Unit 1 Exam Prep Flashcards
What are the two parts of holoenzymes?
Two parts, protein called apoenzyme and non-protein component called the cofactor (could be loosely bound such as coenzymes or tightly bound such as prosthetic groups)
What is compartmentalization?
Isolate the reaction, substrate or product from other competing reactions
Provide favorable environment for the reaction
Organize enzymes into purposeful pathways
What are Isoenzymes?
Different enzymes that catalyze the same reaction
Usually located in different tissues or organelles
Where is chymotypsin produced? What is it a precursor to? What is the function of its active form?
Produced by pancreas as inactive precursor to chymotrypsinogen
Hydrolyses peptide bond on carbon side of Phe, Tyr, or Trp
What are mechanism-based inhibitors used for? What are some examples?
Mimic or participate in intermediate step of reaction
Penicillin – binds tightly to glycopeptidyl transferases that are required for cell wall synthesis
Allopurinol – “suicide” inhibitor of xanthine oxidase, decrease in urate production, used in the treatment of gout
What are covalent inhibitors?
What are Transition State Analogous?
Form covalent bond with functional groups in catalytic site
Bind more tightly than substrate or product
What are some uses for inhibitors?
Chemotherapy – uses drugs to treat disease
Metabolic control – through allosteric or substrate inhibition and activation
Natural poisons – are secondary metabolites, peptides or proteins
Michaelis-Menten
V(0) = Vmax[S]/(Km+[S])
Km
Affinity of enzyme for a particular substrate
Lineweaver burke plot vs Michaelis Menten
Less points, extrapolation easier,
Reversible inhibitor
Non-covalent bonds, enzyme regains activity through dilution
Irreversible inhibitor
Cannot regain activity through dilution. Covalent interaction between inhibitor and enzyme or very tightly bound EI complex
What are allosteric enzymes? What are the forms that they can take?
Allosteric enzymes are enzymes that change their conformation upon binding an effector. Usually consist of multiple subunits
Subunits can exist in relaxed active (R) or taut inactive (T) conformation
Allosteric effectors promote or inhibit conversion from one conformation to another
Competitive inhibition
Inhibitor binds to the same site as substrate
Inhibition can be reversed by high [S]
Vmax does not change, reachable at high [S]
Km increased, more substrate needed to achieve 1/2Vmax
What is cooperativity binding?
Binding of substrate to one subunit facilitates its binding to the other
First binding is slow – enzyme in T conformation
Triggers the changes in subunits adjacent to high-affinity or relaxed R state
What are some of the advantages of allosteric regulators?
Stronger effect than competitive and noncompetitive inhibitors
May act as activators (don’t occupy active site)
Do not require to resemble S or P
Effect is rapid, as concentration changes in the cell
What are the two most common covalent modifications?
Phosphorylation is the most common modification
AND-ribosylation of Arg or Lys in G-proteins by bacterial toxins
What is protein-protein interaction? Give examples
Can regulate conformation of active sites
PKA – inactive when bound to inhibitory R subunit, activated by cAMP, binding of cAMP to inhibitory subunit changes the conformation of the inhibitor dissociating it from the catalytic site, PKA becomes active
Noncompetitive
Substrate and inhibitor binds at different sites Inhibitor can bind to ES complex Can't be overcome by increased [S] Km does not change Vmax decreased
Regulation by conformational changes
Allosteric activation or inhibition
Phosphorylation or other modifications
Protein-protein interactions
Proteolytic cleavage
What are llosteric activators or inhibitors
Compounds that bind to the allosteric site (not catalytic)
Cause conformational changes that affect affinity for substrate
Allosteric inhibition is the example of noncompetitive inhibition
What are four types of regulation in metabolic pathways?
Rate-limiting step – slowest and irreversible, influences the rest of the pathway
Feedback regulation - product controls its own synthesis
Feed-forward regulation – increase of substrate (disposal of toxic compounds, storage)
Tissue isozymes – same function, different kinetics
What does the lack of chemical signals lead to?
Lack of chemical signals: infertilities (lack of gonadotropin), type I diabetes mellitus (lack of insulin), hypothyroidism (reduced thyroid hormone levels), hormone deficiencies
Calmodulin
Calcium binding proteins, binds to and regulates different protein targets. Has four Ca2+ binding sites. Binding of Ca2+ leads to conformational change.
In the liver, binding of Ca2+ activates GPK, which is an activator of glycogen phosphorylase, a key activator in glycogenolysis
What causes hyperactivity to signals?
Lack of regulation (e.g., hyperthyroidism, cAMP overproduction in cholera or whooping cough)
Proteolytic cleavage
Activates proteozymes and zymogens
Why are some enzymes produced as inactive?
In the example of blood clotting, zymogens are activated in times of damaged blood vessel
What happens in Myasthenia gravis?
Autoimmune neuromuscular disease, (muscle weakness, muscle fatigue)
Autoantibodies against the nicotinic ACh receptors
- inhibit ACh binding to the receptor
- enhance the internalization and destruction of the receptor
Low levels of functional ACh receptors on skeletal muscle, (too little signaling)
Explain impairment of acetylcholine signaling II and treatment (organophosphates)
Organophosphates - irreversibly inhibit ACh esterase - excess ACh not destroyed (too much signaling) - contraction/relaxation cycle in the heart is impaired - death
Treatment: atropine, a muscarinic ACh receptor antagonist
5 Major chemical signals and roles
Neurotransmitters – produced by the nervous system
- AA derivatives, neuropeptides
Hormones – produced by the endocrine system (mostly)
Cytokines – produced by the immune system, regulate
immune function
- interferons, interleukins
Eicosanoids – produced in response to injury or inflammation
- arachidonic acid derivatives
Growth factors – regulate cell differentiation and proliferation
- proteins
Water insoluble chemical signals
Steroid hormones, thyroid hormone, Vitamin D3, require transport proteins (albumin or specific transporters), others are soluble
Insensitivity to signaling molecules
deficient receptors, intracellular signaling pathway, interference from other signaling pathways (e.g., type II diabetes mellitus). Lots of insulin, but cells are not able to react
Explain Intracellular receptors (Type I and III), (steroid hormones)
Type I and III receptors are localized in the cytosol in complex with HSP, when hormone is bound to the receptor, HSP is shed and receptors are dimerized, it translocates to the nucleus and induce gene transcription with the help of co-activators
Explain Type II nuclear receptor signaling (retinoid acid, vitamin D3, thyroid hormone)
Type II receptor localized in the nucleus in a dimer form and is bound to DNA, it is unable to initiate transcription due to corepressor, when hormone is bound, corepressor is replaced by a coactivator, receptor-hormone complex can now induce transcription
Treatment to lack of signals (hormones)
administer the hormone to the patient (insulin injection, gonadotropin hormone treatment)
enhance hormone production (dietary iodine to induce more thyroid hormone production)
Explain G-protein linked receptor
Signal attaches to a receptor, activates G-protein leading to a signal cascade
What are the main second messengers
Cyclic AMP (cAMP) Cyclic GMP (cGMP) Ca2+ Diacylglycerol (DAG) Inositol triphosphate (IP3)
Signaling insensitivity or hyper-reactivity
too much hormone: decrease it, biochemically or surgically (hyperthyroidism)
Signaling at the neuromuscular junction
Chemical signal:
- acetylcholine (ACh)
Signal detection (receptors):
- nicotinic ACh receptor (skeletal muscle) Na+/K+ channel
- muscarinic ACh receptor (heart muscle) G protein-linked receptor
Conversion of signal:
- nicotinic ACh receptor lets Na+ in and K+ out
- muscarinic ACh receptor regulates a K+ channel
Regulation:
- acetylcholine esterase, degrades excess ACh
Which signals can pass freely through the membrane?
Hydrophobic, hydrophilic has to go through a receptor to send signal
Ion linked receptor
Chemical signal binds, channel opens or closes. Used in the CNS and the PNS. Example is nicotinic ACh receptor
Adenylyl cyclase
Two receptors, on stimulatory and one inhibitory. Epinephrine/glucagon/ACTH (stimulatory) binds to receptor, it stimulates stimulatory G protein, activates adenylyl cyclase. Prostaglandin E1 and adenosine bind to inhibitory receptors, bind to inhibitory G protein, and deactivates adenylyl cyclase.
What are Enzyme or Enzyme-linked receptors
Either kinases or associated with kinases. Receptor has to dimerize. Signaling requires phosphorylation of receptor. Receptor then binds to signal transducer proteins.
Examples are JAK-STAT, Ser-Thr kinase, and Tyr kinase
What is JAK-STAT used for. What is JAK? What is STAT? Explain the pathway.
Used by most cytokines for signaling.
JAKs are tyrosine kinases associated with the receptor.
STATs are signal transducer proteins.
Receptors bind cytokines, dimerizes, binds JAKs. JAKs phosphorylates each other and the receptor, receptor then binds and phosphorylates STATs. STATs dissociates from receptors, dimerizes, and translocates to nucleus to regulate gene transcription
Explain Ser-Thr kinase receptors
Used by transforming growth factor beta family (TGF-B). R-Smad is the signal transducer that binds to the protein. TGF-B binds to type II receptor, type II phosphorylates type I, which then phosphorylates R-Smad. R-Smad complexes with Co-Smad and translocates to the nucleus to regulate gene transcription
Explain Tyr kinase receptors
Used by many growth factors and insulin. Growth factor binds to the Tyr kinase domain, binds to adaptor proteins, activating ras/raf, which regulates gene transcription
What does MAP-kinase pathway do?
Regulate transcription and translation of genes necessary for glucose metabolism
What does PI3-kinase pathway do?
Glucose transporter (GLUT4) is shuttled to the plasma membrane to enhance glucose uptake by muscle and adipose tissue.
What does PLCy pathway do?
Excess glucose can be stored in glycogen or fatty acids (lipids)
Cholera toxin
Transfers ADP-ribose to stimulatory G-protein complex, adenylyl cyclase remain active. GTP cannot be hydrolyzed to GDP. Causes extreme salt and water efflux from gut epithelial cells to lumen, causing diarrhea.
Explain Thyroid hormone production
Hypothalamus (secretes TSH releasing hormone) —> acts on anterior pituitary —> ant pit releases TSH —> acts on thyroid gland —> releases thyroid hormone —> negative feedback to hypothalamus and anterior pituitary to stop the release of TSH releasing hormone and TSH, respectively
What happens in Grave’s disease (hyperthyroidism)?
Autoantibodies stimulate TSH receptors in the thyroid gland, increasing thyroid hormone production, it down grades TSH production, but has no effect. Negative feedback does not work
Pertussis toxin (whooping cough)
ADP-ribose is bound to inhibitory Gia protein subunit, G protein cannot bind to receptor, adenylyl cyclase cannot be inhibited. Leads to increased mucous in the epithelium
Protein Kinase C G-protein pathway
Signal binds to G-protein linked receptor, activates G subunit, activates phospholipase C, IP3 opens channel in the ER, Ca2+ is released, Ca2+ binds and activates PKC
Ion channel activation
Signal (ACh) binds, activates muscarinic ACh receptor, GDP turns to GTP, opens ion channel
5 mechanisms of signaling regulation
Destruction of signal (ACh esterase destroys ACh)
Decreased synthesis of chemical signal (negative feedback regulation of hormone synthesis in the hypothalamus and the pituitary gland)
Destruction of the functional receptors (desensitization of some receptors to phosphorylation/removal of receptors through endocytosis)
Destructions of second messengers (cAMP/cGMP)
Reversing the effects of kinase (phosphatases)
Trapezius (innervation/artery/action/consequence of damage)
Accessory nerve (CN XI)/superficial transverse cervical artery/elevate shoulders, depress and elevate scapula/shoulder drooping, unable to raise arm overhead
Latissimus dorsi (innervation and artery/action/consequence of damage)
Thoracodorsal nerve (C6-8)/thoracodorsal artery/extend and accuct, rotates humerus (pull up)/unable to pullup
Levator scapulae (innervation and artery/action/consequence of damage)
Dorsal scapular nerve (C5),spinal nerve/C5 artery/elevate scapula/depressed scapula, lateral shift in scapula on injured side)
Rhomboid minor (innervation and artery/action/consequence of damage)
Dorsal scapular nerve (C5)/C5/retract scapula/same nerve injury as levator
Rhomboid major (innervation and artery/action/consequence of damage)
Dorsal scapular nerve (C5)/C5/retract scapula/same as nerve injury as levator
Serratus posterior superior (innervation and artery/action/consequence of damage)
Intercostal nerves 2-5/intercostal arteries 2-5/elevates upper ribs
What is Scapulohumeral rhythm?
Once the humerus passes 30°, scapula must rotate it
Serratus posterior inferior (innervation and artery/action/consequence of damage)
Intercostal nerves T9-T12/arteries/depress lower ribs
What is the composition of cardiolipid? What does it do?
Phospholipid with 4 FA tails - Decrease permeability into mitochondria
Supraspinatus muscle (innervation and artery/action/consequence of damage)
Suprascapular artery
What does Clathrin do?
Helps transport particles from the Golgi by creating vessels. Also used in pinocytosis, the typically nonselective process of ingestion of fluid and small particles. Clathrin comes off after vesicle formation
What are the three types of cytoskeleton?
Microtubules: hollow and polar, used for movement in cell
Intermediate filaments: like a rope, gives integrity
Actin filaments: cell migration, integrity, muscle
What is the function of cytoskeleton?
Structural support (cell shape and protection), intracellular organization (transport of organelles to specific sites), Cell motility (contraction, changes in shape, cell migration, actions of cilia and flagella)
Hematoxylin and eosin (H&E)
Hematoxylin: basic violet dye → binds to ACIDIC structures (DNA)
Eosin: acidic pink dye → binds BASIC structures
Infraspinatus muscle (innervation and artery/action/consequence of damage)
Suprascapular artery/circumflex scapular artery
Serratus anterior (innervation and artery/action/consequence of damage)
Long thoracic nerve (C5-C7)/protraction and rotation of scapula
Ribonucleoprotein particles
Condensation of new RNA (heterogenous or hnRNPS), RNA splicing (remove introns)
What is the function of Microvilli?
Increase surface area for absoption/secretion, and thus are found on cells such as those lining the intestines
What is the function of Cilia?
Transport matter along the cell surface. They are found on columnar cells liking the uterus and oviduct, bronchi, and spinal cord central canal
SER Function
Lipid and cholesterol synthesis
How would you mount a sample with active enzymes and preserved cell components?
Rapidly freezing tissues
Simple cuboidal epithelium location and function
ducts of many glands as well as most kidney tubules. protective barrier and has a secretory and absorptive functions
Simple columnar epithelium location and function
They line the stomach, intestine, uterus, oviducts, small bronchi of the lung, paranasal sinus, ependymal cells of spinal cord, the wall of some large kidney ducts
The major function of simple columnar epithelium is protection, secretion, absorption, and transport
What happens when cells are keratinized?
Cytoplasm and nucleus are replaced with keratin
Basal lamina composition
Collagen type IV, the glycoprotein lamin, the glycoprotein fibronectin, as well as a proteoglycan (heparin sulfate)
Laminin
Means of attaching the basal lamina to the epithelium. It has binding sites for integrins. It is a cross-shaped trimer and it is important for cell recognition and adhesion
Integrins
A class of epithelial cell integral membrane proteins, and collagen type IV and other components of the basal lamina
Basement membrane
Thicker than basal lamina, two basal laminas together. Prominent in tissues such as kidney glomerulus and lung alveoli
What are stereocilia, what are its functions?
Elongated, branched microvilli found only in the epididymis where they increase surface area and the cochlea of the inner ear where they are involved in sensory signal generation
Glycocalyx
Filamentous fuzzy coating overlying the microvilli surface. It helps protect the cell from chemical and physical injuries
Ciliary Dynein
Motor protein attached to a microtubule. It is used for moving cargo along microtubule within a cell. It is necessary for flagellar motion. A mutation in ciliary dynein would most likely result in infertility
Lateral and basal cell specializations
Specializations that are typically involved with either increasing surface area or attachment to adjacent cells or tissue
Zonula occludens or tight junctions
Nearest the apical surface, runs completely around the cell perimeter. Two primary functions, first being the prevention of water-soluble molecules from passing between cells but fusing to the plasma membrane of adjacent cells. The next is to maintain the plasma membrane protein polarity
Zonula adherens or belt desmosomes
Basal to the tight junction in many epithelial cells. They are not meant to prevent leakage, they just connect the cells together. It also provides some rigidity to the apical portion of the cell
Macula adherens or desmosomes
Located below belt desmosomes in epithelia. Makes firm cell-cell attachments and help distribute shear forces
Hemidesmosomes
Attaches basal cell membrane to the underlying basal lamina
Gap junctions
Involves many connexons in adjacent cell membranes forming channels across membranes. Permits movement up to 1.5kD
Hyperplasia
Increase in the number of cells in a tissue. Often arises as inflammation or irritation
Metaplasia
Epithelial tissue transforms to a different type of tissue. This can be triggered by cigarette smoking
Dysplasia
Changes in the normal morphology and organization of cells making up a tissue. Early stage of cancer
What is Glycoprotein and give examples
At least one sugar bound to AA side chains. An example would be fibronectin and laminin
What is Fibronectin? Where is it found?
A type of glycoprotein made up of fibroblasts found in the basal lamina. It is important for cell to cell or cell to substrate recognition and adhesion
Ground substance
Noncellular CT component, GAGs and glycoproteins
GAGs
Linear, unbranched polysaccharide of repeating disaccharide units, hydrophilic, allows for rapid diffusion of water soluble particles
Proteoglycans
Core protein with bound GAGs
Hyaluronic acid
Unique GAGs of many thousand disaccharides, many proteoglycans attached, forming large aggregates. Highly viscous and found in synovial fluid, cartilage, and vitreous humor of the eye. It is highly porous but serves as a barrier to protect from bacteria (can be broken by hyaluronidase)
Collagen
3 alpha chains that are formed in the RER. It is rich in Gly, Lys, and Pro that are hydroxylated. It is first synthesized as a procollagen with propetides at both ends to keep it from prematurely coiling completely. Procollagen is transported out of the cell from the Golgi. N and C procollagen peptidases then cleave procollagen. Collagen monomers can come together to form fibrils
Collagen Type I, how is it stained?
Fibril forming. Found in skin, bones, tendons, blood vessels, and cornea. It is the most abundant and stains red (acidophilic)
Collagen Type II
Fibril forming. Found in hyaline and elastic cartilage, invertebral disk, vitreous body
Collagen Type III
Fibril forming. Found in the blood vessels, fetal skin. Part of reticular CT
Collagen Type IV
Network forming. Found in the basal membrane. It does not form fibers
Adipose function and two types
A type of loose CT. Fat cells (adipocytes), they store and make triglycerides, they are fully differentiated and do not divide.
Two types are white (unilocular), which are most abundant, energy storage and brown (multilocular), which aids in the production of heat. This is mostly found in embryos
Reticular fibers
Very thin, found in hematopoietic organs such as the spleen, lymph nodes, and the red bone marrow. Also found in the liver, endocrine glands, endometrium and smooth muscles. It is made up of loosely packed collagen type III held together by proteoglycans and glycoproteins. It does not stain with H&E, it is argyrophilic, it binds silver salts and it shows up black
Elastic fibers (composition and staining)
Can stretch 150% in length, it is found in expanding tissues such as the lungs, aorta, and the skin. It is poorly stained with H&E, orcein stains it purple-black. It is made up of elastic core and fibrillin (glycoprotein)
Marfan’s syndrome
Mutation of fibrillin, wide range of symptoms such as the weakening of the vascular walls and causing aortic rupture
Fibroblasts
Most common in cells in the CT proper, it makes CT fibers and ground substance. It has a pale nucleus and lots of RER and GA. Fibrocytes are the inactive form, it is smaller, darker nucleus. Myofibroblasts are fibroblasts with actin filament bundles, they are prevalent in wound healing
What are Mesenchymal cells?
Part of embryonic CT. Multi-potential cells from embryonic mesoderm, found only in embryo. They are replaced by pluripotential cells in adults
Mast cells
Inflammatory response cells
Types of mast cells
Secretory granules – fill cytoplasm, contains chemicals for inflammatory response. They are basophilic, therefore they are died blue
Primary mediators – pharmacological agents in granules like heparin (anticoagulant), histamine (vasodilation)
Secondary mediators – not stored in granules, made for immediate release like leukotrienes (cause vasodilation, bronchial contraction, and vascular permeability)
Immediate hypersensitivity reaction – allergic reaction from granule release after antigen introduction
Macrophages (resident/elicited)
Digestion of debris, dead cells, and invaders
Resident – not activated, reside in CT along collagen
Elicited – Mobilized to a site in response to stimulus
What is Reticular tissue? Where is it found?
A type of loose CT. Mostly type III collagen, developing blood cells found in between reticular network, framework for marrow, smooth muscle, lymphoid and liver
Plasma cells
Found throughout CT, they produce antibodies