Protein Structure & Function: Amino Acids, Peptides, & Conformations, Study notes of Earth science

Download Protein Structure & Function: Amino Acids, Peptides, & Conformations and more Study notes Earth science in PDF only on Docsity! BIOCHEM (L3) 1 BIOCHEM (L3) LESSON Midterm Date that was discussed Discussed Add details Protein Proteins serve many functions. Among the most important functions are: 1. Structure: collagen and keratin are the 2 important structural proteins, chief constituents of skin, bone, hair, and nails; function for protection and support, forming connective tissue, tendons, bone matrices, and muscle fiber. 2. Catalysts: virtually all reactions in living systems are catalyzed by proteins called enzymes, without enzymes - reactions would occur so slowly as to be useless 3. Movement: muscles are made up of proteins called myosin and actin. 4. Transport: hemoglobin, a protein in the blood, transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes. 5. Regulation and control: many hormones are proteins, among them insulin, erythropoietin, oxytocin, and human growth hormone 6. Protection: when protein from outside source blood or some foreign antigen enters the body, the body makes its own proteins called antibodies to counteract the foreign protein. Antibody production is one of the major body mechanisms that the body uses to fight diseases. Blood clotting is carried out by protein fibrinogen. Without blood clotting, we would bleed to death from any small wound. 7. Storage: casein in milk and ovalbumin in eggs store nutrients for newborn mammals and birds; ferritin, a protein in the liver, stores iron 8. Regulation: some proteins not only control the expression of genes (regulating the kind of proteins to be synthesized in a cell), but also dictate when such synthesis takes @March 14, 2022 BIOCHEM (L3) 2 place Any individual needs a great many proteins to carry out these varied functions. A typical cell contains about 9000 different proteins; the entire human body has about 100,000 different proteins Two Major Types of Proteins fibrous proteins or Scleroproteins – insoluble in water; used mainly for structural purposes; Scleroprotein superfamilies include keratin, collagen, elastin, actin, myosin, and fibrin. globular proteins or Spheroproteins – more or less soluble in water; used mainly for nonstructural purposes. Examples are hemoglobin, insulin, immunoglobulin and many enzymes in the body. The increased solubility of proteins is all down to the folding of the protein. Amino acid: a compound that contains both an amino group (NH2) and a carboxyl group (COOH). a-Amino acid: an amino acid in which the amino group is on the carbon adjacent to the carboxyl group. Although a-Amino acids are commonly written in the un- ionized form, they are more properly written in the zwitterion (zwi- tər- ī- ˈä- n) or internal salt form. BIOCHEM (L3) 5 Polar Amino Acid with Hydrophobic Side Chain BIOCHEM (L3) 6 Non Polar side chains (at ph 7.0) BIOCHEM (L3) 7 Acidic and Basic side chains (at pH 7.0) Chirality of Amino Acids With the exception of glycine, all protein-derived amino acids have at least one stereocenter (the -carbon) and are chiral. The vast majority of protein-derived -amino acids have the L-configuration at the -carbon. BIOCHEM (L3) 10 zwitterion into a positive ion. Ionization vs pH The net charge on an amino acid depends on the pH of the solution in which it is dissolved. If we dissolve an amino acid in water, it is present in the aqueous solution as its zwitterion. If we now add a strong acid such as HCl to bring the pH of the solution to 2.0 or lower, the strong acid donates a proton to the - COO- of the amino acid turning the zwitterion into a positive ion If we add a strong base such as NaOH to the solution and bring its pH to 10.0 or higher, a proton is transferred from the NH3+ group to the base turning the zwitterion into a negative ion Isoelectric Point (pI) The pH at which the majority of molecules of a compound in solution have no net charge. BIOCHEM (L3) 11 Cysteine The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S- (disulfide). other amino acids Hydroxylation (oxidation) of proline, lysine, and tyrosine, and iodination for tyrosine, give these nonstandard amino acids. BIOCHEM (L3) 12 Peptides In 1902, Emil Fischer proposed: proteins are long chains of amino acids joined by amide bonds. peptide bond: The special name given to the amide bond between the a-carboxyl group of one amino acid and the -amino group of another Peptide: A short polymer of amino acids joined by peptide bonds; they are classified by the number of amino acids in the chain. Dipeptide: A molecule containing two amino acids joined by a peptide bond. BIOCHEM (L3) 15 there are 20 x 20 = 400 dipeptides possible there are 20 x 20 x 20 = 8000 tripeptides possible the number of peptides possible for a chain of n amino acids is 20n. for a small protein of 60 amino acids, the number of proteins possible is 2060 = 1078, which is possibly greater than the number of atoms in the universe! primary structure -The hormone insulin consists of 2 polypeptide chains held together by 2 interchain disulfide Just how important is the exact amino acid sequence? Human insulin consists of 2 polypeptide chains having a total of 51 amino acids; the 2 polypeptide chains are connected by 2 interchain disulfide bonds. In the table, are differences between 4 types of insulin Vasopressin and oxytocin are both nonapeptides but have quite different biological functions. Vasopressin is an antidiuretic hormone -a chemical produced in the brain that causes the kidneys to release less water, decreasing the amount of urine produced. A high ADH level causes the body to produce less urine. A low level results in greater urine production. Oxytocin affects contractions of the uterus in childbirth and the muscles of the breast that aid in the secretion of milk BIOCHEM (L3) 16 Secondary structure conformations of amino acids in localized regions of a polypeptide chain; the way that the linear sequence of amino acids folds upon itself. The most common types of motifs or patterns of secondary structure are α- helix and β- pleated sheet. α-Helix: a type of secondary structure in which a section of polypeptide chain coils into a spiral, most commonly a right-handed spiral. β-Pleated sheet: a type of secondary structure in which 2 polypeptide chains or sections of the same polypeptide chain align parallel to each other; the chains may be parallel or antiparallel; stabilized by H bonds A section of a-helix There are 3.6 amino acids per turn of the helix. The 6 atoms of each peptide bond lie in the same plane. N-H groups of peptide bonds point in the same direction, roughly parallel to the axis of the helix. C=O groups of peptide bonds point in opposite direction, also roughly parallel to the axis of the helix. BIOCHEM (L3) 17 The C=O group of eachpeptide bond is hydrogen bonded to the N-H groupof the peptide bond 4 amino acid units away from it. All R- groups point outward from the helix. β-Pleated Sheet Structure β-pleated sheet In a section of β-pleated sheet: The 6 atoms of each peptide bond lie in the same plane BIOCHEM (L3) 20 tertiary structure Is the overall conformation of an entire polypeptide chain Tertiary structure is stabilized in 4 ways: Covalent bonds, as for example, the formation of disulfide bonds between cysteine side chains. Hydrogen bonding between polar groups of side chains, as for example between the -OH groups of serine and threonine. Salt bridges, as for example, the attraction of the -NH3+ group of lysine and the - COO- group of aspartic acid. Hydrophobic interactions, as for example, between the nonpolar side chains of phenylalanine and isoleucine. The tertiary structure of a native conformation refers to the 3-dimensional organization of all the atoms - including side chain atom - in a protein. Perhaps the best way to visualize what tertiary structure looks like is to imagine taking an amino acid sequence with primary and secondary structure and crumpling BIOCHEM (L3) 21 it up into a ball. Just as each type of protein has its own unique primary and secondary structure, it also has its own unique tertiary structure The quaternary structure of a native conformation refers to the 3-D organization of all the atoms in a multi- subunit protein. Multi-subunit proteins consist of 2 or more individual amino acid chains, each with their own primary, secondary, and tertiary structures. The way these individual chains fit together into an overall three dimensional arrangement is called quaternary structure. Only multi-subunit proteins have quaternary structure. Quaternary Structure the arrangement of polypeptide chains into a noncovalently bonded aggregation; describes the bonding between multiple polypeptides The individual chains are held in together by hydrogen bonds, salt bridges, and hydrophobic interactions. Hemoglobin BIOCHEM (L3) 22 Adult hemoglobin: 2 alpha chains of 141 amino acids each and 2 beta chains of 146 amino acids each chain surrounds an iron- containing heme unit Fetal hemoglobin: 2 alpha chains and 2 gamma chains; fetal hemoglobin has a greater affinity for oxygen than does adult hemoglobin. The 4° Structure of Hemoglobin The term for a completely and properly folded up protein is called the proper conformation of a protein. To achieve the proper conformation, there must be correct primary structure, secondary, tertiary, and quaternary structure. Many proteins function as monomers and so do not require quaternary structure to be considered properly folded. Quaternary Structure Integral membrane protein of rhodopsin made of a-helices. BIOCHEM (L3) 25 Ethanol• safe to use on food-grade surfaces has a quick drying time and does not leave a residual solvent safest method of sanitizing in any food or pharmaceutical setting 70% Solution is Preferred Even though ethanol is diluted to a 70% solution, it’s still effective at killing microbes, bacteria, and other microorganisms on the surfaces of counters and food manufacturing equipment. Two types commonly available in industry: 70% and 95% - also known as 140 proof and 190 proof. 100% but it’s harder to obtain and is only used for specific scientific purposes Ethanol : Disinfectant or Cleaning Agent Pure Ethanol Prevents Cell Death Testing has been done to show that when pure ethanol (at 100%) is poured onto a single celled organism, it will coagulate (clot) its protein. The ethanol penetrates its cellular wall in all directions. The protein located just within the cell wall is what coagulates. It’s much like a defense mechanism. This ring of coagulated protein actually prevents the ethanol from penetrating deeper into the cell wall of the organism. No more coagulation takes place. Basically, this renders the organism dormant, but doesn’t kill it. If the ethanol were to be washed away, then it’s possible the organism would come back to life. This process defeats the purpose of using ethanol to kill microbes. Instead, scientists have found a way to trick these microbes with a lower percentage of ethanol How 70% Ethanol Causes Cell Death? 70% ethanol causes bacterial protein to coagulate, but coagulation occurs at a much slower rate. This actually allowed the ethanol to penetrate the entire bacterial cell before it has a chance for its coagulation to block it. The entire cell is then coagulated, causing the bacterial cell to die. What Microbes Can 70% Ethanol Kill? BIOCHEM (L3) 26 Water that’s been mixed into ethanol slows the drying time, creating a longer contact time. Ethanol needs to have a contact time of at least 10 seconds to kill Staphylococcus aureus and Streptococcus pyogenes. At a 10 second drying time, ethanol kills: Pseudomonas aeruginosa Serratia marcescens E. coli Salmonella typhosa Staphylococcus aureus Streptococcus pyogenes When food is cooked, some of its proteins are denatured. This is why boiled eggs become hard and cooked meat becomes firm. A classic example of denaturing in proteins comes from egg whites, which are typically largely egg albumins in water. Fresh from the eggs, egg whites are transparent and liquid. Cooking the thermally unstable whites turns them opaque, forming an interconnected solid mass. Pouring egg whites into a beaker of acetone will also turn egg whites translucent and solid. The skin that forms on curdled milk is another common example of denatured protein. Keratin in human hair contains high % of disulfide bonds that are responsible for the shape of the hair – straight/curly. A reducing agent cleaves the S-S bonds, allowing molecules to lose their rigid orientation and become more flexible. Oxidizing agent reverses the process. Protein folding is key to whether a globular or membrane protein can do its job correctly; it must be folded into the right shape to function. However, H bonds, which play a big part in folding, are rather weak and thus easily affected by heat, acidity, varying salt concentrations, and other stressors which can denature the protein. This is one reason why homeostasis is physiologically necessary BIOCHEM (L3) 27 Chemical Connections Aspartame (marketed under the trade name NutraSweet) – too sweet peptide The Use of Human Insulin Sickle Cell Anemia Protein/Peptide Conformation-Dependent Diseases Proteomics Quaternary Structure and Allosteric Proteins Laser Surgery and Protein Denaturation State example of an inherited error in protein structure that results in a happy ending rather than a debilitating disease. Soybeans: the only plant food that could serve as a person's sole source of protein because they contain all 8 essential amino acids. Quinoa (keen-wah) is native to the Andes in South America. Chenopodium quinoa plant comes from the same botanical family as sugar beets and spinach, and not the grass family like wheat, rice, and the other grains we typically think of as being cereals. There are 8 essential amino acids (9 for children) — essential in the sense that they cannot be synthesized by the body so they must be supplied by what we eat each day. Quinoa is a better source of these amino acids than many other grains. It contains more lysine than wheat or rice does, and lysine is the amino acid most lacking in these two major sources of dietary protein for many people in the world. But the protein in soy contains substantially more lysine than the protein in quinoa, and by some standards, quinoa falls just short of the lysine needed to be classified as a complete provider of all 8 essential amino acids. So quinoa is quite good when it comes to amino acids, but not quite as good as soybeans.