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Chapter 3 Macromolecules and the origin of life Small molecules containing the hydroxyl group usually dissolve easily

in water Condensation reactions (aka dehydration) o Lose a water o Result in covalently bonded monomers o Polymers form only if energy is added to the system In living systems, energy rich molecules supply this energy Hydrolysis reaction o Water is added to break covalent bonds of a polymer

Protein Energy storage and information storage not done by proteins Contain both carboxyl group and amino group o Because they posses both acid and base, they are amphoteric Amino acids exist in two forms D and L because the alpha carbon is chiral o L-amino acids are common in most organisms o Proline often found at bends or loops in a protein Peptide bonds o Condensation reaction between carboxyl group of one and amino group of another (lose water because it is a condensation reaction) o Goes from N terminus to C terminus o Two characteristics that are important in 3D structure of protein C-N peptide does not rotate due to partial resonance. Inflexibility limits folding of polypeptide chain C=O (partial negative) and N-H (partial positive) charge creates hydrogen bonds Primary structure o Precise sequence of aa determine how protein can twist and fold (determines tertiary structure) o Covalent bonds (peptide bonds) Secondary structure o H-bonding between C=O and N-H o Two types Alpha helix Right hand coil R group extends outward and H bond inward Presence of aa with large R group distorts or prevent formation of helices Very flexible because H bonds break and reform easily Found in keratin (fibrous) stretchy Beta pleated H bonding between N-H and C=O on different polypeptides or can be the same polypeptide but they would be far away from each other o Many proteins contain both alpha helices and beta pleated areas on the same polypeptide Tertiary structure o Outer surface of macromolecule with definite 3D shape can interact with other molecules (if it interacts with protein then makes it a quaternary structure) or other small molecules (acts as an enzyme) o Primarily interactions between R groups H bonding between C=O and N-H responsible for secondary structure o Adding heat energy slowly will break the weaker tertiary bonds. But once you stop the heating, it will go back to its original 3D conformation demonstrating that all information needed to specify shape is in the primary structure Quaternary structure o All sorts of bonds. As Hb binds one oxygen, ionic bonds are broken, exposing buried side chain, that enhances binding of additional oxygen o Subunits Specific shape allows for binding NONCOVALENTLY o Cell junction o Receptor o Membrane o Enzyme o Antibodies Functional groups on surface of protein promote chemical interaction. Property of primary structure Environmental conditions like increase in temperature, change in pH, or high concentration of polar substance (urea) can disrupt nonpolar bonds (but not the covalent bonds)

This loss of proteins normal 3D structure is called denaturationaccompanied by loss of normal biological function of protein, usually irreversible bc aa that were buried in interior of protein might be exposed causing a new structure to form. Example: boiling of an egg.but this is not ALWAYS the case Chaperones o Two occasions where polypeptide binds to wrong ligand. 1. Denaturation. 2. Protein just made not folded completely can present a surface that binds wrong molecule. (Alzheimers disease, misfolded protein accumulate in brain and bind to each other forming fibers in area of brain that control memory, mood, and spatial awareness) o Chaperones prevent inappropriate protein interactions (first discovered in fruit flies as heat shock protein), some work by trapping proteins in a cage. Chaperone is quaternary structure. Protein is locked in this cage and released at appropriate time. o

Carbohydrates General formula for carb is CH2O. In disacc, oligosacc, polysacc, this proportion is different because 2 Hydrogen and oxygen is lost during condensation (glycosidic linkage, also covalent also lose water) (CH2O ONLY APPLICABLE TO MONOSACCHARIDE) Monosaccharides o All living cells contain glucose. Glucose has two forms, straight chain and ring form. (ring form 99% of the time) Two version of ring form (alpha and beta glucose) differ only in orientation of the H and OH attached to carbon 1. Alpha and beta form interconvert and exist in equilibrium when dissolved in water. Alpha D glucose: C1 is OH on the bottom Beta D glucose: C1 OH is on top (fig 3.13) Look at fig 3.15 alpha linkage can be broken down while beta linkage cannot D and L are enantiomers!!!!!! (alpha and beta are conformational isomers) o Hexoses: structural isomers (6 carbons) are glucose, fructose, mannose, galactose. Constitutional isomers. All have C6H12O6 molecular formula o Pentoses: five carbon: ribose deoxyribose are not constitutional isomers important in RNA and DNA distinction Polysaccharide o Starch Alpha linkage. Different starches can be distinguished by number of branches that occur at C1 and C6. Some are unbranched, others are moderately branched, starch readily binds water and when that water is removed (bc it was dried or something), branched starch form H bonds amongst its own polysacc chain which aggregate and harden. (stale bread is due to chains in starch aggregating) Energy storage for plants Branching limits number of H bonds making starch less compact than cellulose o Glycogen Stores glucose in liver and muscles. Serve as energy storage for animals. glucose stored as glycogen because 1000 glucose molec will exert 1000 times more osmotic pressure, causing water to flow into the cell. Glycogen does not. (This is because glucose has a lot of OH that can bind water and bring that in) High amount of branching makes its solid more compact than starch o Cellulose Predominant component of cell wall and most abundant organic compound on earth!!!!! Chemically more stable because of its beta glycosidic linkage; however, this is degradable by chemicals or enzymes Unbranched polymer of glucose. VERY STABLE (starch and glycogen are alpha linkage that can have branching but starch is chemically not as stable as glycogen) MOST compact, no branching Chemically modified carbohydrates with added functional groups o Chitin Adding amino group leads to amino sugar, lead to chitin (amino group replaces OH group) o Peptidoglycan?????????

LIPIDS Insoluble bc of nonpolar covalent bonds Examples include fats, phospholipid, carotenoid (help plant capture light energy), steroids Triglyceride (aka triacylglycerol) o Chemically, fats and oils are in this form, aka simple lipid o Those that are solid at room temp are fats and liquid are oils. o Composed of two types of building block. Glycerol and fatty acid. Glycerol is alcohol with three OH groups. Fatty acid is long nonpolar covalent chain with COOH on it. Triglyceride is three fatty acid with 1 glycerol. Ester linkage o Release water (dehydration condensation) between OH of glycerol and COOH of fatty acid. Carotenoid o Light absorbing pigments found in plants and animals

Beta carotene is one of the pigments that traps light energy in leaves during photosynthesis. This can break into two vitamin A molecules, from which we make pigment rhodopsin, which is required for vision. Carotenoids make colors of carrots, tomatoes, pumpkins, egg yolk, and butter. (eat this for good vision, bc we can make pigment rhodopsin from vitamin A)

Steroids o Cholesterol synthesized in liver and starting material for making testosterone and other steroid hormones, as well as bile salts that help break down dietary fats for digestion. Cholesterol is absorbed from foods such as milk, butter, animal fats. Vitamins o Not synthesized by human body so must be acquired from diet. Vitamins A, D, E, K are also lipids

Nucleic acids Two types of nucleic acids: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) Composed of monomers called nucleotides. Nucleotides: pentose sugar, phosphate group, nitrogen containing base. o Nitrogen containing base is either purine (Adenine, guanine, two rings) or pyrimidine (cytosine, thymine one ring) o Composed of phosphodiester linkages between the sugar of one nucleotide and the phosphate of the next. The phosphate group link carbon 3 in one pentose sugar to carbon 5 in the adjacent sugar o Other important roles ATP acts as energy transducer in many biochemical reactions GTP Serves as an energy source, especially in protein synthesis, transfer of information from environment to cells cAMP transmission of info by hormones ATP is converted to cAMP by taking off two phosphate groups 7 transmembrane G protein, GTP bind to adenylyl cyclase convert ATP to cAMP. cAMP 3 for 1 ATP, leads to signal amplification. cAMP goes on and binds to protein kinase A to phosphorylate protein and carry its function (activation or deactivation of protein)

Questions 1. 2. 3. 4. Most abundant molecule in the cell is a. Water All proteins a. Consist of one or more polypeptide chains Which of following statements about primary structure of a protein is NOT true? a. It may be branched Primary structure of a protein is a. Determined by structure of the corresponding DNA b. Unique to that protein c. Determines the tertiary structure of the protein d. Sequence of aa in the protein

Chapter 4 Cells: working units of life Cell theory o Fundamental units of life o All organisms are made of cells o All cells come from preexisting cells Surface area to volume ratio o Chemical activity, rate of waste production and its need for resources (volume) increases faster than its ability to bring in substances (SA). The smaller the cell, more easily this is accomplished. This explains why large organisms must consist of many small cells. NEED A LARGE SURFACE AREA TO VOLUME RATIO Cell membrane o Maintain constant internal environment or homeostasis o Selectively permeable barrier o Communication with adj cells and environment o Bind and adhere to adjacent cells Prokaryotic cell o Can live in environmental extremes. Generally smaller than eukaryotic cells. o All prokaryotic cell have cell membrane, nucleoid (contain circular stranded DNA), cytoplasm (contain 1. cytosol fluid mostly water that contains dissolved ions, small molecules, and soluble macromolecules like protein//and 2. Ribosome) o Developed specialized structures like cell wall, internal membrane, flagella. (NOT SAYING THAT ONLY PROKARYOTES HAVE THESE STRUCTURES) Most prokaryotes have cell wall located outside the plasma membrane. The cell walls of most bacteria (BUT NOT ARCHAEA) contain Peptidoglycan, (archaea does not have Peptidoglycan in its cell wall) polymer of amino sugars, cross linked by covalent bonds around the entire molecule. Plant and fungi also have cell wall but made of cellulose and chitin, respectively. Penicillin prevent cross linking of peptidoglycan, causing cell wall to weaken and lyse. Some cells have another layer called outer membrane (polysacc rich phospholipid membrane) enclosing peptidoglycan layer. This is not a major permeability barrier unlike plasma membrane. Some have another layer called capsule. Capsule may protect from attack by WBC, help prevent drying out, help attach to other cells. Lysoszyme which is found in tears and saliva destroys Peptidoglycan in bacterial cell wall!! Internal membrane is folded and contains compounds responsible for carrying out photosynthesis (cyanobacteria). Flagella used for motility. Pili used for exchanging genetic info Cytoskeleton to maintain shape. Filamentous structure just inside plasma membrane. Similar in aa sequence to actin in eukaryotic cells. (similar to microfilament) DO NOT HAVE MICROTUBULES Eukaryotic cell o Organelle: membranous compartment as well as other structures (ribosomes) that lack membranes but possess distinctive shape and function are all considered an organelle. o Nucleus Largest organelle in the cell. (the nucleus itself is substantially larger than most prokaryotic cells) Roles include DNA replication, genetic control of cells activities, in the nucleolus begin assembly of ribosomes from RNA and specific proteins Surrounded by two membranes, 3500 nuclear pores (small molecules can enter but larger ones cannot)(larger molecules that are made in cytoplasm and imported into nucleus have a short sequence of aa that is part of the protein called nuclear localization signal. This sequence bind noncovalently to one of proteins in pore that acts as a receptor, binding it changes conformation and lets the protein in) In the nucleus, DNA combine with proteins to form fibrous complex called chromatin. Chromatin consists of exceedingly long, thin threads. Prior to cell division, chromatin aggregates to form discrete visible structures called chromosomes. Nuclear matrix organizes chromatin. Chromatin attached to a protein meshwork called nuclear lamina which is formed by polymerization of proteins called lamins into intermediate filaments. Nuclear lamina maintains the shape of the nucleus by its attachment to both chromatin and nuclear envelope. o Ribosomes In prokaryotes found freely floating ///// eukaryotes found in cytoplasm, RER, mitochondria, or chloroplast. Site where proteins are synthesized under direction of nucleic acids. Consist of a special type of RNA called rRNA to which 50 diff protein are bound noncovalently o RER Segregates certain newly synthesized proteins away from cytoplasm and transport them to other locations in the cell. While inside the RER, proteins can be chemically modified so as to alter their function and eventual destination.

The attached ribosomes are sites for synthesis of proteins that function outside the cytosol (protein that are to be exported from the cell, incorporated into membranes, or moved into the organelles of the endomembrane system (GOLGI)) these proteins enter the lumen of the RER as they are synthesized. RER localization sequence into lumen. In the lumen, proteins undergo several changes, including formation of disulfide bridges and folding them into tertiary structure. Some proteins gain carbohydrate in RER and become glycoproteins. More tubular and less flattened. No ribosomes. Within lumen of SER, some proteins that have been synthesized on the RER are chemically modified. Three other roles. Responsible for chemically modifying small molecules taken in by the cell, especially drugs and pesticides. Site for hydrolysis of glycogen in animal cells. Site for synthesis of lipids and steroids. Lipid synthesized (phospholipid goes to plasma membrane to)

SER

Glandular cells that secrete a lot of things have a lot of ER. WBC which secretes antibodies has a lot of ER. Liver cells that break down glycogen have a lot of SER. o Golgi apparatus Consist of flattened membranous sacs called cisternae. Roles: receives proteins from ER and may further modify them, concentrates packages and sorts proteins before they are sent to their cellular or extracellular destination, where some polysacc for plant cell wall are synthesized. In plants, protist, fungi, invert, stacks of cisternae are individual units and scattered about. Vert cells have a large single more complex golgi. Lysosomes Originating from golgi apparatus Contain digestive enzymes and are sites where macromolecules like protein, polysacc, nucleic acids, lipids are hydrolyzed into their monomers. (aa, monosaccharide, nucleotide, triglyceride) Food extracellular get in by phagoctyosis of the CELL, not the lysosome yet. Small vesicle is in the cytoplasm as a phagosome that is containing food or other material. Phagosome fuses with a primary lysosome, forming a secondary lysosome, in which digestion occurs. Reaction enhanced by acidity of lysosomes interior, where pH is lower than surrounding cytoplasm. Products of lysosome diffuse through membrane of lysosome, providing raw materials for other cell processes. The secondary lysosome then gets exocytosed and released the undigested particles extracellular. Can digest its OWN material called autophagy. Autophagy is an ongoing process in which organelles such as mitochondria are engulfed by lysosomes and hydrolyzed into monomers, which pass out of the lysosome through its membrane into the cytoplasm for reuse. Plant cells do not have lysosomes, but central vacuole of a plant cell may function in equivalent capacity, because it contains many digestive enzymes. Mitochondria Space enclosed by inner membrane is called mitochondrial matrix. Contains ribosomes and DNA that are used to make some of the proteins needed for cell respiration. Plastids (chloroplast) Contain chlorophyll and are sites of photosynthesis. A bunch of thylakoid make a grana. Membranes of thylakoid contain chlorophyll and other pigments that harvest light for photosynthesis. Fluid in which grana is suspended is called stroma. Like mitochondrial matrix, it contains ribosomes and DNA, which are used to synthesize some of the proteins that make up chloroplast. Chromoplast Give color in flowers. No known chemical function. Attraction of animals for seed dispersal. Leucoplasts are storage depots for starches and fats Peroxisomes Organelles that collect toxic peroxides (such as hydrogen peroxide) which are BYPRODUCTS of cellular reactions. These peroxides get safely broken down inside peroxisomes. Glyoxysome Found only in plants Sites where stored lipids are converted into carbohydrates for transport to growing cells

Many eukaryotic cells, but particularly those of plants and protists contain membrane-enclosed vacuoles filled with aq solution containing many dissolved substances. Plant vacuole Storage: plant cells produce a number of toxic by products and waste products, many of which are simply stored within vacuoles. Since they are poisonous, these stored materials deter some animals from eating the plants, contributing to plant survival. Structure: turgor pressure

Reproduction Digestion: developing plant embryo can use as food. Cytoskeleton o Eukaryotic cytoplasm contains a set of long thin fibers called cytoskeleton. o Microfilament Help entire cell or parts of cell to move. Determine and stabilize cell shape. Assembled from actin. Extensively folded and has plus and minus ends. These ends interact with other actin monomers to form long, double helical chains. Reversible (can break down to monomer or reform) In muscle cells: actin associated with myosin for muscle contraction Non muscle cells, actin associated with localized changes of shape in the cell. Flowing movement of cytoplasm and pinching contraction that divide animal cell into two. Involved in pseudopodia Microvilli in intestine o Intermediate filament Stabilize cell structure Resist tension Lamins of nuclear lamina are intermediate filaments. Stabilize and help maintain rigidity in body surface by connecting desmosomes. Hold neighboring cells together. o Microtubule Rigid internal skeleton for some cells or act as framework along which motor proteins can move structures within the cell Assembled from molecules of the protein tubulin. Tubulin is a dimer, molecule made up of two monomers. Alpha tubulin and beta tubulin. Two ends are different. One end is plus and other is minus. Tubulin dimmers added or subtracted at the plus end. Lengthening or shortening microtubule. Radiate from MTOC Serve as tracks for motor proteins. Motor proteins bond to and move along microtubules, carrying materials from one part of cell to another. Essential in distributing chromosomes to daughter cells during cell division. Associated with cilia and flagella movement. Cilia and flagella o Both cilia and flagella have 9+2 arrangement. Both have basal body. Basal body is 9 sets of three microtubules. Central unfused microtubule pair in cilium or flagella do not extend into basal body. (The 2 in 9+2) o Centrioles Found in MTOC, almost identical to basal bodies. 9 sets of 3 microtubules each. Involved in formation of mitotic spindle to which chromosomes attach. Motor protein o Doublets result from sliding of microtubule doublets past each other. Sliding is driven by motor protein called dynein, ATP needed o Another motor protein called kinesin, carries protein loaded vesicles from one part of cell to another o Dynein moves toward minus end, kinesin move towards plus end. Extracellular matrix o Plants Cell wall Semi rigid, provides support, principal chemical component is polysaccharides. Plasmodesmata plasma membrane lined channels permit diffusion of water, ions, small molecules, and RNA and proteins between connected cells. Plant cells are NOT entirely isolated from one another. Although it might look like it because of thick cell wall. Plasmodesmata join adjacent cells together. o Animals Animal cell ECM is made of collagen, proteoglycan, and fibrous proteins that link these two together. Secreted by cells that are near the matrix. fibrous proteins called collagen. (most abundant protein in mammals 25% of protein in human body) Matrix of glycoprotein called proteoglycans consisting primarily of sugars Contribute to physical properties of cartilage, skin, and other tissue. Helps filter materials passing between different tissues. Helps orient cell movement during embryonic development. Plays a role in chemical signaling from one cell to another. Bone and cartilage have large amounts of ECM. Epithelial cells sit on basal lamina.

Peptidoglycan cell wall in prokaryotes other than archaea. Cellulose cell wall in plant cells. Proteoglycan ECM of animal cells.

Chapter 5 Cell membrane Lipids make bulk of membrane Up to 25% of lipid content of membrane may be cholesterol. Cholesterol is important to membrane integrity, and most cholesterol in membranes is not hazardous to health. Cholesterol is commonly situated next to unsaturated fatty acid. Membrane integrity meaning fluidity! In general, shorter chain fatty acid, unsaturated fatty acid, and less cholesterol lead to more fluid membranes.

Membrane proteins are asymmetrically distributed Protein and membrane are independent of each other and react noncovalently. o Integral membrane proteins They have hydrophobic domains and penetrate phospholipid bilayer. Many of these proteins have long hydrophobic alpha helical regions that span the core of the bilayer. Their hydrophilic ends protrude into aq env on either side of membrane. o Peripheral membrane proteins Lack hydrophobic domains and are not embedded in bilayer. They have polar or charged regions that interact with exposed parts of integral membrane proteins or with polar heads of phospholipid molecules. o Transmembrane protein: show diff faces on two membrane surfaces o Peripheral membrane proteins are localized on one side of membrane or other, but not both. This gives two surfaces of membrane diff properties. o How to restrict protein movement Cytoskeleton may have components just below the inner face of membrane that attach to membrane proteins or lipid rafts in semisolid state may trap proteins within a region. (they may have very long fatty acid chains) Their position in membrane is determined by their tertiary structure

MEMBRANES ARE DYNAMIC In eukaryotes, phospholipids are synthesized from SER and rapidly distributed to membranes throughout Membrane proteins inserted from RER Functioning membranes from RER to golgi to fuse with plasma membrane Balanced by removal of membrane in phagoctyosis with fusion of vesicles Membranes of cis face resemble ER in chemical composition but trans face is similar to membrane. As vesicle is formed, mix of proteins and lipids is selected and modified to correspond with target membrane Fluid mosaic apply to both plasma membrane and inner membrane

Membrane carbohydrates are recognition sites Carbohydrate on extracellular are used for recognition sites for other cells and molecules Carbohydrates are added to proteins in the golgi apparatus These are covalently bonded to lipids or to proteins (carbs can bind with a protein OR a lipid) o Glycolipid Carbohydrate covalently bonded to lipid. Carbohydrate of some glycolipid change when cell becomes cancerous. This change may allow WBC to target cancer cells for destruction!!!! o Glycoprotein Carbohydrate covalently bonded to protein. Oligosaccharide chains enable a cell to be recognized by other cells and proteins (hormone binding)

How is the plasma membrane involved in cell adhesion and recognition? Two processes allow cell to arrange themselves in groups: o Cell recognition: one cell specifically binds to another cell of a certain type o Cell adhesion: connection between two cells is strengthened Both processes involve plasma membrane. Easily studied in cells in a tissue are separated, and they adhere to one another again o Example is a sponge which is multicellular and if you put it through a fine wire, they adhere again. They ONLY adhere to its own cell recognizable. Wont bind to other cells from different species of sponges. Glycoprotein is responsible for cell-cell recognition and binding. Homotypic binding: same molecule sticks out of both cells and exposed surface bind to each other most common. Heterotypic binding (binding of diff proteins). Sperm meeting egg binding. Tight junction

Prevent substances go through between epithelial cells (epithelial cells are found on body surfaces or line body cavities). They define different functional regions apical from basolateral and proteins cannot migrate beyond TJ Desmosome o Connect adjacent plasma membranes together. Protein keratin strong fibers provide mechanical stability to epithelial tissues Gap junction o Communication between cells. Made up of specialized channel proteins called connexons that span plasma membranes of two adj cells and the intercell space between them

Diffusion How fast a substance diffuses depends on 4 factors o Diameter of molecule or ion (smaller ions diffuse faster rate of effusion) o Temperature o Electric charge o Concentration gradient Molecules on one side of membrane diffuse across plasma membrane until both sides have equal concentration of molecule. This is termed equilibrium. This does not mean however that molecules are not moving, the rate of them moving in is now equal to rate of them moving out! Increasing concentration gradient is a linear graph unlike carrier proteins which show a logarithmic graph due to saturation!!! Simple diffusion does not have to worry about this because it does not go through a protein The more lipid soluble the molecule, the faster the diffusion rate

Osmosis -

When we say that water moves, this is NET movement of water. Water is still moving in both directions. Turgor pressure: pressure within cell due to water leads to keeping plants upright Obey law of diffusion

Carrier proteins Allow diffusion both into and out of cell, they transport polar molecules like sugar and aa. This is NOT the opening of a channel like voltage or ligand gated channels, but the actually BINDING of transported substance to membrane protein. Glucose transporter: facilitates glucose uptake to the cell. Glucose is broken down instantly in the cell so glucose is always in demand. Enter cell much faster than simple diffusion. Carrier protein is diff from simple diffusion, rate of movement is a logarithmic graph to increase in concentration. Simple diffusion, higher the concentration faster the movement. But carrier proteins are diff because these limited number of proteins can get saturated and increasing the concentration wont affect the rate of transport.

How do substances cross membrane against concentration gradient? Symport and antiport are coupled transporters bc they move two substances at once. There are two types of active transport: primary active transport and secondary active transport. In secondary active transport, its energy is supplied by an ion concentration gradient established by primary active transport. Na/K pump which is a primary active antiport creates a gradient. Na then flow through passive diffusion and this provides energy for secondary active transport of something like glucose into cell against its concentration gradient.

How large macromolecules like protein, polysacc, nucleic acid enter or leave cell Endocytosis o Three types of endocytosis. Phagoctyosis, pinocytosis, and receptor mediated endocytosis Phagoctyosis Cell eating by WBC Pinocytosis Cell drinking, nonspecific bring small dissolved substances. Endothelium Receptor mediated endocytosis Method by which cholesterol is taken up in the liver. Binds to specific molecules in cells environment

Chapter 6 Energy, enzymes, and metabolism Two properties of ATP include ability to release large amount of energy when hydrolyzed and phosphorylate proteins to change its function. ATP is also a nucleotide that can be converted into a building block for nucleic acids! o Consist of adenine bonded to ribose, which is attached to three phosphate groups o Hydrolysis of ATP is about -7.3 kcal/mol (delta G) o Reverse reaction consumes as much free energy as is released by hydrolysis of ATP o ATP is consumed within a second of its formation on average Transition state species o Activation energy is energy needed to change the reactants into unstable molecular form called TS species. They have higher free energies, their bonds might be stretched and unstable. How do enzymes work? o Enzymes orient substrate. If acetyl CoA and oxaloacetate are to form citrate, they must be positioned which is done by enzyme o Induce strain on substrate Lysozymes active site stretches the bonds of bacterial polysaccharide, making it unstable o Temporarily add chemical groups to substrate R group of enzyme react in acid/base catalysis (transfer H to or from substrate, destabilizing covalent bond and permit breakage). Covalent catalysis. Metal ion catalysis. Enzyme can be single polypeptide chain folded or quaternary structure. Other molecules that help enzymes o Prosthetic group (heme, flavin, retinal, TPP) Non amino acid atoms or molecular groupings that are permanently bound to their enzyme (P for prosthetic, P for permanent) TPP is responsible for oxidative decarboxylation (oxidative decarboxylation= pyruvate gets oxidized into acetyl-CoA, NADH; and loses a carbon as CO2) hemoglobin o Cofactors (iron copper zinc) Inorganic ions that bind to certain enzymes (cofactory is a factory that makes iron copper and zinc!!!!) o Coenzymes (NAD, FAD, ATP, biotin, coenzyme A) carbon containing molecules required for action of one or more enzymes, bind temporarily (coenzyme, baby enzyme that are small. Enzyme is made of carbon just like ATP, FAD, NAD!!!!!) ATP and ADP are considered coenzymes bc they are necessary for some reactions, are changed by those reactions, and bind to and detach from enzymes that catalyze those reactions Some coenzymes produced from vitamins (vit B NAD) Enzyme inhibitors o Irreversible inhibition Covalently bond to active site o Reversible inhibition Similar looking to substrate binds noncovalently Competitive inhibitor Noncompetitive inhibitor o Catalytic subunit: active site is present on one such subunit bc many enzymes that are allosterically regulated are proteins with quaternary structure meaning many subunits! o Allostery: the change in enzyme shape due to noncompetitive inhibitor Two possible shapes. Active form and inactive form. In inactive form, it cannot bind to substrate but an inhibitor can bind on a different site so as to make sure it stays inactive. Nonallosteric enzyme has a logarithmic graph (x axis increase in concentration y axis reaction rate) Allosteric enzyme has sigmoid graph First step is commitment step Feedback inhibition (if end product is at high concentration some of it binds to an allosteric site on the commitment step enzyme inactivating it; it is exerted through allosteric effects; it is directed at the enzyme that catalyzes the first committed step in a metabolic pathway, it affects the rate of reaction not the concentration of enzyme; it is example of irreversible inhibition) Enzymes are pH and temperature sensitive o Certain enzymes are activated at certain pH. Pepsin is near acidic, salivary amylase is near basic pH o Temperature thats too high can inactivate enzyme. Enzyme denature and lose function. Noncovalent bonds broken. o Isozymes: adapt to changes in env are a group of enzymes that catalyze the same reaction but have different chemical compositions and physical properties. Some operate at many different temp so if rainbow trout is transferred from warm water to near freezing water, an isozyme is produced that allows continued function.

Chapter 7 ATP made can be used to drive endergonic reactions (reaction that requires heat/energy for a reaction to proceed) Glycolysis (does not require oxygen) goes from glucose pyruvate. Pyruvate can now enter two pathways. If there is oxygen, go through aerobic pathway (pyruvate oxidation, KREB cycle, oxidative phosphorylation (ETC, chemiosmosis) or a anaerobic pathway (fermentation to make lactic acid or ethanol) o Fermentation does not involve oxygen and convert pyruvate into lactic acid or ethanol, breakdown of glucose is incomplete so much less energy is produced In redox reaction, gaining of Hydrogen (hydronium and electron) is reduction and losing hydrogen is oxidation o In metabolism, glucose gets oxidized (lose hydrogen) and O2 gets reduced (gains hydrogen to become H20) Coenzymes o ADP acts as coenzyme when it picks up energy released in exergonic reaction and uses it to form ATP o NAD acts as electron carrier NADH getting oxidized and reducing O2 leads to TREMENDOUS amt of release of energy ATP: 50 kJ/mol NAD: 200 kJ/mol Glycolysis o Convert glucose into pyruvate o No CO2 released o End product: 2 molecules of pyruvate 2 ATP 2 NADH o Pathway Step 1-5 are endergonic (cell is investing free energy) 2 G3P endproduct Step 6 Oxidation reaction Large drop in free energy, this energy lost is stored as chemical energy by reducing two molecules of NAD+ to make two NADH + H+ (NAD+ is limited so it needs to be recycled, if not, glycolytic pathway will end) Step 7-10 Producing ATP by substrate-level phosphorylation (adding phosphate group to ADP) this process is distinguished from oxidative phosphorylation carried out by ETC o (Kinase: any enzyme that catalyzes the transfer of phosphate from ATP to another substrate) Hexokinase and phosphofructokinase (PFK) both phosphorylate glucose from ATP meaning both require ATP PFK Alloesterically inhibited by ATP (negative feedback pathway) Pyruvate oxidation o Pyruvate acetyl CoA o CO2 released KREB cycle (Citric acid cycle) o NADH o FADH2 o ATP o CO2 Fermentation o Uses NADH and reduces pyruvatelactic acid. NAD+ recycled so glycolysis can occur again o This process is all in cytoplasm o Prokaryotes: lactic acid ethanol. Happens in certain yeasts and plant cells. Alcoholic beverage made by anaerobic fermentation of yeast cells using glucose from plant sources like grape or barley Oxidative phosphorylation o ETC o Chemiosmosis: protons diffuse back into mitochondrial matrix through proton channel which couples this diffusion to synthesis of ATP o produce a lot of ATP there is a toll for NADH which needs to pay 1 ATP each to enter inner mitochondrial matrix. NADH enters the inner mitochondrial matrix Metabolic pathway control (degradative pathway) o Catabolic interconversion Polysaccharide: get broken down to glucose to start glycolysis Lipid: broken down to glycerol and fatty acid Glycerol is intermediate in glycolysis Fatty acid gets converted to acetyl CoA (Question I got wrong!) Protein

Intermediate in citric acid cycle and glycolysis Anabolic interconversion Many catabolic pathways can operate in reverse. Glycolytic and CAC intermediates can be reduced and used to make glucose (GLUCONEOGENESIS), acetyl CoA can be used to form fatty acids. Etc.

Questions 1. Pyruvate.. a. It is end product of glycolysis b. It becomes reduced during fermentation i. If pyruvate does not get oxidized to start citric acid cycle, it gets reduced and takes Hydrogen from NADH that was produced. This creates NAD+ which can be used to start glycolysis again IN THE ABSENCE OF O2. c. It is a precursor of acetyl CoA d. It is NOT a protein e. It contains three carbon atoms Which statement about oxidative phosphorylation is true? a. It forms ATP by ETC b. It is brought about my chemiosmosis c. It requires aerobic conditions d. It takes place in mitochondria e. Its functions cannot be served equally well by fermentation

2.

Chapter 8 Photosynthesis Water in plants come from soil up the root to the leaves, exchange of carbon dioxide and oxygen are from stomata. Light is absolutely necessary for production of oxygen and sugar. Oxygen comes from breakdown of water NOT CO2 Light behaves as particle and a wave o Shorter wavelength means greater energy according to E=hv. Photosynthesis involves two pathways o Light dependent Light energy to chemical energy Produce ATP and NADPH + H+ o Light indendent Use ATP and NADPH that reduces CO2 into glucose Although it is called dark reaction, both light dep and light indep stop in dark bc ATP synthesis and NADP+ reduction require light. The difference in free energy between molecules excited state and ground state is approximately equal to free energy of absorbed photon. Makes molecule more reactive since increase in energy boost electron less firmly to a further orbital. If pigment absorbs red and blue, it reflects off green which is what we see in plants Chlorophyll a o Absorb red and blue. Center is a magnesium ion. There is also a long hydrocarbon tail which anchors chlorophyll to integral proteins in thylakoid membrane of chloroplast Accessory pigments o If only chlorophyll were active in photosynthesis, much of visible spectrum would go unused. However, all photosynthetic organism possess accessory pigments which absorb photons intermediate in energy between red and blue and transfer a portion of that energy to chlorophylls. Some include carotenoids, phycobilins Excitation energy moves from pigments that absorb higher energy (short wavelength) to pigments that absorb lower energy (long wavelength). Thus the excitation ends up in one pigment molecule in antenna system that absorbs the longest wavelength: this molecule is in the reaction center of the antennae system!!! Reaction center o Here that converts absorbed light energy into chemical energy. o Always chlorophyll a. Absorb lowest energy. Electron transport o Similar to electron transport in aerobic respiration. Final electron acceptor is NADP+ which gets reduced to NADPH. NADPH is a stable reduced coenzyme. (Whereas NAD+ participates in catabolism (breakdown of glucose), NADP+ is used in anabolic reactions, such as carbohydrate synthesis from CO2, that require energy from reducing power) Cyclic vs noncyclic o Noncyclic ET use PS I and PS II Produce ATP, NADPH, and O2 ATP comes from ETC, NADPH comes from final electron acceptor for NADP+, and O2 comes from breaking of H20 to replace the lost electron from PSII. Photosystem II Light energy to oxidize water, produce e-, H+, and oxygen P680 (lower wavelength more energy) Photosytstem I Light energy to reduce NADP+ to NADPH P700 (higher wavelength less energy. Energy lost as heat or fluorescence) Ferredoxin (Fd) o In PSI, reaction center containing P700 becomes excited which leads to reduction of an oxidizing agent called ferredoxin and the production of P700+. o Cyclic ET use PS I ONLY Produce only ATP Electron passed from an excited chlorophyll molecule at the outset cycles back to same chlorophyll molecule at end of chain of reactions Noncyclic o Protons get pumped into thylakoid interior. Thylakoid interior is more acidic than stroma.

REVIEW CALVIN BENSON CYCLE

Questions

1.

Which statement about chlorophylls is true? a. Chlorophyll absorb light near both ends of visible spectrum b. Chlorophyll can accept energy from other accessory pigments like carotenoids c. Chlorophyll contain Mg d. Excited chlorophyll can either reduce another substance or fluoresce