BIOCHEMISTRY The Chemistry of Living Things Biochemistry, an area that many students find pretty challenging (difficult). While the ideas are abstract, much of the material boils down to memorization. Memorization boils down to studying. Studying boils down to work. Work boils down to effort. So, put your best effort forward & let's get to work! Organic vs Inorganic compounds: "All living things are composed of one or more cells and the products of those cells. Now where have you seen that before? That is 1/3 of the cell theory, right? The chemical compounds that make up the structures in cells are a mixture of organic compounds and inorganic compounds. To keep it simple, remember it this way: organic compounds always contain carbon and hydrogen (and maybe some other elements), inorganic compounds do not contain carbon and hydrogen together. Organic compounds are found in living things, their wastes, and their remains. Examples of organic compounds: carbohydrates (sugars, starches), lipids (fats & waxes), proteins, nucleic acids (DNA & RNA). Examples of inorganic compounds: water, carbon dioxide. The elements (atoms) in organic compounds are held together by covalent bonds, which form as a result of the sharing of two electrons between two atoms. Chemical Formulas: There are three kinds of chemical formulas we should understand. The simplest is the "molecular formula", which tells you the number of atoms of each element present in a compound. An "empirical formula" is basically a molecular formula with the numbers of atoms shown in the smallest possible ratio. A structural formula is like a diagram of the compound. It shows the atoms present and how they are arranged and bonded together in the compound. Here are the molecular, empirical, & structural formulas for one compound that we will all learn to love --- GLUCOSE. Molecular Formula CHEMICAL FORMULAS FOR GLUCOSE Empirical Formula Structural Formula C 6 H 12 O 6 CH 2 O Glucose is an example of a "monosaccharide", a small carbohydrate.
¾The molecular formula tells us that there are 6 carbon atoms, 12 hydrogen atoms, & 6 oxygen atoms in one single glucose molecule. ¾Notice that if you look at the structural formula & tally up each letter (element) you get the molecular formula. ¾Each line (dash) represents the covalent bond holding the atoms together. ¾The ratio of the elements in the molecular formula is 6:12:6, which reduces to 1:2:1 (the number expressed in the empirical formula : CH 2 O --- we don't bother writing the "1"s). ¾Understanding the formulas is very important --- they are like vocabulary in this chapter, if you don't know 'em, it'll be like trying to read & understand this : capt bio forpresident Dehydration Synthesis vs Hydrolysis: All of the organic compounds we will study are examples of polymers. A polymer is a large chemical compound composed of smaller repeating units --- over & over & over again. Like a long choo-choo train is made up of smaller connected, repeating, choo-choo cars. The chemical process that connects the smaller subunits to form large organic compounds is called dehydration synthesis. Remember "synthesis" it means: build. The "dehydration" part of the term refers to the fact that water is lost during the chemical process that bonds the subunits together. We will "see" this in a minute when we get more specific. Hydrolysis is the process that breaks large organic compounds into their smaller subunits. It is the opposite of dehydration synthesis. In HYDROlysis, water (hydro) is added and the large compounds are split ("lysis" means split). The process of hydrolysis is involved in digestion --- when food is broken down into nutrients. So, to summarize: PROCESS STARTS WITH ENDS WITH EXAMPLE dehydration synthesis hydrolysis small molecules (subunits) water & large molecules large molecules & water small molecules (subunits) growth digestion You will do yourself a BIG favor if you can keep these two processes straight. QUESTIONS - Organic Compounds, Formulas, Dehydration Synthesis & Hydrolysis Before we get into specific kinds of organic compounds, let's try some questions about what we've done so far. 1. Which is an example of an organic compound? a)c 17 H 35 COOH b) (NH 4 ) 3 PO 4 c) H 2 O d) NaCl 2. Which type of formula gives the most information about a compound? a) molecular b) empirical c) structural
3. How many atoms of hydrogen in C 12 H 22 O 11? 4. Identify three inorganic compounds in the following reaction: CO 2 + H 2 O + sunlight ---> C 6 H 12 O 6 + O 2 5. Is the following reaction an example of dehydration synthesis or hydrolysis? How do you know? C 12 H 22 O 11 + H 2 O ---> C 6 H 12 O 6 + C 6 H 12 O 6 ANSWERS : THE CHEMISTRY OF LIVING THINGS QUESTIONS :Organic Comp., Formulas, Dehydration Synth. & Hydrolysis Answers & explanations. 1. C 17 H 35 COOH * Organic compounds must have both carbon (C) & hydrogen (H) in them. 2. structural * the structural give you number & types of atoms & their arrangement 3. 22 (the # after the H) 4. CO 2 + H 2 O + O 2 * Organic compounds must have both C & H in them. Anything else is inorganic. 5. * hydrolysis. we know for two reasons : 1) the two molecules we end up with (on the right) are smaller than the one on the left; & 2) water is added CARBOHYDRATES: Elements Present carbon hydrogen oxygen H:O = 2:1 always! Used by organisms for energy structure Building Block monosaccharides (simple sugars) ex: glucose Related Terms & Info dissaccharide = 2 connected monosaccarides (ex: maltose) polysaccharide 3 or more connected monosaccarides (ex: starch, glycogen, chitin, cellulose) NOTES: ¾The 2:1 ratio of hydrogen to oxygen atoms in all carbohydrates is a very important identifying characteristic. ¾Another clue to identifying carbohydrates is their structure. Monosaccharides have a ringlike structure, kind of like a hexagon. So if you are looking at structural formulas and you see "rings", it's probably a carbohydrate; especially if only carbon, hydrogen, & oxygen are present in the molecule. Want to see what I mean?
THE DEHYDRATION SYNTHESIS OF MALTOSE FROM TWO GLUCOSE MOLECULES LOOK... RINGS!!! The ring-thing is a big deal. It will help you. Memorize it. What we have in the equation above is two single rings (monosaccharides) on the left becoming chemically combined to form the two-ringed molecule on the right (a disaccharide). It is a synthesis reaction --- the product is bigger than the individual reactants. In order to combine the two glucose molecules, bonds must become available. This is accomplished by removing a hydrogen ion (H + ) from one glucose & a hydroxyl ion (OH - ) from the other (the dashed box in the equation illustrates this point). These ions bond to form the water molecule that appears on the far right. This happens in every dehydration synthesis reaction --- water is lost as a waste product. If we were to turn the arrow in the equation around & read from right to left, we would be looking at the HYDROLYSIS of maltose. In the hydrolysis of maltose, water would be added to the disaccharide (maltose) causing it to split into its smaller subunits --- the two monosaccharides (glucose molecules). Not to beat a dead horse, but the fact that only C, H, & O are in the molecules, and that the molecules have a ring-like structure should make you very confident in identifying them as carbohydrates. Getting back to the carbohydrate table, chitin and cellulose are examples of carbohydrates with structural functions. Chitin is the material that makes up the exoskeletons of all arthropods (insects, spiders, lobsters, etc.). Cellulose is what the cell wall in plant cells is made of. Starch is the form by which plants store extra carbohydrates. Glycogen (sometimes referred to as "animal starch") is the form by which animals store extra carbohydrates. We store glycogen in our livers.
LIPIDS : (Fats, Oils, & Waxes) Lipids are our 2nd group of organic compounds. Again, organic just means the compound contains carbon & hydrogen together. In the case of lipids, the compounds contain C, H, & O, and that's t. i No other elements in lipid molecules. Nada, none, zippo, zilch. Just those 3. OK? Do you recall another group of organic compounds that are also built with those same 3 elements? Yes, carbohydrates. So how do we keep from confusing our lipids & carbohydrates? No need to panic, it's quite simple. Carbohydrates always have twice as many hydrogen atoms as oxygen atoms (H:O ratio = 2:1). Lipids never do. Also, the structural formulas of carbohydrates have the "ring thing" (remember?) and lipids do not. Here is a summary of Lipid stuff: Elements Present Carbon Hydrogen Oxygen ONLY! There is no specific H:O ratio. Used by Organisms for... Stored Energy Structure (important part of cell membranes) Related Terms & Info saturated fat = C-C bonds are all single bonds unsaturated fat = contain at least one double or triple C-C bond Building Blocks of Lipids fatty acid : glycerol : A fatty acid is nothing more than a long C-H chain with a carboxyl group (COOH) on the end. The 3 "dots" in the diagram above illustrate that the chain is very long. Remember the carboxyl group? The carboxyl group gives a molecule an acidic property. Both of the organic acids you need to remember (fatty ACIDS & amino ACIDS) have carboxyl groups. Glycerol is classified as an alcohol (due to the OH's). It always looks the same: 3 C's with 3 OH's and everything else H's. To build one lipid molecule, we combine 3 fatty acids with 1 glycerol by the process of...
DEHYDRATION SYNTHESIS! Like other dehydration synthesis reactions, we must free some bonds before we combine the 3 fatty acids & glycerol. And like before, this is accomplished by removing water molecules. We remove 3 waters in this reaction because we are bonding 3 fatty acids to the glycerol (we need 3 free bonds). Notice also that there are no ring-shaped molecules, so we are not dealing with carbohydrates. The hydrolysis (digestion) of a lipid could be summarized like so: lipid + water ----> 3 fatty acids + glycerol PROTEINS: Allow me to make my first point about proteins by writing "protein" like this : protein. "N" stands for nitrogen. There is an "N" in the word protein. The element nitrogen is always present in proteins. This will help you. Memorize it. Elements Present carbon hydrogen oxygen NITROGEN (always those 4) phosphorus sulfer (possibly) Used by organisms for... structure & movement (muscles) enzymes antibodies hormones pigments Related Terms & Info peptide bond = the bond that holds amino acids together in protein molecules dipeptide = two connected amino acids polypeptide = 3 or more connected amino acids Building Block of Proteins: amino acids
Well, where to start. Did you notice the "N" in the amino group? Since big protein molecules (which we call polypeptides) are long chains of amino acids, every (every) protein has nitrogen in it. Always. You are responsible for recognizing & identifying the smaller parts of an amino acid. The NH 2 on the left is the amino group, the COOH on the right is called a carboxyl group. The carboxyl group is responsible for giving the amino acids its "acid" properties. The "R" is not an individual atom or element. Instead, the "R" spot is the location at which one of a number of groups of atoms connect to the rest of the amino acid. They are called "side groups". There are 20 different side groups --- so there are 20 different amino acids. So what I am trying to say is that the basic structure of all amino acids is the same except for the side group ("R") spot. And whichever of the 20 variable groups you have bonded there determines which of the 20 amino acids you're dealing with. Let me illustrate with an example: alanine "R" group = CH 3 glycine "R" group = H Both of these are amino acids because they have an amino group (NH 2 ) on the left & a carboxyl group (COOH) on the right. They are two different amino acids because they have different atoms bonded at the "R" group spot. See? That's not so bad, is it? Now, tell me something. By what process are individual amino acids combined to from larger proteins? Very very good... dehydration synthesis. This is THE process by which ANY small organic molecules are combined to form BIG organic molecules. The dehydration synthesis of a protein is typically illustrated like so:
There are two clues that what you are looking at in the above equation is dehydration synthesis. The first is that water is at the end --- a waste product in this process ("dehydration" = loss of water!). The 2nd clue is that the one molecule on the right (the dipeptide) is bigger than the individual reactants (amino acids) on the left (synthesis = build). Now, just like with putting 2 monosaccarides together, we can't combine the two amino acids until we have freed some bonds up. This is accomplished by removing an OH from one amino acid & an H from the other. These atoms bond & live happily ever after as H 2 O (water). The shade in the diagram above is my attempt to emphasize this idea. The removal of OH's & H's & the formation of water as a waste product happens in EVERY dehydration synthesis reaction --- whether it involves carbohydrates, proteins, or lipids. Notice please that the bonds "freed up" after the removal of water form the "peptide bond". "Dipeptide" is just a word for two amino acids that are bonded together. If we continued to add more & more amino acids to the dipeptide we would then call the molecule a POLYpeptide. If you haven't noticed already, "peptide" is a protein word. Dipeptide, polypeptide, peptide bond, --- all protein stuff. The hydrolysis (breakdown) of a dipeptide could be summarized like this: dipeptide + water ---> amino acid + amino acid Notice that water is added at the beginning in hydrolysis, & that our products are smaller than the molecule we start with. i THinK THat we've TRied to STUFF enough into your BRAIN for now. WE'd better make sure SoMe STuFF is STICkiNG. InterESTeD IN a quiz? it's on carbohydrates & proteins. C'mon, give it a shot. POP QUIZ: Carbohydrates & Proteins Questions: 1. Name three elements found in carbohydrates. 2. What is the main function of carbohydrates in living organisms? 3. The ratio of hydrogen atoms to oxygen atoms in a carbohydrate molecule is always? 4. In the list below, circle the polysaccharide(s), underline the disaccharide(s), & put a star next to the monosaccharide(s). cellulose chitin glucose glycogen maltose starch
5. Is the following reaction dehydration synthesis or hydrolysis? Explain your answer. C 12 H 22 O 11 + H 2 O ---> C 6 H 12 O 6 + C 6 H 12 O 6 6. In the diagram below, draw a box around the amino group & circle the carboxyl group. Base your questions to numbers 7-11 on the chemical equation below. 7. How many organic molecules are in this equation? 8. Does this equation represent dehydration synthesis or hydrolysis? Explain your answer. 9. Which molecule contains a peptide bond? 10. Name one molecule (A, B, C, or D) in the equation that could be used an example of a "building block" of protein. 11. Name one clue that indicates that the equation above is related to proteins. POP QUIZ: Answer Key Carbohydrates & Proteins 1. Name three elements found in carbohydrates. carbon, hydrogen, oxygen 2. What is the main function of carbohydrates in living organisms? energy 3. The ratio of hydrogen atoms to oxygen atoms in a carbohydrate molecule is always? 2:1 4. In the list below, circle the polysaccharide(s), underline the disaccharide(s), & put a star next to the monosaccharide(s) cellulose (circle) chitin (circle) * glucose glycogen (circle) maltose starch (circle) 5. Is the following reaction dehydration synthesis or hydrolysis? Explain your answer. C 12 H 22 O 11 + H 2 O ---> C 6 H 12 O 6 + C 6 H 12 O 6 Hydrolysis. Water is a reactant (used in the beginning) & a large 12-carbon molecule is split into two 6-carbon molecules. 6. In the diagram below, draw a box around the amino group & circle the carboxyl group.
The NH 2 on the left should be "boxed", and the COOH on the right should be circled. Base your questions to numbers 7-11 on the chemical equation below. 7. How many organic molecules are in this equation? 3, all of them except the water (which doesn't have a carbon). 8. Does this equation represent dehydration synthesis or hydrolysis? Explain your answer. Dehydration synthesis. Water is a product and the two small molecules on the left are combined to form the large molecule on the right. 9. Which molecule contains a peptide bond? C - Peptide bonds hold amino acids together. 10. Name one molecule (A, B, C, or D) in the equation that could be used an example of a "building block" of protein. A or B. Both are amino acids, the building blocks of proteins. 11. Name one clue that indicates that the equation above is related to proteins. There is nitrogen in the compounds. NUCLEIC ACIDS: DNA & RNA We will save the nitty gritty details of DNA & RNA for later in the year (Genetics). But for now, you should know their functions & basic structure, and how DNA compares to RNA. DNA & RNA (like proteins, carbohydrates, & lipids) are polymers --- long chains of smaller repeating units. The repeating unit in nucleic acids is called a nucleotide. Every nucleotide has the same basic structure:
¾ the phosphate is a PO 4 ¾ the sugar (see the ring?) has 5 carbons (one at each corner) ¾ the N-base is one of four possibilities (more on that in a second...) COMPARISON OF DNA & RNA DNA RNA FULL NAME Deoxyribonucleic acid Ribonucleic acid BASIC STRUCTURE NUCLEOTIDE SUGAR NITROGENOUS BASES LOCATION IN A CELL FUNCTION 2 long twisting strands of nucleotides in the form af a "double helix" Deoxyribose guanine (G) cytosine (C) adenine (A) thymine (T) nucleus (the chromosomes) the hereditary material of a cell, directs & controls cell activities 1 single strand of nucleotides Ribose guanine (G) cytosine (C) adenine (A) uracil (U) nucleus, in the cytoplasm, & at the ribosomes involved in protein synthesis ¾so DNA & RNA are alike in that they are both nucleic acids composed of nucleotides ¾their differences lie in their functions and structure ¾the main structural differences are the number of strands in the molecule, the sugar structure, and one of the N-bases (thymine in DNA, uracil in RNA) Well, congratulations for getting through all this stuff. I hope this stuff helped. Keep pluggin' away.