Advanced Cell Bio Chapter 2 Notes
Advanced Cell Bio Chapter 2 Notes BCMB 311
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This 6 page Class Notes was uploaded by Izabella Nill Gomez on Saturday February 6, 2016. The Class Notes belongs to BCMB 311 at University of Tennessee - Knoxville taught by Dr. Barry Bruce, Dr. J. Park in Spring 2016. Since its upload, it has received 14 views.
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Date Created: 02/06/16
Advanced Cell Bio Chapter 2 Notes! Chemistry of life is based on carbon compounds (organic chemistry); depends on chemical reactions that take place in aqueous solutions and in the narrow temperature ranges on Earth. Enormously complex, dominated and coordinated by polymeric molecules, chains of chemical subunits linked end-to-end whose unique properties enable cells/organisms to grow and reproduce and do all things characteristic of life. Tightly regulated by cell mechanisms. -Matter is made of combinations of elements that cannot be broken down or interconverted by chemical means. The smallest particle of an element that still retains distinctive chemical properties is an atom. Characteristics of substances other than pure elements including materials from living cells depend on which atoms they contain and the way they are linked to form molecules. An atom has a center of positively charged nucleus, surrounded by negatively charged electrons held by electrostatic attraction. Subatomic particles are protons and neutrons. The number of protons determines the atomic number (hydrogen is the lightest element). The electric charge of the proton is equal and opposite to the charge of the electron. Atomic number dictates the chemical behavior. Neutrons contribute to structural stability of nucleus--if too many/few, the atom can disintegrate by radioactive decay--does not alter the chemical properties. Isotopes are physically distinguishable but chemically identical forms of elements (different number of neutrons). Can occur naturally. Atomic weight of an atom or molecular weight of a molecule is mass relative to a 23 Hydrogen atom. Equal to P+N--specified in daltons. Avogadro’s number ( 6∗10 ) atoms allows to relate the quantity of chemicals to numbers of atoms/molecules. If a substance has a molecular weight of M, M grams of the substance contain 23 6∗10 molecules (mole). Organisms are made of only a small selection of elements (C,H,N,O)--constitute 96% of an organism’s weight. Composition is very different from inorganic environments. -In living tissues, electrons are the only parts of atoms that undergo rearrangements. Laws of movement dictate electrons can exist in certain orbits, 2 per energy level (electron shell). Electrons closest to the nucleus are held more tightly--innermost can hold only 2 electrons, 2 ndcan hold eight, 3 can hold eight, 4/5 --18. Electrons are most stable when electrons occupy innermost shells first. An outermost field shell makes the atom stable--chemically unreactive. -Atoms with incomplete outer shells have a strong tendency to react with other atoms. Ionic bonds are formed when electrons are donated by an atom and gained by another, covalent bond formed when 2 atoms share a pair of electrons. H atoms commonly form bonds with C,N,O,P and S. The number of electrons an atom must acquire or lose to fill an outer shell determines the number of bonds. H 2 Molecule: cluster of atoms held by covalent bonds ( ). The shared electrons form a cloud of negative charge that is densest between 2 positively charged nuclei. Attractive and repulsive forces are in balance when nuclei are separated by a distance of bond length. When an atom forms covalent bonds with others, multiple bonds have definite orientations of the shared electrons. Bond angles then form, as well as lengths and energies. Double bonds are shorter and stronger than single bonds and have an effect on 3D geometry--less flexible. Covalent bonds in which electrons are shared unequally are polar covalent bonds. Polar structure is one in which the positive charge is concentrated toward the end of the molecule (positive pole) and the negative charge to the negative pole. O and N atoms attract electrons strongly, H not so much. Bond strength is measured by the amount of energy that must be supplied to break the bond, measured in kcal/mole or kJ/mole. Kcal is the amount of energy to raise the temperature of 1 L of H2O by 1 degree Celsius. **1 kcal= 4.2 kJ. The typical covalent bonds are resistant to being pulled apart by thermal energies/motions, and are broken during specific chemical reactions controlled by enzymes. When water is present, covalent bonds are much stronger than ionic. When an electron (in ionic bonds) jumps from ex: Na to Cl, both atoms become electrically charged ions (Na loses, Cl gains). Because of opposite charges, Na and Cl attract each other and form an ionic bond (called salts)--highly soluble in H2O (polar). Cations=+, anions= --. Associations of transient interactions between molecules are mediated by noncovalent bonds, normally weak, but energies can sum to create an effective force between 2 molecules. Ionic bonds in NaCl are a form of noncovalent bond--electrostatic attraction. Strongest when atoms are fully charged---weaker ones are polar covalent bonds (allow the molecule to interact through electric forces). Any large molecules with polar groups have a pattern of +/- charges on the surface, accompanied by complimentary set of charges, matches with a second molecule. H2O has 2 H-O bonds, with unequal distribution of electrons, with preponderance of + charge on the 2 H atoms and - charge on the O. When + region of H atom comes close to a separate O, electrical attraction can cause a weak hydrogen bond. Much weaker than covalent bond and easily broken by thermal motion--but the combined effect of weak bonds allows water to be liquid at room temperature (constantly breaking and reforming)--without h bonds, life as we know it cannot exist. H bonds can occur in other instances (such as with a large molecule) and help fold into a particular shape. Hydrophilic molecules can dissolve readily in water due to polar bonds (includes sugars, RNA, DNA and many proteins). Hydrophobic molecules are uncharged and form few/no H bonds; do not dissolve in H2O. Hydrocarbons are important hydrophobic cell constituents. H atoms covalently linked to C atoms by nonpolar bonds. Because of no + charge, can’t form good H bonds--helps create lipid molecules for cell membranes. -When a molecule in a highly polar covalent bond dissolves with H, the electron is given up as a proton (H+) is released. The proton is attracted to partial negative charge on the O2 atom of an adjacent H2O molecule; the H+ can dissociate from the original and associate with H2O to form an H3O+ hydronium ion--the reverse reaction takes place readily--back and forth occurs often to find an equilibrium state. Substances that release protons when dissolving in water to form H3O+ are acids. The higher the concentration of H3O+, the more acidic the solution. Concentration of H+ is the pH scale. Strong acids lose protons easily to water--weak ones give up less easily. Sensitivity to changes in pH affect cell function. Acids tend to give up H+ more readily if the concentration is low and accept if high. The opposite of an acid is a base, which includes any molecule that accepts a proton when dissolved in water. Bases raise the concentration of hydroxyl ions (OH-) by removing a proton from a water molecule (becoming alkaline/basic--NaOH is a strong base because it dissociates into Na+ and OH- easily). Weak bases have a weak tendency to accept protons--more important in cells--like NH2 by generating OH-. Increase in OH- concentration decreases H+. Buffers are mixtures of weak acids/bases that adjust proton concentrations to pH 7 and keep the cell neutral. Carbon is outstanding among all elements to form large molecules. An a tom is small and has 4 electrons and 4 vacancies in the outer shell; can form 4 bonds. Can form stable covalent C-C bond for chains and rings and create long/complex molecules. Carbon compounds made by cells are organic molecules. Other molecules, even H2O, are inorganic. Methyl (CH3), Hydroxyl (OH), Carboxyl (COOH), 2−¿ Carbonyl (CO), phosphoryl ( PO ¿ ), amino (NH2) groups occur repeatedly in 3 organic molecules. Each chemical group has distinct chemical and physical properties that influence the behavior of the molecule in which the group occurs, including if it tends to gain/lose electrons and which molecules interact. Small organic molecules of the cell are Carbon compounds with weights between 100-1000 that can have 30 or 50 C atoms. Usually found free in the cytosol and have different roles--some as monomers to construct macromolecules--proteins, nucleic acids, large polysaccharides. Others as energy or potential subunits. Small th organic molecules are less abundant than macromolecules (1/10 ). 4 major families of small organic molecules: sugars, fatty acids, amino acids and nucleotides-- ¿ account for a large fraction of the cell’s mass. Sugars: monosaccharides (CH2O n --n=3, 4, 5, or 6. Larger molecules of sugars (carbs)--depending on the orientation of -OH groups, sugars can be converted into others and have 2 forms, D and L forms, mirror images of each other. Sets of molecules with the same chemical formula but different shape are isomers, and mirror images are optical isomers. Monosaccharides can be linked by covalent bonds (glycosidic) to form larger carbs. 2 monosaccharides make di, 3 tri, so forth. Larger sugars are oligosaccharides (2-10 subunits), and polysaccharides (100eds of subunits). The bond between an -OH on one sugar and -OH on another by condensation reaction, in which molecules of H2O are expelled. Other subunits use the same form--can be broken by hydrolysis, in which one H2O is consumed. Sugar polysaccharides can be branched and large-- arrangement is difficult to know. Glucose has a central role as an energy source for the cell; broken down to smaller molecules by reactions--can be stored as glycogen/starch. Also used for mechanical supports--ex: cellulose (plants), chitin (fungi, insects). Simple oligosaccharides can be linked to proteins to form glycoproteins and lipids for glycolipids (for membranes). Protect cell’s surface and help cells stick to one another. Different in types of cell surfaces: sugars are for blood groups. A fatty acid has a long hydrocarbon chain (hydrophobic) and hydrophilic head. Almost all fatty acids in a cell are covalently linked by carboxylic heads-- amphipathic. -Hydrocarbon tail of palmitic acid is saturated: no 2x bonds between C bonds and a max number of H. Some other like olcic acid have unsaturated tails. With 1 or more 2x bonds along length, creating kinks that inhibit the ability to pack together-- different between head (unsaturated) and soft (saturated) margarine. Many different fatty acids in cells differ only by cell length--serve as concentrated food reserve and can be broken down to use 6x as much energy as glucose. Stored in cytoplasm as fat triglycerol molecules---3 fatty acids joined. Can be broken down into 2 C subunits--identical to glucose. Lipids constitute fatty acids, insoluble in water but soluble in fats/organic solvents (ex: benzene). Can have multiple linked aromatic rings (steroids). Can form lipid bilayer, basis for cell membranes-- composed mostly of phospholipids--glycerol joined to 2 fatty acids, not 3. Leftover -OH links to hydrophilic phosphate group, then is attached to small hydrophilic compounds like choline. Strongly amphipathic. Membranes also have other lipids, such as glycolipids (sugar instead of phosphate). Form a monolayer, phobic tails in air and philic heads in water. 2 layers make a bilayer. Amino acids are small organic molecules that possess a carboxylic acid and amino group both linked to an alpha- Carbon atom. Also has a side chain to alpha-C. Cells use amino acids to make proteins--polymers made of amino acids, joined head to tail in a long chain that folds in a unique 3D shape. Covalent bond between 2 amino acids is a peptide bond; chain is a polypeptide. Always NH2 (N-terminus) and COOH (C terminus) at either end of the chain. Has structural polarity/directionality. 20 types of amino acids--can exist as optimal isomers in D and L forms (only found in proteins). 5/20 can have side chains to form ions and carry a charge (others are uncharged). Amino acids can be polar/nonpolar--philic/phobic. DNA/RNA built from nucleotides. Nucleosides are made of N-ring compound linked to 5-C sugar (ribose/deoxyribose). Nucleotides have nucleoside with 1 or more P groups to sugar--2 forms--rib/deoxyribonucleotides. The N-rings are bases; can bond H proton in acidic conditions to increase OH concentration (C,T,U,G,A). Nucleotides can act as short term carriers of energy--ATP (ribonucleotide) participates in the transfer of energy, 3 P’s linked in series by 2 phosphoanhydride bonds--breaking releases energy. Terminal P is frequently split by hydrolysis. Nucleotides also have a role in storage and retrieval of biological information. Serve as building blocks for construction of nucleic acids--long nucleopolymers linked by phosphodiester bonds between P group to sugar of one nucleotide and hydroxyl to sugar of the next nucleotide. Nucleic acid chains are synthesized from energy-rich nucleoside triphosphates by condensation reaction that releases inorganic pyrophosphate during phosphodiester bond formation. 2 types of nucleic acids--ribonucleic acids (based on sugar ribose) and deoxyribonucleic acids (based on deoxyribose). The based deoxyribonucleic has a hydroxyl at the 2’ position of ribose Carbon ring replaced by H. RNA is usually in a single-stranded polynucleotide, DNA double stranded. Linear sequence of nucleotides in DNA/RNA encodes genetic information. DNA is more stable with H bond helices, long term storage for hereditary information. RNA is the more transient carrier of molecular instructions. On a basis of weight, macromolecules are by far the most abundant of organic molecules in the living cell--principal building blocks from which a cell is built and confer the most distinctive properties of living things. Macromolecules are constructed simply by covalently linking organic monomers/subunits into long chains/polymers. Proteins are especially versatile and perform thousands of distinct functions in cells many proteins act as enzymes that catalyze the chemical reactions that take place in cells. -In nucleic acids, polysaccharides and proteins, each polymer grows by the addition of a monomer onto one end of the polymer down via a condensation reaction, in which a molecule of water is lost with each subunit added. In all cases, catalyzed by specific enzymes. Most macromolecules, although built predictably, are made from a set of monomers slightly different form one another--ex: proteins are built from 20 different amino acids. Polymer chains are not assembled randomly; have a sequence. Sequence is incredibly important for distinction of function. Most of the single covalent bonds that link subunits allow rotation of atoms, giving great flexibility, allows for multiple conformations (affected by thermal energy motions). Shapes highly constrained by weaker noncovalent bonds too--ensures preference to one conformation--determine chemistry/activity. 2 types of noncovalent bonds--electrostatic attractions--weak in water because of partially charged polar groups in attraction are shielded by H2O/inorganic interactions--helps enzyme to substrate guide certain chemicals to place. Hydrogen bonds are important in folding of the polypeptide chain and holding together strands of DNA. Van der Waals attractions are a form of electrical attraction by fluctuating charges when 2 atoms come within a short distance of each other. Weaker than H bonds, hydrophobic interaction expulse hydrophobic molecules form polar ones (like H2O and oil). Creates bonds in hydrophobic molecules. Gathered noncovalent bonds makes it possible for proteins to be enzymes, stabilize associations between macromolecules--can be used for larger structures.
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