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BIO Week 3 Notes

by: Jay Ty

BIO Week 3 Notes 140

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Jay Ty
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Here are some of my original notes for BIO 140 for you guys to refer to! Good luck studying :)
Foundations of Biology I
Kerry Creswawn
Class Notes
Biology, phospholipids, Lipids, saturated, unsaturated, Life Science, Proteins, Proteins and Enzymes
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This 7 page Class Notes was uploaded by Jay Ty on Thursday September 22, 2016. The Class Notes belongs to 140 at James Madison University taught by Kerry Creswawn in Fall 2016. Since its upload, it has received 7 views. For similar materials see Foundations of Biology I in Biology at James Madison University.


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Date Created: 09/22/16
9.20.2016 BIO 140 Cresawn Notes I. Assembling and Breaking Down Proteins a. How many water molecules would be produced in making a polypeptide that is 14 amino acids long? i. 13 ii. Assembling and breaking down proteins (and other polymers) 1. Monomers polymerize through condensation (dehydration) reactions a. That releasea water molecule b. Requires energy c. A + B + Energy  A- B + H2O 2. Hydrolysis is the reversereaction a. That breaks polymers apart by adding a water molecule b. Releases energy c. A – B + H2O  A + B + Energy 3. Condensation reactions create a covalent bond (Peptide bond) which collectivelyform polypeptides iii. Peptide bonds are broken ina hydrolysis reaction 1. Hydro: water 2. Lysis: breaking down 3. The roles of enzymes inhydrolysis… a. Ends in “ase” b. Speed up the rate at which proteins are broken down c. Bind to and cleave the proteinat specific locations resulting in determined fragment sizes iv. APP 1. A specific enzyme that cleaves the intact protein at a specific location via hydrolysis into 2 different peptide fragments a. APP is found in many tissues including brain and spinal cord, but little is known about its function i. Proposedfunction of the in-tact protein: Binds to other proteins on surface of other cells to help cells attach to one another 1. Helps directmovement of nerve cellsduring earlydevelopment ii. Proposedfunctions of the cleaved2 peptide fragments: secreted peptide helps with formations of neurons inbrain before and after birth. 1. Cellular peptide plays role inplasticity: neurons adapting over time in response to experiences and task. iii. An error in hydrolysis 1. A different enzyme is used and cuts at a different location a. Beta secretase enzyme b. This errordestroys neurons, and causes toxicity. II. Connections between TBI (Traumatic BrainInjury), Alzheimer’s (AD) and toxic APP fragments a. Alzheimer’s i. 5.4 million people ii. Risk increases withage iii. Fragments cause plaques iv. # of fragments correlateswith severityof dementia (autopsy studies) v. Why do the enzyme switch insome older people and not others? 1. Not wellunderstood b. TBI i. 5.3 million people ii. 75% due to concussions iii. In 1/3 of TBI brains, fragments and plaques found upon autopsy as early as 2 hours after injury and they persistfor years iv. Specific mechanism by whichconcussions cause the enzyme switch? 1. Not wellunderstood 2. Likely due to damage of neurons and inflammation c. Connection i. Now at much higher riskfor Alzheimer’s III. Question a. Which best explains the difference betweenamyloid precursor protein inhealthy neurons and in neurons after TBI? i. Neuronal damage after TBI causes abnormal hydrolysis of APP producing amyloid peptide fragments that clump together 9/22/2016 BIO 140 Ludwig Notes I. Cell membranes are made up of a class of lipids calledphospholipids a. Important Properties of ALL lipids i. Amphipathic: has two domains: 1. Hydrophobic (nonpolar) 2. Hydrophilic (polar) 3. It is hydrophobic on the inside of the layer, and the outside is hydrophilic ii. 3 classes of lipids 1. Steroids 2. Fats 3. Phospholipids iii. A closer look at a phospholipid 1. There is a polar head group, followedby a nonpolar tail made up of two fatty acid chains iv. Why do lipidsspontaneously come together in this structure when placed in water? 1. The tails are hydrophobic and the heads are hydrophilic, so in order to avoidthe water the tails willcome together 2. These bilayer sheets willalsospontaneously wraparound to form spherical shape holding contents of the cell v. How is the formation of lipid structure similar to the formation of tertiary protein structure? vi. Variations in the molecular make up in fatty acidtails and how that affects lipid and membrane structure 1. Saturated fats: every single carbonavailable is filledwith an equal amount of hydrogen, forming a straight chain 2. Unsaturated fatty acids: missing a hydrogen, making two carbons form a double bond and bringing the carbons closer together. (Forms a kink in the chain) 3. How willthis affect the membrane’s function of keeping unwanted materials out of cells a. Saturated: makes the layer less permeable b. Unsaturated: the kinks create more space and causes the layer to be more permeable 4. What does this have to do with our familiar context of saturated and unsaturated in food? a. Structures of a fat molecule: what are the similarities and differences compared to phospholipids? i. Both olive oil and bacon contain fats like you see above. Which of the two do you predict to have more double carbon bonds? 1. Olive oil has more, because it is a veryfluid membrane, meaning there are kinks 5. Membrane structure alsoimpacted by the presence of another kind of lipid:cholesterol a. The amphipathic structure of cholesterol allowsit to pack tightly with phospholipids. i. Helps maintain the appropriate level of fluidity when membranes in conditions that otherwise alter fluidity like temperature. ii. Cold temperature decrease fluidity iii. Hot temperature increase fluidity. iv. Changing cholesterol levels in membranes helps to stabilize this. vii. Membrane structure also impacted by the presence of proteins (make up 50% of membrane mass) 1. Which of these most closelyresembles the proposedfunction of APP and whichis the function of alpha and beta amylase? 2. The APP is more like the “anchor” a. The anchor is across the membrane, and is a structural component b. It’s to grab things outside of the cell and allowsthem to hook on to the cell,like an anchor c. There’s variationin proteins d. Amphipathic phospholipid layers make it effective for proteins to travel through 3. Are these proteins stationary or mobile? a. Membranes proteins were fluorescently tagged b. A laser used to bleach small area of membrane c. Over time, the bleached area becomes fluorescent i. Shows that the fluorescent molecules are moving into the bleached area gradually ii. These proteins are therefore mobile viii. Membranes are found both surrounding the cell (plasma membrane) and within the cellsurrounding most organelles 1. The structural features of membranes just discussedapply to all ix. Membranes function as selective barrier, theyare “semipermeable” 1. This means membranes have varying levelsof permeability to differen molecules for both entry and exit of cells a. This canchange under different conditions 2. Four key features that impact permeability to specific molecules are a. Structural properties of the molecule in question: polarity and size i. The densely packed phospholipids and hydrophob interactions between these tails create a physical barrier for larger molecules 1. Ex: glucose (large) 2. Which of these two molecules would pass through the membrane more freely? Na+ or O2? a. O2 because heads are polar but spacedfar enough apart that nonpolar molecules can move through them and avoidthe unfavorable interactions b. Tails are nonpolar and more densely packed than the heads. c. [Most] charged molecules cannot “slippast” and avoidinteractions d. A physiologically VERY important exceptionto this rule: i. WATER can getthrough, because it is small ii. Therefore, there is a continuum of permeability dependent on both size and polarity/charge 1. Fast: hydrophobic molecules 2. Slow: small, uncharged polar molecules 3. Can’t pass freelyat all: large polar molecules 4. Can’t pass freelyat all: freelycharged molecules b. Structural properties of phospholipids: tail length and saturation i. Based on what you alreadylearnedabout fatty acid tail saturation, which membrane willbe more permeable in general? 1. A membrane with30% of tails saturated, because 70% would be unsaturated and therefore have more kinks ii. Phospholipid tail length varies from 14-24Carbon atoms, how will# of Carbon atoms impact permeability? 1. This is alsoreflected in relativefluidity of fats when comparing fatty acid tails of beeswaxversus butter a. Shorter tails mean higher permeability b. Longer tails mean lower permeability c. The external environment (ex: temperature) i. Recall the membrane is fluid-like, always in motion ii. Hot temperature causes anincrease in permeability (more kinks) iii. Cold temperature causes a decrease in permeability (less kinks) 1. Some organisms’ bodies respond to decreasingtemperatures inthe environments by increasing the number of double bonds in the lipidportion of the bilayer d. The presence of membrane proteins e. How do these structural features of membranes contribute to membrane function? i. Passive transport (passive diffusion), facilitated diffusion, and active transport 1. Passive diffusion: molecules move from a high concentration to a low concentration until they reachequilibrium, at which point they continue to move II. Equilibrium a. Cells “work toward” steady state (homeostasis) i. Analogy: capacity in a bar. The individuals inthe bar might change, but the total number does not. One out, one in. b. Net movement of solute from the area of higher solute concentration to the area of lower solute concentration i. Occurs randomly c. Osmosis i. Diffusion of water


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