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Kim Dej (39)
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Protein Structure and Function Summary.docx

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Department
Biology
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BIOLOGY 2B03
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Kim Dej

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Protein Structure and Function What is a protein?  String of amino acids, polypeptide chain What is the function of protein?  Structural component of the cell  Sensors for environmental changes and mechanisms for relaying this information to the cell  Enzymes, catalysts for chemical reactions  Gene regulation  Signaling molecules between cells  Molecular motors  Organelle identity and function Diversity of Protein Structure  Shape and structure determines function  Amino acids attached in a linear array to create primary structure of protein- polypeptide  20 different amino acids incorporated into polypeptide  Amino acids attached via peptide bond What is an amino acid?  Monomeric building blocks of proteins  All 20 amino acids have same general structure  Alpha (a) carbon- central carbon attached to 4 components  R-group/side chain properties affect protein structure/conformation and function  Side chain differs in o Size o Shape o Charge o Hydrophobicity o Reactivity  Aa’s classified into groups based on solubility in water (polarity) of side chain  Solubility- property of a molecule that can bond with water for a short time via h- bonding (thermodynamically favourable) Hydrophilic/molecule: at least part of molecule charge-polarized and capable of h- bonding w/ water  Aa’s w/ polar side chain  Tend to be on surface of protein (hydrophilic)  Make protein soluble in aqueous solution  Charged (ionized) at pH 7 o Molecules w/ -OH at one end (O-) o Molecules w/ -NH at2one end (NH ) 3+  Polar + charged o Lysine (Lys) o Arginine (Arg)  Basic, positively charged o Glutamic Acid o Aspartic Acid (Asp)  Acidic, negatively charged o These 4 are prime contributors to overall charge of protein  Polar + uncharged- short side chains that h-bond w/ other polar molecules o Serine (Ser) o Threonine (Thr)  Uncharged at neutral pH but have polar -OH groups that h-bond o Asparagine (Asn) o Glutamine (Gln)  Uncharged but have polar amide groups Hydrophobic/non-polar molecule: not electrically polarized, can’t form h-bonds so water repels them and bonds with itself  Aa’s w/ non-polar side chain: water insoluble or only slightly soluble o Tend to be on interior of protein (when protein is in cytosol) o Often aggregate within hydrophobic core of protein o Ex. anything unable to form h-bonds  Oils, fats, saturated hydrocarbons/alkane (chain of single-bonded carbon- general formula is n Hn+2alkane) o Phenylalanine (Phe) o Tyrosine (Tyr) Aromatic (benzene ring) o Tryptophan (Trp) o Alanine (Ala) o Valine (Val) o Isoleucine (Ile) o Leucine (Leu) Aliphatic (hydrocarbon chain) o Methionine (Met) Special Amino Acids  Cysteine- form di-sulphide bridges (covalent bonds)  Proline- rigid, introduces kink into peptide chain  Glycine-small  Histidine- shifts charge (positive/neutral) depending on pH The Making of a Protein  Amino acids covalently bonded into peptides by formation of peptide bonds (strong covalent bonds) o Peptide bonds formed via condensation rxn between amino group of one aa and carboxyl group of another  Protein chain usually shown w/ amino terminal on left and carboxyl terminal on right Next aa added onto carboxyl end  Peptide bond formation occurs in ribosomal complex (ribosome)  tRNA (transfer RNA carry activated amino acids into ribosome to be added, also recognized groups of nucleotides on mRNA (codons) and translating codon to single amino acid (translation relayed as polypeptide) Protein Structure and Function  Proteins are most structurally complex molecules known, yet 20 aa’s combine to form all known proteins  Structure of protein dependent on amino acid sequence  Polypeptide has be to modified in several ways for folding to occur Primary Structure  Linear arrangement of atoms- amino acid sequence determined by nucleotide sequence of encoding genes  Introns spliced out of mRNA n  # of different polypeptide sequences=20 o n= number of amino acids  protein conformation= 3-d arrangement of polypeptide Secondary Structure- conformation of portion of polypeptide  Polypeptides spontaneously assume a random-coil structure  Local interactions stabilize periodically ordered structures, so the term statistical coil is often used  Interactions between amino acid side chains aren’t covalent bonds (except disulphide bridge)  Ionic bonds o Attraction between a positively charged cation and negatively charged anion  Hydrogen Bonds o Interaction between partially positively-charged hydrogen atom in a molecular dipole (e.g H 2) and unpaired electrons from another atom o Partial charge in water due to polarized covalent bond  Van der Waal forces (London Dispersion forces) o Weak, non-specific attractive force o Results from creation of a temporary dipole when two noncovalently bonded atoms are close enough to disrupt the distribution of electrons in one another (creating temporary dipole) o Responsible for association of nonpolar molecules that can’t form hydrogen or ionic bonds  Hydrophobic effects o Aggregation of nonpolar molecules (side chains) in an aqueous medium to reduce the number of interactions with water. o Reduces hydrophobic surface area exposed to water o Ex. oil droplet in water o In cytosol we have hydrophobic environment that can induce these effects  Non-covalent interactions are individually weak forces (cannot maintain protein structure)  Positions of interacting molecules must correspond to maximize interactions o More interactions = stronger association (accumulated effect of many bonds) Structures  Periodic folding of polypeptide chain into distinct, conserved, geometric arrangements Alpha-Helix  Spiral-rod like structure  Carbonyl oxygen of each peptide bond is H-bonded to the amide hydrogen of the amino acid 4 residues toward the C-terminal  Involves conserved side chains, so develops independently of the specific amino acid side chains o Side chains determine polarity of outer surface of helix  Empty spheres represent alpha carbons Beta-Pleated Sheet  Laterally packed B strands (5-8 amino acid residues long )  H-bonds between carbonyl and amino groups of backbone in adjacent B strands  Forms independent of properties of side chains (determine polarity of surface)  Parallel or anti-parallel arrangements  Inter-or intramolecular interactions o Intra- B-sheet in 1 polypeptide, Inter- B-sheet in 2-3 polypeptide  Core of proteins demonstrate extensive B-sheet formation  Connectors= hinges, turns, loops o Ex. B turns connect segments of B-Sheets (involves 3-4 aa residues) o Carbonyl oxygen of aa-1 H-bonded to amino-H of aa-4 o Proline at aa-2 introduces sharp bend o Glycine at aa-3 minimizes steric hindrance Motifs  Built from particular combinations of secondary structures  Structural units that occur in a variety of proteins  Exhibit particular 3-D architecture  Usually associated w/ a particular function Coiled-Coil motif  2 or more amphipathic a-helices wrapped around one another o amphipathic- hydrophobic hydrophilic parts in same structure  Heptad (7) repeats, w/ hydrophobic residues at position 1 and 4 on repeat  Found in DNA binding protein (fits nicely in groove of double stranded DNA) Zinc Finger motif  A-helix and two b-strands, held in place by interaction of precisely positioned Cys (C) or His (H) residues with a zinc atom  C 2 ,2C 4r C z6nc finger o Zinc reacts w/ all 3, but all have conserved shape/structure  Found in RNA and DNA binding proteins B-barrel motif  4-10 anti-parallel B-strands connected by hairpins  Strands successively added to one another until last strand H- bonded to first strand to complete the barrel (loops back on itself)  Useful in creating a pore across hydrophobic membrane in which r-gr
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