Biological Molecules Learning Materials

Biological Molecules Atoms, Molecules, and Chemical Bonds The structure of atoms dictates their chemical reactivity The smallest unit of an element that retains its defining chemical properties is known as the atom. Atoms are, in turn, composed of sub-atomic particles: positively charged protons and electrically neutral neutrons, which are clustered in a central nucleus and surrounded by negatively charged electrons Electrons are found in discrete states of varying distance from the nucleus, known as shells. The innermost shell contains up to two electrons; the second and third shells can accommodate eight electrons each, and the fourth shell contains up to 18 electrons electron An atom is most stable and chemically unreactive when its outermost electron shell is completely filled, that is, when it contains the maximum number of protons & neutrons electrons for that shell Covalent bonds form when electrons are shared between atoms An atom whose outer shell is not filled is chemically reactive, meaning that it can participate in chemical reactions with other atoms to form molecules By sharing electrons, the atom can achieve a full outer shell and becomes more stable as a result Sharing of electrons between atoms is the basis of covalent bonds, whereby atoms are joined to one another to form molecules. The sharing of one pair of electrons gives rise to a single bond between two atoms. Sharing of two pairs of electrons constitutes a double bond The precise amount of energy needed to break a covalent bond depends on the types of atoms involved and the number of bonds they form with one another, the double bonds generally being stronger than single bonds Shape and flexibility of a molecule are determined by its electrons When an atom participates in a covalent bond with more than one other atom, the covalent bonds will be arrayed in a configuration that is characteristic of the particular atom The number of bonds that are formed between two atoms places an additional constraint on molecular geometry. Although atoms can rotate freely about a single bond, double bonds have properties that create a barrier to rotation The effective size of an atom is determined by its electrons Just as two billiard balls cannot inter penetrate one another, non-bonded atoms can only come within a certain distance of one another before they begin to clash When atoms come closer than the sum of their van def Waals radii, the interaction energy becomes highly unfavorable and they repel one another. When atoms are very far apart - that is, at distances equal to many times their van der Waals radii - they da not interact at all and the interaction energy is therefore nearly zero. However, atoms that are separated by just around the sum of their van der Waals radii weakly attract one another As the distance between the nuclei increases further, however, this attraction decreases until there is no net attraction or repulsion between the two nuclei Electrons are not always shared equally by atoms joined by covalent bonds As a result, the atom with the greater share of the electrons has a partial negative charge and is therefore electronegative, while the atom with the lesser share has a partial positive charge and is therefore electropositive Polar chemical groups interact most favorably with polar molecules such as water, while nonpolar groups prefer to interact with one another rather than with the polar solvent Atoms can become fully charged Because of their energetic preference to have a completely filled outer shell, atoms sometimes gain or lose electrons entirely and therefore become fully electrostatically charged Elements whose outer shells are just one electron short of being filled can acquire an electron and thereby become negatively charged. Conversely, atoms that have just one or two outer shell electrons can lose these electrons and become positively charged Life in Aqueous Solution Water can become ionized Any aqueous solution contains some water molecules that have dissociated into positively and negatively charged ions. A water molecule can lose a proton, denoted H+, from one of its hydrogen atoms, leaving a negatively charged hydroxide ion, OHIn a solution of pure water, only a very small percentage of water molecules will dissociate in this way; the concentration of OH- and H3O+ ions is just 10^-7 M. Importantly, the concentration of OH- and H3O+ ions in a solution are intrinsically linked; the product of the concentration of these two ions is always equal to 10^-14 pH denotes the concentration of hydrogen ions in solution A variety of compounds can become ionized in aqueous solution to release either OH- or H+ ions. The H+ ions (protons) associate with water molecules to form H3O+ ions, whereas the OH- ions remain "free" In solution Molecules that are able to release H+ when they dissolve in a solution are called acids, while molecules that are able to absorb (or "accept") H+ to reduce the concentration of H+ in a solution are called bases Pure water thus has a pH of 7, which we call "neutral", solutions with a pH less than 7 are considered acidic, conversely, solutions with a pH greater than 7 are called basic or alkaline Non-covalent Interactions Non-covalent interactions allow dynamic interactions between molecules The binding interactions that occur between biological molecules involve energies that are far lower than those of the covalent bonds and can therefore be more readily disrupted and reformed as they mediate dynamic processes in the cell These weaker interactions, known as non-covalent interactions, underlie processes that require rapid or transient interactions, such as proteins binding to DNA to regulate gene expression, muscle proteins associating and then disengaging as the muscle fibers contract, and signaling proteins binding at cell surfaces All non-covalent interactions are fundamentally electrostatic in nature, which means that they depend on the attractive forces between opposite charges Types of non-covalent interactions: • Salt bridges, which are ionic interactions • Hydrogen bonds, which are interactions between polar atoms • van def Waals interactions, which arise from a ractive forces A salt bridge is an ionic interaction between charged chemical groups Since the electrostatic field of a fully charged atom extends at equal strength in all directions, the energy of a salt bridge does not depend on the precise orientation of the two oppositely charged groups and is only a function of the distance between them Salt bridge: a non-covalent interaction in which both donor and acceptor atoms are fully charged Hydrogen bonding between two dipoles is a common non-covalent interaction A hydrogen bond arises from electrostatic interactions between the positive end of one dipole and the negative end of another. The positive end is located on A hydrogen atom that is joined by a polar bond to an electronegative atom, and the negative end is located on a different electronegative atom, usually oxygen or nitrogen Hydrogen bond donor: partially positively charged hydrogen atom in a hydrogen bond Hydrogen bond acceptor: partially negatively charged atom participating in a hydrogen bond Hydrogen bonds can impose a high degree of specificity on the interactions between two binding partners, since the interaction energy is most favorable when the hydrogen bond donors and acceptors on each macromolecule pair up at the binding interface so that the hydrogen bonds that form have the appropriate geometry and distance from one another van der Waals interactions can occur between any two atoms The van der Waals interaction arises when the close approach of two atoms causes each atom to induce transient dipoles in the other atom van der Waals interactions can occur between any two atoms and are particularly important in interactions between non-polar atoms or chemical groups that cannot participate in other types of non-covalent interaction The aqueous environment of the cell affects the energy of non-covalent interactions Salt bridges, for example, seldom have the large favorable energy one would expect from the attractive force between full opposite charges because the surrounding water molecules and ions also interact with charged groups, thereby reducing the attractive energy of the salt bridge interaction Polar molecules and highly charged molecules dissolve readily in water because of the many hydrogen bonding interactions they can make with water. By contrast, highly non-polar molecules do not make energetically favorable interactions with water and prefer, instead to associate with one another The distinct behavior of hydrophilic and hydrophobic chemical groups in water dictate the threedimensional S structure of proteins and nucleic acids, the formation of cell membranes, and the way in which biological molecules interact with one another Hydrophobic interactions drive the folding of biological macromolecules In an aqueous environment, the hydrophobic portions of molecules preferentially cluster together, driven by the preference of hydrophobic groups to associate with one another By contrast, hydrophilic regions of a molecule can interact favorably with an aqueous environment and will preferentially lie on the surface of a molecule where they are exposed to the surrounding aqueous medium This partitioning - with hydrophobic regions of a molecule shielded from an aqueous environment, and hydrophilic regions directly exposed to it - is an important driving force behind the way that macromolecules, such as nucleic acids and proteins, fold into their characteristic three-dimensional shapes Non-covalent interactions stabilize the binding of macromolecules at chemically complementary interfaces Whether or not molecules bind to one another, and for how long, depends on the strength of the interaction and on the concentration of each component Favorable chemical interactions arise when hydrophobic groups on one surface interact with hydrophobic groups on the other, when there is pairing of hydrogen bond donors and acceptors, or when positively and negatively charged side chains interact Specificity: preferential binding between two molecules relative to others that have similar properties Nucleotides and Nucleic Acids Nucleic acids play a fundamental role in the processes of life The function of DNA is to store genetic information in all cells and in some viruses. RNA can also store genetic information and forms the chromosomes of other viruses, but has many other functions, including decoding the genetic information in all forms of life and catalyzing the key chemical reactions during protein synthesis Cells contain nucleotides of two general types Nucleotides are small molecules composed of an aromatic group known as a base (also called a nucleobase), a sugar, and one or more phosphate groups DNA bases: • Adenine • Guanine • Thymine • Cytosine RNA only base: • Uracil The bases are planar, conjugated rings that are typically uncharged under physiological conditions but can gain or lose A proton at near physiological pH A nucleotide is formed when one or more phosphate groups are attached by phosphate ester linkages to either the 3' or the 5' hydroxyl groups of the nucleoside sugar, giving rise to ribonucleotides and deoxyribonucleotides DNA and RNA are polymers of nucleotides Each nucleotide is added with a 3' to 5' linkage in the same way, so that a DNA strand has defined directionality, with A 5' phosphate group exposed at one end and a 3' OH at the other end The deoxyribose sugars and phosphodiester linkages comprise a monotonously repeating sugar-phosphate backbone, whereas the base attached to each sugar can vary from one nucleotide to the next along the DNA strand Nucleotide monomers have diverse important functions in cells One of these roles is to store energy derived from the breakdown of food in high-energy covalent bonds within molecules such as ATP. These bonds can then be broken to release energy that can be used to drive chemical reactions and mechanical processes The structure of DNA Single strands of DNA associate non-covalently to form a double-helical structure The bases on opposing strands form hydrogen bonds that cause them to pair with one another in a precise correspondence that is dictated by their geometry; cytosine on one strand makes three hydrogen bonds with the complementary surface of guanine on the other, whereas thyme on one strand makes two hydrogen bonds with the complementary surface of adenine on the other Two complementary DNA strands pair readily with each other when the strands are oriented in opposite directions, so that the 5' end of one strand pairs with the 3' end of the other The hydrophilic sugar-phosphate backbone of each DNA strand lies on the outside of the helix where it can interact with water molecules, while the largely hydrophobic base pairs lie on the inside This arrangement, called base stacking, is energetically highly favorable and is a major factor in stabilizing the structure of double-stranded DNA and thus contributing to the durability required for the robust storage of genetic information DNA can adopt other conformations One of these is the A-DNA helix which has 11 bp per turn, with the base pairs tilted relative to the DNA axis, as well as being displaced farther from the DNA axis than they are in B-DNA. As a result, the A-DNA helix has a narrower, deeper major groove and a shallower, wider minor groove than B-DNA The A-helix conformation can be induced by some proteins that form a complex with DNA. It is therefore thought that some segments of chromosomal DNA that are bound to these proteins may adopt a conformation closer to the A-DNA helix Although we often draw the DNA helix as following a straight path, DNA can bend somewhat, and certain base sequences are more bendable than others. In general, regions of the DNA double helix containing successive A-T followed by T-A base pairs tend to bend more readily than helicase with G-C steps An unusual type of DNA helix that spirals in the opposite direction, and is therefore left-handed, can form under special conditions in DNA strands with alternating G and C bases. This helix is known as Z-DNA DNA can contain topological variations known as supercoiling If the DNA is a closed circle, as is the case for many bacterial and viral chromosomes, it typically looks highly intertwined and tangled when it is isolated from a cell. This is because the DNA is supercoiled, which places the molecule under tension and causes it to twist on itself An initial unwinding of the DNA - which is in the clockwise direction and is equivalent to separating the DNA strands - leads to accumulation of negative supercoils, whereas an initial twisting of the DNA in the counterclockwise direction leads to formation of positive supercoils Supercoiling can also occur in linear fragments of DNA in which the ends are immobilized, and therefore not free to rotate and release superhelical tension If a nick or break is introduced into a supercoiled plasmid or chromosome, one end will swivel around the other to relax the supercoiling, and hence alleviate the strain on the DNA molecule Negative supercoiling favors local unwinding of DNA Negative supercoils in DNA can be removed by unwinding one or more turns of DNA, which is equivalent to separating the strands. In this way, the unfavorable energy of strand separation is partially compensated for by the favorable energy due to relief of negative superhelical tension Since increasing the degree of supercoiling is energetically unfavorable, enzymes that introduce additional supercoils into DNA - usually negative - must use the energy provided by ATP hydrolysis to drive this process Chemical Properties of RNA RNA is chemically distinct from the related nucleic acid DNA Furthermore, it is the ability of RNA to form base pairs with DNA, as well as with RNA, that allows cells to synthesize RNA copies of genes from a DNA or RNA template However, the presence of the 2' OH on ribose and the distinct chemical structure of uracil, as compared with thymine, allow RNA to adopt diverse structures that are not readily formed by DNA RNA is often chemically modified after it is synthesized Many RNA molecules require chemical modification of some of their nucleotides in order to become fully functional. These modifications, which alter the chemical structure of the bases, are introduced after the RNA is synthesized In contrast with DNA methylation, which plays a role in regulating whether a gene is transcribed or not and is reversible, chemical modifications of RNA are largely irreversible and do not play a regulatory role The position and nature of nucleotide modifications in a particular RNA molecule are often conserved among different species. This conservation suggests that these modifications Play important roles in the molecules in which they are found The 2' OH of ribose has important structural and functional consequences The chemical stability of RNA polymers is much lower than that of DNA because the oxygen in the 2' of of ribose facilitates a reaction that can cleave phosphodiester bonds The less stable RNA molecule has been retained as the intermediate messenger, since mRNA is typically needed for only a limited period of time before it degrades chemically or is actively broken down by enzymes in the cell However, the presence of the 2' OH on the ribose causes double-stranded RNA to exclusively adopt the A-type helix for two reasons: First, the 2' OH of ribose would clash with the sugar-phosphate backbone, if RNA were to form a B-type helix Second, the additional hydroxyl group on the 2' position of ribose causes the sugar ring to buckle in a distinct fashion known as C3' endo, which favors the formation of an A-type helix, instead of the C2' endo conformation typically found in B-type helicase RNA Folding and Structure RNA can fold to form compact structures The precise conformation, or fold, of an RNA molecule is determined by its nucleotide base sequence. Together, the fold and nucleotide composition determine the functional properties of the RNA The primary structure of RNA refers simply to the sequence of bases along an RNA strand, reading from the 5' to 3' direction. Portions of the RNA molecule can form short double-helical stretches, and we refer to these regions as RNA secondary structure. The single and doublestranded portions of the RNA molecule come together to form a precise arrangement, which is its tertiary structure Short RNA helices are the building blocks of larger RNA structures If these complementary sequences are relatively close together in the linear or primary RNA sequence, the RNA forms what is called a hairpin structure. The double-helical portion of the hairpin is called the stem, and the unpaired bases are called the loop Unlike DNA helices, RNA helices regularly contain base pairs that do not result from typical Watson-Crick interactions. Termed non-canonical base pairs, these base pairs often feature bases that have been chemically modified in some way One of the more commonly observed non-canonical base pairs is formed between G and U nucleotides. This base pair is stabilized by two hydrogen bonds, just like a Watson-Crick A-U base pair, and is referred to as a "wobble" base pair Short helices assemble to form the final folded RNA structure The strong tendency of base pairs to stack upon one another gives rise to coaxial stacking, in which the helical segments stack with their central axes roughly lined up A second general feature of RNA structure is typed by interactions between nucleotides in unpaired and base-paired regions of a single RNA molecule. Hydrogen bonding interactions involving the 2' OH of ribose or the exposed chemical groups on the bases are particularly common Base triple: three interacting, coplanar bases typically consisting of a Watson-Crick base pair that hydrogen bonds with a third base via its remaining unpaired chemical groups A-minor motif: a commonly seen structural motif in RNA where adenosines found in distant regions interact via their minor-groove face with the minor groove of a neighboring helix, often with their 2' OH groups A potential barrier to the folding of RNA into a compact three-dimensional shape is the high density of negative charge associated with the phosphodiester backbone, which would give rise to electrostatic repulsion when different segments of the backbone come together These positively charged magnesium ions balance the negative charges of the oxygen atoms in the sugar-phosphate backbone, allowing the backbones of different regions of the RNA to pack against one another as they are buried in the interior of the molecule Fundamentals of Protein Structure Proteins are the most versatile macromolecules in biology Proteins can catalyze chemical reactions and form structural components of a cell; they can create channels in a membrane to allow molecules to pass in and out of cells; and they can recognize a vast array of infectious microorganisms This chemical diversity makes it possible for different proteins to adopt highly specialized structures that have been optimized through evolution to perform their particular tasks Amino acids are the building blocks of proteins There are side chains that are largely hydrophobic in character, and those that contain polar chemical groups. A few side chains contain both hydrophobic and hydrophilic groups, and are as a result termed amphipathic side chains The unique chemical properties of each side chain govern the interactions of side chains with one another, with other biological molecules, and with the aqueous environment of the cell Importantly, however, disulfide bonds are only found in extracellular proteins (those that are secreted from the cell) because the interior of the cell is a reducing environment - an environment in which the -S-S- linkage is unable to form Amino acids are joined by peptide bonds to form polypeptides These linkages, called peptide bonds, form through a reaction between the carboxylate group of one amino acid and the amino group of the next, generating one water molecule for each peptide bond that is formed Polypeptides have a repeating series of atoms that form the peptide backbone, from which the amino acid side chains protrude. One end of the polypeptide chain has an exposed amino group and is called the N-terminus, while the other end has an exposed carboxyl group and is called the C-terminus Properties of the peptide backbone govern polypeptide conformation The atoms that make up the peptide bond all lie in a plane due to a phenomenon known as resonance, in which electrons are shared among several atoms of the peptide bond unit. This sharing is what we call delocalization Consequently, each amino acid unit in the polypeptide backbone has only two covalent bonds about which free rotation can occur: the nitrogen-alpha carbon bond, which is defined by the rotation angle phi, and the alpha carbon-carbon bond, which is defined by rotation angle psi While the planarity of the peptide bond restricts the possible conformations of the polypeptide backbone, it still allows proteins to adopt an enormous number of conformations and contributes to the stability of protein structures Protein Folding Proteins fold to adopt defined three-dimensional shapes Each protein adopts a characteristic shape when the polypeptide folds upon itself to yield a much more compact three-dimensional arrangement of atoms. This process of collapse, referred to as protein folding, is driven by non-covalent interactions between atoms in the polypeptide chain The resulting three-dimensional arrangement of the atoms is called the protein's structure, or conformation, and is determined by the sequence of amino acids along the polypeptide chain and by the chemical and physical properties of the polypeptide backbone Primary structure: the amino acid sequence of a polypeptide chain Secondary structure: folded segments of a polypeptide chain with repeating characteristic phi and psi backbone torsion angles, that are stabilized by a regular pattern of hydrogen bonds between the peptide -N-H and C=O groups of different residues Tertiary structure: folded conformation of a protein Quaternary structure: submit structure of a protein The most common forms of secondary structure are alpha helices and beta sheets In an alpha helix, the polypeptide backbone curves in a right-handed helical path, allowing hydrogen bonds to form between the carbonyl oxygen of one residue and the amide nitrogen four residues further along the polypeptide chain Many alpha helices found in proteins have hydrophobic side chains exposed on one face and polar side chains exposed on the opposite face and are hence known as amphipathic alpha helices The beta sheet is formed when two or more segments of the polypeptide backbone, called beta strands, hydrogen-bond to one another through their backbone carbon and amide The ability of a region of a polypeptide chain to adopt one of the distinctive secondary structures described above depends on the primary structure of the polypeptide chain; certain amino acid residues favor the adoption of a given secondary structure more than others Secondary structural elements condense to form the folded protein The tertiary structure of a protein forms when the alpha helices and beta sheets, which are connected by less regular regions of the polypeptide chain, associate in a precise manner to form a defined three-dimensional shape The polar, aqueous environment of the cell drives protein folding by encouraging hydrophobic groups in the polypeptide chain to interact with one another inside the protein, while favoring the exposure of polar groups on the proteins surface Recalling that the secondary structure is stabilized by hydrogen bonding of the peptide backbone, it is energetically more favorable to bury hydrogen-bonded polar atoms in the hydrophobic interior of a protein than to bury unpaired hydrogen bond donor or acceptor atoms When hydrophobic side chains are exposed to water, the nearby polar water molecules tend to orient themselves in a way that cancels out one another's electric dipoles By contrast, when the protein folds, the hydrophobic side chains associate with one another, freeing the water molecules to adopt a larger variety of orientations in their polar surroundings Amino acid sequence determines protein structure There are many proteins that can be unfolded by a change in solution conditions - either by treatment with chemicals that destabilize the protein or by heating to high temperatures - and then spontaneously refold when the solution is returned to the original conditions Since the process of protein folding is so complex and involves an intricate network of noncovalent interactions, we still cannot reliably predict the tertiary structure of a protein solely from its primary amino acid sequence Amino acid sequence can reveal clues about protein function Since the amino and sequence of a protein determines its structure and function, it is sometimes possible to predict the function of a newly identified gene, based on the amino acid sequence of the protein it encodes Protein Folds Protein folds have been conserved through evolution However, some structures look very much like one another in their overall shape, secondary structure content, and the way in which secondary structural elements pack together and are connected by loops We refer to the arrangement of secondary structural elements that characterizes a particular protein as a protein fold. Proteins of identical structure - ones that have an identical arrangement of atoms in space - also have the same fold Two proteins with the same fold can sometimes overlay rather poorly in space because of differences in the precise length of secondary structural elements and the way in which they pack against one another Coiled coil: pair of alpha helices that coil around each other and associate via hydrophobic interactions to form a dimerization interaction Folds also vary greatly in size and secondary structure composition; the homeodomain, which binds DNA, is small and contains only alpha helices, while the much larger immunoglobulins are composed almost entirely of beta sheet Proteins can be composed of multiple domains Each distinctive region is called a domain, which is a compact region of protein structure usually made up of a contiguous segment of the polypeptide chain that is capable of folding on its own Protein-DNA Interactions Each DNA sequence has a distinct chemical signature that can be recognized A given DNA sequence is therefore characterized by a distinct array of hydrogen bond donors and acceptors, as well as by methyl groups that are exposed in the grooves The pattern of functional groups exposed in the major groove is unique to each DNA sequence, whereas there is less variability in the chemical surface exposed in the minor groove. This limited variability in the minor groove occurs because the pattern of hydrogen bond donors and acceptors is the same for A-T and T-A base pairs, and for G-C and C-G base pairs The surface of the protein that recognizes the DNA sequence contains a set of side chain and main chain atoms that can form favorable interactions with the particular array of DNA functional groups that are exposed Shape and charge complementarity are important in protein-DNA interactions If the shape of the protein is complementary to that of the DNA, there is an increased chance that side chains on the surface of the protein will approach functional groups on the DNA closely enough to form favorable non-covalent interactions While the minor groove of B-DNA is normally too narrow to accommodate either a helix or a beta sheet, distortions can be induced by protein binding that open up the groove Any protein that interacts with DNA - whether or not it binds to a specific sequence - must contain chemical features that favor binding to the highly negatively charged sugar-phosphate backbone of DNA Sugars and Carbohydrates Carbohydrates play a variety of roles in the cell Carbohydrates are also a major source of energy for all organisms and are the form in which many cells store energy for future use. Polymers known as complex carbohydrates can form rigid structures that provide mechanical support, such as the cell walls of bacteria and plants or the rigid exoskeleton of insects Simple sugars can form linear or ring-like structures Like the other major biological macromolecules proteins and nuclei's acids, carbohydrates are polymers, in this case built up from fundamental building blocks called monosaccharides Because the monosaccharides contain at least one asymmetrical carbon, they can exist in two non- interconvertible forms, called isomers. The d- or l- designation is defined by the arrangement of atoms around the chiral carbon furthest from the aldehyde or ketone group A structural feature of certain sugars is their ability to form covalently closed, ring-like structures. This occurs when a hydroxyl group reacts with a ketone or aldehyde carbonyl group, yielding A ring-like isomer Monosaccharides can be linked together to form complex carbohydrates The hydroxyl of one monosaccharide can be joined to another in a neighboring molecule by a condensation reaction that releases a water molecule. The resulting disaccharide comprises two sugars joined by a linkage termed a glycosidic bond Because of the many possible ways in which sugars can be linked to form oligo- and polysaccharides, carbohydrates form a much more diverse family of polymers than proteins and nucleic acids, which have only one type of linkage joining one building block with the next Carbohydrates play structural roles in all organisms Plant cell walls contain cellulose, a linear polysaccharide composed of glucose subunits that give plants their rigid structure. The unbranched glucose polymers that comprise cellulose form long, linear chains that line up and hydrogen-bond to one another, thereby strengthening the cell wall Carbohydrates can be attached to proteins and lipids Carbohydrates can be covalently attached to proteins to form glycoproteins, while lipids with covalently attached carbohydrates are called glycolipids The attachment of carbohydrates, termed glycosylation, stabilizes the structure of cell surface proteins and plays an important role in the interactions of cells with each other and with the free proteins surrounding cells Lipids Fatty acid are a key component in most types of lipid The hydrocarbon chain is hydrophobic, whereas the negatively charged carboxylic acid is hydrophilic, which means fatty acids are amphipathic A fatty acid can be saturated, meaning that all the carbon atoms are joined by single bonds, or they can be unsaturated, meaning that there are one or more double bonds joining the atoms in the hydrocarbon chain In biological systems, unsaturated bonds are generally found in the cis configuration, which introduces a kink in the hydrocarbon chain, rather than the trans configuration, which preserves the straight conformation found in saturated chains Saturated hydrocarbon tails are highly flexible molecules that can form extensive interactions with one another. Unsaturated tails, on the other hand, contain kinks caused by their double bonds and so do not generally pack together as tightly Many lipids are composed of fatty acids attached to a head group The head group of the most common phospholipids comprises glycerol, a phosphate group, and an alcohol. Two fatty ands are covalently linked directly to the glycerol, forming the hydrophobic portion of the lipid molecule, while the head group is the hydrophilic part Membranes contain a bilayer of oriented phospholipids The unique properties of phospholipids enable them to form a protective sheath around cells called a plasma membrane, which allows the cell to maintain an intracellular environment that is different from its exterior The amphipathic nature of phospholipids favors their arrangement in a lipid bilayer, with the polar head groups in contact with the surrounding aqueous medium and the hydrophobic fatty acid tails in the interior where they are shielded from water Proteins within the membrane allow communication between the cytoplasm and the cells exterior Cells must have the ability to take in a variety of molecules from the surrounding environment, as well as have a means to communicate with or respond to other cells or organisms Integral membrane proteins are embedded largely within the belayer, whereas some proteins are anchored to the membrane by inserting just a small portion of the protein into the bilayer In all cases, the portion of protein embedded in the membrane must be rich in hydrophobic side chains that interact favorably with the hydrophobic fatty acid chains within the lipid bilayer, with few, if any, polar or charged side chains For this reason, the peptide backbone that is buried within lipid bilayers is generally found in alpha-helical or beta-sheet form, because in these secondary structures the polar backbone atoms are hydrogen-bonded with each other