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BU BIOL 118 - Protein Structure & Function/ Nucleic Acids and the RNA World

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BIOL 118 1st Edition Lecture 4 Outline of Last Lecture I. Ions and Ionic BondsII. The Electron-Sharing ContinuumIII. Key Properties of WaterIV. Water and Hydrogen BondsV. Correlation of Water’s Structure and PropertiesVI. The Importance of CarbonVII. Functional Groups: Determinants of Chemical BehaviorOutline of Current Lecture I. Protein Structure and Functiona. The Nature of Side chainsb. Important Terminologyc. Functional Groups Affect Reactivityd. Primary Structuree. Secondary Structure f. Tertiary Structureg. R-group Interactions That Form Tertiary Structuresh. Summary of Protein Structurei. Protein Function: What Do Proteins Do?j. Folding and Functionk. Protein Folding Is Often Regulatedl. Prions and Protein FoldingII. Nucleic Acids and the RNA Worlda. Summary of DNA’s Secondary Structureb. How Does DNA Replicate?c. Is DNA a Catalytic Molecule?d. RNA Structure and Functione. Glycosidic Linkagesf. Types of PolysaccharidesCurrent LectureProtein Structure and FunctionThe Nature of Side Chains- 20 amino acids differ only in the unique R-group attached to the central carbonThese 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.- The properties of amino acids vary because their R-groups varyImportant Terminology- Side chains= R-groups- Backbone= all the other parts of the amino acids, the same as all the other amino acidsFunctional Groups Affect Reactivity- R-Groups differ in their size, shape, reactivity, and interactions with watero Nonpolar R-groups: hydrophobic; do not form hydrogen bonds; coalesce in watero Polar R-groups: hydrophilic; form hydrogen bonds; readily dissolve in water - Amino acids with hydroxyl, amino, carboxyl or sulfhydryl functional groups in side chains have higher chemical reactivityo More than those only composed of only carbon and hydrogen atomsPrimary Structure- Primary structure is the unique sequence of amino acids- A single change in amino acid can radically alter protein functiono Due to how amino acid R-groups affect a polypeptide’s properties and functiono What happens in the primary structure will affect tertiary structure- Hydrogen bond occurs regularly along amino acid chainSecondary Structure- Hydrogen bonds between the carbonyl group of one amino acid and the amino group of another form a protein’s secondary structure- A polypeptide must bend to allow this hydrogen bonding, forming a-heliceso Can be a-helices or in beta pleats, depends upon amino acid- Secondary structure depends on the primary structure - The large number of hydrogen bonds in a protein’s secondary structure increase its stabilityTertiary Structure- Results from interactions between R-groups or between an R-group and the peptide backboneo Causes the backbone to bend and fold, and contribute to the 3D shape of the polypeptideo R-group interactions include hydrogen bonds, hydrophobic interactions, interactions, covalent disulfide bonds and ionic bondsR-Group Interactions That Form Tertiary Structures- Hydrogen bonds form between hydrogen atoms and the carbonyl group in the peptide-bonded backbone, and between hydrogen and negatively charged atoms in side chains- Hydrophobic interactions within a protein increase stability of surrounding water molecules by increasing hydrogen bonding- Van der Waals interactions are weak electrical interactions between hydrophobic side chains- Covalent disulfide bonds form between sulfur containing R-groupso Very strong bond that helps it stay in tertiary state and makes it stable- Ionic bonds form between groups that have full and opposing chargesQuaternary Structure- Many proteins contain several distinct polypeptide subunits that interact to form a structure; the bonding of two or more subunits produces quaternary structureSummary of Protein Structure- Protein structure is hierarchal- Quaternary structure is based on tertiary structure, which is based in part on secondary structure- All three of the higher level structures are based on primary structure- The combined effects of primary, secondary, tertiary, and sometimes quaternary structure allow for amazing diversity in protein form & functionProtein Function: What do Proteins do?- Proteins are crucial to most tasks required for cells to existo Catalysis- Enzymes speed up chemical reactionso Defense- antibodies and complement proteins attack pathogenso Movement- motor and contractile proteins move the cell or molecules within the cello Signaling- Proteins convey signals between cellso Structure- structural proteins define cell shape and comprise body structureo Transport- transport proteins carry materials; membrane proteins control molecular movement into and out of the cellFolding & Function- Protein folding is often spontaneous, because the hydrogen bonds and van der Waalsinteractions make the folded molecule more energetically stable than the unfolded molecule- A denatured (unfolded) protein is unable to function normallyo Can denature due to high temps or exposure to acid- Proteins called molecular chaperones help proteins fold correctly in cellsProtein folding is often regulated- Since the function of a protein is dependent on its shape it controls when/where it isfolded- Regulates the protein’s activityo The inactive form of a protein has a disordered shape- When active protein is needed it folds into an ordered, active conformationPrions & Protein Folding - Misfolding can be “infectious”- Prions: improperly folded forms of normal proteinso Present in healthy individualso Amino acid sequence does not differ from a normal proteino Shape is radically different Can induce normal protein molecules to change their shape to the alteredformChapter 4Summary of DNA’s Secondary Structure- DNA’s secondary structure consists ofo 2 antiparallel strands twisted into double helix- The molecule is stabilized byo Hydrophobic interactions in its interioro Hydrogen bonding between the complementary base pairs (A-T & G-C)How does DNA Replicate?- Complementary base pairing provides a simple mechanism for DNA replication- each strand can serve as a template for the formation of a new complementary strand- Requires 2 steps:o Separation of the double helixo Hydrogen bonding of deoxyribonucleotides with complementary bases on the original template strand followed by a phosphodiester bond formation to form the complementary strandIs DNA a Catalytic molecule?- DNA has stabilityo Makes


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