation stage – Scurvy **Osteogenesis imperfecta – collagen synthesis halted at the glycosylation stage

**Ehlers-Danlos – peptide cleavage does not occur that would allow collagen fibrils to closslink

Random: collagen and reticular fibers make up the stroma of all lymphoid tissues except the thymus.

Elastin

Elastin is rich in small, nonpolar aliphatic residues such as glycine, proline, alanine, leucine and isoleucine. Contains small amounts of hydroxyproline but no hydroxylysine.

Synthesis similar to collagen; the amino acid sequence of proelastin is Glycine-X-Y, and other residues include proline, lysine, alanine and hydroxyproline

Endopeptidases cleave in the same way as procollagen peptidase and form tropoelastin; tropoelastin molecules cross-link via desmosine, forming elastin fibers

Cross-links involve lysine and oxidized lysine residues, which are covalently linked to produce a desmosine cross-link.

The oxidation of lysine residues in both elastin and collagen is an extracellular process catalyzed by lysyl oxidase.

Plasma Proteins

Plasma proteins act as buffers that help stabilize internal environment pH; intracellular proteins absorb H+ made by metabolism.

Albumin (60%) – maintains plasma ∏ pressure, transports calcium, copper, free FAs, bilirubin, steroid hormones, drugs

o Normal albumin level is 3.5-5g/100mL, but albumin is decreased in malnutrition, liver failure and pregnancy

o Albumins also transport T4 and T3, bile acids, and inorganic ions (along with the things mentioned above)

o Almost all plasma proteins except albumin are glycoproteins; albumin I not glycosylated Fibrinogen (Factor I) – hemostasis

Alpha globulins – transport, substrates for formation of other substances o Lipoproteins (HDL) – transports cholesterol esters

o Prothrombin – hemostasis

o Erythropoietin – erythrocyte synthesis o Angiotensinogen – regulates blood pressure o α2-macroglobulin – protease inhibition

Beta globulins- transport, substrates for formation of other substances o Lipoproteins (LDL) – transport cholesterol

o Transferring – transports iron and copper

Gamma globulins – Ig’s (antibodies); these are the only plasma proteins not made in the liver Complement proteins – bacterial cell lysis, inflammation

Hemoglobin – 1 globin containing two alpha and two beta chains, 4 hemes that reversibly bind a molecule of O2 when the iron is in a reduced ferrous (Fe2+) state

- Heme is a nitrogen-containing organic pigment molecule with a single reduced iron at th center Heme binds CO (carbon monoxide) with a higher affinity than O2

Hb binds only 15% of CO2 carried in venous blood (most travels as HCO3-) Mutations of the alpha or beta subunits results in numerous hemoglobin types:

o Hb A – normal Hb o Hb F – fetal Hb

o Hb C – chronic anemia; lysine replaces glutamic acid, causing reduced plasticity of RBCs! o Hb H – α-thalassemia; defect of alpha chain genes, so Hb is composed of 4 beta chains o Hb M – methemoglobinemia; tyrosine replaces histidine (it cannot function as an oxygen

carrier)

 Fe2+ is oxidized to Fe3+, which can’t bind oxygen; methemoglobin is formed due to decreased activity of methemoglobin reductase, which could be a drug side effect or a hereditary phenotype of increased Hb M

 A group of abnormal Hb’s in which a single amino acid substitution favors formation of methemoglobin

o Hb S – sickle-cell anemia; valine replaces glutamic acid in the beta chain; causes the cells to deform into a sickle shape when exposed to low oxygen (like during exercise or in peripheral circulation); they block small vessels causing pain and impaired circulation, and the cells have a short lifespan; the deoxyHb has decreased solubility; oxygen-carrying capacity is greatly decreased

Heme is a cyclic structure composed of 4 pyrrole rings with a central iron atom.

Myoglobin has only 1 heme, is located in muscle exclusively, is used for O2 storage, and has a much higher affinity for O2 than Hb.

LIPIDS

Fatty acids – all are alipathic carboxylic acids; most are esters, but some exist as unesterified free fatty acids The only essential fatty acids are: linoleic acid and linolenic acid because we lack enzymes to place double bonds at certain positions (omega-3 and omega-6)

Basic structure is carboxylic acid end with a hydrocarbon chain (seen on right ) Classified as:

o Saturated – arachidic, butyric, capric, caproic, caprylic, lauric, myristic, palmitic, stearic o Monounsaturated – erucic, oleic, palmitoleic (note: most monounsaturated fats are in cis

configuration)

o Polyunsaturated – arachidonic, linoleic, linolenic Cells derived energy from FA’s through beta-oxidation TAG’s

3 fatty acids and glycerol; stored in adipose tissue as an energy source Transported in the plasma by lipoproteins

Basic triglyceride structure seen on the right  Phospholipids

2FA’s + phosphate + glycerol; derived from the substance phosphatate Precursors for second messengers and metabolic intermediates

Lecithins (phosphatidylcholines) – water soluble emulsifiers formed from choline

o Upon hydrolysis, lecithins yield 2 fatty acid molecules and 1 each of glycerol, phosphoric acid, and choline

o Also found as membrane constituents

Cephalins (phosphatidylethanolamines) – formed from ethanolamine or L-serine o Have hemostatic properties and found especially in nervous tissue of the CNS

o Resemble lecithin except that they contain either 2-ethanolamine or L-serine in the place of choline

Sphingomyelins – plasma membrane components formed from ceramide; do not contain glycerol!! o Most membrane phospholipids contain glycerol, but sphingomyelin is based on sphingosine

o Found especially in nervous tissue

o Yield sphingosine, choline, a FA, and phosphoric acid upon hydrolysis

o **Remember that Niemann-Pick disease is associated with accumulation of sphingomyelin in the CNS

Steroids

Cholesterol is synthesized throughout the body for cell membranes, but is produced mainly in the liver from acetyl-CoA

Conversion of HMG-CoA  mevalonate via HMG-CoA reductase is the rate limiting step in cholesterol synthesis

Other important intermediates are isopentenyl pyroP and squalene Precursor for bile salts, sex hormones, adrenocortical hormones, vitamin D

Cholesterol is mostly esterified with FA’s when circulating; circulating cholesterol is taken up into liver cells where it inhibits synthesis of more cholesterol from acetyl-CoA via allosteric inhibition of HMG-CoA reductase

Thiolase and HMG-CoA reductase catalyze reversible reactions in cholesterol synthesis Eicosanoids

20-C long polyunsaturated FA’s that are derivatives of arachidonic acid

Phospholipase A2 – releases arachidonic acid from plasma membrane phospholipids upon hormone/cytokine stimulation or cellular damage

o Corticosteroids inhibit PLA-2

Prostanoids – prostaglandins, prostacyclines, thromboxanes (formed by COX) Leukotrienes – formed by lipoxygenase (LOX)

Lipoxins – formed by LOX

**Eicosanoid formation pathway on back (from page 257)

Lipid Transport – Lipoproteins

Composed of nonpolar lipid core (TAG’s, cholesterol esters) surrounded by a single layer of amphipathic phospholipids and free cholesterol

Characterized by the apoprotein embedded in their outer layer

Contain TAG’s, phospholipids, cholesterol, cholesterol esters (in highest %), and free FA’s Choline is essential for the secretion of lipoproteins from hepatocytes, especially VLDL

Familial hypercholesteremia – autosomal dominant defect of the LDL receptor, leading to increased plasma LDL and atherosclerosis

Major lipoproteins

Chylomicron – lowest density (1% protein), major lipid content is TG, carries lipid from the small intestine to extrahepatic tissues

Chylomicron remnants – very low density (7% protine), major lipid content is TG cholesterol, carries lipid from the chylomicrons of extrahepatic tissues to the liver

VLDL – 10% protein, major lipid content is TG cholesterol, carries lipid from the liver to extrahepatic tissues

IDL (VLDL remnant) – 11% protein, major lipid content is TG cholesterol, carries lipid from VLDL of extrahepatic tissues to the liver

LDL – 20% protein, major lipid content is cholesterol, carries lipid from VLDL of extrahepatic tissues to the liver

HDL – highest density (up to 55% protein), major lipid content is cholesterol esters, carries lipid from extrahepatic tissues to the liver

Bile Salts – the two main ones: glycocholic acid and taurocholic acid

Almost exclusively absorbed in the ileum and returned to the liver via the enterohepatic circulation Bile acids are conjugated with either glycine or taurine to give the respective bile salts

Two important actions in the intestinal tract: help in the absorption of FA’s, monoglycerides and cholesterol from the intestine (by forming micelles) and have detergent action that decreases surface tension of particles, allowing agitation from the walls to break fat globules into small sizes.

Lipid storage diseases – inherited disorders of the reticuloendothelial system caused by incomplete lysosomal breakdown of sphingolipids and mucopolysaccharides within phagocytes, leading to their accumulation (most are common to Ashkenazi Jews)

Gaucher’s disease – autosomal recessive β-glucocerebrosidase deficiency  accumulation of glucocerebrosides

o Splenomegaly, hepatomegaly, anemia, skin pigmentation o Most common disease

Niemann-Pick disease – autosomal recessive sphingomyelinase deficiency  sphingomyelin accumulation

o Splenomegaly, hepatomegaly, anemia, CNS degeneration o Rapidly fatal

Tay-Sachs disease – autosomal recessive hexosaminidase A deficiency  accumulation of gangliosides o CNS degeneration, mental retardation, cherry red spots on retina

o Rapidly fatal

Fabry’s disease – X-linked recessive α-galactosidase deficiency  ceramide trihexoside accumulation o Skin lesions (angiokeratomas), renal failure, cardiovascular issues, peripheral neuropathy Glucagon and Epinephrine

Glucagon and epinephrine activate adenylate cyclase in adipocytes, increasing cAMP  protein kinases  activates hormone-sensitive TAG lipase  hydrolysis of TAG’s forming free FA and glycerol. The fatty acids that are released bind to albumin and travel to tissues where they dissociate and diffuse into the cells

The glycerol released by lipase action is phosphorylated by glycerol kinase, and the resulting glycerol-3-P is oxidized to dihydroxyacetone phosphate, which is then converted into glyceraldhyde-glycerol-3-P (by

triose phosphate isomerase); glyceraldehydes-3-P is then oxidized via glycolysis.

Insulin causes activation of a phosphorylase that dephosphorylates the hormone-sensitive lipase and diminishes lipolysis

ENZYMES

Isoenzymes – enzymes with subtle molecular differences that catalyze the same reaction

Metals and B-complex vitamins serve as the majority of non-protein enzyme components (cofactors, prosthetic groups)

Cofactors – organic molecules (coenzymes) or ions (usually metal ions) that are required for an enzyme’s activity; they may be attached either loosely or tightly (prosthetic group) to the enzyme.

o Apoenzyme (inactive) + cofactor  Haloenzyme (active) Enzymes requiring inorganic cofactors

Iron: cytochrome oxidase, catalase, peroxidase, ferredoxin Cu2+: cytochrome oxidase, pyruvate phosphokinase Zn2+: carbonic anhydrase, alcohol DH

Mg2+: glucose-6-Pase, hexokinase, pyruvate kinase Mn2+: ribonucleotide reductase

K+: pyruvate Nickel: urease

Se: glytathione peroxidase

Classifications (others were obvious by name):

Isomerases – catalyze a change in molecular structure

Lyases – catalyze bond cleavage by elimination (break C—O, C—C, or C—N bonds) Ligases – catalyze the union of two molecules

Michaelis-Menten Equation

The Michaelis constant (Km) is the substrate concentration when the initial reaction velocity Vi is ½ of Vmax

Vi = [Vmax * [S]] / [Km + [S]]

Often incorrectly said to equal the dissociation constant of the enzyme-substrate complex; this is not true but it does give a means of comparison of the affinity (reciprocal of dissociation) of an enzyme for different substrates:

o Lower Km = higher relative affinity

Km values increase in the presence of a competitive inhibitor, but are not affected by a noncompetitive inhibitor (but Vmax is reduced in noncompetitive inhibition)

Allosteric enzymes

Have both an active site for its substrate and an allosteric site for an effector

The hallmark of effectors is that when they bind enzymes, they alter the catalytic properties of the active site

Allosteric modifiers may be either the substrate itself or some other metabolite; for example: ATP inhibits phosphofructokinase even though ATP is also a substrate for the enzyme

Frequently catalyze a committed step early in a pathway

Often have 2 or more subunits, each with substrate binding sites that exhibit cooperativity

Allosteric activators cause the enzyme to bind substrate more readily; allosteric inhibitors cause it to bind less readily

Do NOT follow michaelis-mentin kinetics

A non-competitive inhibitor is, by definition, an allosteric inhibitor

An uncompetitive inhibitor will bind away from the active site but ONLY to an enzyme with a substrate already attached!

Covalent modification

Phosphorylation occurs on either Ser-OH, Thr-OH, or Tyr-OH groups

A “modified” enzyme means it is phosphorylated, “unmodified” means unphosphorylated Gibb’s Free Energy Change – determines the direction of the reaction

ΔG = ΔGP - ΔGS

If the reaction is negative (Gs > Gp) then the reaction will proceed forward toward equilibrium when ΔG = 0

Exergonic reactions have negative ΔG, while endergonic reactions have positive ΔG

ΔG provides no information about the reaction rate and is independent of the path of the reaction Equilibrium Constant: Keq = [C][D][enzyme] / [A][B][enzyme]

This shows that enzymes have no effect on reaction equilibrium Reaction Rate - determined by the activation energy, attaining activation energy

Carbonic Anhydrase

Enables red blood cells to transport CO2 from tissues to lungs

Zinc is essential cofactor; the reaction can occur without the enzyme, but it speeds it up significantly in both directions

One of the fastest known enzymes (1 molecule of enzyme can process one million CO2 per second) H2CO3 is formed from waste CO2 in tissues and dissociates so HCO3- reenters plasma for transport to the lungs; in the lungs HCO3- reenters the erythrocyte and makes carbonic acid again then CO2 and H2O; the CO2 diffuses into the alveoli

Because HCO3- is more soluble in plasma than CO2, it allows the blood to carry more CO2 to the lungs

Thrombin – converts fibrinogen found in plasma (essential for clotting) to fibrin; thrombin is produced from the inactive precursor prothrombin formed in the liver. In the presence of thromboplastin and Ca2+, prothrombin  thrombin

Thrombin acts on arginyl-glycine linkages (specific peptide bonds) to produce fibrin

Plasmin (AKA fibrinolysin) – dissolves fibrin; it is present in the blood as plasminogen until plasminogen activators (like urokinase in the kidney) convert it to plasmin, which cleaves the peptide bond in fibrin  breakdown and dissolution of clots

Prothrombin –--thromboplastin thrombin Fibrinogen ---thrombin fibrin

Fibrin ---plasmin fibrin breakdown and dissolution

Zymogens are the inactive precursors of proteolytic enzymes. Pepsinogen is a zymogen produced by the stomach. Those produced by the pancreas are: trypsinogen, chymotrypsinogen, procarboxypeptidase A/B, and proelastase.

Presence of amino acids in the duodenum stimulates release of CCK, which causes the release of pancreatic zymogens and contraction of the gallbladder to deliver bile salts. Trypsinogen  trypsin by enteropeptidase. Trypsin can then activate the zymogens of ALL the pancreatic proteases.

Trypsin cleaves peptide bonds with carboxyl groups from lysine or arginine (the basic amino acids) Chymotrypsin cleaves aromatic amino acids or leucine

Elastase cleaves at the carboxyl end of amino acids with small, unchanged side chains like alanine, glycine or serine

Carboxypeptidase B cleaves basic amino acids lysine and arginine

Pepsinogen is activated to pepsin by low pH in the stomach, or by other activated pepsin molecules.

NUCLEIC ACIDS

Nucleoside – a nucleotide without esterified phosphate groups CUT the Py

A=T/U (2 H-bonds), C=G (3 H-bonds)

Important point: the A=T pair promotes helix stabilization in DNA, but does not do so in RNA! Two forces hold the double helix together: hydrogen bonds and base-stacking interactions Transcription factors and other proteins bind in the major groove

A polynucleotide chain is formed by linking the 5’-hydroxyl group of one nucleotide to the 3’-hydroxyl group of the next with a phosphate in a condensation reaction (phosphodiester bond), so you get alternating phosphate and pentose residues

Backbone is made up of alternating phosphate and pentose units

The catabolism of a nucleotide results in no energy production as ATP (as opposed to catabolism of protein, lipid or carbohydrate)

# purine residues = # pyrimidine residues

DNA backbone is: hydrophilic, constant throughout the molecule, highly polar

The ribose phosphate portion of purines and pyrimidines comes from PRPP—synthesized from ATP and Ribose-5P from the PPP

Purines

Metabolic defects caused by antifolate drugs and anticancer drugs Purines are catabolized  uric acid (pure-ur)

Catabolic defects include: gout, hyperuricemia, G6P deficiency Pyrimidines

Metabolic defects caused by methrotrexate and other anticancer drugs Pyrimidines are catabolized to β-alanine and β-aminoisobutyrate Catabolic defects are rare; pyrimidines are highly water soluble Synthesis of Nucleotides

Catabolism of purines to Uric acid: Purines  xanthine ---xanthine oxidase  Uric acid Nucleic acids, continued…

Extremely polar and hydrophilic

Pentose sugar backbone linked by phosphodiester bonds at the 3rd and 5th carbons… from 5’  3’ the DNA chain goes:

P – O – CH2 (5’) – pentose sugar (deoxyribose) – O – P –O – CH2 etc… (see page 280)

For RNA it is the exact same except for an extra OH instead of an H and the base T is changed to U Hydrolysis of DNA yields: deoxyribose (ribose for RNA), phosphoric acid and nitrogenous base 3 types of RNA

rRNA – synthesized in the nucleolus; most prevalent RNA

tRNA – synthesized in the nucleus; carries amino acids from the cytosol to ribosomes; contains an anticodon

mRNA – synthesized in the nucleus; carries the genetic code from DNA to ribosome; least prevalent; has codons to DNA template

DNA organization

Nucleosome = DNA wrapped around a histone octomer, held by ionic bonds

Histones are composed largely of arginine and lysine (basic, +-charged amino acids that bind the (-) phosphate groups of DNA

Histones neutralize the large negative charge of DNA and stabilize DNA in a compact form Core histones: H2A, H2B, H3 and H4

Linker histones: H1 and H5

Chromatin – consists of nucleosomes, enzymes, gene regulatory proteins, and small amounts of RNA; nucleosome beads-on-string

Each chromosome contains a single molecule of DNA complexed with an equal mass of basic histone protein

Phosphorylation of serine and threonine residues in histones is part of replication, while acetylation of lysine in histones is used for transcriptional activation

Naked DNA  10 nm beads-on-a-string chromatin fibril  30nm chromatin fibril  non-condensed loops on chromosome scaffold  condensed loops on nuclear scaffold  chromosome

DNA Synthesis

After helicase unwinds the DNA molecule, topoisomerase secures the replication fork into leading and lagging strands

o Topoisomerases are responsible for unwinding supercoiled DNA to allow DNAP access to replicate

o Topoisomerases catalyze and guide the unknotting of DNA by creating transient breaks in the DNA then reform them

o The enzyme DNA gyrase reforms the supercoiled structure once the replication fork has passed

Single-strand binding protein stabilizes the two separate strands

DNA polymerase adds 5’  3’ continuously on the leading strand and in Okazaki fragments on the lagging strand

On the leading strand DNA polymerase III is able to synthesize DNA using the free 3' OH group donated by a single RNA primer and continuous synthesis occurs in the direction in which the replication fork is moving.

Along the lagging strand's template, primase builds RNA primers in short bursts. DNA

polymerases are then able to use the free 3' OH groups on the RNA primers to synthesize DNA in the 5'→3' direction. Exonuclease removes the nucleotide primers. DNA polymerase III adds new deoxyribonucleotides to fill the gaps where the RNA was present. DNA ligase then joins the deoxyribonucleotides together, completing the synthesis of the lagging strand.

RNA Synthesis (Transcription)

Occurs in the nucleus; DNA is unwound and replication fork is exposed

RNA polymerase binds to a promoter site on the DNA strand and synthesis occurs 5’  3’ Post-transcriptional modifications:

o Addition of a 5’ cap and a 3’ poly-A tail

o RNA splicing to remove non-coding introns and join the coding exons WIKI

Only one of the two DNA strands is transcribed. This strand is called the template strand, because it provides the template for ordering the sequence of nucleotides in an RNA transcript. The other strand is called the coding strand, because its sequence is the same as the newly created RNA transcript (except for uracil being substituted for thymine). The DNA template strand is read 3' → 5' by RNA polymerase and the new RNA strand is synthesized in the 5'→ 3' direction.

Unlike DNA replication, transcription does not require primers for initiation. However RNA polymerase does require the presence of a core promoter sequence in the DNA, which it is able to bind to in the presence of various specific transcription factors.

Promoters are regions of DNA which promote transcription and are found around -10 to -35 bp upstream from the start site of transcription. Core promoters are sequences within the promoter which are essential for transcription initiation. The most common type of core promoter in eukaryotes is a TATA box. The TATA box, as a core promoter, is the binding site for a transcription factor known as TATA binding protein (TBP). At the start of initiation in bacteria, the core enzyme (RNA polymerase) is associated with a sigma factor (number 70) that aids in finding the appropriate -35 and -10 basepairs downstream of promoter sequences. Transcription initiation is far more complex in eukaryotes, the main difference being that eukaryotic polymerases do not directly recognize their core promoter sequences. In eukaryotes, a collection of proteins called transcription factors mediate the binding of RNA polymerase and the initiation of transcription. Only after certain transcription factors are attached to the promoter does the RNA polymerase bind to it. The completed assembly of transcription factors and RNA polymerase bind to the promoter, called transcription initiation complex.

After the first bond is synthesized the RNA polymerase must clear the promoter. During this time there is a tendency to release the RNA transcript and produce truncated transcripts. This is called abortive initiation and is common for both eukaryotes[4] and prokaroytes[5]. Once the transcript reaches approximately 23 nucleotides it no longer slips and elongation can occur.

Unlike DNA replication, mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be produced from a single copy of a gene. This step also involves a proofreading mechanism that can replace incorrectly incorporated bases.

Prokaryotic elongation starts with the "abortive initiation cycle". During this cycle RNA Polymerase will synthesize mRNA fragments 2-12 nucleotides long. This continues to occur until the σ factor rearranges, which results in the transcription elongation complex (which gives a 35 bp moving footprint). The σ factor is released before 80 nucleotides of mRNA are synthesized.

In Eukaryotic transcription the polymerase can experience pauses. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure. Often the polymerase pauses to allow appropriate RNA editing factors to bind.

Bacteria use two different strategies for transcription termination: in Rho-independent transcription termination, RNA transcription stops when the newly synthesized RNA molecule forms a G-C rich hairpin loop, followed by a run of U's, which makes it detach from the DNA template. In the "Rho-dependent" type of termination, a protein factor called "Rho" destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex. Transcription termination

in eukaryotes is less well understood. It involves cleavage of the new transcript, followed by template-independent addition of A’s at its new 3' end, in a process called polyadenylation.

Translation

Occurs in the cytoplasm on ribosomes; a small ribosomal subunit binds to mRNA Prokaryotes have 70S ribosomes, eukaryotes have 80S ribosomes

Aminoacyl-tRNA synthetase adds each amino acid to the tRNA (based on the anticodon the tRNA is carrying); each enzyme molecule is highly specific for one amino acid!!! Not one

anticodon!!!

The complementary anticodon of tRNA binds to the mRNA start codon A large ribosomal subunit attaches, forming a complete ribosome Synthesis occurs in the 5’  3’ direction until a stop codon is reached No error-checking occurs during translation

WIKI

In activation, the correct amino acid (AA) is joined to the correct transfer RNA (tRNA). The AA is joined by its carboxyl group to the 3' OH of the tRNA by an ester bond. When the tRNA has an amino acid linked to it, it is termed "charged". Initiation involves the small subunit of the ribosome binding to 5' end of mRNA with the help of initiation factors (IF), other proteins that assist the process. Elongation occurs when the next aminoacyl-tRNA (charged tRNA) in line binds to the ribosome along with GTP and an elongation factor. Termination of the polypeptide happens when the A site of the ribosome faces a stop codon (UAA, UAG, or UGA). When this happens, no tRNA can recognize it, but releasing factor can recognize nonsense codons and causes the release of the polypeptide chain.

Many proteins undergo post-translational modification. This may include the formation of disulfide bridges or attachment of any of a number of biochemical functional groups, such as acetate, phosphate, various lipids and carbohydrates. Enzymes may also remove one or more amino acids from the leading (amino) end of the polypeptide chain, leaving a protein consisting of two polypeptide chains connected by disulfide bonds.

**If the anticodon on a tRNA is 5’ ACG 3’ then the corresponding mRNA codon would be 5’ CGU 3’

Point Mutations

Missense: codes for the wrong amino acid Nonsense: results in stop codon

Transverse mutation – a purine is replaced with pyrimidine, or vice versa

Transition mutation – a purine is replaced with another purine, or pyrimidine replaced with another pyrimidine

Frameshift mutation – deletion or insertion of 1 or 2 base pairs, changing the reading frame Repeat mutations – amplification of the sequence of 3 nucleotides

Restriction endonucleases – cleave DNA at various points to allow addition of various vectors, plasmids, or bacteriophages

AZT – a thymidine analog that is a competitive inhibitor of HIV reverse transcriptase

The use of THF acid (TFA) by several enzymes in purine and pyrimidine synthesis have made TFA metabolism a prime target for many antimetabolites such as methrotrexate used in chemotherapy.

UV light produces pyrimidine dimmers in DNA which then interferes with replication and transcription. These lesions are removed by exonuclease, which excises a 12bp fragment surrounding the dimer. DNAP-I then fills in the gap and DNA ligase seals it.

Degenerate nature of the genetic code – many amino acids are designated by more than one codon (same as redundancy)

Only Tryptophan, Methionine and Selenocysteine are coded for by just one codon; the other have 2 or more codons (synonyms)

AUG = initiation codon—codes for methionine, so all proteins begin with Met!! UAA, UAG and UGA – termination codons (AKA stop or nonsense codons)

Southern Blotting – used to detect mutations in DNA and also identify DNA restriction fragments; it uses restriction enzymes and DNA probes

Enzymes used in recombinant DNA technology are: restriction endonucleases, DNA ligases, DNAP-I, reverse transcriptase, exonucleases

Products of current recombinant DNA technology include: human insulin, anticoagulants (tissue plasminogen factor), erythropoietin, hGH

Bacterial cloning vectors include plasmids, bacteriophages, and cosmids.

MEMBRANES SECTION

Phospholipids (50%), steroids and glycolipids make up the bulk of the lipid membrane; examples of phospholipids include sphingomyelin, phosphatidyl choline (lecithin) and phosphatidyl ethanolamine (cephalin)

Small, nonpolar molecules easily pass through

o Only water and gases can easily pass through the bilayer, plus some small nonpolar

molecules (oxygen, CO2, alcohol); large or polar molecules (ions, glucose, urea) cannot cross the bilayer without assistance from active transport systems

Integral proteins and lipids noncovalently linked to allow movement; they’re held by hydrophobic interactions with the lipids

The “fluid mosaic” is lipid + protein

Attractive van der Waals forces between hydrocarbon chains and repulsive forces between polar head groups form the bilayer

Membrane lipids:

o Phospholipids: phosphoglycerides and sphingomyelin o Glycosphingolipids

o Cholesterol

Integral proteins: embedded in either 1 or both portions of the bilayer

Peripheral proteins: weakly bind to hydrophilic head groups on inner or outer membrane surfaces Peripheral proteins are embedded at the periphery, integral proteins span from one side of the membrane to the other side; integral proteins are associated with the hydrophobic phase of the bilayer

Peripheral proteins seldom flip from one side of the membrane to the other, but they move laterally often

The proteins of the cell membrane function as transporters, enzymes, receptors and mediators Carbs attach to proteins and lipids only on the external surface

NEUROPHYSIOLOGY

Thalamus

Ovoid mass of gray matter; part of diencephalon

Ascending input of all sensory stimuli except olfactory is relayed through the thalamus to the cerebral cortex

Descending output from the cortex can also pass through or synapse within the thalamus Hypothalamus

Collection of nerve cells (nuclei) lying subcortical at the base of the cerebrum that controls homeostatic processes

Often associated with the ANS, the hypothalamus regulates: o Autonomic functions: GI and cardiac activity

o Body temperature - the posterior hypothalamus controls both heat generation and heat loss o Appetite, water balance, sexual activity, sleep, emotions

o Pituitary secretions: releasing endocrine hormones to the pituitary

Stimulation of the posterior hypothalamus by a reduction in core temperature will produce shivering Heat Transfer - emission of heat as infrared rays; the body is continuously exchanging heat by radiation with objects in the environment

Conduction – flow of heat energy through direct contact between two objects

Convection – movement of heat by currents in the medium; air molecules exchange heat with body surface and continue to breeze past

Evaporation – includes insensible water loss via respiration and skin, sweating, and active fluid secretion by sweat glands

More effective in low-humidity environments Limbic System

Primitive brain area found deep in the temporal lobe; it communicates with the cerebral cortex to initiate basic drives:

o Hunger, aggression, emotional feelings, sexual arousal It also screens all sensory messages traveling to the cerebral cortex Consists of the:

o Hippocampus – functions in learning and memory

o Amygdala – center of emotions, communicates with the ANS, oxytocin and ADH receptors (for negative feedback)

Motor Control and Coordination

Basal Ganglia – located deep to the cerebral cortex, they control complex patterns of voluntary motor behavior Caudate nucleus

Putamen Globus pallidus Substantia nigra

Subthalamic nuclei

**Parkinson’s, Huntington and Wilson disease are disorders of the basal ganglia; the person has unwanted movements.

**The caudate nucleus and putamen are interposed with the anterior limb of the internal capsule; collectively they are known as corpus striatum.

**The putamen and globus pallidus together resemble a lens and are called the lenticular nucleus

**The cerebral cortex sense info to both the basal ganglia and cerebellum, and both send info back to the cortex via the thalamus. The output of

the cerebellum is excitatory, while the basal ganglia output is inhibitory.

**The basal ganglia (or subcortical nuclei) are the major constituents of the extrapyramidal system Cerebellum – divided into two lateral hemispheres with a middle portion called the vermis

Maintains muscle tone, coordinates muscle movement, controls balance

Basal ganglia and cerebellum modify movement on a minute-to-minute basis; output of the cerebellum is excitatory whereas that of the basal ganglia is inhibitory!!! They work together to achieve smooth, coordinated movements. Movement disorders result from aberration to either of the systems. Motor Pathway:

Precentral gyrus (M1)  upper motor neuron  internal capsule  corticospinal tract  cerebral peduncles  pyramids of medulla (fibers cross)  ventral horn of spinal cord  lower motor neuron  muscle

Brainstem

Midbrain (mesencephalon) – connects dorsally with cerebellum; large voluntary motor nerve tracts pass through the midbrain

o Location of CN III and IV nuclei plus substantia nigra

Pons – between the midbrain and medulla; connects to cerebellum posteriorly o Location of CN V and VI nuclei, motor nuclei of VII, exit points for CN’s 5-7

Medulla Oblongata – contains important regulatory centers for swallowing, cardiac function, vasomotor, respiratory

o Location of nuclei for CNs 8-12 PNS

Somatic NS

o Cranial nerves + 21 pairs of spinal nerves

o Motor: innervates skeletal muscle with no synapse in peripheral ganglia; uses 1 efferent neuron from CNS to end organ

o Sensory: synapse within the dorsal root ganglion prior to CNS entry  Touch, movement, temperature, pain

ANS – no action on skeletal muscle; motor neurons synapse within autonomic ganglia; uses 2 efferent neurons from CNS  effector

Autonomic Nervous System

Pregangionic neuron in CNS  ganglion (cell bodies of postganglionic) outside CNS  postganglionic neuron outside CNS  effector

Autonomic ganglia – collections of cell bodies of postganglionic neurons

o Sympathetic – sympathetic chain ganglia near the spinal cord; short preganglionic, long postganglionic

o Parasympathetic – ganglia at or within the organ; long preganglionic, short postganglionic Exception to rule: sympathetics to sweat glands and blood vessels within skeletal muscle are cholinergic @ muscarinic receptors

Parasympathetic

Composed of CN nuclei and S2-S4

Preganglionic neurons are cholinergic  nicotinic receptors on postganglionic neurons (always excitatory) Each preganglionic parasympathetic neuron synapses on only a few postganglionic parasympathetic neurons

Postganglionic neuron is cholinergic  muscarinic receptors in tissue (can be excitatory or inhibitory)

Postganglionic receptors: NEED TO FIND OUT

THE TRUTH ABOUT THESE!!!!!!

 Located on all effector organs innervated by parasympathetic division, and some innervated by the sympathetic division

o Nicotinic

 Located at the ganglia in both divisions of the ANS

 N1 – found in autonomic ganglia; excitatory only, leading to nerve transmission/postganglionic activation

 N2 – found in motor end plates (@ NMJ); excitatory  muscle contraction ?? WIKI: ACh has two types of effects. The first type is termed muscarinic, which is the parasympathetic effect on the secretory exocrine gland and smooth and cardiac muscles upon their corresponding receptors. The other type of ACh effect is termed nicotinic, which is on the skeletal (voluntary) muscles and not considered to be part of the peripheral autonomic nervous system.

All preganglionic autonomic neurons (both ANS branches) and all postganglionic parasympathetic neurons are cholinergic

Cholinergic effects of preganglionic autonomic systems (at the ganglia) are always excitatory; effects of postganglionic cholinergic fibers are either excitatory or inhibitory, depending on the end organ

**Atropine blocks the action of Ach!

Sympathetic

Composed of spinal segments T1—L3

Exerts widespread effects due to high ratio of postganglionic:preganglionic fibers; each preganglionic neuron branches extensively

Postganglionics – bind adrenergic receptors in tissue, except sweat glands and skeletal muscle blood vessels Three cervical sympathetic ganglia supply the head and neck

Adrenergic receptors

o Membrane-bound G-protein receptors on autonomic effector organs o NE stimulates mainly alpha receptors

o Epinephrine stimulates both alpha and beta equally

Monoamine oxidase (MAO) – an enzyme that catalyzes oxidative deamination of monoamines (including NE, serotonin and Epi); the deamination process increases breakdown/metabolism of excess NT’s that accumulate at postsynaptic terminals

Alpha-1 – excitatory; cause vasoconstriction or contraction in vascular smooth muscle of the skin, mucosa and GI Alpha-2 – found at presynaptic nerve terminals, platelets, fat cells, GI tract wall; inhibitory (relaxation or dilation) Beta-1 – found in the heart, exctitatory—increases HR and contractility

Beta-2 – inhibitory; found in skeletal muscle and smooth muscle; causes vasodilation/bronchodilation **NE stimulates mainly alpha receptors, Epi stimulates both alpha and beta receptors!

**Beta-blockers are used to treat arrhythmias and other cardiac anomalies through reduction in rate/force of heart contractions

Summary of Autonomic Effects Sympathetic Parasympathetic

Pupils Mydriasis (dilation) Miosis (contraction)

Salivation Thick Watery (ready to eat)

Bronchi Bronchodilation Bronchoconstriction

Adrenal Medulla Causes Epi and NE release No effect

SPINAL TRACTS

Axons of a tract have the same origin, termination and function; they’re often named for their origin and termination (e.g. spinothalamic)

Sensory tracts (ascending)

o Spinothalamic – pain and temperature

o Dorsal column, medial lemniscus – touch, pressure, vibration, proprioception Motor tracts (descending)

o Corticospinal (pyramidal) o Extrapyramidal

Receptor  peripheral nerve  DRG  spinal cord  spinal tracts  brainstem nuclei  thalamus  cortex Receptors – 2 broad types according to location of stimuli

Exteroreceptors – receive external stimuli from the body surface: touch, pressure, pain, temperature, light, sound

Interoreceptors (visceroreceptors) – receive input from the internal environment of the body: pressure, pain, chemical changes

o Proprioceptors – type of interoceptor; separate from visual input (which is kinesthetic sense); located in muscles, joints and tendons… communicate with the vestibular apparatus **Types of joint receptors

Nonencapsulated – free nerve endings relaying pain

Encapsulated – Pacinian (vibration, pressure) and Ruffini (stretch) Neuromuscular spindles – stretch

Neurotendons – tension Nonencapsulated

Free nerve endings – pain primarily, but also touch, pressure, tickle, temperature; found in epithelial cells, skin, cornea, GI tract, CT, haversian system of bone, dental pulp

Hair follicle receptors – mechanoreception; bending hair stimulates touch; fiber winds around the hair (transduce hearing and balance)

Merkel’s disc (considered nonencapsulated) – tactile touch, pressure; in hairless skin like the fingertips it senses pressure

Encapsulated

Meissner’s corpuscles – mechanoreceptors allowing 2-pointdiscrimination; in the dermal papilla of skin; the “capsule” is an ovoid stack of Schwann cells

Pacinian corpuscles – mechanoreceptors sensing vibration, pressure; in the dermis, subcutaneous tissue, ligaments and joints; concentric lamellae of flattened cells

o Sense deep cutaneous pressure, vibration, proprioception

Ruffini’s corpuscles – stretch; in the dermis of hairy skin… large unmyelinated fibers ending within bundles of collagen fibers

o Sense continuous touch or pressure, and are found primarily in the dermis of the fingers

*Afferent nerve endings in joints and tendons are called proprioceptors.

*Exteroreceptors – sensory nerve endings associated with the skin that provide info about the external environment *Visceroreceptors provide info about the internal environment

Somatosensory Pathways

Sensory Tracts (ascending) Figure on page 302:

Spinothalamic Tract (anterolateral system)

o Lateral spinothalamic tract – transmits pain, temperature and crude touch from the opposite side; originates in posterior gray column of opposite side and terminates in the thalamus o Anterior spinothalamic tract – transmits crude touch and

pressure; same origin and termination

Sensory nerve  dorsal horn of spinal cord  cross to opposite side of cord  ascend contralateral spinal cord (through anterior or lateral white matter tracts  thalamus  somatosensory cortex

Dorsal Column, Medial Lemniscus System – conveys touch, pressure and vibration

Sensory nerve  dorsal horn  ascends ipsilateral spinal cord in posterior columns (fasciculus gracilis for lower extremities and fasciculus cuneatis for upper extremities)  synapse in the medulla (nucleus gracilis or nucleus cuneatis)  then decussage and ascend the contralateral brainstem in the medial lemniscus  thalamus  somatosensory cortex

**fasciculus gracilis and cuneatus are the largest ascending tracts of the spinal cord; they arise from either cells of the spinal ganglia or from intrinsic neurons within grey matter that receive primary sensory input

Fasciculi gracilis and cuneatus – discriminating touch and pressure, including vibration, stereognosis, and 2-point discrimination; also conscious kinesthesia; originate in the spinal ganglia of the same side and terminate in the medulla

Anterior and Posterior Spinocerebellar – unconscious kinesthesia; go from anterior/posterior gray columns to the cerebellum

Somatosensory cortex (postcentral gyrus) – representation is the homunculus; huge representation of lips, fingertips and hands

- Looking at the lateral brain, the face and tongue are near the bottom of the postcentral gyrus (just above the temporal lobe) and the trunk is near the top of the brain (face, tongue, hand, trunk as you move up)

Descending Motor Tracts (efferent pathways)

Motor area of the brain (precentral gyrus)  upper motor neurons (= descending tracts)  lower motor neurons  skeletal muscle

- Upper motor neurons originate in the white matter of the brain and form 2 major systems: corticospinal and extrapyramidal

- The pyramidal motor system moves your muscles under the direction of your mind; extrapyramidal controls muscle tone, posture and activity without conscious thought

Corticospinal Tract (pyramidal system) – Seen on the right:

o Originates from pyramid-shaped cells in the premotor, primary motor and primary sensory motor areas (80% of cell bodies are in precentral gyrus, AKA the motor strip)

o Direct and monosynaptic tract; axons do not synapse until their final destination in the brainstem or spinal cord

o Fibers of the pyramidal tract that synapse with CN’s form the corticobulbar tract

o 2 components: lateral (70-90%) and anterior/ventral (10-30%) o Travel via M1 through the internal capsule to the medulla

o Decussate in the medulla and continue down opposite side of spinal cord  ventral horn  lower motor neurons  muscles

o Right brain controls left somatic muscles; controls fine, skilled movements of skeletal muscle

o Called the pyramidal system because fibers of the corticospinal tract form pyramids in the medulla

Lateral Corticospinal (crossed pyramidal – 90%)

 Voluntary movement, contraction of individual or small groups of muscles, particularly those moving hands, fingers, feet and toes of the opposite side

 Originates in motor areas of cerebral cortex on opposite side from tract location in cord; ends in lateral columns

Anterior Corticospinal (direct pyramidal – 10%)

 Same as lateral corticospinal but mainly muscles of the same side  Origin is motor cortex but on same side as the location of the cord Extrapyramidal System – collection of smaller tracts

o This motor system works with the ANS to help with posture and muscle tone, and has more influence over midline structures than those in the periphery

o Involved in gross, rather than fine movement, including facial expression o In contrast to pyramidal, it is an indirect, multisynaptic tract

o Relies on dopamine to maintain proper muscle tone and motor stability

o All of the nuclei are synaptically connected to one another, the brainstem, the cerebellum, and the pyramidal system

 Rubrospinal – originates in the red nucleus; the cerebellum sends messages to the spinal nerves along this tract. Information flows from the superior cerebellar peduncle to the red nucleus and finally to the spinal nerves. This info is important for somatic motor control and regulation of muscle tone for posture.

 Coordination of body movement and posture

 Reticulospinal – originates in the reticular nuclei of the pons and medulla to the spinal nerves; involved in somatic control like rubrospinal, but also plays a role in control of autonomic functions

 Lateral reticulospinal – facilitatory influence on motor neurons to skeletal muscle

 Medial reticulospinal – inhibitory influence on motor neurons to skeletal muscle

 Olivospinal –

 Vestibulospinal – originates in vestibular nuclei of lower pons and medulla to the spinal nerves; involved in balance

 Mediates the influences of the vestibular organ and cerebellum upon extensor muscle tone

 Origin is the lateral vestibular nucleus (4th ventricle)

 Tectospinal – points of origin throughout the brainstem, but especially the midbrain, and ends in spinal nerves; involved in control of the neck muscles (tec = neck)

o Travel from the premotor area of the frontal lobe (and other areas) to the pons; decussate in the pons and continue down the opposite side of the spinal cord  ventral horn  lower motor neurons  muscles

o Again, right brain controls left lower motor neurons; this time it controls gross motor movement, posture and balance.

Spinal Cord Lesions

- Lesion on one side causes:

- Same side motor loss (corticospinal tract)

- Contralateral pain and temperature loss (spinothalamic tract)

- If you hemitransect the right side of the spinal cord, you lose right-side motor control and left side pain and temperature sense.

Neurophysiology

- K+ leak out of the cell is the most important determinant of RMP!!!

- Visceral smooth muscle and cardiac pacemaker cells lack a stable resting membrane potential

- Na/K pump creates the gradient that allows K+ leak to occur; 2K+ in for every 3Na+ out = net loss of + from the cell

- Smooth muscle and cardiac pacemakers lack a stable RMP - AP threshold is about +20mV

- K+ conductance (channels stay open and efflux is greater than at rest) is what causes hyperpolarization after an AP

- Hyperpolarization is responsible for the relative refractory period; an influx of Cl- will also hyperpolarize and make AP less likely

Local Anesthetics

- Block sodium channels, decreasing Na+ permeability

- Bind to the inactivation gates of fast, voltage gated Na+ channels, keeping them closed and prolonging the absolute refractory period

- Decrease excitability so can’t generate and AP and there is no nerve impulse conduction - K+, Cl- and Ca2+ conductances are unchanged

- Affect small unmyelinated C fibers first, then small myelinated (pain, temp) then larger A-fibers (touch, proprioception, Golgi)

Inhibitory NT’s – increase membrane permeability to Cl- or K+; examples are: glycine and GABA (both open Cl- channels/increase Cl- permeability)

Spatial summation – 2 inputs arrive at the same time from multiple presynaptic fibers

Temporal summation – 2 inputs arrive at the postsynaptic neuron in rapid succession; ↑ frequency of impulses from a single presynaptic fiber

Nerve Conduction

- Saltatory conduction conserves energy because only Ranvier nodes depolarize, so less energy is required for Na+/K+ ATPase to reestablish resting ion gradients; the pumps only have to work at Ranvier nodes instead of everywhere

o It allows repolarization to occur with less transfer of ions

o Myelin decreases membrane capacitance and increases membrane resistance (good—for saltatory conduction)

- Nodes of Ranvier are located every 0.2 – 2mm along the myelin sheath

- Continuous conduction occurs in unmyelinated fibers and is slow (1m/sec vs. saltatory 100m/s) - Conduction velocity depends on the diameter of fiber; bigger diameter means more resistance to

flow and faster velocity Problems with Nerve Conduction

- Wallerian Degeneration – the axon is cut, and the axon remnant distal to the cut degenerates; regeneration of axons is possible if the endoneurial sheath is intact (when this sheath is intact and regeneration is possible, it is called Axonotmesis).

o Regeneration occurs at a rate of 2-4mm/day

o If the cell body is irreversibly injured, the entire neuron degenerates

- Neuropraxia – transient block (bruise) that causes incomplete paralysis or loss of sensation with rapid recovery

- Neurotmesis – complete transaction of nerve trunk results in: o Motor: flaccid paralysis and atrophy of the organ o Sensory: total loss of cutaneous sensation

Neurilemma – sheath of Schwann; thin membrane spirally enwrapping the myelin layers of nerves or axons of some unmyelinated nerves; all axons of the PNS have a sheath of Schwann cells (and thus a neurilemma made up of the outer layer of Schwann cells)… when a Schwann cell is wrapped successively around an axon, it becomes a myelin sheath.

**If the nerve led to skeletal muscle, the muscle atrophies in the absence of innervation but regrows when the connection is reestablished.

**The CNS has no neurilemma, so regeneration is more difficult.

Chemical synapses are more common than electrical synapses. Chemical NT’s can be:

- Small molecule NT’s contained in vesicles – glutamate, GABA, glycine, Ach, NE, Epi - Neuropeptides (large dense vesicles) – somatostatin, endorphins, enkephalins, opioids

Electrical synapse – cytoplasm of adjacent cells is connected by gap junctions; rare in the CNS but common in cardiac/smooth muscle; also important in embryonic development (morphogenic gradients)

Neuromuscular Junction

- Ach  nicotinic receptor  Na+ opens on motor end plate  depolarizes  voltage-gated Na+ channel on sarcolemma open  AP stimulated  AP travels down transverse tubules  Ca2+ released from SR  contraction

- Ach is synthesized in the presynaptic terminal of the motor neuron: o Acetyl-CoA + choline ---choline acetyltransferase ----> Ach - Breakdown is by acetylcholinesterase located on the muscle end-plate:

o Ach ----AchE---> acetate + choline

o If AChE’s are inhibited, you get prolongation of the end-plate potential whicn can lead to tetany

Special Senses

- Anterior segment of the eyeball is full of aqueous humor; it is divided into anterior and posterior chambers by the iris

- Posterior segment is filled with vitreous humor

- Choroid – very vascular lining of the inner eyeball beneath the retina

- Miosis occurs in response to light, narcotics, parasympathetic stimulation, pathologic conditions - Mydriasis occurs in response to low light, sympathetic, drugs or disease

- Ciliary body – made up of 3 muscles and the iris; the muscles accommodate the lens (they contract, ligaments loosen, lens fattens); the ciliary body also produce aqueous humor,and holds the lens in place

- Four photopigments: rhodopsin, red, green and blue; each photopigment contains: o Opsin – protein bound to retinal; the difference among opsin molecules allows a

photopigment to have specificity for a particular color of light

o Retinal – a chromophore molecule; retinal is constant among all photopigments and is produced from vitamin A

Light  retina rods and cones  bipolar neurons  ganglion cells  optic disc  optic nerve  optic chiasm  lateral geniculate body of the thalamus  optic radiations  visual cortex (area 17) and visual association cortex (18, 19)

Good picture on page 316!!

Lesions along the visual pathway - Left anopsia

- Bilateral hemianopsia

- Right homonomous hemianopsia - Right hemianopsia with macular sparing

Myopia (nearsighted) – the eyeball is too long or the cornea is too steep; the focal point of far objects is focused in front of the retina; near objects are focused correctly ; treatment is concave lenses

Hyperopia (farsighted) – eyeball is too short or the lens cannot become round enough; the focal point of near objects is focused behind the retina; distant objects are focused correctly; corrected with convex lenses Astigmatism – curvature of the lens is not uniform; treatment is with cylindrical lenses

Presbyopia – loss of lens elasticity with age; the eye cannot focus sharply on nearby objects b/c lens doesn’t fatten up; treated with bifocals

HEARING

- External ear

o Auricle (pinna)

o External auditory canal/meatus – contains hair and cerumen; serves as a resonator and conduit

- Middle ear

o Tympanic cavity – surrounds the bones of the middle ear; it is an air filled cavity in temporal bone

 Auditory tube

 Ossicles : eardrum  malleus  incus  stapes  oval window - Inner ear – formed by a bony labyrinth (perilymph) and membranous labyrinth (endolymph)

**endolymph is what stim. Hair cells