Biochemistry Lecture Notes PDF

INTRODUCTION TO BIOCHEMISTRY - Nutrition - Pharmacology and toxicology Biochemistry - Chemistry of life homeostasis -...

INTRODUCTION TO BIOCHEMISTRY - Nutrition - Pharmacology and toxicology Biochemistry - Chemistry of life homeostasis - state of equilibrium - Study of life processes, structures, mechanisms, reactions at the molecular level. CELL AND ITS STRUCTURE - Biology, Chemistry and Genetics (roots of biochemistry) Cell Theory Vitalism - All organisms are composed of one or more cells. - The idea that substances and processes associated with living - Cells are the smallest living units of all living organisms. organisms did not behave according to the laws of physics and - Cells arise kinky by division of a previously existing cells chemistry. - Cells vary in size and shapes. Evidences of Vitalism Cell Requirements - Living things have a high degree of complexity - Genetic Material - Only living things extract, transform and utilize energy from Single circular molecule of DNA in prokaryotes their environment. Double helix located in nucleus in eukaryotes - Only living things are capable of self assembly and self - Cytoplasm: fills cell interior (sugars, amino acids, protein, replication. organelles. Origin of Biochemistry - Plasma membrane: encloses the cell - challenge to vitalism Cell Size - Famous dead scientists - Most are relatively small because as size increases, volume Friedrich Wohler increases much more rapidly. Eduard and Hans Buchner - Cell size and shape are related to cell function. Emil Fisher Scale of Visibility Gregor Mendel Francis Crick Oswald Avery James Watson Colin McLeod Maclyn McCarty Friedrich Wohler - (1828lSynthesized urea (organic) to ammonium cyanate (inorganic) Eduard Buchner - Showed that fermentation did not require living cells ; discovered enzymes - Glucose + dead yeast = alcohol Classification of Cells Emil Fisher Prokaryotic Cells - Proponent of Lock and Key Principle Lacks a nucleus and does not have an extensive system of - Absolute specificity of enzyme internal membranes. James Sumner All bacteria and archaea - Proponent that enzyme is an example of protein Prokaryotes are the simplest cellular organisms 1944 - Have plasma membrane surrounding cytoplasm - Avery, McLeod, and McCarty identified DNA as information without interior compartments. molecule - Some bacteria have additional outer layers to the 1953 plasma membrane - Watson and Crick proposed the structure of DNA (won the Cell wall: comprised of carbohydrates to novel price) confer rigid structure. 1958 Capsule: may surround the cell wall - Francis Crick proposed the Central Dogma of Biology The interior of the prokaryotic cell shows simple organization. Central Dogma of Biology - Cytoplasm is uniform with little or no internal support - The flow of genetic information from DNA to RNA to protein framework Areas of Biochemistry - Ribosomes (site for protein synthesis) are scattered - Structure and function of biological macromolecules throughout the cytoplasm. - Metabolism ( catabolism-destructive ; anabolism-constructive) - Nucleoid region (area where DNA is localized) not - Molecular Genetics (how life is replicated; regulation of protein membrane-bounded, so not a true nucleus. synthesis. Other structure sometimes found in prokaryotes relate to Objective of Biochemistry locomotion, feeding, or genetic exchange. - To determine how the collection of inanimate molecules that - Flagellum (plural, flagellae) is a threadlike structure constitute living organisms interact to maintain and perpetuate made of protein fibers that extends from the cell life. surface. Scope of Biochemistry May be one or many, aids in locomotion and - Different phases of small microorganisms to the most complex feeding. one as human; including viruses(non-living organism) - Pilus (plural, pili) is a short flagellum Cell - have two different nucleic acid (DNA and RNA) Aids in attaching to substrates and in Viruses - have either DNA or RNA exchanging genetic information between cells. Chemical Reaction in Living Organisms - Oxidation: reacts with oxygen, lose of electron (aerobic and anaerobic) - Reduction: gain electrons - Hydrolysis: splitting substance with water - Condensation: two molecules join together to form a larger molecule, releasing water in the process - Decarboxylation: removes carboxyl group - Transfer reaction: transferring one molecule to another Uses of Biochemistry - Agriculture - Clinical chemistry - Medical sciences Eukaryotic Cells Has nucleus and internal membrane-bounded compartments. The interior of lipid bilayer is completely non-polar All organisms other than bacteria and archaea - No water-soluble molecules can freely cross through it. Larger and more complex - Cholesterol is also found in the interior - Have a plasma membrane encasing the cytoplasm Affects the fluid nature of the membrane Internal membranes form compartments called Its accumulation in the walls if blood vessels organelles can cause plaques, which lead to The cytoplasm is semi-fluid and contains a cardiovascular disease network of protein fibers that form a scaffold Another major component of this is the collection of membrane called a cytoskeleton proteins Many organelles are immediately conspicuous under the - Transmembrane proteins: form channels that span the microscope membrane - Nucleus: a membrane-bounded compartment for DNA - Cell surface proteins: attached to the surface of the that gives eukaryotes (literally, “true-nut”) their name membrane and acts as markers - Endomembrane system: gives rise to the internal Nucleus membranes found in the cell, each compartment can Command and control center of the cell and also stores provide specific conditions favoring a particular hereditary information process. The nuclear surface is bounded by a double-membrane called Not all eukaryotic cells are alike the nuclear envelope - The cell of plants, fungi, and many protists have a cell - Group Of proteins form openings called nuclear pores wall beyond plasma membrane. that permit proteins and RNA to pass in and out of the - All plants and protists contain organelles called nucleus. chloroplast The DNA of eukaryotes is packaged into segments and - Plants contains a central vacuole associated with protein, this complex is called chromosomes - Only animal cells contain centrioles - The proteins enable the DNA to be wound tightly and condense during cell division - When the cell is not dividing, the chromosomes exist as threadlike strands called chromatin (protein synthesis occurs when the DNA is in the chromatin form) The cell builds proteins on structures called ribosomes - consists of ribosomal RNA (rRNA) and several different kinds of proteins. - Assembled in a region of the nucleus called the nucleolus Endomembrane System An extensive system of internal membranes Plasma Membrane - Some of the membranes form channels and Conceptualized by the fluid mosaic model interconnection - A sheet of lipids with embedded proteins - Other portions become isolated spaces enclosed by The lipid layer form the foundation of the membranes, these spaces are known as vesicles. membrane The portion of the ER dedicated to protein synthesis is called The fat molecules comprising the lipid layers the rough ER are called phospholipids - surface looks pebbly A phospholipid has a polar head and two non-polar tails - Rough spots are due to embedded ribosomes - Polar region contains a phosphate chemical group and The portion of the ER that aids in the manufacture of is water-soluble carbohydrates and lipids is called the smooth ER - Non-polar region is comprised of fatty acids and js - surface looks smooth because embedded ribosomes water-insoluble are scarce A lipid bilayer forms spontaneously whenever a collection of After synthesis in the ER, the newly-made molecules are phospholipids is placed in water passed to the golgi bodies - Golgi bodies are flattened stacks of membranes scattered through the cytoplasm - Numbers vary depending on the cell - Their function is to collect, package, and distribute molecules manufactured by the cell - Collectively called the golgi complex The ER and golgi complex function together as a transport system in the cell  The golgi complex also gives rise to lysosomes Centrioles are complex structures that assemble microtubules - Contain enzymes that the cell uses to break down in animal cells and the cells of most protists macromolecules - they occur in pairs, found near the nuclear envelope, Worn-out cell parts are broken down and their composed of microtubules components are recycled to form new parts Cellular motion is associated with the movement of actin Particles that the cell has ingested are also microfilaments and/or microtubules digested - some cells “crawl” by coordinating the rearrangement Organelles that Harvest Energy of actin microfilaments Eukaryotic cells contain energy harvesting organelles that - Some cells swim by coordinating the beating of contain their own DNA microtubules grouped together to form flagella or cilia - these appear to have been derived from ancient Cilia and Flagella are hairlike structures projecting from the bacteria that were taken up by eukaryotic cells cell that function to move the cell by their movements Mitochondria: cellular powerhouses, sites for oxidative Cilium (Cilia) - the short, numerous appendages metabolism, surrounded by two membranes Flagellum (Flagella) – the longer, less numerous appendages Chloroplast: sites for photosynthesis, surrounded by two Eukaryotic Cell Surfaces and Junctions membranes Cells interact with their environments and with each other via Both mitochondria and chloroplasts possess their own their surfaces. molecule of circular DNA Plant cells are supported by rigid cell walls made largely of - Cannot be grown free of the cell cellulose. - Totally dependent on the cells within which they occur Plant cells connected by plasmodesmata. Theory of Endosymbiosis Animal cells are embedded in an extracellular matrix - organelles evolved from a symbiosis in which one cell consisting mainly of glycoprotein. of a prokaryotic species was engulfed by and lived - This matrix is responsible for binding cells together in inside of a cell of another species of prokaryote that tissues. was a precursor to eukaryotes Tight junction - prevent leakage of material through the space - the engulfed species provided their hosts with between cells. advantages because of special metabolic activities Gap junction - allow passage of materials between cells - the modern organelles of mitochondria and Adhesion junction - adjacent plasma membranes do not touch chloroplasts are believed to be found in the eukaryotic but are held together by intercellular filaments attached to descendants of these endosymbiotic prokaryotes button-like thickenings. there is a lot of other evidence supporting endosymbiotic theory - mitochondria are about the same size as modern bacteria - the cristae in mitochondria resemble folded membranes in modern bacteria - mitochondrial ribosomes are similar to modern, Eukaryotic Organelles and their Functions bacterial ribosomes in size and structure Manufacture - mitochondria divide by fission, just like modern - Nucleus, ribosomes, RER, SER, Golgi complex bacteria Breakdown Cytoskeleton and Related Structures - Lysosomes, peroxisomes, vacuoles The cytoskeleton is comprised of an internal framework of Energy Processing protein fibers that - Chloroplasts, mitochondria - anchors organelles to fixed locations Support, Movement and Communication Between Cells - supports the shape of the cell - Cytoskeleton, cell walls, extracellular matrix, junctions - helps organize ribosomes and enzymes needed for Transport of Materials synthesis activities Passive Transport The cytoskeleton is dynamic and its components are - Diffusion continually being rearranged - Osmosis Three different types of protein fibers comprise the - Facilitated Diffusion cytoskeleton Active Transport - intermediate filaments; Thick ropes of intertwined - Endocytosis protein - Exocytosis - microtubules; hollow tubes made up of the protein Osmosis and Diffusion tubulin Movement of water and nutrients and elimination if waste out - microfilaments; long, slender microfilaments made up of cell is essential for survival of the protein actin - Occurs across a biological membrane im one of three ways; diffusion, membrane folding, transport through membrane proteins  Molecules move in a random fashion but there is a tendency - Vitamins to produce uniform mixtures Water The net movement of molecules from an area of higher - Essential for life concentration to an area of lower concentration is termed - Polar molecule diffusion - Can form hydrogen bonds, which confers many different Molecules diffuse down a concentration gradient from higher special properties to lower concentrations Unique Properties of Water - diffusion ends when equilibrium is reached Heat storage - water temperature changes slowly and holds temperature well Ice Formation - few hydrogen bonds break at low temperatures - water becomes less dense as it freezes because hydrogen bonds stabilize and hold water molecules farther apart High Heat of Vaporization The concentration of all molecules dissolved in a solution is - water requires tremendous energy to vaporize because called the osmotic concentration of the solution of all the hydrogen bonds that must be broken - if the osmotic concentrations of two solutions is equal, - when water vaporizes, it takes this heat energy with it, the solutions are each called isotonic allowing for evaporative cooling - if two solutions have unequal osmotic concentration, Water molecules are attracted to other polar molecules the solution with the higher solute concentration is said - cohesion: when one water molecule is attracted to to be hypertonic, and the solution with the lower solute another water molecule concentration is said to be hypotonic - adhesion: when polar molecules other than water stick Movement of water by osmosis into a cell causes pressure to a water molecule called osmotic pressure High polarity, in solution, water molecules tend to form the - enough pressure may cause a cell to swell and burst maximum number of hydrogen bonds - osmotic pressure explains why so many cell types are - hydrophilic molecules are attracted to water and reinforced by cell walls dissolve easily in it these molecules are also polar and can form hydrogen bonds - hydrophobic molecules are repelled by water and do not dissolve these molecules are nonpolar and do not form hydrogen bonds Water Ionizes The covalent bond within a water molecule sometimes breaks spontaneously H2O « OH- + H+ This produces a positively hydrogen ion (H+) and a negatively charged hydroxide ion (OH-) The amount of ionized hydrogen from water in a solution can Forms of Endocytosis be measured as pH Phagocytosis is endocytosis of particulate (solid) matter The pH scale is logarithmic, which means that a pH scale Pinocytosis is endocytosis of liquid matter difference of 1 unit actually represents a 10-fold change in hydrogen ion concentration Pure water has a pH of 7 - there are equal amounts of [H+] relative to [OH-] Acid: any substance that dissociates in water and increases the [H+] - acidic solutions have pH values below 7 Base: any substance that combines with [H+] when dissolved in water - basic solutions have pH values above 7 The pH in most living cells and their environments is fairly close to 7 - proteins involved in metabolism are sensitive to any pH changes Organisms use buffers to minimize pH disturbances Exocytosis - a buffer is a chemical substance that takes up or releases hydrogen ions Organic Compounds Carbohydrates – major source of energy Proteins – for tissue repair Lipids – constituents of membranes, also a source of energy Nucleic Acids – genetic material and for protein synthesis Chemistry of Life Inorganic Compounds - Water - Gases - Minerals Organic Compounds - Carbohydrates - Proteins - Lipids - Nucleic acids  BIOCHEMISTRY LECTURE / FIRST SEMESTER CARBOHYDRATES LEARNING OBJECTIVES FUNCTIONS OF CARBOHYDRATES I. Define carbohydrates II. Describe the difference between monosaccharides, 1. Energy Sources: oligosaccharides, and polysaccharides and explain Monosaccharides- glucose, galactose and fructose the system used to categorize monosaccharides Polysaccharides- starch and glycogen III. Identify four important disaccharides and describe 2. Supporting Structures: how the monosaccharide residues in them are joined Bacterial and plant cell walls (cellulose—linear glucose to another polymer) IV. Distinguish homopolysaccharides from Cartilage (modified monosaccharides, ex. glucosamine) heteropolysaccharides Exoskeletons in arthropods (insects, crabs and lobsters) 3. Components of nucleic acids DNA and RNA--ribose and CARBOHYDRATES AND BIOCHEMISTRY deoxyribose 4. Immune system--Oligosaccharides (3-30 sugars) modify cell  Carbohydrates are compounds of tremendous surface proteins to identify native versus foreign cells biological importance: 5. Signal transduction systems--Many cell surface receptor - They provide energy through oxidation proteins have carbohydrate side groups that are critical for - They supply carbon for the synthesis of cell function components - They serve as a form of stored chemical energy CLASSES OF CARBOHYDRATES - They form part of the structures of some cells and tissues  Monosaccharides contain a single polyhydroxy aldehyde or ketone unit  Carbohydrates, along with lipids, proteins, nucleic  Oligosaccharides contain 2 to 10 monosaccharide acids, and other compounds are known as units biomolecules because they are closely  Polysaccharides contain very long chains of associated with living organisms hundreds or thousands of monosaccharide units, which may be either in straight or branched chains CARBOHYDRATES  Most substances of this class have empirical formulas THE STEREOCHEMISTRY OF suggesting that they are carbon hydrates CARBOHYDRATES –a carbohydrate is any molecule that contains the elements C, H, and O in a 1:2:1 ratio –the sizes of carbohydrates vary TWO FORMS OF GLYCERALDEHYDE → simple carbohydrates – made up of one or two monomers → complex carbohydrates – long polymers  Glyceraldehyde, the simplest  These substances have important biological roles carbohydrate, exists in two isomeric forms  Building block is simple sugar or monosaccharide  Carbohydrates or saccharides(saccharon is Greek for “sugar”) that are mirror images of each other: are polyhydroxy aldehydes or ketones, or substances that yield such compounds on hydrolysis  Carbohydrates include not only sugar, but also the starches that we find in food, such as bread, pasta and rice.  The term carbohydrate comes from the observation that when you heat sugars, you get SOPHIA NICOLE POSERIO MACAM carbon and water. UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER CARBOHYDRATES STEREOISOMERS 2^n Rule  These forms are  When a molecule has more than one chiral carbon, stereoisomers of each each carbon can possibly be arranged in either the other. right-hand or left-hand form, thus if there are n chiral  Glyceraldehyde is a chiral carbons, there are 2^n possible stereoisomers. molecule – it cannot be superimposed on its mirror FISCHER PROJECTIONS image. The two mirror- image forms of  Fischer projections are a glyceraldehyde are convenient way to represent enantiomers of each other. mirror images in two dimensions CHILARITY AND HANDEDNESS  Place the carbonyl group at or near the top and the last  Chiral molecules have the achiral CH2OH at the bottom same relationship to each other that your left and NAMING STEREOISOMERS right hands have when  When there is more than one chiral center in a reflected in a mirror carbohydrate, look at the chiral carbon farthest from the carbonyl group: – If the hydroxy group points to right when the carbonyl is up, it is the D-isomer – If the hydroxy group points to the left, it is the L- CHIRAL CARBONS isomer  Chiral objects cannot be superimposed on their mirror images  Achiral objects can be superimposed on the mirror images  Chiral carbon - Any carbon atom which is connected to four different groups will be chiral, and will have two nonsuperimposable mirror What’s so great about chiral molecules? images  Many organic compounds, including  Molecules which are carbohydrates, contain more than one chiral enantiomers of each other have exactly the same physical carbon properties but not their interaction with polarized light CHIRAL CARBON ATOMS  Polarized light vibrates only in one plane; it results from passing light through a polarizing filter OPTICAL ACTIVITY A levorotatory (–) substance rotates polarized light to the left [e.g., l-glucose; (-)-glucose]. A dextrorotatory (+) substance rotates polarized light to the right [e.g., d-glucose; (+)-glucose]. Molecules which rotate the plane of polarized light are optically active. Many biologically important molecules are chiral and optically active. Often, living systems contain only one of the possible stereochemical forms of a compound, or they are found in separate systems. SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER CARBOHYDRATES CLASSIFICATION OF CHEMICAL COMPONENTS OF MONOSACCHARIDES MONOSACCHARIDES  Monosaccharides are classified according to  Reducing power – all monosaccharides and disaccharides the number of carbon atoms they contain: containing the potentially free aldehyde/ketone group NO. OF CARBONS CLASS OF possess reducing properties MONOSACCHARIDES  Osazone formation – reducing sugars form characteristic 3 triose osazone crystals when heated with an excess of 4 phenylhydrazine tetrose  Action of alkalies – reducing sugar heated with an alkali 5 pentose turns to yellow to orange and finally dark brown 6 hexose  Action of acids – disaccharides and other higher  The presence of an aldehyde is indicated by carbohydrates are readily decomposed the prefix aldo- and a ketone by the prefix  Fermentation – decomposition of carbohydrates brought keto- about by the action of microorganisms  Oxidation – monosaccharides and disaccharides (except sucrose) are readily oxidized forming sugar acids  Reduction – sugars undergo reduction with the absorption of energy ; reduction of monosaccharides produce polyhydroxyl alcohols  Monosaccharides do not usually exist in solution in their “open-chain” forms  An alcohol group can add into the carbonyl group in the same molecule to form a pyranose ring containing a stable cyclic hemiacetal or hemiketal PHYSICAL PROPERTIES OF MONOSACCHARIDES  Monosaccharides and disaccharides are white crystalline substance. Starches are amorphous powder. Cellulose is fibrous.  Solubility to ordinary solvents is inversely proportional to the complexity of their structures.  Monosaccharides and disaccharides are sweet. GLUCOSE ANOMERS Starch and cellulose are tasteless.  In the pyranose form of glucose, carbon-1 is chiral, and thus two stereoisomers are possible: one in which the OH group points down (α-hydroxy group) and one in which the OH group points up (β-hydroxy group). These forms are anomers of each other, and carbon-1 is called the anomeric carbon. SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER CARBOHYDRATES OXIDATION OF MONOSACCHARIDES MONOSACCHARIDES DERIVATIVES  Aldehydes and ketones that have an OH group  Deoxy sugars – a hydrogen atom replaces one or more of on the carbon next to the carbonyl group react the –OH groups in a monosaccharide with a basic solution of Cu2+(Benedict’s  Amino sugars – an –OH group of a monosaccharide has reagent) to form a red-orange precipitate of been replaced by an amino (-NH2) group copper (I) oxide (Cu2O).  Alcohol sugars – the carbonyl group of a monosaccharide  Sugars that undergo this reaction are called has been reduced to an alcohol group reducing sugars. (All of the monosaccharides are  Carboxylic acid sugars – an aldehyde or an alcohol group reducing sugars.) of a monosaccharide has been oxidized to form a carboxyl group - Reducing sugar+Cu2+oxidationproduct+Cu2Odeep bluesolutionred-orangeppt FORMATION OF PHOSPHATE ESTERS  Phosphate esters can form at the 6-carbon of aldohexoses and aldoketoses.  Phosphate esters of monosaccharides are found in the sugar-phosphate backbone of DNA and RNA, in ATP, and as intermediates in the metabolism of carbohydrates in the body GLYCOSIDE FORMATION  The hemiacetal and hemiketal forms of monosaccharides can react with alcohols to form acetal and ketal structures called glycosides. The new carbon-oxygen bond is called the glycosidic linkage.  Once the glycoside is formed, the ring can no longer open up to the open-chain form. Glycosides, therefore, are not reducing sugars. IMPORTANT MONOSACCHARIDES 1. Pentose a. Ribose – sugar found in RNA b. Deoxyribose – sugar found in DNA 2. Hexose a. Glucose – dextrose or blood sugar b. Galactose – combined with glucose to produce lactose c. Fructose – fruit sugar, combined with SOPHIA NICOLE POSERIO MACAM glucose to produce sucrose UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER CARBOHYDRATES DISACCHARIDES AND POLYSACCHARIDES OLIGOSACCHARIDES  Most of the carbohydrate found in nature occur in the form Disaccharides of high molecular weight polymers called polysaccharides. – Two  The monomeric building blocks used to generate monosaccharides can be polysaccharides can be varied. linked together through a  The predominant monosaccharide found in polysaccharides glycosidic linkage to form is D-glucose. a disaccharide.  When polysaccharides are composed of a single monosaccharide building block, they are termed homopolysaccharides. DISACCHARIDES  Polysaccharides composed of more than one type of monosaccharide are termed heteropolysaccharides  Disaccharides can be hydrolyzed into their HOMOPOLYSACCHARIDES monosaccharide building blocks by boiling them with dilute acids or reacting them with the 1. Cellulose – is a major importance in the surface of appropriate enzymes. plants, consist of a long chain of β-glucose residues  Disaccharides that contain hemiacetal groups are joined by β-(1, 4). reducing sugars. 2. Starch – Is the major form of stored carbohydrate in plant cells. Its structure is identical to glycogen, except OLIGOSACCHARIDES for a much lower degree of branching (about 20-30 residues). Unbranched starch is called amylose;  Glycosidic bond branched starch is called amylopectin.  Most common are the disaccharides 3. Glycogen – is the major formed of carbohydrate in - Sucrose, lactose, and maltose animals. This crucial molecule is a homopolymer of - Maltose hydrolyzes to 2 molecules of D- glucose in α-(1, 4) linkage; it is also highly branched, with glucose α-(1, 6) branch linkages occurring every 8-10 residues. - Lactose hydrolyzes to a molecule of glucose Glycogen is a very compact structure that results from and a molecule of galactose the coiling of the polymer chains. - Sucrose hydrolyzes to a moledule of glucose and a molecule of fructose HETEROPOLYSACCHARIDES 1. Hyaluronic acid – found in the lubricating fluid that surrounds joints and in the vitreous humor present in the eye; made up of alternating residues of glucosamine and glucuronate connected to another. 2. Chondrotin sulfate – consists of galactosamine sulfate residues alternating with glucuronate 3. Peptidoglycan – found in the cell wall of bacterial cell SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER CARBOHYDRATES GENERAL PROPERTIES TESTS FOR CHO  Physical Properties Molisch’s Test – general test for the presence of 1. Monosaccharides and disaccharides are white carbohydrates; utilize crystalline substance. Starches are amorphous Molisch’s reagent; positive result is formation of violet ring powder. Cellulose is fibrous. Anthrone Test – makes use of anthrone dissolved in 2. Solubility to ordinary solvents is inversely concentrated sulfuric acid; positive result is blue or green proportional to the complexity of their structures. color 3. Monosaccharides and disaccharides are sweet. Starch and cellulose are tasteless Seliwanoff’s Test – specific test for ketose sugar; uses  Chemical Properties resorcinol and HCl; positive result is red color or pink color 1. Reducing powder – all monosaccharides and disaccharides containing the potentially free Tollen’s Phloroglucinol Test – test for galactose; makes aldehyde/ketone group possess reducing properties use of phloroglucinol; positive result is red color 2. Osazone formation – reducing sugars form Bial’s Orcinol-HCl Test – test for pentoses; makes use characteristics osazone crystals when heated wih Bial’s orcinol-HCl reagent; positive result is green solution an excess of phenylhydrazine and precipitate 3. Action of alkalies – reducing sugar heated with an alkali turns to yellow to orange and finally dark Moore’s Test – action of alkalies; makes use of NaOH or brown Ba(OH)2; positive result is dark brown color 4. Action of acids – disaccharides and other Iodine Test – test for the presence of starch; makes use higher carbohydrates are readily decomposed of IKI solution; positive result is blue black color Fehling’s Test – test for reducing power of sugars; makes CHITIN use of Fehling’s reagent (alkaline solution of CuSO4); positive result is yellow to brick red precipitate  Chitin is a polymer of N-acetylglucosamine, an amide derivative of the amino sugar glucosamine, in Benedict’s Test – used to detect reducing sugars; makes which one of the OH groups is converted to an use of Benedict’s reagent; positive result is brick red amine (NH2) group. The polymer is extremely precipitate strong because of the increased hydrogen bonding Nylander’s Test – used to detect reducing sugars; makes provided by the amide groups. use of Nylander’s reagent (bismuth subnitrate); positive result is black metallic bismuth  Chitin is the main component of the cell walls of Picric Acid Test – used to detect reducing sugars; makes fungi, the exoskeletons of arthropods such as use of picric acid; positive result is mahogany red crustaceans and insects, and the beaks of Barfoed’s Test – test for reducing monosaccharide cephalopods. The chitin is often embedded in either sugars a protein matrix, or in calcium carbonate crystals. Since this matrix cannot expand easily, it must be shed by molting as the animal grows. SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER AMINO ACIDS AND PROTEINS LEARNING OBJECTIVES CLASSIFICATION OF AMINO ACIDS I. Define Amino acid and Proteins II. Describe the structure of amino acids and the Amino acids are non-polar, polar acidic, polar basic or polar system used to classify amino acids neutral, depending on the nature of their side chain III. Distinguish between oligopeptides, polypeptides and proteins and describe the 1. Non-polar - the side chain of non-polar amino is usually an bond that joins amino acid residues in these alkyl group, an aromatic ring, or a non-polar collection of atoms. compounds Nonpolar amino acids are glycine, alanine, valine, leucine, IV. Define primary, secondary, tertiary and isoleucine, methionine, praline, phenylalanine and tryptophan. quaternary structure V. Explain what is meant by the term 2. Polar acidic - the side chain of a polar acid amino acid denaturation, and lisyt some ways to contains a carboxyl group. At pH 7, the carboxyl group is found denature a protein in its conjugate base form (-CO₂), which means that the side chains on the two polar acidic amino acids, aspartic acid and AMINO ACIDS glutamic acid, carry a negative charge at this pH.  Amino acids are organic acids containing an amine group. 3. Polar basic - the side chain of polar basic amino acids contains an amino group. At pH 7 the amines exist in their  The most common amino acids are α-amino acids and the conjugate acid form. So polar basic amino acids carry a positive most common α-amino acids are the L- α-amino acids. charge at this pH. Polar basic amino acids are lysine, arginine, histidine. 4. Polar neutral - the side chain of polar neutral amino acids is usually an alcohol, a phenol. None of these functional groups is acidic or basic enough to carry a charge at pH 7. Polar neutral amino acids are serine, threonine, cysteine, tyrosine, asparagine and glutamine. It is important to understand the ff about amino acid  Polarity structure:  R Group 1. Only 20L- α-amino acids are used to make proteins.  Nutrition Rare exceptions are bacterial membrane proteins which contain a few D-amino acids. -Essential AA 2. Side chains or side groups are what distinguish the - Non-essential AA amino acids from each other 3. Amino acids can exist as zwitterions 4. Some amino acids found in cells are not used to make proteins 5. Amino acids are the building blocks of proteins, and are joined by peptide bond SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA BSN- 14 BIOCHEMISTRY LECTURE / FIRST SEMESTER AMINO ACIDS AND PROTEINS SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER AMINO ACIDS AND PROTEINS STEREOISOMERS PROTEINS  A protein is made up of one or more polypeptide chains, each of which consists of amino acid which have been mentioned earlier.  Play more diverse roles in living things than any other class of compounds – Catalysts – Hormones – Transport Molecules – Key Part of Structures (skin, tendons, cartilage, bone) – Muscle Action – Immune Response – Visual Process – Operation of the Nervous System  Amino acids are small molecules with a simple basic structure, a carbon atom to which three THE PEPTIDE BOND groups are added  Peptide bond is another name for amino bond that - an amino group (-NH2) joins one amino acid residue to another. - a carboxyl group (-COOH)  Amino bond is between α-amino and α-carboxyl - a functional group (R) groups.  The functional group gives amino acids their  Two individual amino acids can be linked to form a chemical identity larger molecule, with the loss of a water molecule as – there are 20 different types of amino acids a by-product of the reaction. CLASSIFICATION OF PROTEINS  A protein is classified as being either fibrous or globular. 1. Fibrous proteins – are usually tough and water insoluble, such as collagen and keratin 2. Globular proteins – are spherical in shape, highly folded and tend to be water soluble.  Two molecules linked by peptide bond become what is  Classification according to structure: called a dipeptide. Similar to the system used for – Simple proteins carbohydrates, a combination of three amino acid residues a – Compound proteins tripeptide, a combination of four is a tetrapeptide, and so  Classification according to function: on. Ologipeptides contain between 2 and 10 amino acid – Enzymes residues and polypeptides, more than 10 residues. – Storage – Structural – Regulatory – Defense – Transport Contractile SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER AMINO ACIDS AND PROTEINS PROTEIN STRUCTURE  Protein structure is complex – the order of the amino acids that form the polypeptide affects how the protein folds together – the way that a polypeptide folds to form the protein determines the protein’s function → some proteins are comprised of more than one polypeptide  There are four levels of protein structure: –Primary Structure –Secondary Structure –Tertiary Structure –Quaternary Structure PRIMARY STRUCTURE PROPERTIES OF PROTEINS  Primary structure – the sequence of amino acids  General Properties in the polypeptide chain → Very large molecules  This determines all other levels of protein structure → Have characteristics amino acid composition → Some proteins contain chemical groups other than amino acids and they are called conjugated proteins (amino acid + prosthetic group) like lipoproteins, glycoproteins, metalloproteins  Physical and Chemical Properties → Generally tasteless → Mostly colorless SECONDARY STRUCTURE → Insoluble in fat solvents, but varied degrees of solubility in water, salt, solution, dilute acids and bases  Secondary structure – the initial folding of the → Amphoteric amino acid chains → Very reactive and highly specific  Occurs because regions of the polypeptide that are non-polar are forced together CLASSES OF PROTEINS  The folded structure may resemble coils, helices, or sheets 1. Enzymes – most varied and most highly specialized proteins with catalytic activity 2. Transport – bind and carry specific molecules or ions from one organ to another 3. Nutrient and Storage – store nutrients required for the growth of the seedling 4. Contractile or Motile – endow cells and organisms with the ability to contract, to change shape or move TERTIARY STRUCTURE about 5. Structural – serve as supporting filaments to give  Tertiary structure – the final 3-D shape of biological structures strength the protein 6. Defense – defend organisms against invasion by  The final twists and folds that lead to this other species shape are the result of polarity differences in 7. Regulatory – help regulate cellular or physiological regions of the polypeptide activity QUATERNARY STRUCTURE  Quaternary structure – the spatial arrangement of component polypeptides in proteins comprised of SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA more than one polypeptide chain BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER AMINO ACIDS AND PROTEINS PROTEIN DENATURATION PROTEINS GIVE VARIOUS COLOR REACTIONS  Changes to the environment of the protein may cause it to unfold or denature  increased temperature or lower pH affects hydrogen bonding, which is involved in the folding process  a denatured protein is inactive SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER ENZYMES LEARNING OBJECTIVES ENZYME PARTS I. Define enzyme  The activity of an enzyme depends, at the minimum, on a II. Know the differences among absolute specific protein chain. In many cases, the enzyme specificity, relative specificity and stereospecify consists of the protein and a combination of one or more III. Explain the mechanism of enzyme action parts called cofactors. This enzyme complex is usually simply referred to as the enzyme. IV. Determine the different factors that affect the  Apoenzyme: The polypeptide or protein part of the rate of enzyme reaction enzyme is called the apoenzyme and may be inactive in V. Distinguish between reversible and irreversible its original synthesized structure. The inactive form of the inhibitors apoenzyme is known as a proenzyme or zymogen. The proenzyme may contain several extra amino acids in the protein which are removed, and allows the final specific WHAT ARE ENZYMES? tertiary structure to be formed before it is activated as an  Enzymes are catalysts apoenzyme.  Catalysts are substances that speed up chemical  Cofactors: A cofactor is a non-protein substance which reactions may be organic, and called a coenzyme.  Reactions with enzymes are up to 10 billion times faster than those without enzymes. NOMENLACTURE OF ENZYMES  Enzymes are specific for one particular reaction or group 1. Trivial System of related reactions. – based on the substrate of the enzyme and the type of  Many reactions cannot occur without the correct enzyme present. reaction catalyzed Use of ase ending GENERAL CHARACTERISTICS OF ENZYMES 2. International Enzyme Commission  The catalytic behavior of proteins acting as enzymes is one – Groups enzymes into six classes of the most important functions that they perform in living cells. MAIN ENZYME CLASSES in the  Enzymes are well-suited to their roles in three major ways: IUBMBEC System - They have enormous catalytic power - They are highly specific in the reactions they catalyze - Their activity as catalysts can be regulated Just like any chemical catalysts, what an enzyme does is to lower the activation energy (Ea). Activation energy is the energy needed to cause an effective collision and allow a reaction to proceed forward. The energy profile of a reaction is shown below. All chemical reactions require an initial input of energy called activation energy – the activation energy initiates a chemical reaction by destabilizing existing chemical bonds Reactions become more likely to happen if their activation energy is lowered – this process is called catalysis – catalyzed SOPHIA NICOLE POSERIO MACAM reactions proceed much faster than noncatalyzed reactions UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER ENZYMES PROPERTIES OF ENZYMES  Temperature and pH affect enzyme activity  Enzymes are proteins. – enzymes function within an optimum temperature  Enzymes are catalysts. range – Absolute specificity → when temperature increases, the shape of the – Relative specificity enzyme changes due to denaturing of the protein chains – Stereospecificity – enzymes function within an optimal pH range → the shape of enzymes is also affected by pH → most human enzymes work best within a pH range SPECIFICITY: PROPERTY OF ENZYME of 6 – 8 – exceptions are stomach enzymes that function  Specificity is the ability of an enzyme to discriminate in acidic ranges between two competing substrates.  Inorganic substances (zinc, iron) and vitamins  Its an important property of enzymes whereby the cell (respectively) are sometimes need for proper enzymatic is able to control its chemical reactions. activity.  Specificity is also known as selectivity. Example: Iron must be present in the quaternary  Depending on the enzyme, the degree of selective or structure - hemoglobin in order for it to pick up specificity shown for substrates can vary widely. oxygen. 1. Absolute specificity- which means that the enzyme accepts only one specific substrate, for example urease, which catalyzes the hydrolysis of urea to produce CO2 and NH3, shows how absolute specificity because it catalyzes the hydrolysis of urea bot not any other molecule. 2. Relative specificity – enzymes are much less specific and will react with a range of substrates having the same functional groups or similar structures. For example, alcohol dehydrogenase, which catalyzes the oxidation of a wide range of alcohols. 3. Stereospecificity – some enzymes only react with or produce a particular steroisomer. HOW ENZYMES WORK  Enzymes are the catalysts used by cells to perform particular reactions – enzymes bind specifically to a molecule and stress the bonds to make the reaction more likely to proceed – the active site is the site on the enzyme that binds to a reactant – the site on the reactant where the enzyme binds is called the binding site  The binding of a reactant to an enzyme causes the enzyme’s shape to change slightly - this leads to an “induced fit” where the enzyme and substrate fit tightly together as a complex – the enzyme lowers the activation energy for the reaction the enzyme is unaffected by the chemical reaction and be re-used  Catalyzed reactions may occur together in sequence - the product of one reaction is the substrate for the next reaction until a final product is made - the series of reactions is called a biochemical SOPHIA NICOLE POSERIO MACAM pathway UNIVERSIDAD DE MANILA BSN- 14  BIOCHEMISTRY LECTURE / FIRST SEMESTER ENZYMES MECHANISM OF ENZYME ACTION  First step in enzyme catalysis involves the formation of an enzyme-substrate complex (ES complex) due to the binding of the substrate to an enzyme’s active site. THEORIES ON THE FORMATION OF THE ENZYME-SUBSTRATE COMPLEX HOW CELLS REGULATE ENZYMES  Cells can control enzymes by altering their shape 1. Lock and Key Theory (Emil Fischer in 1894) – allosteric enzymes are affected by the binding of signal molecules  The specific action of an enzyme with a single substrate → some signals act as repressors can be explained using a Lock and Key analogy first – inhibit the enzyme when bound postulated in 1894 by Emil Fischer. In this analogy, the → other signals act as activators lock is the enzyme and the key is the substrate. Only the – change the shape of the enzyme so that it can bind correctly sized key (substrate) fits into the key hole substrate (active site) of the lock (enzyme).  Feedback inhibition is a form of enzyme inhibition where the  Smaller keys, larger keys, or incorrectly positioned teeth product of a reaction acts as a repressor on keys (incorrectly shaped or sized substrate molecules) – competitive inhibition do not fit into the lock (enzyme). Only the correctly → the inhibitor competes with the substrate for the active shaped key opens a particular lock. site → the inhibitor can block the active site so that it cannot bind the substrate – non-competitive inhibition → the inhibitor binds to the allosteric site and changes the shape of the active site so that no substrate can bind 2. Induced Fit Theory (Daniel Koshland in 1958)  The induced-fit theory assumes that the substrate plays a role in determining the final shape of the enzyme and that the enzyme is partially flexible. This explains why certain compounds can bind to the enzyme but do not react because the enzyme has been distorted too much. Other molecules may be too small to induce the proper alignment and therefore cannot react. Only the proper substrate is capable of inducing the proper alignment of the active site. SOPHIA NICOLE POSERIO MACAM UNIVERSIDAD DE MANILA BSN- 14