Flashcards in Medical Physiology Block 1 Week 1 Deck (56):
Medical physiology deals with how the human body functions; It requires an integrated understanding of events at the level of molecules, cells, and organs.
Define Physiological Genomics
integrated understanding of a gene's function at the level of the cells, organs, and whole body
Explain the concept developed by Claude Bernard of the internal milieu
Cells live in a highly protected milieu; internal milieu = extracellular fluid (different from external milieu)
Define homeostasis (steps)
regulation of internal milieu; First, the system must be able to sense the vital parameter (e.g., glucose) or something related to it. Second, the system must be able to compare the input signal with some internal reference value called a set-point, thereby forming a difference signal. Third, the system must multiply the error signal by some proportionality factor (i.e., the gain) to produce some sort of output signal (e.g., release of insulin). Fourth, the output signal must be able to activate an effector mechanism (e.g., glucose uptake and metabolism) that opposes the source of the input signal and thereby brings the vital parameter closer to the set-point (e.g., decrease of blood glucose levels to normal)
Compare and contrast the conditions of equilibrium and steady-state
Equilibrium: force = 0 (no immediate energy needed; energy is needed to create gradients); steady-state: vital parameter is constant/time (ATP may be necessary)
Argue the point that Medicine is Physiology gone awry
It is essential to know how organs and systems function in the healthy person to grasp which components may be malfunctioning in a patient.
Describe the structural organization and characteristic lipid composition of the plasma membrane.
Phospholipid: in general glycerol backbone (3 carbons) + two fatty acids (forming ester bond RCOOR; nonpolar) + phosphate group (another ester bond) + head group (form ester bond with phosphate; name of lipid is derived by head group; polar); outer surface of plasma membrane = phosphatidylcholines; inner surface, phosphatidylserines and phosphatidylethanolamines); remember that they cannot change polarity unless cell is preparing for apoptosis
A compound (in this case, a polypeptide) that has polar and nonpolar properties
How are cholesterol proteins different from other phospholipids found in the bilayer (fluidity?)
found normally in the plasma membrane and not in membranes of organelles; cholesterol may be a regulatory mechanism for blocking ion movement and water (homeostasis in regards to increases in osmotic pressure by increasing membrane rigidity; cholesterol can easily flip or change polarity) (at low concentrations, cholesterol reduces fluidity; at high concentrations, cholesterol inhibits nonpolar forces between phospholipids thus increasing fluidity); remember that fluidity is decreased with saturation and length
Compare and contrast the structural characteristics of the different classes of integral membrane proteins (MIGHT NEED TO MAKE MORE DETAILED)
Single transmembrane domain (involved in phosphorylating other proteins; a subunit of a channel), multiple transmembrane domains (GPCR; sometimes may function as a subunit of a channel), without a transmembrane domain (acetylcholinesterase- has flexibility to move around sequestering ACTH; GPI-linked)
List and explain five major functions of membrane proteins
serve as receptors, serve as adhesion molecules, can be enzymes, can conduct the flow of ions (channel), and can be involved in intracellular signaling (catabolism of the protein; think cleavage of PIP2 in to diacylglycerol and IP3; may also be considered in the context of membrane proteins binding to cytoskeletal filaments)
Describe the unique structural characteristics and critical functions that define the nucleus, the lysosomes, and the mitochondria
Nucleus: double membrane, cytosolic proteins entering must have localization signal (stores, replicates, and transcribes DNA); lysosome: site of digestion of proteins and cellular debris (filled with proton pumps that keep the organelle in an acidic environment); mitochondria: double membrane, site of ATP production (inner membrane), and storage of calcium
Describe the unique structural characteristics and critical functions of the four major types of filaments that comprise the cytoskeleton of mammalian cells
Intermediate filament proteins: structural support (proteins are cell-specific); microtubules: further structural support and motility (chains of microtubules grow at one end and degrade at the other; originate from the centrosome which segregates into centrioles during mitosis (form the mitotic spindle), kinetic proteins traverse these cells in flagella,cilia, and general cell trafficking); thin filaments: functionally similar to tubules (sometimes connected to thick filaments); thick filaments: hydrolysis of ATP produced bending motion
Compare and contrast how soluble secreted proteins versus intrinsic membrane proteins are synthesized within the rough endoplasmic reticulum
Proteins bound for the cytosol are translated on free ribosomes; intrinsic membrane proteins are recruited to the rough ER by binding to a signal recognizing protein that recruits a channel (after a signal is recognized by the translocon the complex disassembles anchoring the protein to the rough ER membrane); secreted proteins follow a similar path to membrane proteins except that they are brought into the cell by the translocon
Describe the mechanisms by which secreted proteins and membrane proteins undergo post-translational modification and folding within the rough endoplasmic reticulum
N-linked glycosylation: an oligosaccharide is attached to an Asp or N residue; cytoplasmic domain may be cleaved and a GPI-protein added to free carboxyl; protein folding occurs in the rough endoplasmic reticulum (normally spontaneous but may be aided by chaperone proteins; hydrophillic residues are on the outside interacting with aqueous environment and hydrophobic residues are hidden inside)
Compare and contrast the processes of constitutive versus regulated exocytotic secretion.
Regulated pathway: protein stored in vesicles prior to receiving signal for release of contents and often calcium is needed to fuse these vesicles with the membrane (think neurotransmitter release)
Explain the roles of clathrin, SNARE proteins, Rab-family GTPases, and SNAPs in the formation, docking, and fusion of secretory vesicles.
clathrin mediates formation of vesicle from trans Golgi; SNARE proteins and SNAPs bind to each to bring the negatively charged phospholipids of two membranes together (electrostatically oppose each other); Rabs function as a switch (like a G-protein coupled receptor)
Compare and contrast the underlying mechanisms and functional roles of fluid-phase endocytosis versus receptor-mediated endocytosis.
Similarities: both are endocytosed by vesicles mediated by clathrins and adaptins and both are transported in an endosome; ; receptor-mediated: acidification of the endosome separates ligand from receptor (receptor get recycled to membrane)
Explain the structural characteristics and functional roles of the tight junctions, adhering junctions, and gap junctions within the polarized cells that comprise epithelial tissues.
Simplest gap junctions: formation of channels between two cells (ion flow); tight junction: separates the cell membrane into apical and basolateral domains that have very different functional properties; adhering junctions: actually form the link between two neighboring cells (through cadherins)
Describe specific examples of how the polarized organization, segregation, and trafficking of membrane proteins can facilitate the specific functions of various epithelial tissues.
the “fence” function of the tight junction separates completely different rosters of membrane proteins between the apical and basolateral membranes. For example, the Na-K pump is restricted to the basolateral membrane in almost all epithelial cells, and the membrane-bound enzymes that hydrolyze complex sugars and peptides are restricted to apical membranes in intestinal epithelial cells.
List the disciplines that were given birth to by Physiology
biochemistry, biophysics, and neuroscience
What is the central organizing concept of physiology?
Two fatty acids + glycerol form what?
diacylglycerol (signaling molecule)
How can you elucidate a peripheral protein?
Treat with high salt concentrations; salt will be compete with peripheral protein in binding to intrinsic proteins (electrostatic interactions)
Explain the role of the Golgi apparatus in the sorting and trafficking of proteins destined for secretion or incorporation into the plasma membrane versus proteins destined for incorporation into specific subcellular organelles
Subtraction of N-linked sugars in the cis Golgi; addition of sugars in the trans Golgi; addition of sugars to oxygen (one of the sugars contains an amino group)
How is a receptor trafficked to the lysosome?
Mannose 6 phosphate is added to receptor in the Golgi (acts as signal for a Golgi receptor); eventually the receptor is packaged into a vesicle and acidification releases the receptor while the vesicle returns the Golgi receptor to the Golgi
Describe the four major modes of intercellular signal transduction
Ligand-gated ion channel: agonist ligands are usually small (AA) with low affinity for the receptor (rapid clearance); receptors are desensitized or inactivated (refractory period); GPCR: GTPase located near receptor and signal from ligand binding is amplified through the interaction of alpha subunit of GTPase interacted with effector protein to yield second messengers; catalytic receptors: have inherited, or recruit, kinases that phosphorylate other proteins (subgroups: serine-threonine kinases, RTK, cytokine (tyrosine-kinase associated); ligands are large and have high affinity; nuclear receptors: located in cytoplasm or nucleus and are highly conserved; ligands are either lipids or lipophilic (alter gene expression)
Explain the roles of protein kinases and GTP-binding regulatory proteins as the major “molecular switches” in the linking of intercellular communication to intracellular signal transduction
To link extracellular signals to target proteins (metabolism, gene expression, and alter shape or movement of cell; amplify or modify signal to produce more profound changes through a cascade)
List the major intracellular “second-messenger” signaling molecules generated in response to activation of receptors for water-soluble hormones/ neurotransmitters
5: cAMP, cGMP, IP3, DAG, and calcium
Describe the structure of a generalized neurotransmitter receptor with intrinsic ligand-gated ion channel activity and identify the structurally significant domains; Explain the similarities and differences between “excitatory” versus “inhibitory” ligand-gated ion channel receptors
multimeric (most often 4 subunits); if channels allows flow of Na, the membrane depolarizes (acetylcholine, serotonin, and glutamate); if channel allows flow of Cl, the membrane hyperpolarizes (GABA and glycine)
Describe the structure of a generalized G protein-coupled receptor (GPCR)
Seven transmembrane domains; N terminus in the extracellular space; loop between alpha helices 5,6 (hydrophilic) is site of G-protein binding (brief)
Describe the structure and functional cycle of the trimeric G proteins that mediate signalling by GPCR
heterotrimer (alpha, beta, gamma unit); alpha subunit is the only component that has GTPase activity; alpha and beta/gamma dimer can interact with effector proteins
List the major effector proteins and second messengers that can be regulated by heterotrimeric G proteins
pairs: adenylyl cyclase (cAMP); phosphodiesterase (gCMP), PLC (DAG, IP3, calcium), PLD (DAG)
Describe four types of enzymatic activities associated with cell surface receptors that have intrinsic catalytic activity
guanylyl cyclases: convert GTP to cGMP; serine/threonine kinases: phosphorylate cellular proteins on serine/threonine residues; RTK: autophosphorylate and phosphorylate cellular proteins on tyrosine residues; receptor tyrosine phosphatases: cleave phosphate from cellular proteins
Describe the structure of growth factor/ hormone receptors that have intrinsic tyrosine kinase activity and identify the functionally significant domains of such receptors
Binding of a ligand, such as IGF, induces a conformational change in the receptor that facilitates the formation of receptor dimers. Dimerization allows the two cytoplasmic catalytic domains to phosphorylate each other (autophosphorylate)
Describe the structure of a generalized receptor complex for cytokine-family signalling molecules and identify its structurally significant domains
multimeric; upon binding to ligand, a non-receptor tyrosine kinase is recruited (JAK/STAT)
Describe the general signaling mechanisms by which cell surface receptors for growth factors or cytokines can regulate the activity of nuclear gene transcription
MAPK: Binding of ligand to RTK; RTK recruits GRB2 (SH2 domain), which recruits SOS activating Ras GTPase which interacts with Raf1 (targets MEK and MAPK, which alters gene expression); JAK/STAT: Interleukin protein binds cytokine receptor (JAK protein is recruited which phosphorylates the receptor and itself recruiting STAT transcription factor
Compare the mechanisms used by different G protein-coupled receptors to increase or decrease synthesis of cyclic AMP
Gs g protein: active alpha subunit communicates with adenylyl cyclase to convert ATP to cAMP; cAMP activates PKA; Gi g protein inhibits AC
Explain how protein kinase A can both mediate the acute regulation of an enzyme’s activity and increase the expression of the gene encoding that enzyme
Its activated by cAMP (removing regulatory proteins) and acts by phosphorylating other proteins and activates CREB, a transcription factor
Explain how the PLC-mediated hydrolysis of the substrate phospholipid, phosphatidylinositol 4,5-bisphosphate (PIP2) can lead to the activation of both Ca2+ signaling and protein kinase C (PKC) signaling.
PLC cleaves PIP2 at the ester bond between a glycerol and the phosphate + head group yielding two products diacylglycerol and IP3; IP3 is a second messenger that acts on a receptor on the ER to release calcium; DAG remains anchored to membrane and recruits protein kinase C (activating the kinase)
Describe the structure of a generalized intracellular receptor (for steroid hormones and other hydrophobic signalling molecules) and identify its functionally significant domains
receptor can be a homodimer or heterodimer; 4-6 domains, include ligand binding domain and DNA binding domain (highly conserved)
What is a receptor for calcium second messenger signaling?
Calmodulin (once it binds to 4 calcium molecules, it can activate other proteins)
What kind of bonds attach DNA to histones and other proteins?
H-bonding and electrostatic interactions provided efficient mechanisms for rapid, repetitive binding and unbinding of proteins; if covalent bonding between histones/proteins and DNA was present in the cell, transcription machinery could not be removed from DNA
What is different from the transcription of master regulator gene and induced gene?
“Master regulator genes” (those needed for viability of the cell) are transcribed at a basal rate (transcription factors and coactivators have very minimal effect)
What is a gene?
a segment of DNA that is transcribed into RNA
What is the central dogma?
A segment of DNA becomes transcribed by RNA polymerase into RNA; RNA is translated into protein on ribosomes
How is DNA packaged into cells?
nucleosome (small segment of DNA that wraps two times around an octamer of histones); The N termini of core histone proteins contain many lysine residues that impart a highly positive charge. These positively charged domains can bind tightly to the negatively charged DNA through electrostatic interactions. Tight binding between DNA and histones is associated with gene inactivity
How can gene expression be regulated?
alteration in chromatin structure (acetylation = access to DNA; DNA methylation prevents transcription; SWI/SNF: use ATP to separate DNA and histones); initiation of transcription (rate limiting step; basal rate is extremely slow); transcript elongation; termination of transcription; RNA processing; nucleocytoplasmic transport; translation; mRNA degradation
What is a transcription factor?
proteins that regulate gene transcription (increase the rate of recruitment of basal transcriptional machinery); Regulatory elements, the site of transcription factor binding, are referred to as cis-acting elements (because they sit on the DNA that they regulate)
Describe the elements of a gene that play a role in the regulation of gene expression (e.g. enhancer, promoter, or repressors elements).
Enhancer: site of transcription factor binding (transcription factors may recruit transactivators or have a transactivation domain that communicates with basal transcription machinery; promoter: site of basal transcription machinery binding (RNA pol II and co), TATA box = TFIID binding site ; repressor elements: binding site for repressive TFs
Discuss how proteins (especially transcription factors) interact with DNA
Mostly bind to major groove of DNA through alpha helical structure (contain lysine and arginine residues (like histones); have specific binding sites (but may bind to neighboring regions with similar sequence)
Describe the process of transcription
5'-3'; RNA pol II must change conformation for increased rate of transcription; elongation and termination;
Breakdown the role proteins and microRNAs play in the expression of genes
phosphorylating the nuclear localization signal (high in arginine and lysine residues) of cytoplasmic transcription factors can alter the rate at which the TF is being shuttled into the nucleus (in other cases affinity of the TF for receptor may be altered or potency of the transactivation domain may change); Site specific proteolysis often converts an inactive precursor protein into an active transcriptional regulator; others: sumolyation, ubiquination, actelyation, and methylation; miRNA combine with a complex to methylate DNA or methylate histones at Lys 9 residues; siRNA can be in complex to cleave mRNA or inhibit translation
Define the determinants of gene expression intensity and duration
Response to changing cellular environment; 3' untranslated region may be stabilized (prevent cleavage) when a gene needs to be transcribed (iron response element on transferrin gene expression)
Explain how signal transduction can regulate gene expression
Phosphorylated CREB binds CBP, which has a transactivation domain that stimulates the basal transcriptional machinery; JAK/STAT: Stat proteins dimerize and then join with another regulatory element to act as transcription factor; The binding of a glucocorticoid hormone to a cytoplasmic receptor causes the receptor to dissociate from the chaperone hsp90. The free hormone-receptor complex can then translocate to the nucleus