Macromolecules I (1) PDF

Macromolecules I  Protein and Nucleic Acid Structure  Nature of monomeric components  Synthesis of the polymers  Properties and functions of the polymer Assumptions regarding chemistry  Basic information regarding atomic structure  Chemical Bonds  Common bond types  Polari...

Macromolecules I  Protein and Nucleic Acid Structure  Nature of monomeric components  Synthesis of the polymers  Properties and functions of the polymer Assumptions regarding chemistry  Basic information regarding atomic structure  Chemical Bonds  Common bond types  Polarity  Chemical nature of common functional groups The Macromolecules of the Cell Most biological macromolecules in cells are synthesized from about 30 common small molecules Diversity of Protein Function  Enzymes serve as  Signaling proteins— catalysts, increasing the communication between rates of chemical reactions cells  Structural proteins—  Receptor proteins— physical support and shape enable cells to respond to chemical stimuli from the  Motility proteins— environment contraction and movement  Defensive proteins—  Regulatory proteins— protect against disease control and coordinate cell function  Storage proteins— reservoirs of amino acids  Transport proteins—move substances into and out of cells All Proteins are Polymers with Common Structural Characteristics The Monomers Are Amino Acids  Only 20 kinds of amino acids are used in protein synthesis  No two different proteins have the same amino acid sequence  Every amino acid has the same basic structure Which of the non-polar amino acids is the only amino acid that does not have separate L and D isomers? Which of the non-polar amino acids is the only amino acid that does not have separate L and D isomers? A) Valine B) Glycine C) Phenylalanine D) Proline E) Tryptophan The Polymers Are Polypeptides and Proteins  Amino acids are linked together stepwise into a linear polymer by dehydration (or condensation) reactions  As the three atoms comprising the H2O are removed, a covalent C—N bond (a peptide bond) is formed Which of these represents an important distinction between a polypeptide and a protein? A) There is no difference. The terms are interchangeable B) “Protein” implies function, while “polypeptide” is a structural term. C) “Proteins” are always made of multiple “polypeptides”. D) A “polypeptide” has multiple “protein” subunits. Monomeric and Multimeric Proteins  Proteins that consist of a single polypeptide are monomeric proteins, whereas multimeric proteins consist of two or more polypeptides  Proteins consisting of two or three polypeptides are called dimers or trimers, respectively  Hemoglobin is a tetramer, consisting of two α subunits and two β subunits Hemoglobin tetramer Several Kinds of Bonds and Interactions Are Important in Protein Folding and Stability  Both covalent bonds and noncovalent interactions are needed for a protein to adopt its proper shape, or conformation  These same bonds and interactions are required for polypeptides to form multimeric proteins  The interactions involve carboxyl, amino, and R groups of the amino acids, called amino acid residues once incorporated into a polypeptide The Importance of Primary Structure (order of amino acids in the polymer)  Primary structure is important genetically because the sequence is specified by the order of nucleotides in the corresponding messenger RNA  Primary structure is always read from N terminus to C terminus (the same order the polypeptide was assembled)  It is important structurally because the order and identity of amino acids directs the formation of the higher-order (secondary and tertiary) structures Secondary Structure  The secondary structure of a protein describes local regions of structure that result from hydrogen bonding between NH and CO groups along the polypeptide backbone  These result in two major patterns, the α helix and the β sheet  The α Helix The α helix is spiral in shape, consisting of the peptide backbone, with R groups jutting out from the spiral A hydrogen bond forms between the NH group of one amino acid and the CO group of a second amino acid that is one turn away from the first  The β Sheet The β sheet is an extended sheetlike conformation with successive atoms of the polypeptide chain located at “peaks” or “troughs” β sheets can be parallel or anti-parallel Common secondary Motifs Proline is referred to as the "helix breaker" because… A) it’s only found in the L form, which is incompatible with helical protein structure. B) it lacks the hydrogen atom needed for hydrogen bonding. C) it lacks a charged functional groups for ionic bonding. D) it is hydrophobic. E) it has a polar functional group. Tertiary Structure  The tertiary structure reflects the unique aspect of the amino acid sequence because it depends on interactions of the R groups  Tertiary structure is neither repetitive nor easy to predict  It results from the sum of hydrophobic residues avoiding water, hydrophilic residues interacting with water, the repulsion of similarly charged residues, and attraction between oppositely charged residues Several Kinds of Bonds and Interactions Are Important in Tertiary Protein Structure  Fibrous Proteins Fibrous proteins have extensive regions of secondary structure, giving them a highly ordered, repetitive structure Fibroin produces silk and is made predominantly of β sheets Keratin is the primary component of hair and is composed of many α helices Globular Proteins  Most proteins are globular proteins that are folded into compact structures  Each type of globular protein has its own unique tertiary structure  Most enzymes are globular proteins Globular Proteins  Most proteins are globular proteins that are folded into compact structures  Each type of globular protein has its own unique tertiary structure  Most enzymes are globular proteins Quaternary Structure  The quaternary structure of a protein is the level of organization concerned with subunit interactions and assembly  The term applies specifically to multimeric proteins  Some proteins consist of multiple identical subunits; others, such as hemoglobin, contain two or more types of polypeptides  The bonds and forces maintaining quaternary structure are the same as those responsible for tertiary structure Which component of DNA and RNA is responsible for the “acidic” part of nucleic acid? A) the phosphate group B) the 5-carbon sugar C) the nitrogenous base D) there is actually nothing acidic about DNA and RNA Nucleic Acids  Nucleic acids are of paramount importance to the cells because they store, transmit, and express genetic information  They are linear polymers of nucleotides  DNA is deoxyribonucleic acid, and RNA is ribonucleic acid Nucleic Acid Components Nomenclature  Nucleotides with one phosphate group can be thought of as nucleoside monophosphates (example: adenosine monophosphate, AMP)  Adenosine diphosphate (ADP) has two phosphate groups, and adenosine triphosphate (ATP) has three The Polymers Are DNA and RNA  Nucleic acids are linear polymers of nucleotides linked by a 3ʹ,5ʹ phosphodiester bridge, a phosphate group linked to two adjacent nucleotides via two phosphoester bonds  The polynucleotide formed by this process has a directionality with a 5ʹ phosphate group at one end and a 3ʹ hydroxyl group at the other  Nucleotide sequences are conventionally written in the 5ʹ to 3ʹ direction Nucleic Acid Synthesis  A preexisting molecule is used to ensure that new nucleotides (NTPs for RNA, dNTPs for DNA) are added in the correct order  This molecule is called a template, and correct base pairing between the template and the incoming nucleotide is required to specify correct order  A complementary relationship exists between certain purines and pyrimidines Complementary relationships between purines and pyrimidines A) allow adenine to form two hydrogen bonds with thymine (or uracil) and guanine to form three hydrogen bonds with cytosine to form double-stranded nucleic acids. B) allow the interaction of the oppositely charged amino acids to form the tertiary structure of proteins. C) allow adjacent bases in a nucleotide chain to stack tightly, stabilizing the DNA double helix. D) provide highly ordered, repetitive bonding to form α helices and β sheets within proteins. E) Both A and C are correct. Complementary Base Pairing A–T G–C anti-parallel The DNA Molecule Is a Double-Stranded Helix Base Pairing and RNA  RNA is normally single stranded  RNA structure is still influenced by complementary base pairing  However, the pairing is usually between bases in different areas of the same molecule and is less extensive than that of DNA