Biochemistry of Cells PDF

Biochemistry of Cells Dr. Hamada Biochemistry is the study of chemical processes within and relating to living organisms Living organisms are made up of cells So the biochemistry of cells means: the study of all sorts of processes that occur within a biological cell...

Biochemistry of Cells Dr. Hamada Biochemistry is the study of chemical processes within and relating to living organisms Living organisms are made up of cells So the biochemistry of cells means: the study of all sorts of processes that occur within a biological cell and also interactions between different cells. Cells are composed of : Water Inorganic ions Organic molecules (carbon-based 1. Water  Water is the most abundant molecule in cells, accounting for 70% or more of total cell mass. Depends on cell type  Water is called the universal solvent (‫)مذيب عام‬ As a result of the interactions between water and the other constituents of cells  Water is used in most reactions in the body 2. Inorganic ions  The inorganic ions of the cell, constitute 1% or less of the cell mass. Including: sodium (Na+) potassium (K+) magnesium (Mg2+) calcium (Ca2+) phosphate (HPO42-) chloride (Cl-) bicarbonate (HCO3-)  These ions are involved in a number of aspects of cell metabolism, and Inorganic ions role in kidney functi thus play critical roles in cell function.. Organic molecules The rest of the cell consists mostly of organic molecules (carbon-based molecules) The study of carbon compounds is known as organic chemistry Why carbon has this importance ? Carbon is a versatile atom Carbon has four electrons in an outer shell that holds  In eight the normal case, the second 1 2 orbital has a capacity of 8 electrons. In carbon only there are 4 electrons in the second orbit. The result of that 3 4 Carbon can share its electrons with other atoms to form up to four covalent bonds.  Carbon is able to form covalent bonds as follows:  Single bond  Double bond  Triple bond he simplest carbon compounds, contain only carbon & hydrogen atoms Hydrocarbons  Four main types of carbon-based molecules are found in living things: Carbohydrates Lipids Proteins Nucleic Acids These compounds are also called macromolecules (Large molecules ‫)الجزيئات الكبيرة‬ The macromolecules constitute 80 to 90% of the dry weight of most lso, some macromolecules are called polymers Polymers are built from smaller molecules called monomers For example,  Carbohydrates include: Monosacchari Disaccharides Polysaccharid des ( ‫سكر احادي‬ ( ‫) سكر ثنائي‬ es ) ( ‫) سكر معقد‬ 1. Monosaccharides ( ‫) سكر احادي‬ Called simple sugars It consists of one molecule (Monomar) of sugar The basic formula for these molecules is (CH2O)n clude glucose, fructose, & galactose  Glucose is found in sports drinks Fructose is found in fruits Honey contains both glucose & fructose Galactose is called “milk sugar”  Glucose, fructose and galactose have the same chemical (C6H12O6), but different structural formulas. This phenomenon is known as Isomer Glucose, fructose and galactose are isomers because they’re structures are different, but their chemical formulas are the same  Monosaccharide properties: 1. In aqueous (watery) solutions, monosaccharides form ring structures 2. The sugar glucose (C6H12O6) is especially important in cells, since it provides the principal source of cellular energy.  2. Disaccharides (‫)سكر ثنائي‬ disaccharide is a double sugar (polymer) Common disaccharides include:  Sucrose (table sugar)  Lactose (Milk Sugar)  Maltose (Grain sugar) They’re made by joining two monosaccharides  Linking Monomers The process which joins two simple sugar to make a double sugar is known as Dehydration During this process, a molecule of water is removed The bond that is produced between the sugar molecules is known as glycosidic bond  Breaking Down Polymers Unlike the dehydration during this process, large molecules (polymers) are broken down into simple molecules, and this process is known as Hydrolysis During this process, a molecule of water is added  Examples of linking monosaccharides to form Disaccharides sugars: nked glucose with fructose to be Sucrose nked glucose with glucose to be Maltose nked glucose with galactose to be Lactose  3. Polysaccharides ( ‫) سكر معقد‬ polysaccharides is a Complex carbohydrates lysaccharides is polymers of monosaccharide chains Composed of many sugar monomers linked together monomer monomer monomer monomer Polymer  Some examples of polysaccharides: 1. Starch Starch is a polysaccharide comprising glucose monomers joined by glycosidic bonds glucose glucose Starch is an example of a polysaccharide in plants Plant cells store starch for energy Potatoes and grains are major sources of starch in the human diet 2. Cellulose Cellulose is a polysaccharide consisting of 3,000 or more glucose units joined by glycosidic bonds Polymer glucos e glucose Humans cannot digest cellulose, but it is important in the diet as a source of fibre. Cellulose is the main substance found in plant cell walls 3. Glycogen Glycoden is similar in structure to starch, a polysaccharide comprising glucose monomers joined by glycosidic bonds glucos glucose e Polym er Glycogen is an example of a polysaccharide in animals Animals store excess sugar in the form of glycogen  B. Lipids Lipids are a substance that is insoluble (Do NOT mix with water) in water and soluble in alcohol hydrophobic Lipids have four major roles in cells; 1. Fats store energy 2. Help to insulate the body 3. Cushion and protect organs 4. Major components of cell membranes Includes: Fats Waxes Steroids Oils. Triglyceride (Fat) Monomer of lipids Composed of Glycerol and 3 fatty acid chains Glycerol forms the “backbone” of the fat Can be broken down for use in energy-yielding reactions. Phospholipids (Fat) Phospholipids is the principal components of cell membranes Consist of fatty acid acids and glycerol Phospholipids is different in structure to triglyceride, It contains phosphate group and only two fatty acid 3. Steroids The carbon skeleton of steroids is bent to form 4 fused rings Cholesterol Cholesterol is the “base steroid” from which your body produces other steroids Estrogen Testosterone Estrogen and testosterone are also steroids  C. Proteins Proteins are polymers made of monomers called amino acids monome r monome r Polymer Proteins are used to build cells, act as hormones and do much of the work in a cell Also, many proteins act as biological catalysts or enzymes Enzymes control the rate of chemical reactions by weakening bonds, thus lowering the amount of activation energy needed for the reaction  Four Types of Proteins: Structural Transport Contractile Storage  All proteins are made of 20 different amino acids linked in different orders  Non polar (10)  Polar (5)  Basic (3); positive charge  Acidic (2); negative charge  Amino acids have a central carbon with 4 things boded to it: Amino group Carboxyl group Hydrogen Side (R) group All amino acids share amino, carboxyl and hydrogen but differ in R group. Leucine Serine Side groups  Linking Amino Acids Cells link amino acids together to make proteins The process is called dehydration synthesis Dehydration Peptide bonds form to hold the amino acids together  When linking amino acids, some concepts have to be distinguished: Oligopeptide is formed of 2-10 amino acids (Monomer);  Dipeptide is formed of 2 amino acids  Tripeptide is formed of 3 amino Polypeptide acids is formed of more than 10 amino acids Polypeptide Dipeptide Oligopeptide Tripeptide Is polypeptide an functional protein  Levels of Protein structure 1. Primary 2. Secondary Protein folding 3. Tertiary 4. Quaternary (subunits) 1. Primary Protein Structure The primary structure is the specific sequence of amino acids in a protein 2. Secondary Protein Structure Secondary protein structures occur when protein chains coil or fold  helix b Sheets 3. Tertiary Protein Structure When protein chains called polypeptides join together, the tertiary structure forms It is also known as the native structure or active conformation 3. Quaternary Protein Structure Results when two or more polypeptide chains form one macromolecule In the watery environment of a cell, proteins become globular in their quaternary structure Hemoglobin  D. Nucleic Acids Two types exist DNA RNA (Deoxyribonucleic acid) (ribonucleic acid)  Store hereditary information  Contain information for making all the body’s proteins In eukaryotic cells, DNA is located in the nucleus. Nucleic acids are polymers of nucleotides The nucleotide consists of three parts: Phosphate group Sugar Base  The Linking of nucleotides (dehydration) The Linking of nucleotides to form nucleic acids DNA and RNA involves the formation of phosphodiester bonds between the 3′ hydroxyl of one nucleotide and the 5′ phosphate of another DNA (Deoxyribonucleic acid) Each DNA nucleotide has one of the following bases: – Adenine (A) – Guanine (G) – Thymine (T) – Cytosine (C) Two strands of DNA join together to form a double helix Double helix  RNA (ribonucleic acid) Each DNA nucleotide has one of the following bases: – Adenine (A) – Guanine (G) – Uracil (U) – Cytosine (C) It has the base uracil (U) instead of thymine  Difference between DNA and RNA 1. In the sugar of nucleotide Thymine (T) Phosphate group Sugar (deoxyribose) DNA RNA Ribose sugar has an extra –OH or hydroxyl group 1. In the base of nucleotide DNA RNA A, G, C and A, G, C and T U 3. In the structure of DNA and RNA DNA RNA Double helix One helix