Cells & the Evolution of Life
Cells & the Evolution of Life BIOL 115
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Chemical Interactions Slide 2 Don t worry We re not going into excruciating detail about the periodic table but it is important to remember that living organisms are governed by the laws of physics and chemistry Out of all the elements listed on the periodic table only a handful of them hydrogen carbon nitrogen oxygen phosphorus and sulfur are vitally important in biological systems At the moment we are particularly interested in looking at how these elements interact and bond together Slide 3 Let s do a quick review of atoms You probably recall that atoms consist of positively charged protons negatively charged electrons and neutral neutrons Atoms are electrically neutral That is they have the same number of protons as electrons so that the electrical charges balance This fact becomes important when we look at the arrangement of electrons around the nucleus The more massive protons and neutrons make up the atom s nucleus while the electrons orbit the nucleus in different shells The rst shell can only hold up to two electrons Each shell beyond that can contain up to eight electrons The bottom line is that electrons Em travel in pairs and all the electron shells want to be full When we say the electron likes this or the electron shells wan that what we really mean is that the atom is more stable when it has what it wants Slide 4 Because atoms are electrically neutral there are only going to be as many electrons as there are protons in an atom and the electron shells will not necessarily be full Let s take a closer look at a phosphorous atom As you can see the two inner shells are complete The first shell has two electrons and the second shell has eight electrons But the third shell only has five electrons This means that there are three unpaired electrons AND an empty shell This is an unstable and unhappy atom Atoms like this one whose outer shells are not full are much more likely to react than those with full outer shells The ways in which atoms maintain electrical neutrality while filling their outer shells with electrons the eetet rule lead to chemical interactions and bonding Slide 5 Ionic bonds are fairly simple to understand They form between atoms with very different electron arrangements The classic case is NaCl or table salt Sodium Na has only one electron in its outer shell 7 that s one lonely electron Chlorine has 7 electrons in its outer shell 7 it wants to get that eighth electron to complete the shell in chemistry this is referred to as the octet rule Both atoms are unstable because of their electron arrangements In ionic bonding there is a complete transfer of that lonely outer electron from sodium to complete the outer shell of chlorine Now there is one negatively charged ion Cl and one positively charged ion Na with a strong attraction for each other The electrical attraction between the two ions holds them together Just remember when it comes to ionic bonding opposites attract Slide 6 Covalent bonding involves a sharing of electrons among atoms Let s think about carbon since it is about the most important biological element Carbon has 4 electrons in its outer shell available to interact with other electrons Gaining or losing one electron as in ionic bonding will not do much to complete carbon s outer shell so atoms like carbon have to do things differently As 2 atoms with unpaired electrons move closer to each other the nuclei with their positively charged protons attract the negatively charged electrons of both atoms The atoms end up sharing a pair of electrons so both atoms are more stable Carbon is most stable if it can nd four atoms with unpaired electrons to share with it as in this example with methane in gure a Figure b simply shows some different ways of representing a covalent bond Covalent bonds may be single 7 where two atoms share one pair of electrons 7 or multiple with more than one pair of electrons shared between 2 atoms Double bonds between carbon and oxygen are pretty common When you get a chance go back and look at the periodic table to gure out why that is Slide 7 Atoms that participate in covalent bonding don t always share the electron pair equally One nucleus may exert a stronger force on the electrons and so pull them a little closer This attractive force that an atom exerts on electrons is called electronegativity Whichever atom tends to pull the electrons closer will have a slightly negative charge to it indicated in the gure as 5 Molecules with a little negative charge at one end and a little positive charge at the other are called polar molecules and the bond is called a polar covalent bond Water is probably the most well known and maybe the most important polar molecule Its polarity is part of what makes it the universal solven This idea of polarity gets very interesting as we start looking at larger molecules There are many simple molecules that can be polar or nonpolar Water is a polar molecule Hydrocarbons are nonpolar In the covalent bonds that form between carbon and hydrogen the electrons are shared equally The ethane molecule in this slide is a nonpolar molecule There are also many large molecules that may have polar or nonpolar regions Slide 8 The last type of bond we are going to look at is the hydrogen bond Hydrogen bonds form between a positively charged 6 hydrogen and the negatively charged 5 end of a polar molecule The most obvious example is water where the oxygen atom from one water molecule is attracted to the hydrogen atom of an adjacent molecule Hydrogen bonding in water gives it many of its rather unusual properties like surface tension and cohesion Remember that hydrogen bonding isn t just found in water Hydrogen bonds help hold proteins together and make the double helix of DNA possible Slide 9 We ve looked at 3 types of bonds so far This table points out the main features of ionic covalent and hydrogen bonds and gives you an idea of which bonds are stronger Covalent bonds are by far the strongest 7 about 10 times as strong as ionic or hydrogen bonds Why are covalent bonds so much stronger Let s recap what forms the three types of bonds Ionic bonds result from the swapping of an electron Hydrogen bonds pull partial positive and partial negative charges together But in a covalent bond an electron is being shared between two atoms It may help to think of it this way if you are sharing a dinner plate with someone you have to sit very close to them so you both have equal access to the food This need for close proximity is what gives a covalent bond its strength Van der Waals forces and hydrophobic interactions are two chemical interactions that are signi cantly weaker than the three main chemical bonds Van der Waals forces which arise from the interaction of electron clouds are relatively weak forces but can produce a big effect in large numbers This type of interaction is what allows a gecko to climb up walls Hydrophobic interactions have to do with the tendency for nonpolar molecules to interact among themselves The classic example of this type of interaction is the oil and water don t mix thing When you put oil in water you get a blob of oil in the water because polar and nonpolar molecules don t like to interact Hydrophobic interactions are part of what makes lava lamps work In this table you can also see some of the conventions for drawing the different types of bonds The solid single or double lines indicate a single or double covalent bond The dotted lines indicate a hydrogen bond and so on You ll see these representations throughout the course Slide 10 Now that you have seen how atoms interact with each other let s look at a few of the biologically important groups they form A functional group is defined as a small number of atoms covalently bonded to each other in a particular way What s interesting about functional groups is that they have the same chemical properties no matter what larger molecule they are a part of Take the hydroxyl group found in alcohols for instance This functional group consists of an oxygen atom covalently bonded to a hydrogen atom No matter where you find this group it has the same chemical properties For example hydroxyl groups can break away from the rest of the atoms they are attached to combine with a hydrogen atom from another molecule and form water In addition to hydroxyl groups there are three other functional groups that you will encounter frequently in biology amino groups carboxyl groups and phosphate groups Amino acids the stuff that makes up proteins all have an amino group and a carboxyl group on either side of a central carbon atom When your cells make proteins these two functional groups interact to form a covalent bond that holds the amino acids together Phosphate groups are found all over the place in your cells This is probably because the properties of phosphate groups make them ideal for energy transfer reactions We ll see a lot more of each of these functional groups and their interactions later on Li ids Slide 2 If something feels greasy or oily when you touch it it is either a lipid or contains lipid components Lipids are carbon containing compounds that are generally insoluble in water These substances are hydrophobic or water fearing compounds Because they are classified according to their property 7 being insoluble in water 7 as opposed to structure the term lipid encompasses a diverse group of molecules Slide 3 There are three main types of lipidsl Fats and oils generally associated with energy storage 2 Phospholipids the main component of cell membranes found in all organisms They also form organelle membranes in eukaryotic cells Most membranes have two lipid layers review cell membrane and 3 Other lipids such as steroids and some pigments For example cholesterol is a sterol and a component of animal membranes It is also a precursor molecule for some of the sex hormones and vitamins found in vertebrates Slide 4 Many lipid molecules consist of two parts 1 A polar group which is the hydrophilic or water loving component The phosphate molecule of a phospholipid is frequently bonded to a small polar molecule such as choline enhancing the hydrophilic properties of the molecule Other lipids such as cholesterol often contain a hydroxyl group as the polar component of the molecule 2 The second part is the nonpolar group which is the hydrophobic or water fearing component The nonpolar group is composed mostly of fatty acid chains These are molecules with a carboxyl group at one end which is attached to a hydrocarbon tail that varies in the number of carbon molecules and the number of double bonds that are present Slide 5 Fatty acid chains are important constituents of lipids Synthesis of fatty acid chains begins with a condensation reaction between acetylCoA and malonyl ACP Two carbon units derived from acetylCoA are then added in a stepwise fashion until the chain reaches a predetermined length usually somewhere between 12 to 20 carbons long In eukaryotes fatty acids are synthesized in endoplasmic reticulum and plant plastids In prokaryotes lipids are synthesized on the inner surface of the existing cell membrane Slide 6 Fatty acid molecules are joined to a second molecule usually a glycerol molecule through the process of dehydration synthesis or condensation reaction forming an ester linkage Slide 7 When three fatty acids are joined to a glycerol molecule a triacylglycerol or triglyceride is produced Triacylglycerols are fat or oil molecules the main type of stored lipid Note that there are no hydrophilic regions associated with this molecule Slide 8 Animal fats are solid at room temperature because they contain saturated fatty acids 7 there are no double bonds between the carbon atoms present in the fatty acid chain This configuration allows the molecules to be closely packed together forming a solid at room temperature Slide 9 On the other hand plant and sh fatty acids are liquid at room temperature The fatty acid chains associated with the triacylglycerol contain one or more double bonded carbon atoms that produce kinks in the fatty acid chain These kinks allow for loosely packed molecules that remain liquid at room temperature Unsaturated fats contain one or more doublebonded carbon atoms in the fatty acid chain a monounsaturated fat has one double bond between two carbon atoms a polyunsaturated fat has more than one double bond in the fatty acid chain Slide 10 Phospholipids the main component of membranes found in all organisms are another important type of lipid Phospholipid molecules are produced when two fatty acid chains compared to three fatty acid chain in the stored lipids join to a glycerol molecule with a phosphate group The hydrophilic component contains a glycerol phosphate and small polar molecule such as choline the hydrophobic component is comprised of the fatty acid chains Phospholipids spontaneously form a bilayer with the fatty acid chains sandwiched between two hydrophilic layers Addition of proteins to the bilayer allows the membrane to be selectively permeable and maintain the internal environment in the cell Slide 11 Finally let s consider some other lipids such as sterols pigments and waxes The basic structure of sterol molecules is four fused rings with a hydroxyl group attached at the carbon3 position Addition of other functional groups produces different molecules that are components of the membrane or may act as signaling molecules within an organism For example cholesterol is important in stabilizing the membrane It can also be remodeled into different molecules such as vitamin D sex hormones and bile salts through subtle changes to the functional groups of the molecule Slide 12 Chlorophyll pigments that produce the green color of plants and carotenoids that produce the yellow orange color of egg yolks and pumpkin are also lipids Vitamin A is produced by splitting molecules of the carotenoid pigment beta carotene Slide 13 Some other lipids such as cutin waxes and suberin are molecules that are made of longchain fatty acids and acyl lipids In combination they form a protective barrier between the surface of an organism and the environment Examples of these protective barriers are evident as water is repelled from the surface of plants hair feathers and beeswax