CHEM123 (LEC_PRELIM).pdf

OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC WEEK 2: CELL EUKARYOTIC CELL vs. PROKARYOTIC CELL CE...

OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC WEEK 2: CELL EUKARYOTIC CELL vs. PROKARYOTIC CELL CELL - Biochemistry explores molecular mechanisms of normal cellular processes as well as diseases. - All higher living organisms including humans are made up MOLECULAR COMPOSITION OF CELL of cells. - Water accounts for about 70- 75% of the weight of the cell. TWO MAJOR CLASSES: - Organic compounds accounts - Prokaryotes for 25-30% of the cell weight. - Eukaryotes - They are nucleic acids, proteins, polysaccharides HISTORICAL NOTES (carbohydrates) and lipids. - Robert Hooke was the first - Inorganic compounds account person to use the term “cell”. for the rest of the cell weight. He referred to the small empty chambers in the structure of EUKARYOTIC CELL cork as cells. - Eukaryotic cells have a - Matthias Schleiden and membrane-bound nucleus and a Theodor Schwann concluded number of other membrane- that all plant and animal bound subcellular (internal) tissues were composed of cells. organelles, each of which has a - Rudolf Virchow proposed the specific function. theory of biogenesis where cells only arise from pre- 1. PLASMA MEMBRANE existing cells. Structure: Phospholipid bilayer containing CELL THEORY cholesterol and proteins - A cell is the basic structural and some carbohydrates; and functional unit of living forms a selectively organisms. permeable boundary of - The activity of an organism the cell. depends on the collective Functions: Acts as a activities of its cells. physical barrier to - According to the principle of enclose cell contents; complementarity, the activities regulates material of cells are dictated by their movement into and out structure (anatomy), which of the cell; functions in determines function cell communication (physiology). lumsyin OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC out specific metabolic activities of the cell. Cytosol provides support for organelles and serves as the viscous fluid medium. Function: It is responsible for various cellular processes. 2. NUCLEUS Structure: It is enclosed within a double membrane called nuclear envelope; contains nucleolus Nucleolus: It consists of RNA and proteins which functions in ribosomal unit assembly. Nucleoplasm: It 4. MITOCHONDRIA surrounds chromatin Structure: Double- and the nucleoli. membrane-bound Function: It contains the organelles containing a DNA that serves as the circular strand of DNA genetic material for Outer membrane is directing protein highly permeable to synthesis. small molecules, due to the presence of a pore- forming protein called porin. Intermembrane contains many proteins that participate in oxidative phosphorylation. Inner membrane has multiple folds projecting inwards, called cristae. 3. CYTOPLASM Function: It is Structure: This can be responsible for the seen between the plasma production of energy in membrane and the the form of ATP. nucleus where the other cellular elements are embedded. Organelles are membrane-bound structures which carry lumsyin OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC membrane network lacking ribosomes 5. LYSOSOMES 7. GOLGI APPARATUS Structure: Spherical Structure: elongated, shaped membrane bound Series of flattened organelles formed from membranous structures. the golgi apparatus; several saclike contain digestive Functions: Modifies, enzymes packages, and sorts The fluid inside materials, that arrive lysosomes is much more from the endoplasmic acidic, at about pH 4.8, reticulum in transport than the normal pH of vesicles about 7.0–7.3. Vesicles transport Function: Digest cellular material. Mature microbes or materials by vesicles are called the cell secretory vesicles. 6. ENDOPLASMIC RETICULUM 6.1. ROUGH ER Structure: Extensive interconnected membrane network that varies in shape; ribosomes attached on the cytoplasmic surfaces Ribosomes are involved in the protein synthesis. Functions: Modifies, transports, and stores proteins produces by attached 8. PEROXISOMES ribosomes Structure: smaller, 6.2. SMOOTH ER spherical membrane ✓ Extensive bound organelles formed interconnected lumsyin OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC from the endoplasmic - Each prokaryotic cell is reticulum. surrounded by a plasma Functions: Detoxify membrane. specific harmful - The cell has no subcellular substances either organelles, only infoldings of produced by the cell or the plasma membrane called taken into the cell mesosomes. - The deoxyribonucleic acid (DNA) is condensed within the cytosol to form the nucleoid. - Some prokaryotes have tail-like flagella. CELL MEMBRANE TRANSPORT 1. PASSIVE TRANSPORT PROCESS Diffusion is the movement of a substance from an area of its higher concentration to an area of its lower concentration. 9. CYTOSKELETON Simple diffusion is the Structure: Organized type of diffusion of network of protein dissolved solutes filaments through the plasma Function: Maintains membrane integral structural Facilitated Diffusion is support and the type of diffusion that organization of cells requires a protein Microfilaments maintain carrier. cell shape. Osmosis is the diffusion Intermediate filaments of water point across a give mechanical support selectively permeable to structures like membrane. nucleus and plasma membrane. 2. ACTIVE TARNSPORT PROCESS Microtubules provides This type of cell structural support. membrane transport uses energy (ATP) IMPORTANT NOTES FOR provided by the cell. PROKARYOTIC CELL For example, cell has - Prokaryotes (Eubacteria and low intracellular Archaebacteria) are the most sodium; but abundant organisms on earth. concentration of - A prokaryotic cell does not potassium inside the cell contain a membrane bound is very high. This is nucleus. maintained by the sodium potassium activated ATPase, lumsyin OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC generally called as Mitosis consists of four sodium pump. stages-prophase, Exocytosis refers to bulk metaphase, anaphase, movement of substance and telophase. The out of the cell by fusion result is two daughter of secretory vesicles nuclei, each identical to with the plasma the mother nucleus. membrane. Endocytosis refers to Prophase- each chromosome consists bulk movement of of two chromatids joined at the substance into the cells centromere. by vesicles forming at the plasma membrane. Metaphase- chromosomes align at the center of the cell Anaphase- chromatids separate at the centromere and migrate to opposite poles. Telophase- two new nuclei assume their normal structure, and cell division is completed, producing two new daughter cells. CELL LIFE CYCLE 1. INTERPHASE It is the longer phase of the cell cycle where the cell is active and preparing for cell division. The DNA molecule is duplicated exactly in a process called DNA replication which occurs toward the end of the interphase. 2. CELL DIVISION Cells arise from the division of other cells. lumsyin OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC Week 3: Carbohydrates CLASSIFICATION OF CARBOHYDRATES OCCURRENCE AND FUNCTIONS OF - Monosaccharides are classified CARBOHYDRATES as aldose or ketose on the basis of the type of carbonyl present. - Carbohydrate oxidation - Disaccharides are glycosides provides energy. formed from the linkage of two - Carbohydrate storage, in the monosaccharides. H HO H H form of glycogen, provides a short-term energy reserve. CHO OH H OH OH - Oligosaccharides are - Carbohydrates supply carbon carbohydrates that contain atoms for the synthesis of other three to ten monosaccharide biochemical substances units. (proteins, lipids, and nucleic acids) - Polysaccharides are polymers - Carbohydrates form part of the in which monosaccharides are the monomers. structural framework of DNA and RNA molecules. - Carbohydrates linked to lipids CHIRALITY are structural components of - Most monosaccharides exist in cell membranes. two forms: a “left handed” and - Carbohydrates linked to “right handed” form. proteins function in a variety of - Superimposable mirror images cell-cell and cell–molecule are images that coincide at all recognition processes. points when the images are laid upon each other. - A carbohydrate is a - Nonsuperimposable mirror polyhydroxy aldehyde, a images are images where not polyhydroxy ketone, or a all points coincide when the compound that yields images are laid upon each polyhydroxy aldehydes or other. polyhydroxy ketones upon - A chiral center is an atom in a hydrolysis. molecule that has four different groups bonded to it in a - The carbohydrate glucose is a tetrahedral orientation. polyhydroxy aldehyde, and the - A molecule that contains a carbohydrate fructose is a chiral center is said to be polyhydroxy ketone. chiral. - A chiral molecule is a molecule whose mirror images are not superimposable. STEREOISOMERISM - The atoms of stereoisomers are connected in the same way but are arranged differently in space. lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC TWO TYPES: highest-numbered chiral center 1. Enantiomers have structures is used to determine D or L that are nonsuperimposable configuration mirror images of each other. 2. Diastereomers have structures that are not mirror images of each other FISCHER PROJECTION FORMULAS - A Fischer projection formula is a two dimensional structural MONOSACCHARIDES notation for showing the - Monosaccharides are often spatial arrangement of groups classified by both their number about chiral centers in of carbon atoms and their molecules. functional group. CHO H O H O - In a Fischer projection formula CH2OH HO a chiral center (Carbon) is - A six-carbon monosaccharide represented as the intersection with an aldehyde functional of vertical and horizontal lines group is an aldohexose; a five carbon monosaccharide with a ketone functional group is a ketopentose. - D and L system used to designate the handedness of glyceraldehyde enantiomers. GLUCOSE AND FRUCTOSE - D-glucose is the most abundant NOTE: always look for the OH in nature and the most group (hydroxyl) to determine if important from a human it’s L or D. nutritional standpoint. - D-Fructose is biochemically the - The D,L system used to most important ketohexose. It designate the handedness of is also known as levulose and glyceraldehyde enantiomers fruit sugar can be extended to other monosaccharides with more than one chiral center. - The carbon chain is numbered starting at the carbonyl group end of the molecule, and the lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC three-dimensional structure of a cyclic form of a monosaccharide GALACTOSE AND RIBOSE D-GALACTOSE ALPHA AND BETA CONFIGURATION 1. Milk sugar - Alpha or Beta configuration is 2. Synthesize in human determined by the position of 3. Used to differentiate between the —OH group on C1 relative to blood types the CH2OH group that 4. Six membered cyclic form determines D or L series. - In a Beta configuration, both of D-RIBOSE these groups point in the same 1. Part of RNA direction 2. Part of ATP - In an Alpha configuration, the 3. Part of DN two groups point in opposite 4. Five membered cyclic form directions. CYCLIC HEMIACETAL FORMS OF D- OH GROUP GLUCOSE - The specific identity of a - Alpha-form: -OH of C1 and monosaccharide is determined CH2OH of C5 are on opposite by the positioning of the other sides —OH groups in the Haworth - Beta-form: -OH of C1 and projection formula. CH2OH of C5 are on same sides - Any —OH group at a chiral center that is to the right in a A cyclic monosaccharide containing a Fischer projection formula six-atom ring is called a pyranose, and points down in the Haworth one containing a five-atom ring is projection formula and any — called furanose because their ring OH group to the left in a structures resemble the ring Fischer projection formula structures in the cyclic ethers pyran points up in the Haworth and furan respectively. projection formula. HAWORTH PROJECTION FORMULAS REACTIONS OF MONOSACCHARIDES - A Haworth projection formula - Oxidation to acidic sugars is a two-dimensional structural - Reduction to sugar alcohols notation that specifies the - Glycoside formation lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC - Phosphate ester formation PHOSPATE ESTER FORMATION - Amino sugar formation - Phosphate ester formation: The hydroxyl groups of a OXIDATION monosaccharide can react with - Oxidation to acidic sugars: The inorganic oxyacids to form redox chemistry of inorganic esters. monosaccharides is closely - Phosphate esters of various linked to the alcohol and monosaccharides are stable in aldehyde functional groups aqueous solution and play present in them. important roles in the - Oxidation can yield three metabolism of carbohydrates. different types of acidic sugars depending on the type of AMINO SUGAR FORMATION oxidizing agent used: - Amino sugar formation: An amino sugar - one of the SUGAR ALCOHOLS hydroxyl groups of a - Reduction to sugar alcohols: monosaccharide is replaced The carbonyl group in a with an amino group monosaccharide (either an - Amino sugars and their N- aldose or a ketose) is reduced acetyl derivatives are to a hydroxyl group using important building blocks of hydrogen as the reducing agent. polysaccharides. GLYCOSIDE DISACCHARIDES - The general name for - Two monosaccharides can react monosaccharide acetals is to form disaccharide glycoside. - The bond that links the two - A glycoside is an acetal formed monosaccharides of a from a cyclic monosaccharide disaccharide (glycoside) by replacement of the together is called a glycosidic hemiacetal carbon -OH group linkage. with an -OR group. CELLOBIOSE BLOOD TYPES AND - Cellobiose is produced as an MONOSACCHARIDES intermediate in the hydrolysis - Blood Types and of the polysaccharide cellulose. Monosaccharides: Human blood - Cellobiose contains two b - D- is classified into four types: A, glucose monosaccharide units B, AB, and O: linked through a b (1—4) - The biochemical basis for the glycosidic linkage. Cellobiose various blood types involves cannot be digested by humans. monosaccharides present on plasma membranes of red blood cells. - The monosaccharides responsible for blood groups are D galactose and its derivatives. lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC MALTOSE - Sucrose (table sugar): The most - Maltose, often called malt abundant of all disaccharides sugar, is produced whenever and found in plants. the polysaccharide starch - It is produced commercially breaks down, as happens in from the juice of sugar cane plants when seeds germinate and sugar be and in human beings during - Sucrose is a nonreducing starch digestion. sugar.ets. - Structurally, maltose is made up of two D-glucose units, one POLYSACCHARIDES of which must be a-D-glucose. THE POLYMER CHAIN - A polysaccharide is a polymer that contains many monosaccharide units bonded to each other by glycosidic linkages. - A homopolysaccharide is a LACTOSE polysaccharide in which only - Lactose is made up of b-D- one type of monosaccharide galactose unit and a b-D- monomer is present. glucose unit joined by a b(1-4) - A heteropolysaccharide is a glycosidic linkage. polysaccharide in which more - Lactose is the major sugar than one (usually two) type of found in milk. monosaccharide monomer is - Lactose intolerance: a condition present. in which people lack the enzyme lactase needed to hydrolyze lactose to galactose and glucose. - Lactase hydrolyzes b(1-4) glycosidic linkages. - Deficiency of lactase can be caused by a genetic defect, physiological decline with age, or by injuries to intestinal mucosa STARCH - A storage polysaccharide is a polysaccharide that is a storage form for monosaccharides and is used as an energy source in cells. - Starch: Starch is a SUCROSE homopolysaccharide lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC containing only glucose monosaccharide units. It is the energy-storage polysaccharide in plants Amylopectin, the other polysaccharide in starch, has a high degree of branching in its CHITIN polyglucose structure. - Similar to cellulose in both All of the glycosidic function and structure linkages in starch (both - Linear polymer with all b amylose and (1→4) glycosidic linkages - it amylopectin) are of the a has a N-acetyl amino derivative type of glucose - Function is to give rigidity to the exoskeleton s of crabs, lobsters, shrimp, insects, and other arthropods GLYCOGEN - Glycogen, like starch, is a polysaccharide containing only glucose units. - Liver cells and muscle cells are ACIDIC POLYSACCHARIDES the storage sites for glycogen in - Acidic polysaccharides - humans. polysaccharides with a - Glycogen is an ideal storage repeating disaccharide unit form for glucose. containing an amino sugar and a sugar with a negative charge due to a sulfate or a carboxyl group. - Structural polysaccharide CELLULOSE present in connective tissue - Linear homopolysaccharide with b (1 → 4) glycosidic bond associated with joints, cartilage, synovial fluids in - Humans don’t have enzymes animals and humans that hydrolyze b (1 → 4) - so humans can not digest cellulose Examples: -- animals also lack these enzymes but they can digest 1. Hyaluronic acid: cellulose because they have Alternating residues of N acetyl-b-D-glucosamine bacteria in their guts to and D glucuronic acid. hydrolyze cellulose Highly viscous - serve as - It serves as dietary fiber in lubricants in the fluid of food-- readily absorbs water and results in softer stools. joints and part vitreous humor of the eye. 2. Heparin: lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC An anticoagulant- prevents blood clots. GLYCOLIPIDS AND GLYCOPROTEINS - A glycolipid is a lipid molecule that has one or more carbohydrate (or carbohydrate derivative) units covalently bonded to it. - A glycoprotein is a protein molecule that has one or more carbohydrate (or carbohydrate derivative) units covalently bonded to it. lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC Week 4: Proteins CHARACTERISTICS OF PROTEINS - A protein is a naturally- occurring, unbranched polymer in which the monomer units are amino acids NON-POLAR POLAR AMINO - Elemental composition - AMINO ACIDS ACIDS Contain Carbon (C), Hydrogen - Hydropho - Hydrophil (H), Nitrogen (N), Oxygen (O), bic ic most also contain Sulfur (S) - Water - Water - The average nitrogen content of fearing loving proteins is 15.4% by mass - Also present are Iron (Fe), SUBTYPES: SUBTYPES: phosphorus (P) and some other - Alkyl - Neutral metals in some specialized - Aromatic - Acidic proteins - Basic AMINO ACIDS 1. Polar Amino Acids - An organic compound that - R-groups are polar contains both an amino (-NH2) Three types: Polar and carboxyl (-COOH) groups neutral; Polar acidic; attached to same carbon atom and Polar basic - The position of carbon atom is 2. Polar-Neutral Alpha (a) - contains polar but -NH2 group is attached neutral side chains at alpha (a) carbon atom - Seven amino acids -COOH group is attached belong to this category at alpha (a) carbon 3. Polar Acidic atom. - Contain carboxyl group - R = side chain –vary in size, as part of the side chains shape, charge, acidity, - Two amino acids belong functional groups present, to this category hydrogen-bonding ability, and 4. Polar Basic chemical reactivity. - Contain amino group as - >700 amino acids are known part of the side chain - Based on common “R” groups, - Two amino acids belong there are 20 standard amino to this category acids NOMECLATURE - Common 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 lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC capitalized followed by next two letters not capitalized except in the case of Asparagine (Asn), Glutamine (Gln) and tryptophan CHIRALITY AND AMINO ACIDS (Trp). - Four different groups - One-letter symbols - are attached to the a- commonly used for carbon atom in all of the comparing amino acid standard amino acids sequences of proteins: except glycine Usually the first In glycine R- letter of the name group is hydrogen When more than - Therefore 19 of the 20 one amino acid standard amino acids has the same contain a chiral center letter the most - Chiral centers exhibit abundant amino enantiomerism (left- and acid gets the 1st right-handed forms) letter - Each of the 19 amino acids exist in left and NON-POLAR AMINO ACIDS right-handed forms POLAR NEUTRAL AMINO ACIDS - 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 POLAR ACIDIC AND BASIC AMINO - The rules for drawing ACIDS Fischer projection formulas for amino acid structures - The — COOH group is put at the top, the R group at lumsyin OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC the bottom to position the carbon chain vertically - The — NH2 group is in a horizontal position. Positioning — CYSTEINE: CHEMICALLY UNIQUE NH2 on the left - AMINO ACID L isomer the only standard amino acid Positioning — with a sulfhydryl group ( — SH NH2 on the right - group). D isomer. The sulfhydryl group imparts cysteine a chemical property ACID-BASE PROPERTIES OF AMINO unique among the standard ACIDS amino acids. In pure form amino acids are Cysteine in the presence of mild white crystalline solids oxidizing agents dimerizes to Most amino acids decompose form a cystine molecule. before they melt Cystine - two cysteine residues Not very soluble in water linked via a covalent disulfide Exists as Zwitterion: An ion bond. with + (positive) and – (Negative) charges on the same molecule with a net zero charge Carboxyl groups give-up a proton to get negative charge Amino groups accept a proton to become positive PEPTIDES Dipeptide: bond between two Amino acids in solution exist in amino acids three different species Oligopeptide: bond between ~ (zwitterions, positive ion, and 10 - 20 amino acids negative ion) - Equilibrium Polypeptide: bond between shifts with change in pH large number of amino acids Isoelectric point (pI) – pH at Every peptide has an N- which the concentration of terminal end and a C terminal Zwitterion is maximum -- net end 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. lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC +H3N-aa-aa-aa-aa-aa-aa-aa-aa- BIOCHEMICALLY IMPORTANT aa-COO SMALL PEPTIDES Many relatively small peptides are biochemically active: Hormones Neurotransmitters Antioxidants Small Peptide Hormones: Best-known peptide hormones: oxytocin and vasopressin Produced by the NOMENCLATURE OF PEPTIDE hypothalamus stored in 1. The C-terminal amino acid the posterior pituitary residue keeps its full amino gland acid name. nonapeptide (nine amino 2. All of the other amino acid acid residues) with six residues have names that end of the residues held in in -yl. The -yl suffi x replaces the form of a loop by a the -ine or -ic acid ending of the disulfide bond formed amino acid name, except for between two cysteine tryptophan, for which -yl is residues added to the name. 3. The amino acid naming sequence begins at the N- terminal amino acid residue. EXAMPLE: Ala-leu-gly has the IUPAC name of alanylleucylglycine ISOMERIC PEPTIDES Oxytocin is a natural hormone that Peptides that contain the same manages key aspects of the female and amino acids but present in male reproductive systems, including different order are different labor and delivery and lactation, as molecules (constitutional well as aspects of human behavior. isomers) with different properties Vasopressin is a hormone that helps For example, two blood vessels constrict and helps the different dipeptides can kidneys control the amount of water be formed between and salt in the body. This helps control alanine and glycine blood pressure and the amount of The number of isomeric urine that is made. peptides possible increases rapidly as the length of the SMALL PEPTIDE peptide chain increases NEUROTRANSMITTERS Enkephalins are pentapeptide neurotransmitters produced by the brain and bind receptor within the brain Help reduce pain lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC Best-known enkephalins: Common proteins Met-enkephalin: Tyr– contain 400–500 amino Gly–Gly–Phe–Met acid residues Leu-enkephalin: Tyr– Small proteins contain Gly–Gly–Phe–Leu 40–100 amino acid residues SMALL PEPTIDES ANTIOXIDANTS More than one peptide chain Glutathione (Glu–Cys–Gly) – a may be present in a protein: tripeptide – is present is in Monomeric : A high levels in most cells monomeric protein Regulator of oxidation– contains one peptide reduction reactions. chain Glutathione is an antioxidant Multimeric: A and protects cellular contents multimeric protein from oxidizing agents such as contains more than one peroxides and superoxides peptide chain Highly reactive forms of oxygen often generated PROTEIN CLASSIFICATION BASED ON within the cell in CHEMICAL COMPOSITION response to bacterial Simple proteins: A protein in invasion which only amino acid residues Unusual structural feature – are present: Glu is bonded to Cys through More than one protein the side-chain carboxyl group subunit may be present but all subunits contain only amino acids Conjugated protein: A protein that has one or more non- amino acid entities (prosthetic groups) present in its GENERAL STRUCTURAL structure: CHARACTERISTICS OF PROTEINS One or more polypeptide A protein is a naturally- chains may be present occurring, unbranched polymer Non-amino acid in which the monomer units are components - may be amino acids. organic or inorganic - A protein is a peptide in which prosthetic groups at least 40 amino acid residues Lipoproteins contain are present: lipid prosthetic groups The terms polypeptide Glycoproteins contain and protein are often carbohydrate groups, used interchangeably Metalloproteins contain used to describe a a specific metal as protein prosthetic group Several proteins with >10,000 amino acid residues are known lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC FOUR TYPES OF STRUCTURES ✓ For two amino acids 1. PRIMARY STRUCTURE OF linked through a PROTEINS peptide bond six Primary structure of atoms lie in the same protein refers to the plane order in which amino ✓ The planar peptide acids are linked together linkage structure has in a protein considerable rigidity, Every protein has its therefore rotation of own unique amino acid groups about the C–N sequence bond is hindered Frederick Sanger (1953) ✓ Cis–trans isomerism sequenced and is possible about C–N determined the primary bond. structure for the first ✓ The trans isomer is protein – Insulin the preferred PRIMARY STRUCTURE OF HUMAN orientation MYOGLOBIN ALPHA-HELIX A single protein chain adopts a shape that resembles a coiled spring (helix): H-bonding between same amino acid chains –intra molecular Coiled helical spring R-group outside of the helix -- not enough room for them to stay inside 2. SECONDARY STRUCTURE OF PROTEINS Arrangement of atoms of backbone in space. The two most common types : alpha-helix (a- helix) and the beta- BETA-PLEATED SHEETS pleated sheet (b-pleated Completely extended amino sheet). acid chains The peptide linkages are H-bonding between two essentially planar thus different chains – inter and/or allows only two possible intramolecular arrangements for the Side chains below or above the peptide backbone for the axis following reasons: lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC subunits a tetramer, and so on). The subunits are held together mainly by hydrophobic interactions between amino acid R groups. An example of a protein 3. TERTIARY STRUCTURE OF with quaternary PROTEINS structure is hemoglobin, The overall three- the oxygen carrying dimensional shape of a protein in blood. It is a protein tetramer in which there Results from the are two identical a interactions between chains and two identical amino acid side chains B chains. Each chain (R groups) that are enfolds a heme group, widely separated from the site where oxygen each other. binds to the protein. In general 4 types of interactions are PROTEIN CLASSIFICATION BASED observed. ON SHAPE 1. Fibrous Proteins: Collagen FOUR TYPES OF INTERACTIONS - Most abundant proteins Disulfide bond: covalent, in humans (30% of total strong, between two cysteine body protein) groups - Major structural Electrostatic interactions: Salt material in tendons, Bridge between charged side ligaments, blood vessels, chains of acidic and basic and skin amino acids - Organic component of ✓ -OH, -NH2, -COOH, - bones and teeth CONH2 - Predominant structure - H-Bonding between polar, triple helix acidic and/or basic R groups - Rich in proline (up to ✓ For H-bonding to occur, 20%) – important to the H must be attached maintain structure on O, N or F 2. Globular Proteins: Myoglobin Hydrophobic interactions: - An oxygen storage Between non-polar side chains molecule in muscles. - Monomer - single 4. QUARTERNARY STRUCTURE OF peptide chain with one PROTEINS heme unit The HIGHEST level of - Binds one O2 molecule protein organization - Has a higher affinity for Most multimeric oxygen than hemoglobin. proteins contain an even - Oxygen stored in number of subunits (two myoglobin molecules subunits a dimer, four serves as a reserve lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC oxygen source for different cells, tissues, and working muscles organs. Insulin and glucagon - 3. Globular Proteins: Hemoglobin regulate carbohydrate - An oxygen carrier metabolism Human growth molecule in blood hormone – regulate body - Transports oxygen from growth lungs to tissues 5. Contractile proteins: Necessary - Tetramer (four peptide for all forms of movement. chains) - each subunit Muscles contain filament-like has a heme group contractile proteins (actin and - Can transport up to 4 myosin). Human reproduction oxygen molecules at depends on the movement of time sperm – possible because of - Iron atom in heme contractile proteins. interacts with oxygen 6. Structural proteins: Confer stiffness and rigidity. Collagen PROTEINS CLASSIFICATION BASED is a component of cartilage a. ON FUNCTION Keratin gives mechanical - The functional versatility of strength as well as protective proteins stems from: covering to hair, fingernails, Ability to bind small feathers, hooves, etc. molecules specifically 7. Transmembrane proteins: Span and strongly a cell membrane and help Ability to bind other control the movement of small proteins and form fiber- molecules and ions. Have like structures, and channels – help molecules can Ability integrated into enter and exit the cell. cell membranes Transport is very selective - allow passage of one type of MAJOR CATEGORIES OF PROTEINS molecule or ion. BASED ON FUNCTION 8. Storage proteins: Bind (and 1. Catalytic proteins: Enzymes are store) small molecules. best known for their catalytic Ferritin - an iron-storage role. Almost every chemical protein - saves iron for reaction in the body is driven use in the biosynthesis by an enzyme of new hemoglobin 2. Defense proteins: molecules. Immunoglobulins or antibodies Myoglobin - an oxygen- are central to functioning of the storage protein present body’s immune system. in muscle 3. Transport proteins: Bind small 9. Regulatory proteins: Often biomolecules, e.g., oxygen and found “embedded” in the other ligands, and transport exterior surface of cell them to other locations in the membranes - act as sites for body and release them on receptor molecules. Often the demand. molecules that bind to enzymes 4. Messenger proteins: transmit (catalytic proteins), thereby signals to coordinate turning them “on” and “off,” biochemical processes between lumsyin OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC and thus controlling enzymatic Fever: >104ºF – the action. critical enzymes of the 10. Nutrient proteins: Particularly body start getting important in the early stages of denatured life - from embryo to infant. Casein (milk) and GLYCOPROTEINS ovalalbumin (egg white) - Conjugated proteins with are nutrient proteins carbohydrates linked to them: Milk also provide Many of plasma immunological membrane proteins are protection for glycoproteins mammalian young. Blood group markers of the ABO system are also PROTEIN HYDROLYSIS glycoproteins - Results in the generation of an Collagen and amine and a carboxylic acid immunoglobulins are functional group. glycoproteins - Digestion of ingested protein is - Collagen – glycoprotein enzyme-catalyzed hydrolysis Most abundant protein - Free amino acids produced are in human body (30% of absorbed into the bloodstream total body protein) and transported to the liver for Triple helix structure the synthesis of new proteins. Rich in 4-hydroxyproline - Hydrolysis of cellular proteins (5%) and 5- and their resynthesis is a hydroxylysine (1%) — continuous process. derivatives Some hydroxylysines are PROTEIN DENATURATION linked to glucose, - Partial or complete galactose, and their disorganization of protein’s disaccharides – help in tertiary structure aggregation of collagen - Cooking food denatures the fibrils. protein but does not change protein nutritional value GLYCOPROTEINS - Coagulation: Precipitation - Immunoglobulins (denaturation of proteins) - Glycoproteins produced as a Egg white - a protective response to the concentrated solution of invasion of microorganisms or protein albumin - forms foreign molecules - antibodies a jelly when heated against antigens. because the albumin is - Immunoglobulin bonding to an denatured antigen via variable region of - Cooking: an immunoglobulin occurs Denatures proteins – through hydrophobic Makes it easy for interactions, dipole – dipole enzymes in our body to interactions, and hydrogen hydrolyze/digest protein bonds. Kills microorganisms by denaturation of proteins lumsyin  OUR LADY OF FATIMA UNIVERSITY – PAMPANGA CAMPUS COLLEGE OF MEDICAL LABORATORY SCIENCE CHEM123 - LEC 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: Chylomicrons: Transport dietary triacylglycerols from intestine to liver and to adipose tissue. Very-low-density lipoproteins (VLDL): Transport triacylglycerols synthesized in the liver to adipose tissue. Low-density lipoproteins (LDL): Transport cholesterol synthesized in the liver to cells throughout the body. High-density lipoproteins (HDL): Collect excess cholesterol from body tissues and transport it back to the liver for degradation to bile acids. lumsyin