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Bio 151, Week 3 Notes

by: Aimee Dennis

Bio 151, Week 3 Notes Bio 151

Aimee Dennis
Cal State Fullerton
GPA 3.16

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These notes are on week 3 notes
Cellular and Molecular Biology
Alison Miyamoto
Class Notes
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This 6 page Class Notes was uploaded by Aimee Dennis on Saturday February 20, 2016. The Class Notes belongs to Bio 151 at California State University - Fullerton taught by Alison Miyamoto in Spring 2016. Since its upload, it has received 9 views. For similar materials see Cellular and Molecular Biology in Biology at California State University - Fullerton.

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Date Created: 02/20/16
Week 3 Spontaneous (energetically favorable): reactions proceed on their own, without any conscious external influences 1) The amount of potential energy I. Products of SR have less potential energy than reactants 2) The degree of order I. Products less ordered than the reactants Equation for Energy: H = G +S  H (enthalpy): energy stored in chemical bonds of a molecule  S (entropy): amount of disorder  G (free energy): energy available to break and reform bonds Equation for change in energy: ∆ G=∆H−T ∆ S  T (Temperature) ∆ - means the change of ∆ G<0 -A non- spontaneous chemical reaction is defined as (Endergonic reaction) -A spontaneous chemical reaction is defined as ∆ G>0 (Exergonic reaction) -Less disorder in the products= positive number Proteins 1. Catalysts: Enzymes that speed up reactions 2. Defense: Immune systems 3. Transport: helping cells move from place to place 4. Movement: Whether or not cells move( myosin, kinesin, cytoskeleton) 5. Structure: Cells walls, cytoskeleton 6. Signaling: controlling all functions Hierarchical: Amino Acids: basic building blocks of life (20 amino acids) (Draw an Amino Acid) Non Ionized and Ionized 1. One end should have an N and one end should have C 2. Amino on the left side, carboxyl on the right side 3. Side Chains are distinguished by their chemical structure To build a protein you need a monomers (amino acid) to form polymer (protein). Peptide bonds link them together. (draw) Condensation reactions build polymers Condensation Reactions: a reaction in which two molecules combine to form a larger molecule, producing a small molecule such as H 2 as a byproduct Protein Structures 1. The shape of the protein is going be determined the order of sequence of amino acids 2. Also determines the interactions 3. 4 levels of protein structure: primary, secondary, tertiary, quaternary 4. Secondary structure: only built on the protein backbone a. Localized interactions within a specific area 5. Tertiary: Uses all noncovalent types of bonds Forming Tertiary Structure -The 3D folding of the whole protein due to interactions between R-groups and peptide backbone (R-R, R-backbone) -Give the number of interactions possible, a diverse array of tertiary structures are possible -Variety in primary amino acid - Secondary Structures is made from hydrogen bonds between the backbone of amino acids Quaternary structure: interactions between two or more separate protein subunits to form a larger functional protein Folding: a physical process by which a protein chain acquires its native 3 dimensional structure -Proteins fold to reach the most stable shape/ conformation - Protein folding is often spontaneous because it is primarily in an aqueous (watery) environment -> increase in entropy Prion Disease: neurodegenerative, misfolding but no change in sequence You are asked to provide data that support the hypothesis that protein structure and function are correlated. The best set of data to support this hypothesis is…  Denatured proteins do not function normally (RNA experiment) -The Tertiary (or Quaternary) Structure of a protein results in the formation of surfaces that can interact with the surrounding environment in different ways Interaction: physical, based on non-covalent bonds -Induced fit of the substrate in the active site of the enzyme Catalysts: increase the rate at which products are formed in a reaction Enzymes: reduce the barriers to chemical reactions (kinetic energy and temp.), function as a catalyst -Enzymes generally have –ase in their name Ex. Kinases, Amylases -Enzymes are not consumed in a chemical reaction A model of enzyme action Consider A + B–C -> AB + C - =covalent bond 1) Initiation: Reactants bind the active site forming a complex enzyme 2) Transition state: Interactions between enzyme and substrate lower, enzyme reduce barriers 3) Termination: Two substrates dissolve themselves, enzyme binds another set of reactants and are not consumed in chemical reaction Regulation of enzyme activity: a) Competitive inhibition: binds to the enzyme’s active site (normal substrates and inhibitors) b) Allosteric regularism: binding to a site away from active site (positive and negative) Activation: Active site available when bound to different site Deactivation: Active site unavailable when bound to a different site Activation energy (Ea): the minimum quantity of energy that the reacting species must possess in order to undergo a specified reaction +∆G −∆G Endergonic reaction = vs. Exergonic reaction = -A catalyst lowers the activation energy of a reaction to increase the rate of reaction Which of the following is true when comparing an uncatalyzed reaction to the same reaction with a catalyst? ∆ G  The catalyzed reaction will have the same value Are there limits to the rate of catalysts?  All enzymes shows this type of saturation kinetics -DNA can store and transmit biological information - Carriers info required for the growing and reproduction of all cells - Sequence of the bases contain the language of nucleic acids DNA and RNA monomers -Nucleotide (triphosphate) - Phosphate is highly negative (charge) - Carbon’s are always counted from the right of the oxygen - Nitrogenous base is bonded to carbon 1 of sugar (N – 1) - Phosphate group is bonded to carbon 5 of sugar (O – 5) 2 5-Carbon Sugars 1) Ribose- OH bond 2) Deoxyribose- H bond 5 Nitrogenous bases 1) Cytosine (C) 2) Uracil (U) 3) Thymine (T) 4) Guanine (G) 5) Adenine (A) Phosphodiester linkage: the linkage between the 3’ carbon atom of one sugar molecule and the 5’ carbon atom of another Sugar-Phosphate backbone: no change between sugar and phosphate nucleotide -Nucleic Acids (like proteins) have chemically distinct ends - If the R group on amino acids is the side chain, the “R” group on nucleic acid is the base - DNA has a secondary structure (double helix) - Hydrogen bonds form between G-C pairs and A-T pairs - DNA contains thymine whereas RNA contains uracil Do both pairs have the same chemical strength? (G &C) (A & T)  G-C has a higher chemical strength than (A-T) because of the number of H bonds -Only purine-pyrimidine pairs fit inside the double helix - Purine-purine pair = Not enough space - Pyrimidine-pyrimidine = Too much space - Combined = Just right G% = C% , A% = T%  The amount of G= the amount of C, the amount of A = the amount of T -DNA can replicate itself 1) Strand separation 2) Bring in monomers to Base-pairing with template 3) Polymerization (original molecule copied) What is the chemical reaction that is required for polymerization?  Dehydration to form a covalent bond Hydrolysis: breaks covalent bonds -The first difference between DNA and RNA is… 1) Sugars - Ribose in RNA (OH) Deoxyribose in DNA (H) 2) Nitrogenous in RNA - Uracil (U) in RNA Thymine (T) in DNA -> more stable DNA RNA Sugar: 2’ – H Sugar: 2’ –OH Base: T (- CH 3 ) Base: U(-H) A,C,G A,C,G -DNA base pairs are held together through non-covalent bonds - RNA’s structures varies whereas DNA is more stable - RNA makes single-stranded loops, might form double helix RNA: is used as transition of DNA as transmission or translation to protein -Goes to ribosomes -> amino acids -> forms protein Which came first DNA or RNA?  RNA because of structural variety, catalyze the polymerization reacting, provides a template for copying itself -Ribosomes are made of both RNA and proteins Ribozyme: enzyme built of RNA, at least partially 5 carbon sugar nitrogenous base


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