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Macromolecules Molecules in the Cell • What’s in a cell? • Water • Ions like Na+, Cl-, Ca2+, PO43-, etc. • Macromolecule subunits and precursors • Macromolecules themselves • Other small organic molecules: enzyme co-factors, secondary metabolites. Four Types of Macromolecule • • • • • “Macromolecule” means “large molecule” Macromolecules are formed from subunits. The subunits are monomers that are joined into a polymer. All cells use the same 4 types of macromolecules, with the same subunits. Macromolecules have a specific sequence of different type of monomers (especially proteins and nucleic acids). Macromolecules also have a specific polarity: a beginning and an end. Synthesis and Breakdown • All of the major types of macromolecule are synthesized through dehydration reactions: removal of H2O from the two molecules being joined together. – Synthesis requires energy input: going from monomers to a polymer is a large reversal of entropy • Breakdown of the macromolecules into their subunits occurs by the reverse reaction: hydrolysis. In hydrolysis, H2O is added to the bond to break it. Carbohydrates • • Carbohydrates are macromolecules composed of simple sugars (monosaccharides). A monosaccharide’s composition has a ratio of 1 carbon to 2 hydrogens to 1 oxygen: (CH2O)n. The simple sugars in living cells have between 3 and 7 carbons, most commonly 5 or 6. – Sugars are often described by the number of carbons: pentose = 5 carbons, hexose = 6 carbons, etc. • Monosaccharides contain several –OH groups and either an aldehyde or a ketone group. – Aldoses have an aldehyde group; ketoses have a ketone group. – Sometimes other functional groups are also attached: amino, carboxylic acid, etc. For example, glucosamine and glucuronic acid, both derived from glucose. Sugar Rings • In aqueous solutions, the C=O group (aldehyde or ketone) reacts with the second-to-last C-OH to form a ring. Sugars can be drawn as linear structures or as rings, but in the cell, they are mostly rings. – Note that the 6 member hexose ring contains 5 carbons and one oxygen, with the sixth carbon outside the ring. – The rings are not planar (as in benzene), but rather they are usually found in a bent configuration (“chair” configuration). Sugar Stereoisomers • • • Many simple sugars differ from each other in the configuration of their –OH groups. Otherwise, these compounds are identical. Hexoses contain 4 asymmetric carbons (carbons with 4 different groups attached). Each asymmetric carbon generates a lefthanded and a righthanded stereoisomer. These stereoisomers are all recognizably different: enzymes in the cell treat them differently. – Note that these are all diastereomers: not mirror images • Below is the set of all D-aldose hexoses. This group includes glucose, galactose, and mannose, which are used in the cell. – There also exist mirror images of each: the enantiomers, with names like L-allose, L-glucose, etc. Sugars Forming Bonds • Sugars bond with other sugars through a dehydration reaction. The sugars are separated by hydrolysis, the reverse of dehydration. • Most sugar-sugar bonds are between the 1carbon (at the right end of the ring) and the 4carbon (at the left end). • The –OH on the 1-carbon can be in the alpha configuration (pointing down) or the beta configuration (pointing up). This leads to alpha 1,4 linkages and beta 1,4 linkages. The difference is very important: the only difference between starch (readily digestible) and cellulose (indigestible) is that the glucoses in starch are linked alpha 1,4 and the glucoses in cellulose are linked beta 1,4. • Some also bond between the 1-carbon and the 6-carbon (outside the ring). Sugar Compounds • Disaccharides: 2 sugars – Maltose (glucose + glucose) – Lactose (galactose + glucose) – Sucrose (glucose + fructose) • Oligosaccharides and polysaccharides: chains linked mostly 1,4, but with branches using 1,6 linkages. Oligosaccharides are shorter than polysaccharides, but the distinction is minor. • Complex oligosaccharides are often attached to proteins or lipids on the cell surface: glycoproteins and glycolipids. Often involve many different simple sugars. Function of Carbohydrates • Two main functions: food storage and structure. • Most organisms use glucose as the primary food molecule, converting many other compounds into glucose, then burning it in the processes of glycolysis and respiration. – Glucose can easily be stored as a polymer. In plants this is starch, which is mostly linear chains of glucose. In animals, glycogen is more highly branched chains of glucose. • Cellulose is the main component of plant cell walls. • Chitin forms the exoskeleton of insects and also the cell walls of fungi. • Peptidoglycan forms the cell walls of bacteria. Peptidoglycan ties linear chains of sugars together with short peptides. Lipids • Lipids are the main hydrophobic molecules in the cell. • Most lipids are composed of fatty acids attached to glycerol, but other types include steroids, waxes, and isoprene compounds. Lipids: Glycerol + Fatty Acids • Fatty acids are long linear hydrocarbon chains with a carboxylic acid group (COOH) attached to one end. Hydrocarbons are carbon atoms linked together, with hydrogens attached to all the unused bonds. – The hydrocarbon chains are usually between 12 and 20 carbons long • Glycerol is a 3 carbon sugar. – If each of the –OH groups is attached to a fatty acid, it is a triacylglyceride (triglyceride), used for long term food storage. – If 2 of the glycerol –OH’s are attached to fatty acids, and the third is attached to a phosphate group, it is a phosopholipid, the main component of cell membranes. Fatty Acid Saturation • Fatty acids are saturated if all the carboncarbon bonds are single bonds, which implies that maximum number of hydrogens are attached. • Unsaturated fatty acids contain one or more carbon-carbon double bonds, which means fewer hydrogens can be attached. • C=C bonds are rigid and planar. This means that the next carbons in the chain can come in from the same side (cis) or opposite sides (trans). – In the cell, most are cis. Trans fatty acids are made by artificially adding H’s to some (but not all) double bonds in unsaturated fats, to make them solid (like margarine). Consequences of Saturation • Saturated fatty acids are very linear. In contrast, a cis bond in an unsaturated fatty acid puts a kink in the chain. • Saturated fatty acids can pack very tightly together. This makes them solid at room temperature: butter and lard, for example. • Cis-unsaturated fatty acids don’t pack together well, so they are liquid at room temperature: things like vegetable oils. Phospholipids and Cell Membranes • Phospholipids are composed of 2 fatty acids attached to glycerol, with the third position on the glycerol having a phosphate group that has a small polar molecule such as choline attached to it. • This structure makes the molecule amphipathic: one end is hydrophilic and the other end is hydrophobic. • When put in water, the hydrophilic ends sit facing the water, and the hydrophobic ends cluster together to avoid the water molecules. This produces the bilayer structure of the cell membrane. – The center of the membrane is hydrophobic, which makes it very hard for most molecules dissolved in water to get through. Other Lipids • Steroid compounds consist of 4 carbon rings attached in a specific way, with various side groups attached. – The most important steroid is cholesterol, a component of cell membranes – Many hormones are steroids. • Isoprene is a 5 carbon compound that can be polymerized in many ways to form things like rubber, scents, waxes. Proteins • • • • • • The most important type of macromolecule. Roles: Structure: collagen in skin, keratin in hair, crystallin in eye. Enzymes: all metabolic transformations, building up, rearranging, and breaking down of organic compounds, are done by enzymes, which are proteins. Transport: oxygen in the blood is carried by hemoglobin, everything that goes in or out of a cell (except water and a few gasses) is carried by proteins. Also: nutrition (egg yolk), hormones, defense, movement Amino Acids • • • • • • Amino Acids are the subunits of proteins. Each amino acid contains an amino group (NH2) and an acid group (-COOH). These groups are attached to a central carbon, called the alpha carbon. Each amino acid also has an R-group, which is different for each of the 20 amino acids used in cells. Amino acids are joined by a dehydration reaction. The bond between them is called a peptide bond, and a chain of amino acids is called a polypeptide. Proteins consist of one or more polypeptides, sometimes with additional small molecules attached. The polypeptide subunits of a protein are attached by non-covalent bonds, including hydrogen bonds, electrostatic interactions, and Van der Waals forces. R-Groups • There are 20 different kinds of amino acids in proteins. Each one has a functional group (the “R group”) attached to it. • Different R groups give the 20 amino acids different properties. They can be classified in many ways, but we will stick to: acidic, basic, polar (hydrophilic) and non-polar (hydrophobic). – Some amino acids don’t fit neatly into these categories. • The different properties of a protein come from the arrangement of the amino acids. Charged Amino Acids • Amino acids whose R group carries a + or – charge at neutral pH. • Basic amino acids all have some version of an amino group (-NH2), which picks up an H to become – NH3+. – Lysine, arginine, and histidine. • Acidic amino acids (aspartic acid and glutamic acid) have a carboxylic acid (-COOH) group, which loses an H to become –COOat physiological pHs. Hydrophobic • Hydrophobic amino acids are non-polar, and are mainly found in the interior of proteins, or the hydrophobic region inside membranes. • Some of them are aromatic (with benzene rings), while others just have hydrocarbon (aliphatic) R groups. Uncharged Hydrophilic R groups • Uncharged hydrophilic amino acids are polar, due to C-N, or C-O bonds. They are mainly found on the surface of proteins, facing the aqueous medium. • The acidic and basic amino acids are also polar and usually found on the protein surface. Protein Structure • After the polypeptides are synthesized by the cell, they spontaneously fold up into a characteristic conformation which allows them to be active. The proper shape is essential for active proteins. – For most proteins, the amino acids sequence itself is all that is needed to get proper folding, but some need help from chaperone proteins. • Proteins fold up because they form hydrogen bonds between amino acids. The need for hydrophobic amino acids to be away from water also plays a big role. Similarly, the polar amino acids need to be exposed to water. Also, the charged amino acids often bond by electrostatic interactions. Proteins • The joining of polypeptide subunits into a single protein also happens spontaneously, for the same reasons. • Enzymes are usually roughly globular, while structural proteins are usually fiber-shaped. Proteins that transport materials across membranes have a long segment of hydrophobic amino acids that sits in the hydrophobic interior of the membrane. • Denaturation is the destruction of the 3-dimensional shape of the protein. Denaturation inactivates the protein, and makes it easier to destroy. This is the effect of cooking foods. Various Proteins Collagen Enolase Myosin ATP Synthase Transmembrane peptide transporter Nucleic Acids • • • • • Nucleotides are the subunits of nucleic acids Nucleic acids store genetic information in the cell. They are also involved in energy and electron movements. The two types of nucleic acid are RNA (ribonucleic acid) and DNA (deoxyribonucleic acid). Each nucleotide has 3 parts: a sugar, a phosphate, and a base. The sugar, ribose in RNA and deoxyribose in DNA, contain 5 carbons (pentoses). They differ only in that an –OH group in ribose is replaced by a –H in DNA. – The –OH group is much more reactive than just an –H, which is one reason DNA is more stable than RNA. • The carbons in the sugar are numbered from 1’ to 5’ (1-prime to 5-prime). – The base attaches to the 1’ carbon – The phosphate is attached to the 5’ carbon – New nucleotides are added to the 3’ carbon Bases • The bases are rings that contain both carbon and nitrogen. The purines have 2 joined rings and the pyrimidines are a single ring. • The purines in DNA and RNA are adenine (A) and guanine (G). • The pyrimidines in DNA are cytosine (C) and thymine (T); in RNA they are cytosine (C) and uracil (U). – Thymine and uracil are almost identical, except that thymine has an extra methyl (-CH3) group attached. • The base is attached to the 1’ carbon of ribose or deoxyribose, using the nitrogen at the bottom of the pyrimidine ring, or the nitrogen at the bottom of the 5 member purine ring. Pyrimidines Phosphates • Nucleotides can have 1, 2, or 3 phosphates attached in a chain to the 5’ carbon of the sugar. These are monophosphate (MP), diphosphate (DP), and triphosphate (TP). • After being polymerized into DNA or RNA, only 1 phosphate remains. Removal of the other two phosphates generates the energy needed for polymerization. Nomenclature • When a base is joined to a sugar, with no phosphates, the molecule is called a nucleoside. The nucleosides are named adenosine, guanosine, cytidine, uridine and thymidine. • When one or more phosphates is added, you have a nucleotide. – The number of phosphates is indicated in the nucleotide’s symbol; for example, ATP is adenosine triphosphate, and CMP is cytidine monophosphate. • Nucleotides can be deoxyribonucleotides, symbolized by a small d: dATP is deoxy adenosine triphosphate. • If the nucleotides have ribose, they are ribonucleotides, which are symbolized without any addition: ATP is a ribonucleotide. • • • Adenine = base only Adenosine = base + sugar (nucleoside) Adenosine monophosphate (AMP) = base + sugar + phosphate (nucleotide) Nucleic Acid Synthesis • Nucleotides are joined by a phosphodiester linkage, between the 3’ carbon of one sugar and the 5’ carbon of the next sugar in the chain. • The synthesis reaction is a dehydration reaction. • Individual nucleotides are added to a growing chain or DNA or RNA. The raw materials are nucleoside triphosphates. Two of the phosphates are removed and the innermost phosphate is attached to the free 3’ – OH group at the end of the growing chain. – The chain is said to grow from 5’ to 3’. The 5’ end is the beginning and the 3’ end is the end of a DNA or RNA molecule. DNA and RNA • DNA uses 4 different bases: adenine, guanine, thymine, and cytosine. • The backbone of a DNA strand is a chain of alternating sugars and phosphates. Two antiparallel DNA strands are twisted into a double helix It is held together by hydrogen bonds that connect the complementary bases in the center of the molecule. – A pairs with T, and G pairs with C. – DNA is a stable molecule which can survive thousands of years under proper conditions • RNA consists of a single chain that also uses 4 bases: however, the thymine in DNA is replaced by uracil in RNA. RNA is much less stable than DNA, but it can act as an enzyme to promote chemical reactions in some situations. – Some of the bases in RNA pair with each other, giving each RNA molecule a characteristic shape. Other Nucleic Acids • The main energy-carrying molecule in the cell is ATP. ATP is an RNA nucleotide with 3 phosphate groups attached to it in a chain. The energy is stored in the phosphoanhydride bonds between the phosphates. • Several coenzymes (small molecules that are used by enzymes) are built from nucleotides. For example, coenzyme A, which is used in generating energy from glucose. It is a modified ADP molecule. • Some nucleotides are used in signalling pathways. For example, cyclic AMP. Extra Two Special Amino Acids • Cysteine has an –SH group at the end of its R group. Two cysteines can be covalently bonded by oxidizing their –SH groups to a single –S-S- , which is called a disulfide bond. – Disulfide bonds help give a protein its three dimensional structure • Proline has an R group that is attached to the amino acid’s amino group. This structure introduces a kink in the polypeptide chain.