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BIO-0013 (28)
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Department
Biology
Course
BIO-0013
Professor
Derek Mc Lachlin
Semester
Fall

Description
09/12/2011 Plasma Membrane – a layer of molecules around the cell that sepeates the interior cell from the external environment Acts as a selective barrier, keeping nasty things out and letting good things in Since it keeps the appropriate chemicals in an enclosed area, reactants collide more frequently and reactions happen more efficiently Lipid – the general term for C-containing compounds that are mainly hydrophobic and nonpolar Part of the Reason they are insoluble is because they are hydrocarbons, and the C-H bonds have almost 0 dipole movement 3 Main Types of Lipids Fats Composed of three fatty acids all connected to a glycerol molecule (3 carbons) Which is why fats are also called triglycerides Glycerol and the fatty acids are joined together by ester linkages Fats are not like macromolecules in the way that amino acids are Steroids Bulky, 4-ring structure Various steroids are distinguished by their R-groups like aminos The R group is hydrophilic while the rest is hydrophobic Important steroid is cholesterol Phospholipids Contain a glycerol connected to a phosphate group and either two chains of isoprene or two fatty acids Critically important to plasma membrane Structure of Membrane Lipids Membrane forming lipids have a polar, hydrophilic region and a nonpolar, hydrophobic region The head of the phospholipid interacts with water while the nonpolar tail doesn’t Amphiphatic – compound that contains both hydrophilic and –phobic regions Phospholipid Bilayer In water, since it doesn’t react with the hydrophobic tails, they are driven together Causes the phospholipids to either form a: Micelle – tiny droplets with heads on the outside and tails on the inside, kind of like a ball Lipid Bilayer – when two sheets of phospholipids align – mainly formed from phospholipids with longer tails Both micelles and bilayers form spontaneously – more energetically stable Researchers used liposomes and planar bilayers to find out what happens when an ion or molecule is added to one side of the bilayer Selective Permeability of Lipid Bilayers – HIGHLY selective Small and nonpolar molecules move quickly across the bilayer while large and charged molecules cross the molecule slowly The leading theory is that the large molecule and charged compounds have a much tougher time passing through the nonpolar hydrophobic tails Lipid StructureAffects Membrane Properties Bond Saturation The C=C double bond can cause a kink in an otherwise straight HC chain Chains without a double bond are said to be saturated and those with a double bond are said to be unsaturated Saturated has more free energy than unsaturated due to the double C=C bond Bond Saturation and Chain Length Change Membrane Fluidity and Permeability When hydrophobic tails are packed together, the kinks in some create more space between the tails, decreasing the force of the hydrophobic interactions Like butter which is very satured (no kinks) and is solid at room temp Oils are unsaturated and have lots of kinks – liquid at room temp These interactions are also stronger when the lengths of the tails are increased Like waxes which are solid at room temp and have long tails Lower permeability = less fluid; higher permeability = more fluid Unsaturated tails have more room for shit to pass through it Cholesterol Reduces Membrane Permeability Adding cholesterol drastically reduces permeability of the lipid bilayers Since cholesterol is bulky, adding it creates a more dense hydrophobic section Temperature’sAffect At room temp, the bilayer has the consistency of oil, and as the temp decreases so does the fluidity and permeability The individual molecules move more slowly in low temps – causes the tails to be packed more tightly At very low temps the tails start to solidify Diffusion Entropy always increases Solutes in the solution have thermal energy and are in constant random motion Movement from their kinetic energy is known as diffusion Solutes move down concentration gradient , from high to low concentrations Happens spontaneously and increases the entropy Once everything is randomly distributed and equal, we reach equilibrium Osmosis Transfer of water from high to low concentration gradient – only occurs across a selective membrane – movement of water is spontaneous Hypertonic If there is more solute outside the cell than inside, water will move out of the cell, causing the cell to shrink and shrivel Hypotonic If there is more solute inside the cell than outside, water will move into the cell, causing the cell to burst or swell Isotonic Equal concentrations on both sides, nothing happens Proteins that are amphiphatic can be inserted into lipid bilayers The amphiphatic quality of proteins come from the fact that R groups can either be polar or nonpolar Fluid-Mosaic Model Proposed 1935 that plasma membranes were like sandwiches Proteins coating both sides of a lipid bilayer Singer and Nicholson proposed 1972 that membranes are mosaics of phospholipids and proteins – the membrane was fluid and dynamic The controversy between the two was solved using scanning electron microscope Allowed researchers to cut plasma membrane in half and see inside This proved that membranes have both integral membrane proteins and peripheral proteins (only on one side) Peripheral proteins are often attached to integral proteins Three main classes of transport proteins: Channels Most ions cross through cells via ion channels Pores in the membrane – ions move from high to low concentration Ions also move with regard to charges Called an electrochemical gradient Channel proteins are selective – each is shaped for a particular molecule i.e.Aquaporins that allow water to cross the plasma membrane 10x faster than normal Pore is hydrophilic but the exterior is hydrophobic Regulated movement through channels Gated proteins – they open/close/ in response to binding of a particular molecule or change in electric charge If the charge outside the membrane changes, the structure of the protein might changes in a way to let potassium through Movement through these channels is always passive – no energy needed Facilitated Diffusion via Carrier Proteins Glucose Transporter – glucose is the most important sugar in the body Would be reasonable to think membranes had some way to aid it Cells have GLUT-1 which helped glucose transport much more easily GLUT-1 – basically glucose binds into the unique fit of glucose, and the act of binding changes the structure of GLUT-1, creating a channel for glucose to shoot into the cell; once its expunged, GLUT-1 goes back to its normal shape Active Transport via Pumps Possible for cells to import molecules against their gradient This requires energy – provided by the phosphate group fromATP Sodium-Potassium Pump Just Review Page 98 nigga SecondaryActive Transport Pumps also set up electrochemical gradients The Na/K pump creates a positively charged interior Sets up cotransport The movement of molecules along a gradient set up by a pump The selective permeability of the membranes creates a very different interior and exterior environment for the cell Able to create an internal environment conducive to life 09/12/2011 Morphology vs. Phylogeny 09/12/2011 Morphology says that the broad classes of cells are eukaryotic and prokaryotic Phylogeny says that the three broad domains are Bacteria,Archaea, and Eukarya For 200 years biologists through prokaryotic cells were very simple – they were wrong Prokaryotic Cells Chromosome – most prominent structure inside a bacteria cell Usually bacterial species have a single, circular chromosome associated with surrounded proteins The DNA has the info but the proteins provide structural support They contain the cell’s genes The DNA double helix coils on itself (with help of enzymes) to form a highly compact structure – supercoiled Chromosomes are found in an area called the nucleoid – center of cell Pretty big area – DNA material not enclosed though Bacterial cells have plasmids along side the chromosomes They contain genes but are independent of the main gene Help cell adapt to unsual circumstances Ribosomes Protein manufacturing units – cells could have 10,000 Complex structures consisting of RNA molecules and proteins Internal Membrane Bacterial cells have an extensive internal membrane that performs photosynthesis The expansive internal membrane gives the cell a lot more surface area to conduct photosynthesis 09/12/2011 Organelles Bacterial cells have membrane-bound compartments inside the cell for particular functions Storing calcium ions; holding crystals of mineral magnetite; Cytoskeleton structures the cell interior Structural fibers help in cell division and help the cell main its shape Plasma Membrane Phospholipid bilayer with proteins that separate cytoplasm from outside world aka life from non- life Flagella Rotation of flagella helps aquatic cells swim through water Cell Wall Tough, fibrous layer that surrounds the plasma membrane Helps resist the pressure of the expanding plasma membrane as water flows into the cell Also contributes to shape Structure and Function of Nuclear Envelope Separates nucleus from the rest of the cell Supported by fibrous nuclear lamina and bounded by two lipid bilayer membranes Nuclear Pores These gate-like structures extend through the membrane and connect the nucleus to the cytosol Structures are made up of over 50 proteins to form an elaborate nuclear pore complex Gold Particle Diffusion Experiment 1960s - researches put gold particles into the nucleus to see where they ended up in the cell 09/12/2011 Turns out that all the gold particles, that leave a black speck on the microscope all started in the nucleus but within 10 minutes they were all over the cell Although DNA doesn’t travel through these pores, they have encoded information that produce RNA which travels outside the nucleus Ribosomal RNAs are produced in the nucleolus where they bind to proteins to form ribosomes, which are then shipped to the cytoplasm mRNAs carry info required to manufacture proteins out to the cytoplasm, where protein synthesis occurs Nucleoside triphosphates and proteins that are integral for copying DNA, synthesizing RNAs, and ribosomal helpers enter the cell Proteins destined for the nucleus have a “zip code” that marks it to be sent to the nucleus – also called Nucleus Localization Signal Pulse-Chase Experiment George Palade treated experimental cells with a large number of labeled molecules and then followed it up with a big amount of unlabeled molecules The idea was just to follow the fate of the labeled molecules over time The ER Signal Sequence Proteins synthesized in the cytosol have a signal sequence of 20 extra amino acids marking it for the plasma membrane The signal sequence, which is bound to a ribosome, binds to a SRP – signal receptor particle The ribosome + signal sequence + SRP attach to a SRP receptor in the ER membrane Once the receptor and SRP are connected, the SRP is released The signal sequence in removed and protein synthesis is completed Once it is inside the ER, it folds into its 3D shape IF it enters the lumen, enzymes catalyze the addition of a sugar to the protein Called glycosylation Proteins move from the ER to the GolgiApparatus via vesicles GolgiApparatus Consists of a stack of flattened vesicles called cisternae New cisternae form as old ones break down 09/12/2011 Monosaccharides 09/12/2011 Carbonyl group is the distinguishing factor for these At the end of the sugar chain, it forms an aldehyde sugar (aldose) Within the chain, it forms a ketone sugar Named differently per number of carbons Triose, pentose, hexose These chains are linear but in aqueous solutions they form rings Each monosaccharide has a unique structure Polysaccharides Many monomers linked together Glycosidic Linkage Condensation between two hydroxyl groups form a covalent bond that binds the simple monomers together Bonding happens on the hydroxyl groups, and each monomer has at least two hydroxyl groups, there is a lot of variety for linkages Alpha vs. Beta bonds Alpha means there is a bond below – Beta means there is a bond above Alphas are easier for enzymes to break Starch – used for energy storage in plant cells Consists of solely alpha-glucose monomers Forms into helixes – can either be Amylose helix which is unbranched Amylopectin helix which is branched but not very frequently 09/12/2011 Glycogen Stores energy in animals – when exercising, enzymes break down glycogen into glucose monomers to supply energy Very highly branched but similar helix to starch Cellulose Major component of the cell wall in plants Beta glucose monomer – generates a linear molecule and permits multiple H bonds to form between adjacent and parallel strands Chitin Stiffens the cell walls of fungi Similar to cellulose but uses NAc monomer instead of glucose Peptidoglycin Used in bacteria to give their cell walls strength and firmness Has a long backbone formed by two monosaccharides that alternate with each other and has beta linkages Also has a string of amino acids attached to it Structure corresponds to function The long parallel strands help withstand pulling and twisting Function Structure Cellulose, chitin, and peptidoglycan They form long and wide sheets that criss cross with one another to form really tough fibers Durability – shape and orientation of Beta linkages make them hard to break, and few enzymes have active sites with correct geometry and reactive groups to do so Durability is important to digestion – helps poop 09/12/2011 Cell Identity Polysaccharides act as signals on the outer membrane of a cell Glycoproteins Proteins that are covalently bonded to a carbohydrate Major parts of cell-recognition and cell signaling – each cell in the body has glycoprotein on the surface that identify it as part of the body Glycoproteins act as an identification method Energy Storage Carbohydrates store and provide chemical energy in cells Carbohydrates store sunlight as chemical energy Photosynthesis The C-H bonds and C-C bonds have much higher potential and free energy Enzymes Hydrolyze Carbs to Release Glucose Glucose subunits are hydrolyzed from starch and then processed – leads to production of chemical energy For glycogen, the important enzyme is phosphorylase For starch, the important enzyme is amylase These are in the body and important for digesting starch ATP The chemical energy from C-H and C-C bonds of carbohydrate is transferred to chemical energy rd in the form of the 3 phosphate group ofATP Energy from sugar helps bring togetherADP and the extra P 09/12/2011 Chemical Formation Theory: 4 step process proposed by Orparin & Haldane Small organic compounds such H2CO and HCN were made from reactants like hydrogen gas and carbon dioxide All those compounds reacted to form mid-sized molecules such as amino acids, nitrogenous bases, and sugars These molecules accumulated in shallow waters, forming a prebiotic soup Bigger, building block molecules linked to form macromolecules Life became possible when one of these large molecules replicated itself – changed chemical evolution to biological evolution Stanley Miller’s Experiment: Tried to recreate first steps of chemical evolution by simulating conditions of ancient Earth Check page 39 for the diagram He had a large flask with ammonia, methane, and hydrogen connected to a small flask with 200 ml water simulating the ocean He boiled the water constantly to have a constant cycle of evaporation and condensation so all the gases are mixing – simulated rain Introduced an electric discharges These pulses of electrical energy “sparked” the reaction and the prebiotic soup started to form within days Follow up experiments showed amino acids could be produced under other Earth conditions Volcanic gases and exposed to high-energy radiation from sunlight Underwater volcanoes spew out boiling water that reacts C and N molecules Meteorites from space had amino acids, proving that amino acids could be produced in outer space Structure of AminoAcids – starts with a central Carbon atom NH2 – amino functional group COOH – carboxyl functional group H – a hydrogen atom “R” group 09/12/2011 For each amino acid, the R group is unique The reactivity of these side chains depends on their composition - the ones with mainly H and C are not as reactive and the ones with S or O The nature of the R groups also affects solubility – if the R group is more polar, the amino acid is hydrophilic; if not, it is hydrophobic AminoAcids link to form proteins Each amino acid is a monomer, which when they link together is called a polymer Linking process is called polymerization Amino acids don’t spontaneously self assemble into macromolecules Moving from simple components to polymers decreases entropy and increases order in the universe, against 2 law of thermodynamics Polymerization reactions are endergonic and nonspontaneous Condensation Hydrolysis reactions Condensation reactions have a loss of a water molecule but a newly formed bond Hydrolysis breaks polymers apart by adding water – the water molecule reacts with the bond linking the polymer, separating a monomer Monomers can be linked in several ways Mix monomers with a strong source of chemical energy and tiny minerals In hot, metal-rich environments of undersea volcanoes, polymerization occurs Polymerization occurs in cooler water if a C or S-containing gas is there Peptide Bond The C-N bond that results from the condensation reaction The carboxyl group loses water and becomes a carbonyl group Polypeptide is when the molecule has a lot of peptide bonds Peptide Backbone of a Polypeptide 09/12/2011 R-groups extend out of the backbone making it possible for them to react Directionality – the free NH2 amino group is always at the left and the free carboxyl group always appears on the right Flexibility – can’t rotate because of double-bond peptide nature, single bonds on the side of it can rotate Polypeptides with <50 = oligopeptide ; with >50 = protein Proteins are very versatile molecules Catalysis – many proteins are enzymes that help speed up reactions in the body Defense – Proteins like antibodies and complement proteins attack and destroy viruses Movement – motor and contractile proteins help move the actual cell or move things in and out of the cell Signaling – proteins receive and carry signals from cell to cell in the body Structure – structural proteins make up body components such as fingernails and hair Transport – proteins allow particular molecules to enter and exit cells and carry specific compounds around the body Protein Structure Proteins serve many purposes because they have so many different shapes and sizes Primary Structure Every protein has a unique sequence of amino acids which is called its primary structure Discovered by Frederick Sanger With 20 different amino acids, the # of possibilities for a string of aminos that could be formed is almost limitless The order and composition of the string of aminos is very important too One small change in a hemoglobin cell can change it from a normal red blood cell to a sickled red blood cell The change in the side chain of just one amino acid fucks everything up Secondary Structure 09/12/2011 Created in hydrogen bonding portions of peptide-bonded backbones These structures are stabilized by H bonding that occurs between the carbonyl oxygen on one amino acid and the Hydrogen on the amino group of another amino acid The oxygen is partial negative due to the its electronegativity and hydrogen is partial positive because of the nitrogen next to it Hydrogen bonding is only possibly when the same polypeptide aligns in a way that carbonyl and amino group are next to each other – happens in two ways Alpha Helix – the polypeptide backbone is coiled Beta Pleated Helix – the backbone bends in 180° and then folds in the same plane Usually secondary structures consist of both but the one that forms depends on the molecule’s primary structure (geometry and properties) Protein may have different secondary structures at different points along the sequence Although individually each H bond is weak, all the them together form a highly stable molecule Tertiary Structure The main overall shape that results from interactions between R-groups or between than and the peptide backbone Each contact between R-groups causes the backbone to bend and fold and contributes to the three-dimensional structure Five types of interactions involving side chains Hydrogen bonding – forms between H and carbonyl group in backbone, and the H and partial atoms with (-) charge in side chains Hydrophobic Interactions In aqueous solution water molecules interact with hydrophilic side chains force hydrophobic side chains to coalesce When these hydrophobic sides of proteins come together, the water molecules form more hydrogen bonds around it, increasing the stability van der Waals Interaction electrical attractions that stabilize hydrophobic side chains These are caused because the constant motion of electrons gives the molecules a tiny charge, which fosters a reaction Very small individually but strong in large numbers 09/12/2011 Covalent bonding Form between sulfur atoms – referred to as bridges Ionic Bonding Form between ionized amino groups and carbonyl groups Quaternary Structure Many proteins contain several distinct proteins, and this structure is the combination of the different polypeptide subunit Proteins with 2 polypeptides subunits = dimer Proteins that consist of single polypeptide lack quaternary structure Most cells have one multienzyme complex, a group of enzymes that are physically joined to each other, each catalyzes a reaction Protein structure is based on a hierarchy Folding and Function Folding can be spontaneous if the hydrophobic interactions, bonds, and van der Waals make the folded molecules more stable Folding in Ribonuclease Anfinson found tat ribonuclease can be denatured by compounds that break H bonds and was unable to function properly Once those compounds were removed, it spontaneously folded and worked properly Folding of proteins is sometimes facilitated by chaperones – these are produced in large quantities after cells denature in high temperature These heat-shock proteins speed the refolding process Folding in Prions Improperly folded proteins can act as disease causing agents called prions Can induce other proteins to get fucked up All prion illnesses are fatal 09/12/2011 Enzymes Part of the reason enzymes are effective catalysts is that they bring the substrate together in certain ways to facilitate electron interactions Energy required for a reaction Amount of free energy required to reach transition state, before shit starts to break up and form new bonds, is called activation energy Reactions happen when reactants have enough KE to reach the transition state The less stable the transition state is, the higher the activation energy will be               Enzymes act as a catalyst, lowering the amount of activation energy needed Also stabilize transition states, making it much more likely for the reaction to occur How Enzymes Work Summarized by the Lock-and-Key model Substrates bind and react in the enzymesActive Site Enzymes are usually big and globular, and the active site is like a cave where the substrates mix Enzymes aren’t rigid either, they are flexible and when the substrates bind the enzymes form to a induced fit to facilitate the reaction – locks them in When the first substrate binds, its held by H bonding, but the second one is held by one or more R groups These R group interactions stabilize the transition state, lowering the activation energy Catalysis Initiation Enzymes orient the substrates instead of having them collide randomly Transition State Facilitation The bound substrate interaction is facilitated in the active site and the reaction goes on 09/12/2011 The substrates have more of an affinity for theActive Spot than do the products Termination Binding ends, products are let out, and the enzyme returns to normal Enzymes make acid base reactions more favorable Enzymes work side by side with cofactors and coenzymes which play an essential role in stabilizing the transition state Cofactors can be metal ions or small organic compounds (coenzymes) Most enzymes are regulated by other molecules Catalysis can be regulated by competitive inhibition – another molecule binds in the active site and competes with the substrate Helps slow down reaction rates Allosteric Regulation – when a molecule binds in another part of the enzyme, changing the shape of the active site and not letting the substrate bind Called allosteric regulation and deregulation Limiting Rates of Catalysis Speed of reaction is a logarithmic curve With not a lot of substrate and more products, it’s a fast reaction At intermediate substrate level, starts to slow down At high substrate levels, reaction rate plateaus at a certain speed At a certain point, active sites hit their max, no matter how much substrate Physical Conditions for Enzymes Enzyme activity is sensitive to conditions that alter its structure Temperature affects KE of substrates and movement of enzymes pH affects makeup of amino acid side chains and reactibility Yes, first living entity was a protein catalyst!!! 09/12/2011 Structure and Function of Extracellular Layer Helps define the cell’s shape and either attaches it to another cell ro acts as the first line of defense Consist of cross-linked networks of long filaments embedded in stiff surrounding material Rods and filaments are good at withstanding stretching and straining forces Stiff surrounding substance withstands pressing forces of compression Cell Wall in Plants Surrounds all plant cells Structures are dynamic – if they’re being attacked, they send out signals Primary Cell Walls Fibrous component consists of long strands of cellulose cross-linked by other polysaccharide filaments and bundles into microfibrils Space between is filled with pectins – pectins are hydrophilic so they keep the cell wall moist Defines the shape of the plant cell Turgor Pressure When water comes into the cell and inflates the plasma membrane Secondary Cell Wall This is inside the primary wall In cells that form wood, the secondary wall includes lignin Helps plants withstand gravity and wind Extracellular Matrix inAnimals Important for structural support The fibrous component is collagen – 3 peptide chains Amatrix of polysaccharides surrounds the collagen Both are very pliable Most ECM components are made in the Rough ER Actin filaments in the ECM are connected to integral membrane proteins called Integrins – integrins bind to fibronectins which bind to collagen This linkage strengthens the cytoskeleton and keeps the cell in place Metastasis If the cytoskeleton-ECM bond breaks, cancer can develop Then they can spread throughout the body 09/12/2011 Structure and Function of ATP ATP makes things happen because of its great deal of potential energy In ATP, four negative charges are forced together – repulsion adds to high PE Hydrolysis in water – outermost phosphate group detaches = exergonic Why it releases energy Entropy of products is higher than that of reactants Large drop in PE when ADP and P1 are formed fromATP Now electrons from phosphate groups are split between two molecules instead of one cluster Negative charges are stabilized by polar water molecules Phosphorylation – addition of a phosphate group to a subst
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