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Biochemistry 380 Week One Notes

by: Mark Hedinger

Biochemistry 380 Week One Notes BCH 380-001

Marketplace > Montana State University - Bozeman > BCH 380-001 > Biochemistry 380 Week One Notes
Mark Hedinger

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Notes taken from "Principles of Biochemistry" covering chapters one and two (Morgan, Horton, Scrimgeour & Perry), along with material covered in class.
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biochemistry, Chapter, Science, Chemistry




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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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