Basic Aspects of Carb, Lipid, Protein and Enzyme PDF

Basic Aspects of Carbohydrates, Lipids, Proteins and Enzymes Dr Bijay Barik Assistant Professor Dept of Biochemistry, Cell Biology and Genetics Office: QC 22  MCB1: Understand the basic structures and functions of the molec...

Basic Aspects of Carbohydrates, Lipids, Proteins and Enzymes Dr Bijay Barik Assistant Professor Dept of Biochemistry, Cell Biology and Genetics Office: QC 22  MCB1: Understand the basic structures and functions of the molecules of life— carbohydrates, lipids, amino acids, proteins, and enzymes By the end of this module, students should be able to: MCB1.1. Recognize carbohydrates based on their basic structure and function. MCB1.2. Recognize lipids based on their composition, function, and location. MCB1.3.Differentiate the 20 standard amino acids based on their side chains and nutritional requirements. MCB1.4. Define denaturation with respect to the bonds needed to stabilize the native structure of a protein. MCB1.5. Recognize the reactions catalyzed by select enzymes: kinase, phosphorylase, phosphatase, glycosylase, hydroxylase, and protease.  Introduction Our body is made up of macromolecules. In our diet we eat all the macromolecules. The complex macromolecules are digested and absorbed in the intestine. Examples of these macromolecules: Carbohydrates, Lipids, and proteins  MCB1: Understand the basic structures and functions of the molecules of life— carbohydrates, lipids, amino acids, proteins, and enzymes By the end of this module, students should be able to: MCB1.1. Recognize carbohydrates based on their basic structure and function. MCB1.2. Recognize lipids based on their composition, function, and location. MCB1.3.Differentiate the 20 standard amino acids based on their side chains and nutritional requirements. MCB1.4. Define denaturation with respect to the bonds needed to stabilize the native structure of a protein. MCB1.5. Recognize the reactions catalyzed by select enzymes: kinase, phosphorylase, phosphatase, glycosylase, hydroxylase, and protease. Functions of Carbohydrates Major source of energy for organisms. Serve as cell membrane component and mediate intercellular communication. Structural component of many organism. Components of nucleic acid, glycoproteins and glycolipids. Definition: Carbohydrates are polyhydroxy aldehydes or polyhydroxy ketones or compounds that can be hydrolyzed to give them. Most abundant organic molecule. Monosaccharides, disaccharides and polysaccharides are the different types No need to memorize the structures Monosaccharide Number of Carbon Functional group Function Glucose 6 (Hexose) Aldehyde Energy source (ATP production), glycosylation reactions in collagen, role in gene regulation in prokaryotes (Lactose Operon) Fructose 6 (Hexose) Ketone Energy source (converted to glucose) Galactose 6 (Hexose) Aldehyde Component of lactose (present in milk) Glycosylation of collagen molecule Mannose 6 (Hexose) Aldehyde - Mannose 6-phosphate tag has a role in protein trafficking* - Glycosylation of proteins Ribose and 5 (Pentose) Aldehyde Part of RNA and DNA synthesis, also part of high energy Deoxyribose compound ATP * In cell biology class on protein trafficking  Pentose sugar No need to memorize the structures  Disaccharides Two monosaccharides joined by a glycosidic bond. Example: Lactose, sucrose and maltose Maltose containing chocolate (Milk contains lactose) (Sucrose is the table sugar)  Polysaccharides More than ten monosaccharides joined by glycosidic bonds. Example: Glycogen and starch  MCB1: Understand the basic structures and functions of the molecules of life— carbohydrates, lipids, amino acids, proteins, and enzymes By the end of this module, students should be able to: MCB1.1. Recognize carbohydrates based on their basic structure and function. MCB1.2. Recognize lipids based on their composition, function, and location. MCB1.3.Differentiate the 20 standard amino acids based on their side chains and nutritional requirements. MCB1.4. Define denaturation with respect to the bonds needed to stabilize the native structure of a protein. MCB1.5. Recognize the reactions catalyzed by select enzymes: kinase, phosphorylase, phosphatase, glycosylase, hydroxylase, and protease.  Lipids Heterogenous group of organic molecules which are insoluble in water and soluble in non-polar solvents. Some have both hydrophobic and hydrophilic groups (amphipathic nature) in the structure. The dietary and stored lipids provide energy. Different Lipids Composition Location Functions Cholesterol Cholesterol Cell membrane - Hydrophobic in nature, helps to synthesize steroid hormone, vitamin D Steroid hormones Steroid hormone Various tissues - Hydrophobic in nature, helps in (Synthesized from growth, energy metabolism, cholesterol) reproduction etc. TAG (Triacylglycerol) Glycerol + three fatty Adipose tissue - Hydrophobic, energy source acids Phospholipids: Examples- [Glycerol + two fatty Cell membrane - PI helps in signal transduction a. Phosphatidylinositol acids +Phosphate+ (PI) Inositol= PI] - PS helps in blood clotting [Glycerol + two fatty b. Phosphatidylserine acids +Phosphate+ (PS) Serine= PS]  MCB1: Understand the basic structures and functions of the molecules of life— carbohydrates, lipids, amino acids, proteins, and enzymes By the end of this module, students should be able to: MCB1.1. Recognize carbohydrates based on their basic structure and function. MCB1.2. Recognize lipids based on their composition, function, and location. MCB1.3.Differentiate the 20 standard amino acids based on their side chains and nutritional requirements. MCB1.4. Define denaturation with respect to the bonds needed to stabilize the native structure of a protein. MCB1.5. Recognize the reactions catalyzed by select enzymes: kinase, phosphorylase, phosphatase, glycosylase, hydroxylase, and protease.  AMINO ACIDS These compounds have an amino (-NH2-) group, a carboxylic acid (-COOH-) group, and a distinctive side chain or R group. 2 functional groups of amino acid: - Amino group → basic - Carboxyl group→ acidic Amino acids represent building blocks for proteins Amino acids are the monomeric units of proteins joined by peptide bonds.  Only 20 amino acids are commonly found as constituents of mammalian proteins: standard amino acids These 20 standard amino acids are the only amino acids encoded by DNA Names of 20 amino acids are: - Glycine (Gly/G), Alanine (Ala/A), Proline (Pro/P), Valine (Val/V), Leucine (Leu/L), Isoleucine (Ile/I), Serine (Ser/S), Threonine (Thr/T), Tyrosine (Tyr/Y), Methionine (Met/M), Cysteine (Cys/C), Aspartate (Asp/D), Glutamate (Glu/E), Asparagine (Asn/N), Glutamine (Gln/Q), Lysine (Lys/K), Arginine (Arg/R), Histidine (His/H), Phenylalanine (Phe/F), and Tryptophan (Trp/W) Different types of amino acids Examples Hydroxyl group (-OH) Tyrosine, Serine and Threonine containing Amino acids Sulfur-containing amino Methionine (S) and Cysteine (-SH) acids Amide group containing Asparagine and Glutamine amino acids Positively charged amino Lysine, Arginine, Histidine acids (Basic amino acids) Different types of amino acids Examples Negatively charged amino Aspartic acid, Glutamic acid acids (Acidic amino acids) Polar (hydrophilic) amino Serine, Threonine, Tyrosine, Cysteine, Asparagine, Glutamine, acids Aspartic acid, Glutamic acid, Lysine, Arginine, Histidine Non-Polar (hydrophobic) Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, amino acids Tryptophan, Methionine and Proline Aromatic amino acids Histidine, Phenylalanine, Tyrosine and Tryptophan  Post translational modification of proteins Phosphorylation (addition of phosphate group) of protein occurs on the hydroxyl group- containing amino acids. O-linked-Glycosylation (addition of carbohydrate moiety) of protein can occur on the hydroxyl group-containing amino acids. N-linked-Glycosylation (addition of carbohydrate moiety) of protein can also occur on the amide group-containing amino acids. Proteins like histones with positively charged amino acids (Lysine and arginine- Basic amino acids) can bind with the negatively charged DNA molecule.  Amino acids based on nutritional requirement A. Essential amino acids: Our body does not synthesize these amino acids so these should be taken in the diet. Examples: Val, Leu, Ile, Lys, Met, Phe, Thr, Trp B. Semi-essential amino acids: These are non-essential in adults, but in children they are essential Example: Arg, His C. Non-essential amino acids: Our body synthesizes these amino acids. So these need not be taken in our diet. Examples: ????  MCB1: Understand the basic structures and functions of the molecules of life— carbohydrates, lipids, amino acids, proteins, and enzymes By the end of this module, students should be able to: MCB1.1. Recognize carbohydrates based on their basic structure and function. MCB1.2. Recognize lipids based on their composition, function, and location. MCB1.3.Differentiate the 20 standard amino acids based on their side chains and nutritional requirements. MCB1.4. Define denaturation with respect to the bonds needed to stabilize the native structure of a protein. MCB1.5. Recognize the reactions catalyzed by select enzymes: kinase, phosphorylase, phosphatase, glycosylase, hydroxylase, and protease.  Proteins A protein molecule (polypeptide chain) has many amino acids joined by peptide bonds. Peptide bond (Covalent bond) stabilizes the primary structure, which is the linear structure. Then the three-dimensional structure of the protein is attained by the proper folding. The following bonds stabilize the secondary, tertiary, and quaternary structures of proteins and help in the proper three-dimensional folding: - Disulfide bond - Hydrogen bond - Hydrophobic interaction - Ionic interaction  Protein Denaturation Definition: Denaturation results in the unfolding and disorganization of a protein’s secondary, tertiary, and quaternary structures without the hydrolysis of peptide bonds. That means after protein denaturation only the primary structure of the protein is maintained. Ex: Heat denatures protein. Protein degradation When the protein is degraded the primary structure is also broken down i.e the peptide bonds are broken.  MCB1: Understand the basic structures and functions of the molecules of life— carbohydrates, lipids, amino acids, proteins, and enzymes By the end of this module, students should be able to: MCB1.1. Recognize carbohydrates based on their basic structure and function. MCB1.2. Recognize lipids based on their composition, function, and location. MCB1.3.Differentiate the 20 standard amino acids based on their side chains and nutritional requirements. MCB1.4. Define denaturation with respect to the bonds needed to stabilize the native structure of a protein. MCB1.5. Recognize the reactions catalyzed by select enzymes: kinase, phosphorylase, phosphatase, glycosylase, hydroxylase, and protease.  Enzymes ▪ Enzymes are biological catalysts that increase the rate of reactions without being changed in the overall process. ▪ So the enzymes help to speed up chemical reactions (catalyst) involved in metabolic pathways, digestion of food, DNA replication, transcription, translation etc. Most enzymes are proteins, synthesized under the direction of genes.  Naming of enzymes: - Most of the enzyme names are with a suffix –ase Which of these two is an enzyme? - Glucose 6-phosphate - Glucose 6-phosphatase - From the name of the enzymes one can guess the reaction it catalyzes. - Example: - Hydroxylase (Adds hydroxyl group) - Kinase (Adds phosphate group) - Phosphatase (Removes phosphate group from a compound) - Phosphorylase (Transfers of phosphate group between compounds) - DNA glycosylase (Breaks the glycosidic bond) - Glycosidase (Breaks the glycosidic bond) - Protease (Proteolytic enzyme- breaks down peptide bond)  Summary - Carbohydrates based on their basic structure and function. (Monosaccharides, disaccharides, polysaccharides, glycosidic bond) - Lipids based on their composition, function, and location. (Cholesterol, TAG, Phospholipids etc.) - Amino acids based on their side chains and nutritional requirements. (Proteins, amino acid types, peptide bonds ) - Protein folding (3D), denaturation and degradation (Different bonds, different structural organization) - Reactions catalyzed by select enzymes: kinase, phosphorylase, phosphatase, glycosylase, hydroxylase, and protease.  References Lippincott Illustrated reviews of Biochemistry, 8th Edition  Thank you Please mail your questions to [email protected]