Chapter 20. Protiens. Chapter 21. Protein and the Amino Acids. These are biopolymers that are constructed from a limited set of amino acids.

Transcription

1 hemistry 121(01) Winter Introduction to rganic hemistry and Biochemistry Instructor Dr. Upali Siriwardane (Ph.D. hio State) ffice: 311 arson Taylor all ; Phone: ; ffice ours: MWF 8:00 am - 10:00 am; TT 9:00 10:00 am & 1:00-2:00 pm. December 18, 2009 Test 1 (hapters 12-13) January 20, 2010 Test 2 (hapters 14,15 & 16) February 8, 2010 Test 3(hapters 17, 18 & 19) March 1, 2010 Test 4 (hapters 20, 21 & 22) March 2, 2010 omprehensive Make Up Exam: hapter 20. Protiens The protein made by spiders to produce a web is a form of silk that can be exceptionally strong. hp hp hapter 20. Proteins 20.1 haracteristics of Proteins 20.2 Amino Acids: The Building Blocks for Proteins 20.3 hirality and Amino Acids 20.4 Acid-Base Properties of Amino Acids 20.5 ysteine: A hemically Unique Amino Acid 20.6 Peptide Formation 20.7 Biochemically Important Small Peptides 20.8 General Structural haracteristics of Proteins 20.9 Primary Structure of Proteins Secondary Structure of Proteins Tertiary Structure of Proteins Quaternary Structure of Proteins Fibrous and Globular Proteins Protein ydrolysis Protein Denaturation Glycoproteins Lipoproteins hapter 21. Protein and the Amino Acids These are biopolymers that are constructed from a limited set of amino acids. They are the most plentiful organic substances in the cell. About half of the dry mass of a cell is composed of proteins. They serve a wide range of functions. hp hp

2 Protein function Enzymes biological catalysts. Types of Proteins Immunoglobulins antibodies of immune system. Transport move materials around -hemoglobin for 2. egulatory hormones, control of metabolism. Structural coverings and support - skin, tendons, hair, bone. Movement muscle, cilia, flagella. hp hp Amino acid 20 standard amino acids Amino acid - An organic compound that contains both an amino (- 2 ) and carboxyl (-) groups attached to same carbon atom The position of carbon atom is Alpha (a) - 2 group is attached at alpha (a) carbon atom. - group is attached at alpha (a) carbon atom. = side chain vary in size, shape, charge, acidity, functional groups present, hydrogen-bonding ability, and chemical reactivity. >700 amino acids are known Based on common groups, there are 20 standard amino acids 2 -Amino Group Side hain -arbon Atom -arboxyl Group All amino acids differ from one another by their -groups Standard amino acids are divided into four groups based on the properties of -groups on-polar amino acids: -groups are non-polar Such amino acids are hydrophobic-water fearing (insoluble in water) nine of the 20 standard amino acids are non polar When present in proteins, they are located in the interior of protein where there is no polarity Polar amino acids: -groups are polar Three types: Polar neutral; Polar acidic; and Polar basic a)polar-neutral: contains polar but neutral side chains Seven amino acids belong to this category b) Polar acidic: ontain carboxyl group as part of the side chains Two amino acids belong to this category c) Polar basic: ontain amino group as part of the side chain Two amino acids belong to this category hp hp

3 on-polar Amino Acids Polar eutral Amino Acids hp hp Polar Acidic and Basic Amino Acids hp Amino Acid omenclature ommon names assigned to the amino acids are currently used. Three letter abbreviations - widely used for naming: First letter of amino acid name is compulsory and capitalized followed by next two letters not capitalized except in the case of Asparagine (Asn), Glutamine (Gln) and tryptophan (Trp). ne-letter symbols - commonly used for comparing amino acid sequences of proteins: Usually the first letter of the name When more than one amino acid has the same letter the most abundant amino acid gets the 1st letter. Both types of abbreviations are given in the following slides hp

4 andedness/hirality of Amino Acids Abbreviations glycine Gly G alanine Ala A valine Val V leucine Leu L isoleucine Ile I methionine Met M phenylalanine Phe F tryptophan Trp W Proline Pro P The amino acids found in nature as well as in proteins are L isomers. Some bacteria do have some D-amino acids With monosaccharides nature favors D-isomers The rules for drawing Fischer projection formulas for amino acid structures is similar to suguars hp hp Practice Exercise ame the following amino acids with correct designation for the enantiomer (chiral carbon is indicated by *). 2 A B * * S 2 2 * 2 Practice Exercise lassify the following amino acids based on the polarity of their -groups onpolar a d. 2 2 on-polar 3 A = L-Isoleusine B = D-ysteine = L-Tyrosine Polar eutral Polar Acidic b. c. 2 2 e Polar Basic 2 hp hp

5 Zwitterion form of amino acids: In pure form amino acids are white crystalline solids Most amino acids decompose before they melt ot very soluble in water Exists as Zwitterion: An ion with + (positive) and (agetive) charges on the same molecule with a net zero charge arboxyl groups give-up a proton to get negative charge Amino groups accept a proton to become positive Isoelectric Point Isoelectric point (pi) p at which the concentration of Zwitterion is maximum -- net charge is zero Different amino acids have different isoelectric points At isoelectric point - amino acids are not attracted towards an applied electric field because they net zero charge L 3 D 3 Low p (net + charge) 3 Zwitter Ion (net neutral charge) 3 igh p (net - charge) eutral p hp hp Peptides Under proper conditions, amino acids can bond together to produce an unbranched chain of amino acids. The length of the amino acid chain can vary from a few amino acids to many amino acids. Such a chain of covalently-linked amino acids is called a peptide. The covalent bonds between amino acids in a peptide are called peptide bonds. Type of Peptides Dipeptide: bond between two amino acids ligopeptide: bond between ~ amino acids Polypeptide: bond between large number of amino acids Every peptide has an -terminal end and a -terminal end + 3 -aa-aa-aa-aa-aa-aa-aa-aa-aa- - -terminal end terminal end Alanine Phenylalanine Serine hp hp

6 Peptide omenclature The -terminal amino acid residue keeps its full amino acid name. All of the other amino acid residues have names that end in -yl. The -yl suffi x replaces the -ine or -ic acid ending of the amino acid name, except for tryptophan, for which -yl is added to the name. The amino acid naming sequence begins at the - terminal amino acid residue. Example: Ala-leu-gly has the IUPA name of alanylleucylglycine Isomeric Peptides Peptides that contain the same amino acids but present in different order are different molecules (constitutional isomers) with different properties For example, two different dipeptides can be formed between alanine and glycine The number of isomeric peptides possible increases rapidly as the length of the peptide chain increases hp hp Biochemically Active Peptides Many relatively small peptides are biochemically active: ormones eurotransmitters Antioxidants Small Peptide ormones: Best-known peptide hormones: oxytocin and vasopressin Produced by the pituitary gland nonapeptide (nine amino acid residues) with six of the residues held in the form of a loop by a disulfide bond formed between two cysteine residues Small Peptide eurotransmitters Enkephalins are pentapeptide neurotransmitters produced by the brain and bind receptor within the brain elp reduce pain Best-known enkephalins: Met-enkephalin: Tyr Gly Gly Phe Met Leu-enkephalin: Tyr Gly Gly Phe Leu hp opyright engage Learning. All 24 hp

7 Protein lassification:hemical omposition Simple proteins: A protein in which only amino acid residues are present: More than one protein subunit may be present but all subunits contain only amino acids onjugated protein: A protein that has one or more nonamino acid entities (prosthetic groups) present in its structure: ne or more polypeptide chains may be present on-amino acid components - may be organic or inorganic - prosthetic groups Lipoproteins contain lipid prosthetic groups Glycoproteins contain carbohydrate groups, Metalloproteins contain a specific metal as prosthetic group hp Four levels of protein structure Primary structure The sequence of amino acids in a protein. Secondary structure Way that chains of amino acids are coiled or folded - ( -helix, -sheet, random coil). Tertiary structure Way -helix, -sheet, random coils fold and coil. Quaternary structure Way that two or more peptide chains pack together. hp Four Types of Structures Primary Structure Secondary Structure Tertiary Structure Quaternary Primary Structure: Primary structure of protein refers to the order in which amino acids are linked together in a protein Every protein has its own unique amino acid sequence Frederick Sanger (1953) sequenced and determined the primary structure for the first protein - Insulin Primary structure All proteins have the same covalent backbone Part of a protein. hp hp

8 Primary Structure of a uman Myoglobin Proteins primary sequence and the source Proteins of the same organism always same sequence (cows, pigs, etc.) Different sources: Insulin from pigs, cows, sheep, humans similar Some differences: Species hain A hain B AA #8 AA #9 AA #10 AA #30 uman Thr Ser Ile Thr Pig (porcine) Thr Ser Ile Ala ow (bovine) Ala Ser Val Ala Due to differences insulin may show some reaction over time ow human insulin produced from genetically engineered bacteria hp hp Secondary Structure of Proteins Arrangement of atoms of backbone in space. The two most common types : alpha-helix ( -helix) and the beta-pleated sheet ( -pleated sheet). The peptide linkages are essentially planar thus allows only two possible arrangements for the peptide backbone for the following reasons: For two amino acids linked through a peptide bond six atoms lie in the same plane The planar peptide linkage structure has considerable rigidity, therefore rotation of groups about the bond is hindered is trans isomerism is possible about bond. The trans isomer is the preferred orientation Three levels of structure: telephone cord hp hp

9 -helix Every amide hydrogen and carbonyl oxygen is involved in a hydrogen bond. Alpha-helix ( -helix) A single protein chain adopts a shape that resembles a coiled spring (helix): -bonding between same amino acid chains intra molecular oiled helical spring -group outside of the helix -- not enough room for them to stay inside hp hp Summary of protein structure primary tertiary secondary quaternary -Pleated sheets Another secondary structure for protein. eld together by hydrogen bonding between adjacent sheets of protein. The hydrogen bonding between the carbonyl oxygen atom of one peptide linkage and the amide hydrogen atom of another peptide linkage. hp hp

10 -Pleated sheets Tertiary Structure of Proteins The overall three-dimensional shape of a protein esults from the interactions between amino acid side chains ( groups) that are widely separated from each other. In general 4 types of interactions are observed. hp hp Four Types of Interactions Disulfide bond: covalent, strong, between two cysteine groups Electrostatic interactions: Salt Bridge between charged side chains of acidic and basic amino acids -, - 2, -, - 2 -Bonding between polar, acidic and/or basic groups For -bonding to occur, the must be attached on, or F ydrophobic interactions: Between nonpolar side chains hp Quaternary structure of protein Quaternary structure of protein refers to the organization among the various peptide chains in a multimeric protein: ighest level of protein organization Present only in proteins that have 2 or more polypeptide chains (subunits) Subunits are generally Independent of each other - not covalently bonded Proteins with quartenary structure are often referred to as oligomeric proteins ontain even number of subunits hp

11 Separation of three amino acids Separation of Lys, Phe, and Glu using electrophoresis after hydrolysis of protein Secondary structure Long chains of amino acids commonly fold or curl into a regular repeating structure. Structure is a result of hydrogen bonding between amino acids within the protein. ommon secondary structures are: - helix - pleated sheet Secondary structure adds new properties to a protein like strength, flexibility,... hp hp The coiled-coil structures ollagen Family of related proteins. About one third of all protein in humans. Structural protein Provides strength to bones, tendon, skin, blood vessels. Forms triple helix - tropocollagen. The coiled-coil structure of the fibrous protein beta kerotin. hp hp

12 ollagen Tertiary structure of proteins esults from interaction of side chains. The protein folds into a tertiary structure. Possible side chain interactions: Similar solubilities Ionic attractions Electrostatic attraction between + and - sidechains ovalent bonding hp hp Tertiary Structure Tertiary Structure of Proteins Sulfide crosslink ydrophobic interaction - S - S Salt bridge ydrogen bonding hp hp

13 Disulfide bonds and tertiary sturcture Four types of interactions between amino acid groups ysteine in the presence of mild oxidizing agents dimerizes to form a cystine molecule. ystine - two cysteine residues linked via a covalent disulfide bond. hp hp Quaternary structure of proteins Many proteins are not single peptide strands. They are combinations of several proteins - aggregate of smaller globular proteins. onjugated protein - incorporate another type of group that performs a specific function. prosthetic group Quaternary structure of proteins Aggregate structure This example shows four different proteins and two prosthetic groups. hp hp

14 Globular Proteins: Myoglobin Globular Proteins: Myoglobin: An oxygen storage molecule in muscles. Monomer - single peptide chain with one heme unit Binds one 2 molecule as a higher affinity for oxygen than hemoglobin. xygen stored in myoglobin molecules serves as a reserve oxygen source for working muscles emoglobin and Myoglobin emoglobin xygen transport protein of red blood cells. Myoglobin xygen storage protein of skeletal muscles. As with the cytochrome example, both proteins use heme groups. It acts as the binding site for molecular oxygen. opyright engage Learning. All 53 hp hp eme Myoglobin myoglobin 1 heme group eme hemoglobin 4 heme groups hp hp

15 emoglobin xygen Transport 2 chains 4 heme 2 chains hp hp Example - cytochrome 550 Sickle cell anemia eme structure ontains Fe 2+ Used in metabolism. Aggregate of proteins and other structures. Defective gene results in production of mutant hemoglobin. Still transports oxygen but results in deformed blood cells - elongated, sickle shaped. Difficult to pass through capillaries. auses organ damage, reduced circulation. Affects 0.4 % of African-American. hp hp

16 omparison of normal and sickle cell hemoglobin Denaturation of Proteins The loss of secondary, tertiary, and quaternary structures 1) p extremes. 2). eat - 3). Mechanical Agitation (foaming) 4). Detergents 5). rganic Solvents 6). Inorganic Salts - ormal Sickle hp hp eat-denaturation of Proteins Permanent for air hp hp

17 Major ategories of Proteins Based on Function Major ategories of Proteins Based on Function atalytic proteins: Enzymes are best known for their catalytic role. Almost every chemical reaction in the body is driven by an enzyme Defense proteins: Immunoglobulins or antibodies are central to functioning of the body s immune system. Transport proteins: Bind small biomolecules, e.g., oxygen and other ligands, and transport them to other locations in the body and release them on demand. Messenger proteins: transmit signals to coordinate biochemical processes between different cells, tissues, and organs. Insulin and glucagon - regulate carbohydrate metabolism uman growth hormone regulate body growth hp opyright engage Learning. All 65 ontractile proteins: ecessary for all forms of movement. Muscles contain filament-like contractile proteins (actin and myosin). uman reproduction depends on the movement of sperm possible because of contractile proteins. Structural proteins: onfer stiffness and rigidity ollagen is a component of cartilage a Keratin gives mechanical strength as well as protective covering to hair, fingernails, feathers, hooves, etc. Transmembrane proteins: Span a cell membrane and help control the movement of small molecules and ions. ave channels help molecules can enter and exist the cell. hemistry 121 Transport Winter 2010 LA is Tech very selective - allow passage of one type hp. of molecule or ion. opyright engage Learning. All 66 Major ategories of Proteins Based on Function Immunoglobulins Storage proteins: Bind (and store) small molecules. Ferritin - an iron-storage protein - saves iron for use in the biosynthesis of new hemoglobin molecules. Myoglobin - an oxygen-storage protein present in muscle egulatory proteins: ften found embedded in the exterior surface of cell membranes - act as sites for receptor molecules ften the molecules that bind to enzymes (catalytic proteins), thereby turning them on and off, and thus controlling enzymatic action. utrient proteins: Particularly important in the early stages of life - from embryo to infant. asein (milk) and ovalalbumin (egg white) are nutrient proteins hemistry 121 Milk Winter also 2010 LA provide Tech immunological protection for mammalian hp young. opyright engage Learning. All 67 Glycoproteins produced as a protective response to the invasion of microorganisms or foreign molecules - antibodies against antigens. Immunoglobulin bonding to an antigen via variable region of an immunoglobulin occurs through hydrophobic interactions, dipole dipole interactions, and hydrogen bonds. opyright engage Learning. All 68 hp