Biochemistry Lecture Notes PDF

1 Jimenez, Marianne B. ​ Discovery of the role of enzymes as NUR240 catalyst ​ Identification of nucleic acids as an BIOCHEMISTRY...

1 Jimenez, Marianne B. ​ Discovery of the role of enzymes as NUR240 catalyst ​ Identification of nucleic acids as an BIOCHEMISTRY information molecules FLOW OF INFORMATION from nucleic LECTURE acids to proteins DNA → RNA→ PROTEIN BIOCHEMISTRY POLYMERS & MONOMERS ​ Chemistry of life or living organism ​ Each type of biomolecules are polymers ​ Science concerned with a chemical that are assemblage from single unit basis of life called Monomers AIM: ​ Each type of molecule in an assemblage ​ To describe and explain in molecular of different type of monomers terms all chemical process of living cell ANABOLIC ​ Build complex molecule from single to SIGNIFICANCE: lager ​ Essential to all life as common ​ Consume energy to proceed this knowledge process CATABOLIC BRANCHES OF BIOCHEMISTRY: ​ Synthesize / breakdown ​ Medical deals with chemical basis of ​ From larger molecule to breakdown human body ​ Release energy to proceed this possess ​ Chemical deals with clinical disease/ pathological condition of human body ​ Clinical diagnosis, therapy and research of medical field CARBOHYDRATES ​ Bacterial biochem deals with bacterial ​ Major source of energy from our diet ​ Plants biochem deals with plants ​ Carbon, Hydrogen, Oxygen ​ Animal biochem deals with animals ​ Called saccharide which means “ sugar” ​ Industrial biochem deals with industrial ​ Cn( H2O)n products involve with microorganism STRUCTURAL PROPERTY ​ BIOCHEM emerged in the late 18th and ​ Handedness early 19th century 1.​ Left handed ​ Introduced by the German Chemist Carl 2.​ Right handed Neuberg 1903 ​ Presence of chiral center ​ 1940’s clinical biochem evolves as an ​ Isomers autonomous field 1.​ Structural isomers 2.​ Stereoisomers NOTABLE BREAKTHROUGHS  2 Stereoisomerism ​ same molecular formula and same structure but different in configuration ​ Different in arrangement of their atoms in space ​ Presence of chiral centers allow the formation of stereoisomers ENANTIOMERS ​ stereoisomers whose molecules ISOMERISM are non superimposable mirror Isomers ​ compound that possessing identical image of each other molecular formula but different DIASTEREOMERS structures ​ stereoisomers whose molecules are not mirror image TYPE OF ISOMERS Structural isomers ​ same molecular formula but different from each other by having different structures OPTICAL ISOMERS ​ Optical activity is the capacity of a substance to rotate the plane  3 polarized light passing through it CLASSIFICATION ​ Monosaccharides simplest EPIMERISM if two monosaccharides carbohydrates differ from each other in their ​ Disaccharides consist of 2 configuration around a single specific monosaccharides carbon (other than anomeric) atom ​ Oligosaccharides 3-10 monosaccharides ​ Polysaccharides contain many monosaccharides MONOSACCHARIDES ​ 3-6 carbon atom ​ Aldehyde and ketone ​ Several hydroxyl group ​ Colorless, crystalline solids ANOMERISM ALDOSE ​ obtained from the change of position of ​ With aldehyde group hydroxyl group attached to the ​ Many hydroxyl (-OH) anomeric carbon ​ TRIOSE 3C ATOMS MUTAROTATION ​ TETROSE 4C ATOMS ​ Change in the specific optical ​ PENTOSE 5C ATOMS rotation by the intervention of ​ HEXOSE 6C ATOMS A and B forms of D-Glucose to an equilibrium mixture D- GLUCOSE ​ Found in fruits, corn, syrup, and honey ​ Aldohexose with the formula of C6H12O6  4 ​ Knows as blood sugar in the body ​ Monosaccharide in polymers of starch, cellulose, and glycogen BLOOD GLUCOSE LEVEL Normal blood level 70-90 mg/dL D-FRUCTOSE ​ A ketohexose C6H12O6 ​ Sweetest carbohydrates ​ Fruit juice and honey ​ Convert glucose in the body Haworth projection was made by Walter Norman Haworth D- GALACTOSE DISACCHARIDES ​ Not found free in nature ​ Form by the condensation of 2 simple ​ C6H12O6 sugar ​ Obtained from lactose, disaccharides ​ If the glycosidic linkage involves the ​ Similar structure to glucose except for carbonyl groups of both sugars (as in the -OH on C4 sucrose) the resulting disaccharides is Non reducing ​ If the glycosidic linkage involves the carbonyl group of the only one sugars (as in maltose) the resulting disaccharides is Reducing ​ Sucrose ( glucose + fructose) ​ Lactose ( glucose + galactose) ​ Maltose (glucose+ glucose)  5 ​ Condensation reaction means removing water ​ Hydrolysis means addition of water MALTOSE ​ Also known as malt sugar ​ Composed of 2 D-Glucose molecules ​ Obtained from the hydrolysis starch ​ Use in cereal, candies, and brewing  6 CLASSIFICATION based on the degree branching BRANCHED ​ Formed from two major type of biochemical polymers therefore forming branches UNBRANCHED ​ Linear polymers POLYSACCHARIDES ​ Formed by the condensation of n molecules of monosaccharides with the removal of n-1 molecules of water ​ Since the condensation involves the carbonyl group f sugars, leaving only one free carbonyl group that at the end of big molecule, polysaccharides are Non reducing CLASSIFICATION based on repeating units HOMOPOLYSACCHARIDES ​ Only one type of monosaccharides monomer unit is present HETEROPOLYSACCHARIDES ​ More than one usually two type of monosaccharides monomer unit are present  7 LIPIDS ​ Organic substance relatively insoluble in organic solvents like chloroform, ether and benzene ​ Fatty acids is building blocks of lipids ​ Relatively insoluble in water FUNCTIONS: ​ Storage form of energy ​ Acts as thermal insulator ​ Protection of internal organs ​ Precursor of many steroid hormones, Vitamin D ​ Structural component of cell membrane ​ Helps in absorption of fat-soluble vitamins ​ Lipoproteins transporting lipids ​ Fats serve as surfactants by reducing surface tension ​ Improve taste and palatability ​ Acts as electric insulators in neurons STRUCTURAL PROPERTY ​ Very divers ​ Some are 1.​ Esters 2.​ Amides 3.​ Alcohols 4.​ Acrylic 5.​ Cyclic 6.​ Polycyclic FATTY ACIDS Oxidize Carboxylic acid ​ Naturally occurring monocarboxylic acid Reduction Alcohol ​ Contain even number of carbon atoms ​ Carbon chain that is unbranched  8 CLASSIFICATION based on total number of ​ Few interactions between chains carbon ​ Low melting points EVEN CHAIN FATTY ACIDS even number ​ Liquid at room temperature of carbon ODD CHAIN FATTY ACIDS odd chain of carbon CLASSIFICATION based on carbon chain length ​ SHORT CHAIN contains 4-6 carbon ​ MEDIUM CHAIN 8-10 carbon ​ LONG CHAIN 12-26 carbon CLASSIFICATION based on number of carbon carbon double bonds ​ SATURATED FATTY ACIDS all carbon bonds are single bonds ​ MONOUNSATURATED FATTY ACIDS one carbon to carbon double bonds ​ POLYUNSATURATED FATTY ACIDS two or more carbon to carbon double bonds PROPERTIES OF SATURATED FATTY ACIDS ​ Only single C-C bonds ​ Closely packed ​ Strong attractions between chains ​ High melting points ​ Solid at room temp. PROPERTIES OF UNSATURATED FATTY ACIDS ​ One or more double bonds ​ Nonlinear chain do not allow molecules to pack closely 9  10 TYPES OF LIPIDS ​ Waxes ​ Fats and oils (triacylglycerides) ​ Phospholipids ​ sphingolipids LIPIDS WITHOUT FATTY ACIDS ​ Steroids TRIACYLGLYCEROL ​ Energy storage lipids ​ Found in adipocytes (adipose cells) ​ Formed by esterification of glycerol and 3 fatty acids ​ Much more efficient at strong energy that glycogen  11 CLASSIFICATION based on fatty acid molecules SIMPLE TRIACYLGLYCEROL ​ Triester formed from esterification of glycerol within 3 identical fatty acids MIXED TRIACYLGLYCEROL ​ triester formed from the esterification of glycerol with more that 1 kind of fatty acids CHEMICAL REACTIONS 1.​ esterifications/ dehydration synthesis 2.​ Hydrolysis 3.​ Saponification 4.​ Hydrogenation 5.​ Oxidation 12  13 SEX HORMONES ESTROGEN ​ Female sex hormones synthesized in the ovaries and adrenal cortex ANDROGENS ​ Male sex hormones synthesized in the testes and adrenal cortex PROGESTINS ​ Pregnancy hormones synthesized in the ovaries in placenta ADRENO CORTICOID HORMONES MINERALOCORTICOID ​ Control the balance of Na+ and K+ ions in cells and body fluids GLUCOCORTICOIDS ​ Control glucose metabolism and counteract inflammation EICOSANOIDS PROSTAGLANDIN ​ Involved in many regulatory function in the body THROMBOXANE ​ Promote formation of blood clots by promoting platelet aggregation LEUKOTRIENE ​ Found in leukocytes and associated with various inflammatory and allergic response  14 BIOLOGICAL WAXES ​ These are 20 amino acids presents are ​ Water insoluble, water repellents lipids called standard amino acids protective coating and lubricating functions PROTEINS ​ Also called polypeptide since it is a chain of amino acids linked by peptide bonds ​ Naturally occurring, unbranched polymer in which the monomer units are amino acids ​ Peptide in which at least 40 amino acids residues are present ​ Hydrogen, oxygen, nitrogen ​ Sometimes contain sulfur and phosphorus FUNCTIONS: Structural components ​ Skin ​ Hair ​ Muscles Chemical messenger ​ Hormones Disease defense ​ Antibodies Enzymes ​ catalase ​ Lactase AMINO ACIDS ​ Building blocks of proteins ​ There are 700 different naturally occurring amino acids but only one normally present in proteins  15 4 CLASSIFICATION OF AMINO ACIDS ​ Based on chain property ​ Based on number of peptide chain ​ Based on chemical composition ​ Based on shape CHIRALITY OF AMINO ACIDS ​ Refer to having mirror image ​ Amino acids have mirror image: right and left based on the location of the amino group ​ Nature prefers the L- isomers of amino acids ​ All 20 standards amino acids have chiral centers except glycine ACIDS BASED PROPERTIES OF AMINO ACIDS ​ Both acidic and basic are present in an a-amino acid  16 ​ If amino acid is in crystal form, it is not soluble with water due to strong intermolecular forces HOW TO NAME PEPTIDES  17 CLASSIFICATION OF PROTEIN BASED ON NUMBER OF PEPTIDE CHAIN MONOMERIC PROTEIN ​ only one peptide chain is present MULTIMERIC PROTEIN ​ more than one peptide chain is present BASED ON CHEMICAL COMPOSITION SIMPLE PROTEIN ​ only amino acids residues are presents CONJUGATED PROTEIN ​ one or more non amino acids entities in its structure in addition one or more peptide chain ​ A complex consisting of amino acids combined with other substances ​ Simple protein + prosthetic group = conjugated protein  18 ALPHA HELIX PROTEIN HYDROLYSIS ​ a telephone chord shape of the alpha ​ Splits peptide bonds to smaller peptides helix is held placed by hydrogen bonds and amino acids between every N-H group and the ​ Occurs in the digestion of proteins oxygen of a C=O group in the next turn ​ Occurs in cells when amino acids are of helix for amino acid down the chain needed to synthesize new proteins and ​ alpha helix is about 11 amino acids long repair tissues ​ In the lab, hydrolysis of a peptide BETA PLEATED SHEETS requires acid or base, water, and heat ​ The pleated sheet structure of the beta ​ In the body, enzymes catalyze the sheet is held together by the hydrogen hydrolysis of proteins bonds between the amide groups of linear polypeptide change ​ The average number of amino acid residues in a typical beta sheet is six with an average of six strand bonding together CLASSIFICATION OF PROTEINS BASED ON SHAPES FIBROUS ​ have an elongated shape with one dimension much longer than the others GLOBULAR ​ Have peptide chains folded into special and globular shapes  19 2.​ Amino acids are the building blocks of protein and are linked via peptide or amide bond 3.​ An amino acids is made up of an amino group, carboxyl group, sidechain H+ 4.​ There are 700 different naturally occurring amino acids but only 20 are normally present in proteins 5.​ There are 9 essential amino acids 6.​ There are 4 possible structures of amino acids 1.Primary 2.Secondary 3. Tertiary 4.Quaternary 7.​ Amino acids are classified based on: a. Based on side chain polarity b. Based on number of peptide chain c. Based on chemical composition d. Based on shape 8.​ When amino acids are condensed to form dipeptide, oligopeptides or polypeptides, their name change is governed by IUPAC standards 9.​ Proteins can be broken down back into amino acids through hydrolysis 10.​ Proteins can have their H+ bonds removed through denaturation SUMMARY 1.​ Proteins have multiple functions in our ENZYMES body ​ Enzyme are catalysts ​ Catalyst are substance that speed up chemical reactions  20 ​ Hence, enzyme are proteins that catalyze or speed up the rate of chemical reactions ​ Enzyme lower the activation energy of the chemical reaction to speed it up ​ After speeding up the chemical reaction, enzymes are unchanged, amd can be reused GLUCOSE AND FRUCTOSE ​ This highlights the function of enzymes WHAT IS ACTIVATION? in catalyzing reactions to break down ​ Is the amount of energy needed to start or build bonds. a reaction ​ Glucose and Fructose can condense to ​ The Chemical reactions they speed are form Sucrose, and Sucrose can be either Anabolic or Catabolic broken down into Glucose and Fructose ​ Anabolic- building large molecules into small ones HOW ENZYME WORKS? ​ Catabolic- breaking down large ​ Enzyme bind to their substrate, causing molecules into small ones a chemical reaction to be catalyzed ​ We call this substances that are built up or broken down as Substrate PARTS OF ENZYME ACTIVE SITE ​ Specific place in the enzyme where substrate bind to ​ Has a specific size, shape, and chemical ​ Enzyme are also highly specific in the behavior rendered by the specific chemical reactions they speed up arrangement of its amino acids ​ There are enzymes for every specific ​ Every type of enzyme has a unique chemical reaction active site, which is why enzymes are specific to particular substrate only AMYLASE ​ Breakdown carbohydrates starch (polysaccharides) into EXAMPLE OF ENZYMES monosaccharides PROTEASE break down protein into amino ​ Starch is polysaccharide made acids up of monosaccharides linked CARBOHYDRASE breakdown carbohydrates together by glycosidic bond into monosaccharides  21 LIPASE breakdown lipids into fatty acids and glycerol CATALASE breakdown hydrogen peroxide into carbon dioxide and water WHAT ARE SUBSTRATES? ​ Molecules that bind to enzymes ​ These substrate are either broken down or built up  22 ENZYME USED IN MEDICINE VITAMINS ​ Discover at the beginning of 20th century ​ DEFINITION: an essential, non caloric, organic nutrient needed in tiny amounts in the diet ​ The role of vitamins is to help make possible the process by which other nutrients are digested, absorbed, and metabolized or built into body structures ​ The only disease vitamins can cure is the one caused by a deficiency of that vitamin DEFINITION AND CLASSIFICATION OF VITAMINS ​ Vitamins fall into 2 classes, fat soluble and water soluble ​ Some vitamins exist as precursor or provitamins  23 2.​ Regulating cell differentiation 3.​ Maintenance of the health of epithelial tissues 4.​ Reproduction and growth THE FAT SOLUBLE VITAMINS A, D, E, K ​ Found in fats and oils of foods ​ Require bile for absorption ​ Store in liver and fatty tissues until needed ​ Not needed in the diet daily ​ Can reach toxic levels if too much is consumed ​ Deficiencies can occur when people eat diets that are extraordinarily low in fat VITAMIN A VITAMIN D ​ Normal dietary intakes provides a ​ Can be self synthesized with the help of person with both performed and sunlight precursor forms of vitamin A ​ Whether made with the help of sunlight ​ beta -carotene- plant -derived precursor or obtained from food, vitamin D ​ Retinol- active stored in the liver undergoes chemical transformation in ​ Converted by cells into its other two the liver and kidneys to activate it active forms, retinal and retinol acid, as 2 MOST IMPORTANT MEMBER OF needed VITAMIN D 4 MAJOR FUNCTION IN THE BODY OF VITAMIN A 1.​ Vision  24 1.​ VITAMIN D3 (cholecalciferol)- produced in the skin by the action of sunlight (UV light) 2.​ VITAMIN D2 (ergocalciferol)- produced by plants through the action of light PRINCIPAL FUNCTION: ​ Maintain normal blood levels of calcium ion and phosphate ion so the bones can absorbed these ions VITAMIN E VITAMIN K ​ Also known as tocopherol ​ To help synthesize proteins that help ​ Anti oxidants blood clot. ​ Oxidative damage occurs when ​ Also necessary for the synthesis of highly unstable molecules also key bone proteins know as free radicals, formed normally during cell metabolism, runamok and disrupt cellular structures 4 FORMS OF VITAMIN E 1.​ alpha -tocopherol 2.​ Beta - tocopherol 3.​ Delta -tocopherol 4.​ Gamma -tocopherol  25 VITAMIN C ​ Simplest structure of the 13 vitamins, exist in two active forms in the human body 1.​ Ascorbic acid- reduced form 2.​ Dehydroascorbic acid- oxidized form B VITAMINS ​ Thiamin, riboflavin, niacin, pantothenic acid,and biotin- participate in the release of energy from the energy nutrients ​ folate e and vitamin B12 help cells multiply vitamin B6 helps the body use amino acids to synthesize proteins THIAMINE ​ Plays a critical role in the energy metabolism of all cells ​ Occupies a site on nerve cell membranes ​ Nerve process and their responding muscles depend heavily on thiamin  26 measure that takes available tryptophan into account RIBOFLAVIN ​ Plays a role in energy metabolism FOLATE ​ When thiamine is deficient, riboflavin ​ Helps synthesized DNA and so is usually is also deficient important for making new cells ​ Deficiency of folate causes anemia, diminished immunity, and abnormal digestive function. ​ Deficiencies are related to increased risk of cervical cancer (in women infected with HPV), breast cancer (in women who drink alcohol) and pancreatic cancer (in men who smoke) NIACIN ​ Participate in energy metabolism of every cell ​ Deficiency disease is pellagra, which appeared in europe in the 1700s when corn from the new world became staple food ​ In the early 1900s in the U.S., pellagra was affecting hundreds of thousands in the South and Midwest ​ The key nutrient that prevents pellagra VITAMIN B12 ​ is niacin Vitamin B12 and folate are closely ​ Or, consuming adequate tryptophan related: each depends on the other for which can be converted to niacin in the activation. body Main roles: helps maintain nerves and is ​ The amount of niacin in a diet is stated a part of coenzymes needed in new in terms of niacin equivalents (NE), a blood cell synthesis.  27 ○​ ○​ BIOTIN AND PANTOTHENIC ACID ​ Also important in energy metabolism ​ Both vitamins are readily available in foods NON B VITAMINS ​ Many substances that people claim are ○​ B vitamins are not ​ Choline- important in fetal development common in foods ​ Carnitine, inositol, and lipoic acid- vitamins because they are non essential common in foods ○​ ○​  28 NUCLEIC ACID ​ Molecules that store information for cellular growth and reproduction ​ Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) ​ Large molecules consisting of long chains of monomers called nucleotides ​ The nucleic acids DNA and RNA consist of monomer called nucleotides that consist of ○​ Pentose sugar ○​ nitrogen - containing base ○​ Phosphate ​ The nitrogen bases in DNA and RNA are ○​ Pyrimidines C, T, and U ○​ Purines A and G  29 PRIMARY STRUCTURE OF NUCLEIC ACIDS ​ Nucleotides Joined by phosphodiester bonds ​ The 3 -OH group of sugar in one nucleotide forms an ester bond to the phosphate group on the 5 carbon of the sugar of the next nucleotide  30 ​ Held in place by two hydrogen bonds that form between the base pairs A-T ​ Held in place by three hydrogen bonds that form between the base pairs G-C DNA DOUBLE HELIX ​ Structure of DNA ​ Has two strands of nucleotides that wind together  31 PROTEIN SYNTHESIS involves ​ TRANSCRIPTION mRNA is formed a gene on a DNA strand ​ TRANSLATION tRNA molecules bring amino acids to mRNA to build protein tRNA ​ Each tRNA has a triplet called an anticodon that complements a codon on mRNA  32 GENETIC CODE ​ is a sequence of amino acids in a mRNA that determine the amino acid order for the protein. ​ consists of sets of three bases (triplet) along the mRNA called codons. ​ has a different codon for all 20 amino acids needed to build a protein. ​ contains certain codons that signal the "start" and "end" of a polypeptide INITIATION OF PROTEIN SYNTHESIS chain. ​ For the initiation of protein synthesis ​ a mRNA attaches to a ribosome. ​ 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 TRANSLOCATION ​ During translocation ​ The first tRNA detaches from the ribosome. ​ The ribosome shifts to the adjacent codon on the mRNA. ​ a new tRNA/amino acid attaches to the open binding site  33 ​ a peptide bond forms and that tRNA detaches. ​ The ribosome shifts down the mRNA to read the next codon TERMINATION ​ all the ribosome reaches a "stop" codon: UGA, UAA, or UAG. ​ there is no tRNA with an anticodon for the "stop" codons. ​ the polypeptide detaches from the ribosome. MUTATIONS ​ alter the nucleotide sequence in DNA. ​ result from mutagens such as radiation and chemicals. ​ produce one or more incorrect codons in mRNA. ​ produce a protein containing one or more incorrect amino acids. ​ produce defective proteins and enzymes. ​ cause genetic diseases  34 REVERSE TRANSCRIPTION ​ a retrovirus, which contains viral RNA, but no viral DNA, enters a cell. ​ The viral RNA uses reverse transcriptase to produce a viral DNA strand. ​ The viral DNA strand forms a complementary DNA strand. ​ The new DNA uses the nucleotides and enzymes in the host cell to synthesize new virus particles