BIOCHEMISTRY-FOR-MEDICAL-LABORATORY-SCIENCE-LEC.pdf

BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] LESSON 1: INTRODUCTION TO BIOCHEMISTRY 5. Frederick Sanger (British) and Walter...

BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] LESSON 1: INTRODUCTION TO BIOCHEMISTRY 5. Frederick Sanger (British) and Walter Gilbert (American) - 1980 → WHAT IS BIOCHEMISTRY Determined sequence of DNA concerned with the chemical basis of life Won Nobel Prize in Chemistry in 1980 concerned with various molecules that occur in living cells and organisms & with their chemical reaction 6. Kary Mullis (American) - 1993 Invention of PCR method Will delve in compounds, chemical expression and Won Nobel Prize in Chemistry in 1993 reactions, and molecular levels Describe the different attributes of life → CELLS ○ Adaptation - ability of living organisms to fit Basic building blocks of life in a certain habitat [ex. Penguin (fat layers)] Smallest living unit of an organism ○ Reproduction - ability to produce offspring May be an entire organism (cellular) or one of billions ○ Metabolism - dynamic processes & different of cells that make up the organism (multicellular) pathways inside the body of living organisms Grow, reproduce, use energy, adapt, respond to their Anabolism - building up environment Catabolism - breaking down Many cannot be seen with the naked eye Aim - to describe and explain in molecular terms, all typical cell size is 10μm; a typical cell mass is 1 chemical processes of living cells nanogram ○ Structure-function (relationship) Design describe the function Hierarchy of Organization of Cells ○ Metabolism and Regulation 1. Precursors Process and control smallest or simple molecules that can be obtained from ○ How life began? the environment of the cell Significance - essential to all life science as the low molecular mass (sum of elements) common knowledge 2. Metabolic Intermediates ○ Genetics, cell biology, molecular biology products or results of the metabolic processes ○ Physiology and immunology (ex. glycolysis → pyruvate) ○ Pharmacology and pharmacy ○ Toxicology, pathology, microbiology 3. Monomers ○ Zoology and botany building blocks (ex. amino acids, simple sugars, nucleotides) Medical students who acquire a sound knowledge of biochemistry will be in a strong position to deal with 4. Macromolecules two central concerns of the health sciences: product when monomers linked with themselves ○ understanding and maintenance of health; (ex. proteins, lipids, carbohydrates, nucleic acid) ○ and effective treatment of disease 5. Supramolecules assembly or complex bonds between macromolecules → HISTORY AND DEVELOPMENT (ex. lipoprotein, glycolipid) 1. Carl Neuberg (German) - 1903 6. Cell Organelles Pioneer non-covalent bonding between supramolecules Father of Biochemistry (ex. hydrogen bonding, london dispersion forces) Editor of first journal of 7. Cells biochemistry 8. Tissues Notable Breakthroughs 9. Individual / Human Body Discover of the role of enzymes as catalysts Two Types of Cells Identification of nucleic acids as A. Prokaryotic Cells information molecules (Greek: pro-before; karyon-nucleus) include various bacteria, archaea, fungi 2. Sir Hans Adolf Krebs (German) - 1937 Lack a nucleus or membrane-bound structures called Discovered Citric Acid Cycle organelles Won Nobel Prize in Physiology or Medicine in 1953 B. Eukaryotic Cells (Greek: eu-true; karyon-nucleus) include most other 3. James Watson and Francis cells (plants, fungie, & animals) Crick (English) - 1953 Have a nucleus and membrane-bound organelles Discovered DNA as double helix (due to hydrogen bonding) Won Nobel Prize in Physiology or Medicine in 1962 4. Frederick Sanger (British) - 1955 Determined insulin sequence and structure of proteins (repeating units of amino acids) Nobel Prize in Physiology or Medicine in 1956 NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] Parts of the Cell Macromolecule Monomer 1. Plasma Membrane Cell’s defining boundary Polysaccharide Simple sugar Providing a barrier and containing transport and signaling systems Protein (Peptide) Amino acid 2. Nucleus Information center (command center) RNA or DNA Nucleotide Double membrane for chromosomes and nucleolus. The place where almost all Lipid Fatty acid DNA replication and RNA synthesis occur. The nucleolus is a site for synthesis of → BIOMOLECULES RNA making up the ribosome. Biomolecules are building block of cells Animal and plant cells = approx. 10,000 kinds 3. Mitochondria Water constitutes 50-95% of cells content by weight The power generator (powerhouse) Ions like Na+, K+, and Ca2 account for 1% ○ Generating of the energy Almost all other kinds of biomolecules are organic inside the cell (ATP) Organic compounds are compounds composed Double membrane with a series of primarily of Carbon skeleton folds called cristae. Functions in energy production through Chemical Composition of a Normal Man metabolism. Contains its own DNA. Constituent Percent (%) Weight (kg) 4. Endoplasmic Reticulum Transport network for molecules Water 61.6 40 a. Rough ER - Covered with ribosomes (“rough” Protein 17.0 11 appearance) → process of synthesizing proteins for secretions or Lipid 13.8 9 localization in membranes b. Smooth ER Carbohydrate 1.5 1 - Site for synthesis and metabolism of lipid and carbohydrates Minerals 6.1 4 5. Ribosomes Protein and RNA complex responsible Carbon for protein synthesis More abundant in living organisms than it is in the rest of the universe 6. Golgi Apparatus What makes Carbon special? Why is Carbon so Process and package the macromolecules different from all the other elements on the periodic Series of stacked membranes. Vesicles table? carry materials from RER to the Golgi The ability of Carbon atoms to bond together to form apparatus. Vesicles move between stacks long chains and rings while proteins are “processed” to mature form. Similarities Among All Types of Cells All cells use nucleic acids (DNA) to store information 7. Lysosomes ○ Except RNA viruses, but not true cells Contains digestive enzymes (incapable of autonomous replication) A membrane bound organelle that is All cells use nucleic acids (RNA) to access stored responsible for degrading proteins information and membranes in the cell All cells use proteins as catalysts (enzymes) for chemical reactions → POLYMERS AND MONOMERS ○ A few examples of RNA based enzymes, Each type of biomolecules are polymers that are which may reflect primordial use of RNA assembled from single units called monomers All cells use lipids for membrane components Each type of macromolecule is an assemblage of ○ Different types of lipids in different types of different types of monomer cells All cells use carbohydrates for cell walls (if present), recognition, and energy generation Macromolecule Monomer Carbohydrates Monosaccharide LESSON 2: CARBOHYDRATES Lipids Not always polymers; → CARBOHYDRATES Hydrocarbon chains A major source of energy from our diet Composed of the elements C, H, and O Proteins Amino Acids Also called saccharides, which means “sugars” ○ sakkharon = “sweet tasting" Nucleic Acids Nucleotides “hydrates of carbon” ○ has a water molecule NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] derived from the formula Cn(H2O)m → ISOMERISM ○ Glucose Isomers C6H12O6 compounds possessing identical molecular formula but C6(H2O)6 different structures polyhydroxy aldehydes, polyhydroxy ketones, or 2n = formula to determine the number of isomers compounds that yield them after hydrolysis ○ Aldehydes - should always be at the terminal Types of Isomerism side of the long chain 1. Structural Isomerism ○ Ketones - it could be on the 2nd, 3rd, or 4th Same molecular carbon because there are 2 R-group attached formula but differ to it from each other by Are produced by photosynthesis in plants having different ○ 6CO2 + 6H2O → (solar energy) C6H12O6 + 6O2 structures Such as glucose are synthesized in plants from CO2, H2O, and energy from the sun 2. Stereoisomerism Are oxidized in living cells (respiration) to produce CO2, Same molecular formula and same structure but differ H2O, and energy in configuration Differ in arrangement of their atoms in space Functions Presence of chiral centers allow the formation of provides energy stereoisomers Glycogen – provides short term energy reserve Types of stereoisomerism associated with glucose are: ○ Glucose = energy that can be used ○ D and L isomerism ○ Glycogen = serves as energy storage ○ Optical isomerism supply Carbon for synthesis of other biochemical ○ Epimerism substances ○ α and β anomerism ○ Carbon is the backbone part of structure of DNA and RNA a. D and L Isomerism linked to lipids – in cell membrane depends on the penultimate carbon (second to the last) linked to proteins – in biological recognition processes Left-handed Right-handed regulation of blood sugar ○ Carbohydrates send signals to pancreas to stimulate insulin spare the use of protein for energy breakdown of fatty acids and preventing ketosis provide flavor and sweeteners source of dietary fibers → STRUCTURAL PROPERTY Handedness ○ Left-handed ○ Right-handed Presence of Chiral Center/s Isomers i). Enantiomers ○ Structural Isomers Stereoisomers whose molecules are ○ Stereoisomers nonsuperimposable mirror images of each other (mirror, nonsuperimposable) Mirror Images Superimposable Mirror Image ii). Diastereomers ○ coincide at all points when images are laid stereoisomers whose molecules are not mirror upon each other images of each other (nonsuperimposable, non mirror) Nonsuperimposable Mirror Image ○ not all points coincide when images are laid b. Optical Isomerism upon each other Optical activity is the capacity of a substance to rotate the plane polarized light passing through it Clockwise direction ○ Dextrorotatory (d) or (+) Counterclockwise direction ○ Levorotatory (l) or (-) Chiral Center atom in a molecule that has four different tetrahedrally bonded to it mirror image are not Chiral compounds rotate polarized light clockwise or superimposable counterclockwise through certain angle NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] c. Epimerism if two monosaccharides differ from each other in their configuration around a single specific carbon (other than anomeric) atom Cyclic Structures the prevalent form of monosaccharides with 5 or 6 carbon atoms d. Anomerism Isomers obtained from the change of position of hydroxyl group attached to the anomeric carbon Pyran Furan e.g. α and β glucose are 2 anomers formed when the hydroxyl group on C-5 ○ In cyclic form reacts with the aldehyde group or ketone Also α and β fructose are 2 anomers group Drawing the Cyclic Structure for Glucose Step 1 Number the carbon chain and turn clockwise to form a linear open chain Mutarotation the change in the specific optical rotation by the interconversion of α and β forms of D glucose to an equilibrium mixture Step 2 Bend the chain to make a hexagon Bond the C5 –O– to C1 Place the C6 group above the ring Write the –OH groups on C2 and C4 below the ring Write the –OH group on C3 above the ring Write a new –OH on C1 → STRUCTURE OF MONOSACCHARIDE Step 3 The new –OH on C1 is drawn Fischer Projection Down for the α anomer the straight chain structural formula Up for the β anomer developed by Hermann Emil Fischer (German) used to represent carbohydrates places the most oxidized group at the top shows chiral carbons as the intersection of vertical and horizontal lines α-D-glucose β-D-glucose X-ray Diffraction Analysis Boat and chair form Haworth Projection α-D-Glucose and β-D-Glucose in Solution Cyclic formula or ring structure When placed in solution: Developed by Walter Norman Haworth (British) ○ cyclic structures open and close Two-dimensional structural annotation that specifies ○ α-D-glucose converts to β-D-glucose and the three-dimensional structure of a cyclic form of back monosaccharide ○ There is only a small amount of open chain NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] 2. D-Fructose Is a ketohexose C6H12O6 ○ Ketone group in the 2nd carbon ○ 4 carbons only in its rings Is the sweetest carbohydrate Is found in fruit juices and honey α-D-glucose D-glucose (open) β-D-glucose Converts to glucose in the body (36%) (trace) (64%) 3. D-Galactose Note: Higher percentage = more stable An aldohexose C6H12O6 Reason: Steric hindrance (they will not collide) Not found free in nature Obtained from lactose, a → CLASSIFICATION: MOLECULAR SIZE disaccharide I. Monosaccharides A similar structure to glucose except The simplest carbohydrates for the –OH on C4 Consist of 3 to 6 carbon atoms, typically A carbonyl group (aldehyde or ketone) II. Disaccharides Several hydroxyl groups Consist of 2 monosaccharides Colorless, crystalline solids Glycosides formed by the condensation of 2 simple sugars a. Aldose If the glycosidic linkage involves the carbonyl groups ○ Monosaccharides of both sugars (as in sucrose) the resulting ○ with an aldehyde group disaccharide is non-reducing ○ with many hydroxyl (─OH) groups If the glycosidic linkage involves the carbonyl group of triose (3 C atoms) only one of the 2 sugars (as in maltose and lactose) the tetrose (4 C atoms) resulting disaccharide is reducing pentose (5 C atoms) hexose (6 C atoms) Important Disaccharides Monosaccharides Disaccharide fructose, a ketohexose Glucose + Glucose Maltose + H2O Glucose + Galactose Lactose + H2O Glucose + Fructose Sucrose + H2O erythrose, an aldotetrose b. Ketose 1. Maltose ○ with a ketone group also known as malt ○ with many hydroxyl (─OH) groups sugar triose (3 C atoms) Composed of two tetrose (4 C atoms) D-glucose molecules pentose (5 C atoms) Obtained from the hexose (6 C atoms) hydrolysis of starch Linked by an Examples of Monosaccharides α-1,4-glycosidic bond 1. D-Glucose formed from the −OH on C1 of the first glucose and Found in fruits, corn syrup, and −OH on C4 of the second glucose honey Used in cereals, candies, and brewing An aldohexose with the formula Found in both the α- and β- forms C6H12O6 Known as blood sugar in the 2. Lactose body Is a disaccharide of The monosaccharide in polymers of starch, cellulose, β-D-galactose and α- and glycogen or β-D-glucose Blood Glucose Level Contains a β In the body, glucose has a normal blood level -1,4-glycosidic bond of 70-90 mg/dL Is found in milk and Glucose tolerance test measures blood milk products glucose for several hours after ingesting 3. Sucrose also known as table sugar obtained from sugar cane and sugar beets Consists of α-D-glucose and β-D-fructose has an α,β-1,2-glycosidic bond NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] Relative Sweetness Include amylose and amylopectin, starches made of Fructose - sweetest-even sweeter than sucrose α-D-glucose Honey - D-fructose and D-glucose Include glycogen (animal starch in muscle), which is made of α-D-glucose. Lactose - almost no sweetness and is sometimes Include cellulose (plants and wood), which is made of added to food as a filler β-D-glucose → CLASSIFICATION: REPEATING UNITS 1. Homopolysaccharide only one type of monosaccharide monomer unit is present 2. Heteropolysaccharide more than one (usually two) type of monosaccharide monomer units are present → CLASSIFICATION: DEGREE OF BRANCHING 1. Branched polysaccharides formed from two major types of → CLASSIFICATION: REACTION TO OXIDIZING AGENTS biochemical polymers therefore forming branch/es 1. Reducing Sugar carbohydrate that gives a positive result with 2. Unbranched Benedict’s and Tollen’s test linear polymers ○ Lactose and Maltose Carbohydrates with a carbonyl group that oxidizes to Structures of Amylose and Amylopectin give a carboxylic acid Undergo reaction with Benedict’s reagent (Cu2+) to give the corresponding carboxylic acid Include the monosaccharides glucose, galactose, and fructose Oxidation of D-Glucose glucose is oxidized to a carboxylic acid Glucose is a reducing sugar Amylose Reduction of D-Glucose A polymer of α-D-glucose molecules Involves the carbonyl Linked by α-1,4 glycosidic bonds group A continuous (unbranched) chain Produces sugar alcohols called alditols Such as D-glucose gives D-glucitol also called sorbitol 2. Non-reducing Sugar negative with Benedict’s and Tollen’s test ○ Sucrose III. Oligosaccharides Amylopectin Consist of 2-10 monosaccharides Is a polymer of α-D-glucose molecules Is a branched-chain polysaccharide IV. Polysaccharides Has α-1,4-glycosidic bonds between the glucose units Contain many monosaccharides Has α-1,6 bonds to branches formed by the condensation of n molecules of monosaccharides with the removal of n-1 molecules of water Since condensation involves the carbonyl groups of the sugars, leaving only one free carbonyl group at the end of a big molecule, α-D-glucose polysaccharides are non-reducing polymers of D-glucose NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] Glycogen polysaccharide that stores α-D-glucose in muscle similar to amylopectin, but is more highly branched Cellulose polysaccharide of glucose units in unbranched chains Has β-1,4-glycosidic bonds Cannot be digested by humans because humans cannot break down β-1,4-glycosidic bonds ‘ Human digestive Human digestive enzymes easily break enzymes cannot break alpha bonds in starch beta bonds in cellulose LESSON 3: PROTEINS → PROTEINS It is also called polypeptide since it is a chain of amino acids linked by peptide bonds It is a naturally occurring, unbranched polymer in which the monomer units are amino acids It is a peptide in which at least 40 amino acid residues are present It contains carbon, hydrogen, oxygen, nitrogen It sometimes contains sulfur and phosphorous Chemical Structure of Amino Amino acid is an organic compound that contains both an amino group and a carboxyl group ○ Common structure is an amine connected with a hydrogen and R group with carboxylic acid (carbonyl with alcohol or hydroxyl) at the end Amino group acts Functions of Proteins like a base and Structural component (skin, hair, muscles) tends to be Chemical messenger (hormones) positive Disease defense (antibodies) Carboxyl group Enzymes (catalase, lactase) acts like an acid and tends to be → AMINO ACIDS negative Building blocks of protein “R” groups is There are 700 different naturally occurring amino acids variable and can but only 20 are normally present in proteins. range from 1 to These 20 amino acids present in proteins are called the 20 atoms Standard Amino Acids Two amino acids can join to form peptide NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] Amino Acid Examples Polar Acidic Amino Acids 1 amino group 2 carboxyl group (1 is part of the side chain) Polar Basic Amino Acids 2 amino group 1 carboxyl group (1 is part of side chain) Polarity depends on the electronegativity of an atom, which is an ability of an atom to pull an electron towards itself. ○ Polar = high electronegativity difference Can be neutral, acidic (-), basic (+) If the side chain contains Oxygen and Nitrogen (0.5) ○ Non-polar= equal sharing of electrons, the pull stabilizes atoms (low to equal difference) If the side chain contains Hydrogen and Carbon (0.1) Pauling Electronegativity Values Non-Polar Amino Acids Commonly, it is bonds between carbon and hydrogen (methyl) → FOUR CLASSIFICATIONS OF AMINO ACIDS Based on side chain polarity Based on number of peptide chain Based on chemical composition Based on shape Polar Amino Acids (Neutral) No positive or negative charge → CLASSIFICATION: SIDE CHAIN POLARITY Classification Description Non-Polar Amino Acids 1 amino group 2 carboxyl group 1 non polar side chain Polar Neutral Amino Acids 1 amino group 1 carboxyl group 1 polar neutral side chain NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] Polar Acidic Amino Acids Nature prefers the L-isomers of amino acids. Negative charge in R group (oxygen) All standard amino acids have chiral centers except Glycine → ACID-BASE PROPERTIES OF AMINO ACIDS Both acidic and basic group are present in an α-amino acid If amino acid is in crystal form, it is not soluble with Polar Basic Amino Acids water due to strong intermolecular forces Positive charge in R group (bond between nitrogen and hydrogen = amine group) → ISOELECTRIC POINT The pH at which an amino acid has no net charge because equal number of positive and negative charges are present → ESSENTIAL AMINO ACIDS Conditionally Essential Non-Essential Non-Essential Histidine Arginine Alanine Isoleucine Cystine Asparagine Leucine Glutamine Aspartate Zwitterion - there are positive and negative one charges Lysine Glycine Glutamate Isoelectric Point (pI) - a pH where the net charge is 0 ○ To compute for pI, add the pKa1 (acidic to Methionine Proline Serine neutral form) and pKa2 (neutral to basic form). The, divide it by 2 Phenylalanine Tyrosine ○ For example, Alanine with a pI of 6.01 Three Different Amino Acids Exist: Threonine 1. Zwitterion Tryptophan It is a molecule that has positive and negative charges. It is made up of two (or more) functional groups. One of its components has a positive charge and another Valine one with a negative charge. Because of this, the net charge of zwitterion is zero. Essential are amino acids that cannot be synthesized by our body. Thus, we need another source (food or medications) Non-Essential are amino acids that can be synthesized by our body. In other words, it can be found and created within our system. → CHIRALITY OF AMINO ACIDS Chirality refer to having a mirror image Amino acids have mirror images: Right and Left based on the location of the amino group. NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] 2. Negative Ion 3. Positive Ion Rule 3 The amino acid naming sequence begins at the N-terminal amino acid residue For example: ○ Valine + Threonine + Cysteine ○ This will form a Tripeptide ○ The N terminal is valine (left side) ○ The C terminal is Cysteine (right side) ○ Hence, Valine + Threonine + Cysteine = ○ Valinyl + Threonyl + Cysteine ○ Final name = Valinylthreonylcysteine → FORMATION OF DIPEPTIDE Amino group = left side = N terminal Carboxyl group = right side = C terminal The condensation or elimination of water molecule Formation of bond between Carbon and Nitrogen Another Example: ○ Glu + Ser + Ala ○ Glutamic Acid + Serine + Alanine ○ Glutamyl + Seryl + Alanine ○ Final Name = Glutamylserylalanine → CLASSIFICATION: NUMBER OF PEPTIDE CHAIN Monomeric Protein only one peptide chain is present Dehydration Synthesis Multimeric Protein Amino Acid + Amino Acid → Dipeptide More than one peptide chain is present Amino Acid + Dipeptide → Tripeptide Amino Acid + Amino Acid + Amino Acid + Tripeptide → → CLASSIFICATION: CHEMICAL COMPOSITION Polypeptide Simple Protein Only amino acid residue are present → NAMING PEPTIDES IUPAC Rules in naming small peptides Conjugated Protein International Union of Pure and Applied Chemistry One or more non-amino acid entities present in its structure in addition to one or more peptide chains IUPAC Rules in Naming Peptides (supramolecules) Rule 1 A complex protein consisting of amino acids combined The C-terminal amino acid residue keeps its full amino with other substances. acid name Simple Protein + Prosthetic Group = Conjugated Protein IUPAC Rules in naming small peptides For example: ○ Glycine + Alanine Class Prosthetic Group Example ○ Glycine is the N-terminal amino acid ○ Alanine is the C-terminal amino acid Hemoproteins Heme unit Hemoglobin ○ Hence, Glycine will become Glycyl Myoglobin ○ While, Alanine gets to keep its name ○ Hence, Glycine + Alanine = Glycylalanine Lipoproteins Lipids LDL HDL, VLDL, and Chylomicrons Glycoproteins Carbohydrate Gamma Globulin Mucin Interferon Phosphoproteins Phosphate Group Glycogen Phosphorylase Nucleoproteins Nucleic Acids Ribosomes Rule 2 Viruses All the other amino acid residue names ending in -ine or -ic acid will be replaced with -yl, except: ○ Tryptophan → Tryptophyl Metalloproteins Metal Ion Ferritin ○ Cysteine → Cysteinyl Alcohol ○ Glutamine → Glutaminyl Dehydrogenase ○ Asparagine → Asparanginyl NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] → STRUCTURE OF PROTEINS → CLASSIFICATION: SHAPE Primary Protein Structure Fibrous Sequence of a chain of amino acids Have an elongated shape with one dimension much longer than the others Globular Have peptide chains folded into spherical and globular shapes Secondary Protein Structure Hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern Fibrous Globular Extended protein structure Compact protein structure Insoluble in water Soluble in water Secondary structure is simple Secondary structure is complex - mixture of α-sheet, β-sheet, loop structures Functions for support and Functions in all aspects of Alpha Helix external protection metabolism The telephone cord shape of the alpha helix is held in place by Hydrogen Bonds between every N-H group and the oxygen of a C=O → PROTEIN HYDROLYSIS group in the next turn of the helix, four amino Splits peptide binds to smaller peptides and amino acids down the chain. acids Occurs in the digestion of proteins Occurs in cells when amino acids are needed to synthesize new proteins and repair tissues In the lab, hydrolysis of a peptide requires acid or base, water, and heat In the body enzymes catalyze the hydrolysis of proteins Beta Pleated Sheets The pleated sheet structure of the Beta Sheet is held together by the Hydrogen Bonds between the amide groups of linear polypeptide chains. The average number of amino acid residues in a typical Beta Sheet is six with an average of six strands bonding together Tertiary Protein Structure Three-dimensional folding pattern of a protein due to side chain interactions → PROTEIN DENATURATION Quaternary Protein Structure - Involves the disruption of bonds in the secondary, Protein consists of more than one tertiary, quaternary structures amino acid chain. - Loss of biological function 1. Heat and Organic compounds break apart H+ bonds and disrupt hydrophobic interactions NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] 2. Acids and Bases Act as thermal insulator break H+ bonds between polar R groups and disrupts ○ Adipose tissue - traps heat which helps ionic bonds maintain body temperature Protection of internal organs 3. Heavy Metal Ions Precursor of many steroid hormones, Vitamin D react with S-S (Sulfur-Sulfur) binds to form solids Structural component of cell membrane Helps in absorption of fat-soluble vitamins 4. Agitation (Whipping or Shaking) Lipoproteins transporting lipids stretches peptide chains until bonds break Fats serve as surfactants by reducing surface tension Improve taste and palatability Applications of Denaturation Acts as electric insulators in neurons Cooking eggs Wiping of alcohol Structural Property Heat used to cauterize blood vessels Very diverse Sterilization of instruments in Some are: autoclave ○ Esters Hair perming ○ Amides ○ Alcohols Protein Hydrolysis vs. Denaturation ○ Acyclic ○ Cyclic Protein Protein ○ Polycylic Denaturation Hydrolysis All are insoluble to water Definition The process of Process of → FATTY ACIDS proteins losing breaking proteins Naturally occurring monocarboxylic acid their shape into their building Always contain an even number of Carbon atoms blocks amino Have a Carbon chain that is unbranched acids → CLASSIFICATION: TOTAL NUMBER OF CARBON What Happens Proteins lose its Proteins convert 1. Even Chain Fatty Acid - even number of Carbon three dimensional into amino acids 2. Odd Chain Fatty Acid - odd number of Carbon structure and shape Even Chain fatty Acid Most of the fatty acids that occur in natural lipids have Factors Affecting High temperature, Enzymes and seen carbon atoms pH changes, chemicals denaturing agents, alkaline, and acid solutions, etc. Result Loss of biological Production of free activity amino acids or peptides LESSON 4: LIPIDS Odd Chain Fatty Acid Seen in milk and microbial cell walls → LIPIDS Organic substance relatively insoluble in water but soluble in organic solvents like chloroform, ether and benzene ○ A diverse group ○ Fatty acids (carboxylic group, carbonyl group, R or side chain (aliphatic chain), glycerol) → CLASSIFICATION: CARBON CHAIN LENGTH Lipids are a diverse group of hydrophobic molecules Lipids are the one class of large biological 1. Short-Chain Fatty Acid - contains 4 to 6 Carbon molecules that do not form polymers 2. Medium-Chain Fatty Acid - contains 8 to 10 Carbon The unifying feature of lipids is having little or 3. Long-Chain Fatty Acid - contains 12 to 26 Carbon no affinity for water Lipids are hydrophobic because they consist → CLASSIFICATION: NUMBER OF CARBON TO CARBON mostly of hydrocarbons, which form nonpolar DOUBLE BONDS covalent bonds 1. Saturated Fatty Acid - all carbon to carbon bonds are The most biologically important lipids are single bonds fats, phospholipids, and steroids 2. Monounsaturated Fatty Acid - with one carbon to carbon double bond Functions 3. Polyunsaturated Fatty Acid - with two or more carbon Storage form of energy to carbon double bonds NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] Properties of Saturated Fatty Acids → NOMENCLATURE Contain only single C-C bonds Naming and Writing Formula Closely packed 1. Trivial Strong attractions between chains General name or common name without basis High melting points Solids at room temperature 2. Systematic Prefix Suffix 4C Buta- 6C Hexa- 8C Octa- If saturated -anoic acid 10 C Deca- Properties of Unsaturated Fatty Acids 12 C Dodeca- Contain one or more double C=C bonds Nonlinear chains do not allow molecules to pack closely 14 C Tetradeca- Few interactions between chains Low melting points Liquids at room temperature 16 C Hexadeca- If 18 C Octadeca- -aenoic acid unsaturated 20 C Eicosa- 24 C Tetraeicosa- Note: cis - if the double bond in a skeletal formula is in the same plane (with both lines oriented or pointing either upward or downward) → FORMULA 1. Condensed trans - if the double bond in a skeletal formula is not in a. Short form - CH3(CH2)14COOH the same plane (with one line oriented or pointed b. Long form - upward and the other downward) CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2 COOH 3. Delta (ΔX) Δ = delta sign X = location of double bond/s (separated by comma for polyunsaturated F.A.) 2. Line-angle/Skeletal 4. Lipid Number (C:D) C = number of carbon atoms D = number of double bonds NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] 5. Omega (ω) or n-x ω = omega sign n = number of carbon atoms from the methyl end to the last carbon to carbon double bond → PHYSICAL PROPERTIES 1. Water Solubility Carbon Chain ↑ Water Solubility ↓ As Carbon Chain increases in length, the more insoluble it is with water 2. Melting Points Carbon Chain ↑ Melting Point ↑ As Carbon Chain increase, melting point increases 3. Melting Points Degree of Unsaturation ↑ Melting Point ↓ The greater the degree of unsaturation, the greater the reduction in melting points Examples: stearic acid (18 C) saturated = MP 69°C ○ stearic acid is saturated and would have a higher melting point than unsaturated fatty acids. oleic acid (18 C) one double bond = MP 13°C ○ linoleic has two double bonds, it would have a lower mp than oleic acid, which has one double bond. linoleic acid (18 C) two double bonds = MP -17°C → ESSENTIAL FATTY ACIDS they are not synthesized in the body must be obtained from diet also called as polyunsaturated fatty acids (PUFA) ○ Linoleic Acid (LA) ○ Linolenic Acid (LNA) ○ Arachidonic Acid (AA) → TYPES OF LIPIDS Lipids with Fatty Acids Waxes Fats and oils (Triglycerides) Phospholipids Sphingolipids Lipids without Fatty Acids Steroids → TRIACYLGLYCEROL Energy storage lipids Found in Adipocytes (Adipose cells) Formed by esterification of glycerol and 3 fatty acids Much more efficient at storing energy than Glycogen NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] → CLASSIFICATION: FATTY ACID MOLECULES Point of 1. Simple Triacylglycerol Omega 3 Omega 6 Difference triester formed from esterification of glycerol with 3 identical fatty acids Source Cold Water Fishes Plant Oils 2. Mixed Triacylglycerol triester formed from the esterification of glycerol with ↓ incidence of more than 1 kind of fatty acid ↑ incidence of Heart Disease Benefits Heart Disease if despite high-fat → CLASSIFICATION: FORMS high-fat diet diet 1. Fats naturally occurring mixtures of triacylglycerol in which many different triacylglycerol molecules are present → CHEMICAL REACTIONS which are solid or semi-solid at room temperature 1. Esterification/ Dehydration Synthesis (25°C) 2. Hydrolysis 3. Saponification 2. Oils 4. Hydrogenation naturally occuring mixtures of triacylglycerol in which 5. Oxidation many different triacylglycerol molecules are present which are liquid at room temperature (25°C) Hydrolysis Triacylglycerol is split by water and acid (H+ or enzyme Points of catalyst) Fats Oils Produce glycerol and 3 fatty acids Difference Reverse of Esterification Form Solid at RT Liquid at RT More SFA than More UFA than Composition UFA SFA Melting Point Higher Lower Source Animals Plants, Fish Good Fat vs. Bad Fat FA Good or Bad Why? ↑ risk of heart SFA Bad disease ↓ risk of heart disease MUFA Food ↓ risk of breast cancer Saponification ↓ risk of heart Triacylglycerol undergoes hydrolysis with a strong base disease and is split into glycerol and salts of fatty acids PUFA Bad and Good The salts of fatty acids are “soaps” ↑ risk of breast cancer → OMEGA 3 AND OMEGA 6 FATS Omega-n Refers to the number (n) of the carbon atom with the first double bond from the methyl end Hydrogenation Unsaturated compounds react with H2 Ni or Pt are catalyst C=C bonds → C–C bonds NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] Converts cis double bonds to trans double bonds → MEMBRANE LIPIDS Trans fatty acids have ill effects on blood chemistry Lipids that are structural components of cell similar to those of Saturated Fatty Acids membrane Phospholipids most abundant type of membrane lipid contains 1 or more fatty acids, a platform molecule, and a phosphate group with an alcohol When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior The structure of phospholipids results in a bilayer arrangement found in cell membranes Phospholipids are the major component of all cell membranes Sphingoglycolipids contains a fatty acid and a carbohydrate component attached to a sphingosine Oxidation C-C double bonds present in Unsaturated FA are subject to oxidation with Oxygen (from air) Results to short chain aldehydes Further oxidation will form short chain carboxylic acids NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] Cholesterol Sex Hormones C27 steroid molecule 1. Estrogen - female sex hormones; synthesized in the component of cell membranes and precursor for other ovaries and adrenal cortex steroid based lipids 2. Androgens - male sex hormones; synthesized in the testis and adrenal cortex 3. Progestins - pregnancy hormones; synthesized in the ovaries and placenta Adrenocorticoid Hormones 1. Mineralocorticoids - control the balance of Na+ and K+ ions in cells and body fluids 2. Glucocorticoids - control glucose metabolism and counteract inflammation Eicosanoids 1. Prostaglandin - involved in many regulatory functions in the body 2. Thromboxane - promote the formation of blood clots by promoting platelet aggregation 3. Leukotriene - found in leukocytes and are associated with various inflammatory and allergic response Biological Waxes Water insoluble, water repellant lipids with protective coating and lubricating functions Summary: Fats are constructed from two types of smaller molecules: glycerol and fatty acids → EMULSIFICATION LIPIDS Glycerol is a three-carbon alcohol with a hydroxyl Lipids that stabilize and disperse water-insoluble group attached to each carbon materials in aqueous solution A fatty acid consists of a carboxyl group attached to a long carbon skeleton Fatty acids vary in length (number of carbons) and in the number and locations of double bonds Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds Unsaturated fatty acids have one or more double bonds → MESSENGER LIPIDS Regulatory lipids that act in the tissue where they are Fats made from saturated fatty acids are called synthesized or at other locations after transport via the saturated fats, and are solid at room temperature bloodstream Most animal fats are saturated Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room temperature Plant fats and fish fats are usually unsaturated A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds These trans fats may contribute more than saturated Steroid fats to cardiovascular disease Steroids are lipids characterized by a carbon skeleton consisting of four fused rings The major function of fats is energy storage Cholesterol, an important steroid, is a component in Humans and other mammals store their fat in adipose animal cell membranes cells Although cholesterol is essential in animals, high levels Adipose tissue also cushions vital organs and insulates in the blood may contribute to cardiovascular diseases the body NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] LESSON 5: ENZYMES It will not work if the substrate does not fit into it. → WHAT ARE ENZYMES? Enzymes are catalyst Catalysts are substances that speed up chemical reactions. Hence, enzymes are proteins that catalyze or speed up the rate of chemical reactions. → PARTS OF ENZYMES ○ They are not consumed during the process Active Site Enzymes lower the activation energy of the chemical This is the specific place in the reaction to speed it up. enzyme where substrates bind to After speeding up the chemical reaction, enzymes are This has a specific size, shae, and unchanged, and can be reused. chemical behavior rendered by the specific arrangement of its amino acids. Each type of enzyme has a unique active site, which is why enzymes are specific to particular substrates only. → EXAMPLES OF ENZYMES 1. Protease Breaks down proteins into amino acids 2. Carbohydrase Breaks down carbohydrate into monosaccharides 3. Lipase Breaks down lipids into fatty acids and glycerol 4. Catalase What is Activation Energy? Breaks down hydrogen peroxide into carbon dioxide The amount of energy needed to start a reaction. and water Generally, the chemical reactions they speed are either 5. Amylase Anabolic or Catabolic. Breaks down carbohydrate starch (polysaccharides) into monosaccharide Anabolic Starch is a polysaccharide made up of monosaccharide Building large molecules from small ones. linked together by glycosidic bonds. Catabolic → STRUCTURE OF ENZYMES Breaking down large molecules into small ones → SUBSTRATES We call these substrates that are built up or broken down as substrate Substrate are molecules that bind to enzymes → MODELS OF ENZYME ACTION 1. Lock and Key Hypothesis Simplest model to represent how an enzyme works The substrate simply fits into the active site to form a reaction just like the key fits in its specific lock. Enzymes are also highly specific in chemical reactions they speed up. ○ They will only bind to a substrate with the same shape. Simply, there are enzymes for every specific reaction. Glucose and Fructose This highlights the function of enzymes in catalyzing reactions to break down or build bonds. Glucose and Fructose can condense to form Sucrose Sucrose can be broken down into Glucose and 2. Induced Fit Hypothesis Fructose In this model, the enzyme, upon binding of substrate, changes shape → HOW ENZYMES WORK? ○ In contrast to the first model, where the Enzymes bind to their substrates, causing a chemical substrate fits directly, here the substrate reaction to be catalyzed. changes shape to fit the active site NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] 2. Non-competitive Inhibitor Attach to parts of the enzyme, other than the active site, to distort the shape of an enzyme. ○ Changes in shape disregards substrate that will bind to it ○ There will be an increase in the binding affinity of our enzymes and substrate → ENVIRONMENTAL EFFECTS ON ENZYME FUNCTION 1. Active sites are very sensitive. They sense even the slightest change in the environment and respond accordingly. 2. The suitable temperature for enzymes to function properly is 37 degrees Celsius. Higher temperatures can denature enzymes, causing them to lose their biological function. 3. Fluctuation in pH can affect these amino acids, making it hard for substrates to bind. → NOMENCLATURE OF ENZYMES Disrupts the bonds 1. Urease The suffix -ase identifies a substance as an enzyme → ENZYME CONCENTRATION Increasing enzyme 2. Oxidase concentration will increase Oxidation - the type of reaction catalyzed by the the rate of reaction, as more enzyme is usually noted in the prefix enzymes will be available to 3. Trypsin bind with substrates. The suffix -in is still being used in some of the first However, after a certain studied digestive enzymes concentration, any increase 4. Glucose Oxidase will have no effect on the The identity of the substrate is usually included. rate of reaction. → CLASSES OF ENZYMES → SUBSTRATE CONCENTRATION Increasing substrate concentration increases the Enzymes Function Example rate of reaction This is because more substrate Oxidoreductase Redox reaction Dehydrogenase molecules will be colliding with Transfer of electron enzyme molecules, so more Results in change of product will be formed oxidation state But again, this effect is valid after certain concentration. Transferase Transfer of Phosphorylase functional group Kinase → INHIBITION OF ENZYME ACTIVITY from one molecule Enzyme Inhibitors to another Reduce or even stop the activity of enzymes in biochemical reactions. Hydrolase Breakdown of a Protease They either block or distort the active site, thus covalent bond using Phosphatase inhibiting the reaction. water Lyase Breakdown of a Decarboxylase covalent bond without water or oxidation (product must contain double bond) Isomerase Rearrangement of Mutase bonds within a 1. Competitive Inhibitor molecule Occupy the active site and prevent a substrate molecule from binding to the enzyme. Ligase Formation of a Synthetase ○ Attach to the active site covalent bond ○ The can increase the Vmax (velocity or between two large maximum rate of reaction) molecules NU MOA (National University - Mall of Asia) John Christhoper B. Dela Cruz Miss Jaymee D. De Dios A.Y. 2024-2025 BIOCHEMISTRY FOR MEDICAL LABORATORY SCIENCE [LEC] - MLSBCHMC MED232 [2ndYR-T1] → ENZYME REGULATION Excretion Not readily Readily excreted It is needed for our enzymes It is to prevents futile cycles and avoids waste of