Biochemistry Part 1; Carbohydrates, Lipids & Proteins
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Biochemistry Part 1; Carbohydrates, Lipids & Proteins

August 31, 2019

Hello! This is the first presentation reviewing basic biochemistry. The focus here is on the carbohydrates, the complex lipids, and proteins, each formed by dehydration synthesis. So let’s quickly review what I showed you earlier. Here is the anabolic synthesis of a polymer, involving removal of a molecule of water. The reaction of course is a dehydration synthesis. Hydrolysis is a catabolic reaction involving the breakdown of a polymer by water addition across the linkages in the polymer. With that bit of review, let’s start with carbohydrates. Here we have a straight chain drawing of a molecule of glucose. Can you identify the optically active carbons, the ‘chiral’ carbons in this molecule? In fact the straight chain glucose is unstable in solution and quickly forms a ring structure, called the ‘hemiacetal’ structure, shown on the right. At equilibrium ninety percent of the dissolved glucose is in this form. Here is that #5 and #1 carbon that was involved in forming that hemiacetal in the first place. A consequence of hemiacetal formation is that the hydroxide on the #1 carbon can end up either above or below the plane of the ring. I’ve got that backwards but you get the idea, creating a racemic mixture of enantiomers of glucose called alpha and beta glucose. The alpha and beta glucose are present in equal proportions in a racemic mixture of hemiacetal glucose. In this slide, we’re going to see the formation of a glucose dimer by water removal, a condensation reaction. Here an alpha 1-4 glycoside linkage has formed between the 2, sugars linking the #1 carbon of glucose on the left with a #4 carbon of glucose on the right. Repetitive addition alpha glucose monomers to a growing chain can form starches in plants and glycogen in animals. The glycoside linkages, which could include alpha 1-4 like the one shown here as well as alpha 1-6 and other alpha linkages, are characteristic of flexible storage polysaccharides that eventually are hydrolyzed to get the sugar out to be metabolized for energy. If beta-glucose enantiomers are polymerized in condensation reactions like the one shown here, the beta glycoside linkages that form (here it’s a beta 1-4 linkage) create a rigid, inflexible polysaccharide like cellulose or chitin. Criss-crossing laminas of cellulose are laid down to form plant cell walls. Not shown here, a modified sugar called N-acetylglucosamine will polymerize to form chitin. Chitin is the main component of fungal cell walls, and is the major component of the hard exoskeleton of insects and crustaceans, like lobsters. Take a quick look at the difference in structure between storage and structural polysaccharides from the 150 textbook used at UWM. Starch is actually made of unbranched alpha 1-4 glycoside-linked glucose polysaccharides called amylose,and a branched glucose polysaccharide called amylopectin. Glycogen in animal cells is just a more highly branched polysaccharide of alpha- linked glucose molecules. Because the beta glycoside linkages are inflexible, cellulose is a pretty much a linear polymer that can form hydrogen bonds along their length with other cellulose polymers to form the sheet like laminar structure illustrated here. It’s these tough unfolded structures to give plant cell walls their strength and allow trees to grow to gravity- defying heights. You should recall that eukaryotic cells are sugar-coated as illustrated in this drawing of the fluid mosaic membrane. This means that short polysaccharides, or oligosaccharides are covalently bound to proteins or to the heads of phospholipids facing outside the cell. The combination of oligosaccharides and either membrane proteins or membrane phospholipids are called glycoproteins or glycolipids, respectively. There are the glycolipids. Note that the sugars are not associated with cytoplasmic surface of the plasma membrane. Okay, let’s take a look at the fats that our cells use as a form of long-term energy storage and the phospholipids that make up the basic structure of membranes. While these are not polymers in the strictest sense of the term and they’re not macromolecules either, their metabolism is based on condensation and hydrolysis reactions. That’s why they’re included in this discussion. Shown here is the structural formula, the ball and stick model and space filling versions of the same fatty acid. The linkage of 3 fatty acids to the 3 carbons of a molecule glycerol in a condensation or water removal reaction makes a triglyceride. Here’s the formation of that triglyceride. Triglycerides are commonly known as fats. The linkage between each fatty acid and the glycerol molecule is called the ester linkage, and the entire molecule again is a triglyceride. Here are some cartoons of fats, or triglycerides. If some other fatty acids in a triglyceride contain double-bonded carbons, they will have kinks, or twists along their length making for a bulkier fat molecule, as seen on the right here. As part of phospholipids, fatty acids play important roles in the structure membranes and will see that in greater detail shortly. The illustration on the left emphasizes the charged phosphate end, and therefore the hydrophilic head of a phospholipid as well as the two uncharged or hydrophobic fatty acid tails. The tendency of the hydrophobic tails to aggregate together and exclude water can result in the formation of the phospholipid bilayer characteristic of cellular membranes. As you can see, the hydrophilic or water loving phosphate heads face the aqueous cytoplasm and the exterior of the cell. An ester linkage again connects 2 of the fatty acids as well as the polar phosphate to the glycerol molecule. Now although cells will synthesize new membranes in a highly regulated series of steps, it’s actually possible to mix phospholipids and water under conditions where they’ll spontaneously form a phospholipid bilayer. Now what does this tell you about the formation of membranes in cells? The next group of true polymers formed by dehydration synthesis reactions that we’ll review are proteins or more correctly, polypeptides. The amino acid monomers shown here will lose a water molecule when they form a peptide linkage, as shown here. Repetitive condensation reactions will add more amino acids to the dimer to form a polypeptide such as the one shown at the bottom of the slide. Twenty amino acids with different side chains, or R-groups, and therefore different physico-chemical characteristics, are used by cells to make proteins. Polypeptides have an amino, or N-terminus and a carboxyl, or or
C-terminus. The NCC repeat, highlighted here in the chain, is called the polypeptide backbone. Of the 20, 19 amino acids have optically active carbons in the backbone. Can you identify which carbon is optically active in each of the amino acids? These 19 optically active amino acids exist in either L or D forms, standing for levorotary or dextrorotary. And cells use only the L-amino acids to make proteins. Many organisms, especially bacteria can synthesize most of the 20 amino acids (if not all of them) from precursors. But for humans, 8 of the amino acids are essential dietary components. We have to eat them. Here’s a table of amino acids emphasizing the essential properties of the R groups which can either gain or lose protons or be polar or be non-polar. The R group of course account for the different chemical properties each of the different amino acids. OK, this is from the BioSci 150 textbook summarizing the four levels of protein structure, beginning with primary structure which is of course just the sequence of amino acids in a polypeptide chain. Here is secondary structure. Shown here is the alpha helix created by a hydrogen bond formation between nearby amino acids in a chain. Secondary structure also includes the beta pleated sheets in a polypeptide, indicated here but not illustrated. We’ll see that a little later. three-dimensional structure or tertiary structure results from interactions between amino acid R groups that are often far apart in a polypeptide chain. The result is that the polypeptide can be caused to fold into unique 3-dimensional shapes. Quaternary structure refers to proteins composed of two or more polypeptides like the hemoglobin molecule illustrated here. Some proteins are made up from more than 10 or 20 or even more polypeptides. Note that the secondary, tertiary and quaternary structures of polypeptides and proteins are stabilized by the additive strength of those many weak interactions like hydrogen bonds or the attraction of oppositely charged R group components. Here then is a brief summary of some major functions of proteins. We’re going to be looking at some of these of course in great detail. Many polypeptides and proteins are themselves insoluble and therefore form parts of cell structures. Perhaps familiar examples include collagen, a protein secreted into the extracellular matrix that helps hold cells and tissues in place in a multi celled organism. Another is keratin, the extracellular protein of hair, fingernails and feathers, and we already saw, can be found inside cells as part of the cytoskeleton. Some proteins serve to store amino acids as nutrients or building blocks. Egg albumen is a perfect example. It’s stored in an egg and used by the developing zygote. Chicken egg whites of course are rich in proteins like albumin. Protein’s function also to transport insoluble molecules in the circulation. A familiar example is hemoglobin which transports oxygen, and two others are HDL and LDL, which transport cholesterol, a lipid that is otherwise insoluble in the blood. Many hormones of course are are proteins. And many other molecular signals are
also proteins. Insulin and growth hormone are two examples of protein hormones. Proteins also function in cell movements. We’ve already seen this when we looked at the elements of the cytoskeleton. The immune system relies on proteins, both on cells and circulating in the blood, including the familiar antibodies that form after the exposure to many disease organisms. Last and of course not least, are the enzymes which are the catalysts for virtually all cellular chemical reactions. Almost all of the enzymes are proteins. We will be revisiting protein structure in somewhat greater detail shortly. So this brings us to the end of this

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