UNIT 2 BIOLOGICAL CHEMISTRY. ORGANIC MOLECULES: Molecules composed of a carbon skeleton
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1 1 UNIT 2 BIOLOGICAL CHEMISTRY ORGANIC MOLECULES: Molecules composed of a carbon skeleton Monomers: single building units Polymers: (macromolecules) Very large molecules composed of many monomers put together. Artificial polymers: Plastics, nylon, Teflon, orlon, polypropylene, FOUR MAIN GROUPS OF BIOLOGICAL ORGANIC COMPOUNDS 1. Proteins (amino acids) CHONS 2. Lipids (Fats, oils) CHO 3. Carbohydrates ( sugar, starch, enzymes) CHO 4. Nucleic Acids (DNA, RNA) CHONP
2 2 CARBON SKELETONS AND ISOMERS Isomer: Compounds w/ the same molecular formula but different structural formulae 3 isomers of pentane C 5 H 12 ( molecular formula) STRUCTURAL FORMULA FUNCTIONAL GROUPS Clusters of atoms that act in specific ways no matter what the rest of the molecule is like. OH Carboxyl group R-COOH C--C=O Found in amino acids and fatty acids
3 3 Amine group --NH 2 H ---N H Amino Acid bond between carboxyl group and amine group + H 2 O Amino acids are the basic building block of proteins. Other important functional Groups: -OH alcohol Condensation rxn : two molecules are joined one loses H and the other OH. This is how polymers are made
4 4 (HYDROLYSIS) Monomer-H + HO Monomer -- Monomer---monomer + H 2 O (CONDENSATION ) CONDENSATION REACTIONS ARE REVERSIBLE. WHEN THEY BREAK UP IT IS CALLED A HYDROLYSIS RXN.
5 5 I. LIPIDS: ( fats, fatty acids, oils, phospholipids, steroids) Characteristics : - Nonpolar - Don t dissolve much in water Elements: C,H,O Uses: (3 main) 1. Waterproofing 2. Energy storage( contain more than twice as much as carbohydrates 10g of fat vs 20g of sugar 3. Insulation :
6 6 A.Fatty Acids These are the simplest Lipids Def: A simple lipid molecule composed of a long hydrocarbon chain w/ a carboxyl group at one end. a. Saturated Fatty acids: All single bonds. ( holding as many H as they can) b. Unsaturated fatty acid: Double and/or triple bonds between C atoms
7 7 Trans vs. Cis fats Hydrophilic : Water loving Hydrophobic: Water fearing -The Carboxyl end of a fatty acid is polar and therefore Hydrophilic. -The hydrocarbon chain end however is hydrophobic because it is non-polar. These characteristics make fatty acids an integral part of cell membranes.
8 Fatty acids found where? 1. Cell and organelle membranes 2. Glycolipids ( Carbohydrate + lipid) 3. Lipoproteins ( fat + protein) see book diagram 8
9 9 B.FATS AND OILS: Pg 39 Fig 3-5 Function: Store energy (energy reserve) Formed by condensation rxn of 3 fatty acid molecules to the alcohol ( glycerol ) ( triglycerides) Fats: room temperature Oils: room temperature due to more unsaturated fatty acids.
10 10
11 11
12 12 C.Phospholipids Pg 39 Fig 3-6 Similar to fats except that one or more fatty acids are replaced by a phosphate group. Function: pg 39 -structural molecules - chief lipid component of biological membranes - polar nonpolar
13 13 D. STEROIDS: ( HAS A CYCLIC 4 CARBON RING ) Qualify as lipids because insoluble in water -Cholesterol is the most abundant steroid - important component of (animal) cell membranes - involved in vitamin D production -Hormones Chemical messengers between different parts of the body. Produced in ( adrenal and pituitary glands) Ex. Cortisone and produced in adrenal sex hormones in sex organs
14 II. CARBOHYDRATES: Sugars, Starches, and related compounds FUNCTION: 1. Energy + energy storage 2. Some structural : cellulose in plant Glucose cell walls, Chitin insect, crustacean, arachnids Exo-skeletons A. Monosaccharides: (Means one sugar) - These are simple sugars - Glucose, Fructose ( know structure of glucose) - These are monomers of larger carbohydrates Note: two monosaccharides are called a di-saccharide Two sugars Sucrose = 2 glucose molecules B. Polysaccharides: - Polymer of monosaccharides Three important forms of polysaccharides 1. Glycogen : animal 2. Starch : Plants 3. Cellulose: Plant cell walls 14
15 A. Glycogen : - This is the major Animal storage molecule - Liver + muscles remove glucose in the blood and assemble it into glycogen to be later broken back down into glucose for energy. 15 B. Starch: Pg 42 - This is the energy storage molecule in Plants - Starch is made up of 2 kinds of glucose o 1. Amylose o 2. Amylopectin
16 16 Amylose consists of a linear, helical chains of roughly 500 to 20,000 alpha-dglucose monomers linked together through alpha (1-4) glycosidic bonds. Amylopectin molecules are huge, branched polymers of glucose, each containing between one and two million residues. In contract to amylose, amylopectin is branched. It contains numerous amyloselike chains of up to 30 glucose residues linked through alpha (1-4) bonds, connected to one another through alpha (1-6) branch points. C. Cellulose - Most abundant organic material on earth - Made of long straight chains of glucose - Cell walls of plants.
17 17 Chitin : i. Structural polysaccharide in arthropod exoskeletons and fungus cell walls
18 18
19 19 III. NUCLEIC ACIDS - These include the largest biological molecules - Contain CHONP - There are two kinds of nucleic acids - DNA, RNA, ATP, ADP, AMP A. Deoxyribonucleic acid 1. Contains organisms genetic material Information for making proteins How to make other nucleic acids B. Ribonucleic acid 1. Directs the building of proteins Both DNA and RNA are named after the sugar they contain. 1. Ribose: Ribonucleic acid 2. Deoxyribose: Deoxyribonucleic acid
20 20 DNA is double stranded while RNA is single stranded Nucleotide: Monomer of nucleic acids Contains: 1. Sugar ( 5 carbon) phosphate groups (PO 4-3 ) 3. Nitrogenous base
21 BASES FOUND IN DNA 1. Adenine 2. Guanine 3. Cytosine 4. Thymine BASES FOUND IN RNA 1. Adenine 2. Guanine 3. Cytosine 4. Uracil 21
22 22 4.PROTEINS -Proteins make up more than 50% dry weight of animals and bacteria. -(Hair, fingernails are made of fibrous protein: collagen)collagen is the most abundant protein by mass in animals. -Hemoglobin is an oxygen carrying protein - The most numerous class of proteins are the enzymes. ( end in ase) Enzymes: speed up chemical reactions Monomer of Proteins: Amino acid : 20 common amino acids
23 The 20 amino acids encoded by the genetic code are: 23
24 24 Amino acids are attached by Covalent bonds called Peptide bonds : formed during the condensation rxn. Dipeptide : 2 amino acids Polypeptide: Long string amino acids
25 25 Protein: Def: a functional unit composed of one or more polypeptide chains. PROTEIN STRUCTURE Proteins are long unbranched chains of Amino acids There are four levels of protein structure 1.primary structure 2.secondary structure 3.tertiary structure 4. quaternary structure
26 1.Primary Structure: is the sequence of amino acids in the polypeptide chain ( help by peptide bonds) 26
27 27 2.Secondary structure: (hydrogen bonding) Is the localized structure caused by hydrogen bonding across a polypeptide chain. Secondary Structure of a Protein or Polypeptide
28 3.Tertiary Structure of a protein 4 Interactions effects these 1. Ionic bonds 2. Hydrogen bonds 3. Disulfide bonds 4. Hydrophobic interactions Nonpolar sections are pushed together by Water 28
29 29 4.Quaternary structure: defined by the way the polypeptides fit together(fig 3-19 pg 47) When polypeptides lose their shape their function and structure are destroyed and they are said to be Denatured : (caused by heat or chemicals )
30 30 Insulin ENZYMES: All enzymes are proteins 1. Proteins act as biological catalysts.. that is they speed up chem. Rxns. (lower activation energy) - Substrates: The reactants in an enzyme-catalyzed rxn are called substrates - Enzymes are named according to their substrates and the rxns they catalyze. Ex. RNA polymerase, Sucrase, Lipase -Over 2000 known enzymes -Some carry out condensation + hydrolysis rxns
31 31 Enzymes combine w/ very specific substrate in what is known as lock and key fit -Enzyme combines w/ substrate and holds it in the correct angel for the rxn to occur. When rxn over the substrate is released and the enzyme can be reused. ( note: enzymes are reuseable) -The substrate binds a a site called the ACTIVE SITE A small groove formed as the protein folds. It recognizes the substrate by its primary structure of amino acids. -Specific point to point connection. -The active site is not rigid but flexible - The size, shape, and electrical charge of the aminoacids R groups are what help identify and fit the substrate at the site.
32 32 -The active site flexes slightly upon connection known as induced fit model. ( more accepted than lock and key) Co-factors: Inorganic ions that bind to the enzyme to help catalyze the reaction Co-enzymes: Organic molecules (not proteins) -generally are bound at the active site and the enzymatic rxn will not work w/o it. Coenzymes are found in small con. Because they are reusable. (vitamins, nucleotides, NAD) NOTE: coenzymes and cofactors are needed in some active sites for enzymes and substrates to bind. FACTORS EFFECTING ENZYME ACTIVITY: 1. Concentration of substrate present 2. Inhibitors: Decrease an enzymes rxn rate. a. Some bind to active site ( competition) b. Some disrupt enzymes 3 dimens. Structure and destroy its function. 3. Temperature: (denatures the protein if too high)
33 33 Generally temperatures above 60 o enzymes. denature 4. ph: ph acids change the shape of the enzymes 3 dimensional structure because H + ion changes overall charge of the molecule and disrupts ionic and hydrogen bonding interactions. (optimum ph for living systems?) Pg 51 ALLOSTERIC ENZYMES (ALLOSTERIC INTERACTIONS)
34 Allosteric Enzymes: Enzymes that can exist in two or more different shapes -Allosteric enzymes have 1. Active site 2. Regulatory site When molecules bind to the regulatory site, it alters the enzymes shape and therefore its activity. 34
35 35 ALLOSTERIC INHIBITORS: Molecules that when bound to the regulatory site cause a change in the active site so it doesn t function anymore. Stimulatory molecules: when attached to the R.S. correct the shape of the active site and let the rxn occur. Allosteric feedback loop: ( negative feedback loop) Often the beginning enzyme is allosteric and the final substrate product is the inhibitor for the regulatory site on the allosteric enzyme.
36 Enzyme product 1C Product 2C-- Product 3c---- Enzyme 2 Enzyme 3 Allosteric inhibitor Product 4c Product 5C --- Product 6C (glucose) Enzyme 4 Enzyme 5 36 Glucose becomes the allosteric inhibitor for enzyme 1 SIMPLE PROTEINS: on hydrolysis include only amino acids: 1. Albumins - soluble in water (distilled), most enzymes 2. Globulins - soluble in dilute aqueous solutions; 3. Protamines - not based upon solubility; small MW proteins with 80% Arginine & no Cysteine 4. Histones - unique/structural: complexed w DNA, high # basic aa's - 90% Arg, Lys, or His 5.Collagen = high Glycine, Proline, & no Cysteine when boiled makes gelatin Keratins - proteins of skin & hair high basic aa's (Arg, His, Lys), but w Cys
37 37 Complex Proteins: on hydrolysis yield amino acids + other molecules lipoproteins - (+ lipids) blood, membrane, & transport proteins glycoproteins - (+ carbohydrates) antibodies, cell surface proteins nucleoproteins - (+ nucleic acids) ribosomes & organelles
38 38
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