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Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED Proteins The position of carbon atom is Alpha (a):...

Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED Proteins The position of carbon atom is Alpha (a): TOPIC OUTLINE  -NH2 group (Amino Group) is attached Alpha carbon = The carbon atom at the center of an amino acid to 1 Characteristics of Protein at alpha (a) carbon atom. which the amino and carboxyl groups are both bonded is referred 2 Amino Acids: The Building Blocks for Proteins  -COOH group (Carboxyl Group) is to as the alpha carbon. 3 Chirality and Amino Acids attached at alpha (a) carbon atom. 4 Acid-base Properties of Amino Acids 5 Peptides  R Group= side chain –vary in size, shape, 6 Biochemically Important Small Peptides charge, acidity, functional groups present, 7 hydrogen-bonding ability, and chemical reactivity. General Structural Characteristics of Proteins 8 Different Structures of Proteins  >700 amino acids are known 9 Classification of Proteins: Based on Shape  Based on common ―R‖ groups, there are 10 Classification of Proteins: Based on Function 20 standard amino acids 11 Protein Hydrolysis 12 Protein Denaturation 13 Glycoproteins 14 Lipoproteins Characteristics of Proteins  A protein is a naturally-occurring, unbranched polymer in which the monomer units are amino acids.  Importance: The R-group will be the  Water accompanies the cell weight. nature to distinguish a-amino acid from  Proteins are considered as most each other. abundant molecule in the cell after water (15%) CHON- S  Elemental composition: Contain Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), most also contain Sulfur (S). Small amount  The average nitrogen content of proteins is 15.4% by cell mass. Tail Head  The presence of nitrogen component set Non-Polar Amino Polar Amino Acids them apart from carbohydrates and lipids. Acids (R-Groups)  Carbohydrates contain carbon, oxygen  Hydrophobic  Hydrophilic and oxygen  Water Fearing  Water Loving  Location:  Attracted to  Also present are Iron (Fe), phosphorus (P) Interior part water and some other metals in some specialized of protein proteins.  Limited contact with water Amino Acids  8 standard amino acids  An organic compound that contains both an Subtypes Subtypes amino (-NH2 ) and carboxyl (-COOH) groups  Alkyl  Neutral attached to same carbon atom AA  Aromatic  Acidic NAB  Basic  Building blocks of protein. Polar amino acids: R-groups are polar TRANSCRIBED BY JEAN HERSHEY REYES 1 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED “MGALF - IWPV”  Three types: Polar neutral; Polar acidic; 9 Non-Polar Amino Acids My Grades Are Like Fights & I Will Prove Victorious and Polar basic  Glycine Polar-neutral  Contains polar but (Gly, G) neutral side chains  It is neither acidic nor basic  7 amino acids belong to this  Alanine category (Ala, A) Polar acidic  Contain carboxyl group as part of the side chains  Bears a Electrical side chain negative charge  Loss it acidic  Valine hydrogen atom (Val, V) VLine  2 amino acids belong to this category Polar basic  Contain amino group as part of the side chain  Leucine 4 (CH) + Cine  Bears a (Leu, L) positive charge  Accepted a Nitrogen of particular amino acid chain proton  2 amino acids  Isoleucine belong to this (Ile, I) category NOMENCLATURE  Common names assigned to the amino acids are currently used.  Three letter abbreviations - widely used for  Proline naming: Protein (Pro, P)  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).  Phenylalanine (Phe, F) Without -OH  One-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 TRANSCRIBED BY JEAN HERSHEY REYES 2 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED  Methionine (Met, M)  Glutamine (Gln, Q) Ring  Tryptophan (Trp, W)  Tyrosine (Tyr, Y) With -OH Polar amino acids (hydrophilic): “STC-NQY” Santa’s Team Crafts New 4 Polar Neutral Amino Acids Quilts Yearly.  Serine 2 Polar Acidic Amino Acids No ring but (Ser, S)  Aspartic acid with -OH (Asp, D)  Cysteine (Cys, C)  Glutamic acid (Glu, E)  Threonine (Thr, T)  Most abundant 3 Polar Basic Amino Acids acid  Histidine compare to (His, H) tryptophan and tyrosine Histo (but i)  Asparagine (Asn, N) TRANSCRIBED BY JEAN HERSHEY REYES 3 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED  Lysine (Lys, K)  Therefore 19 of the 20 standard amino acids contain a chiral center  Chiral centers exhibit enantiomerism (left- and righthanded forms)  They are non-superimposable and superimposable mirror images.  Not go inside of all points.  Each of the 19 amino acids exist in left and right handed forms  Arginine (Arg, R)  The amino acids found in nature as well as in proteins are L isomers.  Bacteria do have some D-amino acids  With monosaccharides nature favors D- isomers The rules for drawing Fischer projection formulas for amino acid structures: Essential Amino Acids  The — COOH group is put at the top,  Essential amino acid is an amino acid needed the R group at the bottom to position in the human body that must be obtained from the carbon chain vertically dietary sources because it cannot be synthesized  The — NH2 group is in a horizontal within the body from other substances in adequate position. amounts. o Positioning:  Arginine is required for growth in children but NH2 on the left - is not required by adults. L isomer o Positioning: The Essential Amino Acids for Humans NH2 on the right  Arginine  Methionine - D isomer.  Histidine  Phenylalanine  Isoleucine  Threonine  Fisher Projection  Leucine  Tryptophan Formula used vertical and horizontal  Lysine  Valine lines. Chirality and Amino Acids  Designation of Mirror handedness in standard  Four different groups are attached to the a- amino acid structures (D & L System) carbon atom in all of the standard amino acids except glycine Amino acid side chain  In glycine R-group is hydrogen atom  Glycine is the simplest of all standard amino acids (achiral) No chiral center TRANSCRIBED BY JEAN HERSHEY REYES 4 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED Acid-Base Properties of Amino Acids Product  Equilibrium aspect or the  In pure form amino acids are white crystalline concentration of the solution when it solids Physical characteristics of a.a comes to the amino acid, it will shift  Most amino acids decompose before they based on the change of their ph. melt Polar Acidic A.A  Not very soluble in water Cysteine: A Chemically unique amino acid  Structure and molecule  The only standard amino acid with a  Exists as Zwitterion: An ion with + (positive) sulfhydryl group (— SH group). and – (Negative) charges on the same molecule with a net zero charge  The sulfhydryl group imparts cysteine a  Carboxyl groups give-up a proton to get chemical property unique among the standard negative charge amino acids.  Amino groups accept a proton to become positive charge  Cysteine in the presence of mild oxidizing agents dimerizes to form a cystine molecule.  Cystine - two cysteine residues linked via a covalent disulfide bond.  Interaction of cystine from another cystine there will be formation of cystine molecule/residue Product consist in cystein  Dimer is a molecule that is made up of two-sub like unit  Cystine from another cystine is what we called Oxidation-Reduction Behavior  Amino acids in solution exist in three different  Oxidation-Reduction Behavior species (zwitterions, positive ion, and negative involves the sulfhydryl group and ion) - Equilibrium shifts with change in pH covalent disulfide bonds.  Isoelectric point (IP) – pH at which the  Consider: The thiol alcohol concentration of Zwitterion is maximum -- net charge is zero  Different amino acids have different isoelectric points Range in the particular aa Isoelectric Point:15 standard amino acid are 4.8- 6.3  At isoelectric point - amino acids are not attracted towards an applied electric field because they net zero charge.  Under Clinical Chemistry  Electrophoresis Method- process of separating charge molecules on the basis of their migration toward Low ph aa= net + charge binding the electric charge  Negative Electrode- Cathode Cut ( - )  Positive Electron- Anode A(+) TRANSCRIBED BY JEAN HERSHEY REYES 5 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED Peptides Isomeric Peptides  Unbranched chain joined to the next by a peptide bond  Peptides that contain the same amino acids but present in different order are different  Dipeptide: bond between two amino acids molecules (constitutional isomers) with  Oligopeptide: bond between ~ 10 - 20 amino different properties. acids  For example, two different dipeptides can  Polypeptide: bond between large number of be formed between alanine and glycine amino acids In terms of chain  The number of isomeric peptides possible  Every peptide has an N-terminal end and a C- increases rapidly as the length of the peptide terminal end chain increases  N-terminal end- located on the left side of the structure  C-terminal end- located on the far right side of the structure  +H3N-aa-aa-aa-aa-aa-aa-aa-aa-aa-COO- Biochemically Important Small Peptides Many relatively small peptides are biochemically active:  Hormones  Biochemical reaction within the body with organs and cells  Neurotransmitters  Respond to a certain stimuli  Antioxidants  Highly reactive to protect ourselves Small Peptide Hormones: Produce milk from mother  Best-known peptide hormones: oxytocin and vasopressin  Produced by the hypothalamus stored in the Peptide Nomenclature posterior pituitary gland  Nonapeptide (nine amino acid residues) with Rule 1: The C-terminal amino acid residue keeps six of the residues held in the form of a loop by a its full amino acid name. disulfide bond formed between two cysteine residues. Rule 2: All of the other amino acid residues have names that end in -yl. The -yl suffix replaces the -ine or -ic acid ending of the amino acid name, except for tryptophan, for which -yl is added to the name. (tryptophyl) Rule 3: The amino acid naming sequence begins at the N terminal amino acid residue Example: Ala-leu-gly has the IUPAC name of alanylleucylglycine TRANSCRIBED BY JEAN HERSHEY REYES 6 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED  Oxytocin regulates the uterine bacterial invasion contractions and lactation.  Labor  Unusual structural feature – Glutamine is  Suck the nipple of mother for bonded to Cystine through the side-chain Hormones uterine contraction carboxyl group.  During Breastfeeding; ejection of milk Nagpipigil ng ihi  Vasopressin is also known as antidiuretic hormone Lead to diabetes incipidus  Regulates the water excretion by the kidneys  Affects the blood pressure.  Urine formation Condition: Deficient of Vasopressin (Diabetes Insipidus) General Structural Characteristics of Proteins  High urine output  A protein is a naturally-occurring,  Urine Specific gravity: It resembles low unbranched polymer in which the monomer units urine specific gravity. are amino acids. SMALL PEPTIDE NEUROTRANSMITTERS  A protein is a peptide in which at least 40 Mostly ginagamit ng athletes amino acid residues are present:  Enkephalins are pentapeptide  The terms polypeptide and protein are neurotransmitters produced by the brain and often used interchangeably used to bind receptor within the brain describe a protein  Help reduce pain  Several proteins with >10,000 amino  Painkillers for athletes acid residues are known  Reduce the effects of injury  Common proteins contain 400–500  Used as local anesthetic during the amino acid residues acupuncture  Small proteins contain 40–100 amino acid residues Best-known enkephalins:  Met-enkephalin: Tyr–Gly–Gly–Phe–Met More than one peptide chain may be present in (Tyrosine, Glycine, Glycine, a protein: Phenylalanine and Methionine)  Monomeric : A monomeric protein contains one peptide chain  Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu (  Multimeric: A multimeric protein contains Tyrosine, Glycine, Glycine, Phenylalanine more than one peptide chain and Leucine) SMALL PEPTIDES ANTIOXIDANTS Protein Classification Based on Chemical Composition  Glutathione (Glu–Cys–Gly) – a tripeptide – is present is in high levels in most cells.  Simple proteins: A protein in which only amino acid residues are present:  Regulator of oxidation–reduction reactions.  Glutathione is an antioxidant and protects  More than one protein subunit may be cellular contents from oxidizing agents such as present but all subunits contain only amino acids peroxides and superoxides.  Highly reactive forms of oxygen often  Conjugated protein: A protein that has one or generated within the cell in response to TRANSCRIBED BY JEAN HERSHEY REYES 7 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED more non-amino acid entities (prosthetic groups) Human structure present in its structure:  Myoglobin associated with muscles  One or more polypeptide chains may be  It is reserve oxygen that is in present line with our working  Non-amino acid components - may be muscle. organic or inorganic - prosthetic groups Factors we considered:  Lipoproteins contain lipid prosthetic 1. Number and kinds of amino acid groups present.  Glycoproteins contain carbohydrate 2. Order of attachment of the amino groups acids  Metalloproteins contain a specific metal 3. Specific protein in the same as prosthetic group manner. 2. Secondary Structures Four Types of Structures 1. Primary Structures  Arrangement of atoms of backbone in space.  Primary structure of protein refers to  The two most common types: the order in which amino acids are alpha-helix (a-helix) and the beta- linked together in a protein. pleated sheet (b-pleated sheet).  They are in a sequence form  The peptide linkages are Amino acid that present  51 amino acids essentially planar thus allows only in insulin sequencing two possible arrangements for the peptide backbone for the following  Every protein has its own unique reasons: amino acid sequence o For two amino acids linked through a peptide bond six o Frederick Sanger (1953) 18 yrs atoms lie in the same plane sequenced and determined the o The planar peptide linkage primary structure for the first structure has considerable protein – Insulin rigidity, therefore rotation of groups about the C–N bond is He is a British biochemist  hindered Insulin regulates the blood  o Cis–trans isomerism is possible glucose level of an about C–N bond. individual o The trans isomer is the Condition: Deficient of Insulin (Diabetes preferred orientation Mellitus) Alpha-helix (a-helix) PRIMARY STRUCTURE OF HUMAN  A single protein chain adopts a shape MYOGLOBIN that resembles a coiled spring (helix): Because of hydrogen bonds o H-bonding between same amino acid chains –intra molecular (single chain folding back itself) o Coiled helical spring o R-group outside of the helix -- not enough room for them to stay inside TRANSCRIBED BY JEAN HERSHEY REYES 8 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED 3. H-Bonding between polar, acidic and/or basic R groups  For H-bonding to occur, the H must be attached on O, N or F 4. Hydrophobic interactions: Between non-polar side chains Beta-pleated sheets Presence of hydrogen bond 4. Quaternary Structures  Completely extended amino acid chains  The HIGHEST level of protein  Resembles as two fully extended organization protein chain segments in the same  Most multimeric proteins contain or different molecules held together. an even number of subunits (two  Tupi factor subunits a dimer, four subunits a  H-bonding between two different tetramer, and so on). chains – intermolecular (between  The subunits are held together mainly two different chain) and/or by hydrophobic interactions intramolecular between amino acid R groups.  Side chains below or above the  An example of a protein with axis quaternary structure is hemoglobin (supplies oxygen), the oxygen carrying protein in blood.  It is a tetramer in which there are two identical a chains and two identical B chains.  Each chain enfolds a heme group, the site where oxygen binds to the protein. 3. Tertiary Structures Classification of Proteins: Based on Shape  The overall three-dimensional 1. Fibrous Proteins: Collagen shape of a protein  Results from the interactions  Fibrous Proteins have an between amino acid side chains (R elongated shape with one groups) that are widely separated dimension from each other.  Simple regular linear structure  In general 4 types of interactions  Form macromolecular structures are observed.  Telephone chord  Most abundant proteins in humans (30% of total body protein) FOUR TYPES OF INTERACTIONS  Major structural material in tendons, (Factors need to be observed) ligaments, blood vessels, and skin  Organic component of bones and 1. Disulfide bond: covalent, strong, teeth between two cysteine groups  Predominant structure - triple helix  Rich in proline (up to 20%) – Amino acid that help 2. Electrostatic interactions: Salt important to maintain structure stability and flexibility Bridge between charged side chains of acidic and basic amino 2. Globular Proteins: Myoglobin acids Reserve oxygen  -OH, -NH2 , -COOH, -CONH2 with in our  Peptide chains that are folded muscle cell TRANSCRIBED BY JEAN HERSHEY REYES 9 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED into spherical or globular shape e.g., oxygen and other ligands, and transport Water molecular subtances  It is connected to hydrophilic and them to other locations in the body and release hydrophobic side chains. them on demand.  Water soluble substances 4. Messenger proteins: transmit signals to  An oxygen storage molecule in coordinate biochemical processes between muscles. different cells, tissues, and organs.  Monomer - single peptide chain  Insulin and glucagon - regulate with one heme unit (binding area of carbohydrate metabolism (pancreas) oxygen)  Human growth hormone – regulate body  Binds one O2 molecule growth (somatotropin)  Myoglobin has a higher affinity for oxygen than hemoglobin. 5. Contractile proteins: Necessary for all forms of  Oxygen stored in myoglobin movement. molecules serves as a reserve  Muscles contain filament-like contractile oxygen source for working proteins (actin and myosin). muscles  Human reproduction depends on the movement of sperm – possible because 3. Globular Proteins: Hemoglobin of contractile proteins.  An oxygen carrier molecule in 6. Structural proteins: Confer stiffness and blood rigidity  Transports oxygen from lungs to  Collagen is a component of cartilage a tissues  Keratin gives mechanical strength as well  Tetramer (four peptide chains) - as protective covering to hair, fingernails, each subunit has a heme group feathers, hooves, etc.  Can transport up to 4 oxygen molecules at time 7. Transmembrane proteins: Span a cell  Iron atom in heme interacts with membrane and help control the movement of oxygen small molecules and ions.  Have channels – help molecules can enter Classification of Proteins: Based on Function and exit the cell.  Transport is very selective - allow The functional versatility of proteins stems from: passage of one type of molecule or ion.  Ability to bind small molecules specifically and strongly 8. Storage proteins: Bind (and store) small  Ability to bind other proteins and form molecules. fiber-like structures, and  Ferritin - an iron-storage protein - saves  Ability integrated into cell membranes iron for future use in the biosynthesis of new hemoglobin molecules. MAJOR CATEGORIES OF PROTEINS BASED ON  Life span of RBC: 120 days FUNCTION  Dead RBC will go throughout through the spleen 1. Catalytic proteins: Enzymes are best known  Myoglobin - an oxygen-storage protein for their catalytic role. present in muscle  Almost every chemical reaction in the body is driven by an enzyme 9. Regulatory proteins: Often found ―embedded‖ in the exterior surface of cell membranes - act 2. Defense proteins: Immunoglobulins or as sites for receptor molecules antibodies are central to functioning of the  Often the molecules that bind to body’s immune system. enzymes (catalytic proteins), thereby  Parasite, fungi and bacteria turning them ―on‖ and ―off,‖ (feedback control mechanism) and 3. Transport proteins: Bind small biomolecules, thus controlling enzymatic action. TRANSCRIBED BY JEAN HERSHEY REYES 10 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED Conjugated proteins with carbohydrates linked to 10. Nutrient proteins: Particularly important in the them: early stages of life - from embryo to infant.  Casein 3/4 (milk) and ovalalbumin 50%  Many of plasma membrane proteins are IgA Human colostrom (egg white) are nutrient proteins glycoproteins IgE  Milk also provides immunological  Blood group markers of the ABO system protection for mammalian young. are also glycoproteins  Collagen and immunoglobulins are Protein Hydrolysis glycoproteins (sugar protein)  Determine our blood type: Type A, B, AB  Results in the generation of an amine and and O carboxylic acid functional groups.  Central process of digestion Collagen-glycoprotein  Reverse formation reaction of a particular peptide bond.  Most abundant protein in human body  It will affect the protein sequencing. (30% of total body protein)  Functional group will be regenerated  Triple helix structure such as amino and carboxyl group.  Rich in 4-hydroxyproline (5%) and 5- hydroxylysine (1%) — derivatives  Digestion of ingested protein is enzyme-  Some hydroxylysines are linked to glucose, catalyzed hydrolysis galactose, and their disaccharides – help  Free amino acids produced are absorbed into in aggregation of collagen fibrils. the bloodstream and transported to the liver for the synthesis of new proteins. Immunoglobulins IgG, IgA, IgM,  Hydrolysis of cellular proteins and their resynthesis is a continuous process  Glycoproteins produced as a protective response to the invasion of microorganisms or foreign molecules - Protein Denaturation antibodies against antigens.  Immunoglobulin bonding to an antigen via  Partial or complete disorganization of variable region of an immunoglobulin Determine Uniquenes protein’s tertiary structure occurs through hydrophobic interactions,  Losing its biochemical activity dipole – dipole interactions, and  Cooking food denatures the protein but does hydrogen bonds. not change protein nutritional value  Coagulation: Precipitation (denaturation of proteins) Visualize the denaturation of protein o Egg white - a concentrated solution Epsi of protein albumin - forms a jelly Fabrigo when heated because the albumin is denatured Cooking:  Denatures proteins – Makes it easy for enzymes in our body to hydrolyze/digest protein  Kills microorganisms by denaturation of proteins  Fever: >104ºF – the critical enzymes of the body start getting denatured  Consist of two heavy polypeptide  Above 37 degree Celsius did not meet the chains and two light polypeptide potential maximum activity chains  They are cross linked by disulfide bridges. Glycoproteins  Purple: Areas of the constant amino TRANSCRIBED BY JEAN HERSHEY REYES 11 Biochemistry for Medical Laboratory Science BACHELOR OF SCIENCE IN MEDICAL LABORATORY SCIENCE LECTURE/RECORDED VIDEO BASED acid regions  High LDL: Cardiovascular Disease.  Red: Variable amino acid region of  Condition: Atherosclerosis and Heart Attack each chain  Area where antigen binds 4. High-density lipoproteins (HDL): Collect excess cholesterol from body tissues and Statin transport it back to the liver for degradation to bile acids  ―Good‖ or ―Happy‖ cholesterol. Helps our arteries clear and free of plaques  Prevent cardiovascular disease  Protect bio-organic molecule: Lipids Clinical Section of Lipoproteins: Clinical Chemistry  Lipid Profile: Fasting State 10-12 hours set of test even lipid cholesterol  Consists of different test: Total cholesterol, Triglycerides, HDL and LDL - no fasting in cholesterol > (some institution consider VLDL)  Attach the chains to the tissues by  Total Cholesterol: Non-fasting State determining the destinations of that immunoglobulin. Immunoglobulins Antigens: IgG, IgA, IgM, IgE, IgD Lipoproteins  A conjugated protein that contains lipids in addition to amino acids  Help suspend lipids and transport them through the bloodstream Four major classes of plasma lipoproteins: 1. Chylomicrons: Transport dietary triacylglycerols from intestine to liver and to adipose tissue.  Extracting patient.  Centrifuge the plasma or serum, floating material 2. Very-low-density lipoproteins (VLDL): Transport triacylglycerols synthesized in the liver to adipose tissue. 3. Low-density lipoproteins (LDL): Transport cholesterol synthesized in the liver to cells throughout the body.  ―Bad‖ or ―Lethal‖ cholesterol. Forms plaques in our arteries causing them to harden and narrow. TRANSCRIBED BY JEAN HERSHEY REYES 12

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