BIOCHEMISTRY NOTES.docx

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Department
Biochem & Molecular Biology
Course
BIOC 2300
Professor
Dr.Carmichael Wallace
Semester
Winter

Description
BIOCHEMISTRY NOTES th January 13 State functions – defined by the difference between the start and the end of the process, not by what’s in the middle. Ex: enthalpy, entropy, free energy First Law – energy is always there. You can’t make it or destroy it, can only change it. Total energy doesn’t change. Second law – intrinsic tendency towards creating disorder drives many reactions - release of energy is spontaneous and increases disorder Universe – think about small closed system. Not usually the “entire universe” System and surroundings can make a unit instead of a universe. Interchangeable terms. Delta G is the measure of spontaneity of a process. Negative means it’s a reaction that releases energy into the system, therefore is spontaneous. If positive, it needs energy input. The reaction is therefore not spontaneous and will not happen on its own. Reaction needs tweaking to make the reaction go. When delta G = 0 it means the reaction is in equilibrium! Means that there is an equal rate of change of the reaction in each direction. Rearrange the equation for delta G so that delta G equals 0. Negative delta H, positive delta S – reaction will always happen no matter what you do to it Hydrophopic effect – water and oil. Nonpolar substances. Standard free energies of reaction – all reactions that occur in living things have standard free energies. The change in free energy is defined by delta G knot. Defined for reactions under standard conditions (25 degree Celsius, 1 atm, 1.0 M). Exception for protons = delta G knot prime because the pH is close to 7. Therefore the concentration is not 1.0 M. Reactants on left, products on right when talking about delta G. Reaction goes left to right. Don’t confuse catalysis (means by which a reaction is speeded up. Reactants are converted to products much more efficiently. Does not affect the direction, only the speed) with delta G(free energy). aA +bB (a or b = molar concentration) Finding the real delta G = take the delta G knot and adding RT In [C]^c[D]^d/[A]^a[B]^b More reactants than products – negative value for In. Overall delta G will be more negative, reaction will be more spontaneous. More negative = more spontaneous. Clue – products in the numerator, reactants in the denominator. Will help you figure out how to manipulate the equation. Coupled reactions – add up the delta Gs. If negative, then both reactions can be spontaneous. Really common in biological conditions. Ex: ATP hydrolysis. It is drived by being coupled to another reaction. Everything you do or don’t do is based on a delta G effect. Try quizzes online from textbook. ------------------------------------------------------------------------------------------------------------------------------- ----------- th January 15 Single arrow indicates a single direction… (?) Delta G indicates which direction is spontaneous, but does not indicate the speed. Pyrophosphate = two phosphates stuck together. Released from ATP to make AMP Need to be familiar with structure of ATP, but do not memorize the structure. Has two phosphoanhydride bonds (bond between phosphates accompanied by a loss of water. Anhydride = bond without water). Negative charges close together in creatine mean that it is more reactive. Delta G knot prime is higher than it is in ATP. Oxidative phosphorylation = occurs in the mitochondria, proton gradient across the membrane, protons go across concentration gradient to area where there isn’t as much… Drives the process to make ATP. We collect it and use it to make most of our energy. Efficient process that makes an abundance of ATP. ------------------------------------------------------------------------------------------------------------------------------- ----------- January 17 th Delta G knot prime of ATP hydrolysis to ADP to release a single phosphate is =30.5 kj/mol… The reverse reaction would be positive. Need to be able to capture and store energy, rather than just burning it like gas. oxidation and reduction. Two half reactions in every redox reaction. Oxidation = loss of electrons. Whatever loses the electron is oxidized. Electron donor. With every oxidation there’s a reduction (the electron has to go somewhere). Losing an electron means it becomes more positively charged. Reduction = gains an electron. Gets reduced. OIL RIG = O xidation Is theL oss of electrons, and R eduction s the G ain of electrons NADP (anabolism) NAD (catabolism) Glycolisis to break down glucose (?) FAD, FADH2 similar to NAD and NADP. Important electron carrier. Want to understand how many electrons they carry and… Easily oxidized and reduced for what is needed in metabolism. Coenzyme is riboflavin. Related molecule RMNH2 (not covering this) We can’t make riboflavin and niacin naturally. Need to consume them in our diet. Need them to make NAD+ and NADH, and FAD, FADH2, molecules that we use all the time. The tendency of electrons to move between molecules easily/readily is expressed as the redox potential (E). We can’t measure E very easily, but can measure the change in E. Redox/reduction potential = defined as delta E (under standard conditions) of the acceptor minus the donor. If delta E is positive, the reaction will occur spontaneously. If the delta E is positive (spontaneous), so somewhere in the equation the delta G (gibbs free energy) is going to be negative. Can measure one and figure out the other one with the right data. Fe + e  Fe (gaining an electron) Cu Cu + e (losing an electron) Large negative reduction potential (positive is spontaneous, negative doesn’t tend to be), top of the chart isn’t spontaneous. At the bottom it is… (ex: 1/2 2 + 2H +2e  H O2has an E knot of +0.82. ½ O 2a a really strong tendency to lose electrons and become oxidized to form H O (2?) … Oxygen is a very good oxidizer. Oxygen loves to lose electrons) What you eat goes through a large amount of electron transfer by managing redox reactions… to fuel oxidative phosphorylation. ------------------------------------------------------------------------------------------------------------------------------- ----------- January 20 th Henderson-Hasselbach Equation  the best buffering occurs between 1 pH unit above and below the pKa - bicarbonate buffer is the principle buffer in the blood - phosphate is the principle buffer in intracellular fluids. Plenty of phosphate around in the cell, just not free. CHAPTER 5 Protein shape partly dictated by the function, there are some strange shapes, particularly when proteins act as molecular machines (ex: turbine out of a protein). - catalase (enzyme), multisub unit - Lysozyme, monomeric, first enzyme ever to have its structure determined - cytochrome c, - collagen, eccentric shapes, fibrous protein that’s essentially structural Generally distinguish proteins by function. Give it a name based on the activity it performs, or maybe it’s source. Shape that determines its function. Protein fold is determined by it’s sequence of amino acid (?), flexibility in it. Can accept fairly conservative changes… Mutation at a permissive site, can get a new functional mutant. Mutation at a site that is not permissive will kill the species (?) Peptides have less than 50 in their amino acid sequence. R group gives each amino acid it’s individual characteristics (personality). Amphoteric molecules = zwitterions. Not net charge at pH around 7. Nonpolar – side chain contains no polar elements. Elements do not have a charge – hydrophobic Tryptophan – incorporates an anine, does have some polarity. Classification is ambiguous. Proline – unusual, is not an amino acid, an animo acid (secondary….?), rigid form Tighter packed, the more defined/rigid structure you’re going to achieve Polar amino acids  groups can interact with water through hydrogen bonding. Hydroxyl groups (hydrogen bond at bar excellence (?)). - tyrosine = planar aromatic ring Basic amino acids = lysine (point charge), arginine (3 nitrogen atoms, a single charge that is delocalized over the nitrogen atoms, defuse charge), histidine (base, but has a partial aromatic character, pK is around 7, very weak base, in equilibrium between two states, useful for catalytic purposes, is a buffer because its pH is around the physiological pH, histidines in hemoglobin can provide buffering in the blood). ***Learn the structures of the amino acids  know the nature of the side chains/functional groups of the amino acids. Knowing the structure will help. Naming will depend on the order of the amino acids. First three letters of the amino acid makes the three-letter abbreviation. Exceptions = Isoleucine (Iso would be too ambiguous), Asparagine, Glutamine, Tryptophan (could be confused with tyrosine). ***Learn the abbreviations One letter abbreviations = the one that is the most common will get the first letter. Ex: Alanine more common than arginine and asparagine (etc), so its one letter abbreviation is A. Leusine more common than lysine, it gets the L. Lysine gets a K (because it’s the nearest letter to L that hasn’t been taken already).Tryptophan has a double ring, so it uses a W (rather than a U), because T is already taken. Indole acetic acid = one of the principle plant hormone. Amino acid derivative. Precursors for synthesis of more complicated molecules = citrulline & … Sometimes amino acids get modified. 20 amino acids give you flexibility… but they can’t do everything. Some of the side chains do not have functional groups at all. They are, to some extent, limited. - Gamma carboxyglutamate – two groups adjacent to eachother (?) Alpha carbon groups can have two stereoisomers…? Names D-(dextro = right) or L-(lilo = left). Direction the light is polarized (?). Generally use L- amino acids. Don’t know why. Some early evolutionary accident perhaps lead to their use. Amino acid sequence leads to the protein conformation – shape of the protein dictates its function. Proteins do have distinct forms/defined structures. - Proteins aren’t random flight polymers… Presence of peptide bond itself ensures this. The C-H bond in the peptide bond has partial double bond character that ensures there is not free rotation around that bond. Rigidified the amide plane. Amide planes are linked together. Limits the number of conformational possibilities because every third bond is rigid. - Steric clashes if rotating the amide planes a certain way around the angles of rotation (?) - sweet zone where you avoid completely steric clashes. Small fraction of conformational space. Linus Paulding got the nobel prize for determining the nature of the peptide bond. A second nobel prize  winner of the peace prize for his efforts in opposing nuclear weapons in the US. Internal crosslinking within a protein (disulfide bridge), interior of most cells is reducing with will usually reduce the disulfide bridge (so it is not common to find one inside most cells)…? - most of the digestive enzymes secreted into the gut are stabilized by… ------------------------------------------------------------------------------------------------------------------------------- ----------- January 22 Primary structure of protein linked by peptide bond. Small collectives of amino acids and peptide bonds gives you a peptide. Ex: glutathione = tripeptide. Very useful. Has a thiol group – a powerful reducing agent. Reducing agent is employed in a variety of functions within the cell. Peptide hormones = Major function of peptides within the body. Agents of communication between cells and organs. Vasopressin (regulates physiological functions) and oxytocin (reproductive functions). Strikingly similar sequences – only two amino acid substitutions in the structure. Still, they have widely different physiological functions. This minor change in the side chains mean they interact with different receptors. Extraordinary degree of specificity….. (?) Glutathione – pentavalent ends… Amino group at the end terminus, the first alpha carbon has an amino group and carboxyl attached to it. Alpha carboxyl group would normally be forming a peptide bond, but in this case the side chain carboxyl is forming the peptide bond. Peptide bond is formed with the wrong carboxylate = isopeptide bond. Found occasionally in biological structures (proteins). Proteins = have an extraordinary number of functions. The workhorses of the cell. Every task that is required within the cell is down to proteins to fulfill. - catalysis (metabolism undertaking by the cell) - structure (form of cytoskeleton holding the cells together, microtubules and actin filaments, also responsible for movement within the cell and intracellular trafficking) - defense (immune systems dependent upon various kinds of proteins as well as antibodies, intrinsic immunity with interleukins) - regulation (communication, hormones and hormone receptors, ex:insulin) - transport (transporters built into membranes that are able to pump material in and out of cells) -storage (in the form of nutrition, amino acids stored in the form of proteins) - stress response (can use proteins to repair cells using the stress response system) Sometimes proteins can have multiple functions = moonlighting proteins (holding down two jobs at the same time). -a particular type of protein will have varying structures from species to species, neutral mutation (variations within the primary sequence of the protein). Sometimes such a protein can diverge into two separate streams (two related functions with specific…). Ex: myoglobin (oxygen transport in the bloodstream. Globular protein found in muscles and other tissues, is the intercellular oxygen store) and hemoglobin. Proteins also divided into shapes: globular and fibrous. Divided by classification: simple or conjugated (?) Space filling model = gives the full flesh, useful for… Can’t see the skeleton though… Divide structure up into primary, secondary (the way in which the bits of primary structure gets organized into regular patterns), tertiary (corresponds to the 3D structure (fold of the protein)), and quaternary (the way in which multi-sum units of proteins are assembled. Combo of tertiary structures. Ex: a lot of globular proteins assembled into a string to make a fibre). Primary structure can vary. Call what we regard as the same protein from different species = homologues. Didn’t arise independently. Sufficiently similar in form that it is clear they arose from a common ancestor. Lots of good reasons for determining protein structure: to understand the 3D structure of the protein. When we determine that structure we create an electron density map through electron crystallography… if we know the amino acid sequence we can pick out the shapes and find out where those chains go… When we introduce artificial substitutions we can make an interpretation of the structure function relationships…. -sometimes we cannot easily determine the structure of the protein. A difficult thing to do. Depends on being able to get good crystals of a protein. Need to be able to grow the crystals to put a beam through it (?). - Ways of trying to predict the 3D structure through the linear sequence. Can allow you to predict what units of secondary structure may exist from a given primary sequence. Does the pattern match any structures known in the databank? Can use modelling and try and build the 3D structure. To find the gene = most amino acid sequencing is done by knowin
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