BIO Midterm 2 - Units 6 & 7 PDF

UNIT 6 and 7 1) what are the 3 stages of the the cell signaling process? 1) Reception 2) Transduction 3) Response Reception the target cell detects a signaling molecule (chemical) that binds to a receptor protein on the cell surface OR inside the cell...

UNIT 6 and 7 1) what are the 3 stages of the the cell signaling process? 1) Reception 2) Transduction 3) Response Reception the target cell detects a signaling molecule (chemical) that binds to a receptor protein on the cell surface OR inside the cell OR: physical touch in the surface of cells Transduction the binding of the signaling molecule alters the receptor and initiates a signal transduction pathway→ RELAYING the message to the interior of the cell often occurs in a series of steps: ○ CONVERTS it to the intracellular signals that PRODUCE a RESPONSE in the cell Response the transduced signal triggers a specific response in the target cell various types of cell responses can occur: ○ cell to divide ○ cell to be activated ○ cell to move ○ cell to start/stop producing specific proteins types of cell signaling RECEPTION of the message 1) Direct cell signaling→ touch 2) Indirect cell signaling→ through released chemicals Direct cell signaling→ Touch cells pass signal from 1 to the next by contact of their plasma membranes→ proteins w/ oligosaccharides from cell 1 interacts w/ other proteins/receptors w/oligosaccharides from cell 2 cells communicate w/each other by cell-cell contact or touch cell-cell contact/touch signaling the signal= the touch→ the contact between 2 cells EX= the dividing cells that are covering a wound make direct physical contact w/ each other once they heal and trigger responses which is to stop dividing they use signals and receptor molecules in their plasma membrane TOUCH signaling signal→ Touch: by proteins in the membrane of cell 1 signal detection→ by receptors in the membrane of cell 2 response→ stop dividing what does touch signaling play an important role in? wound healing→ cells stop growing when they touch each other and the wound= closed Indirect cell signaling most cells communicate w/each other through: secreted signal molecules ○ divided into 2 categories based on the distance over which signals are transmitted: ○ PARACRINE signaling ○ ENDOCRINE signaling Paracrine signaling cells communicate using secreted chemicals that travel only SHORT distances target cells= nearby the signal molecules diffuse locally through the extracellular fluid, remaining in the neighborhood of the cell that secretes them examples of paracrine signaling→ immune cells in immune cells→ many chemical signals are secreted by some cells and act on nearby cells, regulating inflammation at the site of an infection example of paracrine signaling→ neurons synaptic signaling occurs in the ANIMAL nervous system when a neurotransmitter is released in response to an electric signal (action potential) this signal will reach the target cell receptor in the post-synaptic neuron passing the signal from 1 neuron to the next Endocrine signaling in LONG-distance signaling, the chemical signals travel to reach target cells ○ the chemical signals= hormones hormones are secreted by specialized cells→ endocrine cells (in endocrine glands) hormones are secreted to the blood, and they get to their target cells via the circulatory system Endocrine signaling  in LONG-distance signaling, the chemical signals travel to reach target cells ○ the chemical signals= hormones hormones are secreted by specialized cells→ endocrine cells (in endocrine glands) hormones are secreted to the blood, and they get to their target cells via the circulatory system YES receptors and NO receptors regardless to the type of signaling system, the ability of cells to respond to a signal depends on whether or not they have a receptor SPECIFIC to that hormone/signal: ○ YES receptor→ response ○ NO receptor→ NO response endocrine glands endocrine cells in glands secrete the hormones to the blood there are 8 major endocrine glands in the body; that produce around 50 different hormones types of hormones 1) Large, hydrophilic, peptide, protein hormones 2) Steroid hormones Large/Hydrophilic/Peptide/Protein hormones CANNOT cross the plasma membrane bc they are hydrophilic/large they act by binding to cell-surface receptors on their target cells examples of protein/amino acid hormones: AMINE hormone→ amino acids w/ modified groups; ex: norepinephrine’s carboxyl group is replaced w/ a benzene ring PEPTIDE hormone→ short chains of linked amino acids PROTEIN hormone→ long chains of linked amino acids steroid hormones small lipid hormones → small, hydrophobic signaling molecules able to diffuse across the plasma membrane→ SIMPLE diffusion they bind INTRACELLULAR receptors (in the cytoplasm or in the nucleus) examples of steroid hormones steroid hormones→ derive from cholesterol sex hormones→ estrogen, testosterone, progesterone cortisol thyroid hormones what are the 3 stages of the cell signaling process? 1) Reception of the signal 2) Transduction of the signal 3) Response (cellular response) Reception the target cell detects a signaling molecule that binds to a receptor protein on the cell surface (or: in the cytoplasm/nucleus), causing it to change its shape what are the 2 main types of receptors? 1) Surface receptors 2) Cytoplasmic receptors Surface receptors ON the plasma membrane of the target cells for large/hydrophilic/protein hormones receptors for hydrophilic signals→ amino acid, peptide, and protein hormones Cytoplasmic receptors INSIDE the cytoplasm of the target cells→ steroid hormones what are the 2 types of surface receptors? 1) G protein-coupled receptors (GPCRs) 2) Receptor protein-Tyrosine kinase (RTKs) G protein-coupled receptors (GPCRs) the largest family of cell-surface receptors most water-soluble signal molecules bind to specific sites on receptor proteins that span the plasma membrane humans have at least 100 different types of GPCR located ON the plasma membrane what characterizes a GPCR? characterized by 7 transmembrane α-helixes where the ligand (chemical hormone) binds they all have a large INTRACELLULAR domain which binds a G-protein how do GPCRs work?  GPCRS are cell-surface transmembrane receptors that work with the help of a G protein close by in the inner portion of the membrane G proteins= proteins that bind the energy-rich GTP ○ when bound to GTP→ they are ON ○ when bound to GDP→ they are OFF Activation of GPCR→ STEP 1 - there is a G protein (bound to GDP) loosely attached to the cytoplasmic side of the membrane, close to the GPCR the G protein functions as a molecular switch which is ON or OFF depending on whether GDP or GTP is attached: ○ GDP= OFF (**D for dead) ○ GTP= ON (**T for thriving) Activation of GPCR→ STEP 2 when the hormone binds to the extracellular side of the receptor, the receptor is activated and changes shape ○ its cytoplasmic side then binds to inactive G protein, causing a GTP molecule to attach and displace the GDP, so the G-protein= turned ON Activation of GPCR→ STEP 3 activated G protein separates from the receptor, diffuses along the membrane and binds to enzymes close by, altering their shape and activating them ○ once activated→ these enzymes can produce a second messenger→ travels through the cytoplasm and binds to other proteins causing a cellular response Activation of GPCR→ STEP 4 changes in the enzyme and G protein are only temporary bc the G protein looses its P forming ADP ○ the G protein is reused and goes back to the GPCR Tyrosine-kinase receptors (TKR) another type of membrane receptor that when stimulated, can attach phosphate groups(P) to proteins (to the amino acid Tyrosines) abnormal functioning of TKRS→ associated w/ many types of cancers Steps of the activation of TKR each tyrosine in the tails will get phosphorylated→ these phosphorylated INTRACELLULAR activated sections will serve as DOCKING PLATFORMS for many intracellular proteins the cytoplasmic proteins that are activated by TKRS have specific protein domains→ SH2 domains→ able to recognize and bind to specific phosphorylated TYR many different proteins w/SH2 domains will come by and attach and become activated, so multiple proteins get activated at the same time Intracellular receptors intracellular receptor proteins are found in the cytoplasm of target cells small or hydrophobic chemical messengers can readily cross the membrane and activate receptors ○ EX: steroid+thyroid hormones the hormone gets inside the cell, binds to the receptor, and then the hormone-receptor complex travels to the nucleus acting as transcription factors, turning on specific genes reception of steroid hormones receptors are NOT in the surface of the plasma membrane; they are inside the cell→ in the cytoplasm EX of a malfunctioning receptor→ Androgen Insensitivity Syndrome (AIS) the Y chromosome contains a “male-determining gene”→ SRY gene, that causes the development of testes in the embryo and the production of testosterone→ results in the development of external+internal male genitalia ○ the X-chromosome contains the gene for the TESTOSTERONE RECEPTOR ○ the androgen receptor, located on the X-chromosome, binds to androgens like testosterone ○ in AIS→ the androgen receptor is defective due to mutations in the AR gene; even though the SRY gene may be functioning correctly, leading to the formation of testes and androgen production, the body’s tissues are unable to respond to these hormones due to the faulty receptor ○ result→ individuals w/ AIS will develop female or ambiguous physical traits bc the body cannot properly respond to androgens Transduction cascades of molecular interactions that relay signals from receptors to target molecules in the cell leading to a cellular response ○ signal transduction usually involves multiple steps ○ multistep pathways can greatly amplify a signal and provide MORE opportunities for coordination and regulation of the cellular response Signal transduction pathways the binding of a signaling molecule to a receptor TRIGGERS the first step in a chain of molecular interactions the activation of the receptors will ACTIVATE enzymes that release SECOND MESSENGERS ○ second messengers then will activate specific proteins INSIDE the cell→ falling domino effect→ the receptor activates another protein, which activates another, and so on, until the protein producing the response is activated ○ at each step, the signal is transduced into a different form, usually a shape change in a protein Second Messengers small, non-protein molecules or ions that spread throughout a cell by diffusion after a primary messenger (hormone or ligand) has bound to the receptor participate in BOTH pathways initiated by GPCRs and RTKs bind to specific proteins in the cell and modify cell’s activity  Cyclic AMP (cAMP) and calcium ions= COMMON second messengers Adenylyl Cyclase an enzyme in the plasma membrane, converts ATP→ cyclic AMP (cAMP) in response to an extracellular signal Second Messenger: Cyclic AMP (cAMP) one of the most widely used second messengers cAMP then will activate Protein Kinase A that will ADD phosphates to target proteins and ACTIVATE them ○ this way, the message= passed on to the inside of the cell activating many proteins Second Messenger: Calcium (Ca2+) activation of both receptors GPCR and TKR in the membrane can activate another membrane enzyme called: Phospholipase C ○ Phospholipase C chops the head off a membrane phospholipid PIP2, generating IP3→ that diffuses into the cytosol and DAG (that remains in the membrane) IP3 IP3 diffuses through the cytoplasm and binds to Calcium channels in the membrane of the smooth endoplasmic reticulum (SER) ○ they OPEN the Ca2+ channels ○ Ca2+→ flushes OUT of SER where it is stored ○ Ca2+→ acts as a second messenger that will activate some other types of protein kinases (PKC) ○ this will lead → to activating other proteins spreading the signal to the inside of the cell leading → cellular responses Protein kinases enzymes that ADD phosphate groups to target proteins ○ adding phosphates to proteins make them→ turn ON Protein Phosphorylation a widespread cellular mechanism for regulating protein activity when proteins are phosphorylated= have a P→ they are turned ON in this process→ protein kinases TRANSFER phosphates from ATP→ Protein ○ many relay molecules in signal transduction pathways are protein kinases, creating a→ phosphorylation cascade Phosphorylation- depending on the protein a phosphorylation could EITHER: stimulate protein activity OR prevent it, depending on the protein, BUT normally→ it activates→ turns the protein ON Protein Dephosphorylation a widespread cellular mechanism for regulating proteins when proteins are dephosphorylated= REMOVE the P→ they are turned OFF Molecular switch- Phosphorylation and Dephosphorylation system this system acts as a molecular switch→ turning activities ON and OFF or UP and DOWN, as requried types of Cellular Responses many different types of responses depending on the type of proteins that are activated: ○ control the behavior of the cell ○ opening or closing ion channels ○ altering cell metabolism→ activate or inhibit metabolic enzymes ○ altering gene expression (turning genes ON or OFF) ○ altering SHAPE and MOVEMENT of the cell ○ make cells divide or stop cells from dividing ○ Cell differentiation ○ induces APOPTOSIS (programmed cell death) Apoptosis cells may receive a signal to “destroy themselves”→ APOPTOSIS ○ also known as programmed cell death or cell suicide can be triggered by signals from OUTSIDE the cell or from INSIDE the cells as ○ INTERNAL signals→ can result from permanent damage to DNA, OR during embryonic development Process of Apoptosis: results from activation of intracellular signaling cascades that course the events in cell suicide Response→ it activates a series of proteins that will lead to the digestion of the cell from within ○ clean ○ NO inflammation is involved WHY does apoptosis occur? if cells are no longer needed, cells will undergo apoptosis using an intracellular death program mechanism apoptosis is ALSO used to shape and sculpture organs during embryonic development EX of apoptosis eliminating a body part: when a tadpole changes into a frog at metamorphosis, the cells die as the tail= not needed in the frog ○ the unneeded cells DIE by apoptosis what stimulates the changes and the induction of apoptosis in the tadpole tail during metamorphosis? an increase in thyroid hormone in the blood EX of shaping/sculpture of organs during Apoptosis: individual fingers and toes SEPARATE during embryonic development ○ hands+feet=sculpted by apoptosis ○ start as spade-like structures and the fingers/toes separate bc the cells BETWEEN them die Necrosis another type of cell death NOT programmed cause→ damage the process of Necrosis organelles+plasma membrane= damaged, swell, become leaky eventually→ the cell BURSTS and SPILLS all of its components→ causes a general inflammatory response involuntary much MORE messy immune cells are called to clean the area→ phagocytosis what causes necrosis? Ischemia→ low blood flow and hypoxic (low oxygen) injury→ in strokes, heart attacks ○ causes cells to NOT receive oxygen, which interrupt generation of energy (ATP) so the cells die Chemicals→ caused by TOXIC chemicals→ poisons, cell receptors, nerve communication, etc Infections→ many microorganisms damage cells directly or stimulate the immune system to destroy infected cells→ bacteria, viruses, fungi Physical+Mechanical damage→ temperature (low-frostbite, high-burns), electrical (generates heat that burns cells), radiation (radiation injure cell directly by creating free radicals that react w/cell components, esp DNA), atmospheric (air pollutants), mechanical (trauma) Energy in Cells virtually every task performed by living organisms requires energy every organism’s living cells constantly USE energy living organisms use METABOLISM Energy Flow most life-forms on earth obtain their energy from the sun plants use photosynthesis→ to CAPTURE sunlight, and herbivores EAT those plants to obtain energy carnivores EAT the herbivores, and decomposers digest PLANT/ANIMAL matter Metabolism all the chemical reactions in the cell that provide: ○ cell’s energy to maintain cellular function ○ cell’s using raw materials/energy to build complex molecules EX’s of metabolism ex→ using glucose to obtain energy ex→ using amino acids/energy to make proteins, using CO2 + H2O and solar energy to make sugars why do cells need “matter” and “energy”? to maintain life, our cells require “matter” and “energy” from outside sources (food), bc we are heterotrophs ○ food needs to be broken down into SMALL nutrient molecules (digested), and the nutrients are absorbed into each cell of the body ○ foods digested by digestive system in animals, absorbed in the intestines, transported to ALL cells in the body through circulatory system, and then absorbed by ALL cells in the body what happens once the cells are inside? a series of enzymatically-driven chemical reactions→ metabolic reactions will break DOWN the nutrients to RELEASE→ matter and energy the “energy” will be used by the cells to perform work once INSIDE the cells, a series of enzymatically-driven chemical reactions (METABOLIC reactions) can use the building blocks to BUILD more complex molecules 2 main types of Metabolic Reactions ANABOLIC reactions: require energy→ endergonic→ “build-up” CATABOLIC reactions: release energy→ exergonic→ “break-down (**catapolt** of energy**) Catabolism breaking down Food is made of the BIOMOLECULES which make our cells: carbohydrates, lipids, proteins, nucleic acids through digestion→ food is BROKEN DOWN to smaller molecules that can pass to our blood stream and then be distributed to all cells in the body ○ Polysaccharides/Disaccharides→ Monosaccharides→ Fats→ Glycerol+Fatty acids+Proteins→ Aminoacids+Nucleic acids→ Nucleotides molecules in Catabolism these molecules (monosaccharides: glucose, fructose, aminoacids, fatty acids, etc) will then be incorporated by each cell and degraded even further to obtain ENERGY out of them where is the energy stored? in the nucleotide molecule ATP→ stores the chemical energy used by the cell cells require a CONSTANT supply of ENERGY to generate and maintain their cellular functions structure of ATP 1 base→ Adenine 1 pentose sugar→ Ribose 3 phosphates what are the 3 phosphate groups? Gamma phosphate group Beta phosphate group Alpha phosphate group ATP the cell’s PRIMARY energy currency→ ATP acts like **batteries in the cell ○ they BIND to specific sites on protein molecules, providing energy to the protein so it can perform its function ○ once the bond of one of the P groups is broken, ATP becomes→ ADP+P has an adenosine backbone w/ 3 phosphate groups attached breakdown of ATP: high energy bonds between the P groups store energy breaking the last P bond→ releasing energy that can be then used by the cell ○ ATP → ADP + ENERGY ADP→ recharging the batteries ADP (rechargeable batteries) can be recharged with ENERGY ○ can be recharged BACK to ATP in the mitochondria during AEROBIC cellular respiration EX: ATP needed by the cell to do work→ Transporting substances across membranes Active transport using the sodium-potassium pump in cell membranes Exocytosis of digested bacteria from white blood cells EX: ATP needed by the cell to do work→ Anabolic reactions synthesis of DNA from nucleotides synthesis of protein from amino acids EX: ATP needed by the cell to do work→ Movement cellular movement of chromosomes via the spindle mechanical contraction of muscles EX: ATP needed by the cell to do work→ Maintaining body temperature ONLY occurs in mammals/birds why must cells constantly generate energy? BC if NO energy is supplied, ALL processes that require ATP will stop functioning and the cell dies→ necrosis in order to keep producing the energy they need→ cells need a constant supply of fuel molecules from food and oxygen Energy requirement of: the BRAIN → the organ that has HIGHER metabolic needs= needs more energy for their functioning→ action potentials, membrane Na/K pump, vesicle transport, etc) it takes abt 6 minutes before brain cells start to die WITHOUT new ATP being made if a person has a cardiac arrest OR lack of oxygen to the brain (suffocation, drowning), resuscitation has to begin WITHIN this time to be successful ○ the time may be prolonged if the body= cooled (ex= drowning in ice cold water) Energy requirement of: MUSCLE cells muscle cells also have a very HIGH demand for ATP ○ muscle contraction REQUIRES energy→ muscle cells and cardiac cells what amount of time can each organ survive without constant oxygen supply? heart→ a muscle; needs CONSTANT oxygen supply brain→ 4-6 mins Kidneys→ 30 mins Muscles→ 2-4 hours GI tract→ 12 hours Bone/tendon/skin→ 8-12 hours Catabolic reactions chemical reactions that break down COMPLEX organic compounds into SIMPLE ones, with the net release of energy ○ breaking down sugars for energy; fat for energy what kind of reaction is a Catabolic reaction → exergonic (releases energy as it breaks down molecules) - EX= cellular respiration→ glucose is broken down, releasing energy in the form of ATP what happens when sugar molecules burn in the cell? sugar molecules= a HIGH energy compound when sugar molecules burn in the cell→ the LOW energy compounds carbon dioxide and water are the result the released energy is captured in ATP, which then does useful work w/ the energy BEFORE it escapes into the environment part of the energy is LOST in the form of→ heat Anabolic reactions taking what is in your food and forming LARGE complex molecules ○ when sugars are joined together to create GLYCOGEN= anabolic reaction ○ when amino acids are joined together to create PROTEINS= anabolic reaction ○ when fatty acids are joined together to create a TRIGLYCERIDE= anabolic reaction ○ when a plant makes SUGARS in photosynthesis= anabolic reaction what kind of reaction is an Anabolic reaction? → endergonic (require the input of energy to proceed) energy supplied from an outside source when LOW-energy compounds are COMBINED or MODIFIED to produce HIGH-energy compounds→ energy must be supplied from an outside source or the reaction WONT happen ○ some of the energy from the outside source is stored in the products in the form of high-energy bonds EX of energy supplied from an outside source: carbon dioxide and water→ 2 very LOW energy compounds, can be forced together into 1 molecule of glucose→ a HIGH energy compound ○ the source of this energy→ sunlight ○ the reaction takes place in very highly ORGANIZED cellular compartments→ chloroplasts ○ oxygen= byproduct of the process ENZYMES proteins that act as biological CATALYSTS by accelerating chemical reactions in the cell enzymes SPEED UP chemical reactions more than a million times→ allowing vital chemical reactions to take place at normal temperatures and conditions  NO chemical reaction would occur in the cells WITHOUT enzymes there are more than 2000 different enzymes in the human body how do enzymes work? they act on SUBSTRATES and release PRODUCTS ○ the reaction takes place in a small area of the enzyme→ the ACTIVE SITE ○ the rest of the protein acts as scaffolding holding the active site TOGETHER enzymes= specific the arrangement of the amino acids in the active site makes it specific for only ONE type of substrate enzymes= VERY specific; they work as **”lock and key”** with their substrates EX of the process of an enzyme acting on a substrate: 1) substrates ENTER active site→ FORMS enzyme/substrate complex 2) enzyme CHANGES shape slightly as substrate binds→ shape change PROMOTES reaction 3) product RELEASED; leaving active site of enzyme= ready again 2 substrates→ 1 product OR 1 substrate→ 2 products characteristics of enzymes 1) highly SPECIFIC→ each enzyme typically ONLY reacts with 1 type of substrate+performs 1 type of reaction 2) enzymes are REUSABLE→ enzymes are not used up during the reaction→ once an enzyme binds to a substrate and catalyzes the reaction, the enzyme= released and UNCHANGED→ can be used for another reaction (*an enzyme will be catalyzing reactions all of its life unless its stopped by inhibition or degradation) 3) enzymes act by LOWERING the activation energy of the reaction what is the activation energy of a reaction? in order for the reaction to take place→ some or ALL of the chemical bonds in the reactants must be BROKEN so that new bonds, those of the products, can form to get the bonds into a state that allows them to break, the molecule must be contorted (deformed or bent) into an unstable state→ the transition state ○ a HIGH- energy state; where some amount of energy (activation energy) must be added in order for the molecule to REACH it naming the enzymes  enzymes can be named according to their substrate, to their product, or are named based on the reaction they perform, adding the suffix “ASE” why might enzymes need help? they need assistance to perform their functions→ to CATALYZE reactions some enzymes employ small non-protein molecules to catalyze reactions→ COFACTORS ○ without them, the enzyme WONT work Cofactors help enzymes CARRY OUT their catalytic function they BIND to the enzymes, close to the active site ORGANIC cofactors coenzymes→ derivatives of vitamins INORGANIC cofactors minerals→ zinc, iron, copper (small+metals) factors that affect enzyme activity: BC enzymes=proteins→ anything that can AFFECT the structure of a protein (denaturation) can AFFECT the activity of an enzyme ○ PHYSICAL factors= temperature, pH, salts, molecules that attach and blocks the enzyme ○ if enzymes=denatured→ the substrate does NOT fit in the active site enzyme inhibitors molecules that are able to bind to SPECIFIC enzymes inhibiting them what are the 2 mechanisms of enzyme inhibition? Competitive inhibition + Noncompetitive inhibition COMPETITIVE inhibition the inhibitor will BIND to the active site of an enzyme and COMPETE with the normal substrate, BLOCKING the entry of the substrate→ inactivating the enzyme ○ shape/chemical structure of the inhibitor= SIMILAR to the substrate NONCOMPETITIVE inhibition the inhibitor BINDS to the enzyme at a different location AWAY from the active site ○ binding of the inhibitor to the allosteric site causes the enzyme to LOSE its shape, so the substrate CANNOT fit into the active site→ the enzyme WONT work