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Molecules Chapter 2 Introduction to Biochemistry and Review Covalent Bonds - SPONCH Non polar – Equal sharing of the electrons Polar – Unequal sharing of the electrons Water and Hydrogen Hydrogen Bonds Water Water contains polar covalent bonds Oxygen and hydrogen do not share electrons equally Oxygen exerts a greater pull on the electrons and gains a negative charge Hydrogen as a result has a positive charge Dipole As a result – the water molecule has a positive end the Hydrogens The oxygen is slightly negative This forms a dipole – a polar covalent molecule Hydrogen bonds One of the most significant consequences of the polar covalent bond is the production of inter molecular bonds with other water molecules Water as the universal solvent Water is able to dissolve small non polar covalent molecules, ionic compounds, and other polar covalent molecules Water soluble molecules are described as hydrophilic Those molecules that are not soluble in water are hydrophobic Properties Adhesion- water molecules stick to unlike surfaces such as glass or plastic( -) Meniscus Cohesion – water molecules stick to each other – “ sticky Mickeys” – drop of water Water exists in three states on Planet earth ( Liquid – aquatic environment outside us and inside us) More Specific heat – Water does not change temperature as rapdily as air- high specific heat Density of water = 1g/ml Surface tension – Solutions – universal solventDissolves – salts( ionic bonds), sugar( non polar covalent), and polar covalent( unequal sharing) Molecules in water polar Yea or Nay Hydrophilic – water loving Hydrophobic – water hating or fearing Polar molecule? Water and hydrogen ions http://www.biology.arizona.edu /biochemistry/problem_sets/p h/ph.html Acid and Base Acids are hydrogen donors or proton donors COOH COO- + H+ Bases are hydrogen acceptors or proton acceptors NH2 NH3+ Acids and Bases pH pH = The concentration of H+ ions The negative logarithm of the hydrogen ion concentration in an aqueous solution. pH = - log[ H30+] pH and measurementpHydrion paper pH measurement – pH meter Carboxylic acids ( Organic acids) The acidic functional group in organic acids is the carboxl group The carboxyl group is a proton donor COOH COO- in water solution Buffering capacity Organic bases Proton acceptors – gain a hydrogen and become positively charged in water solution The amino group - NH2 becomes NH3+ Amino acids Contain both an amino group and a carboxyl group They are amphoteric “zwitterions” Amino acids Amino Acid Structure Alanine Amino acids http://www.johnkyrk.com/amin oacid.html Formulas Structural formulas show the atoms and the arrangement of the atoms in the compound Molecular formulas tell the number of each type of atom in the compound, C6H12O6 Structural formula and condensed Complete Structural Formula H H H | | | H-C-C-C-H | | | H H-C-H H | H Condensed Structural Formula CH3CHCH3CH3 or CH(CH3)3 Isomers These molecules have the same structural formula but a different arrangement of the atoms Macromolecules Proteins Lipids Carbohydrates Nucleic acids p a c e G r o u p 2 1 2 1 2 1 Protein Facts Proteins: Polymers of Amino Acids Proteins are polymers of amino acids. They are molecules with diverse structures and functions. Each different type of protein has a characteristic amino acid composition and order. Proteins range in size from a few amino acids to thousands of them. Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids. Proteins are polymers Proteins are polymers of amino acids. They are molecules with diverse structures and functions. Polymers are made up of units called monomers The monomers in proteins are the 20 amino acids Proteins: Polymers of Amino Acids Each different type of protein has a characteristic amino acid composition and order. Proteins range in size from a few amino acids to thousands of them. Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids. Polar side chains Non Polar Hydrophobic side chains Electrical charged hydrophilic Functions of proteins Hormones – Growth hormone Receptors – to Receive information so that cell can communicate with other cells Neurotransmitters – messenger molecules – to send information between neurons Cytoskeleton – actin, myosin, and collagen – the structure of connective tissue and muscles Antibodies – Immunoglobulins to fight disease Function of Proteins continued Enzymes – Biological catalysts Transport of small molecules – Albumin and haptoglobin Transport of oxygen – hemoglobin and myoglobin Membrane proteins – to assist in support Channels in membranes – to allow the passage of molecules or ions Electron carriers in electron transport in the production of ATP Functions( continued)i Clotting proteins Immune proteins to fight infectious agents Histones – DNA binding proteins Toxins to repel or kill other organisms Bacteriocins – molecules produced by bacteria against bacteria Biochemical Reactions Polymerization reactioncondensation and dehydration synthesis – involves the loss of water between two amino acids and the formation of a peptide bond ( OH is lost from the carboxyl group and H is lost from the hydroxyl) requires energy Hydrolysis – the addition of water causes the peptide bond Polymerization Hydrolysis Four levels of Protein Structure There are four levels of protein structure: primary, secondary, tertiary, and quaternary. The precise sequence of amino acids is called its primary structure. The peptide backbone consists of repeating units of atoms: N—C—C— N—C—C. Enormous numbers of different proteins are possible. The causes of Tertiary structure Carbohydrates Diverse group of compounds based on the general formula CH2O Range in moleclular mass from less than 100 to hundreds of thousands of daltons Energy Energy storage Structural Monosaccharides ( Hexoses) CH2O – Molecular formula C6H12O6 Simple sugars ( hexoses) Glucose – blood sugar Galactose Fructose – fruit sugar Hexoses D isomers Optical isomers Isomers These monosaccharides have the same molecular formula but a different arrangement of C, H , and O Glyceraldehyde – the simplest sugar Monosaccharides( Pentoses) Ribose Deoxyribose Disaccharides Glucose Lactose When + Galactose two monosaccharides are combined they form a disaccharide. The bond that connects the two sugars is an alpha glycosidic linkage Disaccharides Dehydration synthesis to form disaccharides Glucose + Glucose Maltose alpha beta This forms an alpha glycosidic linkage Beta glycosidic linkages Glucose + Glucose Cellobiose beta beta This combination forms a beta glycosidic linkage. Polysaccharides Macromolecules Amylose – giant molecule formed by thousands of glucose molecules connected by an alpha glycosidic linkage Amylose Plant starch Stores energy Found in tubers, grains, seeds Hydrolysis releases sugar molecules for glycolysis Glycogen Animal starch Found in muscle and liver in the human body Glycogen hydrolysis produces glucose for the blood stream Glycogen has energy storage for musclesprovides sugars for mitochondria Cellulose Formed by glucose molecules Forms the cell walls of plants Connected by beta glycosidic linkages Bond cannot be broken down or degraded Energy stored in bonds – not released during digestion Derivative sugars These are derivative carbohydrates Carbon 6 in glucose may be oxidized from CH2OH to a carboxyl group producing glucuronic acid Glucose + O2 Glucuronic acid Phosphorylated sugars Phosphate group attached to glucose Glycolytic pathway intermediate Release of energy Amino group added to basic glucose molecule Basic molecules for chondroitin sulfate and hyaluronic acid the foundation of connective tissue Chitin Chitin forms the basis of the insect exoskeleton Hard outer covering – prevents dehydration and holds the water inside and protects the organism Lipids Chemically diverse group of molecules Non polar molecules Hydrophobic Not really macromolecules because they are not polymers constructed from monomers Lipids have diverse cellular roles Energy production Energy storage Hormones Carotenoids help to capture light energy Structural – forming cell membranes Phospholipids Form the basis of cell membranes Formed from phosphate groups that are hydrophilic joined to Two long chain non polar fatty acid chains Fatty acids( fats and oils) Saturated and unsaturated Saturated fatty acids have all single bonds and have a maximized number of hydrogens attached to the carbons Unsaturated fatty acids have a double bond Molecular structure Saturated fatty acids are linear [inflexible] Unsaturated fatty acids have a kink [flexible] Cis and Trans Fatty Acids When plants and animals build fatty acids they make the cis forms Food manufacturers found that foods like chips with the trans form have a longer “shelf Cis fatty acids Natural However they turn rancid and spoil The cis form is used by the body. When the trans form is eaten in foods the body tries to use it for the same functions Cis are flexible and trans are not flexible which causes them adhere to surfaces Polyunsaturated These molecules have more than one double bond Kinks - prevent stacking – lend flexibility Triglycerides Glycerol + 3 fatty acid chains = a triglyceride Triglycerides are fat storage molecules Provide slow release of energy Steroids Family of organic molecules Made of multiple rings Important constituent of membranes They are hormones – signaling molecules and messenger molecules Cholesterol Synthesized in the liver Basis for the formation of sex hormones Used in cell membranes Cause a problem when it is deposited in the lining of blood vessels May lead to arteriosclerosis and heart attacks Nucleic Acids Informational molecules Information storage Transmission of information Linear polymers Catalytic properties( RNA) Gene Expression Regulation(RNA) Structural( Ribosomes) DNA Deoxyribonucleic Giant acid polymer Basis of heredity Purines( Adenine and guanine) Pyrimidines( Cytosine and Thymine) Sugar – Deoxyribose Phosphate group Nucleotides Bases Bases form hydrogen bonds in the middle of the helix DNA The backbone of DNA is made from sugar and phosphates The sugar and phosphates are connected by phosphodiester bond or linkage One end has an end with an OH-this is called the 3’ end The other end has a PO4- this is called the 5’end DNA The molecule is made of two strands They are antiparallel 3’------------------5’ 5’------------------3’ The molecule is linear with purine and pyrimidines in a sequence The purines are bonded to the pyrimidines with hydrogen RNAs RNAs are made complementary to DNA Single stranded molecules Vary in function Transfer RNA Ribosomal RNA Nc RNAs( noncoding RNAs) Transcriptional regulators Translational regulators RNAi Anti sense