Human Bioscience

Vitamin A (retinol)

• Not synthesized by humans; hence, must depend ultimately on plant pigment, β-carotene., eat a plant or an animal that ate a plant • Deficiency leads to night blindness (nyctalopia); retinal rods (more prone to harm) do not respond normally to dim light. cone cells also depent on vit A, about 20x more rods than cones, but rids get affected way more often and more quicly than cones • Chromophore of visual pigment molecule, rhodopsin (needs Vit A to function). Vitamins that are fat soluble - ADEK, water soluble - B's and C

Erythrocyte

• Of total protein, ~ 1/3 has MW > 200,000 - spectrin. • ~ 1/3 has MW > 100,000 - anion channel (anion exchange protein; Cl- / HCO3- exchanger), both have to move through • Remainder - at least 9 components with MW 15 - 90 kD; major one is glycoprotein called glycophorin.

• Organization of skeletal muscle

• Organization of skeletal muscle •Fascicles --> •Fibers (muscle cell) --> •Myofibrils --> •Muscle filaments (in regular arrangement) --Thick --Thin tendon connects muscle to bone

Phospholipases and Sphingolipids

• Phospholipases - catalyze degradation of phospholipids. • Sphingolipids - involved in determining human blood groups; e.g., sphingomyelin. • Some inherited genetic diseases (e.g., Tay-Sachs disease, usually fatal around ages 1-2) result from abnormal breakdown of certain membrane lipids.

Reduction Potential

• Reduction potential (E) - Affinity for electrons (substance being reduced, accepting electron. The higher the E, the higher the affinity); higher E, higher affinity - Electrons transferred from lower to higher E ΔE°' = -(RT/nF)ln (Keq) = ΔG°'/nF ΔE°' = E°'(e- acceptor) - E°'(e- donor) ΔG°' = -nFΔE°' For negative ΔG need positive ΔE E(acceptor) > E(donor)

Glucose Metabolism

• Regulation different in muscle vs. liver. • In muscle, main function is to produce ATP. • In liver, main function is to keep blood glucose level constant. Produces and exports glucose when cells need it; imports and stores glucose when there is dietary excess.

Blood Clotting

• Series of zymogen activations; enzymatic cascade. • Very small amounts of initial factors trigger cascade b/c of catalytic nature of activation process. • Large amplification; assures rapid response to trauma. • Both pathways needed for proper clotting; clotting disorders can be caused by a deficiency of a single protein in one of the pathways.

Two great classes of living cells

-Autotrophic cells - CO2 is carbon source; e.g., photosynthetic cells and some bacteria. -Heterotrophic cells - cannot use CO2 but must obtain C from environment in reduced form, such as glucose; e.g., cells of higher animals and most microorganisms.

Energy sources of cells

-Energy sources of cells - light vs. oxidationreduction reactions. Require a transfer of electrons (redox reactions) -Aerobic, get O2 via blood vessels (different cells and different tissues can get most of energy anaerobically. Ex cornea and lens) vs. anaerobic. -cornea - gets most anaerobically, 80% (has peripheral blood vessels) -Lens - metab done anaerobically

Red/Slow

-Myoglobin -Rich in mitochondria -Small fibers -Rich in capillaries -Slow contraction speed -Aerobic metabolism -High resistance to fatigue -High proportion in postural muscles in the back

White/Fast

-Myoglobin absent -Mitochondria sparse -Large fibers -Capillaries less profuse -Rapid contraction speed - Anaerobic metabolism - Low resistance to fatigue - High proportion in muscles necessary for fast movements like in joints biceps

Smooth muscle excitation Contraction Coupling, Contraction

-Myosin Light Chain Kinase (MLCK) MLCK is a regulatory light chain on the neck of myosin -Activated MLCK phosphorylates Myosin molecule and lifts inhibition by Calponin and Caldesmon -When phosphorylated, regains ATP activity and can bind actin -10‐20 times slower than skeletal muscle contraction due to increased number of steps

Junctional complexes

-Tight junctions (aka occluding junctions or zona occludens) -Adherens junctions (aka zonula adherens) -desmosomes (aka macula adherens) -Hemidesmosomes -Gap junctions

malonate

-added malonate (a compound inhibitor to succinate dehydrogenase), blocked reaction -confirmed that succinate was present --> inhibited the enzyme -anything before blocking accumulates, anything after block stops -blocked at different points to determine sequence

DNP

-an uncoupler, weak acid -moves across mito space, produces H+ -diminishes electrical and chemical potential by moving H+ inside mito -if uncoupler just changes gradient, diminishes electrical but not chemical gradient (however DNP affects both)

High energy vs low energy phosphate compounds

-can give phosphate to ADP --> ATP, or take phosphate from ATP --> ADP

disfunctional enzyme in metabolism

-can only really measure A and Arg in normal system, when forms B it quickly converts to B and so on -possible solutions: inhibit A so you do not get a build up of intermediate (which may be toxic) -could also attempt to solve conversion of D --> Arg (in mut 1)

Velocity change when you increase ADP

-cannot use MM equation because of sigmoid shape

ETC

-chemical potential - change in [H+] -electrical potential - inside becoming more negative relative to outside

Latchbridge formation

-gives constant tension •When myosin is dephosphorylated when still attached to actin •Sustained contractions •Slow cycling rate •Minimal ATP requirement

glucokinase

-glucokinase important when eating a lot of sugar or diabetic (have hyperglycemia)

image of ATP production in mito

-hyperpolarization increases the potential across the gradient

in vivo vs in vitro reactions

-in vitro - many more water molecules, they interact with enzymes, possibly slowing down reaction to a factor of 10^9. Protein folding from scratch also takes hours -in vivo - often in a much more hydrophobic reaction (much more efficient. Protein folding from scratch takes about 2 minutes, must be an enzymatic system that increases rate of rxn in cell

Zymogen

-inactive precursor to active form of enzyme -two peptide bonds must be broken (via a protease that breaks peptide bonds adj to an aromatic AA residue) for enzyme to become active. the disulfide bonds go from all intramolecule to two intramolecule and two intermolecule ( hold together the 4 peptide chains) -cell secretes enzyme in an inactive form for several reasons, one maybe so it can be secreted in one area, travel to another, and become activate where necessary

Smooth muscle thick filaments

-no regular arrangement of thick and thin filaments. -spontaneous generation of AP is random, monitored by ion pumps, no standard, resting potential is constantly changing 2 heavy chains (head and neck regions), myosin molecule -Head contains -->ATPase activity -->Actin binding site -->Sidepolar arrangement (allows shortening to a greater degree) head faces in opposite direction, thin filaments slide past each other during contraction, allows for greater level of shortening 2 pairs of light chains •Each pair contains -->1 essential light chain -->1 regulatory light chain (MLC - Myosin Light Chain), activates myosin light chain kinase

Phospholipids structure

-one position is usually saturated -two position is usually unsaturated -head group distinguishes among phospholipids

Glycerides

(acylglycerols; neutral fats) • Fatty acid esters of glycerol; mono-, dior triglycerides.

second rate determining step

-main control point determining if metabolism is turned on or turned off -metabolism is stopped if you have enough ATP -high levels of ATP turn off rxn -high levels of ADP turn on rxn --> exception - in the lens of the eye (unlike most tissues), the first reaction involving glu --> G6P is major regulator. It is very sensitive to high levels of glucose

Sickle Cell Anemia

-most common in African descent • Genetic disease; 4/1000; autosomal (not sex linked); recessive; homozygous (these two go together) • Heterozygotes have sickle cell trait; 1/10. • Mutated Hb molecules cannot bind O2. Solubility of deoxyHb lo; deforms cells. • Sickling can create vessel blockage, esp. at lo [O2].

entire metabolism image

-most products end up as Acetyl-CoA -TCA cycle generates electrons via H ions. Electrons enter electron transport chain to generate ATP

lateral transport modes on the cell surface

A. transient confinement by obstacle clusters, something is moving in a way that suggests it is bumping into things, but there is nothing actually there B. or by the cytoskeleton, actual movement C. directed motion, has to go from one side of cell to the other D. free random diffusion

Epithelia, Functions

Functions • Protection • Strength • Secretion • Absorption

gap junctions - Gating factors, Permeability

Gating factors • Ca2+ • pH • Phosphorylation • Membrane potential changes • Potential difference across the junction Permeability • Ions • Water • 1000 MW proteins and molecules

smooth muscle membrane systems

•Caveoli, pits in CM --> Saclike inpockets in place of T‐tubule --> Contain L‐type calcium channels • Ca2+ channel on surface of Sarcoplasmic reticulum --> Ca2+ induced Ca2+ release (CICR) channels --> Inositol triphosphate‐gated (IP3‐gated) Ca2+ channels, can open up calcium channels, increase cytoplasmic calcium

Woven bone

•only see after a fracture •Allows breaks to heal quickly •Produced by osteoblasts rapidly •Haphazard arrangement of collagen fibers •Appearance of fabric - very irregular •Mechanically weak, but does it's job to fix break quickly •Occurs in all fetal bone and gradually replaced by mature (lamellar) bone •In adults it is created after fractures or in Paget's disease

Bone types

Woven bone, Lamellar bone

Steps in bone remodeling

around 20% of bone is being turned over

Acid-Base Catalysis of Organic Reactions

(level of importance increases from 1 to 3) 1) specific acid-base catalysis; ~ [H+] or [OH-]. rate enhancement relative to [H+] or [OH-] 2) general acid-base catalysis; ~ [proton donor] or [proton acceptor]. rate is proportional to [proton donor] or [proton acceptor] 3) (most important) catalysis by Lewis acids (e- pair acceptor, electrophilic and positively charged) and bases (e- pair donor, nucleophilic with R groups with unshared e-); electrophilic and nucleophilic.

Phospholipids

(phosphoglycerides), basic component of CM • Found almost exclusively in cell membranes. • All are amphipathic; contain polar head group and two nonpolar hydrocarbon tails. • Form micelles in H2O.

Thin filaments

- Actin, 3 components •G actin (globular) --> F Actin (2) --> Double helix •2 regulatory proteins in the chains •Tropomyosin (double helix) •Troponin complex, 3 proteins •Troponin C - binds calcium •Troponin I - inhibitory, inhibits binding of acting to myosin at rest •Troponin T - connects to tropomyosin. holds tropomyosin in a place where it blocks myosin binding site during rest

Energy source to skeletal muscles

- Creatine phosphate - quick source of energy, quickly depletes ATP - Glycolysis-Lactic acid system (anaerobic) - gives 2 ATP - Aerobic metabolism (oxidative phosphorylation) - takes longest time to generate, most amount of ATP

Disease of muscles cont

- Metabolic myopathies (defects with metabolic enzymes) -Myotonia --> Prolonged relaxation after a contraction --> Na+ and Cl- channel related disorders

Disease of muscles - Muscular dystrophy

- Muscular dystrophy, generalized disfunction of dystrophin (dystrophin-glycoprotein complex disorders). dystrophin connects microfibrils to proteins in CM. complex connects to laminen which connects to ECM --> Duchenne's muscular dystrophy - dystrophin absent ---->Utrophin (usually in NM junction) upregulation can replace dystrophin function -->Becker's muscular dystrophy - altered or reduced dystrophin -->Limb girdle muscular dystrophy - sarcoglycan gene mutations

Thick filaments

- Myosin, around 200 •2 heavy and 4 light chain (yellow and green) polypeptides •Head (ATP and actin binding sites, on heavy chain), Neck (two light chains) and Tail (forms alpha helix) regions •2 bundles of 100 myosin molecules joined tail to tail

simple sugars as reducing agents

they are oxidized, causing something else to be reduced

structure of integral protein

- green = carbohydrates for recognition site -green + circle = entire glycoprotein -red and blue = charged AA

pentose shunt

-10-15% of glucose -generates reducing equivalents (NADPH) from G6P -provides energy for many biosynthetic reactions that require energy --> 85% of glucose goes down citric acid cycle

Electron transport chain inhibition

-2 electrons produces 3 ATP if enter ETC at the beginning. -If block at site 1, can still produce 2 ATP of electrons enter at Q

types of glycerols

-3 carbons, 3 OHs -mono (one FA attached) and di (2 FA attached)- polar, free OH, readily forms micelles -tri - non-polar, all 3OH groups tied with FAs. source of FA in our diet (over 98% of what we eat) FAs need to come off vi hydrolysis

Lipids

• H2O insoluble; extracted with nonpolar solvents. • 4 general functions: 1) Structural components of cell membranes (most important) 2) Intracellular storage of fuel for metabolism 3) Transport form of metabolic fuel 4) Protective components

Hemidesmosomes

• Hemidesmosomes • Only one half of the desmosome - just cell on top • Cell membrane connected to the extracellular matrix (not other cells) • Integrin is the connecting protein --> provides strength as well

Fluid Mosaic Model

• Integral vs. peripheral membrane proteins • Membranes assymetrical in terms of both protein and lipid distribution (compositional assymetry); membrane always has polarity. • Membranes held together entirely by hydrophobic and polar interactions; no covalent bonds; hence, quite fluid.

sickle cell shape

-only one peptide fragment was different. -HbA vs HbS -for sickle cell - one AA changes from glutamic acid (pK of R group is much lower than pH of blood, therefore fully dissociated (-1) charge) to valine -only one mutated AA out of around 650 in two different positions (have same alpha chains, and position 6 in both B chains is different) -the two negative charges are close together in space, therefore repel creating space. -since there are no negative charges in HbS, molecules stick together, creating a "sticky patch", this collapses entire molecule

molecularity of reaction

-overall reaction is bi-molecular, two molecules in overall reaction -order or reaction is only depended on slow step, therefore is a 1st order reaction --> if you don't know the rates of rxn cannot determine the order

protein folding in enzyme kinetics

-protein may not fold into the lowest delta G value, not completely native allowing protein to react with a variety of different target molecules.

cataracts

-proteins have matured and clumped together, clouding lens -chaperones prevent this if working properly

Proximity and orientation

-proximity - how close are the two groups that are going to react. Tested importance by bringing attacking group closer -orientation - in 3D space, much more important

blood letting

-removing blood from the body, removing some of the iron -the bacteria releases enzyme like structure that ruptures RBC -free heme with iron is released --> the primary source of iron for bacteria, bacteria prefers iron from theme rather than just any iron -if bloodletting, removes some of the blood, therefore not enough iron for the bacteria to survive and bacteria will die off

Skeletal muscles

-striated - skeletal and cardiac muscles, regular arrangement of filaments •Voluntary muscles (involuntary is smooth and cardiac, controlled by ANS) •Body movement •Arranged in antagonistic pairs - during flexion/ extension, one muscle contracts while another relaxes. ex - biceps and triceps •Arrangement allows extension and flexion •40% of body mass

first rate determining step

-substantial negative delta Go

H+ gradient across mito membrane

-the electrical potential gradient stores energy -this gradient is used to create ATP -system wants to maintain homeostasis with relation to pH

uncouplers

-uncouples energy flow with production of ATP. energy still released, energy still transferred, but ATP is not produced

test to see if all of enzyme is necessary for function

-used a protease to cut an intact ribonuclease into two -eliminated some AA, full activity still possible with some AA missing not all are necessary -created 2 chains an S peptide and S protein, and saw if either part of chain was active individually (neither was), then mixe the two together and added substrate and the reaction worked. The two bonds were still separated, but 3D shape went back to original, indicating that the bond was not neccessary for molecule to adopt native shape (went to lowest delta G shape anyways). Both chains had necessary AA for function

systole vs diastole

-when ventricle fills with blood (diastole), muscles are being stretched -during systole phase, contractile force is determined by amount of stretching (how much blood has filled) --> cardiac output depends upon ventricular end diastolic volume

Noncompetitive (Mixed) Inhibition

1) I does not resemble S; I binds to E at some site other than the active site. 2) I and S can bind simultaneously to E. 3) Vmax permanently < by I and cannot be restored by > [S] because they are not competing for the same active site -inhibitor makes it so enzyme is not working as efficiently, could function in many different ways, can deform structure so product doesn't form the normal way, can take away a metal cofactor, etc.

Two structural features that determine substrate specificity of enzyme:

1) substrate must contain specific chemical bond that can be attacked by enzyme. Often an acyl group 2) substrate contains another functional group which binds to enzyme and helps position substrate molecule on catalytic site. Happens before chemical event, substrate must be positioned at the active site

Regulation of a metabolic pathway

1. Basic parameters affecting enzymatic reaction rates; e.g., [enzyme], pH, [intermediate], [coenzyme]. 2. Regulatory enzymes 3. Hormones 4. Genetic control -symptomology cannot tell you which level is at fault

Catabolism vs. anabolism

1. Catabolic and anabolic pathways between precursor and product usually not identical. -Glycogen --(enzymatic degredation)--> lactic aid (12 steps) -backwards direction <--(biosynthesis)-- 9 steps the same, 3 different (want to get rid of phosphate, using ADP would be a waste of energy, can use an enzyme) 2. Catabolic and anabolic pathways may differ in their intracellular location. -FA --(oxidative)--> acetate (in mito) -Acetate --(synthesis)--> FA (in cytoplasm) 3. Independent genetic regulation.

Four specific functions of metabolic processes

1. Extract chemical energy from environment, either from organic nutrients or sunlight. Don't synthesize amino acids, must break it down from other organisms 2. Convert exogenous nutrients into precursors of macromolecular components of cells. 3. Assemble precursors (building blocks) into proteins, lipids, etc. 4. Form and degrade biomolecules required for specialized cell functions.

All intermediates between glucose and pyruvate are phosphorylated. Pi groups have 3 functions:

1. Polar, negatively charged; impermeable to cell membrane. 2. Serve as binding group in formation of ES complex. 3. Become terminal Pi of ATP, chemical basis of energy storage

3 kinds of chemical transformations

1. Reactions involving carbons 2. reactions involving ATP or ADP 3. Redox reactions (electron transfer

Three kinds of skeletal muscle fibers

1. Red/Slow 2. White/Fast (1 and 2 have contrasting features) 3. Red/Fast fibers are intermediate between red/slow and white/fast fibers

Smooth muscle arranged around hollow organs

1. Tubular structures with diameter change e.g., capillaries 2. Tubular structures with mixing movements e.g, gut wall, can have circular and longitudinal layers 3. Sacular structures with overall size change e.g., glands, only purpose is to contract whole structure, not unifom

CO2 regulation of Hb

> CO2 releases O2 -during active metabolism, CO2 is released. The body requires O2 when this is going on • In rapidly respiring tissue, e.g. muscle, higher levels of CO2 and H+ in capillaries promote release of O2 from oxyHb (Bohr effect). • Reciprocal effect in alveolar capillaries of lungs where hi [O2] unloads H+ and CO2 from Hb.

Excitation contraction coupling

Action potential is an electrical event and muscle contraction is a mechanical event. The transduction from electrical to mechanical occurs by a process known as excitation‐contraction coupling AP = electrical Contraction = mechanical

delta G for aerobic metabolism vs anaerobic metabolism

Aerobic: Glu + 2ADP + 2Pi --> 2LAC + 2ATP + 2H2O Delta G = -32.4, very favorable Anaerobic: Glucose --> 2LAC Delta G = -47.0 Kcal/mol -net gain of 2 ATP (one ATP has a delta Go = -7.3 (-14.6 for two), not a very energy efficient system)

Allosteric properties of Hb

Allosteric properties of Hb arise from interactions between its subunits. Binding of O2, H+, CO2 and BPG by Hb are linked. These molecules bind at different points and communicate with each other thru changes in quaternary structure of protein.

Smooth muscle Contractile units (continued)

Assembly •Contractile units arranged generally parallel to the long axis of the cell. extend all over cell, randomly organized •Thick and thin filament lengths are variable •Dense bodies equivalent of Z‐lines define the Sarcomere, these dense bodies (red structures) connect with thin filaments

Disaccharide mech

Disaccharide - two monosaccharides joined by glycosidic bond

Michaelis-menton limitation

ES and EP form actual products, not just transition states

Connective tissue Types

Embryonic connective tissue (mesenchyme) Specialized connective tissue • Cartilage • Bone • Hematopoietic tissue and blood • Lymphatic tissue • Adipose tissue Connective tissue proper (forms the extracellular matrix) • Loose connective tissue (holds organs in place) • Dense connective tissue (tendons, ligaments, fibrous capsules) • Reticular connective tissue (blood vessels, muscles, liver)

Irreversible Inhibition

Enzyme is chemically modified to such an extent that it becomes inactive. • Enzyme inhibition serves as biochemical control mechanism. • Many drugs and toxins which inhibit enzymes. • Ethanol used therapeutically to treat ethylene glycol poisoning by inhibiting alcohol dehydrogenase and, hence, ultimate formation of oxalic acid; oxalate crystals injure kidneys.

Regulatory Enzymes

Feedback Inhibition • Overall reaction rate regulated by product inhibiting enzyme. • Enzyme which is inhibited called allosteric or regulatory enzyme. • Inhibitor called effector or modulator. • I binds to E at regulatory site which is different from catalytic site.

Connective tissue composition

Fibroblasts, Structural proteins, Elastic fibers, Ground substance

Classification of bone cont.

Flat • Generally curved •2 layers of compact bone sandwiching spongy bone •Flat bone growth occurs by intramembranous (different from endochondral) ossification, a bunch of osteoblasts lay out •Bones of the skull Sesamoid •Embedded in tendons •Patella and pisiform Irregular •Irregular shape •Thin layers of compact bone surrounding spongy interior •Bones of the spine, hip, ethmoid and sphenoid bones

Hb trends in tissues and lungs

Hb needs to function at both ends of the spectrum -picks up O2 in lungs, needs high affinity -releases O2 in tissues, needs low affinity

chymotrypsin 3 D space

Histidine (57) and serine (195) are actually very close to each other due to folding, and also ideally situated to react with a molecule -histidine is involved in positioning, the benzene molecule provides a hydrophobic pocket that is involved in situations substrate on surface to maximize interaction -serine is involved in chemical reaction -Asp and Gly

Lactic Acid - Performance- Enhancing Drug cont.

• New research (rat muscle fiber preparations) - The lower pH resulting from the production of lactic acid (metabolic acidosis) decreases Cl- channel activity which in turn sustains the action potential. • Accumulation of extracellular K+ is key component of muscle fatigue b/c it results in action potentials becoming less effective trigger of Ca++ release (necessary for muscle contraction) • When Cl- channel activity is diminished, Na+ current increases which stimulates the action potential and triggers Ca++ release.

smooth muscle organization

• No myofibrils • Assemblies of sarcomeres stretch across the cell's length •Vimentin and desmin rich intermediate filament suspend filaments from cytoskeleton •Dense plaques (purple) - tether contractile arrays to sarcolemma via thin filaments - constitute adherens junctions, dense plates bind •Gap junctions

Polysaccharides (Glycans)

• Polymers; starch (main polysacc in plants) vs. glycogen (main polysacc in humans) • Cellulose - structural homopolysaccharide (only one sacc in many forms); structure stabilized by H-bonding. -are first broken down into monosacc then stored in the form of glycogen

Prion Diseases

• Prion - misfolded protein. • May be implicated in cystic fibrosis, Alzheimer's disease, Creutzfeldt-Jakob disease, Huntington's chorea.

Quaternary (4o) structure

• Quaternary (4o) structure - more than 1 pp chain; e.g., hemoglobin. -hemoglobin binds a single element (iron), which binds to oxygen. 4 Fe bound, 4 oxygens can bind • Quaternary structure is formed by the assembly of individual polypeptides into a larger functional cluster

Sialic acid residues

• Sialic acid residues (remains on protein until it is no longer functional) (acidic sugar; -COO- group) at ends of oligosaccharide chains of soluble glycoproteins carry a message that determines whether protein continues to circulate in blood or is removed by liver (protein is no longer functional, needs to be broken down). -Removal of sialic acid is one way to mark "old" proteins for degradation and replacement; also, "old" cells (also looses the sialic acid) like erythrocytes thru membrane glycoproteins.

Simple Epithelia

• Simple, usually very thin (Facilitate exchange between apical surface and vasculature) • Simple squamous (pulmonary) - line alveoli, nee to allow for exchange of gas • Simple cuboidal (renal tubule & glandular ducts) - facilitate exchange of material, cuboidal shape, more regulation, more mito, larger • Simple columnar (distal (before enters collecting duct) renal tubule & intestine)

Cofactors

• Some enzymes depend for their activity only on their structure as proteins, while others require in addition nonprotein structures, or cofactors, for activity. • Cofactor - metal ion or complex organic molecule (coenzyme). • Cofactors bind to enzymes with varying degrees of affinity. -ex. hemoglobin used iron (metal) and another non-protein compound that binds iron -rhodopsin used an organic molec (VitA) to function

Spectrin and Ankyrin

• Spectrin - inner surface of cell membrane. Forms extended network of filaments; double helix. Interacts with other proteins to stabilize and regulate shape of erythrocyte membrane. • Ankyrin - tethers anion channel protein to spectrin, thereby limiting lateral mobility.

Classification of Enzymes

• Substrate - molecule on which enzyme exerts catalytic action. • Many enzymes named by adding suffix -ase to name of substrate; e.g., urease. • Trivial vs. systematic names. Systematic name based on nature of chemical reaction catalyzed by enzyme; hexokinase (hexo - P group transfer, kinase - 6 C sugar, not necessarily glucose) vs. ATP:glucose phosphotransferase (P group being transferred by ATP, substrate must be glucose)

Gluconeogenesis

• Synthesis of glucose from PYR or LAC. • All rxs. of glycolysis but 3 freely reversible (have very negative delta G, most other reactions have a delta G around 0). Reverse of these 3 occur via different mechanism and enzyme; e.g., PFK vs. phosphatase. • Enzymes unique to each pathway reciprocally related by common allosteric effectors; coordinate regulation. If you increase [ATP] turn on enzyme, if you increase [ADP] turn off enzyme

Active Site

• Takes up relatively small part of total volume of enzyme. these AA can be anywhere on linear sequence due to folding, but must be close in space • Is a 3-dimensional entity made up of residues from different parts of linear AA sequence. • S bound to E through multiple weak interactions. • Active sites are indentations, a physical location. • Specificity of binding depends on precise arrangement of atoms in active site. Can be broad (ex. hexokinase interacts with 6C sugars) or precise (ex glucokinase only interacts with glucose

Tertiary (3o) structure

• Tertiary (3o) structure - folded and compact. Structure determined by X ray diffraction. • Each protein has distinct structure adaptedfor its particular biological function. • Common properties: hydrophobic AA inward (away from H2O); hydrophilic AA on surface. • Structure stabilized by many H-bonds, some ionic interactions and (often) -S-S- bonds. • Denaturation - via heat (around 55-60 degrees, physiologica = 37); pH extremes (change charge characteristics of certain AA); detergents (breaks H bonds. Disrupt 3o structure.

Determining protein composition

• To determine how proteins oriented relative to membrane, first use SDS to solubilize and identify all proteins associated with membrane. • Then use either: 1) proteolytic (breaks peptide bonds) enzyme, e.g., pronase - only degrades exterior proteins; or 2) fluorescent or radioactive label. Interacts with portion of protein it can get to, must be in ECM • Then, lyse cell to create "ghost"; both exterior and interior proteins now labeled.Can now detect proteins on inside

Transmembrane Channel

• Transmembrane (provides a hydrophilic membrane, lowers the activation energy) passage of polar compounds or ions facilitated by proteins that lower activation barrier by providing alternative path thru membrane; transporters or permeases; facilitated (easier) diffusion or passive (higher conc to lower) transport. • Similar to enzymes; bind their substrates thru many weak, nonconvalent interactions.

Apical specializations

• Villi and microvilli - not capable of movement • Motile cilia (picture) --> 9+2 arrangement of microtubules (allows for movement) --> Dynein arms --> Upper airways (flushing fluid), brain ventricles (moving CSF), fallopian tubules • Sensory cilia --> Renal tubule cilia - monitor flow rates of sodium and chloride in order to monitor BP --> Olfactory epithelial cilia - odorant receptors, can change membrane potential and signal brain --> Stereocilia (hair cells move)- Inner ear and vestibular apparatus (head rotation, orientation)

Diabetes, Hyperglycemia and Glycosylated Hemoglobin (HbA1C)

• [HbA1C] (can be used to measure glucose levels in blood) dependent on [glucose] in blood and duration of hyperglycemia. In prolonged hyperglycemia, [HbA1C] may reach 12% or > of total [Hb]. (Severe gyperglyc. Normal is < 6%) • Diabetics have hi [ ] of blood glucose and hi amounts of HbA1C. • Changes in [HbA1C] in diabetics can be used to monitor effectiveness of treatments. -type 1 - lack of insulin (insulin dependent) -type 2 - (85-90% of people) insulin resistance

Lacrimal gland

• exocrine glands, lined by cuboidal epithelial cells • Multiple lobules • Lobes contain acini • Intralobular ducts • Interlobular ducts --> found on top and laterally

Meibomina gland

• found below tarsal gland in lid • Mainly produce meibum • Rich in lipids • Prevent tear evaporation • Upper and lower lids • Inside tarsal plate • Acini and ductal system • Ducts open in lid margin

Structure of retinal pigment epithelium

• non-neural part of the retina • Hexagonal cells • Single layer • Between Bruch's membrane (basal surface faces here) and photoreceptor outer segment (apical surface faces here) • Infoldings on basal surface • Processes extending from apical surface along the outer segment of photoreceptors • Adherent junctions and tight occluding junctions between RPE • Pigment containing melanosomes --> Pigment absorbs some light to prevent scatter

Glycophorin

• pp with CHO at one end attached to external membrane surface. -CHO region - influenza virus receptor; responsible for large net negative charge of human erythrocyte which prevents cells from clumping together. -Also, rigidity.

Junctional complexes structure

Junctional complexes -fused proteins, generally occludins -restrict what gets into body via paracellular routes. Are leaky, let Na+ or H2O get in, but very selective

rhodopsin pathway

LCA - mutation making much more retinal isomerase inactive. Cannot restore native levels of rhodopsin -bleaching of rhodopsin (when light hits), purple to almost transparent, must be a regenerative process

Classification of bone

Long •Parts --> Shaft (Diaphysis), Mainly compact bone --> End (Epiphysis), Mainly trabecular (cancellous or spongy) bone --> Metaphysis •Long limbs, fingers and toes •Lenghtening occurs in the metaphysis region (Endochondral ossification) Short •Cube shaped •Bones of the wrist and ankle

Terpenes

Multiples of isoprene

Stage 3 - Electron transfer and oxidative phosphorylation

NAD - organic molecule, oxidyzed, accepts electron in form of hydrogen ions and becomes reduced released energy is stored in form of ATP, get some energy in stage one, but most in stage 3

NADH absorbance

NAD+ and NADH have different absorbance -UV spectrum. see an increase in absorption as NAD+ --> NADH at a wavelength of around 340

stage 1 vs stage 2 of metabolism

Net gain of ATP - 2

Chaperones

No lingering.The model shows that chaperones assist proteins during their folding in the ER. Proteins with low folding efficiency are partially released from chaperones and become Omannosylated by Pmt1/2. -chaperones allow it to fold into proper structure -aggregate needs to be avoided -sugar part of chaperone is what binds to protein. Also targets protein that needs to be eliminated

Choroid epithelial layers

Pars plana (posterior portion) • Pigmented and non pigmented epithelium • Secretions into vitreous Pars plicata (anterior portion), see ciliary bodies • Pigmented and non pigmented (closest to ciliary bodies) epithelium • Secretions into posterior chamber -basement membrane between pig and non-pig layers, filters capillaries in order to monitor secretions that form aqueous humor

Types of smooth muscles

Phasic (unitary, anatomical term) - all muscle fibers contract together as one unit •Gap junctions •Pacemakers - in the gut •Action potentials - fibers capable of self-generating AP, membrane potential is constantly changing, can cause AP -Walls of GI tract, Walls of Urinogenital tract Tonic (multiunit) - multiple units between muscle mass, only muscle fibers innervated b that axon contracts -Vascular muscles, Airway muscles, Sphincters, Ciliary body and iris muscle

deltaG of hydrolysis

Phosphate bond energy - difference in free energy when a phosphate group is hydrolyzed from a phosphate compound -p-creatine - stores phosphate bond energy for potential future use

Epithelia Types (based on morphology)

Simple, Stratified, Glandular

Steroids and Sterols

Steroids - decreases level of inflammation, a little can be helpful but a lot can be harmful • Examples include bile acids, male and female sex hormones, adrenocortical hormones. Sterols - imp in membrane structure • Cholesterol; lanosterol.

Epithelia structure

Structure • Apical surface - faces outside, either lumen or external body • Basal surface • Basement membrane --> Basal lamina - one end, cell is attached, other en, often connective tissue --> Lamina reticularis (aka reticular lamina) --> Junctional complexes

Tight junctions

Tight junctions (aka occluding junctions or zona occludens) strength and regulation • Membranes of adjacent cells fused at the level of transmembrane proteins (occludin, claudin) • Serve as paracellular barriers for solute and water • Very tight or leaky

Glycerol phosphate shuttle

Unidirectional, production of ATP -NADH does not enter mito itself, dontates electrons to glycerol P (which can enter mito) -the dehydrogenase removes electrong from glycerol P and electrons are funneled into ETC -2ATP per 2 electrons, electrons coming in are feeding into the chain at a point in the middle (if entering from the beginning would get 3 ATP per 2 e-)

measuring V0 cont.

When V0 = (1/2)Vmax, Km = [S] can determine Vmax via y-int can determine Km via slope

Stress monitoring system

When bone formation is complete osteoblasts die by apoptosis or persist as osteocytes or bone lining cells and monitor bone stress and integrity.

TCA cycle (names and structures)

[oxaloacetate acid] remains constant, is being used but also being regenerated

movement of lipids in membrane

a. generally only happens if there is a reason for movement to occur, polar head group has to move across membrane . flippase allows this to happen in a reasonable time frame c. happens by itself and all the time, fluidity of cell membrane

when no chaperone present

aggregated protein is dangerous, cannot function properly

RPE replenishes retinal rod cells

aldehyde, essential component of rhodopsin (retinal + opsin) undergoes conformational change from 11-cis to all-trans -this detaches it, moves into the RPE -bleached (excessive light) must be restored by RPE then brought back to rods

3 major classes of redox enzymes

all oxidized form, can accept H 1. Pyridine-linked dehydrogenases (NAD, NADP coenzyme) 2. Flavin -linked dehydrogenases (FAD, FMN coenzyme) 3. Cytochromes (Fe-porphyrin ring system)

Malate shuttle

bidirectional -get 3 ATP per 2 electrons -direction of electron flow is dictated by requirements of organism --> may need e- for reductive biosynthesis rather than ATP production

Abnormal Collagen Synthesis

collagen breaks down • Collagen most abundant protein in humans. • Abnormal collagen synthesis or structure can cause dysfunction of heart, bone (fragility), joints (arthritis), skin and eyes (dislocation of lens). • These diseases may result from genetic mutations or abnormal posttranslational modification.

Stratified Epithelia

contains multiple layers, where there is a lot of wear and tear • Mouth, esophagus, vagina, Skin (keratinized (strengthens)) - often one basal cell layer that's constantly building, slothing off older top layers • Urinary bladder, ureters, urethra ‐ Translational or urothelium (needs to be capable of stretching)

Sorbital pathway

glucose --> sorbital --> fructose --> F6DiP -last step requires ATP

glycogen to G1P

glycogen - storage form of glucose -glucose gets broken off and phosphorylate at 1 position -in order to participate in metabolism, phosphate must move from 1 --> 6 -an enzyme adds a phosphate to the 6 position, then takes away a phosphate from the 1 position

multienzyme complex

if you remove one enzyme in the series, either the reaction will not occur or the reaction will occur at a slower rate -all enzymes need to be present for complex to function properly -enzyme complex is associated with the cell membrane

iron

iron is either in the +2 or +3, if in the +3 form can accept an electron and becomes +2 -->then can hand off electron and go back to +3 -iron is the only functional part of the heme • FerroHb (+2) vs. ferriHb (+3); only Fe(+2) can bind O2. • Mb - 1 pp chain; 153 AA; MW 16.7 kD • Very compact; mainly α-helix. • Interior almost entirely nonpolar (want to get away from H2O molecules, could be "filler molecules") residues. • Only polar (must perform some function in order to overcome the less favorable location) residues inside Mb - 2 HIS.

Protein folding process

kept denaturing agent present -1st he removed mercaptoethanol (breaks disulfide bonds), disulfide bonds formed but not in original formation -2nd he removed urea (denatures, breaks weak interactions), fully active native state returned --> refolding process does not require any outside help, protein will fold to lowest delta G shape

Sterol content

moderate extremes of solidity and fluidity -below solid-fluid temp (relatively solid) - limits how solid inside of cell can become by inserting itself in membrane -when more fluid, limits movement of FAs

Carriers - Ionophores

red circles - oxygens, hydrophilic center valinomycin (an ionophores antibiotic), transports ions (in this case K+) inside cell, bringing positive charges in decreases the electrical pot gradient, pump no longer works, organism dies

heme group structure

rings - very rigid, planar -every other c=c bond is a double bond -conj pi system (necessary in order to absorb light) -electrons are delocalize, can move around in a greater volume of space

Pathways are controlled in order to regulate levels of metabolites

system is designated to provide max efficiency -negative regulation, product of enzyme 5 inhibits enzyme 1

•Muscle filaments

thick and thin filaments

nonpolar vs polar part of heme

very compact, alpha helix structure throughout

measuring V0

want to characterize enzyme catalytic properties by finding Km and Vmax

important nucleophilic groups of proteins

when histidine has unshared electrons, is a strong nucleophile and can accept an H+ ion (strong base) when it accepts a H+, it becomes a strong acid (likely to give it up)

Glucose permease of erythrocytes

• Glucose permease of erythrocytes - e.g. of passive transport system. -Glucose uptake can be analyzed using Michaelis-Menten formalism. Shows 3 hallmarks of passive transport system: 1. hi rate of diffusion down concentration gradient 2. saturability, reaches Vmax 3. specificity, specific for glucose, not any other kind of sugar

Glycoproteins and glycolipids

• Glycoproteins and glycolipids - oligosaccharides covalently bonded to protein or lipid. Add bulkiness and negative charge (increases probability that glycoprot will not clump together. Also function as receptor (recognition) sites.

Hb

• Hb - biological necessity to regulate Hb is much greater than for Mb - 4 pp chains; held together by noncovalent interactions; 2 α and 2 β; each contain 1 heme and 1 O2; MW 64.5 kD • Molecule nearly spherical; 4 O2 binding sites far apart. when a Hb molecules binds O2, goes under a conformational change and becomes move likely to bind another O2 • α and β chains resemble Mb in shape even though AA sequences very different. degenerate, more than one sequence can have similar result • All Hb's have nonpolar core.

Hb as an allosteric (regulatory) protein

• Hb is allosteric protein; Mb is not, but Mb always has a stronger affinity for O2 than Hb • Binding of O2 enhances binding of additional O2's. -Hb has < O2 affinity than Mb; hyperbolic vs. sigmoidal curve

Lysosomal Acid Lipase Deficiency

• Human lysosomal acid lipase (breaks down lipids) (hLAL) - triglycerides → free f.a. + glycerol cholesteryl esters → cholesterol + f.a. • Cholesteryl ester (needs to be destarified, release ester in order to be function) storage disease (CESD) and Wolman's disease - genetic disease; deficiency of hLAL; autosomal; recessive. --> ester is the storage form, change OH --> OR to it can traverse membrane much more readily, is much less polar • CESD - hypercholesterolemia; severe atherosclerosis; adults. • Wolman's disease - infants; usually fatal by age 1.

Hyaluronic acid

• Hyaluronic acid - e.g. of GAG; hyaluronate at physiological pH (totally dissociated, in anionic form); MW > 106; clear, viscous solution. • Covalent bonds between GAG's and core protein are glycosidic bonds (elim of H2O) between saccharides and -OH groups of SER (R group contains an OH) residues in protein.

Carbohydrates in cell recognition

• In contrast to AA's in proteins (and nucleotides in nucleic acids) which can bond together in only one way, monosaccharide units in polysaccharides can attach (many OHs) to one another at multiple points.

Enzyme-limited vs. Substrate-limited Reaction

• In every metabolic pathway, there is at least one rx. that, in vivo, is far from equilibrium b/c enzyme that catalyzes it has relatively low activity; enzyme-limited; rds (rate determining step). • These reactions tend to have large -ΔG in vivo and, hence, are irreversible. • Enzymes are allosteric (metabolic regulation)

Lipid Motion Within Membranes

• Lateral diffusion vs. "flip-flop" (transverse or transbilayer diffusion) • Degree of fluidity depends on temperature and lipid composition, cells generally occur at a constant temp • At lo temp., relatively little lipid motion - paracrystalline state. • Solid-to-fluid transition temperature: 1. Saturated vs. unsaturated fatty acids 2. Sterol content • Proteins can diffuse laterally in bilayer; 2-dimensional mobility.

Lubricant in synovial fluid

• Lubricant in synovial fluid of joints; vitreous humor; extracellular matrix of cartilage and tendons, contributing tensile strength (due to rigidity) and elasticity (has flexibility because of H bonding).

Cell Membranes

• Mainly protein and lipid (about 90%); a little carbohydrate (glycoprotein or glycolipid). • Membranes from different species have different lipid and protein compositions. • In general, membranes impermeable to polar or charged solutes, but permeable to nonpolar compounds.

Formation of NADH can be monitored by UV-spectrophotometry

• Measure the change of absorbance at 340 nm • Very useful signal when studying the kinetics of NAD-dependent dehydrogenases

Transport

• Membrane transport systems - mainly protein-mediated processes. 3 basic types: transmembrane channels, pumps, carriers. • Simple diffusion - movement of solute molecules across permeable membrane which is concentration dependent.

Metal ion cofactor vs coenzyme

• Metal ion cofactor - functions as bridging group binding substrate and enzyme together through formation of coordination complex; serves as catalytic group. • Coenzymes usually function as intermediary carriers of electrons or of specific atoms or functional groups that are transferred in enzymatic reaction.

Modulators for allosteric enzymes

• Modulators for allosteric enzymes may be either inhibitory or stimulatory. • When modulator (activator) is substrate itself, have homotropic enzyme; active and regulatory site are the same. • When modulator is molecule other than substrate, enzyme is heterotropic. • Homotropic allosteric enzymes do not follow M-M kinetics; sigmoid vs. hyperbolic curve.

Carbohydrates

• Monosaccharide (simple sugar) - single polyhydroxy aldehyde or ketone. • Oligosaccharide - short chains of monosaccharides; glycosidic linkage. • Disaccharide - e.g., lactose - glucose + galactose; sucrose - glucose + fructose.

Na+ - K+ - ATPase Pump

• Most animal cells have hi K+ and lo Na+ compared to surrounding medium. • > 1/3 of ATP consumed by animal at rest (just the basic properties needed to keep us alive) used to pump these ions. • Na+ - K+ gradient controls cell volume, is responsible for generation of action potential that excites nerve and muscle cells, and drives accumulation of sugars and amino acids (secondary active transport).

Fibroblasts

• Motile • Continually synthesized • Secrete structural protein precursors and ground substance • Essential for maintaining ECM and wound healing

NAD-linked dehydrogenases

• NAD-linked dehydrogenases function in respiration; transfer e-'s from substrates to O2 • NADP-linked dehydrogenases transfer e-'s from substrates generated during catabolism to reductive biosynthetic rxs. Electrons are not used to produce ATP, but provide biosynthesis reactions • Many pyridine-linked dehydrogenases contain divalent cation cofactors; e.g., alcohol dehydrogenase has Zn++.

O2-binding Proteins

• Needed to overcome relatively low solubility of O2 in H2O. • Myoglobin (Mb) and hemoglobin (Hb) • O2 binds to heme (organic group which complexes iron, which in turn binds oxygen) which of Hb or Mb; chromophore (absorbs light) or prosthetic group.

Glycocalyx

• Network of sugar moieties associated with different glycoproteins. • "sugary coating" • Inhibits protein movement. passageway for things moving in and out of cell, should not be moving

Choroid

• rich in connective tissue • Suprachoroid - right under sclera --> Loose connective tissue --> Melanocytes - pigment containing cells, light not captured by photoreceptors captured here to attempt to prevent scattering --> Tapetum of animals • Haller's layer - contains large caliber blood vessels • Sattler's layer - med caliber blood vessels • Choriocapllaris - rich in capillaries, exchange in nutrients, gas, the primary supply of oxygen and nutrients to photoreceptors • Bruch's membrane - right next to retinal epith cells, barrier between retinal epith and capillaries --> Basement membrane --> Elastic fibers and collagen

Basolateral membrane specializations

• usually have tight junctions, very close to blood vessels, face interior space • Basolateral membrane contains unique complement of ion channels and transporters e.g., Na+‐K+ ATPase (maintains normal Na+ and K+ gradients) • Basolateral membrane may be folded • Basolateral membrane faces vasculature

Triad arrangement

•1 T‐tubule (runs inbetween term cisternae) and 2 terminal cisternae of adjacent SR •Dihydropyridine receptors on T‐tubule membrane (purple) •Rynodine receptor on terminal cisternae

Bone

•206 bones in the human skeleton •Work in conjunction with --> Cartilage (between bones, ribs) --> Ligaments (attach bone to bone) --> Tendons (attach muscle to bone) --> Skeletal muscles •Bone design is a compromise between strength (bearing a lot of weight) and weight (if bone is too heavy, will interfere with movement)

Excitation contraction coupling mech

•Action potential enters the T‐tubule •Triad role --> Sarcoplasmic Ca2+ conc increases from 0.1micromol/L to 10micromol/L within a fraction of a second --> calcium binds to C trop, conformational change, rolls, exposes t-trop. also pulls away I trop --> opens up binding site that binds with myosin, therefore myosin binds actin •Crossbridge cycling --> Troponin is activated --> Troponin pulls tropomyosin deeper into the groove of actin filament --> Myosin binding sites exposed --> Contraction begins (Follow steps 1‐5 on Right) •Relaxation 2 z discs get pulled towards center

•Active and passive tension

•Active tension is the tension developed by cross bridge formation •Passive tension is the tension developed by stretching the muscle. If fiber is long, lots of stretching and the greater the tension •Total tension is the sum of active and passive tension. increases with muscle length, but if force increases further it drops

Bone marrow (soft tissue in center)

•Bone marrow (soft tissue in center) - almost always red in development Red - still in spine, vertebrae, clavicle, and several others •Source or Red cells, white cells and platelets •Contain Hematopoeitic multipotent stem cells •Location of mesenchymal stem cells (give rise to osteoblasts and chondrocytes) Yellow •Red marrow is replaced by yellow marrow during adulthood in most bones •Stores fat •Can be converted to red marrow depending on demand

smooth muscle Excitation Contraction Coupling, Calcium source

•Calcium influx from extracellular fluid 1. L‐type (long lasting) calcium channels in Caveoli (voltage‐gated) 2. Receptor‐operated calcium channels (ROCCs), NT can bind to receptors and ope channels -->Muscarinic - Visceral smooth muscles -->Adrenergic - Vascular smooth muscles 3. Stretch activated calcium channels, increasing stretch opens calcium channels --> Vascular smooth muscles •Calcium induced calcium release (from sarcoplasmic reticulum) •Inositol triphosphate pathway (from sarcoplasmic reticulum)

Muscle tension‐length relationship

•Contractile force depends on the number of cross bridges that can be recruited for power strokes •The number of cross bridges recruited will depend on the length of the muscle fiber before contraction begins. The shorter, the smaller the contraction •Stretching a muscle to optimize actin and myosin interaction is known as preloading, thin fibers are further from thick, tension decreases because acting and myosin are not in right config •Maximum contractile force will be generated for intermediate lengths (preloads) of muscle fiber •Contractile speed depends on the speed of cross bridge recycling

Neuromuscular junction (smooth muscle)

•Controlled by ANS --> Sympathetic, parasympathetic or enteric nervous system control •Varicosities (swellings) at the end of ANS efferents can contact several muscle fibers

Dihydropyridine receptors

•Dihydropyridine receptors on T‐tubule membrane (purple) •L‐type Ca2+ channels (long-lasting) •Tetrads •Voltage sensitive •Causes Ca2+ movement from t‐tubule lumen into muscle cell, voltage sensitive, activated by AP •Ca2+ Entering via these channels is negligible for muscle contraction

Vasculature

•Enter via periosteum (outer covering) •Penetrate the bone cortex to reach the medulla •Travel in the Haversian and Volkmann canals

Transverse tubules

•External membrane specialization •Aligned with Z disks •Carry action potentials into the cell, SR must depolarize to release calcium, senses through T-tub

Sarcoplasmic reticulum

•Internal membrane specialization •Ca2+ storage when cell is at rest •Douse myofibrils with Ca2+ to initiate contraction, releases into cytoplasm •Ca2+ ATPase on surface to pump Ca2+ back in •Contains calsequestrin a Ca2+ binding protein. keeps calcium in SR lower, so the gradient of calcium of SR and sarcoplasm is more favorable in allowing calcium to go back in •Terminal cisternae - specializations at the end of each sarcoplasmic reticulum

Isotonic (constant tension) vs. isometric contraction (constant length)

•Isotonic contraction is one where the muscle changes in length when the tension developed is constant. --> An example is bending the elbow from straight to fully flexed •Isometric contraction is one where the muscle develops tension with no change in muscle length. --> An example is carrying an object in front of you as the weight of the object is pulling your arms down but your muscles are contracting to hold the object at the same level.

bone composition

•Mineral component --> Carbonated hydroxy‐apatite (Calcium and phosphate) --> brittle, can't expand or contract --> all cemented to a think wall of collagen strand alpha helix •Collagen matrix (Type I) --> Crosslinked polypeptide triple helix --> can expand a little, why bone has a little give Ground substance •Glycosaminoglycans •Proteoglycans •Salts •Water •Saturated with Calcium and phosphate •Collagen and ground substance together termed osteoid

bone cont.

•Mineralized connective tissue •Honeycombed with tunnels and cavities --> Teeming with cells --> Channels for blood vessels and nerve fibers •Central chamber filled with bone marrow --> Manufacture blood cells --> Store fat •Dynamic tissue constantly remodeled and turned over

Recruitment

•Motor unit - The motor neuron and the muscle fibers it innervates •Recruitment of multiple motor unit is another way to increase tension -if need fine and precise movement, motor neuron innervates one muscle fiber. to increase strength, innervates many muscle fibers

Lamellar bone

•Regular pattern of collagen arrangement •Mechanically strong •Comprises compact and trabecular/cancellous or spongy bone regions •Laid down in concentric rings that form cylinders called osteones or Haversian systems •Haversian canal in center ‐ Throughfare for blood vessels and nerves

Rynodine receptor

•Rynodine receptor on terminal cisternae •Ca2+ release channels •Activated by active dihydropyridine receptors. Dihydro relays depol to rynodine receptor • Released stored Ca2+ from SR into cytoplasm •Ca2+ released by the SR brings about muscle contraction

Skeletal muscle summation

•Twitch response, tension that is developed in response to a single AP •Summation - one way to increase muscle tension •Tetanus - prolonged period of contraction

Sarcomere (basic contractile unit)

•Z disks (delineates the far end of a sarcomere) •M line •A band (wide dark band) •H band (narrow light band in the middle of A band) •I band (intermediate width light band around z disk) •Structural proteins --> Actinin binds actin to z disk --> Titin binds myosin to z disk --> Dystrophin binds Z disk to cytoskeleton and plasma membrane

Osteocytes

•all connexted, creates a complex and can sense stress. communicates with bone lining cells •Entombed (old) osteoblasts - can't form new bone anymore •Reside in lacunae - get caught inside •Detects mechanical stress to bone •Signal remodeling when there is a microfracture •Long thin dendrites •Canaliculi - microscopic channels •Gap junctions between osteocytes and bone lining cells

Structural proteins

• Collagen • Fibrous protein • High tensile strength • 28 different types

BPG

BPG < O2 affinity of Hb causing Hb to unload O2 in tissue capillaries the green line is still a sigmoidal plot, just increases so quickly that you can't see it • Within a few hours after climbing from sea level to altitude of 3700 m, BPG level >, thereby < affinity of Hb for O2. p O2 < at hi altitudes, so facilitates release of O2 in tissues. Reverse occurs when people acclimated to hi altitudes move to sea level. • > in BPG level in people with hypoxia due to inadequate function of lungs or circulatory system. not a cure, just helps initially • Fetal Hb (Hb F) has > O2 affinity physiologically than Hb A (adult) b/c Hb F binds BPG < strongly than does Hb A, thereby allowing O2 flow from maternal oxyHb to fetal deoxyHb.

Bone lining cells and Nutrient supply

Bone lining cells •On surface •Monolayer •Communicate between Osteocytes and exterior Nutrient supply •Via canaliculi •Blood vessels only in Haversian and Volkman's canals

Cornea Connective tissue

Bowman's layer (connects the two) • Stroma bound to the epithelial basement membrane • Lacks fibroblasts, contains proteins and ground substance Stroma - thickest part • Fibroblasts • Collagen - regular arrangement, responsible for transparency of cornea • Proteoglycans • Ground substance Descemet's membrane - similar to BL, connects endothelium and stroma • Basement membrane of endothelium • Collagen • Proteins like fibronectin

CN- inhibition of fuel oxidation

CN- shuts down oxidative metabolism -no longer has energy for pump to function -[lactose] decreases until [lactose] inside is equal to [lactose] outside cell

major solar energy pathway

COHN -COH - digested nutrients -N - nitrogen from environment

smooth muscle excitation Contraction Coupling, Relaxation

Calcium renormalization - calcium levels must drop to normal levels, autonomic innervation closes calcium channels •End of excitatory signal •Sarcolemmal Ca2+ATPase activity •Na+Ca2+ exchanger activity on sarcolemma •Sarcoplasmic reticulum Ca2+ATPase activity •Store Operated Ca2+channel (SOC) Deactivation of MLCK Myosin phosphatase (dephosphorylases) activity predominates

Lens

Capsule - covers lens, where zonules are inserted Epithelium • Only on anterior surface of lens • Simple cuboidal epithelium • Gives rise to new cells, constantly dividing • New cells converted to lens fibers • New lens fibers form outer shells • Old fibers pushed to the center --> gets compacted over time, optical density of tissue increases, possibly causing cataracts and change in refractive index Fibers

Metabolism divided into catabolism and anabolism.

Catabolism Large nutrient molecules → lactic, acetic acids; CO2, NH3, urea Free energy released and stored as ATP. Anabolism Simple precursors → molecular cell components Free energy input from ATP.

bone composition cont.

Cells •Osteoblasts (bone forming), can be regenerated, destroyed by apoptosis or become osteocytes •Bone lining cells (initiate bone remodeling) - recruit new osteoblasts and osteoclasts •Osteocytes (entoumbed osteoblasts) •Osteoclasts (bone digesting) - bone remodeling, mostly occurs in interior parts The above composition of bone helps to •Resist mechanical impact •Also makes it flexible enough to torque and bend

monosaccharides cyclic form

Common monosaccharides occur in cyclic form

Two types of lamellar bone

Compact (aka cortical or dense) bone •Hard outer layer •Extremely dense so low porocity •Strong •Accounts for 80% of total bone mass Trabecular (aka cancellous or spongy, much smaller portion) bone •Fills the interior •Lacy and porous •Large surface area (10x of compact bone), because is porous •First to release calcium when plasma calcium levels fall •Rebuilt when calcium and phosphate levels renormalize •Do not contain osteones or Haversian canal

gap junctions - Connexin gene mutations

Connexin gene mutations • Idiopathic atrial fibrillation, contractional structures connected via gap junctions. Irregular heartbeat • Hearing loss • X‐linked form of Charcot‐Marie‐Tooth (CMT) disease • Congenital cataract - nutrients don't spread, things accumulate in glands • Oculodentodigital dysplasia - eye, dental, 2 fingers together

3 physiologically important forms of iron

• 3 physiologically important forms differ in 6th coordination position: (+2) deoxyMb - empty (+2) oxyMb - O2 (+3) ferriMb - H2O, oxygen cannot bind if valence state is in +3 state • pp chain of Mb necessary to allow reversible oxygenation, or else oxygen will remain bound. keeps oxygen bound for the necessary period of time, prevents oxygen from binding between two hemes (intermediate) • CO poisons ferroMb and ferroHb and blocks O2 transport. Isolated heme binds CO ~ 25,000 X more strongly than it binds O2. In Mb and Hb, binding affinity for CO relative to O2 only ~200X as great b/c binding of CO sterically hindered by distal HIS (E7). still very dangerous. --> in a normal situation, [CO] is very low and therefore doesn't matter

Lipid Aggregation

• 3 types of lipid aggregation a) micelle b) bilayer c) liposome

Cornea Epithelium

• 6‐8 layers of cells • Basement membrane • Basal cells - columnar (transformation #1), bottom cells, attached to basement membrane. able to divide, push cells up • Wing cells - several layers (2), freshly formed cells • Squamous cells - several layers (3), flat, less mito and other structures, facilitates diffusion, gets slotched off • 10 day life cycle • Junctional complexes --> Desmosomes --> Hemidesmosomes --> Adherens junctions

Functions of retinal pigment epithelium

• Absorption of light not captured by photoreceptors • Supplies nutrients to the photoreceptors, including O2, primary source of nutrients for photoreceptors • Helps to control the ionic microenvironment of the extracellular space • Replenishes retinal to reconstitute photopigments after a visual bleach • Phagocytoses shed photoreceptor outersegments in a renewal process • Secretes a variety of growth factors that aid in maintaining structural integrity of retinal neurons, more specifically the photoreceptors

Acini

• Acini contain only serous cells (not mucus cells) • Acini contain central lumen -line by epithelial cells, aqueous secretions -gets inside, then drained in ducts

Active Transport

• Active - against concentration gradient, gains free energy (delta G is greater than 0); passive - with concentration gradient, looses free energy. • Thermodynamic definition: active transport - system gains free energy; passive transport - system loses free energy.

Adherens junctions

• Adherens junctions (aka zonula adherens) - main function is to provide strength • Bridge that connects the actin of cytoskeleton of adjacent cells • Transmembrane linkers are cadherin or integrin • Provides strength to the tissue

pH regulation of Hb

• Affinity for O2 regulated by pH, CO2 and organic phosphates (BPG - biphosphoglycerate). • < pH releases O2 -ex. metabolism, you need O2 during these mechanism

Fatty Acids

• All have hydrocarbon tail and terminal -COOH group; chain may be saturated (all C-C bonds), monounsaturated (one C=C bond) or polyunsaturated (2 or more C=C bonds, PUFA)

Ground substance

• Amorphous gel • Proteins (mainly proteoglycans made of glycosaminoglycans) • Extracellular fluid

diabetes

• An estimated 30.3 million people of all ages (or 9.4% of the U.S. population) had diabetes in 2015. • This total included 30.2 million adults aged 18 years or older (12.2% of all U.S. adults), of which 7.2 million (23.8%) were not aware of or did not report having diabetes. • The percentage of adults with diabetes increased with age, reaching a high of 25.2% among those aged 65 years or older. • Compared to non-Hispanic whites, the ageadjusted prevalence of diagnosed and undiagnosed diabetes was higher among Asians, non-Hispanic blacks, and Hispanics during 2011-2014.

Erythrocyte cont.

• Anion channel - single pp chain; 929 AA residues; MW ~ 106 kD; each cell contains ~ 106 molecules. • Globular shape; straddles bilayer; most buried ion membrane. Held in place by spectrin and ankyrin (anchors it in place). • Allows HCO3 - and Cl- to equilibrate across erythrocyte membrane. --> important to keep it in one place because it is allowing things to come through

LDH (lactate dehydrogenase)

• At least 5 different isozymes. • Contain different ratios of 2 kinds of pp's that differ in AA composition and sequence: A chain (also M, for muscle) and B chain (also H, for heart). • In skeletal muscle, predominant form is A4 ; in heart, B4. In other tissue, mixture of A4, A3B, A2B2, AB3, B4. Have different KM and Vmax.

Lactic Acid - Performance- Enhancing Drug

• Athletes experience muscle fatigue with accumulation of lactic acid • Approaches used to enhance performance - creatine supplementation, carbohydrate loading, training at high altitude. • Muscle fatigue has been synonymous with accumulation of lactic acid. • The new idea is that lactic acid, rather than being a cause of muscle fatigue, actually combats it. -The decrease f pH in particular - metabolic acidosis, decrease in Cl- channel activity, which sustains AP

ECM

• Bacterial cell walls contain polysaccharides; degraded by lysozyme. • Extracellular matrix - gel-like material that fills extracellular space in animal tissue -holds cells of a tissue together (structural function) and provides porpous pathway for diffusion of nutrients and O2 to cells. -Composed of interlocking meshwork of heteropolysaccharides (glycosaminoglycans, GAG's) and fibrous (keeps GAGs in place) proteins. -GAG's attached to extracellular proteins to form proteoglycans. -also helps get rid of waste products, provides a proper medium

enzyme people

• Buchner (1897) - extracted enzymes that catalyze alcoholic fermentation in yeast cells. • Sumner (1926) - isolated urease in pure crystalline form; recognized that enzymes are proteins. • Northrop (1930-36) - isolated crystalline pepsin, trypsin and chymotrypsin; protein nature of enzymes firmly established.

microorganisms and causing disease

• Carbohydrates can carry much more information per unit weight than either proteins or nucleic acids. due to the increase number of structures that can be formed • To cause disease, microorganisms must be able to attach themselves to a cell. don't want cell to have a recognition site that's unfamiliar. -Infectious agents lacking that capability are swept away from potential sites of infection by the body's normal cleansing mechanisms.

Gout

• Catabolism of purines, N-containing heterocyclic compounds. • Excess of uric acid in blood; precipitates as urate crystals. these get stuck in capillaries, usually in feet • Stimulates release of lysosomal enzymes which digest cellular components.

Chaperones

• Chaperone - prevents aggregation (may make proteins inactive) of partially denatured proteins by binding transiently to exposed hydrophobic areas in different molecules, thereby preventing them from clumping together, stops unfolding protein and allows them to properly fold; stress proteins (e.g., heat shock proteins). Also function in this way normally when pp chain being assembled on ribosome. • What happens to misfolded proteins? Some remain in ER and are sequestered and degraded there w/o being secreted. Some are secreted and degraded extracellularly. Some molecular chaperones involved in targeting irreversibly misfolded proteins for degradation in ER. -due to crowding, proteins may form an aggregation via H-bonding, chaperones prevent this

Chloride-bicarbonate exchanger

• Chloride-bicarbonate exchanger - another passive transport system. > permeability of erythrocyte membrane to HCO3- by factor of > 106 . • Coupling of Cl- and HCO3- obligatory; e.g. of cotransport system.

FAs

• Cis (electrons are closer together, steric hindrance) vs. trans (always more stable). Cis predominates in naturally occurring fatty acids. • Long chain fatty acids insoluble in H2O; their Na+and K+ salts (soaps) form micelles in H2O. • Unsaturated fatty acids (much more reactive) undergo addition reactions at their double bonds, more likely to spit up --> a saturated FA can only go undergo substitution with H ions.

Structure of Collagen

• Collagen is an important constituent of connective tissue: tendons, cartilage, bones, cornea of the eye • Each collagen chain is a long Gly- and Pro-rich • The triple helix has higher tensile strength than a steel wire of equal cross section • Many triple-helices assemble into a collagen fibril

Competitive Inhibition

• Competitive Inhibition 1) I chemically resembles S; I binds to E at active site. 2) EI cannot form product. 3) > [S] relative to [I], < amount of inhibition.

Sclera

• Connective tissue • Episclera - superficial • Stroma (order of layers from fibroblasts to ground subs --> Fibroblasts --> Collagen - lack of transparency because not a regular arrangement --> Proteoglycans --> Ground substance • Lamina fusca • Endothelium

Monosaccharides

• Crystalline solids; soluble in H2O; insoluble in nonpolar solvents. • Have assymetric centers (chiral C's). -can only use monosaccharides in metabolism

Membrane Structure

• Davson and Danielli (1935) - lipid-protein bilayer model. • Accounts for several properties of cell membranes: 1) Phospholipids form bilayer spontaneously in aqueous medium; represents minimum energy configuration. 2) Hydrocarbons poor conductors; accounts for hi resistance. 3) Nonpolar molecules dissolve readily in hydrocarbon phase while charged ions do not; accounts for permeability characteristics. 4) Consistent with electron micrographs; e.g., electron dense lines represent polar head groups.

Desmosomes

• Desmosomes (aka macula adherens) mechanical • Also act as bridge that connects the cytoskeleton of adjacent cells • Bridging proteins are connected to membrane associated proteins on the cytosolic side (a plaque), which in turn are attached to keratin or desmin • Transmembrane linkers are cadherin (for desmosomes) • Acts as rivets (protein plates, connected to cytoskeleton structure) and provides strength to the tissue

Isozymes

• Different molecular forms of an enzyme. catalyze the same reaction, but have different forms depending on where reaction is occurring and what's going on • Generally differ in kinetic or regulatory properties, in form of cofactor (e.g., NADH vs. NADPH for dehydrogenases), or in their subcellular distribution (soluble vs. membrane bound). • Usually have similar but not identical AA sequences.

Elastic fibers

• Elastin • Glycoprotein microfibrils (fibrillin, fibulin etc.) • Lungs, arteries, veins

Substrate Specificity

• Enzymes vary in their degree of specificity; narrow (lock and key, enzymes interact with a very specific molecule, some could even differentiate between cis vs trans, L vs D) vs. broad (induced fit, enzyme often involved in many functions of many different cells) • Lock and key hypothesis. • Induced fit.

Conjunctiva

• Epithelial tissue • Interspersed with mucin producing goblet cells -covers where sclera is exposed, goes under eyelids -protective, produces mucin, transparent

Erythrocytes

• Erythrocytes contain membrane = glycoprotein. Also, many soluble glycoproteins, e.g., carrier (transport) proteins and Ig's in blood and many of the proteins within lysosomes.

Glandular Epithelia

• Exocrine glands (Sweat, salivary, mammary glands) - secretions occurs into open space • Serous • Watery secretion • Bicarbonate ions • Enzymes • Antibacterial agents - e.g. lactoferrin • Mucous (mucin - glycoprotein) • Endocrine glands - secretes hormones into blood

Smooth muscle thin filaments

• F actin double helix made of G actin molecules • No troponin or tropomyosin •Contains Cladesmon and calponin -->Actin‐associated myosin ATPase inhibitors -->Inhibition relieved by ---->High Ca2+ calmodulin (CaM) conc, activates kinase ---->Phosphorylation by Ca2+ calmodulin dependent kinases, Phosphorylation of myosin head allows for ATPase activity, lifting inhib

Prostaglandins

• First found in prostate glands of mammals. • Function as modulators of hormone activity, e.g., stimulate muscle contraction. • Formed from polyunsaturated fatty acids (PUFA's) by oxidative closure of five-membered C-ring in middle of fatty acid chain.

Gap junctions (location of gap junction channels)

• Formed by two connexon hemichannels, facilitates movemont • Connexons --> Contains 6 connexin monomers • Connexins --> 21 connexin isoforms in humans • Gating factors - may or may not be gated • Permeability • Connexin gene mutations

Lipid Bilayer

• Forms spontaneously. • Has properties similar to cell membranes re: permeability. • Since hydrocarbon phase has low dielectric constant (is nonpolar) and is poor conductor, bilayer has hi electrical capacitance (ability to store energy) and resistance

Living systems extract energy

• From sunlight - plants - green bacteria - cyanobacteria • From fuels - animals - most bacteria • Energy input is needed in order to maintain life