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TAMU BIOL 213 - Proteins, Nucleic Acids, and Thermodynamics
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BIOM 213 1nd Edition Lecture 4Outline of Last Lecture II. MolarityA. DefinitionB. Tips on how to do the molarity problems III. Acids, Bases and pHa.Definitions of acid and baseb.Ionization of water; Kw c.Tips on how to do problems involving pHd.BuffersIV. Review of the most common chemical groups in biological moleculesa. A list, their formulas, a unique characteristic, and where they’re commonly foundV. Macromoleculesa. “Monomers” of allb. Condensation reactionVI. Polysaccharidesa. Descriptioni. Major functionsb. Structurei. How the flipping of an –O and –OH can change the sugarc. Glucose i. Alpha and betaVII. Lipidsa. Descriptioni. Ester linkageb. Basic structurei. Hydrophobic and hydrophilic partsii. Saturated vs Unsaturatedc. Propertiesd. Two main different kinds covered in lecturei. Triacylglycerolii. Phospholipid1. PhosphatidylserineVIII. Cholesterola. Basic structureb. Main functionsThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.i. Hormones IX. Proteinsa. Descriptioni. Major functionsb. Amino Acidsi. Structureii. Classification (nonpolar, charged, or uncharged polar)iii. We need to be able toOutline of Current Lecture1. Finishing up proteinsa. Polar moleculesb. Structure = function2. Nucleic acidsa. Main functionsb. Structural polarityc. Basic structurei. Nucleotidesd. DNA vs. RNA3. Central dogma of biologya. DNA synthesis  transcription  translation4. Noncovalent bonds in macromoleculesa. Bonds macromolecules to themselvesb. Bonds together multiple macromolecules5. Basic overview of macromoleculesa. Small subunits join together to make macromolecules, which can join together tomake macromolecular complexes6. Thermodynamicsa. 1st and 2nd lawsb. Entropy 7. Free energy, Ga. –ΔG = energetically favorableb. What it depends onc. When ΔG = 0, at equilibrium8. Review of oxidation and reductiona. Oxidation = lossb. Reduction = gainc. The more highly reduced molecule has more energy9. Energy in biologya. When a biological reaction has a – ΔGi. Coupled reactions: sequential “siphoning” and activated carriersb. Activation energyi. Enzymes Current Lecture1. Finishing up proteinsa. The condensation reaction that joins together amino acids is an amide linkage which results in a peptide bondb. Must be able to draw this reactionc. Proteins are polar moleculesi. The order of amino acids matters – it determines what the protein isii. Always start reading a protein from the amino group / N- terminus and end at the carboxyl group / C- terminusd. Structure = functioni. The structure of a protein is determined by the sequence of 20 different amino acidsii. The structure of each amino acid is determined by the sequence of 4 different nucleotidesiii. Therefore, there can be a nearly infinite number of different sequences, and therefore functions1. This number is never seen in natureiv. If you switch the sequence/structure of the amino acids, it creates a different protein than originally intended, which has a different function1. Because the shape of the protein determines what molecules it can react with based on the number of noncovalent interactions the two canform2. Nucleic acidsa. The last main group of macromoleculesb. Most commonly known: DNA, RNA and ATPc. Main functionsi. Energy carriers (ATP)1. Adenine triphosphateii. Storage and expression of genetic information (DNA & RNA)d. Have structural polarity (like proteins) – the sequence and direction matteri. 5’ end1. Always add nucleotides to this end2. This is the end of the nucleic acid that has the phosphate group3. Five = Phosphate4. 5 looks like and S (as in start)ii. 3’ end1. Always the end of a nucleic acid2. This is the end with a free hydroxyl groupe. Made up of nucleotides (monomer) i. Joined together to make nucleic acid via condensation reaction, which results in a phosphodiester linkage1. –O from the phosphate group and 2. –OH (bonded to the 3rd carbon) from the pentose sugarii. Nucleotide = nitrogenous base + pentose (5 carbon) sugar + phosphate groupiii. Nitrogenous base1. Pyrimidinesa. Cytosineb. Thymine (DNA)c. Uracil (RNA)2. Purines a. Adenineb. Guanine c. Remember: we AGs are PURe3. Pyrimidines always pair up with purines and purines always pair up with pyrimidinesa. C – Gi. Form 3 hydrogen bonds with each otherb. A – Ti. Form 2 hydrogen bonds with each otherc. A – U i. Form 2 hydrogen bonds with each otherd. Because of this, we can know the arrangement of both DNA strands by only looking at oneiv. Pentose sugar1. Ribosea. Found in RNAb. Has a hydroxyl group attached to the 2nd carbonc. Causes the ribose to be more unstable and more catalyticd. This is why RNA is not the main genetic material2. Deoxyribosea. Found in DNAb. Only has a hydrogen atom attached to the 2nd carboni. One fewer oxygen atom than ribose, hence its name: deoxyribosec. The absence of the hydroxyl group causes the deoxyribose to bemore stable and less catalyticd. This is why DNA is the main genetic materialv. Phosphate group1. Binds to the 5th carbon of the pentose sugarf. DNA vs RNADNA RNAStructure Mostly double-stranded = helicalMostly single-strandedFunction Genetic information storageGenetic expression, storageSugar 2-Deoxyribose RiboseNitrogenous bases A, T, G, C A, U, G, C3. Central dogma of biologya. DNA synthesis (replication)i. Always begin at the 5’ endii. Emphasis on this with Dr. Gomerb. Transcription i. RNA synthesisii. This is when the genetic code is just copied. It stays in the same “language”c. Translationi. Protein synthesisii. This is when the genetic code is “translated” into the protein “language”4. Noncovalent bonds in macromoleculesa. Long-stranded molecules aren’t very stable when they’re left free as a long strandb. This is where Noncovalent bonds come in handyc. Different parts of the molecule interact with itself via noncovalent bonds to “fold up” into a tighter, more globular, conformationi. This makes it more stabled. Multiple molecules can interact with each other tooi. When the surfaces of two or more molecules match up, they can form these noncovalent bonds with each otherii. The more similar the surfaces, the stronger the bondsiii. This is the phenomenon seen it enzyme-substrate interactionse. The number of interactions determines the strength of the bond5. Basic overview of macromoleculesa. Small molecules assemble into large


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TAMU BIOL 213 - Proteins, Nucleic Acids, and Thermodynamics

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