Important Concepts in Biology - Cell and Molecular Biology | BIOL 1441, Study notes of Cellular and Molecular Biology

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Important Concepts in Biology

What is the difference between polar and nonpolar covalent bonds?

In order to answer this question, begin with the basics: what is a covalent bond? Two atoms in a covalent bond share electrons. Remember electrons like to be in pairs. Each atom contributes an electron so there are two- which both atoms share. The electrons will spin around one atom, then the other. Electrons are always in constant movement- meaning they never stop orbiting the atoms. The electrons can spin around the atoms two ways: 1) spending more time around one atom than the other or 2) spending the same amount of time around each atom. Scenario 1 describes a polar covalent bond. Scenario 2 describes a nonpolar bond. POLAR COVALENT BONDS Polar covalent bonds result from atoms sharing the electrons unequally. This depends on each atom’s electronegativity value. Electronegativity is a measure of an atom's ability to draw its bonding electrons to itself. Each atom has a numeric value corresponding to its electronegativity. www.beyondbooks.com/psc92/3c.asp The more electronegative an atom, the more it will attract or “pull” the electron to itself. Meaning- the electrons spin around the electronegative atom more than the other atom it is bonded to. Think of the electronegative atom like a bully- it does not play nice! It is an electron hog. It does not like to share. How do I determine the electronegativities of the atoms??? Good question. I do NOT expect you to memorize those values on the chart above- save that for chemistry class. I’m going to make it easy on you & tell you which ones are the most electronegative! The two most electronegative atoms that we deal with in biology are OXYGEN and NITROGEN. These guys are the bullies- the electron hogs. Carbon and hydrogen are often associated with these bullies because C, H, O, & N are the four most common elements that compose all living matter. Carbon and hydrogen have similar electronegativities. They are not bullies when bonded together; they cannot pull the electron more than other one can. Oxygen and nitrogen are both more electronegative than either carbon or hydrogen.

If you covalently bond a hydrogen atom with an oxygen atom or a hydrogen atom with a nitrogen atom, what do you think will happen?! You guessed it, oxygen and nitrogen will hog those electrons from poor little hydrogen. Oxygen and nitrogen will also hog those electrons from carbon. What is the consequence of one atom being more electronegative than the other in a covalent bond? Well consider that the electrons are negatively charged. If the electrons are spinning around the more electronegative atom (O or N) more often compared to the other atom (H or C), than the electronegative atom gains a partial negative charge and leaves the other atom with a partial positive charge. NONPOLAR COVALENT BONDS Nonpolar covalent bonds result from atoms sharing the electrons equally. The atoms in this type of covalent bond have the same level of electronegativity. Meaning- the electrons spin around the both atoms the same amount of time. These atoms play nice- they share their electrons equally! Because the electron is spinning around both atoms equally, there are no partial charges associated with either atom (even though the electron has a negative charge). REMEMBER: Carbon and hydrogen have similar electronegativities, so when they covalently bond electrons are shared equally and there is no charge (nonpolar). Examples: C-C nonpolar O-H polar H-H nonpolar O-C polar O-O nonpolar N-H polar N-N nonpolar N-C polar C-H nonpolar Don’t worry about O-N, I won’t ask that! (technically it is polar)

How does polar/nonpolar relate to hydrophilic/hydrophobic?

Hydrophilic means water “loving” and hydrophobic means water “fearing” (phobia). Molecules that have polar covalent bonds have a partial charge associated with them and may be called polar molecules. Water is called a polar molecule because the oxygen creates two polar covalent bonds with the hydrogens.

Molecules that have charges are attracted to each other (positive and negative charges attract). This includes molecules that have polar covalent bonds (partial charges associated with them) and ions (charged molecules or atoms due to gaining (- charge) or losing (+ charge) an electron). These charged molecules or ions dissolve in water. Like dissolves like. In this case charged water dissolves molecules with charges- they are alike b/c they both have CHARGES. We call these charged molecules or ions hydrophilic- water loving b/c they are attracted to water and interact with it. An example would be alcohols which have a hydroxyl group (-OH). The hydroxyl group is a polar covalent bond between oxygen and hydrogen. That functional group has a partial charge associated with it and interacts with water. Alcohols and other molecules with hydroxyl groups are hydrophilic and readily dissolve in water. Molecules with nonpolar bonds have no charge and referred to as nonpolar. Because nonpolar molecules have no charge (no region of + or -), they do not interact with water (which is polar and has a charge). We therefore consider nonpolar molecules hydrophobic or water “fearing”. An example would be hydrocarbons- hydrogen and carbon play nice and SHARE the electron equally and therefore have no charge associated with them. Fats are mostly hydrocarbons (fatty acids) and tend to repel water, like oil floating on top of water. What if you put a protein with amino acids that have side groups (R groups) with polar and nonpolar functional groups into an aqueous solution (water-based)? The amino acids with polar side groups (-OH, -COOH, -CO, -NH 2 , -SH) all have polar covalent bonds and like to interact with water. Amino acids that have a charged R group (ion) will also interact with water. The amino acids with nonpolar side groups (-CH 3 ) will not want to interact with water. The protein will fold accordingly to its amino acids’ “preferences”. The amino acids with polar side groups/ions (all charged) will be the exterior while the amino acids with nonpolar side groups (no charge) will fold to the interior. Remember like dissolves like. So charged solutions/molecules will mix with other charged molecules and uncharged solutions/molecules will mix with other uncharged molecules, BUT charged and uncharged will not mix with each other!

How can I tell which amino acid is polar/nonpolar or hydrophilic/phobic?

Amino acids are classified only by their side groups (R groups). Every amino acid has an amino group (orange box below), an asymmetric carbon (except glycine), a carboxyl group (yellow box), a hydrogen and an R group (white box). The amino acid “skeleton” or backbone is the amino group, asymmetric carbon, carboxyl group and hydrogen- because it is the EXACT same for every amino acid. The only difference between the amino acids is their R-groups. Generic Structure of every amino acid: Amino Acid backbone in purple, R group in white: If the amino acid R group can form a hydrogen bond or has a charge (ion) it is POLAR! Identify the functional groups that make up the R group. Every functional group is polar, except the methyl group (CH 3 ). If you read above, you already know this because remember carbon and hydrogen play nice and share electrons- no charge, nonpolar. If there is a hydroxyl, carboxyl, carbonyl, thiol functional group- it is most likely classified as a POLAR amino acid which is hydrophilic. If the R group (not the backbone) has a charge it is POLAR. If it has only methyl groups or hydrocarbon chains (-CH) it is nonpolar and therefore hydrophobic. What if it has a polar and nonpolar functional group? In this case, it is still classified as polar because it will be able to form a hydrogen bond with other molecules. Examples below (observe the functional groups). Polar-hydrophilic Polar- hydrophilic Nonpolar- hydrophobic

pH Problems *recall [ ] indicates concentration

pH is simply the concentration of hydrogen ions in a solution [H+], i.e. how many H+ are in that solution. A solution at standard conditions will always have a product of [H+] and [OH-] equal to 10-14^ M. (Recall product means you multiply two numbers. 12 is the product of 3 x 4) That means if you count all the H+ and then you count all the OH- and multiply those numbers, they will equal 10-14^ M or 0.00000000000001 mol/ L. We cannot easily work with those numbers, so we use the log scale to measure the concentration of hydrogen ions in solution. pH does NOT measure the hydroxide ion concentration!!!! pH = -log [H+] We can determine the hydroxide ion concentration if we know they hydrogen ion concentration and vice versa. How? Their product is always 10-14^ M! Math: when multiplying two numbers with the same base, keep the base the same, add the exponents.

10 -5^ x 10-9^ = 10-14^10 -3^ x 10-11^ = 10-14^10 -6^ x 10-8^ = 10-

Get it?! The exponents have to add up to 14. When dividing two numbers with the same base, keep the base the same, subtract the exponents.

10 -14^ / 10-5^ = 10-9^10 -14^ / 10-11^ = 10-3^10 -14^ / 10-8^ = 10-

(-14) – (-5) = -9 Got it?! Why didn’t you tell me this was so easy?!

Rule Example

Two like signs become a positive sign

+(+) 3+(+2) = 3 + 2 = 5

-(-) 6-(-3) = 6 + 3 = 9

Two unlike signs become a negative sign

+(-) 7+(-2) = 7 - 2 = 5

-(+) 8-(+2) = 8 - 2 = 6

If you need a math refresher on exponents try this site! http://mathrefresher.blogspot.com/2005/05/exponents.html Examples: You have a solution with [OH-] = 10-4^ M, what is the [H+]? Look at the exponent: -14 - -4 = - Answer: [H+] = 10-10^ M What is the pH of this solution? The pH of the [H+] is simply the exponent associated with the [H+], no negative signs, just the number. Answer: pH = 10 Why isn’t the answer 4??? Because 10-4^ M is the concentration of OH- not H+!!! pH is a measure of the H+ concentration NOT OH-. Why isn’t the answer -10? Because pH = - log [H+], so a – x -10 = 10. See the rules above.

Keep it simple! The log of any number with a base of 10 is simply the exponent. In this case it will always be a negative exponent and you will always multiply it times another negative sign, so it will always be a positive whole number! [H+] = 10-5^ M pH = 5 [H+] = 10-7^ M pH = 7 NOTE: This only works with the [H+], not the [OH-]. [OH-] = 10-10^ M, pH = 4 ([H+] = 10-4^ M) [OH-] = 10-3^ M, pH = 11 ([H+] = 10-11^ M) You have a solution with a pH of 8. What is the hydrogen ion concentration? Answer: [H+] = 10-8^ M *Just make the pH number an exponent and put a negative sign in front of it. What is hydroxide ion concentration of this solution? Answer: [OH-] = 10-6^ M (-14 - -8 = -6) Is this solution acidic or basic? Answer: Basic [H+] = 0.00000001 M [OH-] = 0.0000001 M (this is the bigger number, remember -8 is smaller than -6!) There are more hydroxide ions than hydrogen ions in solution, therefore it is a basic solution. If there are more hydrogen ions in solution than hydroxide ions, it is an acidic solution. pH 1-6 is ACIDIC solution, more hydrogen ions in solution than hydroxide ions. pH 7 is neutral- hydrogen ions equal hydroxide ions in solution. pH 8-14 is BASIC solution, more hydroxide ions in solution than hydrogen ions. Do NOT confuse the functional group hydroxyl (-OH) with the hydroxide ION which is OH-. The hydroxide ION is a covalently bonded oxygen to a hydrogen with an extra electron, it is an ION , a charged molecule. A hydroxyl group is a functional group with a polar covalent bond between oxygen and hydrogen AND whatever other atom the oxygen is bound to. It is NOT an ion!!! It does not have an extra electron. It has a partial charge due to the polar covalent bond. If you are struggling with the math, please go back to elementary school or high school and apologize to your math teacher who you complained to repeatedly, “Why do I have to learn this stuff? I’m never going to use it.”