5th Midterm_Proteins 2 PDF
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This document is an outline for a biochemistry lecture focusing on proteins, including their characteristics, amino acids, and structures. Topics covered include the building blocks, classification based on shape, and roles in different processes.
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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