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Molecular Biosciences 305: Macromolecules Lecture 24 [Speaker: Consetta Helmick]

Slide # 1 Slide Title: WSU Online Title Slide Title: Macromolecules Instructor: Consetta Helmick online.wsu.edu Audio: [Music]

Slide # 2 Slide Title: Macromolecules Macromolecules

Macromolecules or Food

Carbohydrates

Lipids

Proteins

Vitamins and Minerals

Nucleic Acids Audio: Lecture one macromolecules or food. Why do we eat? We eat to gain nutrients so that cellular processes can occur. We will be discussing carbohydrates, lipids, proteins, vitamins and minerals, and nucleic acids.

Slide # 3 Slide Title: Macromolecules and Their Component Macromolecules and Their Component

Macromolecules: large molecules - Four major classes

Proteins Carbohydrates Nucleic acids Lipids

- Polymers formed via dehydration synthesis Yields water

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- Reverse reaction is hydrolysis Requires addition of water

[Diagrams of dehydration synthesis and hydrolysis] Audio: Macro or large so macromolecules. Macromolecules are a series of subunits that are linked together to make the product. Proteins are made up of subunits amino acids. Carbohydrates such as lactose are made up of two subunits galactose and glucose to produce that particular product. When we think about this polymers or subunits have to be brought together to make the product. And then what we are going to see is that we have to digest them out, whether it is you or a bacteria. So to break things out we can use this in the process of hydrolysis where we add water and water will break out the bond and release a subunit. Or we can use enzymes. Enzymes again are things that can break down components also. Or if we have to make a macromolecule. So we could use dehydration synthesis or condensation. So in bringing two subunits together we will actually form water as a byproduct. Now if you think about it, you eat something a large component, you eat an apple. You chew it, you digest it, you swallow it, winds up in the small intestine, small intestine produces enzymes and water that are going to break that large macromolecule down to those individual subunits. The individual subunits, whether it is a carbohydrate or lipid or an amino acid, cross the intestinal barrier, travel to your cells and enter your cells and provide a product, either produce energy or produce protein or nucleic acids or whatever. Now bacteria do the same thing. So bacteria have to again break down large macromolecules into small macromolecules so they can also again run cellular processes.

Slide # 4 Slide Title: Carbohydrates Carbohydrates

Diverse group includes sugars and starches - Energy source, energy storage - Carbon source - Component of DNA and RNA - Structural components of cell

Carbon, hydrogen, oxygen in 1:2:1 ratio - General formula (CH2O)n (literally “hydrate of carbon”)

[Images of carbohydrates] Audio: Let’s start with carbohydrates. Another word for carbohydrates are sugars, starches, cell walls. And the whole purpose of a carbohydrate is to produce energy, ATP, whether it is you or a bacterial cell. So energy source, energy storage. In our cells, human cell, we bring in glucose. If we don’t use it for energy we store it in the form of glycogen. In plants, plants take glucose and

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they store it in the form of a cell wall. In our bacteria we have a number of organisms that can use carbohydrates in a number of ways. A lipidpolysaccharide, many lipids liked together with many sugars, gram-negative bacteria. A peptidoglycan layer, gram-positive cell wall. The glycan again is a sugar component. So depending on the organism and depending where the carbohydrate may be needed primarily it is used for energy but it can also be used for a number of cellular processes. So think about when you are looking at that carbohydrate and what that organism could be doing. Eventually we will be talking about metabolism and we actually will be seeing how the carbohydrate molecule glucose is run through the process of metabolism in eukaryotic cells, you, and prokaryotic cells.

Slide # 5 Slide Title: Carbohydrates Carbohydrates

Monosaccharides have single unit - 5-carbon include ribose, deoxyribose - 6-carbon include glucose, galactose, fructose, mannose

Structural isomers: distinct properties, names - Can exist in alpha (α) or beta (β) form depending on location of hydroxyl group

[Images of carbohydrates] Audio: Our carbohydrates, again sugars, are our smallest subunit is referred to as a monosaccharide. This is a single unit sugar. And what we see under the monosaccharides are glucose, galactose, fructose, and mannose. If we also think about monosaccharide we also have to think about nucleic acid, the five carbon sugar, that is found in RNA or DNA. So if it is RNA it is a ribose sugar, if it DNA it is deoxyribose. So depending again on the structure of the glucose molecule you are going to be producing or storing glucose as glycogen. Or we have our different again monosaccharides that you and prokaryotes can use as an energy source.

Slide # 6 Slide Title: Carbohydrates Carbohydrates

Disaccharides are two monosaccharides - Joined by covalent bond - Common ones include

Sucrose (glucose + fructose) Lactose (glucose + galactose) Maltose (glucose + glucose)

- Dehydration synthesis between hydroxyl groups forms Loss of water

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- Reverse reaction is hydrolysis Addition of water; yields two monosaccharides

[Diagram of dehydration synthesis] Audio: Linking molecules together. So we go from a monosaccharide to a disaccharide. Disaccharide means two sugars linked together. So we find this in a number of places. So sucrose, table sugar, is glucose plus fructose. Lactose which we find in milk, milk sugar, is glucose plus galactose. Maltose is glucose plus again glucose to form a maltose molecule. Now when an organism ingests or digests a disaccharide it has to break apart that bond to release the two subunits. Or if the carbohydrates are in a cell they can actually reform those monosaccharides into a disaccharide. If we think about like milk sugar, lactose, so you have galactose and glucose that are linked together. Our bacteria can produce lactase that again will break that sugar bond. And they use that again for an energy source. Your intestinal tract also produces lactase to break apart the lactose molecule so that you can absorb the glucose and galactose and fructose. Now your cells can’t use galactose or fructose as an energy source. So galactose and fructose are actually sent to the liver and chemically converted into glucose and then sent back out to the blood supply so that you can use that glucose again for energy.

Slide # 7 Slide Title: Carbohydrates Carbohydrates

Polysaccharides are chains of monosaccharides - Often made from glucose - Structural diversity from branching, linkages - Oligosaccharides are shorter chains

Important polymers of glucose: - Cellulose - Starch - Glycogen - Dextran

Chitin, agar also important Audio: Many sugars can also be linked together to form what are called polysaccharides. So many saccharides linked together. And the importance of this again is to form structures. So if we look at some of the important macromolecules that are polysaccharides one of the things that we see is cellulose. Cellulose is the cell wall of plants. And because animals such as ruminant animals that, elk, deer, cow, that have millions of organisms that live in their rumen, they can actually break apart the cellulose molecule, release the individual glucose molecule so that caw, deer, elk can use that glucose again as an energy source. We don’t have that capability as

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humans. So we cannot digest out cellulose. But we do use the fiber for intestinal health. Starch, if you think about a potato it has starch. And again that is glucose linked together. For us we can actually use that starch as a food source. We can break out the glucose molecules and use it for energy. And most microorganisms can too. Glycogen is the stored form of glucose in our cells. If you do not use that glucose we store it in the form of glycogen. We link glucose molecules together to form glycogen again as a storage unit. And dextran again is another form of sugar that we see in plants that give the sweetness again to our plants. Chitin also is important in agar so it gives our stability to agar and it allows for a food source for our bacteria in agar when we grow them on plates.

Slide # 8 Slide Title: Lipids Lipids

Lipids are non-polar, hydrophobic molecules - Diverse group defined by this physical property - Highly soluble in organic solvents

E.g., ether, benzene, chloroform - Not composed of similar subunits

Simple lipids contain carbon, hydrogen, oxygen o Fats most common

Glycerol linked to fatty acids via dehydration synthesis Fatty acids are long chains of bonded C, H atoms with carboxyl group at one end

[Diagram of dehydration synthesis] Audio: The lipids, when we think of lipids we actually have to think of three forms of lipids: phospholipids that we find in cell membranes, sterols such as cholesterol, and our triglycerides again used for certain functions. Lipids are non-polar. They are hydrophobic molecules which means they do not like water. They have a very diverse physical property. Highly soluble in organic solvents such as ether, benzene, chloroform. Not composed of similar substructures. Simple lipids contain carbon, hydrogen, and oxygen. We refer to these primarily as fats, especially when we think of triglycerides. So this is the gristle that you find on your steak, it is the layer of fat that you find between your muscle and your skin. So what we see is that we have a glycerol backbone and carbon, hydrogen, oxygen coming off that glycerol backbone. We can also again break out the fatty acid chains through the process of hydrolysis or using enzymes. Then we can also rebuild a triglyceride through the process of dehydration synthesis. A lot of times we don’t think of bacteria and again fat. But if you think about a bacteria breaking down butter it becomes rancid that is the organism again using the fatty acids for a food source. If you think about an animal decomposing in the woods. There is a lot of triglycerides in that animal and bacteria have the ability to break that down.

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Slide Title: Lipids Lipids

Fatty acids: two groups - Saturated: no double bonds

Tails pack tightly so solid at room temperature (fats) - Unsaturated: double bonds

Kinks prevent tight packing so liquid at room temperature (oils) Monounsaturated: 1 double bond Polyunsaturated: >1 double bond

o Most natural fatty acids are cis: hydrogens attached to same side of double bond o Trans have hydrogens on opposite sides of double bond

[Images of fatty acids] Audio: When we think of the triglycerides we always think of oils or butter or lard. Basically this is comprised of the fatty acid chains. Tri meaning three fatty acid chains linked to one glycerol backbone. The saturated fatty acid has no double carbon bonds, the tails are packed tightly together, and they stay solid at room temperature. Again butter, the fat, the gristle that you find on your steak. Unsaturated double fatty acids have double carbon bonds that again prevents the tight packing so they stay liquid at room temperature. So corn oil, vegetable oil, all of our different oils. We have monounsaturated which means there is one double carbon bond. Polyunsaturated means more than one double carbon bond again depending on the product itself. Most natural fatty acids are cis hydrogens attached to the same side of the double bond. Trans have hydrogens on opposite sides of the double bond. When we think of trans fatty acids the ones that are causing the issues right now are being accused of causing heart disease. Again it is that trans state that is causing the issues. But when it comes to bacteria they don’t really care. A prokaryote can pretty much digest or use any form of triglyceride or fatty acid chain to bring in the carbon, hydrogen, oxygen that those organisms again need for energy production.

Slide # 10 Slide Title: Lipids Lipids

Compound lipids include other elements

Phospholipids important - Phosphate group linked to polar molecule

Yields hydrophilic head group Hydrophobic fatty acid tails Form lipid bilayer with polar heads oriented outward toward aqueous

environments

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Essential component of cytopia membranes [Images of lipids] Audio: The next type of lipid are the phospholipids. Phospholipids are found everywhere. Phospholipid bilayers comprise all cell membranes whether it is plants and animal, bacteria, you or I. If we look at the phospholipid what we’ll see is that the head is hydrophilic, which means water loving, and the tail is hydrophobic, which means water hating. The tail is comprised of two fatty acid chains, one saturated one unsaturated. The thing that makes the phospholipid different is that it has a chloride backbone group attached to it also. If we look at the illustration it is a phospholipid bilayer which makes up all cell membranes. If you remember from cell membranes they are selective barriers. Some items can go through the phospholipid through simple diffusion. Some items require a facultative protein, a helper protein, a transport protein. And some items require active transport to get them across that selective barrier. So as stated earlier every life form every cell membrane are made of that phospholipid bilayer.

Slide # 11 Slide Title: Lipids Lipids

Steroids are simple lipids

Characteristic four-ring structure - Classified as lipids due to water insolubility - Sterols have hydroxyl group attached to one of the rings

E.g., cholesterol - Other steroids include hormones

E.g., cortisone, progesterone, testosterone [Images of steroid ring and sterol] Audio: The last form of lipids are the sterols or the steroids or this case we think of always cholesterol. This particular lipid is in a ring shape. And what we see is that this is a backbone. This is a precursor molecule for a number of other components that cells use. It is usually water insoluble. The sterols have a hydroxyl group attached to one of the rings, example again cholesterol. Cholesterol is a precursor molecule. It is a precursor molecule for the sex hormones estrogen and testosterone. It is a precursor molecule or the starting point for bile which again is an emulsifier in the intestinal tract, keeps lipids in suspension. It can also again be a precursor molecule for vitamin D. So you have to have cholesterol in your diet to make pre-vitamin D that can be changed into vitamin D for calcium absorption. For the longest time cholesterol got a bad rap. It was linked to heart disease, causing heart attacks in the 1980s until further research was done primarily by the port industry that was disputing the claim. People would take their kids off cholesterol diets because their fear again heart attacks. We find it in butter, we find it in

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pork, we find it in fats, we find the cholesterols in a number of locations.

Slide # 12 Slide Title: Proteins Proteins

Proteins

More than half of dry weight of cell

Versatile, many important roles - Catalyze reactions - Transport molecules - Move cells -Provide cellular framework - Sense and respond to conditions outside cell - Regulate gene expression

Audio: Protein, you are made up about half your weight is going to be protein. Bacterial cells, protein. This is one of the most diverse macromolecules there is. The thing is with protein too your cells produce it. So you eat something that is made up of protein which is made up of amino acids. You digest out those amino acids, absorb them, send them to your cells, the amino acids cross into the cells, they go through the process of protein synthesis, and you make the proteins your body requires. Prokaryotes do the same thing. Everything from enzymes are proteins, transport proteins in cell membranes, flagella, proteins, fibrium, pili, again proteins. Cytoskeletons, proteins, hormones, proteins, except for the sex hormones those are cholesterol. Gene regulation expression, proteins, muscle, your skeletal muscle, proteins. The list just goes on and on and on and on when you think of all the things that you are made up of that are protein structures and again think about your prokaryotes and all the things that they have that are protein structures.

Slide # 13 Slide Title: Amino Acids Amino Acids

Proteins made up of amino acids - Infinite possible combinations of 20 amino acids - Protein characteristics depend mainly on shape - Shape determined by amino acid sequence - Amino acids share common structure

Side chain (R group) differs [Image of amino acid]

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Audio: Proteins are comprised of amino acids, that is the smallest subunit. The most amazing thing about proteins though is that there are only twenty amino acids that make up thousands and thousands of proteins. If you think about it think about like the alphabet. There are twenty six letters in the alphabet and how many proteins or letters, words can we make from those particular letters? So if I start with the word bat, change the first letter cat, hat, mat, tat. Those are all again individual words that come from three simple letters. Think about your amino acids doing the same thing for your proteins. If we look at insulin, insulin is a thirteen amino acid structure that again is involved in glucose uptake for energy production. So when amino acids come together we create what are called peptide bonds. Then the peptide bonds and how the amino acids come together are basically dictated by your DNA. Your DNA is your huge protein cookbook. Every recipe for every protein that you require is in the DNA. Once that DNA is transcribed, the messenger RNA is produced, the messenger RNA is sent to the cytoplasm, it is read by a ribosome in the process of translation, it will produce a very specific sequenced amino acid, and eventually put it into the correct shape and you have the protein that your body or your bacterial cell requires.

Slide # 14 Slide Title: Protein Structure Protein Structure Determinants:

Hydrogen bonding

Polar groups

Non-polar groups

Covalent bonds [Images of protein structures] Audio: Proteins have to be created. So when the ribosome reads the messenger RNA it is taking those amino acids and putting them in a very specific sequence based on the information from the DNA. Its first structure is referred to as a polypeptide chain. The polypeptide chain is actually produced in the endoplasmic reticulum, the endoplasmic reticulum ships that protein to the Golgi apparatus which twists it, folds it, bends it, adds sulfur, adds whatever component it requires to become that very specific protein. Then that protein is produced and shipped out to the cell for cellular use or becomes a structural protein. So what we see is that the next secondary structure of the protein is called the alpha-helix or the beta-sheet. So all we are doing is just taking that amino acid and making it into a very specific structure. And then we can also take that protein and make it into a tertiary structure so it is three dimensional. And then we can make it into a quaternary structure. So a quaternary structure can be a combination of all three additional structures again producing that protein structure. Since bacteria don’t have an endoplasmic reticulum or Golgi apparatus.

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Slide # 15 Slide Title: Protein Structure Protein Structure

Protein domains - Associated with specific functions

Substituted proteins - Have covalent bonds with other molecules

Protein denaturation - High temperature, extreme pH, solvents can break bonds

[Images of protein structures] Audio: Since bacteria don’t have endoplasmic reticulums or again Golgi apparatus if you remember when we talked about the nucleoid transcription translation occur simultaneously in bacteria. But they still do the same thing; they make the polypeptide chain, the secondary structures, the quaternary, and whatever structure again that particular protein requires or is required by the cell. You can have substitution proteins that may affect the structure of the protein, it may not. One amino acid substitution like mentioned before can cause Sickle Cell Anemia. Proteins can be denatured which means they can be destroyed or their shape can be changed. Shape dictates function on a protein. So when a protein is denatured, this can occur by high temperatures. If you think about a raw egg being cooked into a cooked egg, that is protein denaturation. That protein is never going to go back to that raw egg shape. Extreme pHs can also change proteins. Solvents can also denature proteins. So when you think about protein that shape dictates function proteins are very sensitive to a number of external conditions that can affect the protein itself. And this can occur in prokaryotes and eukaryotes.

Slide # 16 Slide Title: Vitamins and Minerals Vitamins and Minerals

B-Vitamins ATP Production

Vitamin A Vitamin E

Vitamin D Vitamin K

25 Different Minerals Audio: When we think about the macromolecules we always seem to forget the vitamins and the minerals, in prokaryotes and eukaryotes. All B vitamins are required for energy production. Each step of ATP production requires a number of the B vitamins. If you think about NADH, this comes from niacin, a B vitamin. If you think of FADH this comes from the B vitamin riboflavin.

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And these are important in prokaryotes and eukaryotes. Also our fat soluble vitamins, vitamin A, vitamin D, vitamin E, and vitamin K are very important in eukaryotes. Vitamin K for again blood clot production and vitamin E and A as antioxidants. Vitamin E, D again involved in calcium absorption. We don’t see too many of the fat soluble vitamins being important in prokaryotes as we do again in eukaryotes. In addition to the vitamins every living organism requires twenty five different minerals. Everything from selenium to iron to calcium to phosphorus. If you think about phosphorus, ATP adenosine triphosphate. Nucleic acids have a phosphorus backbone. Calcium is involved in a number of chemical reactions, muscle contraction, a number of important things, neurons being fired. If you think of hydrogen, oxygen, hydrogen protons. So there is a huge number of minerals that all prokaryotes and actually eukaryotes require.

Slide # 17 Slide Title: Elements and Small Molecules in Cell Elements and Small Molecules in Cell

~1% dry weight is inorganic ions - Na+ (sodium) - K+ (potassium) - Mg2+ (magnesium) - Ca2+ (calcium) - Fe2+ (iron) - Cl- (chloride) - PO4

3- (phosphate) - SO4

2- (sulfate)

Organic compounds - Have important functional groups

[Table 2.4] Audio: Elements and small molecules in cells. Less than one percent of dry weight is made up of inorganic ions such as sodium, potassium, magnesium, calcium, iron, sulfate, phosphate, and so forth. Organic compounds important functions too. If we look at table 2.4 this is basically your functional groups. So each one of your functional structures again are important in each one of the processes that we talked about and it is going to be extremely important in our metabolism as we get into that. So for the functional group aldehyde, this is what makes our carbohydrates. Amino acids made our protein structures. Carboxyls again involved in organic acids and fatty acids. The hydroxyls again carbohydrates, fatty acids, alcohol. We will be talking about alcohol production. Ketones carbohydrates again and polypeptides. Methyl, some amino acids attached to again the DNA. Phosphate, adenosine triphosphate, nucleic acids, signaling molecules. And the sulfur again part of the amino acid. This is what gives the protein its structure and when we talk about the sulfur also we’ll find out that in our prokaryotes sulfur can be a final electron acceptor in one of the energy pathways of our prokaryotes.

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Slide # 18 Slide Title: Elements and Small Molecules in Cell Elements and Small Molecules in Cell

Adenosine triphosphate (ATP) - Energy currency of cell - Three negatively charged phosphate groups repel

Bonds inherently unstable, easily broken Releases energy to drive cellular processes High energy phosphate bonds denoted by ~ ATP → ADP + Pi

[Image of ATP] Audio: All life forms require energy. This is your gas, this is your fuel in your cells. And if we look at this you can see the importance of again our functional groups and our minerals. Adenosine triphosphate, three negatively charged phosphate groups repel. The bond is easily broken; it is a high energy bond so when the phosphate bond breaks it releases energy. We capture that energy and we use it for cellular energy, mechanical energy. So we will be seeing how this is going to be produced through the process of metabolism. After the ATP bond is broken we are going to be having ADP plus a phosphate bond, adenosine diphosphate. How do we go and make adenosine triphosphate? This is the process of metabolism. Taking a glucose molecule, running it through aerobic cellular respiration, and again producing ATP. Our next section the material will be going into a lot of detail on metabolism and metabolic functions. In prokaryotes and eukaryotes.

Slide # 19 Slide Title: Nucleic Acids Nucleic Acids

Nucleic acids carry genetic information in sequence of nucleotides

DNA: deoxyribonucleic acid - Nucleotide sequence encodes all of cell’s properties - Information transcribed into form of RNA

Ribonucleic acid (RNA) is single-stranded RNA is then translated into protein

- Nucleotides have three parts Deoxyribose Phosphate group Nucleobase

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[Image of nucleic acid] Audio: The nucleic acids again carry genetic information. Your DNA is your heritable genes. This is how you get your characteristics: you tall or are you short, you have blue eyes, green eyes. Also again this is your Betty Crocker cookbook for every protein that your body will require. Prokaryotes again, genetic material. Even though they go through binary fission one to two to four to eight and so forth to sixteen, they are still passing on genetic information. And then remember we talked about genetic variability in prokaryotes: transformation, transduction, and conjugation. So DNA is DNA whether it is in plant, an animal, or a prokaryotic cell. Same thing with messenger RNA. Messenger RNA is a copy of the DNA during the process of transcription. We have to be able to copy that recipe, send the messenger RNA to a ribosome, have it translated into that polypeptide sequence so that we can produce again the protein that we require. So messenger RNA is produced pretty much the same way whether we are talking about a prokaryote again or a eukaryotic cell.

Slide # 20 Slide Title: Nucleic Acids Nucleic Acids

Nucleotides include nucleobase - Purines adenine (A), guanine (G)

Two fused rings - Pyrimidines cytosine (C), thymine (T)

Single ring structure Uracil (U) is found only in RNA

[Images of purines and pyrimidines] Audio: The last thing we have to think about when we think about our nutrients, our macromolecules, are the nucleic acids. Even though they are not really a nutrient, we can’t exist without our DNA and our messenger RNA. But again when you think about it DNA has a phosphate back bone, a five carbon sugar, a deoxyribose, and then the nucleotides that make up again the DNA. Same thing again with messenger RNA. It has a phosphate backbone, a five carbon sugar ribose, and then again our nucleic acids that make up the messenger RNA. In the process of life our DNA and our messenger RNA is just as important as any other macromolecule that we will be talking about. So the next couple lectures from here on out will be getting into metabolism, metabolic pathways, we’ll be looking how eukaryotic cells can produce energy and byproducts. And we’ll be seeing how prokaryotic cells can produce energy and byproducts.