A BEGINNER S GUIDE TO BIOCHEMISTRY Life is basically a chemical process Organic substances: contain carbon atoms bonded to other carbon atom 4 classes: carbohydrates, lipids, proteins, nucleic acids Chemical properties derived from functional groups o Sugars: ketone group ( C==O), aldehyde group ( C O), hydroxyl group ( OH) o Alcohols: hydroxyl group ( OH) o Organic acids, amino acids, fats: carboxyl group ( COOH) o Amino acids (proteins): amino group( NH 2 ) o Fats, oils, waxes: methyl group ( CH 3 ) o ATP, DNA, RNA: phosphate group ( PO 4 ) -3 The 3-D orientations of atoms in organic molecules promote or discourage interactions with other substances: FUNCTION IS DERIVED FROM SHAPE Single bond (C C) is the most flexible: rotational freedom linear carbon-carbon chains form the most stable portion of most biological molecules H H H H H H H H C C C C C C C H H H H H H H H - can add functional groups or form into a ring or the rings can be joined! Double bond (C == C) is more rigid Triple bond (C === C) is least flexible, but is also the least common bond 5 Classes of Chemical Reactions in Biology (All enzyme -mediated): 1. Functional group transfer (between donor & acceptor molecules) 2. Electron transfer (1 or more electrons moved) 3. Rearrangement (juggling of internal bonds) 4. Condensation or dehydration synthesis (2 molecules combine to form a larger one; byproduct is water; can be used to create polymers) 1 AP Biology Krabath monomer + monomer + monomer + monomer polymer + 3 H 2 0 5. Cleavage (molecule splits into 2 smaller ones): Hydrolysis is a special type of cleavage reaction in which water is added to break the bonds polymer + 3 H 2 0 monomer + monomer + monomer + monomer
Carbohydrates The Structure of Carbohydrates C, H, O atoms General formula: C(H 2 O) NOTE: not all carbohydrates conform precisely to the formula not all compounds which conform to the formula are carbohydrates (EX: C 2 H 4 O 2 is acetic acid) Simpler carbohydrates have names ending in ose (sucrose, glucose, maltose, etc.) 2 main uses: energy & structure 3 main groups: monosaccharaides, disaccharides (oligosaccharides), polysaccharides Monosaccharides Can t be broken down into simpler substances by condensation Sugars: low molecular weights, water soluble, sweet taste EX: glucose, fructose, galactose, ribose Glucose: C 6 H 12 O 6 6-sided ring structure also called dextrose most abundant monosaccharide found in honey, most sweet fruits & virtually all body cells where energy is metabolism most polysaccharides yield glucose on hydrolysis Fructose: C 6 H 12 O 6 5-sided ring structure found in honey and sweet fruits Galactose: C 6 H 12 O 6 6-sided ring structure similar structure to glucose except for the orientation of the OH group in carbon #4 constituent of lactose (milk sugar) also found in nerve tissues, seaweeds, mosses, lichens, and as a component of certain proteins Ribose: pentose five-sided ring structure found in RNA and DNA (as deoxyribose) 2 AP Biology Krabath Disaccharides Contain between 2 and 10 monosaccharide units per molecule 3 common disaccharides: sucrose, maltose, lactose
Sucrose (cane sugar): found in sugar cane, sugar beets, many plants formed from condensation of glucose and fructose Maltose (malt or grain sugar): doesn t occur in the free state in nature liberated from starch during the manufacture of beer formed from glucose monomers only Lactose (milk sugar): formed from condensation of glucose and galactose least sweet of the sugars Polysaccharides Complex, high mol. wt., low solubility in water, bland taste Commonly formed entirely of glucose units (100 s or 1000 s) 4 VIP polysaccharides: starch, glycogen, cellulose, chitin Starch: food supply in plant cells (esp. cereal grains, tubers, legumes, and unripen fruits) mixture of 2 types of polysaccharides: amylose & amylopectin amylose: long, unbranched chains of glucose units joined by alpha linkages between carbons #1 & #4; arranged as a helix amylopectin: highly branched molecule easier for enzymes to digest Glycogen: counterpart in animals (esp. in liver & muscle) more branched than amylopectin yields glucose when digested by the body (balance coiled between liver glycogen & blood glucose is controlled by spirals insulin more water soluble than plant starch Cellulose: probably the most abundant organic compound on earth supporting structure of plant tissues (cell walls, woody stable parts of plants) long unbranched chains of glucose units joined by beta linkages between carbons #1 & #4 only certain microorganisms have the enzyme cellulose; humans can t digest it Chitin: found in exoskeletons of fungi & exoskeletons of insects & crustaceans nitrogen is attached to hydrocarbons adds strength 3 AP Biology Krabath
Carbohydrate Structures I. Monosaccharide: C 6 H 12 O 6 C 5 H 10 O 5 Glucose Fructose Galactose Ribose II. Disaccharide C 12 H 22 O 11 1. Sucrose (glucose + fructose) 2. Maltose (glucose + glucose) 3. Lactose (glucose + galactose) 4 AP Biology Krabath
III. Polysaccharide Starch Glycogen Cellulose 5 AP Biology Krabath
The Structure of Proteins 1. Primary Structure: Chains of amino acids. Twenty amino acids essential to life. All proteins are made from these twenty amino acids. When amino acids bind together a molecule of water is eliminated. Many amino acids joined together would be called a polypeptide. Most protein chains range from 50 to 2000 amino acids. Peptide bond 2. Secondary Structure: Within the long protein chains there are regions in which the chains are organized into regular structures known as alpha-helices (alpha-helixes) or beta-pleated sheets. These structures are held together by hydrogen bods between the lone pairs of oxygen and hydrogen. Alpha-helix secondary structure Beta-pleated sheets secondary structure 3. Tertiary Structure: When the chain folds on itself into a 3- dimensional shape the This structure is held together by interactions between the side chains. There are several ways that this could happen including ionic interactions, hydrogen bonds, and sulfur bridges. 4. Quaternary Structure: Multiple polypeptides bind together into a single, larger protein. Hemoglobin is a good example of quaternary structure due to the binding of two alpha globin and two beta globin polyproteins. 6 AP Biology Krabath
The Structure of Nucleic Acids Genetic code of life Include DNA, RNA, mrna, trna, rrna Made up of: 1. a phosphate group 2. a five-carbon sugar 3. made of nitrogen (N) atoms DNA is double stranded RNA is single stranded Bases will join A to T and C to G In RNA Uracil replaces Thymine phosphate sugar base 7 AP Biology Krabath