BIOL 118 1st Edition Lecture 4 Outline of Last Lecture I Ions and Ionic Bonds II The Electron Sharing Continuum III Key Properties of Water IV Water and Hydrogen Bonds V Correlation of Water s Structure and Properties VI The Importance of Carbon VII Functional Groups Determinants of Chemical Behavior Outline of Current Lecture I Protein Structure and Function a The Nature of Side chains b Important Terminology c Functional Groups Affect Reactivity d Primary Structure e Secondary Structure f Tertiary Structure g R group Interactions That Form Tertiary Structures h Summary of Protein Structure i Protein Function What Do Proteins Do j Folding and Function k Protein Folding Is Often Regulated l Prions and Protein Folding II Nucleic Acids and the RNA World a Summary of DNA s Secondary Structure b How Does DNA Replicate c Is DNA a Catalytic Molecule d RNA Structure and Function e Glycosidic Linkages f Types of Polysaccharides Current Lecture Protein Structure and Function The Nature of Side Chains 20 amino acids differ only in the unique R group attached to the central carbon These 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 vary Important Terminology Side chains R groups Backbone all the other parts of the amino acids the same as all the other amino acids Functional Groups Affect Reactivity R Groups differ in their size shape reactivity and interactions with water o Nonpolar R groups hydrophobic do not form hydrogen bonds coalesce in water o 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 reactivity o More than those only composed of only carbon and hydrogen atoms Primary Structure Primary structure is the unique sequence of amino acids A single change in amino acid can radically alter protein function o Due to how amino acid R groups affect a polypeptide s properties and function o What happens in the primary structure will affect tertiary structure Hydrogen bond occurs regularly along amino acid chain Secondary 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 helices o 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 stability Tertiary Structure Results from interactions between R groups or between an R group and the peptide backbone o Causes the backbone to bend and fold and contribute to the 3D shape of the polypeptide o R group interactions include hydrogen bonds hydrophobic interactions interactions covalent disulfide bonds and ionic bonds R Group Interactions That Form Tertiary Structures Hydrogen bonds form between hydrogen atoms and the carbonyl group in the peptidebonded 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 groups o Very strong bond that helps it stay in tertiary state and makes it stable Ionic bonds form between groups that have full and opposing charges Quaternary Structure Many proteins contain several distinct polypeptide subunits that interact to form a structure the bonding of two or more subunits produces quaternary structure Summary 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 function Protein Function What do Proteins do Proteins are crucial to most tasks required for cells to exist o Catalysis Enzymes speed up chemical reactions o Defense antibodies and complement proteins attack pathogens o Movement motor and contractile proteins move the cell or molecules within the cell o Signaling Proteins convey signals between cells o Structure structural proteins define cell shape and comprise body structure o Transport transport proteins carry materials membrane proteins control molecular movement into and out of the cell Folding Function Protein folding is often spontaneous because the hydrogen bonds and van der Waals interactions make the folded molecule more energetically stable than the unfolded molecule A denatured unfolded protein is unable to function normally o Can denature due to high temps or exposure to acid Proteins called molecular chaperones help proteins fold correctly in cells Protein folding is often regulated Since the function of a protein is dependent on its shape it controls when where it is folded Regulates the protein s activity o The inactive form of a protein has a disordered shape When active protein is needed it folds into an ordered active conformation Prions Protein Folding Misfolding can be infectious Prions improperly folded forms of normal proteins o Present in healthy individuals o Amino acid sequence does not differ from a normal protein o Shape is radically different Can induce normal protein molecules to change their shape to the altered form Chapter 4 Summary of DNA s Secondary Structure DNA s secondary structure consists of o 2 antiparallel strands twisted into double helix The molecule is stabilized by o Hydrophobic interactions in its interior o 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 helix o Hydrogen bonding of deoxyribonucleotides with complementary bases on the original template strand followed by a phosphodiester bond formation to form the complementary strand Is DNA a Catalytic molecule DNA has stability o Makes it a reliable store for genetic information o Less reactive than RNA o More
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