Biomolecules II PDF

BIOL S103F ESSENTIAL BIOLOGY STRUCTURES, PROPERTIES, AND FUNCTIONS OF BASIC BIOMOLECULES (PART II) Week 3 Proteins 2  Very diverse, with tens of thousands of different proteins  Each with a specific structure & function in the human body  Polymers composed of different arrangements of a common se...

BIOL S103F ESSENTIAL BIOLOGY STRUCTURES, PROPERTIES, AND FUNCTIONS OF BASIC BIOMOLECULES (PART II) Week 3 Proteins 2  Very diverse, with tens of thousands of different proteins  Each with a specific structure & function in the human body  Polymers composed of different arrangements of a common set of just 20 amino acid monomers  A polypeptide chain contains hundreds or thousands of amino acids linked by peptide bonds  The amino acid sequence causes the polypeptide to assume a particular shape  Functions of different types of proteins depend on their individual shapes Groove Groove @2015 Pearson Education, Inc. Functions of Proteins 3 1. 2. 3. 4. Enzymes  Serve as catalysts & regulate virtually all chemical reactions within cells  e.g. Lactase Transport proteins  Embedded in cell membranes to move molecules into / out of cells  e.g. Haemoglobin Defensive proteins  Protect against disease  e.g. Antibodies of the immune system Signal proteins  Help coordinate body activities  e.g. Many hormones & other chemical messengers @2015 Pearson Education, Inc. Functions of Proteins (cont’d) 4 5. 6. 7. 8. Receptor proteins  Built into cell membranes, receiving & transmitting signals into cells Contractile proteins  Found within muscle cells  e.g. Actin & myosin Structural proteins  Form the long, strong fibers of connective tissues  e.g. Collagen & keratin Storage proteins  Serve as biological reserves of metal ions & amino acids  e.g. Ovalbumin in egg white @2015 Pearson Education, Inc. Amino Acids 5   Amino acids all have 1. An amino group NH2 2. A carboxyl group COOH (which makes it an acid) Also bonded to the central carbon is 3. A hydrogen atom 4. A side chain (R group)  Determines the specific properties of each of the 20 amino acids used to make proteins  Hydrophobic vs Hydrophilic Hydrophobic Leucine (Leu) Hydrophilic Serine (Ser) Aspartic acid (Asp) @2015 Pearson Education, Inc. Types of amino acids 6 Essential Conditional http://www.personal.psu.edu/staff/m/b/mbt102/bisci4online/chemistry/chemistry8.htm Polypeptides 7   Range in length from a few to more than a thousand monomers Each polypeptide has a unique linear sequence of amino acids  With a carboxyl end (C-terminus) & an amino end (N-terminus)  Amino acid monomers are linked together in a dehydration reaction  Peptide bond  Additional amino acids can be added by the same process to create a chain of amino acids  Polypeptide @2015 Pearson Education, Inc. A Protein’s Functional Shape Results from 4 Levels of Structure 8   A functional protein is one or more polypeptide chains precisely coiled, twisted, & folded into a unique three-dimensional shape A protein can have 4 levels of structure 1. Primary structure  Unique linear sequence of a.a. determined by inherited genetic information 2. Secondary structure  Coiling (alpha helix) or folding (beta pleated sheet) of polypeptide chain  Regular interaction of groups in the peptide backbone  Hydrogen bond pattern A Protein’s Functional Shape Results from 4 Levels of Structure 9 3. Tertiary structure  Overall 3D shape of a polypeptide resulting from interactions between R groups  Determines the function of a protein 4. Quaternary structure  Association of multiple (identical / different) polypeptide subunits 10 @2015 Pearson Education, Inc. Denaturation of Protein 11    In addition to primary structure, physical & chemical conditions can affect structure Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel Denaturation  Loss of a protein’s native structure (native conformation)  In the process of denaturation, a protein  Unravels  Loses its specific shape  Loses its function  A denatured protein is biologically inactive @2015 Pearson Education, Inc. Sickle-Cell Disease: a Change in Primary Structure 12 @2015 Pearson Education, Inc. Protein Folding in the Cell 13  Hard to predict a protein’s structure from its primary structure  Most proteins go through several stages on their way to a stable structure   Chaperonins  Protein molecules that assist the proper folding of other proteins Diseases associated with misfolded proteins  e.g. Alzheimer’s, Parkinson’s, mad cow disease @2015 Pearson Education, Inc. Types of Nucleic Acids 14 Nucleic acid is polymer of nucleotides  DNA and RNA  Deoxyribose Nucleic Acids (DNA)  Ribose Nucleic Acids (RNA)   Messenger RNA (mRNA)  Ribosomal RNA (rRNA)  Transfer RNA (tRNA) Nucleotides 15    DNA & RNA are composed of monomers (nucleotides) Nucleotides have 3 parts: 1. A 5-carbon sugar  Ribose in RNA  Deoxyribose in DNA 2. A phosphate group Phosphate 3. A nitrogenous base group  Adenine (A)  Thymine (T) in DNA / uracil (U) in RNA  Cytosine (C)  Guanine (G) Nitrogenous base (adenine) Sugar Nucleoside  The portion of a nucleotide without the phosphate group @2015 Pearson Education, Inc. Components of Nucleic Acids 16  2 families of nitrogenous bases  Pyrimidines have a single 6-membered ring  Cytosine, thymine, uracil  Purines have a 6-membered ring fused to a 5-membered ring  Adenine, guanine @2015 Pearson Education, Inc. Polynucleotide 17  Adjacent nucleotides are joined by covalent bonds between  -OH group on the 3’ carbon of one nucleotide  Phosphate on the 5’ carbon on the next  By dehydration reactions  Produces a repeating sugar-phosphate backbone with protruding nitrogenous bases  Phosphodiester linkages Nitrogenous base (adenine) Phosphate group Sugar @2015 Pearson Education, Inc. Polymerisation of Nucleotides 18   Condensation or dehydration between nucleotides Nucleoside triphosphate      Adenosine triphosphate Thymidine triphosphate Guanosine triphosphate Cytidine triphosphate Uridine triphosphate https://www.chegg.com/homework-help/questions-and-answers/lets-create-energy-story-reaction-reactants-select-polymer-3-oh-ctp-polymer-3-oh-atp-polym-q34898982 Nucleic Acids 19   Amino acid sequence of a polypeptide is programmed by a discrete unit of inheritance known as a gene Genes consist of DNA (deoxyribonucleic acid), a type of nucleic acid  Inherited from an organism’s parents  Provides directions for its own replication  Programs a cell’s activities by directing the synthesis of proteins  Does not build proteins directly  Works through an intermediary, RNA (ribonucleic acid)  DNA is transcribed into RNA in a cell’s nucleus  RNA is translated into proteins in the cytoplasm @2015 Pearson Education, Inc. DNA vs RNA 20       RNA is usually a single polynucleotide strand DNA is a double helix (2 polynucleotide strands wrap around each other)  The 2 strands are associated because particular bases always hydrogen-bond to one another, producing complementary base pairs  A pairs with T; C pairs with G In the DNA double helix, the 2 backbones run in opposite 5’ → 3’ directions from each other (antiparallel) C C One DNA molecule includes many genes The base sequence along a DNA / mRNA polymer is unique for each gene Cellular functions  DNA: Stores hereditary information Transmit it from one generation to another  RNA: Gene expression (direct protein synthesis) G G T A C G A Base pair T A T G C A A T T T A @2015 Pearson Education, Inc. Complementary Base Pairing of Nucleotides 21  Adenine pairs with Thymine or Uracil  Guanine pairs with cytosine  Complementary base pairing is mediated by hydrogen bond  Adenine and thymine/uracil forms two hydrogen bonds  Guanine and cytosine forms three hydrogen bonds Complementary Base Pairing of Nucleotides 22 Complementary base pairing allows the formation of doubled stranded structure Structure of Nucleic Acids 23     Nucleic acid is polymer of nucleotides Nucleic acid has a helical structure DNA is double stranded RNA is usually single stranded but sometimes is double stranded Functions of Nucleic Acids 24     DNA  Carries inheritance information mRNA  Carrying information from DNA for protein production rRNA  Part of the ribosome structure tRNA  Participate in RNA synthesis Functions of Nucleotides 25  Nucleotides are different from nucleic acids  Nucleotide is the monomer of nucleic acids  Energy molecules (ATP, GTP)  Coenzyme molecules / Electron acceptors   Nicotinamide adenine dinucleotide (NAD+) Flavin adenine dinucleotide (FAD) Functions of Nucleotides 26 Nicotina mide adenine dinucleoti de (NAD+) Flavin adenine dinucleoti de (FAD) Vitamins 27  Organic compounds Present in trace amount Essential to normal physiological function Deficiency cause specific syndrome  Fat soluble vitamin      Vitamin A, D, E, K Water soluble vitamin  Vitamin B, C, folic acid http://www.compoundchem.com/2015/01/13/vitamins/ Vitamins 29 https://www.pinterest.com/pin/261560690830384657/ https://www.pinterest.com/pin/261560690830384657/ Water 31  Two important parameters to characterize water    Water content / moisture content    Water content / moisture content Water activity/ water availability (aw) A measure of amount of water present in food Weight of water / dry weight of food (%w/w) Water activity/ water availability (aw)    A measure of unbound water present in food Partial vapour pressure of food / partial vapour pressure of pure water (0-1) Increase as temperature increase