Biology Week 2

There are four classes of biomolecules:

Carbohydrates Lipids Proteins Nucleic acids Carbon is the essential ingredient in all biomolecules. The carbon chain of a biomolecule is its skeleton or backbone. Reactivity of a biomolecule is largely dependent on the attached functional groups.

Steroids

Cholesterol Sex hormones testosterone and estrogen

Fatty acids

Saturated - no double bonds between carbon atoms Unsaturated - one or more double bonds between carbon atoms Trans fats - often found in processed food

Proteins are the most versatile of life's biomolecules 50% of dry weight of most cells Several functions:

Support Metabolism Transport Defense Regulation Motion The monomers of proteins are amino acids. Amino acids are joined by dehydration. Peptide - two or more amino acids joined together by peptide bonds Polypeptide - chain of many amino acids

Introduction to macromolecules

*Introduction* Think back to what you ate for lunch. Did any of your lunch items have a "Nutrition Facts" label on the back of them? If so, and if you had a look at the food's protein, carbohydrate, or fat content, you may already be familiar with several types of large biological molecules we'll discuss here. If you're wondering what something as weird-sounding as a "large biological molecule" is doing in your food, the answer is that it's providing you with the building blocks you need to maintain your body - because your body is also made of large biological molecules! Just as you can be thought of as an assortment of atoms or a walking, talking bag of water, you can also be viewed as a collection of four major types of large biological molecules: carbohydrates (such as sugars), lipids (such as fats), proteins, and nucleic acids (such as DNA and RNA). That's not to say that these are the only molecules in your body, but rather, that your most important large molecules can be divided into these groups. Together, the four groups of large biological molecules make up the majority of the dry weight of a cell. (Water, a small molecule, makes up the majority of the wet weight). Large biological molecules perform a wide range of jobs in an organism. Some carbohydrates store fuel for future energy needs, and some lipids are key structural components of cell membranes. Nucleic acids store and transfer hereditary information, much of which provides instructions for making proteins. Proteins themselves have perhaps the broadest range of functions: some provide structural support, but many are like little machines that carry out specific jobs in a cell, such as catalyzing metabolic reactions or receiving and transmitting signals. We'll look in greater detail at carbohydrates, lipids, nucleic acids, and proteins a few articles down the road. Here, we'll look a bit more at the key chemical reactions that build up and break down these molecules. *Monomers and polymers* Most large biological molecules are polymers, long chains made up of repeating molecular subunits, or building blocks, called monomers. If you think of a monomer as being like a bead, then you can think of a polymer as being like a necklace, a series of beads strung together. Carbohydrates, nucleic acids, and proteins are often found as long polymers in nature. Because of their polymeric nature and their large (sometimes huge!) size, they are classified as macromolecules, big (macro-) molecules made through the joining of smaller subunits. Lipids are not usually polymers and are smaller than the other three, so they are not considered macromolecules by some sources^{1,2} 1,2 start superscript, 1, comma, 2, end superscript. However, many other sources use the term "macromolecule" more loosely, as a general name for the four types of large biological molecules^{3,4} 3,4 start superscript, 3, comma, 4, end superscript. This is just a naming difference, so don't get too hung up on it. Just remember that lipids are one of the four main types of large biological molecules, but that they don't generally form polymers. *Dehydration synthesis* How do you build polymers from monomers? Large biological molecules often assemble via dehydration synthesis reactions, in which one monomer forms a covalent bond to another monomer (or growing chain of monomers), releasing a water molecule in the process. You can remember what happens by the name of the reaction: dehydration, for the loss of the water molecule, and synthesis, for the formation of a new bond. Dehydration synthesis reaction between two molecules of glucose, forming a molecule of maltose with the release of a water molecule. In the dehydration synthesis reaction above, two molecules of the sugar glucose (monomers) combine to form a single molecule of the sugar maltose. One of the glucose molecules loses an H, the other loses an OH group, and a water molecule is released as a new covalent bond forms between the two glucose molecules. As additional monomers join by the same process, the chain can get longer and longer and form a polymer. Even though polymers are made out of repeating monomer units, there is lots of room for variety in their shape and composition. Carbohydrates, nucleic acids, and proteins can all contain multiple different types of monomers, and their composition and sequence is important to their function. For instance, there are four types of nucleotide monomers in your DNA, as well as twenty types of amino acid monomers commonly found in the proteins of your body. Even a single type of monomer may form different polymers with different properties. For example, starch, glycogen, and cellulose are all carbohydrates made up of glucose monomers, but they have different bonding and branching patterns. *Hydrolysis* How do polymers turn back into monomers (for instance, when the body needs to recycle one molecule to build a different one)? Polymers are broken down into monomers via hydrolysis reactions, in which a bond is broken, or lysed, by addition of a water molecule. During a hydrolysis reaction, a molecule composed of multiple subunits is split in two: one of the new molecules gains a hydrogen atom, while the other gains a hydroxyl (-OH) group, both of which are donated by water. This is the reverse of a dehydration synthesis reaction, and it releases a monomer that can be used in building a new polymer. For example, in the hydrolysis reaction below, a water molecule splits maltose to release two glucose monomers. This reaction is the reverse of the dehydration synthesis reaction shown above. Hydrolysis of maltose, in which a molecule of maltose combines with a molecule of water, resulting in the formation of two glucose monomers. Dehydration synthesis reactions build molecules up and generally require energy, while hydrolysis reactions break molecules down and generally release energy. Carbohydrates, proteins, and nucleic acids are built up and broken down via these types of reactions, although the monomers involved are different in each case. (In a cell, nucleic acids actually aren't polymerized via dehydration synthesis; we'll examine how they're assembled in the article on nucleic acids. Dehydration synthesis reactions are also involved in the assembly of certain types of lipids, even though the lipids are not polymers^3 3 start superscript, 3, end superscript. In the body, enzymes catalyze, or speed up, both the dehydration synthesis and hydrolysis reactions. Enzymes involved in breaking bonds are often given names that end with -ase: for instance, the maltase enzyme breaks down maltose, lipases break down lipids, and peptidases break down proteins (also known as polypeptides, as we'll see in the article on proteins). As food travels through your digestive system - in fact, from the moment it hits your saliva - it is being worked over by enzymes like these. The enzymes break down large biological molecules, releasing the smaller building blocks that can be readily absorbed and used by the body.

Microtubules

- made of tubulin Maintain cell shape and create tracks along which organelles move

Lysosomes

- vesicles produced by the Golgi Low internal pH and hydrolytic enzymes Important in recycling cellular material and digesting worn-out organelles Tay Sachs disease occurs when a particular lysosomal enzyme is nonfunctional.

The cell theory states

1. A cell is the basic unit of life. 2. Organisms are made up of cells. 3. New cells arise only from preexisting cells

The cytoskeleton maintains cell shape and assists movement

All eukaryotic cells have a *cytoskeleton* Network of protein fibers within the cytoplasm In animals, used for support and cell shape Fibers can assemble and disassemble rapidly. Anchors organelles in place but also allows them to move Types of fibers: Actin filaments Intermediate filaments Microtubules

Nucleic acids

Introduction Nucleic acids, and DNA in particular, are key macromolecules for the continuity of life. DNA bears the hereditary information that's passed on from parents to children, providing instructions for how (and when) to make the many proteins needed to build and maintain functioning cells, tissues, and organisms. How DNA carries this information, and how it is put into action by cells and organisms, is complex, fascinating, and fairly mind-blowing, and we'll explore it in more detail in the section on molecular biology. Here, we'll just take a quick look at nucleic acids from the macromolecule perspective. Roles of DNA and RNA in cells Nucleic acids, macromolecules made out of units called nucleotides, come in two naturally occurring varieties: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material found in living organisms, all the way from single-celled bacteria to multicellular mammals like you and me. Some viruses use RNA, not DNA, as their genetic material, but aren't technically considered to be alive (since they cannot reproduce without help from a host). DNA in cells In eukaryotes, such as plants and animals, DNA is found in the nucleus, a specialized, membrane-bound vault in the cell, as well as in certain other types of organelles (such as mitochondria and the chloroplasts of plants). In prokaryotes, such as bacteria, the DNA is not enclosed in a membranous envelope, although it's located in a specialized cell region called the nucleoid. In eukaryotes, DNA is typically broken up into a number of very long, linear pieces called chromosomes, while in prokaryotes such as bacteria, chromosomes are much smaller and often circular (ring-shaped). A chromosome may contain tens of thousands of genes, each providing instructions on how to make a particular product needed by the cell. From DNA to RNA to proteins Many genes encode protein products, meaning that they specify the sequence of amino acids used to build a particular protein. Before this information can be used for protein synthesis, however, an RNA copy (transcript) of the gene must first be made. This type of RNA is called a messenger RNA (mRNA), as it serves as a messenger between DNA and the ribosomes, molecular machines that read mRNA sequences and use them to build proteins. This progression from DNA to RNA to protein is called the "central dogma" of molecular biology. Importantly, not all genes encode protein products. For instance, some genes specify ribosomal RNAs (rRNAs), which serve as structural components of ribosomes, or transfer RNAs (tRNAs), cloverleaf-shaped RNA molecules that bring amino acids to the ribosome for protein synthesis. Still other RNA molecules, such as tiny microRNAs (miRNAs), act as regulators of other genes, and new types of non-protein-coding RNAs are being discovered all the time. Nucleotides DNA and RNA are polymers (in the case of DNA, often very long polymers), and are made up of monomers known as nucleotides. When these monomers combine, the resulting chain is called a polynucleotide (poly- = "many"). Each nucleotide is made up of three parts: a nitrogen-containing ring structure called a nitrogenous base, a five-carbon sugar, and at least one phosphate group. The sugar molecule has a central position in the nucleotide, with the base attached to one of its carbons and the phosphate group (or groups) attached to another. Let's look at each part of a nucleotide in turn. Image of the components of DNA and RNA, including the sugar (deoxyribose or ribose), phosphate group, and nitrogenous base. Bases include the pyrimidine bases (cytosine, thymine in DNA, and uracil in RNA, one ring) and the purine bases (adenine and guanine, two rings). The phosphate group is attached to the 5' carbon. The 2' carbon bears a hydroxyl group in ribose, but no hydroxyl (just hydrogen) in deoxyribose. _Image modified from "Nucleic acids: Figure 1," by OpenStax College, Biology (CC BY 3.0)._ Nitrogenous bases The nitrogenous bases of nucleotides are organic (carbon-based) molecules made up of nitrogen-containing ring structures. [Why is it called a base?] ^+ start superscript, plus, end superscript Each nucleotide in DNA contains one of four possible nitrogenous bases: adenine (A), guanine (G) cytosine (C), and thymine (T). Adenine and guanine are purines, meaning that their structures contain two fused carbon-nitrogen rings. Cytosine and thymine, in contrast, are pyrimidines and have a single carbon-nitrogen ring. RNA nucleotides may also bear adenine, guanine and cytosine bases, but instead of thymine they have another pyrimidine base called uracil (U). As shown in the figure above, each base has a unique structure, with its own set of functional groups attached to the ring structure. In molecular biology shorthand, the nitrogenous bases are often just referred to by their one-letter symbols, A, T, G, C, and U. DNA contains A, T, G, and C, while RNA contains A, U, G, and C (that is, U is swapped in for T). Sugars In addition to having slightly different sets of bases, DNA and RNA nucleotides also have slightly different sugars. The five-carbon sugar in DNA is called deoxyribose, while in RNA, the sugar is ribose. These two are very similar in structure, with just one difference: the second carbon of ribose bears a hydroxyl group, while the equivalent carbon of deoxyribose has a hydrogen instead. The carbon atoms of a nucleotide's sugar molecule are numbered as 1′, 2′, 3′, 4′, and 5′ (1′ is read as "one prime"), as shown in the figure above. In a nucleotide, the sugar occupies a central position, with the base attached to its 1′ carbon and the phosphate group (or groups) attached to its 5′ carbon. Phosphate Nucleotides may have a single phosphate group, or a chain of up to three phosphate groups, attached to the 5' carbon of the sugar. Some chemistry sources use the term "nucleotide" only for the single-phosphate case, but in molecular biology, the broader definition is generally accepted^1 1 start superscript, 1, end superscript In a cell, a nucleotide about to be added to the end of a polynucleotide chain will bear a series of three phosphate groups. When the nucleotide joins the growing DNA or RNA chain, it loses two phosphate groups. So, in a chain of DNA or RNA, each nucleotide has just one phosphate group. Polynucleotide chains A consequence of the structure of nucleotides is that a polynucleotide chain has directionality - that is, it has two ends that are different from each other. At the 5' end, or beginning, of the chain, the 5' phosphate group of the first nucleotide in the chain sticks out. At the other end, called the 3' end, the 3' hydroxyl of the last nucleotide added to the chain is exposed. DNA sequences are usually written in the 5' to 3' direction, meaning that the nucleotide at the 5' end comes first and the nucleotide at the 3' end comes last. As new nucleotides are added to a strand of DNA or RNA, the strand grows at its 3' end, with the 5′ phosphate of an incoming nucleotide attaching to the hydroxyl group at the 3' end of the chain. This makes a chain with each sugar joined to its neighbors by a set of bonds called a phosphodiester linkage. Properties of DNA Deoxyribonucleic acid, or DNA, chains are typically found in a double helix, a structure in which two matching (complementary) chains are stuck together, as shown in the diagram at left. The sugars and phosphates lie on the outside of the helix, forming the backbone of the DNA; this portion of the molecule is sometimes called the sugar-phosphate backbone. The nitrogenous bases extend into the interior, like the steps of a staircase, in pairs; the bases of a pair are bound to each other by hydrogen bonds. Structural model of a DNA double helix. Image credit: Jerome Walker/Dennis Myts. The two strands of the helix run in opposite directions, meaning that the 5′ end of one strand is paired up with the 3′ end of its matching strand. (This is referred to as antiparallel orientation and is important for the copying of DNA.) So, can any two bases decide to get together and form a pair in the double helix? The answer is a definite no. Because of the sizes and functional groups of the bases, base pairing is highly specific: A can only pair with T, and G can only pair with C, as shown below. This means that the two strands of a DNA double helix have a very predictable relationship to each other. For instance, if you know that the sequence of one strand is 5'-AATTGGCC-3', the complementary strand must have the sequence 3'-TTAACCGG-5'. This allows each base to match up with its partner: 5'-AATTGGCC-3' 3'-TTAACCGG-5' These two strands are complementary, with each base in one sticking to its partner on the other. The A-T pairs are connected by two hydrogen bonds, while the G-C pairs are connected by three hydrogen bonds. When two DNA sequences match in this way, such that they can stick to each other in an antiparallel fashion and form a helix, they are said to be complementary. Hydrogen bonding between complementary bases holds DNA strands together in a double helix of antiparallel strands. Thymine forms two hydrogen bonds with adenine, and guanine forms three hydrogen bonds with cytosine. Image modified from OpenStax Biology. Properties of RNA Ribonucleic acid (RNA), unlike DNA, is usually single-stranded. A nucleotide in an RNA chain will contain ribose (the five-carbon sugar), one of the four nitrogenous bases (A, U, G, or C), and a phosphate group. Here, we'll take a look at four major types of RNA: messenger RNA (mRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), and regulatory RNAs. Messenger RNA (mRNA) Messenger RNA (mRNA) is an intermediate between a protein-coding gene and its protein product. If a cell needs to make a particular protein, the gene encoding the protein will be turned "on," meaning an RNA-polymerizing enzyme will come and make an RNA copy, or transcript, of the gene's DNA sequence. The transcript carries the same information as the DNA sequence of its gene. However, in the RNA molecule, the base T is replaced with U. For instance, if a DNA coding strand has the sequence 5'-AATTGCGC-3', the sequence of the corresponding RNA will be 5'-AAUUGCGC-3'. Once an mRNA has been produced, it will associate with a ribosome, a molecular machine that specializes in assembling proteins out of amino acids. The ribosome uses the information in the mRNA to make a protein of a specific sequence, "reading out" the mRNA's nucleotides in groups of three (called codons) and adding a particular amino acid for each codon. Image of a ribosome (made of proteins and rRNA) bound to an mRNA, with tRNAs bringing amino acids to be added to the growing chain. The tRNA that binds, and thus the amino acid that's added, at a given moment is determined by the sequence of the mRNA that is being "read" at that time. Image credit: OpenStax Biology. Ribosomal RNA (rRNA) and transfer RNA (tRNA) Ribosomal RNA (rRNA) is a major component of ribosomes, where it helps mRNA bind in the right spot so its sequence information can be read out. Some rRNAs also act as enzymes, meaning that they help accelerate (catalyze) chemical reactions - in this case, the formation of bonds that link amino acids to form a protein. RNAs that act as enzymes are known as ribozymes. Transfer RNAs (tRNAs) are also involved in protein synthesis, but their job is to act as carriers - to bring amino acids to the ribosome, ensuring that the amino acid added to the chain is the one specified by the mRNA. Transfer RNAs consist of a single strand of RNA, but this strand has complementary segments that stick together to make double-stranded regions. This base-pairing creates a complex 3D structure important to the function of the molecule. Structure of a tRNA. The overall molecule has a shape somewhat like an L. Image modified from Protein Data Bank (work of the U.S. government). Regulatory RNA (miRNAs and siRNAs) Some types of non-coding RNAs (RNAs that do not encode proteins) help regulate the expression of other genes. Such RNAs may be called regulatory RNAs. For example, microRNAs (miRNAs) and small interfering RNAs siRNAs are small regulatory RNA molecules about 22 nucleotides long. They bind to specific mRNA molecules (with partly or fully complementary sequences) and reduce their stability or interfere with their translation, providing a way for the cell to decrease or fine-tune levels of these mRNAs. These are just some examples out of many types of noncoding and regulatory RNAs. Scientists are still discovering new varieties of noncoding RNA.

Carbohydrates (Khan Academy)

Introduction What's in a spud? Besides water, which makes up most of the potato's weight, there's a little fat, a little protein...and a whole lot of carbohydrate (about 37 grams in a medium potato). Some of that carbohydrate is in the form of sugars. These provide the potato, and the person eating the potato, with a ready fuel source. A bit more of the potato's carbohydrate is in the form of fiber, including cellulose polymers that give structure to the potato's cell walls. Most of the carbohydrate, though, is in the form of starch, long chains of linked glucose molecules that are a storage form of fuel. When you eat French fries, potato chips, or a baked potato with all the fixings, enzymes in your digestive tract get to work on the long glucose chains, breaking them down into smaller sugars that your cells can use. Carbohydrates are biological molecules made of carbon, hydrogen, and oxygen in a ratio of roughly one carbon atom (\text CCC) to one water molecule (\text H_2\text OH 2 ​ OH, start subscript, 2, end subscript, O). This composition gives carbohydrates their name: they are made up of carbon (carbo-) plus water (-hydrate). Carbohydrate chains come in different lengths, and biologically important carbohydrates belong to three categories: monosaccharides, disaccharides, and polysaccharides. In this article, we'll learn more about each type of carbohydrates, as well as the essential energetic and structural roles they play in humans and other organisms. Monosaccharides Monosaccharides (mono- = "one"; sacchar- = "sugar") are simple sugars, the most common of which is glucose. Monosaccharides have a formula of (\text {CH}_2\text O)_n(CH 2 ​ O) n ​ left parenthesis, C, H, start subscript, 2, end subscript, O, right parenthesis, start subscript, n, end subscript, and they typically contain three to seven carbon atoms.[How is that formula different from carbohydrates in general?] \text CC\text H_2\text O H, start subscript, 2, end subscript, O \text CC\text H_2\text O H, start subscript, 2, end subscript, O \text HH\text OO\text CC Most of the oxygen atoms in monosaccharides are found in hydroxyl (\text {OH}OHO, H) groups, but one of them is part of a carbonyl (\text C=\text OC=OC, equals, O) group. The position of the carbonyl (\text C=\text OC=OC, equals, O) group can be used to categorize the sugars: If the sugar has an aldehyde group, meaning that the carbonyl C is the last one in the chain, it is known as an aldose. If the carbonyl C is internal to the chain, so that there are other carbons on both sides of it, it forms a ketone group and the sugar is called a ketose. Sugars are also named according to their number of carbons: some of the most common types are trioses (three carbons), pentoses (five carbons), and hexoses (six carbons). Structures of monosaccharides. By carbonyl position: glyceraldehyde (aldose), dihydroxyacetone (ketose). By number of carbons: glyceraldehyde (triose), ribose (pentose), and glucose (hexose). Structure of aldehyde: carbonyl bonded to a H on one side and to an R group (carbon-containing group) on the other. Structure of ketone: carbonyl bonded to R and R' groups (carbon-containing groups) on both sides. Image modified from OpenStax Biology. Glucose and its isomers One important monosaccharide is glucose, a six-carbon sugar with the formula \text C_6\text H_{12}\text O_6C 6 ​ H 12 ​ O 6 ​ C, start subscript, 6, end subscript, H, start subscript, 12, end subscript, O, start subscript, 6, end subscript. Other common monosaccharides include galactose (which forms part of lactose, the sugar found in milk) and fructose (found in fruit). Glucose, galactose, and fructose have the same chemical formula (\text C_6\text H_{12}\text O_6C 6 ​ H 12 ​ O 6 ​ C, start subscript, 6, end subscript, H, start subscript, 12, end subscript, O, start subscript, 6, end subscript), but they differ in the organization of their atoms, making them isomers of one another. Fructose is a structural isomer of glucose and galactose, meaning that its atoms are actually bonded together in a different order. Glucose and galactose are stereoisomers (have atoms bonded together in the same order, but differently arranged in space). They differ in their stereochemistry at carbon 4. Fructose is a structural isomer of glucose and galactose (has the same atoms, but bonded together in a different order). Image modified from OpenStax Biology. Glucose and galactose are stereoisomers of each other: their atoms are bonded together in the same order, but they have a different 3D organization of atoms around one of their asymmetric carbons. You can see this in the diagram as a switch in the orientation of the hydroxyl (\text{OH}OHO, H) group, marked in red. This small difference is enough for enzymes to tell glucose and galactose apart, picking just one of the sugars to take part in chemical reactions^1 1 start superscript, 1, end superscript. Ring forms of sugars You may have noticed that the sugars we've looked at so far are linear molecules (straight chains). That may seem odd because sugars are often drawn as rings. As it turns out both are correct: many five- and six-carbon sugars can exist either as a linear chain or in one or more ring-shaped forms. These forms exist in equilibrium with each other, but equilibrium strongly favors the ring forms (particularly in aqueous, or water-based, solution). For instance, in solution, glucose's main configuration is a six-membered ring. Over 99% of glucose is typically found in this form^3 3 start superscript, 3, end superscript. Even when glucose is in a six-membered ring, it can occur in two different forms with different properties. During ring formation, the \text OOO from the carbonyl, which is converted to a hydroxyl group, will be trapped either "above" the ring (on the same side as the \text{CH}_2\text{OH}CH 2 ​ OHC, H, start subscript, 2, end subscript, O, H group) or "below" the ring (on the opposite side from this group). When the hydroxyl is down, glucose is said to be in its alpha (α) form, and when it's up, glucose is said to be in its beta (β) form. Linear and ring forms of glucose. The linear form can convert into either the alpha or the beta ring form, with the two forms differing in the position of the hydroxyl group derived from the carbonyl of the linear form. If the hydroxyl is up (on the same side as the CH_2 2 ​ start subscript, 2, end subscriptOH group), then the molecule is beta glucose, while if it is down (on the opposite side), then the molecule is alpha glucose. Also pictured ring forms of ribose and fructose. Unlike the six-membered glucose rings, these rings are five-membered. Image modified from OpenStax Biology. Disaccharides Disaccharides (di- = "two") form when two monosaccharides join together via a dehydration reaction, also known as a condensation reaction or dehydration synthesis. In this process, the hydroxyl group of one monosaccharide combines with the hydrogen of another, releasing a molecule of water and forming a covalent bond known as a glycosidic linkage. For instance, the diagram below shows glucose and fructose monomers combining via a dehydration reaction to form sucrose, a disaccharide we know as table sugar. (The reaction also releases a water molecule, not pictured.) Formation of a 1-2 glycosidic linkage between glucose and fructose via dehydration synthesis. Image credit: OpenStax Biology. In some cases, it's important to know which carbons on the two sugar rings are connected by a glycosidic bond. Each carbon atom in a monosaccharide is given a number, starting with the terminal carbon closest to the carbonyl group (when the sugar is in its linear form). This numbering is shown for glucose and fructose, above. In a sucrose molecule, the 111 carbon of glucose is connected to the 222 carbon of fructose, so this bond is called a 111-222 glycosidic linkage. Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of glucose and galactose and is found naturally in milk. Many people can't digest lactose as adults, resulting in lactose intolerance (which you or your friends may be all too familiar with). Maltose, or malt sugar, is a disaccharide made up of two glucose molecules. The most common disaccharide is sucrose (table sugar), which is made of glucose and fructose. Common disaccharides: maltose, lactose, and sucrose Image credit: OpenStax Biology. Polysaccharides A long chain of monosaccharides linked by glycosidic bonds is known as a polysaccharide (poly- = "many"). The chain may be branched or unbranched and may contain different types of monosaccharides. The molecular weight of a polysaccharide can be quite high, reaching 100,100,100, comma000000000 daltons or more if enough monomers are joined. Starch, glycogen, cellulose, and chitin are some major examples of polysaccharides important in living organisms. Storage polysaccharides Starch is the stored form of sugars in plants and is made up of a mixture of two polysaccharides, amylose and amylopectin (both polymers of glucose). Plants are able to synthesize glucose using light energy gathered in photosynthesis, and the excess glucose, beyond the plant's immediate energy needs, is stored as starch in different plant parts, including roots and seeds. The starch in the seeds provides food for the embryo as it germinates and can also serve as a food source for humans and animals, who will break it down into glucose monomers using digestive enzymes. In starch, the glucose monomers are in the α form (with the hydroxyl group of carbon 111 sticking down below the ring), and they are connected primarily by 111-444 glycosidic linkages (i.e., linkages in which carbon atoms 111 and 444 of the two monomers form a glycosidic bond). Amylose consists entirely of unbranched chains of glucose monomers connected by 111-444 linkages. Amylopectin is a branched polysaccharide. Although most of its monomers are connected by 111-444 linkages, additional 111-666 linkages occur periodically and result in branch points. Because of the way the subunits are joined, the glucose chains in amylose and amylopectin typically have a helical structure, as shown in the diagram below. Top: amylose has a linear structure and is made of glucose monomers connected by 1-4 glycosidic linkages. Bottom: amylopectin has a branching structure. It is mostly made of glucose molecules connected by 1-4 glycosidic linkages, but has glucose molecules connected by 1-6 linkages at the branch points. Image credit: OpenStax Biology. That's great for plants, but what about us? Glycogen is the storage form of glucose in humans and other vertebrates. Like starch, glycogen is a polymer of glucose monomers, and it is even more highly branched than amylopectin. Glycogen is usually stored in liver and muscle cells. Whenever blood glucose levels decrease, glycogen is broken down via hydrolysis to release glucose monomers that cells can absorb and use. Structural polysaccharides Although energy storage is one important role for polysaccharides, they are also crucial for another purpose: providing structure. Cellulose, for example, is a major component of plant cell walls, which are rigid structures that enclose the cells (and help make lettuce and other veggies crunchy). Wood and paper are mostly made of cellulose, and cellulose itself is made up of unbranched chains of glucose monomers linked by 111-444 glycosidic bonds. Cellulose fibers and molecular structure of cellulose. Cellulose is made of glucose monomers in the beta form, and this results in a chain where every other monomer is flipped upside down relative to its neighbors. Image modified from OpenStax Biology. Unlike amylose, cellulose is made of glucose monomers in their β form, and this gives it very different properties. As shown in the figure above, every other glucose monomer in the chain is flipped over in relation to its neighbors, and this results in long, straight, non-helical chains of cellulose. These chains cluster together to form parallel bundles that are held together by hydrogen bonds between hydroxyl groups^{4,5} 4,5 start superscript, 4, comma, 5, end superscript. This gives cellulose its rigidity and high tensile strength, which are important to plant cells. The β glycosidic linkages in cellulose can't be broken by human digestive enzymes, so humans are not able to digest cellulose. (That's not to say that cellulose isn't found in our diets, it just passes through us as undigested, insoluble fiber.) However, some herbivores, such as cows, koalas, buffalos, and horses, have specialized microbes that help them process cellulose. These microbes live in the digestive tract and break cellulose down into glucose monomers that can be used by the animal. Wood-chewing termites also break down cellulose with the help of microorganisms that live in their guts. Image of a bee. The bee's exoskeleton (hard outer shell) contains chitin, which is made out of modified glucose units that have a nitrogenous functional group attached to them. Image credit: Louise Docker. Cellulose is specific to plants, but polysaccharides also play an important structural role in non-plant species. For instance, arthropods (such as insects and crustaceans) have a hard external skeleton, called the exoskeleton, which protects their softer internal body parts. This exoskeleton is made of the macromolecule chitin, which resembles cellulose but is made out of modified glucose units that bear a nitrogen-containing functional group. Chitin is also a major component of the cell walls of fungi, which are neither animals nor plants but form a kingdom of their own.

3A Controlling Obesity

Obesity is an excess accumulation of body fat. Afflicts 30% of adults and over 16% of children and adolescents in US Disorders associated with obesity include: Diabetes type 2 Cardiovascular disease Lose weight by lowering caloric intake and increasing exercise.

Orders of protein structure

Primary structure The simplest level of protein structure, primary structure, is simply the sequence of amino acids in a polypeptide chain. For example, the hormone insulin has two polypeptide chains, A and B, shown in diagram below. (The insulin molecule shown here is cow insulin, although its structure is similar to that of human insulin.) Each chain has its own set of amino acids, assembled in a particular order. For instance, the sequence of the A chain starts with glycine at the N-terminus and ends with asparagine at the C-terminus, and is different from the sequence of the B chain. [What's up with those S-S bonds?] Image of insulin. Insulin consists of an A chain and a B chain. They are connected to one another by disulfide bonds (sulfur-sulfur bonds between cysteines). The A chain also contains an internal disulfide bond. The amino acids that make up each chain of insulin are represented as connected circles, each with the three-letter abbreviation of the amino acid's name. image credit: OpenStax Biology. The sequence of a protein is determined by the DNA of the gene that encodes the protein (or that encodes a portion of the protein, for multi-subunit proteins). A change in the gene's DNA sequence may lead to a change in the amino acid sequence of the protein. Even changing just one amino acid in a protein's sequence can affect the protein's overall structure and function. For instance, a single amino acid change is associated with sickle cell anemia, an inherited disease that affects red blood cells. In sickle cell anemia, one of the polypeptide chains that make up hemoglobin, the protein that carries oxygen in the blood, has a slight sequence change. The glutamic acid that is normally the sixth amino acid of the hemoglobin β chain (one of two types of protein chains that make up hemoglobin) is replaced by a valine. This substitution is shown for a fragment of the β chain in the diagram below. Image of normal and sickle cell mutant hemoglobin chains, showing substitution of valine for glutamic acid in the sickle cell version. Image modified from OpenStax Biology. What is most remarkable to consider is that a hemoglobin molecule is made up of two α chains and two β chains, each consisting of about 150 amino acids, for a total of about 600 amino acids in the whole protein. The difference between a normal hemoglobin molecule and a sickle cell molecule is just 2 amino acids out of the approximately 600. A person whose body makes only sickle cell hemoglobin will suffer symptoms of sickle cell anemia. These occur because the glutamic acid-to-valine amino acid change makes the hemoglobin molecules assemble into long fibers. The fibers distort disc-shaped red blood cells into crescent shapes. Examples of "sickled" cells can be seen mixed with normal, disc-like cells in the blood sample below. Image credit: OpenStax Biology modification of work by Ed Uthman; scale-bar data from Matt Russell. The sickled cells get stuck as they try to pass through blood vessels. The stuck cells impair blood flow and can cause serious health problems for people with sickle cell anemia, including breathlessness, dizziness, headaches, and abdominal pain. Secondary structure The next level of protein structure, secondary structure, refers to local folded structures that form within a polypeptide due to interactions between atoms of the backbone. (The backbone just refers to the polypeptide chain apart from the R groups - so all we mean here is that secondary structure does not involve R group atoms.) The most common types of secondary structures are the α helix and the β pleated sheet. Both structures are held in shape by hydrogen bonds, which form between the carbonyl O of one amino acid and the amino H of another. Images showing hydrogen bonding patterns in beta pleated sheets and alpha helices. Image credit: OpenStax Biology. In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids. The R groups of the amino acids stick outward from the α helix, where they are free to interact^3 3 start superscript, 3, end superscript. In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet^3 3 start superscript, 3, end superscript. The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other). Certain amino acids are more or less likely to be found in α-helices or β pleated sheets. For instance, the amino acid proline is sometimes called a "helix breaker" because its unusual R group (which bonds to the amino group to form a ring) creates a bend in the chain and is not compatible with helix formation^4 4 start superscript, 4, end superscript. Proline is typically found in bends, unstructured regions between secondary structures. Similarly, amino acids such as tryptophan, tyrosine, and phenylalanine, which have large ring structures in their R groups, are often found in β pleated sheets, perhaps because the β pleated sheet structure provides plenty of space for the side chains^4 4 start superscript, 4, end superscript. Many proteins contain both α helices and β pleated sheets, though some contain just one type of secondary structure (or do not form either type). Tertiary structure The overall three-dimensional structure of a polypeptide is called its tertiary structure. The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein. R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding, dipole-dipole interactions, and London dispersion forces - basically, the whole gamut of non-covalent bonds. For example, R groups with like charges repel one another, while those with opposite charges can form an ionic bond. Similarly, polar R groups can form hydrogen bonds and other dipole-dipole interactions. Also important to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules. Finally, there's one special type of covalent bond that can contribute to tertiary structure: the disulfide bond. Disulfide bonds, covalent linkages between the sulfur-containing side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary structure. They act like molecular "safety pins," keeping parts of the polypeptide firmly attached to one another. Image of a hypothetical polypeptide chain, depicting different types of side chain interactions that can contribute to tertiary structure. These include hydrophobic interactions, ionic bonds, hydrogen bonds, and disulfide bridge formation. Image modified from OpenStax Biology. Quaternary structure Many proteins are made up of a single polypeptide chain and have only three levels of structure (the ones we've just discussed). However, some proteins are made up of multiple polypeptide chains, also known as subunits. When these subunits come together, they give the protein its quaternary structure. We've already encountered one example of a protein with quaternary structure: hemoglobin. As mentioned earlier, hemoglobin carries oxygen in the blood and is made up of four subunits, two each of the α and β types. Another example is DNA polymerase, an enzyme that synthesizes new strands of DNA and is composed of ten subunits^5 5 start superscript, 5, end superscript. In general, the same types of interactions that contribute to tertiary structure (mostly weak interactions, such as hydrogen bonding and London dispersion forces) also hold the subunits together to give quaternary structure. Flowchart depicting the four orders of protein structure. Image modified from OpenStax Biology's modification of work by the National Human Genome Research Institute. Denaturation and protein folding Each protein has its own unique shape. If the temperature or pH of a protein's environment is changed, or if it is exposed to chemicals, these interactions may be disrupted, causing the protein to lose its three-dimensional structure and turn back into an unstructured string of amino acids. When a protein loses its higher-order structure, but not its primary sequence, it is said to be denatured. Denatured proteins are usually non-functional. For some proteins, denaturation can be reversed. Since the primary structure of the polypeptide is still intact (the amino acids haven't split up), it may be able to re-fold into its functional form if it's returned to its normal environment. Other times, however, denaturation is permanent. One example of irreversible protein denaturation is when an egg is fried. The albumin protein in the liquid egg white becomes opaque and solid as it is denatured by the heat of the stove, and will not return to its original, raw-egg state even when cooled down. Researchers have found that some proteins can re-fold after denaturation even when they are alone in a test tube. Since these proteins can go from unstructured to folded all by themselves, their amino acid sequences must contain all the information needed for folding. However, not all proteins are able to pull off this trick, and how proteins normally fold in a cell appears to be more complicated. Many proteins don't fold by themselves, but instead get assistance from chaperone proteins (chaperonins).

What is a cell

Right now your body is doing a million things at once. It's sending electrical impulses, pumping blood, filtering urine, digesting food, making protein, storing fat, and that's just the stuff you're not thinking about! You can do all this because you are made of cells — tiny units of life that are like specialized factories, full of machinery designed to accomplish the business of life. Cells make up every living thing, from blue whales to the archaebacteria that live inside volcanos. Just like the organisms they make up, cells can come in all shapes and sizes. Nerve cells in giant squids can reach up to 12m [39 ft] in length, while human eggs (the largest human cells) are about 0.1mm across. Plant cells have protective walls made of cellulose (which also makes up the strings in celery that make it so hard to eat) while fungal cell walls are made from the same stuff as lobster shells. However, despite this vast range in size, shape, and function, all these little factories have the same basic machinery. There are two main types of cells, prokaryotic and eukaryotic. Prokaryotes are cells that do not have membrane bound nuclei, whereas eukaryotes do. The rest of our discussion will strictly be on eukaryotes. Think about what a factory needs in order to function effectively. At its most basic, a factory needs a building, a product, and a way to make that product. All cells have membranes (the building), DNA (the various blueprints), and ribosomes (the production line), and so are able to make proteins (the product - let's say we're making toys). This article will focus on eukaryotes, since they are the cell type that contains organelles. A diagram representing the cell as a factory. The cell membrane is represented as the "factory walls." The nucleus of a cell is represented as the "blueprint room." The ribosome is represented as the "production room" and the final protein made by the ribosome is represented as the "product." What's found inside a cell An organelle (think of it as a cell's internal organ) is a membrane bound structure found within a cell. Just like cells have membranes to hold everything in, these mini-organs are also bound in a double layer of phospholipids to insulate their little compartments within the larger cells. You can think of organelles as smaller rooms within the factory, with specialized conditions to help these rooms carry out their specific task (like a break room stocked with goodies or a research room with cool gadgets and a special air filter). These organelles are found in the cytoplasm, a viscous liquid found within the cell membrane that houses the organelles and is the location of most of the action happening in a cell. Below is a table of the organelles found in the basic human cell, which we'll be using as our template for this discussion. Organelle Function Factory part Nucleus DNA Storage Room where the blueprints are kept Mitochondrion Energy production Powerplant Smooth Endoplasmic Reticulum (SER) Lipid production; Detoxification Accessory production - makes decorations for the toy, etc. Rough Endoplasmic Reticulum (RER) Protein production; in particular for export out of the cell Primary production line - makes the toys Golgi apparatus Protein modification and export Shipping department Peroxisome- Lipid Destruction; contains oxidative enzymes Security and waste removal Lysosome- Protein destruction Recycling and security Diagram of a cell highlighting the membrane bound organelles mentioned in the table above. Nucleus Our DNA has the blueprints for every protein in our body, all packaged into a neat double helix. The processes to transform DNA into proteins are known as transcription and translation, and happen in different compartments within the cell. The first step, transcription, happens in the nucleus, which holds our DNA. A membrane called the nuclear envelope surrounds the nucleus, and its job is to create a room within the cell to both protect the genetic information and to house all the molecules that are involved in processing and protecting that info. This membrane is actually a set of two lipid bilayers, so there are four sheets of lipids separating the inside of the nucleus from the cytoplasm. The space between the two bilayers is known as the perinuclear space. Though part of the function of the nucleus is to separate the DNA from the rest of the cell, molecules must still be able to move in and out (e.g., RNA). Proteins channels known as nuclear pores form holes in the nuclear envelope. The nucleus itself is filled with liquid (called nucleoplasm) and is similar in structure and function to cytoplasm. It is here within the nucleoplasm where chromosomes (tightly packed strands of DNA containing all our blueprints) are found. Cartoon showing a close up the nucleus and highlighting structures specific to the nucleus. A nucleus has interesting implications for how a cell responds to its environment. Thanks to the added protection of the nuclear envelope, the DNA is a little bit more secure from enzymes, pathogens, and potentially harmful products of fat and protein metabolism. Since this is the only permanent copy of the instructions the cell has, it is very important to keep the DNA in good condition. If the DNA was not sequestered away, it would be vulnerable to damage by the aforementioned dangers, which would then lead to defective protein production. Imagine a giant hole or coffee stain in the blueprint for your toy - all of a sudden you don't have either enough or the right information to make a critical piece of the toy. The nuclear envelope also keeps molecules responsible for DNA transcription and repair close to the DNA itself - otherwise those molecules would diffuse across the entire cell and it would take a lot more work and luck to get anything done! While transcription (making a complementary strand of RNA from DNA) is completed within the nucleus, translation (making protein from RNA instructions) takes place in the cytoplasm. If there was no barrier between the transcription and translation machineries, it's possible that poorly-made or unfinished RNA would get turned into poorly made and potentially dangerous proteins. Before an RNA can exit the nucleus to be translated, it must get special modifications, in the form of a cap and tail at either end of the molecule, that act as a stamp of approval to let the cell know this piece of RNA is complete and properly made. Cartoon showing mRNA preparing to leave the nucleus and enter the cytoplasm. Nucleolus Within the nucleus is a small subspace known as the nucleolus. It is not bound by a membrane, so it is not an organelle. This space forms near the part of DNA with instructions for making ribosomes, the molecules responsible for making proteins. Ribosomes are assembled in the nucleolus, and exit the nucleus with nuclear pores. In our analogy, the robots making our product are made in a special corner of the blueprint room, before being released to the factory. A diagram representing the cell as a factory. The cell membrane is represented as the "factory walls." The nucleus of a cell is represented as the "blueprint room" while the nucleolus is represented as a "special product corner" within the blueprint room. The ribosome is represented as the "production room" and the final protein made by the ribosome is represented as the "product." Endoplasmic Reticulum Endoplasmic means inside (endo) the cytoplasm (plasm). Reticulum comes from the Latin word for net. Basically, an endoplasmic reticulum is a plasma membrane found inside the cell that folds in on itself to create an internal space known as the lumen. This lumen is actually continuous with the perinuclear space, so we know the endoplasmic reticulum is attached to the nuclear envelope. There are actually two different endoplasmic reticuli in a cell: the smooth endoplasmic reticulum and the rough endoplasmic reticulum. The rough endoplasmic reticulum is the site of protein production (where we make our major product - the toy) while the smooth endoplasmic reticulum is where lipids (fats) are made (accessories for the toy, but not the central product of the factory). Rough Endoplasmic Reticulum The rough endoplasmic reticulum is so-called because its surface is studded with ribosomes, the molecules in charge of protein production. When a ribosome finds a specific RNA segment, that segment may tell the ribosome to travel to the rough endoplasmic reticulum and embed itself. The protein created from this segment will find itself inside the lumen of the rough endoplasmic reticulum, where it folds and is tagged with a (usually carbohydrate) molecule in a process known as glycosylation that marks the protein for transport to the Golgi apparatus. The rough endoplasmic reticulum is continuous with the nuclear envelope, and looks like a series of canals near the nucleus. Proteins made in the rough endoplasmic reticulum as destined to either be a part of a membrane, or to be secreted from the cell membrane out of the cell. Without an rough endoplasmic reticulum, it would be a lot harder to distinguish between proteins that should leave the cell, and proteins that should remain. Thus, the rough endoplasmic reticulum helps cells specialize and allows for greater complexity in the organism. Smooth Endoplasmic Reticulum The smooth endoplasmic reticulum makes lipids and steroids, instead of being involved in protein synthesis. These are fat-based molecules that are important in energy storage, membrane structure, and communication (steroids can act as hormones). The smooth endoplasmic reticulum is also responsible for detoxifying the cell. It is more tubular than the rough endoplasmic reticulum, and is not necessarily continuous with the nuclear envelope. Every cell has a smooth endoplasmic reticulum, but the amount will vary with cell function. For example, the liver, which is responsible for most of the body's detoxification, has a larger amount of smooth endoplasmic reticulum. A diagram showing the structure of the rough endoplasmic reticulum, the golgi apparatus, and the smooth endoplasmic reticulum. Figure 6. The rough endoplasmic reticulum (3) is continuous with the nucleus (1) and makes proteins to be processed by the Golgi apparatus (8), which it is not continuous with. The smoother endoplasmic reticulum is more tubular than the rough, and is not studded with ribosomes. Golgi apparatus (aka Golgi body aka Golgi) We mentioned the Golgi apparatus earlier when we discussed the production of proteins in the rough endoplasmic reticulum. If the smooth and rough endoplasmic reticula are how we make our product, the Golgi is the mailroom that sends our product to customers . It is responsible for packing proteins from the rough endoplasmic reticulum into membrane-bound vesicles (tiny compartments of lipid bilayer that store molecules) which then translocate to the cell membrane. At the cell membrane, the vesicles can fuse with the larger lipid bilayer, causing the vesicle contents to either become part of the cell membrane or be released to the outside. Different molecules actually have different fates upon entering the Golgi. This determination is done by tagging the proteins with special sugar molecules that act as a shipping label for the protein. The shipping department identifies the molecule and sets it on one of 4 paths: Cytosol: the proteins that enter the Golgi by mistake are sent back into the cytosol (imagine the barcode scanning wrong and the item being returned). Cell membrane: proteins destined for the cell membrane are processed continuously. Once the vesicle is made, it moves to the cell membrane and fuses with it. Molecules in this pathway are often protein channels which allow molecules into or out of the cell, or cell identifiers which project into the extracellular space and act like a name tag for the cell. Secretion: some proteins are meant to be secreted from the cell to act on other parts of the body. Before these vesicles can fuse with the cell membrane, they must accumulate in number, and require a special chemical signal to be released. This way shipments only go out if they're worth the cost of sending them (you generally wouldn't ship just one toy and expect to profit). Lysosome: The final destination for proteins coming through the Golgi is the lysosome. Vesicles sent to this acidic organelle contain enzymes that will hydrolyze the lysosome's content. Cartoon representing the golgi apparatus sorting proteins into one of the four paths described above: the cytosol, the cell membrane, secretion, or lysosome. Lysosome The lysosome is the cell's recycling center. These organelles are spheres full of enzymes ready to hydrolyze (chop up the chemical bonds of) whatever substance crosses the membrane, so the cell can reuse the raw material. These disposal enzymes only function properly in environments with a pH of 5, two orders of magnitude more acidic than the cell's internal pH of 7. Lysosomal proteins only being active in an acidic environment acts as safety mechanism for the rest of the cell - if the lysosome were to somehow leak or burst, the degradative enzymes would inactivate before they chopped up proteins the cell still needed. Peroxisome Like the lysosome, the peroxisome is a spherical organelle responsible for destroying its contents. Unlike the lysosome, which mostly degrades proteins, the peroxisome is the site of fatty acid breakdown. It also protects the cell from reactive oxygen species (ROS) molecules which could seriously damage the cell. ROSs are molecules like oxygen ions or peroxides that are created as a byproduct of normal cellular metabolism, but also by radiation, tobacco, and drugs. They cause what is known as oxidative stress in the cell by reacting with and damaging DNA and lipid-based molecules like cell membranes. These ROSs are the reason we need antioxidants in our diet. Mitochondria Just like a factory can't run without electricity, a cell can't run without energy. ATP (adenosine triphosphate) is the energy currency of the cell, and is produced in a process known as cellular respiration. Though the process begins in the cytoplasm, the bulk of the energy produced comes from later steps that take place in the mitochondria. Like we saw with the nuclear envelope, there are actually two lipid bilayers that separate the mitochondrial contents from the cytoplasm. We refer to them as the inner and outer mitochondrial membranes. If we cross both membranes we end up in the matrix, where pyruvate is sent after it is created from the breakdown of glucose (this is step 1 of cellular respiration, known as glycolysis).The space between the two membranes is called the intermembrane space, and it has a low pH (is acidic) because the electron transport chain embedded in the inner membrane pumps protons (H+) into it. Energy to make ATP comes from protons moving back into the matrix down their gradient from the intermembrane space. Mitochondria are also somewhat unique in that they are self-replicating and have their own DNA, almost as if they were a completely separate cell. The prevailing theory, known as the endosymbiotic theory, is that eukaryotes were first formed by large prokaryotic cells engulfing smaller cells that looked a lot like mitochondria (and chloroplasts, more on them later). Instead of being digested, the engulfed cells remained intact and the arrangement turned out to be advantageous to both cells, which created a symbiotic relationship. So far we've discussed organelles, the membrane-bound structures within a cell that have some sort of specialized function. Now let's take a moment to talk about the scaffolding that's holding all of this in place - the walls and beams of our factory. Cytoskeleton Within the cytoplasm there is network of protein fibers known as the cytoskeleton. This structure is responsible for both cell movement and stability. The major components of the cytoskeleton are microtubules, intermediate filaments, and microfilaments. Microtubules Microtubules are small tubes made from the protein tubulin. These tubules are found in cilia and flagella, structures involved in cell movement. They also help provide pathways for secretory vesicles to move through the cell, and are even involved in cell division as they are a part of the mitotic spindle, which pulls homologous chromosomes apart. Intermediate Filaments Smaller than the microtubules, but larger than the microfilaments, the intermediate filaments are made of a variety of proteins such as keratin and/or neurofilament. They are very stable, and help provide structure to the nuclear envelope and anchor organelles. Microfilaments Microfilaments are the thinnest part of the cytoskeleton, and are made of actin [a highly-conserved protein that is actually the most abundant protein in most eukaryotic cells]. Actin is both flexible and strong, making it a useful protein in cell movement. In the heart, contraction is mediated through an actin-myosin system.

Surface area

The more surface area a cell has, the more work it can do. • Which would have more surface area? - Large cells or small cells? - Which cells could do more work?

Turgor Pressure

The pressure of cell contents against the plant cell wall.

Polymers

are constructed by linking together many identical subunits. The subunits are monomers

Fats and oils are

composed of glycerol and fatty acids. Sometimes called triglycerides Insoluble in water Rich source of chemical energy

Disaccharides

contain two monosaccharides joined by a dehydration reaction.

An enzyme

is a molecule that speeds a reaction by bringing reactants together. Food is rich in biomolecules. Polymers are broken into monomers by digestion

A hydrolysis reaction

splits polymers into monomers by adding water. In order for these reactions to occur in a cell, an enzyme must be present.

A dehydration reaction

synthesizes polymers from monomers by removing water.

What is a cell?

• A cell is the basic unit of life. • All cells come from pre-existing cells. • Some basic features of cells: - All cells have a plasma membrane. - The cells cytoplasm contains its organelles. - All cells have genetic material.

George Palade used

*pulse-labeling* to observe the pathway of protein secretion. Radioactive amino acids (pulse) followed by nonradioactive amino acids (chase)

Who first discovered cells?

Robert Hooke Credited with making the first microscopes (1660), and who coined the term "cell;" Antonie van Leeuwenhoek Credited with "perfecting" microscopes (1673).

Actin filaments

Contain 2 strands of actin Associate with mysoin in muscles Motor molecule that pulls actin

Eukaryotic cells

Domain *Eukarya* Protists, plants, fungi, and animals Cytoplasm bound by plasma membrane Compartmentalized into *organelles* Perform specific functions Most are membranous

Mitochondria

Found in nearly all eukaryotic organisms Cellular respiration uses carbohydrates to make ATP. Takes in oxygen and release carbon dioxide

Phospholipids

Hydrophobic tails and hydrophilic heads Form bilayer plasma membranes

Denaturation

Irreversible change of protein shape caused by heat, pH, or chemicals Levels of Organization Primary - sequence of amino acids Secondary - takes on orientation in space Tertiary - final 3D shape for a single polypeptide Quaternary - arrangement of two or more polypeptides in a protein Comparing nucleotide sequences of many organisms helps determine how they are related and the history of life. Molecular evolutionists want to associate new gene mutations with advantages that are selected by the environment. Bacterial laboratory studies Occurrence of mutations Studies in the wild Flowers and their pollinators

Prokaryotic cell structure

No membrane-bound nucleus *Cytoplasm* bound by *plasma membrane* Ribosomes for protein synthesis Long, looped *chromosome* found in nucleoid Reproduce by splitting in two Can share DNA by various means Cyanobacteria can photosynthesize *Cell wall* outside plasma membrane May be surrounded by a capsule May have *pili* (attachment) or *flagella* (movement)

Structure of DNA

Nucleotides contain the sugar deoxyribose Double-stranded Covalently-bonded sugar and phosphate molecules make up sides of ladder Hydrogen-bonded bases make up rungs Bases held together by hydrogen bonds Complementary bases Thymine (T) is always paired with adenine (A) Guanine (G) is always paired with cytosine (C) Base sequence of all the genes is called the genome

Chloroplasts

Plants absorb solar energy using chlorophyll Photosynthesis uses carbon dioxide to produce carbohydrates, and releases oxygen

Waxes

Used for waterproofing Resistant to degradation Found in plants and animals

Ribosomes

Where protein synthesis occurs Found in both prokaryotes and eukaryotes Made of two subunits Some float free in cytoplasm, others attached to *endoplasmic reticulum (ER)* Messenger mRNA (mRNA) is a copy of a gene that tells a cell how to make a particular polypeptide at a ribosome.

Nucleus contains DNA

*Chromatin* - network of strands that condenses to form chromosomes *Nucleolus* - dark region of chromatin where ribosomal subunits are made *Nuclear envelope* A double membrane with nuclear pores Separates the nucleus from the cytoplasm

4A Microscopes allow us to see cells

*Compound light microscope* Multiple lenses increase magnifying power. A condenser lens focuses light through specimen. An objective lens magnifies the specimen's image. An ocular lens magnifies the image into the eye. *Electron microscope* More magnifying power than light microscope A transmission electron microscope passes electrons through the specimen. A scanning electron microscope collects and focuses electrons scattered by the specimen's surface.

2 fundamentally different types of cells

*Eukaryotic cells* Have a nucleus *Prokaryotic cells* Lack a membrane-bound nucleus Are smaller than eukaryotic cells *Two domains:* Bacteria Archaea

Differences between Prokaryotes and Eukaryotes?

2. Complexity - eukaryotes have numerous organelles (most them membrane-bound) organelle = little organ structures inside cells carries out specific functions In fact, prokaryotes have no membrane-bound organelles! membrane-bound organelles (nucleus, mitochondria, chloroplasts) 3. Ribosomes - both prokaryotes and eukaryotes have ribosomes but there are important structural differences!

Cell Theory

A very important concept in biology. • The theory that the cell is the fundamental unit of life. • Through the mid 1800's: - The nucleus was discovered. - Comparisons of plants to animal cells. - Organelles were discovered. - Rudolph Virtow (1855) disproved spontaneous generation.

Nucleic Acids

DNA - deoxyribonucleic acid Genes are segments of DNA. Genes control structure and function of cells and organisms by coding for proteins. Nucleotides (monomers) make up nucleic acids (polymers).

Lipids

Fats and oils A fat molecule consists of two kinds of parts: a glycerol backbone and three fatty acid tails. Glycerol is a small organic molecule with three hydroxyl (OH) groups, while a fatty acid consists of a long hydrocarbon chain attached to a carboxyl group. A typical fatty acid contains 12-18 carbons, though some may have as few as 4 or as many as 36. To make a fat molecule, the hydroxyl groups on the glycerol backbone react with the carboxyl groups of fatty acids in a dehydration synthesis reaction. This yields a fat molecule with three fatty acid tails bound to the glycerol backbone via ester linkages (linkages containing an oxygen atom next to a carbonyl, or C=O, group). Triglycerides may contain three identical fatty acid tails, or three different fatty acid tails (with different lengths or patterns of double bonds). Synthesis of a tryacylglycerol molecule from a glycerol backbone and three fatty acid chains, with the release of three molecules of water. Image modified from OpenStax Biology. Fat molecules are also called triacylglycerols, or, in bloodwork done by your doctor, triglycerides. In the human body, triglycerides are primarily stored in specialized fat cells, called adipocytes, which make up a tissue known as adipose tissue^1 1 start superscript, 1, end superscript. While many fatty acids are found in fat molecules, some are also free in the body, and they are considered a type of lipid in their own right. Saturated and unsaturated fatty acids As shown in the example above, the three fatty acid tails of a triglyceride need not be identical to each other. Fatty acid chains may differ in length, as well as in their degree of unsaturation. If there are only single bonds between neighboring carbons in the hydrocarbon chain, a fatty acid is said to be saturated. (The thing that fatty acids are saturated with is hydrogen; in a saturated fat, as many hydrogen atoms as possible are attached to the carbon skeleton.) When the hydrocarbon chain has a double bond, the fatty acid is said to be unsaturated, as it now has fewer hydrogens. If there is just one double bond in a fatty acid, it's monounsaturated, while if there are multiple double bonds, it's polyunsaturated. The double bonds in unsaturated fatty acids, like other types of double bonds, can exist in either a cis or a trans configuration. In the cis configuration, the two hydrogens associated with the bond are on the same side, while in a trans configuration, they are on opposite sides (see below). A cis double bond generates a kink or bend in the fatty acid, a feature that has important consequences for the behavior of fats. Saturated fatty acid example: stearic acid (straight shape). Unsaturated fatty acid examples: cis oleic acid (cis double bond, bent chain), trans oleic acid (trans double bond, straight chain). Image credit: OpenStax Biology. Saturated fatty acids tails are straight, so fat molecules with fully saturated tails can pack tightly against one another. This tight packing results in fats that are solid at room temperature (have a relatively high melting point). For instance, most of the fat in butter is saturated fat^2 2 start superscript, 2, end superscript. In contrast, cis-unsaturated fatty acid tails are bent due to the cis double bond. This makes it hard for fat molecules with one or more cis-unsaturated fatty acid tails to pack tightly. So, fats with unsaturated tails tend to be liquid at room temperature (have a relatively low melting point) - they are what we commonly call oils. For instance, olive oil is mostly made up of unsaturated fats^2 2 start superscript, 2, end superscript. Trans fats At this point, you may be noticing that I've left something out: I didn't say anything about unsaturated fats with trans double bonds in their fatty acid tails, or trans fats. Trans fats are rare in nature, but are readily produced in an industrial procedure called partial hydrogenation. In this process, hydrogen gas is passed through oils (made mostly of cis-unsaturated fats), converting some - but not all - of the double bonds to single bonds. The goal of partial hydrogenation is to give the oils some of the desirable properties of saturated fats, such as solidity at room temperature, but an unintended consequence is that some of the cis double bonds change configuration and become trans double bonds^3 3 start superscript, 3, end superscript. Trans-unsaturated fatty acids can pack more tightly and are more likely to be solid at room temperature. Some types of shortening, for example, contain a high fraction of trans fats^3 3 start superscript, 3, end superscript. Partial hydrogenation and trans fats might seem like a good way to get a butter-like substance at oil-like prices. Unfortunately, trans fats have turned out to have very negative effects on human health. Because of a strong link between trans fats and coronary heart disease, the U.S. Food and Drug Administration (FDA) recently issued a ban on trans fats in foods, with a three-year deadline for companies to remove trans fats from their products^4 4 start superscript, 4, end superscript. Omega fatty acids Another class of fatty acids that deserves mention includes the omega-3 and omega-6 fatty acids. There are different types of omega-3 and omega-6 fatty acids, but all of them are made from two basic precursor forms: alpha-linolenic acid (ALA) for omega-3s and linoleic acid (LA) for omega-6s. The human body needs these molecules (and their derivatives), but can't synthesize either ALA or LA itself^5 5 start superscript, 5, end superscript. Accordingly, ALA and LA are classified as essential fatty acids and must be obtained from a person's diet. Some fish, such as salmon, and some seeds, such as chia and flax, are good sources of omega-3 fatty acids. Omega-3 and omega-6 fatty acids have at least two cis-unsaturated bonds, which gives them a curved shape. ALA, shown below, is quite bent but isn't the most extreme example - DHA, an omega-3 fatty acid made from ALA by the formation of additional double bonds, has six cis-unsaturated bonds and is curled up almost in a circle! [What makes a fatty acid omega-3 or omega-6?] Image of alpha-linoleic acid (ALA), showing its curled shape due to its three cis double bonds. Image credit: OpenStax Biology. Omega-3 and omega-6 fatty acids play a number of different roles in the body. They are precursors (starting material) for the synthesis of a number of important signaling molecules, including ones that regulate inflammation and mood. Omega-3 fatty acids in particular may reduce the risk of sudden death from heart attacks, decrease triglycerides in the blood, lower blood pressure, and prevent the formation of blood clots. Role of fats Fats have received a lot of bad publicity, and it's true that eating large amounts of fried foods and other "fatty" foods can lead to weight gain and cause health problems. However, fats are essential to the body and have a number of important functions. For instance, many vitamins are fat-soluble, meaning that they must be associated with fat molecules in order to be effectively absorbed by the body. Fats also provide an efficient way to store energy over long time periods, since they contain over twice as much energy per gram as carbohydrates, and they additionally provide insulation for the body. Like all the other large biological molecules, fats in the right amounts are necessary to keep your body (and the bodies of other organisms) functioning correctly. Waxes Waxes are another biologically important category of lipids. Wax covers the feathers of some aquatic birds and the leaf surfaces of some plants, where its hydrophobic (water-repelling) properties prevent water from sticking to, or soaking into, the surface. This is why water beads up on the leaves of many plants, and why birds don't get soaked through when it rains. Image of shiny leaf surface covered with wax. Image credit: OpenStax Biology. Structurally speaking, waxes typically contain long fatty acid chains connected to alcohols by ester linkages, although waxes produced by plants often have plain hydrocarbons mixed in as well^6 6 start superscript, 6, end superscript. Phospholipids What keeps the watery goo (cytosol) inside of your cells from spilling out? Cells are surrounded by a structure called the plasma membrane, which serves as a barrier between the inside of the cell and its surroundings. Specialized lipids called phospholipids are major components of the plasma membrane. Like fats, they are typically composed of fatty acid chains attached to a backbone of glycerol. Instead having three fatty acid tails, however, phospholipids generally have just two, and the third carbon of the glycerol backbone is occupied by a modified phosphate group. Different phospholipids have different modifiers on the phosphate group, with choline (a nitrogen-containing compound) and serine (an amino acid) being common examples. Different modifiers give phospholipids different properties and roles in a cell. Structure of a phospholipid, showing hydrophobic fatty acid tails and hydrophilic head (including ester linkages, glycerol backbone, phosphate group, and attached R group on phosphate group). A bilayered membrane consisting of phospholipids arranged in two layers, with their heads pointing out and their tails sandwiched in the middle, is also shown. Image modified from OpenStax Biology. A phospholipid is an amphipathic molecule, meaning it has a hydrophobic part and a hydrophilic part. The fatty acid chains are hydrophobic and do not interact with water, whereas the phosphate-containing group is hydrophilic (because of its charge) and interacts readily with water. In a membrane, phospholipids are arranged into a structure called a bilayer, with their phosphate heads facing the water and their tails pointing towards the inside (above). This organization prevents the hydrophobic tails from coming into contact with the water, making it a low-energy, stable arrangement. If a drop of phospholipids is placed in water, it may spontaneously form a sphere-shaped structure known as a micelle, in which the hydrophilic phosphate heads face the outside and the fatty acids face the interior of this structure. Formation of micelle is an energetically favored because it sequesters the hydrophobic fatty acid tails, allowing the hydrophilic phosphate head group to instead interact with the surrounding water^{7,8} 7,8 start superscript, 7, comma, 8, end superscript. [More details] ^{7,8} start superscript, 7, comma, 8, end superscript Steroids Steroids are another class of lipid molecules, identifiable by their structure of four fused rings. Although they do not resemble the other lipids structurally, steroids are included in lipid category because they are also hydrophobic and insoluble in water. All steroids have four linked carbon rings and several of them, like cholesterol, also have a short tail. Many steroids also have an -OH functional group attached at a particular site, as shown for cholesterol below; such steroids are also classified as alcohols, and are thus called sterols. Examples of steroids: cholesterol and cortisol. Both have the characteristic structure of four fused hydrocarbon rings. Image credit: OpenStax Biology. [Stereochemistry of cholesterol] Cholesterol, the most common steroid, is mainly synthesized in the liver and is the precursor to many steroid hormones. These include the sex hormones testosterone and estradiol, which are secreted by the gonads (testes and ovaries). Cholesterol also serves as the starting material for other important molecules in the body, including vitamin D and bile acids, which aid in the digestion and absorption of fats from dietary sources. It's also a key component of cell membranes, altering their fluidity and dynamics. Of course, cholesterol is also found in the bloodstream, and blood levels of cholesterol are what we often hear about at the doctor's office or in news reports. Cholesterol in the blood can have both protective effects (in its high-density, or HDL, form) and negative effects (in its low-density, or LDL, form) on cardiovascular health.

Connecting the Concepts: Chapter 3

Four types of large biomolecules are present in all cells. DNA is the genetic code: the sequence of bases determines what types of proteins can be made. DNA → mRNA → proteins DNA mutations are a source of genetic variety for evolution. ATP has the same structure and function in all cells.

3.9 DNA stores coded information

Genetic information flows from DNA to RNA to proteins. RNA is synthesized from a gene (DNA). Uracil replaces thymine, and pairs to adenine. Messenger RNA (mRNA) is a copy of the gene. Several types of RNA in a cell Sequence of bases in mRNA determines sequence of amino acids in a protein

How the Eukaryotic Cell Evolved

The fossil record tells us that the prokaryotic cell was present about 3.5 BYA (billion years ago). Eukaryotic cells evolved in stages. Nuclear envelope and nucleus may have arisen around 2 BYA from an infolding of the plasma membrane. The theory of endosymbiosis states that mitochondria and chloroplasts were once free-living organisms. Outer double membrane Have their own DNA Reproduce by splitting like bacteria

Hydrocarbons

are chains of carbon atoms bonded exclusively to hydrogen atoms. Branching or rings

Vacuoles

are larger than vesicles. Provide storage in protists and plants. The sap-filled central vacuole supports a plant cell.

Isomers

are molecules that have identical molecular formulas but a different arrangement of atoms. Isomers with different functional groups will react differently in chemical reactions.

Complex Carbohydrates

are polymers of monosaccharides, and therefore are called *polysaccharides* Some are used for short-term energy storage. Animals store glucose as glycogen. Plants store glucose as starch. Some are used for structure. Chitin in animals and fungi Peptidoglycan in bacteria Cellulose in plants

Monosaccharides

are single sugar molecules. Glucose is C6H12O6. Isomers - fructose, galactose Ribose and deoxyribose are found in nucleic acids.

Peroxisomes

are small, membrane-bound organelles resembling empty lysosomes. Contain enzymes to digest excess fatty acids Products used by mitochondria to make ATP Produce H2O2 that is broken down Produce cholesterol and phospholipids found in brain and heart tissue

The Golgi apparatus

consists of a stack of slightly curved, flattened saccules. One side is directed toward the ER and the other toward the plasma membrane. It receives, processes, and packages proteins and lipids, so that they may be sent to their final destination in the cell. Forms transport *vesicles* May become *lysosomes* May be released during *secretion* or *exocytosis*

The endoplasmic reticulum (ER) is physically

continuous with the outer membrane of the nuclear envelope. Consists of membranous tubules and flattened sacs Types *Rough ER (RER)* - studded with ribosomes Proteins modified inside *Smooth ER* (SER) - no attached ribosomes Lipid synthesis, detoxification

Adenosine triphosphate (ATP) is a high

energy molecule. Composed of adenosine (adenine plus ribose) plus three phosphate groups Hydrolyzed to form adenosine diphosphate (ADP) and phosphate Breakdown of ATP releases energy Coupled to energy-requiring processes

Genetic mutation

is a change in the sequence of bases in a gene. Can result in altered amino acid sequence in a protein Without mutations, evolution would be impossible because mutations can result in adaptive changes. Sickle-cell disease Inherit a double mutation - disease Inherit a single mutation - advantage in avoiding malarial parasite infection

The endomembrane system

is a series of membranous organelles that work together and communicate by transport vesicles. Includes: ER Golgi apparatus Lysosomes Transport vesicles

A functional group

is a specific combination of bonded atoms that always reacts in the same way, regardless of the particular carbon skeleton

Organic chemistry

is the branch of chemistry devoted to carbon compounds. Carbon has only 6 electrons. 4 in outer shell Almost always shares electrons with CHNOPS

Surface-area-to-volume ratio requires cells to

stay small. A cell needs a surface area large enough to allow sufficient nutrients to enter and wastes to exit. Actively metabolizing cells need to be small. A chicken egg is large but is not actively metabolizing. Cells that specialize in absorption have modifications to increase the surface-area-to-volume ratio.

Prokaryotic Cells

• No nucleus! - But, have "nucleiod region with naked DNA • Ribosomes: the factory for polypeptides • Bacterial cell wall • Some have: - Flagella - Pili - A sticky capsule

Cell SA/V comparisons:

• Three comparisons on previous slide: - Small (6:1), middle (3:1), large (2:1). • More SA/V ratio means the cell works more: - Which cell does the most work? • Prokaryotes are smaller, and have more surface area compared to its volume. - Yet eukaryotes do more work than prokaryotes. - Why???