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by: Udbluehen03

Lecture_3___Protein_Structure.pdf BISC401

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These notes cover protein structure
Molecular Biology of the Cell
Class Notes
molecularbiology, cellandmolecularbio, Biology
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This 6 page Class Notes was uploaded by Udbluehen03 on Friday September 9, 2016. The Class Notes belongs to BISC401 at University of Delaware taught by Lachke,Salil in Fall 2016. Since its upload, it has received 15 views. For similar materials see Molecular Biology of the Cell in Biology at University of Delaware.


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Date Created: 09/09/16
Class 3 – 9/6/2016, Protein Structure Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish Amino Acids - There are 20 types of amino acids - Hydrophobic Alanine Valine Isoleucine Leucine Methionine Phenylalanine Tyrosine Tryptophan - Hydrophilic o Basic Acidic Polar Special Lysine Aspartate Serine Cysteine Arginine Glutamate Threonine Glycine Histidine Asparagine Proline Glutamine - When amino acids (all 20) are incorporated into a protein polymer they are called residues - All amino acids have a characteristic structure consisting of a central alpha carbon atom (Cα) - An amino acid is bonded to four different chemical groups o An amino (-NH2) group o A carboxyl or carboxylic acid (-COOH) group o A hydrogen (H) group o One variable group called a side chain or R group - The α-carbon in all amino acids except glycine is asymmetric o Chiral or asymmetric α-carbon lends itself to formation of mirror images called isomers or stereoisomers. o The molecules can exist in two mirror image forms  D (dextro) isomers  L (levo) isomers o With rare exceptions, only the L form of amino acids are found in proteins o D amino acids are prevalent in bacterial cell walls and other microbial products - Amino acids can be classified into several broad categories based on o Size Class 3 – 9/6/2016, Protein Structure Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish o Shape o Charge o Hydrophobicity (measure of water solubility) o Chemical reactivity of their side chain - Humans and other mammals can synthesis 11 of the 20 amino acids o The rest are essential amino acids (9)  Must be included in diet  Phenylalanine  Valine  Threonine  Tryptophan  Isoleucine  Methionine  Leucine  lysine  Histidine Hydrophobic Amino Acids - Amino acids with nonpolar side chains - Poorly soluble in water - Linear or branched are called Aliphatic Amino Acid o They don’t form ring o They are  Alanine  Valine  Isoleucine  Leucine  Methionine - Aromatic Amino Acid o They contain a ring o They are  Phenylalanine  Tyrosine  Tryptophan Class 3 – 9/6/2016, Protein Structure Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish Hydrophilic Amino Acids - The most hydrophilic amino acid is the subset with side chains that are charged (ionized) at the pH typical of biological fluids (≈7) both inside and outside the cell. - Arginine and Lysine o Have positively charged side chains - Histidine o Has a side chain containing a ring with two nitrogens called imidazole o Can shift from being positively charged to uncharged in response to small changes in the acidity of its content - Asparagine and glutamine o Uncharged o Side chains: amide groups with extensive hydrogen-bonding capacities - Serine and Threonine o Uncharged o Have polar hydroxyl groups Special Amino acids - Cysteine, Glycine, Proline - Unique properties because of their side chains - Cysteine o Side chain: sulfhydryl group (SH) o SH releases H+ to form S- (thiolate) o Thiolate anions play important roles in catalysis o Each of two adjacent sulfhydryl groups can be oxidized, each releasing a proton and electron, to form a covalent disulfide bond (-S-S-) o Disulfide bonds  Serve to cross link regions within(intra) and between (inter-molecular) polypeptides  Stabilize folded structure - Glycine o No chiral carbon o Smallest amino acid o Its small size allows it to fit into tight spaces - Proline o Its side chain bends around to form a ring by covalently bonding to the nitrogen atom in the amino acid attached to the α-carbon o Very rigid Class 3 – 9/6/2016, Protein Structure Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish o The presence of proline in a protein creates a fixed kink in the polymer chain, limiting how it can fold in the vicinity of the proline residue Chemically Modified Amino Acids - They have important biological roles - Phosphorylation: Serine, Threonine, Tyrosine - Glycosylation: Asparagine, Serine, Threonine - Methylation: Arginine, Histidine - Acetylation: Lysine, other amino acids (Most common) - Hydroxylation: Proline, Lysine (Collagen protein) Overview of Protein Structure and Function - Different sizes and shapes - The linear, unbranched polymer of amino acids will fold into one or a few closely related three-dimensional shapes called conformation - The conformation of a protein + the distinctive chemical properties of its amino acid side chains determines its function - The function of a protein can change when the protein noncovalent/covalently associates with other molecules - Classes of protein 1. Structural protein o Determine the shapes of cells and their extracellular environment o Serve as guide wires or rails to direct the intracellular movement of molecules and organelles 2. Scaffold proteins o Bind two or more proteins together to perform specific functions 3. Enzymes o Catalyze chemical reactions 4. Membrane Transport Proteins o Allow the flow of ions and molecules across cellular membranes 5. Regulatory Proteins o Act as signals, sensors, and switches to control the activities of cells by altering the functions of other proteins and genes Class 3 – 9/6/2016, Protein Structure Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish o Include signaling proteins (e.g. hormones) 6. Motor proteins o Move other proteins, organelle, cell - Proteins have a hierarchical structure - A polypeptides linear sequence of amino acids linked by peptide bonds (primary structure) folds into local helices or sheets (secondary structure) that pack into a 3 - dimensional shape (tertiary structure) - A polypeptide’s primary structure determines the secondary structure - There are four levels of protein structure o Primary o Secondary o Tertiary o Quaternary - Primary structure o Sequence of amino acids in a polypeptide o Bonds: covalent - Secondary structure o Structural motifs in a polypeptide o Bonds: Hydrogen bonds (between NH and CO groups in the backbone of the polypeptide o The principal secondary structures are  The alpha (α) helix  The beta (β) sheet  The short U-shaped beta (β) turn - Tertiary structure o Folding up a single polypeptide chain o Bonds: various bonds; covalent (disulfide bond) hydrogen bonds, ionic, van de Waals, hydrophobic o Not rigidly fixed because the stabilizing interactions are often weak - Quaternary o Association of multiple folded protein subunits into a larger multimeric protein o Bonds: various bonds Peptide bonds - Amino acids are joined by peptide bonds - It is a covalent amide group - It has a partial double bond character Class 3 – 9/6/2016, Protein Structure Dr. Salil Lachke Molecular Cell Biology, 8 edition - Lodish o Dipoles are set up due to resonance effect (partial) sharing of two pairs of electrons between the carbonyl oxygen and the amide nitrogen - Protein structure is limited by the flexibility of the peptide backbone o Double bond character of C-N bond prevents rotation around the peptide bond itself o Electrons are distributed between C-O and C-N bonds - Peptide bonds can make two H-bonds, ne with its N-H in one direction, the other with its C=O in the other direction Protein Shape and Function - Fibrous Protein o Long strands or sheet o Collagen: α-helix conformation o Fibroin: β-sheet conformation - Globular Protein o Water soluble o Compactly folded structure o For example, myoglobin, hemoglobin, most enzymes and soluble proteins in the cell o Usually have both α-helices and β-sheet Secondary Structure: The α-Helix - Within an α-helix, all the backbone amino and carboxyl groups are hydrogen bonded to one another except at the very beginning and end of the helix - Side chains face out (away) from the helix - The α-helix is a semi-rigid structure - It bends only slightly in a protein - Amino acids commonly found in α-helix: Leucine, Methionine, Glutamate - All the hydrogen bond acceptors (i.e. the carboxyl groups) have the same orientation - In water-soluble proteins, hydrophilic helixes tend to be found on the outside surfaces - Hydrophobic helices tend to be buried within the core of the folded protein


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