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Biology 1002B Notes

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Department
Biology
Course
Biology 1002B
Professor
Tom Haffie
Semester
Winter

Description
Biology Lecture 1 - Chlamydomonas Roles of light as used by life • Light is used as a source of energy and as a source of information about the environment Characteristics of Chlamydomonas that make it a useful model system • Genome sequence is useful to study because it has attributes of both animal and plant cells. • Some human diseases are caused by mutations that make the cilia in humans develop poorly -- Chlamy is helpful for looking at flagella and cilia structure and function because it is a eukaryote and the flagella is identical in chlamy as it is in humans. • Good for looking at light energy and information because it has an eyespot that detects light and then orients chlamy in relation to the light (can either swim towards light or away from it) • Has a good genetic system that has mutants in different pathways, mutants enable you to elucidate the pathway. • We want to elucidate the pathway between the eyespot and the photoaxis- (cells movement in relation to where the light comes from), to find out which genes are involved in light reception, and controlling the flagella so that the cell moves. • It is homologous with the human eye (this is just a hypothesis) Function of basic components of Chlamydomonas cells • Nucleus - gene expression/transcription • Basal Body - organelle found at the base of any flagellum • Where the microtubules develop to produce the flagella • Ribosome - site of protein synthesis • Mitochondria - ATP factories of the cell (has more than one mitochondria) • Chloroplast - energy transducing factory of the cell (just 1 cholorplast) • Within cholorplast is pyrenoid - where carbon fixation takes place Occurs in Calvin Cycle Carbon fixation - process by which photosynthetic organisms such as plants turn inorganic carbon (i.e - CO2) into organic compounds (i.e - carbs) •Also within the chloroplast is the eyespot - enables single chlamy cell to orient itself in relation to light Relative usefulness of various biological characteristics as measures of complexity • Cell size - Human cells > Chlamy > E.cole , the bigger the cell, the more space it needs to carry out complex processes and compartmentalize. • Genome size - can be useful sometimes although some similar organisms have very different genome sizes (some inconsistencies) • Protein coding genes (PCG) - How many proteins does your genome code for •Both genome size and PCG can be misleading (due to junk DNA , etc) Advantages to Chlamydomonas in being phototactic • Eyespot is used for photoaxis - movement towards or away from light • Chlamy can thus move toward light because they want to harvest photons for photosynthesis Reasons why Chlamydomonas might move away from a light source • If too much light is absorbed, too much product is formed and as a result too much oxygen is formed and this can lead to reactive oxygen species which can destroy the cell if there’s too many of them. Basic structure of rods and cone as photoreceptor cells • Photoreceptor cells (rods and cones) have photoreceptors which are the ‘blue’ dots found on the disk which harvest the light(their is a stack of disks making up rods and cones) and each disk has many photoreceptors and these individual photoreceptors trap the light. Major components involved in phototransduction and their role • Pigment found within the discs ‘change’ when light is harvested, this change activates a pathway called phototransduction - when this pathway is active, it activates another protein - transducin. • SO the membrane complex grabs the photon of light which causes a change(in the discs) that then activates transducin which in turn activates the enzyme phosphodiesterase The sodium pump located on the membrane is regulated by cyclic GMP, • So when cyclic GMP is bound, sodium is transported into the cell and there is a sodium influx (excess) • The phosphate group in cyclic GMP is bound to the ribose of GMP at the 5’ and 3’ position. SO when phosphodiesterase cleaves the 3’ bond, a 5‘GMP is generated. •This results in the cyclic GMP detaching from the transporter and as a result the transporter SHUTS OFF and sodium cannot enter the cell. • Light through the processes mentioned above, shuts down the sodium pump which hyper polarizes the membrane which leads to an electrical signal being sent down the membrane surrounding the rod or cone • The signal moves along the optic nerve and reaches your brain at an incredibly fast speed (as a result you see) Lecture 2 - Light Relationship between excited states of a pigment and its absorption fluorescence emission spectrum • The energy of the fluorescence emission spectrum is always less in energy and longer than the excited state due to the heat loss that occurs from the lower energy level to the sub-lover energy level. Region of the electromagnetic spectrum known as “visible light” • Ranges from 400nm wavelength (most energy) to 700nm (least energy) • Only area of the spectrum visible to the human eye Relationship between wavelength and energy content of a photon • They are inversely proportional - as wavelength increases, energy decreases. As energy increases, wavelength decreases. • Most energy - Gamma rays (shortest) / Least energy - Radio waves (longest) Molecular characteristic of visible pigments that make them absorb light. • Pigments have a conjugated system: •alternates b/w double bonds and single bonds •has many non bonding pi-orbital electrons • these electrons are not required for bonding so they’re readily accessible to trap energy (interact with photons of light) • MOST pigments absorb light and have no role in bonding • exceptions apply - retinal (involves bonding electrons) Relationship between pigments and associated protein Pigments (such as chlorophyl or retinal) are bound to proteins • • If you isolate the protein and are careful enough you can keep the pigment attached - causing the isolated protein to have color • When a pigment is bound non covalently to the protein, it is called a pigment protein complex • If detachment of the pigment occurs - there will be free pigment floating around (at the top of the test-tube) • If the protein does not have a pigment attached, you must stain in with color to see the bands of the protein (in an electrophoresis) Four “fates: of the excited state of chlorophyll resulting from absorption of photons Absorbed photon by an electron will either reach higher excited state or lower • excited state depending on the energy of the photon • Regardless, the HES decays to the LES after 10^-12 seconds due to heat loss • Once in LES one of 4 fates occurs: 1. Energy is lost as heat resulting in the electron going back to ground state 2. Little energy is lost as heat and energy goes to sub excited state - remainder of energy is lost as fluorescence which has less energy and longer wave length than original absorbed light (darker color) 3. Using the light to do work - and the work is photochemistry -- light is used to change a molecule / change the structure of a pigment 4. Transferring the energy of the excited state pigment to a neighboring pigment. Reasons why relative fluorescence is different in isolated cholorophyll vs intact cells when exposed to light • There is less fluorescence in an intact cell when exposed to light because the energy absorbed from exciting the electrons is used to power photosynthesis - thus leaving little to no energy for fluorescence to be released. • In an isolated chlorophyl the excited electrons have nothing to contribute there energy towards and thus release it as fluorescence. • Thus there is more fluorescence released in an isolated chlorophyl What accounts for the fact that chlorophyll is green in color • It is green in color because it does not have a green excited state • Green photon has more energy than red and less than blue and there is no excited state in chlorophyl at that point so the photon is either reflected or transmitted through the pigment Quantitative relationship between photons and excited electrons • Only 1 photon can excite 1 electron - photon cannot excite more than one electron and many photons cannot excite one electron. MUST BE 1:1 Relationship between photon and energy required to excite electrons in order for photons to be absorbed. • For the energy to be absorbed, the energy that’s in the photon must match the amount of energy required to get from the ground state to one of the excited states. General structure of photosystem • When chlorophyll in antenna absorbs photon of light - electron gets excited to a higher energy state - the excited state then Chlorophyll transfers to a neighboring Molecule chlorophyll molecule • The excited state then moves through the antenna (no photochemistry occurs yet) until the photon reaches the reaction centre where the cholorophyll molecule is excited and then oxidized • The electron released from the Antenna reaction is then used to drive electron transport in the thylakoid membranes of chloroplast (and Reaction Centre bacteria) Similarities and differences of the light capturing and photochemistry of phototransduction (retinal) vs. photosynthesis (chlorophyll) Similarities Differences How are excited states of antennae pigments organized to provide for energy transfer to reaction center • The pigments are very close to one another (6 angstroms - atomic distances) and they are organized as so : • Excited states get progressively lower to account for heat loss between each shift. Structure of rhodopsin • Rhodopsin = retinal + opsin • Opsin surrounds the retinal Effect of photon absorption by 11-cis retinal on retinal structure followed by association with opsin protein followed by interaction of transducing with opsin • Retinal found in its 11-cis configuration (cis means hydrogens are on the same side of double bond) and can be found in all-trans configuration (hydrogens on opposite sides) • Structurally different molecules but have the same molecular weight •To go from cis to trans - the double bond must be broken When retinal absorbs a photon of light you go from 11-cis to all-trans • retinal because the photon of light excited one the pi electrons in the double bond - the energy breaks the bond , the molecule swivels and then the double bond is reformed and it is in its all-trans configuration (photochemical event occurring in our eyes) • Once in trans configuration the retinal becomes linear molecule and no longer fits the bonding site within the opsin - and so it detaches from the opsin. • This now causes the shape of the protein to change (changes the shape of opsin) - creating a little cleft so that transducin can interact • Once transducin interacts it activates phosphodiesterase and through a series of processes an electrical signal is sent along the optic nerve to the brain. •Opsin can no longer absorb light so it must be recycled so that a new cis- retinal can be incorporated inside the opsin. Reasons why life has evolved to detect the narrow band of energy represented by “visible light” • It is the most abundant and dominant light at the top of the atmosphere and on the surface of the earth and is energetically perfect to interact with biological molecules • Ozone sucks in a lot of the ultraviolet light at the surface of the atmosphere and and at the surface of the earth (so theres very little UV on/around earth) • Gamma Rays have too much energy so they would obliterate/ionize pigments and molecules. They would also disassociate all the bonds in molecules. • Radio waves/ micro waves have too little energy and would simple warm up the molecule (cause slight vibration) rather than exciting the electrons Side note • In order to absorb a photon of light, white light must be shined on a molecule (chlorophyl for example) and one of the non bonding pi-electrons absorbs the photon. Lecture 3 - Protein Structure and Function (ISO) Basic structure of an amino acid and what are the different classes of amino acids. • Generalized structure of an amino acid has a central carbon atom attached to an amino group ( --NH2) , a carboxyl group (--COOH) , and a hydrogen atom •The remaining bond of the central carbon is 1 of 20 different side groups represented by the R. R group is called the side chain. • Differences in side group give the amino acids their individual properties Different classes of amino acids : non-polar , uncharged polar, negatively charged(acidic) polar, and positively charged (basic) polar amino acids. Chemistry of the peptide bond and how it is formed • Peptide bond - link b/w each pair of amino acids in a polypeptide. •It is formed by a dehydration synthesis reaction between the - NH2 group of one amino acid and the --COOH group of a second. The four levels of protein structure 1. Primary structure: the proteins complete amino acid sequence (determined by nucleotide sequence in coding region of the proteins corresponding gene) Hydrogen bonds forms between N--H group of the 2. Secondary structure: regions of alpha helixes (formed by hydrogen bonds), backbone and the =O group of the amino acid beta sheet , or random coils, in a polypeptide chain. The sheet is formed by hydrogen bonds between atoms of each strand. ( O - - - H--N) 3. Tertiary Structure: overall three-dimensional folding of a polypeptide chain due to ionic bonds, hydrogen bonds, hydrophobic interactions and disulfide bridges. 4. Quaternary structure: the arrangement of polypeptide chains in a protein that contains more than one chain. (Two or more polypeptides coming together to form a functional protein) Bonds in: Primary - peptide bonds Secondary - Hydrogen Bonds Tertiary - ionic, hydrogen, hydrophobic interaction and disulfide bridges Quaternary - N/A How are alpha helices and beta sheets formed Alpha is formed when hydrogen bonds form between every N--H group of the • back-bone and the C=O group of the amino acid • Beta sheet is formed by side-by-side alignment of Beta strands. Sheet is formed by hydrogen bonds between atoms of each strand. Lecture 3: Protein Structure & Function Reasons why photosystems have antenna proteins while they eye doesn’t INFORMATION VS ENERGY •A photosystem wants to harvest as much light as possible so that it can use it as energy • Photosynthetic systems don’t care about information, just light harvesting •A photoreceptors arrangement of rods and cones is attempting to harvest light as information - because where there photons come from conveys information. Points of control for regulation of protein abundance 1. Controlling transcription - the conversion of DNA into mRNA. Transcription makes the proteins mRNA and is thus vital 2. Translation is also a regulated process and so if it is halted or controlled conversion of mRNA to protein • There’s a level of control at the level of transcription and translation that can be altered to impact protein abundance. Factors affecting mRNA transcript abundance. Amount of (specific) mRNA you have for a certain protein is affected by: Transcription Rate: If transcription rate is high you should make lots of transcript, however this is not always true due to: •mRNA decay - when mRNA is made - they float around for a varying time (20 minutes to hours) before they start to break down . •Transcript abundance - the balance between mRNA decay and Transcription rate (both controlled processes that compete) • mRNA decay is a very important control point Steps in making a Northern Blot for measuring mRNA transcript abundance. 1. Isolate the total RNA (from tissue samples for example) 2. Quantify how much total RNA you have and load the same amount of micrograms of RNA into every lane and then run on gel electrophoresis 3. Transfer the RNA to a (nylon) membrane (gel breaks too easy) 4. Incubate the membrane with a solution of probe that washes over the membrane. The probe is a single stranded molecule of DNA that is complementary in sequence to the sequence you are interested in detecting that is stuck on the (nylon) membrane. 5. Once incubated, the probe will hybridize with the complimentary sequence on the membrane 6. Each DNA probe has a radioactive group attached to it so you can detect its location and abundance on the membrane by exposing the membrane to a piece of x-ray photographic film. Relative abundance of various types of RNA in typical cells. •97% of total RNA is ribosome RNA •3% of total RNA is mRNA -- of that 3% there is an EXTREMELY small percentage of mRNA that expresses a certain protein (e.g - hexokinase - there would be 100-1000 copies of the specific mRNA that codes for hexokinase) Steps in making a Western Blot for measuring protein abundance 1. Stain gel if they aren’t pigmented protein complexes. 2. Insert equal amount of protein (maybe its from a tissue sample) into 5 lanes of gel electrophoresis (and one marker lane) & run gel. 3. Afterwards gel is transferred to a membrane 4. An anti-body raised in a rabbit/chicken..etc that is specific to a protein (hexokinase) and that antibody then sticks to the corresponding An anti body to hexokinase is made. (It protein(hexokinase) 5. Easy to detect the hexokinase in the lab and thus you know where that tracks it down) specific protein is. Usually done by attaching a reporter enzyme to the antibody so that when the Characteristics of constitutive vs. induced vs. repressed gene expression antibody encounters the kinetics. protein, the enzyme releases color. •Constitutive expression -> when the abundance of protein or transcript doesn’t respond to heat. • Eg. Actin shows constitutive protein abundance • Because it’s a house keeping protein, it does not respond to change in temperature (many genes show constitutive expression) Induced expression -> transcript or protein abundance increases as heat increases Repressed expression -> transcript or protein abundance decreases with exposure to heat shock over time. (As Temp increases, abundance decreases) Varieties of defects that might account for lower levels of functional photoreceptors •There could be a defect in transcription and/or translation - there are alot of enzymes required to make opsin and thus trans.c and trans.l are important. •mRNA decay could be ‘going nuts’ and thus barely any transcript is accumulated •Recycling of opsin needs a transcription factor so there could be a mutation in the transcription factor. •mutation to the opsin gene as a result of poor folding (which is due to mutations) Maybe too much light is absorbed due to a mutation and light is damaging the • photoreceptor •Defect in retinal(NOT a protein)-- without retinal you cannot produce rhodopsin • retinal not coded for by a gene - it is the product of a biosynthetic pathway - E.G: no gene that makes beta-carotene BUT genes code for the enzymes which regulate the biosynthetic pathway and change the chemical structure of beta-carotene. •Defect in retinal biosynthesis (due to malfunctioning enzymes) Relationship among polypeptide, apoprotein, cofactor and functional protein Retinal is a cofactor not a protein - it is required for rhodopsin to work and thus A cofactor is a non- • it binds to opsin protein chemical •Opsin is the apoprotein (protein before it accepts the cofactor) - together they compound that is bound come together to produce a functional rhodopsin (or a functional protein) to a protein and is required for the protein's biological activity. • If any one of the two is malfunctioning or defected then rhodopsin as a whole is defected. • Apoproteins (opsin) synthesized on the ribosome are not functional until they PTM doesn’t happen all the time - HOWEVER, all protein accept their corresponding co-factor (retinal), when they do accept it, it is pigment protein complexes would known as post translational modification have to go through this BUT not all proteins Post-translational Relationship between protein folding and function. • A protein must fold into its correct 3-D(a.k.a conformation) shape to function modification (PTM) is the chemical modification of a properly protein after its translation. • Polypeptide is string of a.a’s and once that ‘string’ folds, you have a protein. • Enzymes 3-D shape must be very exact to be functional. MUST FOLD THE SAME WAY EVERY TIME • To get the exact fold the polypeptide must go from primary to tertiary (a.k.a - native confirmation of protein) Factors affecting proper protein folding (Anfensen’s dogma) • Got a simple enzyme to catalyze a simple reaction (measured the product by observing color change) •A low amount of enzyme produced a lot of color which means the enzyme is catalyzing the reaction the way he expected it to. •Once he added urea - it disrupted the bonding arrangements that contribute to the tertiary structure of the protein •As a result the protein falls apart and so if you add urea and do the same experiment (reaction) you get NO color. (enzymes messed up) He then got rid of urea thought a series of processes (centrifuge/pour it off/rinse • it, etc) and then put the enzyme back into a buffer that doesn't have urea and that reconstituted the enzyme (it works again)(refolded in the perfect orientation - it fold back correctly 90% of the time.) • He showed that folding is VERY FAST and is spontaneous - you don’t need any Even before translation energy for folding to occur. is finished, the amino end of the polypeptide •Also showed that the ONLY thing that dictates folding is the primary starts to fold. sequence of the polypeptide (the order of the amino acids) Lecture 4 : Energy & Enzymes (ISO) Isolated system - does not exchange matter or energy with its surroundings Closed system - exchanges only energy with its surroundings Open system - exchanges both energy and matter with its surroundings. First law of thermodynamics - energy can be transformed from one form into another or transferred from one place to another, but it cannot be created or destroyed. Second law of thermodynamics: the total disorder of a system and its surroundings always increases. What is meant by the phrase “it takes energy to maintain low entropy” • In the course of the thousands of chemical reactions that take place to generate order, living things give off heat and by-products of metabolism such as carbon dioxide that are much less ordered and increase the disorder or entropy of the surroundings. •Thus without energy, we cannot undergo processes/reactions that produce order in our cells and as a result we’d die. ▯ Heat ENERGY Lecture 4 : Energy & Enzymes Definitions Potential Energy - A form of energy that has potential for a reaction, though at present is in a stored form. Chemical Energy - Energy released in a chemical reaction (often in the form of heat) Kinetic Energy - Energy released due to motion. Entropy (S) - The amount of disorder in a system Spontaneous Reaction - A reaction that occurs spontaneously without the input of energy. Enthalpy (H) - Measure of the total energy of the system Delta H - The change in Internal energy of a system Exothermic - energy is released A-->B (A has more energy than B) Endothermic - energy is absorbed , B has more energy than A Gibbs Free Energy - Indicates whether a process will occur spontaneously Exergonic - reaction occurs spontaneously Endergonic - reaction does not occur spontaneously Delta G - change in Gibbs free energy Catalyst - A substance that increases the rate of a chemical reaction Rate of reaction - the speed at which a reaction occurs Energy of Activation - minimum amount of energy required to initiate a reaction (energy needed to reach transition state) Transition state - bonds are strained and ready to break. Point at which reactant molecules will form products. Kinetic Stability - without external energy applied, reaction occurs EXTREMELY SLOWLY or not at all Active Site - part of the enzyme where substrates bind Catalytic Cycle - Process of a substrate binding to an enzyme and forming an enzyme substrate complex, then catalysis occurs - substrate is converted to product after the reaction and produce is released and you are left with an enzyme. Why life does not go against the second law of thermodynamics • Cells maintain low levels of entropy due to the huge input of energy they receive but as a result, CO2/other molecules are given off which in turn increase the disorder of the surroundings. Heat produced and motion of molecules Why life needs to consume energy also increases entropy of surroundings. • Life needs to consume energy so that it can stay ordered. If living things stopped brining in energy and as a result became disordered - they would die. Components of Gibbs Free Energy equation • Delta G - Change in free energy • Delta H - Change in enthalpy • Delta S - change in entropy (multiplied by temperature) Whether or not a given reaction will be spontaneous given Delta G • If DG is + , the reaction is endergonic and will NOT proceed spontaneously If entropy is + , more • If DG is - , reaction is exergonic and will proceed spontaneously disorder If entropy is -, less disorder Role of enzymes in endergonic vs exergonic reactions • Spontaneity indicates nothing about the rate of a reaction! If enthalpy is positive - endothermic • Some reactions can take millions of years to occur spontaneously but with If enthalpy is negative - enzymes a spontaneous reaction that can take 78 million years occurs in 20ms exothermic • Thus, enzymes speed up exergonic reactions and have NO effect on endergonic reactions -- enzyme cannot change the sign in free energy or the value of Delta G Relationship between activation energy and rate of reaction • The amount of energy needed to get to the transition state determines how fast spontaneous reactions happen. Amount of energy needed to get to transition state is energy of activation (or Activation energy) • The lower the activation energy the higher the rate of reaction (the faster) How enzymes increase rate of chemical systems • Enzymes lower the energy required to get to the transition state. Once the activation energy is lowered, more molecules can acquire the energy to get to the transition state. • Starting and ending free energy does not change - only the path the reaction takes changes ( SAME DELTA G) • Enzymes increase the rate of a reaction by increasing the number of substrate molecules that attain the transition state conformation, done by: • Precise orientation of two substrates - two molecules will rarely come together in the correct orientation to get to the transition state. • Binding to the active site actually forces the molecules into the orientation they need thereby mimicking the transition state. This speeds up the reaction drastically • Charge interactions - sometimes the substrate needs a certain charge across them but if you add an enzyme - the amino acids that make the active site of the enzyme provide a charge - it is MUCH easier for the energy of activation to be lowered Conformational strain - substrate may need to be strained, which happens • more frequently in the presence of an enzyme which uses its active site to distort the substrate molecule into a conformation that mimics the active site. Why biological systems need enzymes Reactions need to proceed relatively quickly. This is usually done (by chemists • for e.g) by raising the temperature. However, biological molecules cannot handle high temperature or high pressure so enzymes increase the rate of a reaction without increasing the temperature Importance of tertiary structure to enzyme function • Enzyme must have correct 3-D structure and the structure must have some Molecule upon which an flex. This is because when a substrate molecules get close to the enzyme it causes the shape of the enzyme to change - induced fit enzyme acts Correct tertiary structure also ensures that the active site is functioning and in • the correct place. (POSITION OF ACTIVE SITE CANNOT BE DETERMINED BY THE PRIMARY SEQUENCE) Link between enzyme function and growth rate • Growth rate is a function of enzyme activity • Enzymes need to come in contact with substrates in order for catalysis to occur. • The rate of molecular motion increases with temperature so then catalysis occurs at a faster rate Thus, enzymes are more active the higher the temp so they can process more substrate and the cell can grow faster (divide more) (optimum), the catalytic cycle is operating the fastest. • HOWEVER, if the temperature gets too high (beyond 40 degrees for bacteria) - the enzymes will denature How tertiary structure bonding arrangements are different depending upon the temperature habitat of the organism. • Hyperthermophiles live at high temps, and so they have stronger/more intramolecular forces between the bond of the protein and as a result have a higher disassociation temperature Takes longer for these enzymes to denature • • Psychrophiles live at low temps and have weaker ‘bonds and such’ and so they dissociate at much lower temperatures • There are bond energies associated with the bonds in the tertiary bonding arrangements of enzymes/proteins and if that bond energy is exceeded, the bond will break • Heat can denature proteins, PH can affect ionic interactions and urea detergents interfere with the ability of the groups to form bonds. Lecture 5 - Membrane Structure & Transport Role of fatty acids in membrane structure •They are hydrophobic and therefore position themselves away from aqueous environments in cell - as a result can form lipid membrane spontaneously Relationship of fatty acid saturation levels on membrane fluidity •If the fatty acids are fully saturated (no double bonds) , they align very close and pack close together and as a result membrane is less fluid •If fatty acid tails is unsaturated,the tail then has a kink in it and this gives a more fluid membrane • The more unsaturation - the more fluid the membrane will be at any given temperature Relationship of temperature on membrane fluidity •At a low temperature desaturase transcript abundance increases because at low temperatures the membrane is not fluid Graph for bacteria enough (too cold and rigid - gel like) and thus grown at different desaturase introduces double bonds in the temperatures fatty acid tails (causing kinks) which increases the fluidity of the membrane. •If temperature is raised, membrane is fluid enough as is and so transcript abundance of desaturase decreases, if at extremely high temperature, there should be no unsaturated fatty acids at al !! Relationship of fluidity to membrane functions such as transport •Fluidity of membrane must maintain itself within a certain range - if it gets too hard, things can’t move between the membrane. If it’s too lose, ions will leak from one side to the other. Properties of saturated vs. unsaturated fats • Saturated : every Carbon has 4 Hydrogen bonds (no double bonds) •Very linear Unsaturated : Have double bonds causing a kink in the tail. There can be many • sites of unsaturation (many double bonds) Role of desaturases in fatty acid biosynthesis • Fatty acids are synthesized through a biosynthetic pathway in a totally saturated form (linear) and then to make it unsaturated the enzyme desaturase introduces double bonds Relationship of bacterial desaturase expression vs. temperature • Bacteria could have 3 desaturase genes that code for different desaturase enzymes. The reason they have different desaturase enzymes is because they differ in where they incorporate/introduce the double bond. • At high temperature - low desaturase transcript abundance. At low temperature - increase in temperature abundance. Cells that don’t maintain a constant body temperature can modulate fatty acid Role of size and charge in movement of molecules across biological membranes abundance and fatty acid unsaturation. • Small and uncharged molecules get right through the semi permeable membrane • However a bigger size and a charge are two things that impede movement across a membrane • To get certain molecules across (glucose for e.g) , proteins are needed. Characteristics of transmembrane proteins that enable them to interact with hydrophobic core of membrane 1) They could have many alpha helices - the hydrogen bonding that gives rise to the alpha helical structure minimizes the charges of the protein backbone. Thus the alpha helical structure can interact with the hydrophobic tails. 2) Membrane proteins - they have a tail-tail signature. •Part of the protein that interacts with the membrane tends to be made up of non- polar (NOT CHARGED) amino acids. •Usually 17-20 a.a traverse the lipid bilayer •A transmembrane protein can be detected based on the primary sequence of a protein (when you see 17-20 non polar amino acids in a row - you know it traverses the bilayer) 3 stretches of it partially spaced out means it crosses 3 times. Factors influencing simple and facilitated diffusion • Simple diffusion is influenced by concentration gradient. Oxygen/CO2 diffuse DOWN a concentration gradient [high] --> [low] Free Energy Change drives diffusion - the more F.E the more ability there is to • do work. •More molecules on one side than other --> High free energy Diffusion then •Equal amounts of molecule on both sides --> lower free energy decreases the free energy by balancing it out. Facilitate diffusion operates under the same principles, but it cannot get through the membrane on its own and thus needs a channel to facilitate the diffusion. Example : Sodium Ion • Many pores (pores are inside channel) are very specific to certain molecules and may only let one molecule through at a time. (one will go through its specific channel one by one) Transport against a concentration gradient (active transport) • Molecule is moved from a region of low concentration to a region of higher - because this is against free energy change , it requires energy Role of electrochemical gradient in determining equilibrium concentration of ions • In left chamber the membrane is only permeable to potassium. Potassium wants to move from high concentration (150mM) to low concentration (5mM) - chemical aspect • However, potassiums movement is retarded by the electrical gradient -- Strong negative charge due to Cl- attracts the K+ molecules and prevents them from going to the right side - electricity aspect • This causes a charge difference of -92mV **** Charge is always mentioned inside in relation to the outside - orange on left side is more negatively charged than blue. ▯ On right side orange is more positively charged (+62mV) Basis for electrical gradient across photoreceptor cell IN DARK • Charge exists due to all the anions in the cell (proteins, amino acids, etc) There is also lots of sodium outside the cell and lots of potassium inside the cell and they both leak down an electrochemical gradient • K leaks OUT and Na leaks IN -- NaK pump then moved them back to there original place (pumps 3 Na out and 2 K in) • Cyclic GMP gated channels on the plasma membrane are active when cGMP is bound to and this causes a huge influx of sodium which keeps the difference across the membrane smaller than it would otherwise be. IN LIGHT • In light, cyclic gmp gated channels are shut off once they are metabolized by phosphodiesterase. As a result, positively charged sodium cannot get into the cell to minimize the negative charge (as it usually would in the dark) Potential difference across membrane becomes even greater as positive • potassium leaves the cell. This causes hyper-polarization of the cell and causes a trigger that blocks the release of glutamate and triggers the electrical impulse. ▯ Usually (in the dark) sodium is coming in (+) and potassium is leaking out (+) so the negative state of -30mV of the photoreceptor cell is maintained. However in the light hyper-polarization occurs. DARK ^^^ LIGHT ^^^ Basic structure of ABC transporter • Used in active transport and human genome codes for 100’s of different ABC transporters ABC Transporters are one group of molecules • Composed of two parts : 1)Transmembrane domain - part that transports the molecule - different depending on which molecule its designed to transport of active transporters 2) ATP binding cassette - binds ATP to it and uses energy of ATP breakdown (hydrolysis) to fuel the transport Genetics underlying cystic fibrosis Is a homozygous recessive disease (if both parents are heterozygous for it - • child has a 1/4 chance of getting two mutant copies of CFTR • 1 wild type and 1 mutant CFTR does not lead to CF • Cystic fibrosis is a defect in CFTR (an ABC transporter) • CFTR is 6000 bases long and is composed of 1480 a.a’s Most common mutation to CFTR is the ΔF508 (70% of cases) • • ΔF508 mutation is when CFTR lacks a phenylaneline at the position 508 Cystic Fibrosis Phenotype • CF leads to problems with lungs and gastrointestinal tract CFTR is located on the membrane of epithelial cells that are lined with cilia with • mucus. • Cilia and mucus must be kept wet to get good clearance (be able to cough out any bacteria or dirt that gets in the lungs) • Cilia and mucus stay wet due to CFTR - it pumps chloride out into the epithelial space and in response there is an osmotic movement of water - water will move from the epithelial cell to the epithelial lining and keep the mucus wet. • With CF, CFTR cannot pump chloride out and as a result lung tissue sticks together, gas exchange is inhibited, etc. Relationship of CFTR synthesis and folding in the intra-cellular secretory system • For CFTR to get to the plasma membrane it must be moved through the secretory pathway • Wild-type CFTR moves perfectly well through the secretory pathway What happens to the ΔF508 form of CFTR • Mutant form gets to the E.R where it is detected by the quality control system - it is detected by the quality control system in the E.R because due to the ΔF508 mutation the protein doesn’t fold perfectly and the native conformation of the protein is not perfect • Thus, chaperone proteins in the E.R detect the faulty folding of the protein and tag it • The tagged CFTR is then sent to the proteosome - a giant complex of proteases (enzymes that break down proteins) - broken/malfunction proteins go there to be degraded • **ΔF508 mutant is PERFECTLY FUNCTIONAL (functions 50% as well as the wild type, but it would still be good enough to not cause CF. The only problem is the defective protein never gets a chance to get to the plasma membrane because it is tagged in the E.R and consequently; degraded. Lecture 6 - Energy Transformation I - ISO Catabolic Pathway - A metabolic pathway where energy is released by the breakdown of complex molecules to simple compounds • An example is cellular respiration whereby energy is extracted from the breakdown of food such as glucose (Glucose --> ATP,H20,CO2) • Overall Delta G is negative ,, but both types of pathways can be made of a mixture of both endergonic and exergonic reactions Anabolic Pathways - consume energy to build complicated molecules from simpler ones; often called biosynthetic pathways • An example is photosynthesis (CO2 --> glucose) as well as the synthesis of macromolecules such as proteins and nucleic acids • Overall Delta G is positive How is the structure of ATP linked to the fact that its hydrolysis is strongly exergonic The components of a water molecule are added as molecules • Both products of the hydrolysis reaction (ADP and Pᵢ) carry a negative charge, are split into smaller subunits and the repulsion between these ionic products favors hydrolysis Pᵢ - Orthophosphate ion or inorganic • Release of the terminal phosphate allows greater opportunity for hydration , and phosphate this an energetically favored state • The orthophosphate group (Pᵢ) can exist in a wide variety of resonance forms, not all of which are available when it is bonded. Thus release of the orthophosphate increases the disorder of the system Lecture 6 - Energy Transformation 1 Structure of Chloroplast •Outer membrane covers entire surface of the chlorplast •Inner membrane lies just inside the outer membrane. •Between the inner and outer membrane is the is the inter-membrane compartment •Stroma is the aqueous component filled with enzymes (wher
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