BB 450 Unit 3

What happens in the common pathway?

1. Activation of Factor 10 by either the extrinsic or intrinsic pathways 2. Factor 5 (another cofactor) helps Factor 10's activity and activated factor 10 converts prothrombin into thrombin 3. Thrombin is an important central molecule (physiologically) as we go in to find out fibrin is a monomer that loves to stick to other fibrin 4. The protein blocks of fibrinogen are cut off by thrombin

Describe the receptor tyrosine kinase pathway?

1. Binding of the hormone to RTK in membrane 2. Receptor Dimerization The 2 subunits come together 3. Autophosphorylation of receptors -> on the cytoplasmic side the tails of those receptors autophosphorylate and it becomes at this point an active tyrosine kinase 4. Signal Complex Assembly-> Using an SH2 domain to recognize that this is indeed an active phosphotyrosine 5. Message is communicated to the cell, it can happen in a variety of different ways

How do cells control the activity of an enzyme?

1. Cells use ~Allosterism~ to control enzyme activity by binding small molecules to the enzyme. When this happens, it's not completely an on or off mechanism. Instead it just says how much of the pool of that enzyme gets to be active at any given time. 2. Cells also control enzymes by covalent modifications * Breaking peptide bonds is usually an activation of the enzyme * Phosphorylation and dephosphorization are also covalent modifications (These can be activating or not activating) 3. Controlling synthesis of an enzyme is another mechanism that makes sure that the cell is allowing the right amount of enzyme to be active. AKA being transcribed, translated, or folded properly Whether an enzyme is present at all is clearly a way of controlling its levels 4. Activism can also activate enzymes and not just inactivate them.

Prothrombin Summary

1. Converts Fibrinogen to Fibrin 2. Serine protease 3. MUST bind calcium to be at site of wound 4. Carboxylation of glutamate side chains requires vitamin K 5. Carbonylated glutamate side chains bind calcium 6. Blocking vitamin K action reduces clotting (blood thinner)

What is the big picture of the blood clotting response?

1. Damage to the epithelial tissue (that lines the blood vessels) exposes collagen. This exposure of collagen where it shouldn't tells the body to start the clotting process in that local area 2. Platelets bind collagen-binding surface receptors 3. Platelet integrins get activated and bind tightly to the extracellular matrix to anchor to site of wound 4. von Willebrand factor (a blood glycoprotein that helps it all stick together) forms additional links btw. the platelets' glycoprotein and the fibrils of the collagen 5. Signal amplification begins with release of platelet factor 4 (inhibits heparin which is an anti-clotting factor usually present in the blood so we don't get clots for no reason, inhibiting heparin allows clots to form right at the site of the wound) and thromboxane A2 (increases platelet stickiness) 6. Calcium (helps w/ molecular response) is released from intracellular stroes (Gq cascade)

What happens in the EGF pathway?

1. EGF receptor becomes a dimer when EGF binds 2. It autophosphorylates on tyrosines in the cytoplasmic domain 3. A signaling complex assembles on the phosphotyrosines. Made up of GRB2, SOS, and RAS Ras is the G-coupled protein in this case, GTP makes Ras active

Relate G-coupled protein receptor to PKA to cAMP.

1. GPCR binds epinephrine and makes a conformational change in the receptor. The alpha subunit is holding GDP 2. The alpha subunit breaks off from the beta and gamma subunits and tales off to do its own thing 3. The alpha subunit activates and uses ATP, it activates adenylate cyclase and then adenylate cyclase uses ATP to activate a molecule called cyclic AMP (cAMP) If cyclic AMP is not activated then you would not have PKA be active either So G-coupled proteins are important for they synthesis or lack thereof of these molecules

What are two types of blood clotting diseases? How do they work?

1. Hemophilia: When blood clotting is not working correctly * Deficiency of FVIII leads to Hemophilia A (about 1 in 5000-10000 male birth) * Deficiency of FIX (9) produces Hemophilia B (about 1 in 20,000 - 35,000 male births) Correlated to male births because it is linked to the X chromosome, to be a female and have hemophilia A you would have to have 2 mutated copies of the gene and usually you don't. A woman could have one mutation and then be a carrier but the other X chromosome would take care of you just fine. 2. Von Willebrand disease ---> Similar to hemophilia ---> von Willebrand factor is a large multimeric glycoprotein present in blood plasma and also produced in the endothelium lining of blood vessels. It does a lot of jobs and in its absence these processes won't happen. ---> Anchor platelets near the site of the wound in cellular response ---> Binds to platelet glycoprotein, heparin and helps moderate its action, collagen, FVIII in the molecular response, playing a protective role for it. ---> In the absence of the von Willebrand factor, FVIII is destroyed.

What happens in the Ras/Raf signaling cascade? What is the outcome?

1. Ras travels to Raf kinase and activates it, then everything goes through what is called the MAO kinase signaling pathway 2. RAF/Ras activates MEK Kinase 3. MEK activates the MAP Kinase Cascade Outcome: Transcription, Cell Division, and Cell Differentiation. We see an overwhelming signal for the cell to divide, the point is for the transcription of genes for DNA replication and cell division.

What types of pathways get changed by signaling?

1. Signal binds receptors 2. Affects one or more intermediary molecules 3. Affects target molecule(s) which regulate gene expression or metabolic pathways ---> They change, turn on, or turn off genes OR they tell the cell it's time to grow, break down glycogen, or build up their stores using glucose

Blood Clotting Summary

1. Tissue damage initiates a cellular response that starts to plug the wound (sticky platelets) and releases calcium necessary for the cellular response. 2. Tissue damage signals initiation of the intrinsic and extrinsic pathways (molecular response) 3. The intrinsic pathway and extrinsic pathway are molecular responses that converge to favor polymerization of fibrin 4. The molecular responses involve an initiation phase that activates a small amount of thrombin 5. The small amount of active thrombin results in the amplification of factors FXa and FVa by many fold, which in turn activates thrombin by millions fold 6. Thrombin activates fibrinogen to make fibrin and form the clot.

How is the clotting signal amplified?

1. Tissue damage stimulates formation of TF-FVIIIa complex. 2. TF-FVIIIa, FIXa, Platelet Membrane Phospholipid (PL) and Calcium (from the cellular response) inefficiently convert FX to FXa 3. FXa, FV, PL, and calcium inefficiently convert prothrombin (zymogen) to a tiny amount of thrombin 4. Thrombin is key to the amplification phase of the molecular response Factor 8 usually is bound with a von Willebrand factor but it gets released and activated by thrombin Factor II favors the production of more factor 9 and that activates factor 10 Then 10 and 8 make factor 10a (and a lot of it!) Factors 5a and 10 make thrombin, thrombin stimulates other factors that activate it in a positive feedback loop

What happens when a ligand binds, in a general way?

A conformation change ---> The receptor needs to tell the cell that something is bound, and now if it's embedded in the membrane it's saying, somethings bound to the outside of the cell. That's sending the signal and doesn't even need to come in. It just needs to make the conformation change. Internal receptors also have a conformation change that will allow them to have an activity And so the signal is transduced via other messenger proteins in the cell due to the conformational change, it will cause something else The end result is it might affect transcription, or affect enzyme activity that controls metabolism.

What is a kinase and what covalent modification does it catalyze?

A kinase is an enzyme that catalyzes the transfer of a phosphate group from ATP to a specified molecule.

What is negative feedback?

A response to a change in the body that counteracts or opposes the initial change. Negative feedback occurs to reduce the change or output: the result of a reaction is reduced to bring the system back to a stable state.

In the case of ATCase: what are the roles of ATP and CTP?

ATP: High Energy, Purine Acts as an activator, indicating that there's plenty of energy available Stabilizes/Favors the R state which increases the reaction rate (shifts/increases the velocity). CTP: End of Product Pathway (negative feedback) When CTP is sensed it tells the cell to end the reaction of pyrimidines Favors the T state, it is a heterotrophic effector and decreases V0

What are some types of allosteric regulators?

Allosteric Regulation: Enzymes can have an allosteric site (can be anywhere and an enzyme can also have a number of them) which are places on the enzyme where any enzyme regulator can bind Allosteric activators: increase enzymatic activity and activate enzymes Allosteric inhibitors: decrease enzymatic activity and inhibit enzymes

How do allosteric inhibitors and activators affect Km?

Assuming [S] to be constant, there are two ways to influence enzymatic activity (or V0) Activators: Increase Vmax and decrease Km Inhibitors: Decrease Vmax and increase Km

What is a ligand?

Any molecule that binds specifically to a receptor site of another molecule Ligands are the signaling molecule used by the body for various cells to communicate with other cells.

What is apoptosis? How does it work?

Apoptosis: Method by which faulty cells that pose a threat to an organism will undergo self destruction ~essentially programmed cell death~ Apoptosis involves cellular agents chopping up everything within a cell. All the DNA and organelles become fragmented and the cell itself shrinks to form lobes Lobes are then pinched off and digested by specialized cells called scavenger cells. This is important because if the dying cell simply leaked its components these could potentially be incorporated into other cells and initiate the same faulty mechanisms in those.

What are two major ways apoptosis can happen?

Apoptotic Signaling Pathways: signals can initiate from outside or inside of the cell. If Outside: nearby cells release signaling molecules that initiate ~signal transduction~ that results in the expression of genes whose protein products carry out apoptosis If DNA inside the cell becomes damaged beyond repair, a series of ~protein-protein interactions~ can act as a signal that triggers apoptosis

Why is aspartate a homotropic effector of ATCase? What state is favored?

Aspartate is a homotrophic effector because it both acts as a substrate and affects the enzyme Binding of aspartate favors the R state ---> That means that bc. it favors the R state additional substrate binding is favored. (when aspartate is bound, then the enzyme will be in the R state)

Why do aspirin and NSAIDs stop pain?

Aspirin's ability to suppress the production of prostaglandins and thromboxanes is due to its irreversible inactivation of the cyclooxygenase (COX) enzyme. NSAIDs also block the COX enzyme

Why is a G protein called that?

Because it binds to guanine nucleotides.

Why does this promote cancer? What are the several ways?

Before an oncogene becomes mutated, it is called a proto-oncogene, and it plays a role in regulating normal cell division. Cancer can arise when a proto-oncogene is mutated, changing it into an oncogene and causing the cell to divide and multiply uncontrollably. Mutations (changes) in a proto-oncogene may cause it to become an oncogene, which can cause the growth of cancer cells.

Possible consequence of a mutation in a protooncogene?

Cancer Protooncogene mutations cause the protein to be on FOREVER. A mutation in the DNA at the location of a proto-oncogene and not a neutral mutation but something that changes the DNA and changes the codon to produce the wrong amino acid causes the increased amount of cell division. Causes the first step towards cancer, NEOPLASIA, or new growth

What is a caspase and how does it work?

Caspases are a type of protease and the role of a protease is that they chop proteins and DNA. Caspases more specifically are important in the process of apoptosis and the killing of cells. Caspases exist in all cells as inactive precursors, or procaspases, which are usually activated by cleavage by other caspases, producing a proteolytic caspase cascade.

Exposure of what molecule triggers clotting?

Collagen ---> Exposure of collagen where it shouldn't be tells the body to start the clotting process in that local area

How is the clot stabilized?

Crosslinking by Factor 13a (FXIIIa) ---> This enzyme catalyzes the joining of the carboxamide of glutamine to the amine side chain of lysine ---> And so a covalent bond is made, these bonds are pretty stable, so the clot hardens and becomes stable as well

What other, non-cancer-related, cell functions use apoptosis? Why?

Electron Transport Chain: Uses cytochrome C but outside of the mitochondrial matrix it acts as an apoptotic factor Apoptosis is sometimes a last resort for misbehaving cells, it is often important for organismal development ---> Occurs in varying degrees within different vertebrates to produce hands, feet, paws, and other such limbs ---> Required for the normal development of the nervous system ---> Occurs in most eukaryotic life, even single celled yeast Problems with apoptosis also lead to a variety of degenerative diseases such as Alzheimer's and Parkinson's ---> Protein aggregation can activate an enzyme that triggers apoptosis, resulting in the death of neurons and loss of brain function

What kinds of signals do hormones send?

Endocrine Signaling * Tell cells to divide, to break down glycogen, make glucose, etc. * They're known for being made in one tissue and exerting their effects on another tissue The first signal is the "first messenger", however, people usually call it a signal or receptor binding

What is EGF for?

Epidermal Growth Factor (EGF) is a protein that signals the growth of the cell, and it signals differentiation which is telling a cell to go from a stage where it could become several different types of cells or tissue or parts of tissue to only be one thing and that's it. When a cell is differentiated it is less likely to become cancerous because it doesn't have a lot of pluripotency

What is an example of the RTK pathway?

Epidermal Growth Receptor Insulin Receptor

What are some hormones used in signaling?

Epinephrine (aka Adrenaline) Thyroid Hormone Epidermal Growth Factor (a protein, proteins can also act as ligands) Progesterone (based on the structure of cholesterol and it is made from cholesterol)

What types of signals get transduced?

Extracellular Signals / Molecular Signals

What does the extrinsic pathway expose?

Extrinsic pathway is triggered by substances outside of the blood. The extrinsic pathway exposes tissue factor which is a membrane protein in sub epithelial tissue that's not normally exposed to blood. When exposed the tissue factor binds to factor 7 which is already active in the blood and this goes on to activate the common pathway. Tissue factor and Factor 7a help each other and are co-factors.

What helps fibrin crosslink into a clot?

Factor XIII (13) helps fibrin mesh to cross link and become even stronger. Lots of signal amplification and positive feedback.

What is a feedback loop? How do they work, for example?

Feedback occurs when outputs of a system are routed back as inputs as part of a chain of cause-and-effect that forms a circuit or loop. The system can then be said to feed back into itself. When you have downstream products regulate upstream reactions Feedback loops can be positive or negative Good Control points are "committing steps" Ones that are very negative or positive which means that they are not easily reversible Phosphofructokinase is an example of a negative feedback loop: It is involved in glycolysis, catalyzes the conversion of fructose six phosphate and ATP to form fructose 1, 6 -bisphophate and ADP It is negative bc making ATP slows down glycolysis and rate or ATP production. ATP is a homotrophic inhibitor AMP is the allosteric activator that uses up ATP

How is apoptosis related to cancer?

If an enzyme can't carry out self destruction, a cell will proliferate until a tumor forms This is precisely why mutations in genes that code for enzymes that regulate apoptosis are extremely common causes in causes of cancer.

Describe the pathway of a G-coupled protein receptor? Give an example?

G-coupled protein receptor: Binds a ligand on the outside of the cell, they're embedded in the lipid bilayer 1. Hormone is on the outside of the cell, it's getting near the cell membrane 2. Hormone is binding to the receptor that's specific for it. 3. Then there's a structural change in the receptor. The receptor is actually bound to an internal protein (a G-protein) 4. This affects the interaction when a ligand binds and there's a conformational change in the receptor that causes the G protein to let go of GDP and then grab GTP instead (occurs at the alpha subunit). 5. Alpha subunit breaks off and transmits a signal by activating an enzyme. And that enzyme or one downstream of it will be what affects the change. Sometimes it takes several steps. You're amplifying the signal the whole time 6. The alpha subunit turns itself off by breaking GTP down to GDP and then it will go back and bind to the beta and gamma subunits where it is normally anchored

What is an example of hormone signaling that uses a heat shock protein (Hsp)?

Glucocorticoid Hormone Signaling 1. Hormone enters the cell 2. Hormone finds a receptor and forms a complex, a HSP is then kicked off 3. Dimerization occurs and then it travels through the nuclear pore 4. Transcription is then activated

What does heparin do?

Heparin is an anti-clotting factor that is present in the blood so blood clots don't form for no reason. Inhibiting heparin allows for clots to form right at the site of the wound.

How does a phosphate group get removed from a signaling molecule?

Hydrolysis

How substrate affects enzyme binding Compare the hyperbolic and sigmoidal plots.

Hyperbolic: Tells us that the substrate does not change enzyme binding of the substrate Can read the Vmax and see the Vmax/2 relationship to Km Sigmoidal: Tells us that the substrate does change enzyme binding of the substrate. This effect is allosterism

How can the cell tell if there are plentiful amino acids and nucleotides and energy?

If this reaction is occurring it means that the cell understands that there are enough amino acids to go around and the energy status is good. Therefore the cell can undergo DNA replication if it needs to. ~ It knows this due to the presence of aspartate/aspartic acid ~

What is the Philadelphia Chromosome made from? What fusion protein does it make? Why is that fusion protein oncogenic? What type of cancer has the Philadelphia Chromosome? Why would you not just use a tyrosine kinase inhibitor against this type of cancer? What drug works against it in a very specific way?

It is made when there's a breakage and fusion between chromosomes 9 and 22. The point at which it breaks part of a protein called BCR is joined to a part of a protein called ABL and ABL has tyrosine kinase activity. The fusion is the Philadelphia Chromosome (bcr-abl fusion) The fusion protein is oncogenic because on chromosome 9 abl exists at low levels and bcr is expressed at high levels but when the two are joined abl is expressed at high levels and has high activity. This higher level of expression is a hallmark for chronic myelogenous lukemia. Cancer: Chronic myelogenous leukemia You would not use a tyrosine kinase inhibitor because it would affect ALL the tyrosine kinase in the cell which would have a lot of adverse effect. The treatment would be too general. Would target things like hair, and intestinal lining so that's why there needs to be a period btw the chemotherapy sessions Treatment Drug: Gleevec (made at OHSU)

Where do signals originate?

It originates when the signal binds to the receptor which is either on the outside of the cell OR The signal will somehow get into the cell and bind to a receptor internally

How does vitamin K regeneration work?

It starts off with Vitamin K epoxide which must be recycled. It does this by performing... Vitamin K epoxide reductase where a water molecule is lost. This then regenerates Vitamin K

Contrast the insulin pathway with the beta-adrenergic pathway in terms of their outcomes?

The beta-adrenergic pathway releases glucose. Blood glucose levels rise Whereas the insulin pathway takes up glucose back into the cell. Blood glucose levels fall. The movement of glucose is switched

What signaling molecules can go right through the lipid bilayer?

Lipid Bilayer: Charged polar head group on the outside facing the external environment and also facing the inside of the cell and then the hydrophobic tails are on the inside of the lipid bilayer Most molecules can't readily travel through this But, HORMONES derived from cholesterol can Cholesterol is often a component of the membrane Hormones are a type of molecule that produces signals and travels a long distance in the bloodstream. It is not fast and takes some time to travel through the bloodstream and end up at the cell type they're looking for.

How is lysine changed by acetylation?

Lysine: an amino acid that has an extra amino group on its side chain that can act as a base and carry a positive (+) charge Ig you acetylate the lysine residue and add an acetyl group to the amino and nitrogen (a covalent modification) the e- withdrawing effect of the acetyl group will prevent the nitrogen from carrying a positive charge and modify the behavior of the AA. The loss of the positive charge (+) on the side chain affects... ---> acidity/basicity: since it can no longer exchange protons ---> Electrostatic interactions with other charged molecules

Name some post-translational modifications?

Methylation: Addition of a methyl group (CH3) to a protein Acetylation: Addition of an acetyl group Glycosylation: Addition of a sugar molecule Translation: synthesis of AA polymers Post Translational: Events that take place after the initial synthesis Small: Adding or subtracting small functional groups

The molecular response ---> Blood Clotting

Molecular response converges on polymerization of fibrin (resulting from intrinsic and extrinsic pathways) to make the blood clot Intrinsic Pathway: Also known as the contact activation pathway Extrinsic pathway: Known as the tissue factor pathway (more important)

Which is faster, hormones or nerve impulses?

Nerve impulses

What is the outcome of a steroid receptor binding a steroid hormone? If Hsp70 is involved, what is its job?

Outcome: Transcription ---> When it's done the signal is turned off and the receptor may even be recycled and used in the cytoplasm again If Heat shock protein is involved... 1. It binds to the receptor in the cytoplasm and stays in the cytoplasm 2. Once the receptor binds the hormone then it drops HSP70 by conformational change in the receptor What happened when the HSP70 got released is a nuclear localization signal was revealed on the receptor protein. So now the whole complex can be transported into the nucleus and it acts as a transcription factor when it gets there.

What covalent modifications of enzymes did we go over? What are some examples?

Phosphorylation - Kinase Cascade and Signaling Acetylation - Histones (and DNA replication) Formylation - All Prokaryotic Proteins Acylation - Anchored Membrane Proteins (SRC) acyl = fat ADP Ribosylation - Transcription Factors Sulfation - Serine Protease Inhibitors Ubiquitination - Many proteins, tags proteins for degradation by the 26S proteasome Gamma-Carboxylation - Clotting Proteins

How are blood clots dissolved?

Plasmin dissolves blood clots Plasminogen is the zymogen that gets cleaved to plasmin and it's controlled so we don't have it being at odds w/ clotting all the time Cells controls the levels of the enzyme and how active they are. The enzymes tissue plasminogen activator (tPA), Urokinase, Factor XIa, XIIa, and Kallikrein activate plasminogen tPA is a serine protease that breaks down clots in the body and you can give it to patients if they have a clot and you catch it in time. Plasmin when activated does have inhibitors so that activity doesn't get to be too much Plasmin cleaves fibrin clots and von Willebrand factors Collagenases that'll break down collagen that shouldn't be showing at the wound site are activated by plasmin so the exposed collagen no longer signals to get broken down and inform the body of a wound.

How do prostaglandins work? What do they do?

Prostaglandins are hormone like but they act very locally ---> Unlike hormones they don't travel to a distant part of the body from where they are made because they are not very stable They are important for pain, uterine contraction, and the cells around in an injury will make prostaglandins and it will cause swelling and pain in the local area The prostaglandins are a group of lipids made at sites of tissue damage or infection that are involved in dealing with injury and illness. They control processes such as inflammation, blood flow, the formation of blood clots and the induction of labour.

Why would an enzyme be held in an inactive state?

Protein digesting enzymes are secreted in an inactive form to protect the organs and glands from digestion by the enzymes. So that the enzyme is not constantly active * prevent any kind of reaction of the enzymes with other cells or tissues. * they would otherwise digest the protein contents of the cell where they are produced, which could cause the cell to die.

What is a protooncogene? Give an example?

Proto-oncogenes are a group of genes that cause normal cells to become cancerous when they are mutated Part of normal cell growth but if they go rouge then it could morph into an oncogene especially if it's mutated in such a way that messes up the EGF pathway. It becomes overexpressed which means there's too much being transcribed and translated or it's mutated and cant be turned off. These can al contribute to some of the steps towards cancer but it still has a normal job in the cell. They're just over or underdoing they're normal job. Can also be called proto-oncoprotein An example is Ras

Why is Ras potentially problematic if over expressed?

Ras is actually a family of proteins and like many proteins there are other homologous proteins sometimes they're called something different because they're in a different cell or tissue type Ras is a GTPase converting GTP to GDP it can turn itself off when it does that If overexpressed it would lead to uncontrolled cell growth and researchers have been unable to develop treatments that can directly target altered RAS proteins, and many have written off RAS as being "undruggable." RAS is the most commonly mutated oncogene in human cancers

How can ATCase shut down pyrimidine synthesis?

Reaction that requires ATCase: Starts w/ bicarbonate and then you end up w/ carbamoyl phosphate. Then the carbonyl phosphate acts w/ ATCase to make carbamoyl aspartate. What we need to make this whole reaction occur is phosphate, nitrogen, and energy. As [S] increases, the ATCase goes from being mostly in the T state to mostly in the R state It can shut down pyrimidine synthesis by being inhibited by CTP (which is a pyrimidine) CTP creates a negative feedback loop. The large amounts of CTP tell our body that we probably need more purines. So purine/ATP is what turns the self inhibition on

What is a second messenger and why is it called that?

Second messengers are small molecules and ions that relay signals received by cell-surface receptors to effector proteins. Second messengers are the key distributors of an external signal, as they are released into the cytosol as a consequence of receptor activation and are responsible for affecting a wide variety of intracellular enzymes, ion channels and transporters. Ex. Calcium ions, cyclic AMP (cAMP), Cyclic GMP (cGMP), Inositol 1,4,5 Trisphosphate (IP3)

Where is the receptor for a steroid hormone located? Describe the pathway?

Since steroid hormones are lipid-soluble, receptors are located WITHIN the cytoplasm or nucleus of target cells. Taken within the cell due to conformational change through nuclear transport and then it binds to the DNA Since steroid hormones are lipid-soluble, receptors are located WITHIN the cytoplasm or nucleus of target cells.1. Steroid hormone is diffused across the plasma membrane. 2. Steroid hormone binds to the receptor, changing its conformation 3. The hormone-receptor complex enters the nucleus, and binds to a section of DNA. This induces an alteration of gene activity Steroid hormones cross the membrane either on their own or sometimes with a protein partner. There may be a receptor that when they bind to it dimerizes but for sure, at least, the receptor experiences a conformational change.

What does Src (for "sarcoma") do when mutated as an oncogene?

Src is controlled (gets turned on and off) by phosphorylation BUT the mutated form makes it so it can't be phosphorylated Phosphorylated tyrosines block access to its SH2 Domain and prevent it from participating in signaling leaving it inactive Mutations changing these tyrosines leave the protein always activated stimulating uncontrolled cell division

How does a typical pathway for steroid hormones differ from the other types?

Steroid hormones are derived from cholesterol. Steroid hormones and thyroid hormone are lipid soluble. All other amino acid-derived hormones are water soluble. This allows them to cross the lipid bilayer They signal the cell about metabolism at the levels of allosteric regulation and gene expression and covalent modification and so normally they're going to affect gene expression. And they take a little time traveling through the bloodstream, it's not as instantaneous as the nervous system. It could even take hours

Why do you think steroid hormones get inside the cell so easily?

Steroid hormones can pass through the plasma membrane by simple diffusion because they are LIPID DERIVED hormones They are fat/lipid soluble

Describe a form of inhibition that is covalent and cannot unbind?

Suicide Inhibition Suicide inhibition is a form of irreversible inhibition in which the substrate in the first catalytic cycle is converted into a chemically reactive product which remains bound to the active site through covalent bonding. The enzyme is rendered permanently inactive. Such inhibitors have potential as drugs.

What molecule is the target of the drug Herceptin? What type of molecule is it? What type of cancer can it cause?

Target: HER2 Molecule: Monoclonal Antibody Cancer: Breast Herceptin in a monoclonal antibody to treat HER2 caused breast cancers. Prevents the dimerization of the HER2 receptor Some mutations cause too much of a quantity of a protein rather than affecting its structure or activity, a great example is the HER2 receptor. AKA too much transcription More HER2 = more cell division HER2 is inserted into the membrane and forms dimers There doesn't need to be any epidermal growth factor, HER2 binds the growth factor to form a dimer

Which subunit binds the guanine nucleotide?

The alpha subunit of the G-protein

What is meant by amplification of the signal?

The amplification of signals, defined as an increase in the intensity of a signal through networks of intracellular reactions, is considered one of the essential properties in many cell signaling pathways. Signals are amplified at the intermediary and target molecule steps

Do kinases turn things on or off or both?

The covalent modification will change the proteins activity either by turning it on or off. Phosphorylation can do either and it depends on what site on the protein that phosphorylation is activating or repressing

What is the end result of the insulin pathway?

The fall/decrease of blood glucose levels

Where are the digestive zymogens made?

The pancreas! They get moved around btw. organs and you want them to be able to move and not be in the active enzyme form.

What is signal transduction?

The transfer of molecular signals from the exterior to the interior of a cell. How cells and tissues manage to respond to signals they are recieving Often these are in the form of molecules traveling through the bloodstream. Those molecules arrive at the cells and they give them instructions of what to do. The signals could be stop or go, on or off, do more or less, and the signals originate on the outside of the cell membrane but they have to change processes on the inside of the cell.

What are homotropic and heterotropic effectors? How do they differ?

They are both allosteric effectors: Homotropic effector: Is both a substrate and has the ability to change the enzyme (regulatory molecule). * Makes the sigmoidal curve, and is the control on the [S] vs. Reaction Velocity plot. Heterotropic effector: Is NOT a substrate, it's just something that affects the enzyme. It could be activating or inhibitory but it's not happening at the active site. * ATP is an activator * CTP is an inhibitor

How does the beta-adrenergic pathway work (i.e., epinephrine or adrenaline)? What is the outcome?

This pathway works to control the breakdown of glycogen. It's great for when you have an adrenaline rush. Binds epinephrine (aka adrenaline) and the rush is very temporary 1. Protein Kinase A phosphorylates a molecule called phosphorylase kinase and glycogen synthase 2. Phosphorylase kinase phosphorylates glycogen phosphorylase 3. Glycogen phosphorylase converts glycogen to glucose-1-phosphase Outcome: Releases glucose in the bloodstream

How does thrombin perform positive feedback?

Thrombin, the enzyme that is used to call upon platelets, form fibrin and activate Factor 13, can also be used in positive feedback loops. Thrombin goes back to the beginning of the cascade and also activates Factor 8, Factor 11 and Factor 5 in an effort to amplify the amount of prothrombinase that is formed.

How does the receptor become active?

Through dimerization (joining together) and then the autophosphorylation Dimerization happens when the ligand is bound and they have to use ATP to phosphorylate the target protein

How do you turn off the beta-adrenergic receptor?

Through modification or undoing an activating event that's happened to it (this is all under very tight regulation) There is a kinase that will add a phosphate to the cytoplasmic side. This would cause a protein called arrestin to prevent the G protein from interacting with the receptor and the whole thing would be endocytosed We also need to turn off the G-protein too ---> If the receptor hasn't let go of the ligand then we still need to turn off the G-coupled protein

What is the goal of blood clotting/coagulation?

To create a fibrin mesh to stop bleeding Fibrin can only polymerize when its active site is exposed. Fibrinogen has a protein block over the active site. To become activated it needs a protease enzyme to chop off the protein block. The protease enzyme also has a protein block over its active site that requires a different protease enzyme to cut off its protein block.

How is chymotrypsinogen activated?

Trypsin cleaves/cuts after Arg-15 that triggers tertiary changes (disorder ---> order) This creates the partially active pi-chymotrypsin. Then self digestion occurs at Leu-13, Tyr-146, and Asn-148 by pi-chymotrypsin. The the pieces (Ser-14+Arg-15 and Thr-147+Asn-148) are what makes the enzyme active because it exposes the active site so it can bind substrates The new Ile-16 a-amino group forms an ionic bond with Asp-194 to form the substrate binding site. This gives us the fully active form alpha chymotrypsin Before these enzyme will digest other proteins other enzymes. They'll also digest themselves so that's why they zymogenic form is needed.

How does vitamin K work in blood clotting?

Vit K is a fat soluble molecule stored in fat tissue ---> Roles in blood clotting and bone health ---> Absence leads to uncontrolled bleeding ---> Deficiency is rare Vitamin K helps to make four of the 13 proteins needed for blood clotting, which stops wounds from continuously bleeding so they can heal. Vit K is key for the carboxylation of glutamates of the factors 2, 7, 9, and 10. Gamma carboxylation modifies the side chains of glutamates. The glutamate has two carbonyl groups and it an bind calcium where it couldn't before 2 is prothrombin and it's key for anticlotting factors There are 4 different forms of Vit K ~Vitamin K is a cofactor for glutamate carboxylase~ ---> The Vit K becomes Vit K epoxide, but it needs to be converted back to Vit K for the person to have they're Vit K levels restored

What do coumadin and warfarin do?

Warfarin (brand name of coumadin) is a Vitamin K inhibitor given to heart patients. It lowers the levels of vitamin K to thin the blood (aka reduce clotting) ---> It's a blood thinner ---> Reduces clot forming capabilities ---> Warfarin is rat poison that causes rats to bleed internally It blocks vitamin K recycling The lack of Vit K stops protein carboxylation Low protein carboxylation slows blood clotting It's given in small doses to prevent stroke and patients have to be careful bc. if they get injured they could end up with internal bleeding It's also given to people with irregular heartbeats

Why do other ligands stay on the outside of the cell?

Water-soluble ligands are polar or charged and cannot readily cross the plasma membrane. So, most water-soluble ligands bind to the extracellular domains of cell-surface receptors, staying on the outer surface of the cell. The molecules are hydrophilic and cannot penetrate the hydrophobic interior of the plasma membrane.

What happens when a ligand-gated ion channel gets opened?

When a ligand-gated ion channel opens: ---> Lets calcium into the cell ---> Changes the formation and opens the gate so a signal that wouldn't normally be able to do anything to the lipid bilayer or come through binds to the receptor embedded into the bilayer. ---> The channel allows ions that couldn't get in before a chance to do so Now there is a voltage differential across the membrane because the calcium ions have come in. This is a signal that is common in nerve cells

How do we get a fibrin clot?

When tissue damage results in bleeding, fibrinogen is converted at the wound into fibrin by the action of thrombin, a clotting enzyme. The amplification phase of the molecular response requires factors from the intrinsic and extrinsic response: 1. FVIII is normally bound in a complex with the von Willebrand factor and is inactive until it is released by action of thrombin 2. FXIa helps favor the production of more FIXa 3. FIX1 plus FVIIIa stimulate production of a considerable amount of FXa (3-4 orders of magnitude) 4. FVa joins FXa and calcium to make a much larger amount of thrombin (3-4 orders or magnitude) 5. Fibrinogen cleaved to fibrin, which polymerizes Thrombin converts fibrinogen into fibrin, it self polymerizes and assembles itself into a longer polymer

What covalent modification does a zymogen receive?

Zymogens are inactive precursor enzymes that are regulated by irreversible covalent modification Ex. Digestive enzymes from the pancreas like trypsinogen are moved to the intestine and then in there it's covalently modified by the enzyme enterokinase which converts it to it's active form trypsin

Where are zymogens used in blood clotting?

Zymogens are really important for this process, they can form a clot from proteins in our blood where there wasn't a clot before In the molecular response: There is a cellular response that works via platelets. (This is a specific cell response that forms the clot) Then the focus of activity comes from fibrin that forms polymers that make a clot and it comes from the zymogen fibrinogen. Thrombin converts it o the active form of fibrin. Thrombin also has a zymogen which is prothrombin. Most of the factors in the initiation and amplification phase have an active and zymogen form. The activation of the zymogens comes from the intrinsic or extrinsic pathways which have some overlap but they converge to make this process happen The whole cascade ends up w/ activating thrombin, fibrin, and factor 13a

What is a zymogen? Can you give some examples?

Zymogens are... Precursors of active enzymes, the enzyme is not active if in zymogenic form because you don't necessarily want all your enzymes active at all times but you want them standing ready Especially important in digestive enzymes or else it would chew up proteins they encounter that look specific enough to them or when they're moving through the body btw organs you want them to not be active. Suffix: -ogen Prefix: pro- or prepro - Examples: Proenteropeptidase ---> Enteropeptidase Trypsogen ---> Trypsin Proelastase ---> Elastase Procarboxypeptidase ---> Carboxypetdidase Chymotrypsinogen ---> Chymotrypsin Prolipase ---> Lipase

What happens when insulin binds to its receptor?

it causes signal transduction which includes glucose coming into cell. GLUT4 protein is the glucose transporter that will take glucose back into the cell. Glucose is then used as an energy substrate The insulin is the catalyst for the next step which is autophosphorylation. Without the insulin the autophosphorylation would not occur even if the receptor was dimerized

What is a receptor?

protein that detects a signal molecule and performs an action in response transmembrane proteins, which bind to signaling molecules outside the cell and subsequently transmit the signal through a sequence of molecular switches to internal signaling pathways.