Biochemistry 380 Week One Notes
Biochemistry 380 Week One Notes BCH 380-001
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This 11 page Class Notes was uploaded by Mark Hedinger on Friday September 2, 2016. The Class Notes belongs to BCH 380-001 at Montana State University - Bozeman taught by Staff in Fall 2016. Since its upload, it has received 123 views.
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Date Created: 09/02/16
Biochemistry 380 Week 1 Chapters 1-2 “Principles of Biochemistry” Schlick Chapter 1 1.2 Chemical Elements of Life Six nonmetallic elements which are important for organisms because they can form stable covalent bonds during chemical reactions within the body CHNOPS o Carbon o Hydrogen o Nitrogen o Oxygen o Phosphorous o Sulfur Essential Ions—present in all species 2+ o Calcium (Ca ) + o Potassium (K ) o Sodium (Na ) + o Magnesium (Mg ) 2+ o Chloride (Cl ) Common Linkages in Organisms o Ester and ether linkages Fatty acids and lipids o Amide linkages Proteins o Phosphate ester and phosphoanhydride linkages Nucleotides In vivo o Referring to reactions that take place within an organism In vitro o Referring to reactions that take place within a laboratory (or laboratory conditions) 1.3 Important Macromolecules Condensation reactions (removing water) o Biological macromolecules are normally found in the form of polymers (large molecule) which is formed through condensation reactions between small monomers (small organic molecules) Functional Groups (pg. 5) o Organic compounds Alcohol, Aldehyde, Ketone, Carboxylic acid, Thiol, Amines o Functional Groups of the organic compounds Hydroxyl, Acyl, Carbonyl, Carboxylate, Thiol, Amino, Phosphate, Phosphoryl o Linkages formed between the functional groups of organic compounds Ester, Ether, Amide, Phosphate ester, Phosphoanhydride Levels of Complexity of Organisms 1. Atoms 2. Molecules 3. Macromolecules 4. Organelles 5. Cells 6. Tissues 7. Organs 8. Organism Relative molecular mass (M )r o Mass of molecule relative to 1/12 the mass of Carbon-12 1 dalton = 1 atomic mass unit o Molecular mass a.k.a molr mass 1 mole = 6.022 x 10 23molecules 1 mole = 38 kilograms Proteins Each amino acid contains o Amino group o Carboxylate group o R group—unique to each amino acid Peptide bond o Bond between a carbon atom of one amino acid and a nitrogen atom of another Polysaccharides (carbohydrates) Primarily made up of o Carbon, oxygen, and hydrogen Polysaccharide residues and all monosaccharide’s contain multiple hydroxyl groups o They are all polyalcohol’s Ribose is the most common 5-Carbon sugar o Contains a covalent bond between Carbon (C1) and the C4 hydroxyl group Glucose is the most common six carbon sugar o Forms cellulose, glycogen and starch Cellulose Structural function Glycogen and starch Storage function o Formed by a covalent bond between C-1 and a hydroxyl group A.k.a. glycosidic bond o Most abundant bipolymer Cellulose Nucleic Acids Large macromolecules made up of smaller monomers (Nucleotides) o A nucleotide is made up of a five-carbon sugar, a heterolytic nitrogen base, and one (or more) phosphate groups Purines o Adenine (A) o Guanine (G) Pyrimidines o Cytosine (C) o Thymine (T)—only in DNA o Uracil (U)—only in RNA Link between ribose and a-phosphoryl o Phosphodiester linkage Linkage between β and γ -phosphoryl groups (Make up ATP) o Phosphoanhydride linkage (don’t involve carbon) Linkage between adjacent nucleotides o Phosphodiester linkage Energy carrier in the body o ATP RNA—contains ribose o Four kinds Messenger RNA—transfers information from DNA to protein Transfer RNA—required for protein synthesis Ribosomal RNA—component of ribosomes Small RNA—multiple different functions DNA—contains deoxyribose Lipids and Membranes Contain few, if any, oxygen Abundant in carbon and hydrogen o Not water soluble Many contain a hydrophobic tail, and a polar hydrophilic head Simplest lipids = fatty acids o Commonly make up larger molecules such as glycerophospholipids Other kinds of lipids o Steroids Cholesterol Sex hormones o Waxes Ear wax Beeswax Membranes o Largest and most complex cell structure 1.4 Energy of Life Life requires an input of energy o The ability to produce energy is one of the criteria to be considered “alive” Photosynthesis o Key process essential for life o Plants make energy via photosynthesis and organisms eat plants for energy Reaction Rates/Equilibria Brackets indicate concentration o [A] = “Concentration of A” Expressed in moles per liter (M) Rate Constant (k) o Forward rate = 1 k1 o Reverse rate = E-1ilibrium: k = k-1 [C][D] k o K eq= [ ][B] Thermodynamics ∆ G --Change in Gibbs free energy o ∆ G <0 reaction favors products Spontaneous Energy is released o ∆ G >0 reaction favors reactants Not spontaneous Must input energy o ∆ G = 0 reaction at equilibrium ∆ S --Change in Entropy o Amount of disorder/ randomness ∆ H --Change in Enthalpy o Change in heat content Gibbs Free Energy Change Equation o ∆ G=∆H−T ∆S o Tis always∈Kelvin o Depends on the concentration of reactants and products Higher concentration of reactants reaction favors products Higher concentration of products reaction favors reactants Standard Conditions o 25 ℃ ’(298 K), 1 atm, 1.0 M concentration o ∆ G° ' C [D] o ∆ GA=∆G° +RTln A [B] [ ] R= 8.315kJ Free Energy and Reaction Rates Activation Energy o The excess of energy required in order for a reaction to proceed o Determines the rate of a reaction o Other factors that contribute to the rate of a reaction Temperature Concentration Kinetic energy of the molecules Orientation of the molecules o **The reactions inside cells are accelerated by enzymes because the reactions are very slow by themselves. 1.5 Biochemistry and Evolution Prokaryotes o No membrane bound nucleus DNA in nucleoid region of cytoplasm o No internal membrane compartments o Cell wall o Periplasmic space Crucial in biochemical processes o Pili Protein fibers that attach to other cells o Flagella Allows bacteria to move o Due to their high surface area to volume ratio (they are small), simple diffusion is adequate for the transportation of material within the prokaryote Eukaryotes o Complex internal structure—very crouded o Membrane bound nucleus Site of Transcription Nucleolus Site of ribosome synthesis o Many organelles o Have a cell membrane (not a cell wall) Usually a phospholipid bilayer o Endoplasmic Reticulum and Golgi Apparatus Rough ER (RER) Site of protein synthesis Smooth ER (SER) Lipid synthesis Golgi Chemically modifies, stores, packages and transports in vesicles o Due to its small surface area to volume ratio, simple diffusion is not enough to transport material throughout the cell o Mitochondria Site of oxidative energy metabolism ATP production o Chloroplasts (plants only) Site of photosynthesis ATP production in plants o Specialized Vesicles Lysosomes—digestive vesicles Peroxisomes Carry out oxidation reactions o Create peroxide as a toxic byproduct Peroxide is destroyed by peroxisomal enzyme catalase Vacuoles (plants only) Storage sites for water and nutrients The Cytoskeleton o Three types of protein filaments Actin Filaments Most abundant Movement within and by the cell Microtubules Made of tubulin Form mitotic spindle fibers in mitosis Create cilia and flagella Intermediate filaments Inside nuclear envelope Help cell resist mechanical stresses 1.9 The Living Cell Molecular collisions are fully elastic (energy is conserved) Small nonpolar molecules can diffuse freely Charged, polar or large molecules cannot diffuse through the membrane o Must use channels, pores, or pumps Chapter 2 Water makes up 60-90% the mass of a cell 2.1 Polar Water Molecule A water molecule’s angle is 104.5 ° The outer shell can contain four pairs of electrons o One pair in the s orbital o Three pairs in the p orbital Can form covalent bonds Water is polar because the oxygen atom is more electronegative than the hydrogen atoms o Can dissolve other charged or polar molecules o “Like dissolves like” 2.2 Hydrogen Bonding in Water A hydrogen bond is formed due to attractive forces between it (it has a partial pos charge) and another molecule with a partial negative charge (like an oxygen atom) o Strength of hydrogen bonds 20 kJ mol -1 The stability increases if the hydrogen bond forms in a straight line with another molecule This arrangement is why ice is less dense than liquid water—multiple hydrogen bonds form tetrahedrals Water expands below 4 ℃ Specific Heat o Amount of heat required to raise 1 gram of substance 1 ℃ Water has a high specific heat which reduces temperature fluctuations within cells Heat of vaporization of water 2260 J g -1 2.3 Water as a Solvent Water is an excellent solvent due to its polar properties, low viscosity, and small molecules relative to other solvents Water dissolves polar and ionic substances Ionization o Gain or loss of an electron resulting in an atom or molecule with a net charge Electrolytes—molecules that can form ions Hydrophilic o Water loving o Substances that dissolve in water Solvation sphere o Shell of water around a substance Solvated o A substance surrounded by solvent molecules o A.k.a hydrated when the solvent is water o An increase in polar groups on a molecule increases its solubility Cellular Concentrations/ Diffusion Three reasons solutes diffuse slowly in cytoplasm 1. The viscosity of cytoplasm is higher than water 2. Charged molecules bind to each other and tend to restrict movement 3. The cytoplasm is very crowded a. This is the main reason this move slowly Osmotic Pressure A solvent (such as water) diffuses from high concentration to low concentration o Aka osmosis when the solvent is water o The osmotic pressure is depends on the total molar concentration of solute Condensing small molecules into large ones is a way of controlling osmotic pressure. Hypotonic solution o Lower concentration of solutes outside cell Hypertonic solution o Higher concentration of solutes outside cell Isotonic solution o Equal concentrations of solutes in and outside cell 2.4 Nonpolar substances Insoluble in water Known as hydrophobic o Water fearing Hydrophobic effect o A very important factor in the folding of proteins into specific shapes Amphipathic o Have a polar end and a non polar end (phospholipids) Micelles form because water creates an organized structure around the nonpolar particles in order to minimize order amongst the water cells o Chaotropes Enhance solubility of nonpolar substances in water by disordering water molecules 2.5 Noncovalent Interactions (electrostatic interactions) Four major noncovalent interactions o Hydrogen bonds Strong enough to assist in structural stability but easily broken when needed All functional groups are able to form hydrogen bonds o Charge-charge interactions Strongest noncovalent forces Interaction between two charged particles Ion paring + - o E.g. Na + Cl = NaCl Plays a role in the recognition of one molecule by another molecule Helps in the formation of protein shape o Van der Waals forces Weakest of the forces Involve attraction and repulsion forces When involved in attraction forces they are known as London dispersion forces Have an optimal packing distance where the attraction is strongest and the protons aren’t too close that they repel each other o Hydrophobic Interactions Weaker than covalent bonds but stronger interaction than van der Waals Give protein its three-dimensional structure 2.6 Water is Nucleophilic Nucleophiles o Have a negative charge or free electrons o Attack electrophiles o Most common nucleophiles in biology Oxygen Nitrogen Sulfur Carbon **All proteins will eventually be degraded by hydrolysis o hydrolysis reactions are energetically favorable G is negative, and the reaction is always spontaneous o Synthesis of molecules is unfavorable but that is why the cells require ATP to drive the reactions! 2.7 Water Ionization Cations—have a net positive charge Anions—have a net negative charge Acids o Proton Donors (Bronsted-Lowry) o Electron Acceptors (Lewis) Bases o Proton Acceptors (Bronsted-Lowry) o Electron Donors (Lewis) Equilibrium constant of water o 1.8 x 10 -16M Concentration of water at 25C o 55.5 M 2.8 The pH Scale pH o –log[H ] A change in pH one unit = a 10-fold change in concentration of + H Acids o pH<7 o Remember “Party-goers drop acid” Bases o pH>7 Normal blood pH is 7.4 o Physiological pH 2.9 Acid Dissociation Constants—Weak Acids Strong acids o Dissociate completely in water Weak acids o Don’t dissociate completely in water o Henderson-Hasselbalch Equation conjugatebase pH = pKa + log acid Acids become the conjugate base Bases become the conjugate acid 2.10 Buffer Solution The ability of a solution to resist changes in pH after a small amount of acid or base is added Buffer solution is most effective when pH = pKa o An extremely important buffering system in the body is the carbon dioxide-carbonic acid-bicarbonate buffer system Caused by a reaction between water and carbon dioxide See page 51 for a more in-depth view of the buffering system Other than the previously mentioned buffer system, the second most important buffer system in the body is the hemoglobin buffer system in blood cells o Changes in CO hel2s restore equilibrium If someone is hyperventilating they are expelling too much CO an2 will become alkalotic Why we instruct them to breath into a paper bag, to retrieve some of the expelled CO 2 Acidosis (Acidotic individuals) are the reverse of the previously stated. No breathing hold too many hydrogen ions in one’s body resulting in acidosis.
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