Before Midterm 1 Notes PDF

Friday The Chemical Basis of Life I: Atoms, Molecules, and Water (chapter 2): Subatomic Particles: Protons Neutrons Electrons Except for ions, the number of protons and electrons are equal Ex. Hydrogen is 1 proton and 1 electron, Helium is 2 protons, 2 electrons, or 2 ne...

Friday The Chemical Basis of Life I: Atoms, Molecules, and Water (chapter 2): Subatomic Particles: Protons Neutrons Electrons Except for ions, the number of protons and electrons are equal Ex. Hydrogen is 1 proton and 1 electron, Helium is 2 protons, 2 electrons, or 2 neutrons Isotopes: Same number of protons in their nuclei and position on periodic table but differ due to different number of neutrons in their nuclei Determines stability Can be used in radiotherapy Can be used for labeling Electron orbital/shells: Three-dimensional region in which there is a 95% likelihood of finding and election Each orbital is a greater distance from nuclei Further the orbital more energy is required to stay there n=1, n=2, n=3 Different orbitals, different calls, different energy level, different number of electrons Valence electrons: Outermost shell Participate in chemical bonds Outer electron pairs are important in biology Electron pair: Two electrons occupying the same molecular orbital A pair is considered stable If electrons are not in a pair they will be looking for another molecule to pair with Pair electrons on outside are happy, unpaired are unhappy Shell accommodations: First shell 2 electrons Next shells have 8 electrons Love t have complete electrons in cells Most abundant in living organisms (95% of total mass) Oxygen - Atomic # 8 Carbon - Atomic # 6 Hydrogen - Atomic # 1 Nitrogen - Atomic # 7 Mineral elements (less than 1% of total mass) Calcium Chlorine Magnesium Phosphorus Potassium Sodium Sulfur Electronegativity: Symbolized as X Electronegativity is the tendency for an atoms of an element to attract shared electrons More electronegative atom means that they will pull the electrons stronger than less electronegative More electronegative Water is charged and oxygen is more electronegative than hydrogen 1.8 is ionic (electrons transferred) *question on exam would be identifying what type of bond it is based on electronegativity or calculating electronegativity Ionic Bonds: Attraction between positive and negative ions Anion - has a net positive charge (loses electron) Cation - has a net negative charge (gains electron) Covalent Bonds: - Two atoms whose outer shells are not full share a pair of electrons - Are electrons always shared equally? Hydrogen bonds: Polar covalent Polar covalent Electrostatic force of attraction between H and another highly electronegative atom or group (N,O,F) Water is a universal solvent Weak bond Many hydrogen bonds Partial negative atoms bond with partial positive atoms Protein and DNA is hydrogen bonding Water is an example of hydrogen bonds  Arrangement of Covalent Bonds: Methane (CH4) Ammonia (NH3) Water (H2O) Hydrogens are equally distanced Hydrogens are equally distanced Rotation of Covalent Bonds: Covalent bond types Single bond Double bond Triple bond Single bond is rotatable Double and triple bonds do not rotate Free Radicals: Any molecular species capable independent existence that contains an unpaired electron in an atomic orbital Can be used to kill bacteria and are released by immune system during illness Used by the body as a form of communication Reactive Oxygen Species ○ Natural outcome of mitochondria procuring energy Antioxidants are chemicals that provide an electron for a free radical to neutralize it Role of Water: Universal solvent in biology Every biochemical is a function of interaction of water Ions and polar molecular dissolve in water Cells are surrounded on all sides by fluids Substances dissolved are known as solutes Liquid in which solutes are dissolved is called solvents  Solutes and solvents form a solution Chemical bases of like II: Organic Molecules Chapter 3 *Assigned reading 2.4 (pH and buffers) Hydrophobic: Does not interact/dissolve in water (non-polar) Hydrophilic: Interacts/dissolves in water (polar) Amphipathic: One end hydrophobic (non-polar) and the other end is hydrophilic (polar) Carbon: Forms both polar and non-polar bonds C-C and C-H bonds are electrically neutral and nonpolar Hydrocarbons are hydrophobic (non-polar) C-O bonds are polar as oxygen is more electronegative than Glucose has 6 carbons In glucose, Carbon has a polar bond with O but non-polar with H and C Strong interactions between polar molecules (POLAR MOLECULES ARE STICKY - will be term used on exam) - high melting and boiling point. Polar molecules have positive and negative parts which makes them have a strong attraction. Weak interactions between non-polar molecules - low melting point and boiling point Functional groups: Grouping of specific atoms with specific properties -OH is hydroxyl -NH3 is amino, amino acids (proteins) -weakly basic COOH is carboxyl - amino acids, fatty acids, acidic, forms part fo peptide bonds Isomers: Structural isomers: Same molecular formulas (number and types of atoms), but different bonding arrangement of atoms. They have different properties. Functional groups on same side of molecule is CIS and different sides is TRANS Only single bonds can rotate Enantiomers are mirror images of each other Stereoisomers molecules have the same molecular formulas and bonding of atoms but different spatial arrangement. They have different properties. Synthesis and breakdown of biomolecules, polymers, condensation, and hydrolysis reactions: Polymer begins as two monomers combine in a dehydration (condensation) reaction Elongation of the polymer continues with additional dehydration reactions The final polymer may consist of many monomers Polymers are broken down one monomer at a time by hydrolysis reactions To build something you need condensation (dehydration) To build something down you need hydrolysis Major Biomolecules: Carbohydrates: General formula: Cn(H2O)n (n is a whole number) Key functions: Simply carbohydrates are broken down to make ATP (energy) Larger carbohydrates store energy or play a structural role as in plant walls Stored like a starch in plants Stored as glycogen in animals and humans Or stored as cellulose Some carbohydrates function as molecular tags allowing recognition of specific cells and molecules Examples: Simple sugars, such as glucose; larger polymers such as glycogen, starch, and cellulose Monosaccharides - 1 molecule of sugar (two mono makes a di) Disaccharides - 2 molecules of sugar (ex. glucose and fructose make sucrose) Hexose - any simple sugar with 6 carbons Pentose - any simple sugar with 5 carbons Glycosidic bond between sugars Either linear or ring structure Fatty acids: General formula: Many hydrocarbons linked together Carboxyl group at the and of hydrocarbon chain (which is polar/hydrophilic) Non-polar Hydrophobic Key functions: Prostaglandins (PG) are a group of active lipid compounds called eicosanoids that have diverse hormone-like effects (including fever and pain) in animals - Arachidonic acid (20 carbons with 5, 8, 11, and 14 being double bonds) is tylenol, ibuprofen, aspirin, which fights PG Saturated has single bonds is straight and is mainly fats Saturated is all long non-polar tails Unsaturated has double bonds and is mainly oils Unsaturated fats are made from hydrogenation Unsaturated fats are a mix of short and long polar and nonpolar tails Trans fatty acids are trans and come from packaging and manufacturing (squishing fats into small spaces) Natural fats are cis Bonded by glycosidic bonds Examples: Triglycerides (lipids) are made of 3 fatty acids and a glycerol Phospholipids (triglycerides/lipids) are a phosphate head with two fatty acid tails and a glycerol ○ Hydrophilic, polar head ○ Hydrophobic, non-polar tail Steroids ○ Estrogen ○ Testosterone ○ Cholesterol ○ Cortisol Suppresses immune system  Makes memory better Increases blood pressure Reduces bone formation Aids in the metabolism of fat Counteracts insulin Increasing sodium water reaction Activates under psychological stress, physical stress, pain (ex. An exam) Carboxyl group of one amino acid reacts with amino group of the next amino acid in a condensation reaction (produces water and makes a peptide bond) Peptide bonds is between the double bonded O and the N bond Polypeptide is a linear chain of amino acids (many peptides together) Primary ○ The linear sequence of amino acids Secondary ○ Certain sequences of amino acids for hydrogen bonds that cause a spiral or sheet shape Tertiary ○ Secondary structures and random coiled rejoins fold into a 3-dimensional shape Quaternary structure ○ Two or more polypeptides may bind to each other to form a functional protein First amino acid has a three amino group and last amino acid has a carboxyl group Nucleotides and Nucleic acids: Deoxyribose sugar is used in DNA Ribose sugar is used in RNA Sugar is labeled with a prime numbers (‘) 3’ has a hydroxy and 5’ has a phosphate 3’ and 5’ is where phosphodiester bond (bond between nucleotides) is linked through a condensation reaction ○ PHOSPHATE GROUP LINKES 5’ TO 3’ HYDROXY IN PHOSPHODIESTER BOND CONNECTING THE 5’ POINT OF ONE BASE TO THE 3’ POINT OF ANOTHER BASE 5’ to 3’ in DNA connection In DNA ○ two hydrogens are on 2 and 3 prime ○ Tells us why DNA can store  In RNA ○ one hydroxide and hydrogen in 2 and 3 prime (respectively) ○ Tells us why RNA is unstable that likes to interact and destroy bonds DNA and RNA: Bases are hydrophobic Phosphates are charged hydrophilic 3.24 - Find if given how much of one molecule you have how much % DNA ○ Deoxyribonucleic acid ○ Adenine and Thymine ○ Cytosine and Guanine RNA ○ Ribonucleic acid ○ Adenine and Uracil ○ Cytosine and Guanine Names of bases and nucleotides: Bases: Nucleotides: Thymine - Thymidine (deoxythymidine thymidine) Adenine -Adenosine Cytosine - Cytidine Guanine - Guanosine Uracil - Uridine Ether monophosphate (one M), diphosphate (two, D), triphosphate (or three, T) A d in front makes is deoxy-root-# of phosphates Pyrimidine Nucleotides: Single rings Cytidine, Uridine, and Thymidine Cytosine, Urail, and Thymine Purine Nucleotides: Double rings Adenosine and Guanosine Adenine and Guanine ALWAYS PAIRING BETWEEN ONE PYRIMIDINE WITH ONE PURINE pH and Buffers: Pure water can dissolve into OH- (hydroxide) and H+ (hydrogen ions) In pure water the concentrations of H+ and OH- are both 10 -7 (subscript) Product of H+ and OH- is 10-14 (from multiplying the two concentrations) Substances that release hydrogen ions in a solution are called acids Hydrochloric acid is a strong acid because it completely dissociates into H+ and Cl- when added into water Carbonic acid is a weak acid because some of it remains in the H2CO3 state when dissolved in water A base decreases the H+ concentration Some bases release OH- when dissolved in water (such as sodium hydroxide) When a base raises the OH- concentration, some of the hydrogen ions bind with the hydroxide ions to form water, increasing the OH lowers the H pH is a measure of the H+ in a solution 1 unit in pH represents 10 units in H+ concentration change Lower than 7 is acidic, more than 7 is basic, and 7 is neutral In living cells, pH ranges from about 6.5-7.8 Human blood normal pH is 7.35-7.45 Basic is also called alkaline Kidneys secrete acidic or alkaline compounds when blood chemistry becomes imbalanced Buffers: A way in which pH fluctuation are managed in the fluids of living organisms Pair of substances, an acid and its related base Can impact pH in both directions Ex is carbonic acid and bicarbonate ions in blood of animals As the pH of an animal's blood increases, the reaction proceeds left to right, and the increased H+ concentration (made in the equation) decreases pH. When the pH gets too low, the reaction runs in reverse, using up the H+ to make more CO2 and H2O with the bicarbonate, increasing the H+ and increasing the pH. Buffers found in living organisms function most effectively at the normal range of pH values THE MORE H+ THERE IS THE LOWER THE pH IS!!!! Concepts in Energy and Thermodynamics: Entropy (S): The degree of disorder of a system (ex. untidy room has increased entropy) 2nd Law of thermodynamics: Entropy always increases in a reaction Enthalpy (H): The total energy of a system Free energy (G) The amount of a system’s energy that is available and can be used to promote change Total energy (H, Enthalpy) = Usable energy (G, free energy) + unusable energy (TS, Entropy) H=G+TS ΔG=ΔH - TΔS +ΔG value is not favourable and not spontaneous (energy required) - endergonic -ΔG value is favourable and is spontaneous (no energy required) - exergonic To find: Free energy of the products-Free energy of reactants To be endergonic - reactions are bigger than products To be exergonic - products are bigger than reactants Ex. ΔG=+3.3kcal/mol is not spontaneous as it is positive but -3.3kcal/mol would be spontaneous as it is negative and favourable Exergonic: Produce outside work Endergonic Δ above 0 and requires help Catalysts: Agent that speeds up the rate of a chemical reaction without permanently changed or consumed during the reaction Enzymes are made of protein Ribozymes are made of RNA RNaseP cleaves RNA molecules acting on others Ex. ATP using sugar but us not running out Activation energy (EA): An initial input of energy in a chemical reaction that allows the molecules to get close enough to cause a rearrangement of bonds  For a reaction to work the reactants must be given enough energy to make it over the bump, this is done through activation energy In the body, enzymes work by lowering the energy needed to make reactions go faster, lower activation energy and speeding up the reaction Enzymes only affect the activation energy and not the products or reactants Saturday Metabolic Reactions: Metabolic pathway: ○ In living cells a coordinates series of chemical reactions in which each step is catalyzed by a specific enzyme Catabolic reaction: ○ A chemical reaction where a molecule breaks down into smaller components, usually releasing energy, frequently ATP, cleaning up, or producing useful molecules Anabolic reaction: ○ A chemical reaction involving the synthesis of larger molecules (biosynthetic reaction) from smaller precursor molecules, usually requires an input of energy Oxidation: The removal or one or more electrons from an atom or molecule; may occur during the breakdown of small organic molecules Reduction: The addition of one or more electrons to an atom or molecule Ex. NAD+ to NADH Redox reaction (reduction-oxidation): Where one electron is removed during the oxidation of an atom or molecule and is transferred to another atom or molecule which is being reduced Metabolic pathway regulation: Are regulated Regulation levels: Genetic (switch of genes on or off) Cellular (Cell signaling pathways, e.g. protein kinases, hormones) Biochemical (feedback inhibition of enzymes) Did not mention Vmax, Km, Inhibition (competitive, and non-competitive) - do not worry about them  Chapter 7 - Cellular Respiration and Fermentation: Mitochondria: 2 membranes (inner and outer) All cellular respiration occurs in the mitochondria except for The release of energy during cellular respiration: Glucose + Oxygen —-------> Carbon Dioxide + Water C6H12O6 + 6O2 —-------> 6CO2 + 6H2O Oxidation and Reduction: NAD+ —> NADH is reduction NADH —-> NAD+ is oxidation Need to Invest: In order to make ATP you need to spend ATP Energy investment phase (put in ATP) Cleavage phase (split up ATP into 2) Energy liberation phase (double ATP value) Ex. if you put 2 in and end with 4, there is a net of 2 Glycolysis: Located in Cytoplasm 10 Steps: 1. Glucose is phosphorylated by ATP as Glucose-6-phosphate is more easily trapped in cell than glucose Glucose made 2. Glucose-6-phosphate structure is rearranged to Fructose-6-phosphate Glucose-6-phosphate made 3. Fructose-6-phosphate is phosphorylated to fructose-1,6-biphosphate Fructose-6-phosphate made 4. Fructose-1,6-biphosphate cleaved to dihydroxyacetone phosphate and glyceraldehyde-3-phosphate Fructose-1,6-biphosphate made 5. Dihydroxyacetone is rearranged (isomer) and forms another glyceraldehyde-3-phosphate Glyceraldehyde-3-phosphate made (x2) 6. Glyceraldehyde-3-phosphate oxidised into 1,3-bisphosphoglycerate and upper left phosphate is destabilized, allowing bond to break in highly exergonic reaciton. NADH produced. 1,3-biphosphoglycerate made (x2) 7. Phosphate removed from 1,3-biphosphoglycerate forming 3-phosphoglycerate. Removed phosphate is transferred to ADP, making ATP in substrate-level phosphorylation 3-phosphoglycerate made (x2)  8. Phosphate group from 3-phosphoglycerate is moved to new location making 2-phosphoglycerate 2-phosphoglycerate made (x2) 9. Water molecule removed from 2-phosphoglycerate forming phosphoenolpyruvate. In this, phosphate group is unstabilized, bond will break in highly exergonic reaction. Phosphoenolpyruvate made (x2) 10. Phosphate removed from phosphoenolpyruvate, forming pyruvate. Removed phosphate transferred from ADP to make ATP via substrate-level phosphorylation. Pyruvate made (x2) Control: 1. Substrate level Energy levels how much glucose is there in the system, how much demand for glucose is there Glucagon converts glycogen back into glucose (when sugar is low) Insulin converts glucose back into glycogen (when sugar is high) 2. Inhibition When you make enough product production will stop from substrate inhibition 3. Enzyme 3 part of enzymatic control Kinase means adds phosphate Hexokinase (Only phosphorylated glucose can enter the cycle, if you can control hexokinase you can control the cycle, controls entry to glycolysis) Phosphofructokinase (controls commitment to glycolysis) Pyruvate kinase (controls end of glycolysis) Breakdown (oxydation) of pyruvate: Pyruvate made in the cystol in glycolysis and moves through ourer membrane and H+/pyruvate symporter in the inner membrane to reach mitochondrial matrix Pyruvate is oxidised via pyruvate dehydrogenase to an acetyl group and CO2. NADH made. Acetyl group is transferred to coenzyme A (CoA) and later removed and enters citric acid cycle. Is how pyruvate (3 carbon) is moved from outer/middle shell and into mitochondria Pyruvate loses one of the carbons (2 carbon left) Passed by sulfur and turned into Coenzyme A (CoA) which uses an NADH in its formula Pyruvate dehydrogenase is responsible for removing carbon from pyruvate and adding CoA 2 pyruvate is broken down into 2CO2 + 2 acetyl CoA Citric Acid Cycle: Located in Mitochondria One turn makes 2 molecules of CO2, 3 NADH, 1 FADH2, and 1 ATP Total, 4 CO2, 6 NADH, 2 FADH2, and 2 ATP made No energy from breaking down carbons, only using up carbons at at a time Steps 1. Acetyl group from acetyl CoA is attached to oxaloacetate to form citrate, CO2 removed ○ Citrate made 2. Citrate is rearranged to isomer called isocitrate, CO2 removed ○ Isocitrate made 3. Isocitrate is oxidised to ketoglutarate. CO2 is released an NADH is formed (reduced from NAD+), CO2 removed ○ α-ketoglutarate made 4. Ketoglutarate is oxidised when combining with CoA to form succinyl CoA. CO2 is released and NADH is formed (reduced from NAD+) ○ Succinyl-CoA made 5. Succinyl CoA is broken down to CoA and succinate. The exergonic reaction synthesis GTP to transfer phosphate to ADP, making ATP ○ ATP and succinate made 6. Succinate is oxidised to fumarate and FADH2 is made (reduced from FAD, redox reaction) ○ Fumarate made 7. Fumarate combines with water to make malate ○ Malate made 8. Malate is oxidised to oxaloacetate. NADH is made (reduced from NAD+) and the cycle begins again. ○ Oxaloacetate made Isocitrate dehydrogenase ○ NADH, ATP, feedback inhibitors ○ NAD+, ADP, activators ○ Isocitrate dehydrogenase is floating around and wanting to bond with NADH and ATP, when there is more the reaction stops but at the right level of NADH and ATP, it will run nicely (substrate product inhibition) it is regulatory OVERALL REACTION ○ Acetyl-CoA + 2H2O + 3NAD+ + FAD + GDP2- + Pi2- = CoA-SH + 2CO2 + 3 NADH + FADH2 + GTP4- + 3H+ All delta G in reaction is negative so it is exergonic and spontaneous (no energy required) on all steps Catabolic kinds of metabolic reaction Up to this point in all of cell resp, we have made 4 ATp, 10 NADH, and 2 FADH2 Oxidative phosphorylation: Located in Mitochondria 30-34 ATP made Oxidation NADH FADH2 —--> ATP H+ pumping Making ATP from the 10 NADH and 2FADH2 that have been made already Electron transport chain or respiratory chain  4 protein complexes and small molecules in the inner mitochondrial membrane ○ Mitochondria has an outer and inner membrane and the matrix is in the inner membrane ○ Inner membrane acts as a barrier to charged protons ○ Matrix has fewer protons ○ Complex 1, 2, 3, 4 Complex 1 NADH deposits two high energy electrons where they are passed along a line or redox centres (cluster of atoms based on unique affinity for electrons based on configurations) and a small amount of energy is released as it is passed along between redox centres. Complex 1 harnesses the energy and uses it to pass along protons. Last redox centre donates 2 electrons to a coenzyme Q molecule Donate electrons to complex 3 Complex 2 FADH2 deposits two high energy electrons and sends them though redox centres until it is deposited into Coenzyme 2 Does not use energy liberated to pump protons Donate electrons to complex 3 Complex 3 - Uses energy from complex 2 to power One electron is recyclable and can enter complex 3 later Other passes through 2 redox centres until it reacher cytochrome C Cytochrome C carries electron to complex 4 Complex 4 - Last stage of the ETC Reaction involving 4 electrons converts molecule of oxygen into 2 water molecules and eventually Proton gradient is strengthened because 4 protons from the matrix are incorporated into water molecules and another 4 are pumped into intermembrane space In absence of oxygen the ETC comes to a halt and so does ATP synthesis H+ electrochemical gradient production Electrons (protons) from NADH and FADH2 are donated (oxidized) There is a movement of electrons to the redox centre If electrons escape somewhere on the ETC, you get free radicals (buy antioxidants to fight/mop up escaped electrons) As they move down, they lose energy and the excess energy is used to pump hydrogen Protons go to complex 1,3 and 4 and are pumped from the matrix to membrane space Complex 2 promotes proton pumping in complex 3 and 4  A low pH concentration has more protons (H+), so as protons are pumped out, pH decreases If you have a lot of ATP and you do not need any more, ATP will bond to Isocitrate dehydrogenase and stop production (Regulation) Protons form the NADH and FADH2 will be pumped from matrix to intermembrane (using ATP), generating an electrochemical gradient (REMEMBER) ATP synthase ○ ATP synthase uses electrochemical gradient to spin protons into ATP but if there is no gradient, the pump will not work ○ Turns ADP + Pi into ATP from outside the matrix to inside ○ Highly conserved enzyme that catalyses the formation using rotary motor mechanism ○ Located in the inner membrane of the mitochondria, in the thylakoid membrane of chloroplasts, and plasma membrane of bacteria ○ Fo in the membrane has a lots of Cs that interact with protons ○ F1 contains alpha, beta subunits ○ Parts of ATP synthase WATCH VIDEO ONLINE FIND IT Fo motor Proton powered Protons flow through a channel open to intermembrane space where they bind to a ring of protein subunits, rotate 360 degrees, and exit through another channel exposed only to matrix Force from flow of protons generate rotation F1 motor Torque generated in Fo motor is transferred to the F1 motor by central stalk or shaft Generates ATP by additional phosphate to ADP Top of the central stalk causes conformational changes of the catalytic subunits Catalytic unit is made of a dimer of subunits and there are three arranged in a ring Catalysis occurs at the interface between the dimers ○ ADP and phosphate bind to catalytic side ○ Central staff rotates 120 degrees to rearrange molecules ○ Enzymes undergoes another 120 degree rotation, fusing ADP and phosphate together making ATP ○ Enzyme rotates back and the ATP and ADP are released so phosphate can be bound for the next cycle of catalysis Catalytic subunits must remain stationary in respect to a rotating central staff (performed by a dynamic scaffold on the outside called a peripheral stalk) Dimerises to turn mitochondrial inner membrane into cristae shape and be more efficient by focusing proton gradient in ATP synthase In three beta subunits  ○ Conformation 1 ADP and Pi bind with good affinity ○ Conformation 2 ADP and Pi bind so tightly that ATP is made ○ Conformation 3 ATP binds very weakly and is released ○ Once ATP bind, the gamma interacts, rotates 120 degrees, and squeezes so tight that the ADP and Pi becomes ATP Then the gamma rotates again 120 degrees and ATP is released Gamme rotates again to bring more substrate in Beta subunit is where ATP is made with ADP and Pi Beta unit moved gamma unit Also make Coenzyme Q10 Energy of protons drops as they move through the ATP For every molecule of NADH that is oxidised and each molecule of ATP made, two chemical reactions of oxidative phosphorylation NADH + H+ + ½ O2 —--> NAD+ + H2O ADP2- + Pi2- = ATP4- + H2O Fatty acids also contribute to Acetyl-CoA, can go straight into glycolysis Look at figure 7.14 Sunday Fermentation: In muscles - lactic acid fermentation ○ In absence of oxygen ○ Glucose is oxidized into 2 pyruvate molecules so that glycolysis can work and ATP can be made ○ Two pyruvate are reduced to 2 lactate molecule ○ If you keep making NADH, you will run out of NAD+ and if you do, you will collapse because no more ATP can be made ○ So, to make more NADH, the power created from reducing the pyruvate into lactic acid oxidizes NADH back to NAD+ (redox reaction) ○ Lactate builds in muscles and is excreted through kidneys In yeast - alcoholic fermentation ○ Glucose is oxidized into 2 pyruvate molecules ○ Two acetaldehyde molecules are reduced to 2 ethanol molecules which oxidizes NADH to NAD+ ○ Alcohol is made ○ Used in wine making PET scans: Warburg effect  Positron emission tomography Uses radioactive substances call radiotracers to visualize and measure changes in metabolic processes Fluorodeoxyglucose (FDG) is commonly used to detect cancer FDG can not be properly phosphorylated so it can enter glycolysis but can not move through, so it builds up and has a lot of glycolysis (which is why tumors are visible on PET scans) Amino acids and proteins: Starts with alpha carbon in the middle of amino acid Add amino group to alpha carbon Add carboxyl group to alpha carbon Add hydrogen to alpha carbon And one unique “R” group that changes between amino acids Key functions: There are 20 amino acids 9 are essential but how many you have depends on diet Are divided into polar and nonpolar groups Some are essential, conditional essential, and some are non-essensial Nonpolar: Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (ile) Proline (Pro) Phenylalanine (Phe) Tryptophan (Trp) Cysteine (Cys) Methionine (Met) Polar (uncharged): Some things are good tasting Serine (Ser) Threonine (Thr) Asparagine (Asn) Glutamine (Gln) Tyrosine (Tyr) Polar (charged): Amazing Actor Glues His Legs Aspartic acid (Asp) Glutamic acid (Glu) Histidine (His) Lysine (Lys) Arginine (Arg) Nine essential amino acids: Have to get them from your diet  Histidine (His) Isoleucine (lle) Leucine (Leu) Lysine (Lys) Methionine (Met) Phenylalanine (Phe) Threonine (Thr) Tryptophan (Trp) Valine (Val) Conditional essential: If you need them depends on age, where you live, who you are, diseases Arginine (Arg) Cysteine (Cys) Glutamine (Gln) Glycine (Gly) Proline (Pro) Tyrosine (Tyr) Non-essential: Almost all girls act so strongly psycho Alanine (Ala) Aspartic acid (Asp) Glutamic acid (Glu) Asparagine (Asn) Serine (Ser) Selenocysteine (Sec) Pyrrolysine (Pyl) (not used by the human body)  Monday Chapter 8 - Photosynthesis Cyanobacteria, eukaryotic algae, and plants combine two photosystems in a linear electron transport chain. Photosynthesis: Algee, plants, and some bacteria can transform light energy to chemical energy (covalent bonds) by a process called photosynthesis Making covalent bond to make organic molecules Opposite of process of metabolic breakdown of sugars (cellular respiration) Heterotroph ○ Breaks down compounds in the environment for energy Autotroph ○ Produces its own sources of energy and feeds themselves by energy from the sun to make organic molecules ○ Algee, plants, some bacteria General Redox Equation of Photosynthesis: CO2 + 2H2A + Light energy = CH2O + A + H2O Where A is oxygen or sulfur and CH2O is the general formula for a carbohydrate. This is a redox reaction in which CO2 is reduce H2A is oxidyzed In plants and algae, A is oxygen and A2 is a molecule of oxygen, written as O2. Therefor this equation becomes CO2 + 2h2O + Light energy = CH2O + O2 + H2O When carbohydrate produced is glucose, we multiply each side of the equation by 6: 6 CO2 (reduced) + 12H2O (oxidized) + Light energy = C6H12O6 + 6O2 + 6H2O +685 kcal/mol Requires energy to go Cyanobacteria, eukaryotic algae, and plants combine two photosystems in a linear electron transport chain. In algae and plants this occurs in organelles called chloroplasts. Leafs: 4 layers of cells ○ Epidermal on top ○ Mesophyll on the bottom ○ Two layers of each ○ Where oxygen circulates In the mesophylls ○ Chloroplasts Have equivalent structures to mitochondria Two membranes and inner is used and pumped out in both Have another thylakoid membrane Where the chlorophyll are found  ○ Two forms of chlorophyll are a and b Looks like pennies stacked on eachother (or pancakes) Contains chlorophyll pigment Stages of Photosynthesis: Capture energy and convert it to usable and then use that to make carbohydrates Carbon dioxide + Water = Sugar + Oxygen ○ Light reactions Occur at the thylakoid membrane, produce ATP, NADPH, and O2 Light reactions 12 H20 + 12NADP + 18 ADP + 18 P1 + light and chlorophyll = 6O2 +12 NADPH + 18 ATP Oxygen is produced as the waste product ○ Calvin cycle Products from light reactions are fed into calvin cycle to be used In the stroma and uses CO2, ATP, and NADPH to make carbohydrates Light: Only see small part of light (toward blue higher energy and toward red lower energy) We can see 380mm to 740mm Deposits energy in the form of a photon Photons can hit a molecule and can be absorbed by electrons in the orbital and then the excited electron joins another orbital Electron jumps from ground state to excited state when hit by photon Plants and algae use excited electron, make it lose the atom and gets transferred from one chlorophyll molecule to another until it hits the sink that absorbs the electron (primary electron acceptor) Makeup: chlorophyll Porphyrin ring Non-polar, hydrophobic tail Has an electron that can move all over the place until it gets hit by a photon and then leaves the chlorophyll all together Stroma is on outside of thylakoid Protons in photosystem hop around until they reach they are dumped out so energy they contain can be harvested by the P680 (receives them) Photosystem II - P680 wavelength - P680 donor consists of a heterodimer of two distincts molecules 1. Light energy is absorbed by a pigment molecule. This boots an electron in the pigment to a higher level  2. Energy is transferred among pigment molecules via resonance energy transfer until it reacher P680 converting it to P680+ 3. THe high-energy electron on P680 is transferred to the primary electron acceptor (pheophytin) where it is very stable. P680 becomes P680+ 4. A low-energy electron from water is transferred to P680+ to convert it to P680. O2 is produced. - Water comes in and is split - Electrons go through the system - Electrons are thrown in the chain and as they go from high to lower energy they hit photosystem I - Water splits, oxygen comes out Photosystem 1: P700 - NADPH is made - Uses electron from oxygen - Hydrogens fed through ATP synthase to make ATP Just need to remember that in photosystem II and I the electron transport chain is harvesting ATP from the electrons, wavelengths of both photosystems, but do not need to know the specific parts of the ETC in photosystem II and I, must remember reaction Reason that plants have different plants have different colours is because different pigments absorb different wavelengths Why do leaves turn red: Have an orange carotene chlorophyll as well as the normal green one In the fall you lose green chlorophyll (gets depleted) and only the carotene becomes visible Wavelenths absorb all colours but the greens, which is why trees are green And carotene only absorbs in colour such at the yellow and red which is why trees turn colour in the fall when less chlorophyll is present Calvin Cycle RuBisCO enzyme - take CO2 and RuBP and puts them together RuBP ribulose biphosphate (five atoms of carbon and a phosphate group on each end) Co2 + NADPH + ATP = CH2O + NADP + ADP+Pi It takes six turns on the calvin cycle to make one carbohydrate molecule (one for each carbon dioxide molecule fixed). The remaining G3P molecules regenerate RuBP Starts with 3 carbons and adds them each turn until there are 6 LOOK AT FIGURE 8.16 AND FIND RIGHT STOICHIOMETRY AND ADDING NUMERS OF ATP NADPH AND CO2 FOR MAKING GLUCOSE EX QUESTION HOW MANY ATP TO MAKE GLUCOSE Answer is 18 Question: what is photosystem II electron donor Answer: P680 Phase 1: Carbon fixation Phase 2: Phase 3: Regeneration of RuBP Midterm notes: Everything covered in lecture up to next friday 30 multiple choice questions 50 minutes Need dark pencils Also answer questions on exam script and scantron and whatever answer is on exam script and put name and student number on both Leave quietly after handing in exam Don’t sit next to eachother No material from the lab included Tuesday Mendelian Patterns of Inheritance - Chapter 17 What is a gene A gene is the basic physical and functional unit of heredity Specify traits or characteristics Made of DNA and located in chromosomes Act as instructions to make proteins (for body function) but most do not code for RNA Human genome has over 60000 genes and from those 19900 (RNA) are used to make proteins Genes that code for proteins are mRNA forcing different proteins RNA producing genes is the final product Inheritance Acquisition of traits by their transmission from parent to offspring Humans have two copies of each gene (homologous pair), one inherited from each parent except for the mitochondrial genes and sex chromosomes Many genes are identical in all humans but some differ in DNA sequence and function Mendelian Genes Chromosomes Chromosomes are threadlike structures made of protein and one molecule of DNA that carry genetic information from cell to cell  Chromosomes reside in the nucleus (in plants and animals) Humans have 22 pairs of chromosomes (autosomes) and one pair of sex chromosomes (XX or XY), for a total of 46 Sex chromosomes involved in sex determination Humans and most other animals hae=ve two sex chromosomes (X,Y) that determine the sex of an individual Females have XX chromosomes and males have XY Each pair of chromosomes has one chromosomes from each parent meaning that children inherit half of their chromosomes from their mother and half from their father Y chromosomes (little) only transmitted from father to son Alleles Forms of the same gene with differences in their sequence of DNA bases Different version of each trait Contribute to each person’s unique physical features Mendelian Inheritance Diploid Haploid Homozygous Two alleles are identical in diploid there called homozygous for that gene Heterozygous Two alleles are not identical in duploids theres called heterozygous for that gene Evolution Changes in what alleles and the population carries around E.g. being immune to HIV Phenotype An organism's actual observed properties such as morphology, development, or behaviour Genotype Organisms full hereditary information Distinction between geno and phenotype is fundamental in the study of inheritance of traits and their evolution Dominance Dominant phenotype in individual who have one copy of the allele which can come from just one parent Recessive To produce recessive phenotype, the individual must have two copies, one from each parent Medel: Studied genetic traits in peas ○ Flower colour (purple, white) ○ Flower position (arial, terminal) ○ Seed colour (yellow, green) ○ Seed shape (round, wrinkled) ○ Pod colour (green, yellow) ○ Pod shape (smooth, concentrated) ○ Height (tall, dwarf) All categories are controlled by one gene each Parent (P) generation (tall (TT), dwarf (tt) ○ Gamete (T and T), and (t and t) F1 Generation (tall (Tt) Mendel's law of segregation (and dominance) ○ The two alleles of a gene separate (segregate) from each other during the process that gives rise to gametes so every gamete receives only one allele ○ Gametes Specialised sex cells responsible for transmitting genetic information Contain only half of genetic material of a diploid, complete, organism (e.g. haploid) Two alleles of a gene separate (segregate) from each other during the process that gives rise to gametes so every gamete receives only one allele (at random) Segregation Alleles separate into different haploid cells that eventually give rise to gametes Fertilization During fertilization, male and female ○ Single factor crosses A monohybrid cross is one in which both parents are heterozygous (or hybrid) for a single (mono) trait Some Human Traits Determined by Single Genes: Ear lobes ○ Dominant allele results is free earlobes and recessive for attached PTC (phenylthiocarbamide) tasting ○ For 75% of people, PTC tastes bitter and other 25% is tasteless ○ Tasting is dominant meaning you have one tasting copy and non tasters have two copeis of the recessive non tasting allele  Freckles ○ Controlled by the MC1R gene ○ Freckles show a dominant pattern (parents with freckles tend to have kids with freckles) Tongue curing ○ Affected by environmental factors and genes ○ 70% of identical twins share the trait Red/green colourblindness ○ Recessive trait ○ Single gene on the X-chromosome ○ More common in boys (1 in 12) than girls (1 in 250) Mom has one normal and one defective x-chromosome (but normal vision) Dad has one normal x-chromosome and one y-chromosome (normal vision) Daughters have 1 in 2 chance of being carries X (mom) X (dad) non carrier with normal vision X (mom, with color blindness trait) X (dad) carrier with normal vision (not portrayed but in gene) Sons have 1 in 2 chance of being colour blind X (mom) and Y (dad) normal vision X (mom, with color blindness trait), Y (dad) colourblind Pigmented iris ○ Person with B allele has brown eyes (dominant) ○ Recessive allele (b) encodes blue eyes ○ Model works most of the time with the main blue eye gene (OCA2)  ○ Blue or brown describes only a portion of eye colour. There are intermediate variations of green and hazel, as well as albino eyes, which lack pigment entirely-all examples for which the simple Mendelian model does not apply. Geneticist Victor McKusick stated, "The early view that blue is a simple recessive has been repeatedly shown to be wrong by observation of brown-eyed offspring of two blue-eyed parents* ○ We now know that eye colour is actually a complex genetic trait, involving interaction of some major genes and many minor genes. This Mendelian-Complex genetic explanation for eye colour also crosses over into the genetics of many other eye diseases such as age-related macular degeneration and glaucoma. Many people can look at the eye colours in their own families and draw their own pedigrees to see how the Mendelian model applies. Punnett Squares Table in which all possible outcomes for a genetic cross between two individual with know genotypes gives Allows to determine relative properties of genotypes and phenotypes of offspring  T T t Tt Tt t Tt Tt T t T TT Tt t Tt tt Outcome is 3 tall and one short Testcross: Dominant phenotype for tall plant could be TT or Tt and recessive (dwarf) must be tt If plant with dominant phenotype is TT all offspring will be tall If plant with dominant phenotype is Tt half the offspring with be tall and half will be dwarf T T t Tt Tt t Tt Tt T t t Tt tt t Tt tt Two traits of characteristics 2 factor cross Mendel's law of independent assortment Alleles of two or more genes get assorted into gametes independent of each other Every possible combination of alleles for every gene is equally likely to occur Gametes proceed bake the F1 generation YR yr YR YYRR YyRr  yr YyRr yyrr Parent YYRR (YR) and yyrr (yr) F1 generation: YyRr YR YR YR YR yr YyRr Yy Yy Yy Rr Rr Rr yr YyRr Yy Yy Yy Rr Rr Rr yr YyRr Yy Yy Yy Rr Rr Rr yr YyRr Yy Yy Yy Rr Rr Rr For f2: Crossing Two hypotheses Linked assortment makes gametes based on linking (uppercase (dominant) with uppercase and lowercase (recessive) with lowercase always linked together) Independent assortment find all combinations of genotypes from the parents Look at figure 17.8 Pedigree analysis: In a family pedigree, black squares indicate the presence of a trait in a male and white squares are males without the trait. White circles are females. A trait in one generation can be inherited but not outwardly apparent before two more generations (compare black squares). Circles are females Squares are males Dark square or circle has the interested trait  Cystic fibrosis disease ○ Approximately 3% of Americans in european descent are heterozygous carriers of the recessive CFTR allele but do not exhibit symptoms ○ Individuals who are homozygous for this allele exhibit disease symptoms which include abnormalities of the lungs, pancreas, intestines, and sweat glands. Figure 17.14 Sex chromosomes: X-Y in mammals X-O in certain insects Z-W in birds ○ ZZ for males ○ ZW for females Haplodiploid in bees ○ Females 16 haploid ○ Mals 32 diploid Hemophilia Sex-linked XH Y XH XHXH (unaffected female) XHY (Unaffected male) Xh-A XHXh-A (carrier female) Xh-AY (has disease) Looking next at chapter 16: Locus (location) - single and LocI (location)- double Chromosome in the cell is made of a what looks like a ball of yarn made of chromatin Chromatin is combination of protein and DNA To get metaphase chromosome ○ Have chromosomes all over (stands or chromatids) ○ Replicate chromosomes do inside (chromatids) becomes double stranded (double helix)  ○ And do chromosome condensation by being joined by centromere and keep replicated chromosomes (made of chromatin) together by joining them If chromatin is relaxed it is euchromatin and if it is condolences it is heterochromatin (into the distinct shapes)