Later, we will talk. We will start here! A) Water. * Others are. not: Propane. this!) individual water characteristics for life: heat of

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1 1 PART II-BIOCHEMISTRY - 2 types of molecules: 1) ORGANIC compounds containing carbon * Some are biologically important molecules: carbohydrates, proteins, lipids (fats), HCO 3 -, etc. * Others are not: Propane is organic, and petroleum contains many organic molecules. NOTE: not everything organic is "good for you". Gasoline, mushroom poison, and urea are organic molecules. (Theree are exceptions molecules that have carbon but are not t classified as organic. Ignore this!) Later, we will talk about why carbon gets its own category! 2) INORGANIC - everything else (not carbon containing). * Water, salts, many acids, etc. We will start here! I) INORGANIC COMPOUNDS A) Water - Most abundant compound found in organisms; 60%-70% of volume. - Recall the special characteristics of water from the chemistry section: Due to the polarity of the water molecule, the individual water molecules attach to each other via H-bonds (an intermolecular bond). The H-bonds between individual water molecules give liquid water some indispensable characteristics for life: 1) High Heat Capacity - water absorbs a lot of heat before changing physical states. Therefore, water is a good "environment for biological processes" ". * Acts as a "vacuum cleaner" for heat water sucks it up! Our organs and cells are protected because they are surrounded by water. 2) High Heat of Vaporization - Therefore, it helps keep our bodies cool. As it evaporates and takes heat away. * Other liquids, like alcohol, etc. have low heat of vaporization, so they do not cool as well. 3) Polarity/Solvent Properties-wate = the "universal solvent"; other materials dissolve in it due to its polar properties. * Put salts, acids, polar covalent bonds in water in water = they dissolve. * Not true of other liquids 4) Highly Reactive - HOH = important reactant. - Water often used to break bonds, and to build them. cell s use, and we can also form polymers: We can make building blocks available for our Catabolism via Hydrolysis, and Anabolism via Dehydration Synthesis Our body s cells need nutrients ( building block molecules ). Catabolism is breaking things down. Inside the digestive tract, digestion of food occurs chemically via a process called "OXYDATION" = "add oxygen". When this is done using water, it is called HYDROLYSIS (= "water splitting").

2 2 You end up with the Building Block molecules your body needs to build your tissuess and organs (technical namee = residuals ). Monomer refers to a single unit.

3 3 - Conversely, when bonds are formed (Anabolism), water is often a byproduct. In other words, we form bonds by removing water. This is called DEHYDRATION SYNTHESIS (Dehydration = "remove water". Synthesis = "making" or "forming"). * If the resulting molecule is a long, repeating chain, we call it a POLYMER MOLECULE (polymerization = formation of a polymer): - During this process, the molecule becomes LESS SOLUBLE IN WATER (hydrophobic polymer). This is because you have removed charges from the molecules (another way to look at it you removed water each time you attached another subunit!).

4 4 Polymers are often used (among other things) ): 1. Energy storage (they are insoluble, which is a good way to store things in water) complex carbohydrates. 2. Structure (it is good to build the body out of something that does not dissolve well in water) - proteins - When the body is ready to use the individual subunits, it is broken down, so its parts can be re-used (hydrolyses the polymer). The subunits are MORE SOLUBLE in water: * Now, easy to transport the hydrophilic subunits in the bloodstream. 5) Water is Resilient-absorbs impacts well; good "cushion". * This also protects against changes in temperature! * Water protects your cells and organs from pressure and temperature changes. 6) Water exhibits both adhesion (it sticks to other molecules) and cohesion (sticks to other water molecules). * Water forms a great lubricating surface, and it exhibitss (among other things) capillary action. B) Salts - SALT - an ionic compound containing a cation and an anion. * For our purposes, cation other than an H+ and an anion other than OH- (in other words, an ion that is NOT an acid or a base). - Why are ions important? MANY functions, including: * Ionic solutions are electrolytes (conduct electricity). * Small charged particles in water can move quickly, attach to things, and start physiological processes. Na+ & K+ ions are important for muscle & nerve impulses (= electrical current!). Na+ is vital nutrients. for absorption of almost all other Ca++ important for heart function, and bone structure. Cl- important for exocytosis, movement of mucus, acid balance in the body. LOTS of examples!!!!

5 5 * Also - ions have an ATTRACTIVE force to other chargedd particles - often used to "carry things. ** Oxygen is carried in blood by an iron ion found in red blood cells w/in the blood. Iron Oxide (FeO2) is red in color, that's why blood is red (color of rust)!

6 C) Acids & Bases & Buffers: a special case of an important ionic compound (salt) - First: a review of concentration: RECALL: CONCENTRATION ( [ ] ) = percent of total of a SOLUTE (= substance dissolved in a liquid substance called the SOLVENT) ) Water will be our solvent; Solute will often be saltss & minerals inn biological systems * If add ionic compound (salt) to water see image 6 - It is important to know the concentration of H+ in a solution of water, because it is so destructive. * The hydrogen atom consists of 1 p+ & 1 e-. If the e- is lost, you only have a proton. Therefore: A hydrogen ion = a proton (H+ = p+) * Now, you have a free proton in water, which is very destructivee to other bonds. Lot of kinetic energy, which disruptss other bonds easily. - Ionic compounds that change the concentration of hydrogen ion (H+) are special...and therefore get their own names: Acids & Bases * For us, WATER IS ALWAYS ASSUMED TO BE THE SOLVENT. So we onlyy have to worry about 1 type of acid- base: acids and bases in water. ** There are other definitions of acids and bases. But....we don t have to worry about them. 1) ACID - anything that donates ("gives up") a hydrogen ion (H+ +), which equals a proton (p+ +), in solution. - EXAMPLE: Hydrochloric acid (HCl) NOTE: the arrows in chemical reactions always goo both ways. The reaction will go in the direction of the longer arrow, unless forced by some energy input, or some other factor.. - What makes a strong acid STRONG? It greatly increases the [H+]. * Weak acids: only increase the [H+] a little. See later. HCl too strong for your body s tissuess (releases tooo many H+ s),, while citric acid is not!

7 7 - Characteristics of acids: * Conduct electricity (electrolytic solution). * Can be very destructive, if in high enough concentration. POLYPROTIC ACIDS - donate more thann 1 H+. We won t be dealing with these. * Sour taste ( sour is your tongue s detection of H+!!). 2) BASE - anything that acts as a proton acceptor in solution ("eats up H+s out of the solution ). * Synonym: alkaline - EXAMPLE: bicarbonate ion - NOTE: anything with a negative charge, if you put it in water, will actt basic! Maybe not a strong base, but it will be basic! ALSO NOTE: anything that donates an OH- when in water is a strong base, as the OHwill immediately "eat up" any available H+ +'s to form water. In other words...we form the solvent! - What makes a strong base STRONG? It greatly increases the [OH-].. * Weak bases: only increase the [OH-] a little. See later. - Characteristics of bases: * Conduct electricity (electrolytic solution) * Can also be very destructive if in high enough concentration. Fats in a strong base turn into soap! * Bitter taste ( bitter is your tongue s detection of OH-!!) * Slippery feel 3) Strength of Acids & Bases, and Neutralizing Them - NOTE: if you mix acids and bases, they neutralize each other (and you get water) _ HCO 3 Bicarbonate = a base + HCl Hydrochloric acid Neutralized! *the above example is especially important to biological systems - it is how your body neutralizes the acid produced in your stomach.

8 8 **if your blood becomes too acidic, pancreas makes bicarbonate; we mimic this with Alka-Seltzer. - So, an acid or base is something that ionizes in water, giving up H+'s (acids) or removing the H+'s (bases; some do this by giving up OH-'s). If an ionic compound, their strength depends on how much they ionize. * Strong acid - all or almost all of the molecules ionize. * Strong base - all or almost all of the molecules accept an H+ (or, increases greatly the [OH-]). Is it a strong acid? Is it a strong base? We need to know the [H+] and [OH-] in water! This takes us to the next topic... 4) ph Scale - ph = "potential of hydrogen" = [H+] = ACIDITY or ALKALINITY ("base-ness") of a solution. * Often in question, since any extra H+'s tend to react with other chemicals (you know what acid does to your skin & clothes! Bases have an equally strong effect!). * However, since the [H+] is so small, even in an acidic solution, % is difficult to use. [H+] of pure water = moles/liter or 1 X 10-7 * water ionizes itself...so there are always somee H+ s and OH- s, even in a glass of pure water. -in 1909, Sorensonn (Swedish chemist) proposed using thee ph scale as shorthand. ph = - log [H+]

9 - LOG SCALE - uses the exponent as the scaling variablee 9 value ph Since exponents of decimal numbers are negative, ph scale uses the NEGATIVE LOG (the negative of a negative is a positive number!!). - 2 little quirks to LOG scales in general, and the ph scale in particular: 1. 0 does not mean none, because 10-0 = 1 (which would mean pure ). 0. So, neutral is not - Neutrality on the scale = the ph of pure water (= [H+]] of pure water) at room temperature. * Arbitrary distinction? Why use pure water? Water is the only substance in thee universe where: [H+] = [OH-] This is because all of the H s andd OHs came from a water molecule (ratio of 1:1). So neutral is defined as the condition where [H+] = [OH-]. Therefore, a glass of pure water is neutral, even though it has both H+ and OH-! [H+] of water at room temperaturee = [OH-] = 1 x 10-7 moles/liter = ph of Since we are really dealing with negative exponents, higher numbers on the scale are less H+, andd lower numbers on the scale are more H+ +. That is because 10-7 is a smaller amount than 10-6 (for example), so a ph of 7 is LESS than a ph of 6! Therefore, low ph numbers mean more acid, while high numbers mean more base * Acids have a high [H+], but a LOW ph (small #s the scale). ph on Moreover, increased Acids have a smaller (-) exponent = a lower # on the ph scale. every time you go up or down 1 number on the scale, you have actually decreased or [H+] by 10X (since it is an exponent). **NOTE: since ph scale is a log scale, there is a big difference (for example) between a ph of 6 and a ph of 7 (10X difference!)

10 10 1 **NOTE: since ph scale is a log scale, there is a big difference (for example) between a ph of f 6 and a ph of 7 (10X difference!) So, as we [H+] goes move up in number on the ph scale, [OH-] goes up,, as down. * Bases have a low [H+], but a HIGH ph. - Some examples of ph (just to give you an idea): (i) ph lemon juice: [H+] = 1/100 = 10-2 = ph of 2 = highly acidic! (ii) ph of milk of magnesia: super low [H+] = = ph of 11 = highly basic! REMEMBER: when we refer to an increase or decrease in number, we are referring to the scale number (to go from a ph of 6 to a ph of 7 is an increase). 5) Buffers: Controling ph (Homeostasis) Bases have fewer H+ ions, therefore a larger (-) exponent, so they have a higher # on the ph scale. ** So: ph of 7 = Neutral ph > 7 = Basic or Alkaline ph < 7 = Acidic Why the heck do we care about this in the first place! Homeostasis of ph in the body. - Because, your body maintains strict control of the body'ss ph using feedback loops, since high or low [H+] (acidity or alkalinity) will destroy cells and proteins, and that can lead to death (rather painful death, I might add)! WHY? Because changes in [H+] up or down affect how proteins, etc. do their job by changing the shape of proteins (look what vinegar does to a raw egg!). Therefore, it is important that acidity levels (ph) remain stable DESPITE THE FACT that many biochemical reactions cause H+ +s to either be released or used up, which changes ph (for example, digesting an orange releases citric acid into the system, temporarily lowering ph!). Basic everyday activities such as eating, moving your muscles, etc. produce acids and bases, which end up in your blood. - Maintaining a stable ph is accomplished by different means in different organisms. For many, the first line of defense involves BODY FLUID BUFFERS. * BUFFER - any substance that, when added to a solution, prevents ph change by: By removing H+ ions if they are added. By adding H+ if they are removed from solution.

11 11 1 You have blood buffers to help maintain blood ph. They act like an acid if the ph increases, and act like a base if the ph decreases: One example of how a buffer might work: Another way to say it: Buffers are a weak acid-base pair. The buffer acts like a base if the solution becomes acidic, and the buffer acts like an acid if the solution becomes basic. 6) Different ph s in different parts of the body reflect different needs: * Blood - ph of blood must be maintained between (approximately) pretty neutral. Slightly basic due to components within blood, especially carbohydrates and proteins which tend to be negatively charged. Buffers in blood maintain this when you eat an orange, bread, etc.; anything would change blood ph if not for buffers. Low blood ph = ACIDOSIS ( osis = "condition") Buffers are what let you take an aspirin (acetylsalicylic acid) without going into acidosis. High blood ph = ALKALOSIS. Buffers are what let you take milk of magnesia without going into alkalosis. * Stomach = low ph (acidic) as stomach uses HCl to digest & store food (kill bacteria). ** pancreas adds bicarbonate to neutralize the juice in the intestines so it doesn t kill you. * Vaginal secretions = slightly acidic to help fight against microbial infection. ** Semen = slightly basic to help neutralize the acid so sperm can survive.