Enzymes Combined PDF

1. Oxidoreductase I. GENERAL PROPERTIES - is an enzyme that catalyzes an oxidation–reduction...

1. Oxidoreductase I. GENERAL PROPERTIES - is an enzyme that catalyzes an oxidation–reduction reaction. ENZYME - An enzyme is a compound, usually a protein, that catalyzes a biochemical reaction. ENZYME STRUCTURE 1. Simple Enzyme 2. Transferase - is an enzyme composed only of protein - is an enzyme that catalyzes the transfer of a (amino acid chains). functional group from one molecule to 2. Conjugated enzyme another. Two major subtypes of transferases amino groups - is an enzyme that has a nonprotein part in phosphate are trans-aminases and kinases. addition to a protein part. Apoenzyme is the protein part of a conjugated enzyme. Po + cofactor A holoenzyme is the biochemically & - active conjugated enzyme produced from an apoenzyme and a cofactor A cofactor is the non protein part of a conjugated enzyme. II. CLASSIFICATION OF ENZYMES 3. Hydrolase - is an enzyme that catalyzes a hydrolysis reaction in which the addition of a water molecule to a bond causes the bond to break.  4. Lyase ENZYME- SUBSTRATE COMPLEX - is an enzyme that catalyzes the addition of a - Is the intermediate reaction species that is group to a double bond or the removal of a formed when a substrate binds to the active group to form a double bond in a manner site of an enzyme. that does not involve hydrolysis or oxidation. LOCK-AND-KEY MODEL - The active site in the enzyme has a fixed, COO- COO- rigid geometrical conformation. Only | fumarase | substrate with a complementary geometry C—H + H2O HO—C—H can be accommodated at such a site, much || | as a lock accepts only certain keys. H—C H—C—H | | COO- COO- Furminate L-malate 5. Isomerase - is an enzyme that catalyzes the isomerization (rearrangement ofatoms) of a substrate in a reaction, converting it into a molecule isomeric with itself. COO- COO- | | INDUCED-FIT MODEL H—C—OH H—C—O—P - Allows for small changes in the shape or | | geometry of the active site of an enzyme to CH2O—P CH2OH accommodate a substance. 3-Phosphoglycerate 2-Phosphoglycerate - Induced-fit model is a result of the enzyme’s flexibility; it adapts to accept the incoming 6. Ligase substrate. - is an enzyme that catalyzes the bonding together of two molecules into one with the participation of ATP. IV. ENZYME SPECIFICITY III. MODELS OF ENZYME ACTION ENZYME SPECIFICITY - Is the extent to which an enzyme’s activity is restricted to a specific substrate, a specific group substrate, a specific type of chemical bond, or a specific type of chemical reaction. TYPES OF ENZYME SPECIFICITY 1. ABSOLUTE SPECIFICITY - the enzyme will catalyze only one reaction. - Catalase is an enzyme with absolute specificity. ENZYME ACTIVE SITE It catalyzes the conversion of hydrogen peroxide - Is the relatively small part of an enzyme’s (H2O2) to O2 and H2O. Hydrogen peroxide is structure that is actually involved in the only substrate it will accept. catalysis.  2. GROUP SPECIFICITY - the enzyme will act only on molecules that have a specific functional group, such as hydroxyl, amino, or phosphate groups. - Carboxypeptidase is group specific, it cleaves amino acids, one at a time, from a carboxyl end of a peptide chain. 3. LINKAGE SPECIFICITY - the enzyme will act on a particular type of chemical bond, irrespective of the rest of the molecular structure. - Phosphatases hydrolyze phosphate-ester bonds ENZYME CONCENTRATION in all types of phosphate esters. - Because enzymes are not consumed in the - Linkage specificity is the most general of the reactions they catalyze, the cell usually common specificities. keeps 4. STEREOCHEMICAL SPECIFICITY - the enzyme - The number of enzymes is low compared will act on a particular stereoisomer. with the number of substrate molecules. - L-amino acid oxidase will catalyze the oxidation This is of the L-form of an amino acid but not the - efficient; the cell avoids paying the energy D-form of the same amino acid. costs of synthesizing and maintaining a large - work force of enzyme molecules. V. FACTORS THAT AFFECT ENZYME ACTIVITY VI. ENZYME INHIBITION ENZYME ACTIVITY - Is a measure of the rate at which an enzyme covers substrate to products in a biochemical ENZYME INHIBITOR reaction. - Is a substance that slows or stops the normal catalytic function of an enzyme by binding TEMPERATURE to it. - Is a measure of the kinetic energy (energy of motion) of molecules. At higher REVERSIBLE COMPETITIVE INHIBITION temperatures, molecules are moving faster - Is a molecule that sufficiently resembles an and colliding more frequently. enzyme substrate in shape of charge - Optimum Temperature is the temperature distribution that it can compete with the at which an enzyme exhibits maximum substrate for occupancy of the enzyme’s activity. active site. - For human enzymes, the optimum temperature is around 37°C, normal body temperature. PH - The pH of an enzyme’s environment can affect its activity. The charge on acidic and basic amino acids located at the active site depends on pH. REVERSIBLE NONCOMPETITIVE - Optimum pH is the pH at which an enzyme INHIBITION exhibits maximum activity. - Is a molecule that decreases enzyme activity - Pepsin in the stomach functions best at 2.0 by binding to a site on an enzyme other pH. Trypsin in the small intestine functions than the active site. best at 8.0 pH. SUBSTRATE CONCENTRATION - When the concentration of an enzyme is kept constant and the concentration of substrate increases, the enzyme activity pattern shown in the figure below is obtained. - This activity pattern is called a saturation curve.  REVERSIBLE INHIBITION VIII. COVALENT MODIFICATION OF ENZYMES (UNCOMPETITIVE) - is a molecule that inactivates enzymes by forming a strong covalent bond to an amino COVALENT MODIFICATION acid side-chain group at the enzyme’s active - a process in which enzyme activity is altered site. by covalently modifying the structure of the - In general, such inhibitors do not have enzyme through attachment of a chemical structures similar to that of the enzyme’s group to or removal of a chemical group normal substrate. from a particular amino acid within the - Will only bind to the substrate if it is already enzyme’s structure. binded. VII. REGULATION OF ENZYME ACTIVITY PHOSPHORYLATION - The process of addition of the phosphate group to the enzyme ALLOSTERIC ENZYMES - Is an enzyme with two or more protein chains (quaternary structure) and two kinds DEPHOSPHORYLATION of binding sites (substrate and regulator). - the removal of the phosphate group from the - Substances that bind at regulatory sites of enzyme. allosteric enzymes are called regulators. - This phosphorylation/dephosphorylation - The binding of a positive regulator process is the off/on or on/off switch for the increases enzyme activity; the shape of the enzyme. For some enzymes the active active site is changed such that it can more (“turned-on” form) is the phosphorylated readily accept substrates. version of the enzyme; however, for other enzymes it is the dephosphorylated version FEEDBACK CONTROL that is active. - is a process in which activation or inhibition of the first reaction in a reaction sequence is PROTEIN KINASES controlled by a product of the reaction - Effect the addition of phosphate groups and sequence. phosphatases catalyze removal of the phosphate groups. Usually, the phosphate group is added to (or removed from) the R group of a serine, tyrosine, or threonine VIII. PROTEOLYTIC ENZYMES AND ZYMOGENS amino acid residue present in the protein (enzyme). PROTEOLYTIC ENZYME GLYCOGEN PHOSPHORYLASE - is an enzyme that catalyzes the breaking of - An enzyme involved in the breakdown of peptide bonds that maintain the primary glycogen to glucose is activated by the structure of a protein. addition of a phosphate group. ZYMOGEN GLYCOGEN SYNTHASE - Is the inactive precursor of a proteolytic - An enzyme involved in the synthesis of enzyme. glycogen is deactivated by phosphorylation. BIOCHEMISTRY: PROTEINS Ms. Angelica C. Lopez, RPh | Week 3 | SSCTI - BSN 1G | S.Y 2024-2025 Topic Outline: 4 Categories of Standard Amino Acids Nonpolar Amino Acids - Hydrophobic I. Characteristics of Proteins (“water-fearing”), not II. Amino Acids: The Building Blocks for Proteins attracted to water molecules. III. Essential Amino Acids -Found in the interior of IV. Acid- Base Properties of Amino Acids proteins, where there is V. The Two Types of Protein-Energy Malnutrition limited contact with water VI. Peptide, Insulin, Immunoglobulin, Glucagon and Hormones Polar Neutral Amino Acids -The side chain of a polar VII. General Structural Characteristics of Proteins neutral is neither acidic nor a. Primary Structure of Proteins basic. b. Secondary Structure of Proteins - More soluble in water and c. Tertiary Structure of Proteins the R group present can d. Quaternary Structure of Proteins hydrogen bond to water. PROTEINS Polar Acidic Amino Acids Bears negative charge Building blocks of life Polar Basic Amino Acids Bears a positive charge They are the most complex and most diverse in chemical composition, conferring upon the different tissues. Note: Only L isomer are constituents of proteins Protein molecules contain elements of C, H, O, N It has a molecular weight of 5,000 to 3,000,000 Proteins are polymers consisting of 20 kinds of amino acids. Serves as transport and messenger molecules AMINO ACIDS An organic compound that contains both an amino (-NH2) group and a carboxyl (-COOH) group. The general structural formula for an amino acid is The R group present in an amino acid is called the amino acid side chain, defines the chemical nature Amino acid are amphoteric - able to react both as a base and as an acid Only 20 standard amino acids are normally Carboxylic Acids present in proteins. pKa is 2 to 5 The names are often abbreviated using Amino Groups three-letter codes pKa is usually 9-10 Abarico, Marks, Pique, Octaviano | 1  pH=1: +H3N – CH2 - COOH Low pH Proton concentration is high pH=7: +H3N – CH2 – COO- Both amines and carboxylic acids are protonated pH=12: H2N - CH2- COO- At acidic 2 TYPES OF PROTEIN-ENERGY MALNUTRITION High pH Proton concentration is low Both amines and carboxylic acids are deprotonated At basic Neutral pH Amines are protonated and carboxylates are deprotonated Zwitterionic Form A molecule having a positive charge on an atom, a negative charge on a different atom, having no net charge. Kwashiorkor Is a Ghanian word that means “the disease that the first child gets when the new child comes” Characteristic symptom: swollen abdomen Energy intake could be adequate, but protein consumption is too low. ESSENTIAL AMINO ACIDS Marasmus An amino acid needed in the human body must be Means “to waste away” or “dying away”, and obtained from dietary sources because it cannot be thus occurs in individuals who have Severely synthesized within the body from other substances in limited energy intakes. adequate amounts. Insufficient proteins and energy intake The Essential Amino Acids for Humans Bony PEPTIDE Chain of covalently linked amino acids 1. Dipeptide- 2 AA 2. Tripeptide- 3 AA 3. Oligopeptides- 10-20 AA residues 4. Polypeptides- long unbranched chain of ACID-BASE PROPERTIES OF AMINO ACIDS AA CYSTEINE Acid-Base Properties of Amino Acids Draw the following Only standard AA that has a side chain that chemical structures for glycine: (Non-existent form:) H2N contains sulfhydryl group – CH2 - COOH Abarico, Marks, Pique, Octaviano | 2  LEVELS OF PROTEIN STRUCTURE Primary Protein Structure Linear sequence of amino acid Order in which the individual amino acids making up the protein are linked together through peptide bonds Twisting about various bonds in the polypeptide backbone gives proteins a variety of shapes. Location of disulfide bonds INSULIN Insulin is the smallest protein, with 51 amino acids in two chains linked by cystine (disulfide) cross links GLUCAGON Although the injection of insulin lowers the blood sugar, administration of glucagon, another pancreas hormone, raises the blood sugar level. Straight peptide chain of 29 amino acids. It has been synthesized. The structure of glucagon is Secondary Protein Structure free of cystine and isoleucine. Localized regional structures Help drive the peptide folding that gives rise to IMMUNOGLOBULINS tertiary structure Antibodies, proteins that combat foreign Hydrogen bonding between carbonyl oxygen substances in the body and nitrogen atoms of amino acids Antibodies are associated with the γ-globulins Alpha helix and beta sheet aka immunoglobulins. Immunoglobulins Superfamily Characteristics Ig-like domain analogous to antibody structure Transmembrane glycoproteins ○ Trans- within ○ Membrane- plasma membrane ○ Glyco- presence of carbohydrate ○ Protein- polypeptide Cellular adhesion Molecules (CAMs) ○ Cell-Cell Tertiary Protein Structure ○ Cell-Extracellular Matrix Overall shape of proteins ○ Cell-Protein Water soluble proteins fold into compact HORMONE structures with nonpolar cores Thyrotropin-releasing Hormone – Secreted by 8 alpha helices; 154 amino acids; porphyrin ring hypothalamus; causes anterior pituitary gland to with iron release thyrotropic hormone Interaction between R group of amino acids Vasopressin (antidiuretic hormone) – cause folds in the protein Secreted by posterior pituitary gland; causes Includes ionic bonds, disulfide bonds, hydrogen kidney to retain water from urine bonds and hydrophobic interactions. Peptide bonds have partial double bond character due to resonance that limits rotation about this bond Abarico, Marks, Pique, Octaviano | 3 Quaternary Protein Structure Interactions between proteins Arises when multiple polypeptide chains fold together to form a single protein Includes ionic bonds, disulfide bonds, hydrogen bonds and hydrophobic interactions. PROTEIN DENATURATION Partial or complete disorganization of proteins characteristic three-dimensional shape as a result of disruption of its secondary, tertiary, and quaternary structural interactions. - Destruction of the tertiary structure of a protein molecule and the formation of random polypeptide chains EXAMPLE: 1. Cooking 2. Sealing of blood vessels 3. Temperature above 41 4. Applying isopropyl or ethyl alcohol (70%) 5. Rebonding PHYSICAL AND CHEMICAL DENATURING AGENTS Abarico, Marks, Pique, Octaviano | 4  MC 2: BIOCHEMISTRY CELLS (Angelica C. Lopez, RPh) August 31, 2024 TOPIC OUTLINE: ③ Metabolism - Reactions allow for the extraction & I. Definition of Biochemistry transformation of environmentally acquired II. Characteristics of Living Cells III. Levels of Organization energy. IV. Molecular Organizations of Level V. The Cell G Genetic Material VI. The Cell as Basis of Living - All life contains DNA, the hereditary VII. Organisms Organelles of Eukaryotic material which is passed down to future Cells generations. ⑧ Evolution BIOCHEMISTRY - DNA mutation over time leads to - Scientific discipline that seeks to explain life at adaptation and improved fitness in the organisation level. changing environments. - Uses the tools and terminology of chemistry to describe the various attributes of living organisms. LEVELS OF ORGANIZATION (simplest to complex) CDSHRMGE CHON CHARACTERISTICS OF LIVING CELLS 1. Atoms - such as Oxygen, Carbon, Hydrogen, Nitrogen, Phosphorus. ① Cells 2. Molecules - such as Water, Oxygen Gas, - The cell is the basic and most (combination of atoms Carbon Dioxide. fundamental unit of life. main topic 3. Macromolecules - such as Proteins, ② A Dynamic Organized Carbohydrates, Lipids, Nucleic Acid. - Organisms are not random and are highly parts of the cell 4. Organelles - such as Nucleus, organized using simpler atoms to build Mitochondria, Chloroplast, Plasma/Cell larger molecules & structures to survive. Membrane. Stimuli ③ 5. Cells - such as Myocytes, Neurons, - Can respond to specific triggers from the Erythrocytes. environment. 6. Tissues - such as Muscle, Epithelial, ④ Homeostasis Connective, Nervous. - Mechanisms for regulating & 7. Organs - such as Heart, Stomach, Brain. maintaining/stabilizing their internal 8. Organ System - Cardiovascular System, chemistry. Digestive System, Nervous System. ⑤ Reproduction 9. Multicellular Organism - such as Human, - The capacity to produce more life, either Leopard, Whale. sexually or asexually.  MC 2: BIOCHEMISTRY CELLS (Angelica C. Lopez, RPh) August 31, 2024 MOLECULAR ORGANIZATION OF CELL Rudolf Virchow (1821-1902) - Stated that “Every cell comes from a cell”. CELLS ARE THE BASIS OF LIVING ORGANISMS Four (4) Types of Biomolecules (ACNL) Level 1: Monomeric Units M 1. Amino Acids M Among the simplest compounds are the Level 2: Macromolecules amino acids, so named because they S Level 3: Supramolecular Complexes contain an amino group (NH2) and a carboxylic acid group (COOH). Under Level 4: The cell and its organelles C physiological conditions, these groups are actually ionized to NH3+ and COO– THE CELL - The basic unit of life. - According to conventional definitions, a living organism is composed of one or more organisms. - Can grow, reproduce and respond to stimuli, and has some other characteristics. These characteristics are mainly based on the cell. 2. Carbohydrates Robert Hooke (1635-1703) Simple carbohydrates (also called - Termed the “cell” (cella, a Latin word monosaccharides or just sugars) have the means ‘small container’) which he saw formula (CH2O)n, where n is ≥ 3. Glucose, through a microscope when he observed a monosaccharide with six carbon atoms, a slice of cork. has the formula C6H12O6; Rene Dutrochet (1776- 1882) - Declared in 1824 that “The cell is the Polyhydroxy aldehyde, a polyhydroxy fundamental element in the structure of ketone or a compound that yields living bodies, forming both animals and polyhydroxy aldehyde or polyhydroxy plants through juxtaposition.” ketone upon hydrolysis Theodore Schwann (1810-1882) - Created the term “Cell Theory” and declared that plants consisted of cells. - A similar declaration was made by Matthias Schleiden (1804-1881) on the units forming animals. MC 2: BIOCHEMISTRY CELLS (Angelica C. Lopez, RPh) August 31, 2024 Proteins ( - peptide bonds Nucleic Acid , prophodiester bond 3. Nucleotides 2. Polymers of amino acids are called A five-carbon sugar, a nitrogen-containing polypeptides or proteins. Twenty ring, and one or more phosphate groups different amino acids serve as building are the components of nucleotides. blocks for proteins, which may contain many hundreds of amino acid residues. Linked to each other by amide bonds called peptide bonds. 4. Lipids. 3. Nucleic Acids Polymers of nucleotides are - These compounds cannot be described by termed polynucleotides or nucleic a single structural formula since they are a acids, better known as DNA and RNA. diverse collection of molecules. Each nucleic acid is made from just four different nucleotides. For example, the Au residues in RNA - bases adenine, cytosine, guanine, and uracil, whereas the ACGT residues in DNA contain adenine, cytosine, guanine, and thymine. linked by phosphodiester bond Three (3) Major Kinds of Polymers 1. Universal feature of nature: A few kinds of building blocks can be combined in different ways to produce a wide variety of larger structures  MC 2: BIOCHEMISTRY CELLS (Angelica C. Lopez, RPh) August 31, 2024 ORGANELLES OF EUKARYOTIC CELLS genetic make-up; 2 forms: euchromatin & 1. NUCLEUS heterochromatin. control center - Control center of the cell. 2. ENDOPLASMIC RETICULUM Complex folded - Appears as an intricate, complex, folded net in the cytoplasm. PARTS OF NUCLEUS: - Encased in a double membrane called PARTS OF ENDOPLASMIC RETICULUM: the Nuclear Envelope. Rough Endoplasmic Reticulum ribosomes - Outer Membrane - fused with the ER ; - Contains ribosomes which gives it a contains ribosomes & ribosomes rough appearance site for protein lamines - Inner Membrane - contains lamines synthesis; proper protein folding; glycosylation "ER stress" - apoptosis by important for maintaining envelope celt mitochondria. structure, division and interaction Smooth Endoplasmic Reticulum no ribosomes between chromatins. - Nuclear Pores - facilitate transport of - No ribosomes site for lipid synthesis like fatty acids, phospholipids, cholesterol; molecules between the cytoplasm and CYP450; glucose-6-PO4 metabolism; the nucleus. stores calcium ions. - Nucleolus - contains genes for making ribosomal RNA (rRNA); copies of rRNA 3. GOLGI APPARATUS synthesized in the nucleoli are bound to - (Camillo Golgi) proteins are processed, ribosomal proteins that are transported modified, and prepared for export from to the nucleus from the cytoplasm. After the cell; a stack of 10 to 20 hollow, flat assembly of bosomes in nucleoli, they structures: Proteins are received from the ER and passed through layers of the are exported through the nuclear pores it where polysaccharides are back into the cytoplasm. synthesized and attached to proteins to - Chromatin - contains primarily DNA and make glycoproteins, or to lipids to make proteins (specifically histones), making glycolipids.  MC 2: BIOCHEMISTRY CELLS (Angelica C. Lopez, RPh) August 31, 2024 - Contain 40 different hydrolytic enzymes including proteases, nucleases, glycosidases, lipases, phosphatases, and sulfatase in order to break down macromolecules; - Cell renewal by digesting old or damaged cellular components (autophagy/autolysis). 4. PLASMA MEMBRANE 6. PEROXISOMES - Consists of a lipid bilayer (head = phospholipid; tail fatty acid), phosphate - Similar to lysosomes; and carbohydrate components, and a large number of proteins; maintains the physical integrity of the cell and prevents the contents of the cell from leaking into the fluid environment. - Contain three detoxification enzymes: catalase, urate oxidase and D-amino acid oxidase; use molecular oxygen to remove hydrogen atoms from specific substrates in oxidation reactions; Integrins receptor — adhesion degradation of long chain fatty acids. Form lipids (plasmalogen) and cholesterol; Detoxification of alcohol. 5. LYSOSOMES sals - Membrane-bounded sacs. 7. MITOCHONDRIA powerhouse - Powerhouse of the cell;  MC 2: BIOCHEMISTRY CELLS (Angelica C. Lopez, RPh) August 31, 2024 - Contains inner and outer membrane; - Intermediate Filaments - which cristae, mitochondrial matrix. facilitates mainstay of cell to - ATP synthesis via oxidative extracellular proteins, mainstay of cell to phosphorylation; another cell and mainstay of different - Metabolic reactions occur including organelles intracellularly. heme biosynthesis, rea formation, fatty acid oxidation, initiation of apoptosis; gluconeogenesis, ketogenesis. 8. RIBOSOMES membrane bound (protein syntness) - "Free" or membrane-bound ribosomes. - Microtubule - contains tubulin to transport different substances inside the cell (ATP- dependent); separate chromatid during cell division; cell movement (flagella and cilia). - Cytosolic proteins used intracellularly; - Protein synthesis in cells. 9. CYTOSKELETON END OF TRANSCRIPTION - Microfilaments - contain "actin"; they are involved in cytokinesis, diapedesis of white blood cells and phagocytosis of white blood cells. ○ PPT OF MA'AM LOPEZ Nucleic Acids DNA & RNA LEARNING OBJECTIVES 1. Classify nucleic acids and give their functions. 2. Identify the building blocks of nucleic acids and the components of a mononucleotide. 3. Describe the components and structure of nucleotides 4. Distinguish levels of organizations of nucleic acid structures: primary, secondary and tertiary 5. Compare the structural organizations of DNA and RNA and prove that DNA is the genetic material. 6. Illustrate the biosynthetic replication process from transcription and translation. 7. Discuss the central dogma of molecular biology LEARNING OBJECTIVES 8. Differentiate spontaneous from induced mutations and give examples. 9. Give examples of physical, chemical and biological mutagens. 10. Correlate gene mutations to tumor, cancer and genetic disorders. Loading… 11. Demonstrate repair system of the cell. 12. Describe recombinant technology and discuss applications of recombinant DNA technology in medical diagnosis and therapy.  What are they ? The 4th type of macromolecules The chemical link between generations The source of genetic information in chromosomes  What do they do ? Dictate amino-acid sequence in proteins Give information to chromosomes, Loading… which is then passed from parent to offspring Central Dogma of Molecular Biology  Nucleic acid and Hereditary Processes in the transfer of genetic information: Replication: identical copies of DNA are made Transcription: genetic messages are read and carried out of the cell nucleus to the ribosomes, where protein synthesis occurs. Translation: genetic messages are decoded to make proteins. 7 The nucleus contains the cell’s DNA (genome) RNA is synthesized in the nucleus and exported to the cytoplasm Nucleus Cytoplasm replication DNA transcription RNA (mRNA) translation Proteins  Two types of Nucleotides (depending on the sugar they contain) 1- Ribonucleic acids (RNA) The pentose sugar is Ribose (has a hydroxyl group in the 2nd carbon- --OH) 2- Deoxyribonucleic acids (DNA) The pentose sugar is Deoxyribose (has just an hydrogen in the same place--- H) Deoxy = “minus oxygen”  Definition Nucleic acids are polymers of nucleotides Nucleotides are carbon ring structures containing nitrogen linked to a 5- carbon sugar (a ribose) 5-carbon sugar is either a ribose or a deoxy-ribose making the nucleotide either a ribonucleotide or a deoxyribonucleotide  Nucleic acid function DNA Genetic material - sequence of nucleotides encodes different amino acid RNA Involved in the transcription/translation of genetic material (DNA) Loading… Genetic material of some viruses  Nucleotides Structure Despite the complexity and diversity of life the structure of DNA is dependent on only 4 different nucleotides Diversity is dependent on the nucleotide sequence All nucleotides are 2 ring structures composed of: 5-carbon sugar : b-D-ribose (RNA) b-D-deoxyribose (DNA) Base Purine Pyrimidine Phosphate group A nucleotide WITHOUT a phosphate group is a NUCLEOSIDE  Nucleotides Structure Despite the complexity and diversity of life the structure of DNA is dependent on only 4 different nucleotides Diversity is dependent on the nucleotide sequence All nucleotides are 2 ring structures composed of: 5-carbon sugar : b-D-ribose (RNA) b-D-deoxyribose (DNA) Base Purine Pyrimidine Phosphate group A nucleotide WITHOUT a phosphate group is a NUCLEOSIDE  Nucleotides and Nucleosides Nucleotide = Nitrogenous base Pentose Phosphate Nucleoside = Nitrogenous base Pentose Nucleobase = Nitrogenous base PURGA PYRCU  T Nucleotide Formation 1. Sugar and base react to form two units called nucleoside  Nucleotide Formation 2. The nucleoside reacts with a phosphate group to form the three-subunit entity called nucleotide. base（purine、pyrimdine）+ribose（deoxyribos N-glycosyl linkage nucleoside+phosphate phosphoester linkage nucleotide phosphodiester linkage nucleic acid Pentose Sugars There are two related pentose sugars: - RNA contains ribose - DNA contains deoxyribose The sugars have their carbon atoms numbered with primes to distinguish them from the nitrogen bases  Nucleotide Function Building blocks for DNA and RNA Intracellular source of energy – Adenosine triphosphate (ATP) Second messengers - Involved in intracellular signaling (e.g. cyclic adenosine monophosphate [cAMP]) Intracellular signaling switches (e.g. G-proteins)  Nucleotide Structure - 4 Phosphate Groups Phosphate groups are what makes a nucleoside a nucleotide Phosphate groups are essential for nucleotide polymerization Basic structure: O O P O X O  Nucleotide Structure - 4 Phosphate Groups Number of phosphate groups determines nomenclature Monophosphate O e.g. AMP O P O CH Free = inorganic 2 phosphate (Pi) O Diphosphate O O e.g. ADP O P O P O CH Free = Pyro- 2 O O phosphate (PPi)  Nucleotide Structure - 4 Phosphate Groups Triphosphate O O O e.g. ATP O P O P O P O CH 2 No Free form exists O O O Purine and Pyrimidine Pyrimidine contains two pyridine-like nitrogens in a six- membered aromatic ring Purine has 4 N’s in a fused-ring structure. Three are basic like pyridine-like and one is like that in pyrrole 25  Nucleotide Structure - 2 Bases - Purines NH2 Adenine N N A N N N 6 H 7 5 1 N 8 9 4 3 2 O N N N NH G Guanine N N NH2 H  Nucleotide Structure - 3 O Bases - Pyrimidines H3C Thymine NH T N O 4 3 5 N H 2 6 NH2 1 N N C Cytosine N O H  Nucleotide Structure - 4 Bases - Pyrimidines Thymine is found ONLY in DNA. In RNA, thymine is replaced by uracil Uracil and Thymine are structurally similar Loading… Uracil O 4 3 5 N NH 2 6 U 1 N N O H Nitrogen Bases The nitrogen bases in nucleotides consist of two general types: - purines: adenine (A) and guanine (G) - pyrimidines: cytosine (C), thymine (T) and Uracil (U) DT R U?  Nucleosides and Nucleotides A nucleoside consists of a nitrogen base linked by a glycosidic bond to C1’ of a ribose or deoxyribose Nucleosides are named by changing the the nitrogen base ending to -osine for purines and –idine for pyrimidines A nucleotide is a nucleoside that forms a phosphate ester with the C5’ OH group of ribose or deoxyribose Nucleotides are named using the name of the nucleoside followed by 5’-monophosphate Names of Nucleosides and Nucleotides 1  1 DNA Watso Cric n k Died in 2004 DEFINITION 2 DNA stands for deoxyribose nucleic acid This chemical substance is present in the nucleus of all cells in all living organisms DNA controls all the chemical changes which take place in cells The kind of cell which is formed, (muscle, blood, nerve etc) is controlled by DNA DNA molecule 3 DNA is a very large molecule made up of a long chain of sub-units The sub-units are called nucleotides Each nucleotide is made up of a sugar called deoxyribose a phosphate group -PO4 and an organic base Nucleic Acids and Nucleotides Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are the chemical carriers of genetic information Nucleic acids are biopolymers made of nucleotides, aldopentoses linked to a purine or pyrimidine and a phosphate 38 Deoxyribonucleotides found in DNA dA dG dT d C The Deoxyribonucleotides 40  Hydrogen Bonding Interactions Two bases can hydrogen bond to form a base pair For monomers, large number of base pairs is possible In polynucleotide, only few possibilities exist Watson-Crick base pairs predominate in double-stranded DNA A pairs with T C pairs with G Purine pairs with pyrimidine  DNA Nucleotides Composition (3 parts): 1- Deoxyribose sugar (no O in 3rd carbon) 2- Phosphate group 3- One of 4 types of bases (all containing nitrogen): - Adenine - Thymine (Only in DNA) - Cytosine - Guanine Base Pairing in DNA: The Watson–Crick Model In 1953 Watson and Crick noted that DNA consists of two polynucleotide strands, running in opposite directions and coiled around each other in a double helix Strands are held together by hydrogen bonds between specific pairs of bases Adenine (A) and thymine (T) form strong hydrogen bonds to each other but not to C or G (G) and cytosine (C) form strong hydrogen bonds to each other but not to A or T 43 The Difference in the Strands The strands of DNA are complementary because of H- bonding Whenever a G occurs in one strand, a C occurs opposite it in the other strand When an A occurs in one strand, a T occurs in the other 44  Primary Structure of Nucleic Acids The primary structure of a nucleic acid is the nucleotide sequence The nucleotides in nucleic acids are joined by phosphodiester bonds The 3’-OH group of the sugar in one nucleotide forms an ester bond to the phosphate group on the 5’-carbon of the sugar of the next nucleotide Generalized Structure of DNA 47  Reading Primary Structure A nucleic acid polymer has a free 5’- phosphate group at one end and a free 3’-OH group at the other end The sequence is read from the free 5’-end using the letters of the bases This example reads 5’—A—C—G—T—3’ Describing a Sequence Chain is described from 5 end, identifying the bases in order of occurrence, using the abbreviations A for adenosine, G for guanosine, C for cytidine, and T for thymine (or U for uracil in RNA) A typical sequence is written as TAGGCT 49  Secondary Structure: DNA Double Helix In DNA there are two strands of nucleotides that wind together in a double helix - the strands run in opposite directions - the bases are are arranged in step-like pairs - the base pairs are held together by hydrogen bonding The pairing of the bases from the two strands is very specific The complimentary base pairs are A-T and G-C - two hydrogen bonds form between A and T - three hydrogen bonds form between G and C Each pair consists of a purine and a pyrimidine, so they are the same width, keeping the two strands at equal distances from each other Properties of a DNA double helix – Secondary Structure/3D The strands of DNA are antiparallel The strands are complimentary There are Hydrogen bond forces There are base stacking interactions There are 10 base pairs per turn  The sides of the ladder are: Untwisted it P = phosphate looks like this: S = sugar molecule The steps of the ladder are C, G, T, A = nitrogenous bases (Nitrogenous means containing the element nitrogen.) A = Adenine (Apples are T = Thymine Tasty) A always pairs with T in DNA C = Cytosine (Cookies are Good) G = Guanine Nucleotide C always pairs with G in DNA Hydrogen bonding possibilities are more favorable when A-T and G-C base pairing occurs  Model of DNA: The model was developed by Watson and Crick in 1953. They received a nobel prize in 1962 for their work. The model looks like a twisted ladder – double helix.  Nucleic Acid Structure “Base Pairing” DNA base-pairing is antiparallel i.e. 5’ - 3’ (l-r) on top : 5’ - 3’ (r-l) on 5’ 3’ T A G C A C A T C G T G 3’ 5’  17 PO PO 4 The strands 4 PO separate PO 4 4 PO PO 4 4 PO PO 4 4 PO PO 4 4 PO PO 4 4 PO PO 4 4 PO PO 4 4 Practice DNA Base Pairs GATTACA Practice DNA Base Pairs GATTACA CTAATGT Nucleic Acid Structure The double helix Minor Groov e Major Groov e Before a cell divides, the DNA strands unwind and separate (DNA Helicase] Each strand makes a new partner by adding the appropriate nucleotides The result is that there are now two double- stranded DNA molecules in the nucleus So that when the cell divides, each nucleus contains identical DNA This process is called DNA replication  DNA Replication When a eukaryotic cell divides, the process is called mitosis - the cell splits into two identical daughter cells - the DNA must be replicated so that each daughter cell has a copy DNA replication involves several processes: - first, the DNA must be unwound, separating the two strands - the single strands then act as templates for synthesis of the new strands, which are complimentary in sequence - bases are added one at a time until two new DNA strands that exactly duplicate the original DNA are produced  bond Hellcase -> broken hydrogen STEP 1 Hydrogen bonds between DNA molecule base pairs are broken by the separates into enzyme DNA helicase and complementary halves DNA molecule unzips  Nucleic Acid Structure Polymerization 5’ 3’ Sugar Phosphate “backbone” Base T A G C A C s 5’ 3’ TAGCAC  Nucleic Acid Structure Polymerization P P P N P P P N C C S Phosphodiesterase S + P P P N C (PPi ) S P P P N C S  STEP 2 Nucleotides match up with complementary bases Free nucleotides abundant in nucleus  STEP 3 into 2 new strands of DNA by Nucleotides are linked the enzyme, polymerase—DNA polymerase also proofreads for copying errors New Strand Original Strand Mutations occur when copying errors cause a change in the sequence of DNA nucleotide bases Diagram Examples of DNA Replication: (You could see DNA replication represented different ways.)  DNA Replication The process is called semi- conservative replication because one strand of each daughter DNA comes from the parent DNA and one strand is new The energy for the synthesis comes from hydrolysis of phosphate groups as the phosphodiester bonds form between the bases  Storage of DNA (Nucleus] In eukaryotic cells (animals, plants, fungi) DNA is stored in the nucleus, which is separated from the rest of the cell by a semipermeable membrane The DNA is only organized into chromosomes during cell replication Between replications, the DNA is stored in a compact ball called chromatin, and is wrapped around proteins called histones to form nucleosomes  Figure 5-14 Schematic representation of the strand separation in duplex DNA resulting from its heat denaturation. P a g e 9 0  Direction of Replication The enzyme helicase unwinds several sections of parent DNA At each open DNA section, called a replication fork, DNA polymerase catalyzes the formation of 5’-3’ester bonds of the leading strand The lagging strand, which grows in the 3’-5’ direction, is synthesized in short sections called Okazaki fragments The Okazaki fragments are joined by DNA ligase to give a single 3’-5’ DNA strand Spaces between “nicks” 5'-3'-leading strand 3-5- lagging strand short-okazaki fragments Segments  RNA Nucleotides Composition ( 3 parts): 3rd Carbon 1- Ribose sugar (with O in 3rd carbon) 2- Phosphate group 3- One of 4 types of bases (all containing nitrogen): - Adenine - Uracyl (only in RNA) - Cytosine - Guanine  RNA—Ribonucleic Acid RNA is a messenger that allows the instruction of DNA to be delivered to the rest of the cell RNA is different than DNA: 1. D The sugar in RNA is ribose; the sugar in DNA is deoxyribose 2. ② RNA is a single strand of nucleotides; DNA is a double strand of nucleotides 3. ③ RNA has Uracil (U) instead of Thymine (T) which is in DNA 4. ⑧ RNA is found inside and outside of the nucleus; DNA is found only inside the nucleus There are three main types of RNA: - ribosomal (rRNA), messenger (mRNA) and transfer (tRNA) - subtypes: heterogenous nuclear RNA (hnRNA) & small nuclear RNA (snRNA) Types of RNA  Transfer RNA Transfer RNA translates the genetic code from the messenger RNA and brings specific amino acids to the ribosome for protein synthesis Each amino acid is recognized by one or more specific tRNA tRNA has a tertiary structure that is L-shaped - one end attaches to the amino acid and the other binds to the mRNA by a 3-base complimentary sequence The Parts of Transfer RNA There are 61 different tRNAs, one for each of the 61 codons that specifies an amino acid tRNA has 70-100 ribonucleotides and is bonded to a specific amino acid by an ester linkage through the 3 hydroxyl on ribose at the 3 end of the tRNA Each tRNA has a segment called an anticodon, a sequence of three ribonucleotides complementary to the codon sequence 80  Ribosomal RNA and Messenger RNA Suburt Large Ribosomes are the sites of protein synthesis Small subunit - they consist of ribosomal DNA (65%) and proteins (35%) - they have two subunits, a large one and a small one Messenger RNA carries the genetic code to the ribosomes - they are strands of RNA that are complementary to the DNA of the gene for the protein to be synthesized  How DNA Works 1- DNA stores genetic information in segments called genes 2- The DNA code is in Triplet Codons (short sequences of 3 nucleotides each) 3- Certain codons are translated by the cell into certain Amino acids. 4. Thus, the sequence of nucleotides in DNA indicate a sequence of Amino acids in a protein. Transcription Process Several turns of the DNA double helix unwind, exposing the bases of the two strands Ribonucleotides line up in the proper order by hydrogen bonding to their complementary bases on DNA Bonds form in the 5 3 direction, Loading… 83 Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003 Transcription of RNA from DNA Only one of the two DNA strands is transcribed into mRNA The strand that contains the gene is the coding or sense strand The strand that gets transcribed is the template or antisense strand The RNA molecule produced during transcription is a copy of the coding strand (with U in place of T) 84 Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003 Example of RNA Primary Structure In RNA, A, C, G, and U are linked by 3’-5’ ester bonds between ribose and phosphate  Protein Synthesis The two main processes involved in protein synthesis are - the formation of mRNA from DNA (transcription) - the conversion by tRNA to protein at the ribosome (translation) Transcription takes place in the nucleus, while translation takes place in the cytoplasm Genetic information is transcribed to form mRNA much the same way it is replicated during cell division  RNA Polymerase During transcription, RNA polymerase moves along the DNA template in the 3’-5’direction to synthesize the corresponding mRNA The hnRNA is released at the termination point Processing of mRNA Genes in the DNA of eukaryotes contain exons that code for proteins along with introns that do not Because the initial mRNA, called a pre-RNA/hnRNA includes the noncoding introns, it must be processed before it can be read by the tRNA While the mRNA is still in the nucleus, the introns are removed from the pre-RNA The exons that remain are joined to form the mRNA that leaves the nucleus with the information for the synthesis of protein Removing Introns from mRNA Splicing Process of removing introns from an hnRNA molecule and joining the remaining exons together to form an mRNA molecule. The process involves the snRNA which facilitates splicing to occur. snRNA is found complexed with protein together called small nuclear ribonucleoprotein particles snRNPs (pronounced as snurps) A large complex of snurps is called a spliceosome. Spliceosome is a large assembly of snRNA molecules and proteins involved in the conversion of hnRNA molecules to mRNA molecules  Transcription Several steps occur during transcription: - a section of DNA containing the gene unwinds (governed by RNA polymerase) - one strand of DNA is copied starting at the initiation point, which has the sequence TATAAA - an hnRNA is synthesized using complementary base pairing with uracil (U) replacing thymine (T) - the newly formed mRNA moves out of the nucleus to ribosomes in the cytoplasm and the DNA re-winds In DNA-RNA base pairing the complementary base pair are: DNA-RNA A----U G----C C----G T-----A RNA molecules contain the base U instead of the base T Regulation of Transcription A specific mRNA is synthesized when the cell requires a particular protein The synthesis is regulated at the transcription level: - feedback control, where the end products speed up or slow the synthesis of mRNA - enzyme induction, where a high level of a reactant induces the transcription process to provide the necessary enzymes for that reactant Regulation of transcription in eukaryotes is complicated and we will not study it here The Ribonucleotides 102  The Genetic Code The genetic code is found in the sequence of nucleotides in mRNA that is translated from the DNA aminoacia & A codon is a triplet of bases along the mRNA that codes for a particular amino acid MET-AUG Each of the 20 amino acids needed to build a protein has at least 2 codons There are also codons that signal the “start” and “end” of a polypeptide chain The amino acid sequence of a protein can be determined by reading the triplets in the DNA sequence that are complementary to the codons of the mRNA, or directly from the mRNA sequence The entire DNA sequence of several organisms, including humans, have been determined, however, - only primary structure can be determined this way - doesn’t give tertiary structure or protein function Genetic code 1 19 The sequence of bases in DNA forms the Genetic Code CODOMS A group of three bases (a triplet) controls the production of a particular amino acid in the cytoplasm of the cell The different amino acids and the order in which they are joined up determines the sort of protein being produced Coding 21 For example↑ cano a4d ↳ Cytosine 3 pas Adenin Codes for Valine e Thymin e Cytosine (C) Guanine (G) Codes for Alanine Adenine (A) Triplet code 22 This is known as the triplet code Each triplet codes for a specific amino acid CGA - CAA - CCA - CCA - GCT - GGG - GAG - CCA - Ala Val Gl Gl Arg Pro Leu Gl y y y Specific The amino acids are joined together in the correct sequence to make part of a protein Ala Val Gl Gl Arg Pro Leu Gl y y y mRNA Codons and Associated Amino Acids Reading the Genetic Code Suppose we want to determine the amino acids coded for in the following section of a mRNA 5’—CCU —AGC—GGA—CUU—3’ According to the genetic code, the amino acids for these codons are: CCU = Proline AGC = Serine GGA = Glycine CUU = Leucine The mRNA section codes for the amino acid sequence of Pro—Ser—Gly—Leu The Structure of tRNA 111 Based on McMurry, Organic Chemistry, Chapter 28, 6th edition, (c) 2003  tRNA and anticodon - Interaction between codon and anticodon  Translation and tRNA Activation Once the DNA has been transcribed to mRNA, the codons must be translated to the amino acid sequence of the protein The first step in translation is activation of the tRNA Each tRNA has a triplet called an anticodon that complements a codon on mRNA A aminoacyl tRNA synthetase anticodon enzyme uses ATP hydrolysis to attach an amino acid to a specific tRNA  Initiation and Translocation Initiation of protein synthesis occurs when a mRNA attaches to a ribosome On the mRNA, the start codon (AUG) binds to a tRNA with methionine The second codon attaches to a tRNA with the next amino acid A peptide bond forms between the adjacent amino acids at the first and second codons The first tRNA detaches from the ribosome and the ribosome shifts to the adjacent codon on the mRNA (this process is called translocation) A third codon can now attach where the second one was before translocation Initiation Initiation Initiation Elongation - Elongation -o Elongation Elongation Termination After a polypeptide with all the amino acids for a protein is synthesized, the ribosome reaches the the “stop” codon: UGA, UAA, or UAG There is no tRNA with an anticodon for the “stop” codons Therefore, protein synthesis ends (termination) The polypeptide is released from the ribosome and the protein can take on it’s 3-D structure (some proteins begin folding while still being synthesized, while others do not fold up until after being released from the ribosome)