Proteins: Wide range of func2ons Proteins coded in DNA account for more than 50% of the dry mass of most cells Protein func9ons structural support storage transport cellular communica9ons movement defense against foreign substances Polypep2des Polypep2des polymers built from the same set of 20 amino acids Amino acid monomers Protein consists of one or more polypep9des Folded into func9onal 3-D form Amino acids Amino Acid Monomers Nonpolar organic molecules with carboxyl and amino groups Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) differ in their proper9es due to differing side chains Methionine (Met or M) Phenylalanine (Phe or F) Trypotphan (Trp or W) Proline (Pro or P) called R groups Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Electrically charged Acidic Basic Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) 1
Amino Acid Polymers pep2de bonds Covalent bond between C and Peptide bond Polypep9des N linking amino acids range in length from a few to (a) more than a thousand monomers Amino acid sequence dictates type Peptide bond Side chains Backbone of polypep9de (b) Amino end (N-terminus) Carboxyl end (C-terminus) and ul9mately type of protein Protein Structure and Func2on func9onal protein consists of one (or more) polypep9de(s) twisted, folded, and coiled into a unique shape Groove Groove (a) A ribbon model of lysozyme (b) A space-filling model of lysozyme Protein Structure and Func2on Sequence of amino acids determines a protein s three-dimensional structure Protein s structure determines its func9on Fit substrate in in specific lock and key fashion Antibody protein Protein from flu virus 2
Primary structure (1 ) sequence of amino acids Secondary structure (2 ) ini9al folding alpha(α) helices or beta(β) sheets in the polypep9de chain Ter9ary structure (3 ) interac9ons among side chains (R groups) combina9ons of α-helices and β- sheets Quaternary structure (4 ) protein consists of mul$ple polypep9de chains Primary structure Sequence of amino acids Dictated by sequence of nucleo9des in DNA Codon set of three nucleo9des code for a specific amino acid secondary structure result from hydrogen bonds between backbones of amino acids α helices Not R groups coiled H-bond between every fourth amino acid α kera9n - hair β pleated sheet Accordian folds Amyloid plaques of Alzheimers amino acid subunits β pleated sheet Secondary Structure α helix 3
Ter2ary structure Combina9ons of helices and pleated sheets determined by interac9ons between R groups, rather than interac9ons between backbone cons9tuents covalent bonds hydrogen bonds ionic bonds hydrophobic interac2ons van der Waals interac9ons Strong covalent bonds called disulfide bridges may reinforce the protein s structure Quaternary structure results when two or more polypep9de chains form one macromolecule Collagen fibrous protein consis9ng of three polypep9des coiled like a rope Hemoglobin globular protein with four polypep9des: two alpha and two beta chains Tertiary Structure Quaternary Structure Polypeptide chain β Chains Iron Heme Collagen α Chains Hemoglobin Fig. 5-21 Primary Structure Secondary Structure Tertiary Structure Quaternary Structure β pleated sheet + H 3 N Amino end Examples of amino acid subunits α helix 4
What Determines Protein Structure? In addi9on to primary structure physical and chemical condi9ons can affect structure ph salt concentra9on Temperature other environmental factors can cause a protein to Denaturation unravel Denatura2on loss of a protein s na9ve structure Now biologically inac9ve Normal protein Renaturation Denatured protein Protein Folding in the Cell It is hard to predict a protein s 3D structure from its primary structure Sequences of 1.2 million proteins known Only 8,500 3-D shapes known Most proteins probably go through several states on their way to a stable structure Chaperonins protein molecules that assist the proper folding of other proteins Cap Polypeptide Correctly folded protein Hollow cylinder Chaperonin (fully assembled) Steps of Chaperonin Action: 1 An unfolded polypeptide enters the cylinder from one end. 2 The cap attaches, causing the 3 cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. Nucleic Acids Store and transfer gene9c informa9on Gene unit of inheritance codes for the amino acid sequence of a polypep9de Genes are made of DNA, a nucleic acid 5
The Roles of Nucleic Acids Two types of nucleic acids: Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA provides direc9ons for its directs synthesis of own replica9on messenger RNA () controls protein synthesis Protein synthesis occurs in ribosomes Fig. 5-26-1 DNA 1 Synthesis of in the nucleus NUCLEUS CYTOPLASM Fig. 5-26-2 DNA 1 Synthesis of in the nucleus NUCLEUS CYTOPLASM 2 Movement of into cytoplasm via nuclear pore 6
Fig. 5-26-3 DNA 1 Synthesis of in the nucleus NUCLEUS CYTOPLASM 2 Movement of into cytoplasm via nuclear pore Ribosome 3 Synthesis of protein Polypeptide Amino acids The Structure of Nucleic Acids Polynucleo2des Nucleic acid polymer Nucleo2de 5ʹ end 5ʹC Nitrogenous bases Pyrimidines monomers of a polynucleo9de 3ʹC Nucleoside Nitrogenous base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines a nitrogenous base, a pentose sugar, and a phosphate group Phosphate group 5ʹC 3ʹC (b) Nucleotide 3ʹ end (a) Polynucleotide, or nucleic acid Sugar (pentose) Adenine (A) Guanine (G) Sugars Nucleoside Deoxyribose (in DNA) Ribose (in RNA) por9on of a nucleo9de without the phosphate group (c) Nucleoside components: sugars Two families of nitrogenous bases: Nucleo2de Monomers Pyrimidines (cytosine (C), thymine (T), and uracil (U)) single six-membered ring Purines (adenine (A) and guanine (G)) deoxyribose six-membered ring fused to a fivemembered ring Sugar in DNA ribose Sugar in RNA 7
Nucleo9de Polymers linked together to build a polynucleo9de Adjacent nucleo9des joined by phosphodiester bonds (covalent) between the OH group on the 3ʹ carbon of one nucleo9de and the phosphate on the 5ʹ carbon of the next Create a backbone of sugar-phosphate units with nitrogenous bases as appendages Nucleo2de Polymers Double helix two polynucleo9des spiraling around an imaginary axis, forming a DNA molecule Nitrogenous bases bond with one another in the middle in complementary fashion An2parallel A-T; C-G two backbones run in opposite 5ʹ 3ʹ direc9ons from each other in the DNA double helix One DNA molecule includes many genes Equals one chromosome The DNA Double Helix You should now be able to: 1. List and describe the four major classes of molecules 2. Describe the forma9on of a glycosidic linkage and dis9nguish between monosaccharides, disaccharides, and polysaccharides 3. Dis9nguish between saturated and unsaturated fats and between cis and trans fat molecules 4. Describe the four levels of protein structure 5. Dis9nguish between the following pairs: pyrimidine and purine, nucleo9de and nucleoside, ribose and deoxyribose, the 5ʹ end and 3ʹ end of a nucleo9de 8