Exam 1

Prions Are Infectious Protein Molecules

- Prion proteins are abnormally folded versions of normal cellular proteins. - has no genome - Some biologists speculate that a similar mechanism is responsible for the plaques of misfolded proteins that are found in the brains of deceased Alzheimer disease patients

Secretory Vesicles

- Once processed by the Golgi apparatus, secretory proteins and other substances intended for export from the cell are packaged into secretory vesicles. - These vesicles from the Golgi region move to and fuse with the plasma membrane and discharge their contents to the exterior of the cell by the process of exocytosis.

The Endoplasmic Reticulum

- The endoplasmic reticulum consists of tubular membranes and flattened sacs, or cisternae (singular: cisterna), that are interconnected. - The internal space enclosed by the ER membranes is called the lumen - The ER can be either rough or smooth.

A Membrane Is a Lipid Bilayer with Proteins Embedded in It

- When exposed to an aqueous environment, amphipathic molecules undergo hydrophobic interactions. * In a membrane phospholipids are organized into two layers: Their polar heads face outward toward the aqueous environment on both sides, and their hydrophobic tails are hidden from the water by interacting with the tails of other molecules oriented in the opposite direction. Thus, resulting to the structure called lipid bilayer.

Characteristics of Cells

- general characteristics of cells * the organizational complexity and molecular components of cells, the sizes and shapes of cells, and the specializations that cells exhibit.

The Importance of Selectively Permeable Membranes

- A cellular membrane is essentially a hydrophobic permeability barrier that consists of phospholipids, glycolipids, and membrane proteins. - In most organisms other than bacteria, the membranes also contain sterols—cholesterol in the case of animal cells, etc. - Most membrane lipids and proteins. They typically have both hydrophilic and hydrophobic regions and are therefore referred to as amphipathic molecules. * The distinguishing feature of amphipathic phospholipids is that each molecule consists of a polar head and two nonpolar hydrocarbon tails. *The polarity of the hydrophilic head is due to the presence of a negatively charged phosphate group that is often linked to a positively charged functional group

Fatty Acids Are the Building Blocks of Several Classes of Lipids

- A fatty acid is a long, unbranched hydrocarbon chain with a carboxyl group at one end. * The fatty acid molecule is therefore amphipathic; the carboxyl group renders one end (often called the "head") polar, whereas the hydrocarbon "tail" is nonpolar. * The usual range is from 12 to 20 carbon atoms per chain. - Fatty acids without double bonds are referred to as saturated fatty acids because every carbon atom in the chain has the maximum number of hydrogen atoms attached to it. * Saturated fatty acids have long, straight chains that pack together well. - unsaturated fatty acids contain one or more double bonds, resulting in a bend or kink in the chain that prevents tight packing * Much concern has arisen recently over a particular type of unsaturated fatty acid known as a trans fat. * Trans fats contain unsaturated fatty acids with a particular type of double bond that causes less of a bend in the fatty acid chain, thus causing them to resemble saturated fatty acids in both their shape and their ability to pack together more tightly than typical unsaturated fatty acids. * Trans fats have been linked to changes in blood cholesterol that are associated with increased risk of heart disease.

Water Has a High Temperature-Stabilizing Capacity

- An important property of water that stems directly from the hydrogen bonding between adjacent molecules is the high specific heat that gives water its temperature-stabilizing capacity. * Specific heat is the amount of heat a substance must absorb per gram to increase its temperature 1°C. * The specific heat of water is 1.0 calorie per gram. *In water, the energy is used instead to break hydrogen bonds between neighboring water molecules, buffering aqueous solutions against large changes in temperature. *If not for the extensive hydrogen bonding and the resulting high specific heat of water molecules, this release of energy would pose a serious overheating problem for cells, and life would not be possible. - Water also has a high heat of vaporization, which is defined as the amount of energy required to convert 1 gram of a liquid into vapor. * This value is high for water because of the hydrogen bonds that must be disrupted in the process.

Water Molecules are polar

- An unequal distribution of electrons gives the water molecule its polarity *polarity is an uneven distribution of charge within a molecule. - The water molecule is bent rather than linear in shape, with the two hydrogen atoms bonded to the oxygen at an angle of 104.5° rather than 180°. * The oxygen atom is highly electronegative—it tends to draw electrons toward it. So, O has a partial negative charge (denoted as δ−) and each of the two hydrogen atoms has a partial positive charge (δ+). * The extensive association of water molecules with one another in either the liquid or the solid state is due to hydrogen bonds

- There Are Several Limitations on Cell Size

- Bacterial and archaeal cells are usually about 1-5 μm in diameter. - most cells of higher plants and animals have dimensions in the range of 10-100 μm. - Several factors limit cell size, but the three most important are: * (1) the requirement for an adequate surface area/volume ratio - Surface area is critical because it is at the cell surface that the needful exchanges between a cell and its environment take place. - The cell's internal volume determines the amount of nutrients that will have to be imported and the quantity of waste products that must be excreted. - Cell size can increase only as long as the membrane surface area is still adequate for the passage of materials into and out of the cell. * (2) the rates at which molecules diffuse - Because the rate of diffusion decreases as the size of the molecule increases, this limitation is most significant for macromolecules such as proteins and nucleic acids. * (3) the need to maintain adequate local concentrations of the specific substances and enzymes involved in necessary cellular processes. - the need to maintain adequate concentrations of the essential compounds and enzymes needed for the various processes that cells must carry out. In the absence of a concentrating mechanism, this obviously taxes the cell's synthetic capabilities.

Hershey and Chase Showed That DNA Is the Genetic Material of Viruses

- Bacteriophages are viruses that infect bacteria. * Some of the most thoroughly studied phages are the T2, T4, and T6 (the so-called T-even) bacteriophages, which infect the bacterium Escherichia coli. - Hershey and chase used T4 bacteriophage and E.Coli to demonstrate DNA as the genetic material. - Ran parallel experiments of radioactive virus 1. Radioactive protein 2. radioactive DNA Through a few phases were performed * initiate infection, half infection, centrifuge, analyze supernatant vs pellet - He found that radioactive protein were found in the supernatant, while radioactive DNA was found in pellet.

Lipid Bilayers Are Selectively Permeable

- Because of its hydrophobic interior, a lipid bilayer is readily permeable to non-polar and small molecules. * Also known as Passive/Facilitated Diffusion where concentration of molecules move from high to low concentration. - works best for non-polar and small molecules - requires carrier protein (transport protein) - However, it is quite impermeable to most polar molecules and is highly impermeable to all ions * the smallest ions are effectively excluded from the hydrophobic interior of the membrane. E.g Na+ or K+ ions - Primary Active Transport use ATP directly to pump for example Na+/K+ ions - Secondary Active Transport uses gradient potential energy to transport in or out glucose for example in the small intestine. - Because most cellular constituents are either polar or charged, they have little or no affinity for the membrane interior and are effectively prevented from entering or escaping from the cell. Small, uncharged molecules are an exception, however. * E.g. Water is an especially important example of a very small molecule that, though polar, diffuses rapidly across membranes and can readily enter or leave cells. - Large, uncharged polar molecules, such as glucose and sucrose, can diffuse across the membrane, but to a lesser extent than small molecules. - To transport ions such as Na+ and K+ but also a wide variety of polar molecules into and out of the cell, biological membranes are equipped with a wide variety of transport proteins. * A transport protein: is a specialized transmembrane protein that serves either as a hydrophilic channel through an otherwise hydrophobic membrane or as a carrier that binds a specific solute on one side of the membrane and then undergoes a conformational change to move the solute across the membrane. * Whether a channel or a carrier, each transport protein is specific for a particular molecule or ion * Moreover, the activities of these proteins can be carefully regulated to meet cellular needs. - Active Transport * requires for molecules to be moved against a concentration gradient. * requires energy input.

Water Molecules Are Cohesive

- Because of their polarity, water molecules are attracted to each other so that the electronegative oxygen atom of one molecule is associated with the electropositive hydrogen atoms of adjacent molecules. * Thus forming a hydrogen bond, which is a type of non-covalent interaction that is about one- tenth as strong as a covalent bond. - Water is thus, characterized by an extensive three-dimensional network of hydrogen-bonded molecules. * Each molecule of water in the liquid state is hydrogen-bonded to at least three neighbor molecules at any given time. - It is this tendency to form hydrogen bonds between adjacent molecules that makes water so highly cohesive. - This cohesiveness accounts for the high surface tension of water, as well as for its high boiling point, high specific heat, and high heat of vaporization. * The high surface tension of water allows some insects to move across the surface of a pond without breaking the surface. * The high surface tension of water results from the collective strength of vast numbers of hydrogen bonds. * High surface tension is also important in allowing water to move upward through the conducting tissues of plants.

Macromolecules Are Synthesized by Stepwise Polymerization of Monomers

- Because the elimination of a water molecule is essential in all biological polymerization reactions, each monomer must have both an available hydrogen (H) and an available hydroxyl group (-OH) on the molecule. - For a given kind of polymer, the monomers may differ from one another in other aspects of their structure; but each monomer possesses an available hydrogen and hydroxyl group. - A different kind of carrier molecule is used for each kind of polymer. (from the image, step a) * For protein synthesis, amino acids are activated by linking them to carriers called transfer RNA (or tRNA) molecules. * Monosaccharides are activated by linking them to derivatives of nucleotides. * Note that nucleic acid synthesis needs no specific carrier molecules because the nucleotides themselves (e.g., ATP or GTP) are high-energy molecules. - Once activated, monomers can react with each other in a condensation reaction that releases the carrier molecule. (step 2 in the image) * This is also known as dehydration synthesis because, as each monomer is added during polymer synthesis, one molecule of water is removed. - One activated monomeric unit is added at a time, thus lengthening the elongating polymer by one unit. (step 3 in the image) - Polymer synthesis always involves activated monomers joined via condensation reactions, and ATP or a similar high-energy compound is required to activate the monomers by linking them to an appropriate carrier molecule. - The degradation, or breakdown, of macromolecules occurs in a manner opposite to the condensation reactions used for synthesis. * monomers are removed from the polymer by hydrolysis—the addition of a water molecule that breaks the bond between adjacent monomers. In the process, one monomer receives a hydroxyl group from the water molecule and the other receives a hydrogen atom, re-forming the original monomers.

Carbon-Containing Molecules Can Form Stereoisomers

- Carbon-containing molecules are capable of still greater diversity because the carbon atom is a tetrahedral structure. - When four different atoms or groups of atoms are bonded to the four corners of such a tetrahedral structure, two different spatial configurations are possible; being mirror images of one another. * mirror-image forms of the same compound are called stereoisomer. - A carbon atom that has four different substituents (atoms or groups attached) is called an asymmetric carbon atom or chiral *Because two stereoisomers are possible for each asymmetric carbon atom, a compound with n asymmetric carbon atoms will have 2n possible stereoisomers. * Chirality leads to additional specificity of chemical interactions.

Using Centrifugation to Isolate Organelles

- Centrifugation separates different organelles and macromolecules based on differences in their physical properties in a solution. - When a particle is subjected to centrifugal force by spinning a cellular extract at extremely rapid rates, the rate of movement of the particle through a solution will depend on its size and density, as well as on the solution's density and viscosity. * starting at low C-force and centrifuging in multiple steps (with C-force at every step). * researchers can collect multiple samples with different size components. - The relative size and density of an organelle or macromolecule is expressed in Svedberg units (S), which describe its sedimentation coefficient. * This is a measure of how rapidly the particle sediments when subjected to centrifugation. * Larger and/or denser particles have higher sedimentation coefficients. * mass is the major factor contributing to S values. - Using density gradient centrifugation, we can separate the components of a single pellet because each has a slightly different density.

H bonds of bases in DNA and RNA

- Complementary relationships between purines and pyrimidines allow A to form two hydrogen bonds with T (or U) and G to form three hydrogen bonds with C - This pairing of A with T (or U) and G with C is a fundamental property of nucleic acids. Genetically, this base pairing provides a mechanism for nucleic acids to recognize one another.

The discovery of DNA and proving that it is the genetic material.

- DNA was discovered by Friedrich Miescher, a Swiss physician. * Miescher reported the discovery of the substance now known as DNA in 1869. - Around 1910 to the 1940s, most scientists believed that genes were made of protein rather than DNA. * DNA was thought to be a simple polymer consisting of the same sequence of four bases repeated over and over, thereby lacking the variability expected of a genetic molecule. - British physician Frederick Griffith was studying a pathogenic strain of a bacterium. * Griffith discovered that this bacterium exists in two forms, called the S strain and the R strain. * When injected into mice, S-strain (but not R-strain) bacteria trigger a fatal pneumonia. * When Griffith autopsied the animals that had been injected with the mixture of live R-strain and dead S-strain bacteria, he found them filled with live S-strain bacteria. - He concluded that the nonpathogenic R bacteria were somehow converted into pathogenic S bacteria by a substance present in the heat-killed S bacteria that had been co-injected. * He called this phenomenon genetic transformation. - Oswald Avery and his colleagues continued Griffith's work. * They fractionated cell-free extracts of S-strain bacteria and found that only the nucleic acid fraction was capable of causing transformation. * Moreover, the activity was specifically eliminated by treatment with deoxyribonuclease, an enzyme that degrades DNA. - This and other evidence convinced them that the transforming substance of pneumococcus was DNA.

Discovery of DNA structure Chargaff, Crick and Watson double helix model, and Rosalind Franklin's X-ray of the Chromosomes.

- Erwin Chargaff, used chromatographic methods to separate and quantify the relative amounts of the four bases—adenine (A), guanine (G), cytosine (C), and thymine (T)—found in DNA. - The number of adenines is equal to the number of thymines (A = T), and the number of guanines is equal to the number of cytosines (G = C). - This meant that the number of purines is equal to the number of pyrimidines (A + G = C + T). The significance of these equivalencies, known as Chargaff's rules, became clear when Watson and Crick proposed the double-helical model of DNA in 1953. - The most profound implication of the Watson-Crick model was that it suggested a mechanism by which cells can replicate their genetic information: the two strands of the DNA double helix could simply separate from each other before cell division so that each strand could function as a template, dictating the synthesis of a new complementary DNA strand using the base-pairing rules. * without Franklin's X-ray diffraction data, then Watson and Crick couldn't have proposed the model.

The Extracellular Matrix and Cell Walls Are Outside the Plasma Membrane

- For many animal cells, the extracellular matrix (ECM) consists primarily of collagen fibrils and proteoglycans. - For plant and fungal cells, the extracellular structure is the rigid cell wall, which consists mainly of cellulose microfibrils embedded in a matrix of other polysaccharides and small amounts of protein. - neighboring plant cells, though separated by the cell walls between them, are actually connected by numerous openings, called plasmodesmata which pass through the fused cell walls. * The plasma membranes of adjacent cells are continuous through each plasmodesma, such that the channel is membrane-lined. * The diameter of a typical plasmodesma is large enough to allow water and small solutes to pass freely from cell to cell.

Glycolipids Are Specialized Membrane Components

- Glycolipids are lipids containing a carbohydrate group instead of a phosphate group and are typically derivatives of sphingosine or glycerol. -The carbohydrate group attached to a glycolipid may contain one to six sugar units, which can be d-glucose, d-galactose, or N-acetyl-d-galactosamine. - These carbohydrate groups, like phosphate groups, are hydrophilic, giving the glycolipid an amphipathic nature.

Vacuoles

- In animal and yeast cells, vacuoles are used for temporary storage or transport. - Phagocytosis is a form of endocytosis that involves an infolding of the plasma membrane around the desired substance. - This infolding is followed by a pinching-off process that internalizes the membrane-bounded particle as a type of vacuole, known as a phagosome. - Plant cells also contain vacuoles. * most mature plant cells contain a single large vacuole, which occupies much of the internal volume of the cell, leaving the cytoplasm sandwiched into a thin region between the vacuole and the plasma membrane. sometimes called the central vacuole and its role in maintaining the turgor pressure that keeps plant tissue from wilting. * The vacuole has a high concentration of solutes; thus, water tends to move into the vacuole, causing it to swell. As a result, the vacuole presses the rest of the cell constituents against the cell wall, thereby maintaining the turgor pressure.

The Lysosome

- Lysosomes are used by the cell as storage containers for hydrolases, enzymes capable of digesting specific biological molecules such as proteins, carbohydrates, or fats. - Like secretory proteins, lysosomal enzymes are synthesized on the rough ER, transported to the Golgi apparatus, and then packaged into vesicles that can become lysosomes.

Functional groups in carbon

- Most biological compounds contain, in addition to carbon and hydrogen, one or more atoms of oxygen and often nitrogen, phosphorus, or sulfur as well. - These atoms are usually part of various functional groups * Functional groups: specific arrangements of atoms that confer characteristic chemical properties on the molecules to which they are attached. e.g. Animo (NH3+), carboxyl (COO-), phosphate (POOO), hydroxyl (OH), sulfhydryl (SH), carbonyl (CO), aldehyde (COH)

Macromolecules Are Critical for Cellular Form and Function

- Most cellular structures are composed of small, water-soluble organic molecules (Level 1) that cells either obtain from other cells or synthesize from simple nonbiological molecules such as carbon dioxide, ammonia, or phosphate ions. - Small organic molecules known as monomers polymerize to form biological macromolecules (Level 2) such as polysaccharides, proteins, or nucleic acids. - These macromolecules may function on their own, or they can then be assembled into a variety of supramolecular structures (Level 3). These supramolecular structures are themselves components of organelles (Level 4) that make up the cell itself (Level 5). - A general principle emerges and it states that the macromolecules that are responsible for most of the form and order characteristic of living systems are generated by the polymerization of small organic molecules into long chains; by linking together small repeating units (monomers), forming a polymer.

The Monomers Are Nucleotides

- Nucleic acids are informational macromolecules and contain nonidentical monomeric units in a specified sequence. * The monomeric units of nucleic acids are called nucleotides - DNA and RNA each contain only four different kinds of nucleotides. * each nucleotide consists of a five-carbon sugar to which is attached a phosphate group and a nitrogen-containing aromatic base. * The sugar is either d-ribose (in RNA) or d-deoxyribose (in DNA). * The phosphate is joined by a phosphoester bond to the 5′ carbon of the sugar, and the base is attached to the 1′ carbon. - The base may be either a purine or a pyrimidine * DNA contains the purines adenine (A) and guanine (G) and the pyrimidines cytosine (C) and thymine (T). * RNA contains the purines adenine (A), guanine (G), and the pyrimidines cytosine (C) and Uracil (U). - Without the phosphate, the remaining base-sugar unit is called a nucleoside * As the nomenclature indicates, a nucleotide can be thought of as a nucleoside monophosphate because it is a nucleoside with a single phosphate group attached to it. - nucleotides play two roles in cells: They are the monomeric units of nucleic acids, and several of them—ATP most notably—serve as intermediates in various energy-transferring reactions.

Water Is an Excellent Solvent

- One of the most important properties of water is its excellence as a general solvent. *A solvent is a fluid in which another substance, called the solute, can be dissolved. - It is the polarity of water that makes it so useful as a solvent. - Solutes that have an affinity for water and therefore dissolve readily in water are called hydrophilic ("water-loving"). Most small organic molecules found in cells are hydrophilic. * Examples are sugars, organic acids, and some of the amino acids. - Molecules that are not very soluble in water are termed hydrophobic ("water-fearing"). * Among the more important hydrophobic compounds found in cells are the lipids and proteins found in biological membranes. - When NaCl (salt and its polar or hydrophilic) is placed in water, both the sodium and chloride ions become involved in electrostatic interactions with the water molecules instead of with each other, and the Na+ and Cl− ions separate and become dissolved. *Because of their polarity, water molecules can form spheres of hydration around both Na+ and Cl−, thus neutralizing their attraction for each other and decreasing their likelihood of reassociation. - the sphere of hydration around a cation such as Na+ involves water molecules clustered around the ion with their negative (oxygen) ends pointing toward it. - For an anion such as Cl−, the orientation of the water molecules is reversed, with the positive (hydrogen) ends of the solvent molecules pointing in toward the ion. - Hydrophobic molecules such as hydrocarbons, on the other hand, have no such polar regions and therefore show no tendency to interact electrostatically with water molecules. - Because typical cells are primarily water and most other biological molecules in cells contain hydrogen, the chemical and physical properties of the hydrogen atom can be exploited for medical imaging purposes. * E.g magnetic resonance imaging (MRI) takes advantage of this abundance of water to image internal body tissues in a noninvasive manner

Phospholipids Are Important in Membrane Structure

- Phospholipids are similar to triacylglycerols in some chemical details but differ strikingly in their properties and their role in the cell. * phospholipids are important in membrane structure due to their amphipathic nature and are a key component of the bilayer structure found in all membranes. * phospholipids are classified as phosphoglycerides or sphingolipids. - A phosphoglyceride consists of fatty acids that are esterified to a glycerol molecule, the fatty acids are attached to the 3rd carbon that is also attached to P. P is also attached to the functional group (R group). * the basic component of a phosphoglyceride is phosphatidic acid, which has just two fatty acids and a phosphate group attached to a glycerol backbone * membrane phosphoglycerides have, in addition, a small hydrophilic alcohol linked to the phosphate by an ester bond - groups that contribute to the polar nature of the phospholipid head group, or alcohols (e.g. serine). - The combination of a highly polar head and two long nonpolar chains gives phosphoglycerides the characteristic amphipathic nature that is so critical to their role in membrane structure. - In addition to the phosphoglycerides, some membranes contain another class of phospholipid called sphingolipids, which are important in membrane structure and cell signaling. * Sphingolipids are present predominantly in the outer monolayer of the plasma membrane bilayer, where they often are found in lipid rafts, which are localized microdomains within a membrane that facilitate communication with the external environment of the cell.

Noncovalent Bonds and Interactions Are Important in the Folding of Macromolecules

- Polypeptides can fold and self-assemble without the input of further information, and the three-dimensional structure of a protein or protein complex is remarkably stable once it has been attained. - Every protein or other macromolecule in the cell is held together by strong covalent bonds. * But, many cellular structures are held together by non-covalent bonds and interactions— typically much weaker forces that occur within and among macromolecules. - The most important non-covalent bonds and interactions in biological macromolecules are hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions. * Hydrogen bonds involve weak, attractive interactions between an electronegative atom such as oxygen (or nitrogen) and a hydrogen atom that is covalently bonded to a second electronegative atom. * Ionic bonds are strong non-covalent electrostatic interactions between two oppositely charged ions. In the case of macromolecules, ionic bonds form between positively charged and negatively charged functional groups such as amino groups, carboxyl groups, and phosphate groups. * Van der Waals interactions (or forces) are weak attractive interactions between two atoms that occur only if the atoms are very close to one another and are oriented appropriately. The van der Waals radius of a specific atom specifies the "personal space" around it that limits how close other atoms can come. * Hydrophobic interactions describes the tendency of nonpolar groups within a macromolecule to associate with each other as they minimize their contact with surrounding water molecules and with any hydrophilic groups in the same or another macromolecule.

The Polymers Are Storage and Structural Polysaccharides

- Polysaccharides typically perform either storage or structural roles in cells. * The most familiar storage polysaccharides are starch, found in plant cells and glycogen, found in animal cells and bacteria. - Both of these polymers consist of α-d-glucose units linked together by α glycosidic bonds. - In addition to α(1→4) bonds that link carbon atoms 1 and 4 of adjacent glucose units, these polysaccharides may contain occasional α(1 → 6) linkages along the backbone, giving rise to side chains. * Storage polysaccharides can therefore be branched or unbranched polymers, depending on the presence or absence of α(1→6) linkages. - Glycogen is highly branched, with α(1→6) linkages occurring every 8 to 10 glucose units along the backbone and giving rise to short side chains of about 8 to 12 glucose units. * E.g. In our bodies, glycogen is stored mainly in the liver and in muscle tissue. - Starch, the glucose reserve commonly found in plant tissue, occurs both as unbranched amylose and as branched amylopectin. * amylopectin has α(1→6) branches, occur once every 12 to 25 glucose units and longer side chains of 20 to 25 glucose units are common. - A common example of a structural polysaccharide is the cellulose found in plant cell walls. * cellulose is a polymer of glucose; however, the repeating monomer is β-d-glucose, and the linkage is therefore β(1→4). * Mammals do not possess an enzyme that can hydrolyze this β(1→4) bond and therefore cannot use cellulose as food. - Peptidoglycan contain peptide along with carbohydrates, found in bacterial cell wall. - chitin found in insect exoskeletons, crustacean shells, and fungal cell walls.

The Monomers of proteins Are Amino Acids

- Proteins are linear polymers of amino acids (a single chain is called a polypeptide) * only 20 kinds are used in protein synthesis - Every amino acid has the basic structure with a carboxyl group, an amino group, a hydrogen atom, and a side chain known as an R group all attached to a central carbon atom known as the α carbon. * The R group is different for each amino acid and gives each amino acid its distinctive properties. - All amino acids have four different groups attached to the α carbon. This means that all amino acids except glycine exist in two stereoisomeric forms that are mirror images of each other and cannot be superimposed. These two mirror-image forms are called d- and l-amino acids, but only l-amino acids occur in proteins.

Rough endoplasmic reticulum (rough ER)

- Rough ER appears "rough" in the electron microscope because it is studded with ribosomes on the side of the membrane that faces the cytosol. - These ribosomes are actively synthesizing polypeptides that either accumulate within the membrane or are transported across the ER membrane to accumulate in the space inside the ER (its lumen). - In general, secretory proteins and membrane proteins are made by ribosomes on the rough ER, whereas proteins intended for use within the cytosol or for import into organelles are made on free ribosomes.

The Nucleus Is the Information Center of the Eukaryotic Cell

- Separated from the rest of the cell by a membrane boundary, are the DNA-bearing chromosomes of the cell. - The boundary around the nucleus consists of two membranes, called the inner and outer nuclear membranes. Taken together, the two membranes make up the nuclear envelope. - The nuclear envelope has numerous small openings called pores. * Each pore is a channel through which water-soluble molecules can move between the nucleus and cytoplasm. * This channel is lined with transport machinery known as a pore complex that regulates the movement of macromolecules through the nuclear envelope. - The nucleolus (plural: nucleoli), the structure responsible for synthesizing ribosomal RNA and beginning the assembly of the protein components needed to form ribosomes.

Steroids Are Lipids with a Variety of Functions

- Steroids are derivatives of a four-ringed hydrocarbon skeleton which, makes them structurally distinct from other lipids. The 3rd ring with six carbons and 4th ring with 5 carbons. - they are relatively nonpolar and therefore hydrophobic. * Because most of the molecule is hydrophobic, cholesterol is insoluble in water and is found primarily in membranes except the inner membranes of mitochondria and chloroplasts. - Steroids are found almost exclusively in eukaryotic cells. * The most common steroid in animal cells is cholesterol. - Cholesterol is an amphipathic molecule, with a polar head group and a non-polar hydrocarbon body and tail. - Help mediate fluidity in cell membranes. - Cholesterol is the starting point for the synthesis of all the steroid hormones, * E.g. male and female sex hormones; estrogens produced by the ovaries of females and the androgens produced by the testes of males. * E.g. Aldosterone which regulates water balance and blood pressure.

The Golgi Apparatus

- The Golgi apparatus consists of a stack of flattened vesicles. - The Golgi apparatus plays an important role in processing and packaging secretory proteins and in synthesizing complex polysaccharides. - Transition vesicles that arise by budding off the ER go to the Golgi apparatus. - The processed contents are then passed on to other components of the cell in vesicles that arise by budding off the Golgi apparatus.

A DNA Molecule Is a Double-Stranded Helix

- The double helix consists of two complementary chains of DNA twisted together around a common axis to form a right-handed helical structure that resembles a spiral staircase. * The two chains are oriented in opposite directions along the helix, with one running in the 5′→3′ direction and the other in the 3′→5′ direction. * The phosphate groups are charged, and the sugar molecules contain polar hydroxyl groups. Therefore, it is not surprising that the sugar-phosphate backbones of the two strands are on the outside of the DNA helix, where their interaction with the surrounding aqueous environment can be maximized. * The pyrimidine and purine bases, on the other hand, are aromatic compounds with less affinity for water (more hydrophobic). - Accordingly, they are oriented inward away from water, forming the base pairs that hold the two chains together. - To form a stable double helix, the two component strands must be antiparallel (running in opposite directions). They also must be complementary, each base in one strand will pair with one specific base directly across from it in the other strand. * one member of the pair is a pyrimidine (T or C) and the other is a purine (A or G). - RNA structure also depends in part on base pairing, but this pairing is usually between complementary regions within the same strand and is much less extensive than the inter-strand pairing of the DNA duplex. * Of the various RNA species, secondary and tertiary structures occur mainly in rRNA and tRNA.

Bonds and Interactions Involved in Protein Folding and Stability.

- The initial folding and subsequent stability of a polypeptide depend on (a) covalent disulfide bonds as well as on several kinds of noncovalent bonds and interactions, including (b) hydrogen bonds, (c) ionic bonds, (d) van der Waals interactions, and hydrophobic interactions. * A special type of covalent bond that helps stabilize protein conformation is the disulfide bond, which forms between the sulfur atoms of two cysteine amino acid residues. Such intramolecular disulfide bonds stabilize the conformation of the polypeptide. In the case of multimeric proteins, a disulfide bond may form between cysteine residues located in two different polypeptides. Such intermolecular disulfide bonds link the two polypeptides to one another covalently. * non- covalent bonds and interactions are also important in maintaining protein structure (hydrogen bonds, ionic bonds, van der Waals interactions, and hydrophobic interactions). - Hydrophobic interactions: Polypeptide folding to form the final protein structure is, in part, a balance between the tendency of hydrophilic groups to seek an aqueous environment near the surface of the molecule and the tendency of hydrophobic groups to minimize contact with water by associating with each other in the interior of the molecule. - The stability of the folded structure of a polypeptide depends on an interplay of covalent disulfide bonds and four noncovalent factors: hydrogen bonds between R groups that are good hydrogen bond donors and acceptors; ionic bonds between charged amino acid R groups; transient van der Waals interactions between nonpolar molecules in very close proximity; and hydrophobic interactions that drive nonpolar groups to the interior of the molecule.

Several Kinds of Bonds and Interactions Are Important in Protein Folding and Stability

- The initial folding of a polypeptide into its proper shape, or conformation, depends on several different kinds of bonds and interactions, including the covalent disulfide bond and several noncovalent interactions. - the association of individual polypeptides to form a multimeric protein. These interactions primarily involve the R groups of the individual amino acid residues, the name given to the amino acids once they are incorporated into the polypeptide. - Disruption of these interactions by heat, high salt, or chemical treatment can result in denaturation, or unfolding, of the polypeptide

The Polymers Are DNA and RNA

- The phosphate group already attached by a phosphoester bond to the 5′ carbon of one nucleotide becomes linked by a second phosphoester bond to the 3′ carbon of the next nucleotide. * The resulting linkage is known as a 3′,5′phosphodiester bridge, which consists of a phosphate group linked to two adjacent nucleotides via two phosphoester bonds (one bond to each nucleotide). - The polynucleotide formed by this process has an intrinsic directionality, with a 5′ phosphate group at one end and a 3′ hydroxyl group at the other end. - Nucleic acid synthesis requires both energy and information. * To provide the energy needed to form each new phosphodiester bridge, each successive nucleotide enters as a high-energy nucleoside triphosphate. - For DNA synthesis, dATP, dCTP, dGTP, and dTTP. For RNA synthesis, ATP, CTP, GTP, and UTP * Information is required for nucleic acid synthesis because successive incoming nucleotides must be added in a specific, genetically determined sequence. - a preexisting molecule is used as a template to specify nucleotide order. For both DNA and RNA the template is DNA.

The Plasma Membrane Defines Cell Boundaries and Retains Contents

- The plasma membrane defines the boundaries of the cell, ensuring that its contents are retained. The plasma membrane consists of phospholipids, other lipids, and membrane proteins and is organized into two layers. * The phospholipid molecules orient themselves in the two layers of the membrane such that the hydrophobic hydrocarbon tails of each molecule face inward and the hydrophilic phosphate-containing heads of the molecules face outward. * The resulting lipid bilayer is the basic structural unit of virtually all membranes and serves as a permeability barrier to most water-soluble substances. * Membrane proteins are also amphipathic, with both hydrophobic and hydrophilic regions on their surfaces. * Types of proteins: - Integral proteins span the entire membrane, many proteins span the membrane multiple times. - Peripheral proteins associated only with outer or inner membrane, mostly outer * The proteins present in the plasma membrane play a variety of roles. - Some are enzymes, which catalyze reactions known to be associated with the membrane—reactions such as cell wall synthesis. - Transport proteins: responsible for moving specific substances (ions and hydrophilic solutes, usually) across the membrane. - Receptor proteins: Membrane proteins are also important as receptors for external chemical signals that trigger specific processes within the cell. - Anchor proteins: anchors for structural elements of the cytoskeleton.

The Polymers Are Polypeptides and Proteins

- The process of stringing individual amino acids together into a linear polymer involves the stepwise addition of each new amino acid to the growing chain by a condensation (or dehydration) reaction. - As the three atoms of H2O are removed, the carboxyl carbon of one amino acid and the amino nitrogen of a second are linked directly by a covalent bond. This C—N bond linking two amino acids is known as a peptide bond. As each new peptide bond is formed by condensation, the growing chain of amino acids is lengthened by one amino acid. - The chain of amino acids formed in this way has an intrinsic directionality because it always has an amino group at one end and a carboxyl group at the other end. The end of the chain with the amino group is known as the N- (or amino) terminus, and the end with the carboxyl group is known as the C- (or carboxyl) terminus. - A protein is a polypeptide chain (or a complex of several polypeptides) that has attained a unique, stable, three-dimensional shape and is biologically active as a result. Although a polypeptide is itself a polymer, the entire polypeptide is sometimes a monomeric unit of a multimeric protein. If a multimeric protein is composed of two polypeptides, it is referred to as a dimer; and if it has three polypeptides, it is known as a trimer.

Quaternary Structure

- The quaternary structure of a protein is the level of organization concerned with subunit interactions and assembly. * Quaternary structure therefore applies only to multimeric proteins * Some multimeric proteins contain identical polypeptide subunits; others, such as hemoglobin, contain two or more different kinds of polypeptides. - The bonds and forces that maintain quaternary structure are the same as those responsible for tertiary structure: hydrogen bonds, electrostatic interactions, van der Waals interactions, hydrophobic interactions, and covalent disulfide bonds. - Disulfide bonds may be either within a polypeptide chain or between chains. * When they occur within a polypeptide, they stabilize tertiary structure. * When they occur between polypeptides, they help maintain quaternary structure, holding the individual polypeptides together - chaperones are required to ensure proper assembly.

The Monomers Are Monosaccharides

- The repeating units of polysaccharides are simple sugars called monosaccharides. - A sugar can be defined as an aldehyde or ketone that has two or more hydroxyl groups. * there are two categories of sugars: the aldosugars, with a terminal carbonyl group. * the ketosugars, with an internal carbonyl group at carbon 2. - Most sugars have between three and seven carbon atoms and thus are classified as trioses (three carbons), tetroses (four carbons), pentoses (five carbons), hexoses (six carbons), or heptoses (seven carbons).

Secondary Structure

- The secondary structure of a protein describes local regions of structure that result from hydrogen bonding between NH and CO groups along the polypeptide backbone. * These local interactions result in two major structural patterns, referred to as the α helix and β sheet conformations. - α helix: * n α helix is spiral in shape, consisting of a backbone of amino acids linked by peptide bonds with the specific R groups of the individual amino acid residues sticking out from it. * The distance between these peptide bonds (3.6 amino acids per turn) is , in fact, just right for the formation of a hydrogen bond between the NH group adjacent to one peptide bond and the CO group adjacent to the other. * These hydrogen bonds are all nearly parallel to the main axis of the helix and therefore tend to stabilize the spiral structure by holding successive turns of the helix together. * Hydrogen bonding in an α helix is invariably intramolecular (within the same polypeptide) - β sheet conformations: * this structure is an extended sheetlike conformation with successive atoms in the polypeptide chain located at the "peaks" and "troughs" of the pleats. * The R groups of successive amino acids stick out on alternating sides of the sheet. * The β sheet is characterized by a maximum of hydrogen bonding. * Hydrogen bonding in the β sheet can be either intramolecular (between two segments of the same polypeptide) or intermolecular (linking two different polypeptides). * If the two interacting regions run in the same N-terminus-to-C-terminus direction, the structure is called a parallel β sheet; if the two strands run in opposite N-terminus-to-C-terminus directions, the structure is called an antiparallel β sheet. - Whether a specific segment of a polypeptide will form an α helix, a β sheet, or neither depends on the amino acids present in that segment. - An α-helical region is represented as either a spiral or a cylinder, whereas a β-sheet region is drawn as a flat ribbon or arrow with the arrowhead pointing in the direction of the C-terminus. * A looped segment that connects α-helical and/or β-sheet regions is called a random coil that is intrinsically disordered.

Carbon ability to have 1,2, and 3 bonds

- The sharing of one pair of electrons between atoms results in a single bond. Methane, ethanol, and methylamine are simple examples of carbon-containing compounds containing only single bonds between atoms - Sometimes two or even three pairs of electrons can be shared by two atoms, giving rise to double bonds or triple bonds. Ethylene and carbon dioxide are examples of double-bonded compounds

Glucose (C6H12O6)

- The single most common monosaccharide in the biological world is the aldohexose d-glucose, represented by the formula C6H12O6. - The formula CnH2nOn is characteristic of sugars and gave rise to the general term carbohydrate because compounds of this sort were originally thought of as "hydrates of carbon"—Cn(H2O)n - the carbons of glucose are numbered beginning with the more oxidized end of the molecule, the carbonyl group. Because glucose has four asymmetric carbon atoms (carbon atoms 2, 3, 4, and 5), there are 2^4 = 16 different possible stereoisomers of the aldosugar C6H12O6. But, we will concern ourselves only with d-glucose, which is the most stable of the 16 isomers. - In reality, glucose exists in the cell in a dynamic equilibrium between the linear (or straight-chain) configuration and the ring form. * The ring forms when the oxygen atom of the hydroxyl group on carbon atom 5 forms a bond with carbon atom 1. * The six-membered ring, formed by five carbon atoms and one oxygen atom, is called a pyranose ring, which are more stable energetically than the linear form. - The formation of the pyranose ring structure results in the generation of one of two alternative forms of the molecule, depending on the spatial orientation of the hydroxyl group on carbon atom 1. These alternative forms of glucose are designated α and β. α-d-glucose has the hydroxyl group on carbon atom 1 pointing downward in the Haworth projection, and β-d-glucose has the hydroxyl group on carbon atom 1 pointing upward.

The smooth endoplasmic reticulum (smooth ER)

- The smooth endoplasmic reticulum (smooth ER) has no role in protein synthesis and hence no ribosomes. - Smooth ER is involved in the synthesis of lipids (fatty acids, triglycerides, sterols) and steroids such as cholesterol and the steroid hormones derived from it. - smooth ER is responsible for inactivating and detoxifying drugs such as barbiturates and other compounds that might otherwise be toxic or harmful to the cell.

Cells Contain Three Different Kinds of Macromolecular Polymers

- The three major kinds of macromolecular polymers found in the cell are proteins, nucleic acids, and polysaccharides. - Lipids, though considered macromolecules, are not polymers consisting of a long chain of monomers. - For nucleic acids and proteins, the exact order of the different monomers is critical for function. - polysaccharides are typically composed of a single monomer or of two different monomers. - Nucleic acids (both DNA and RNA) are often called informational macromolecules because the order of the four kinds of nucleotide monomers in each is nonrandom and carries important information. * A critical role of many DNA and RNA molecules is to serve a coding function, meaning that they contain the information necessary to specify the precise amino acid sequences of particular proteins. - Proteins are a second type of macromolecule composed of a nonrandom series of monomers—in this case, amino acids. * the monomer sequence does not transmit information but rather determines the three- dimensional structure of the protein dictates its biological activity * 20 different amino acids found in proteins * proteins have a wide range of functions in the cell, including roles in structure, defense, transport, catalysis, and signaling. - Polysaccharides typically consist of either a single repeating subunit or two subunits occurring in strict alternation, and usually do not carry specific information. Polysaccharides may be branched and therefore not strictly linear. * Most polysaccharides are either storage macromolecules, which act as an energy source, or structural macromolecules, which provide physical support to cells.

Triacylglycerols Are Storage Lipids

- The triacylglycerols, also called triglycerides, consist of a glycerol molecule with three fatty acids linked to it. * glycerol is a three-carbon alcohol with a hydroxyl group on each carbon. * Fatty acids are linked to glycerol by ester bonds, which are formed between a carboxyl and a hydroxyl group by the removal of water. * Triacylglycerols are synthesized stepwise, with one fatty acid added at a time. * Each fatty acid in a triacylglycerol is linked to a carbon atom of glycerol by means of a condensation reaction. - The main function of triacylglycerols is to store energy. * In some animals, triacylglycerols also provide insulation against low temperatures. * Triacylglycerols containing mostly saturated fatty acids are usually solid or semisolid at room temperature and are called fats. - Fats are prominent in the bodies of animals. * In plants, most triacylglycerols are liquid at room temperature, as the term vegetable oil suggests (unsaturated fatty acids). - vegetable oils have lower melting temperatures than most animal fats do. Triglycerides also support, provide structure and protect the cell.

All Organisms Are Bacteria, Archaea, or Eukaryotes

- There are two fundamentally different types of cellular organization: * a simpler one characteristic of bacteria * a more complex one found in all other kinds of cells. - Organisms have been traditionally divided into two broad groups, * the prokaryotes (bacteria and archaea) * the eukaryotes (plants, animals, fungi, algae, and protozoa). - The most fundamental distinction between the two groups is that eukaryotic cells have a true, membrane-bounded nucleus, whereas prokaryotic cells do not. - All organisms belong to one of three domains—the Bacteria, the Archaea, or the Eukarya (eukaryotes). * The bacteria include most of the commonly encountered single-celled, non-nucleated organisms that were traditionally referred to as prokaryotes. * The archaea include many species that live in extreme habitats on Earth and have very diverse metabolic strategies. Unique features of archaea include their ribosomal RNAs and their membrane phospholipids

Carbon Containing Molecules are Stable

- This stability is expressed as bond energy * Bond energy: the amount of energy required to break 1 mole (about 6×10^23) of such bonds. - Bond energies are usually expressed in calories per mole (cal/mol). - It takes a large amount of energy to break a covalent bond; most energy required to break out of a single, double and triple bonds are the triple bonds, while double bonds are 2nd, and single bonds require the least amount of energy to break its bond. - Covalent bonds are much higher in energy than hydrogen bonds and are therefore much more stable. * H bonds are weak but numerous. They generally occur when H is bonded to either N or O (N or O have high electronegativity; e's towards themselves). Therefore, H bonds gets partial charges and thus weak attractions.

The Endosymbiont Theory Proposes That Mitochondria and Chloroplasts Were Derived From Bacteria

- This theory, proposed by Lynn Margulis (then Lynn Sagan) in 1967, proposes that mitochondria and chloroplasts evolved from ancient bacteria that established a symbiotic relationship (a mutually beneficial association) with primitive nucleated cells 1 to 2 billion years ago. - theory suggests that the ancestor of eukaryotic cells (called a protoeukaryote) developed at least one important feature distinguishing it from other primitive cells: * the ability to engulf and ingest nutrients and particles—including smaller bacteria and cyanobacteria—from the environment by phagocytosis ("cell eating"). * Following engulfment, the smaller cells were not digested. Instead, surrounded by host cell membrane, they took up residence in the cytoplasm of the protoeukaryote and eventually evolved into mitochondria and chloroplasts, which are surrounded by a double membrane. - Evidence supporting endosymbiotic theory * mitochondria and chloroplasts still retain their own DNA * mitochondria and chloroplasts make ribosomes and produce some of their own proteins * organelle DNA has both structural and sequence similar to prokaryotic DNA, not eukaryotic.

The Structures of the 20 Amino Acids Found in Proteins.

- Those in Group A have nonpolar, hydrocarbon R groups and are therefore hydrophobic. The others are hydrophilic, either because the R group is polar (Group B) or because the R group is acidic or basic and thus is charged at cellular pH (Group C). * Nine of these amino acids have nonpolar, hydrophobic R groups (Group A). As you look at their structures, you will notice the hydrocarbon nature of the R groups, with few or no oxygen and nitrogen atoms. found in the interior of proteins when the proteins are in an aqueous environment. * The remaining 11 amino acids have hydrophilic R groups that are either distinctly polar (Group B) or actually charged at the pH values characteristic of cells (Group C). Two acidic amino acids are negatively charged and that the three basic amino acids are positively charged. Hydrophilic amino acids tend to occur on the surface of proteins in solution.

- Viruses

- Viruses are acellular, parasitic particles that are incapable of a free-living existence. * therefore depend on the cells they invade for most of their needs. * They typically consists of only a few different molecules of nucleic acid and protein. - However, viruses can invade and infect cells and redirect the synthetic machinery of the infected host—host cell enzymes and ribosomes—toward the production of more virus particles. After replication, the viral progeny typically erupt from the host cell and, in the process, destroy it. - Despite their morphological diversity, viruses are chemically quite simple. * Most viruses consist of little more than a coat (or capsid) of protein surrounding a core that contains one or more molecules of either RNA or DNA, depending on the type of virus. - Some viruses are surrounded by a membrane that is derived from the plasma membrane of the host cell in which the viral particles were previously synthesized and assembled. Such viruses are called enveloped viruses. - very diverse in their genomes - many DNA viruses, some even have single-stranded DNA genomes. - many RNA viruses, can be single stranded or double stranded - SS RNA viruses may be + or - * + SS RNA viruses can be directly translated into protein * - SS RNA viruses, their complement strand must be produced in order to be translated into protein.

Importance of carbon

- carbon atom has a valence of four, thus being able to form four chemical bonds with other atoms. - atoms that share e's in this way are held together and are said to be joined by a covalent bond. - stable organic compounds have four covalent bonds for every carbon atom. This gives carbon-containing molecules great diversity in molecular structure and function. - Carbon atoms are most likely to form covalent bonds with other carbon atoms and with atoms of oxygen (O), hydrogen (H), nitrogen (N), and sulfur (S). - When only hydrogen atoms are bonded to carbon atoms in linear or branched chains or in rings, the resulting compounds are called hydrocarbons.

Oxidation and reduction

- carbon-containing compounds will lose electrons to other molecules such as molecular oxygen. This process is called oxidation and typically involves degradation and releases energy, as in the oxidation of glucose to carbon dioxide and water. - carbon-containing compounds gain electrons, is known as reduction and typically is biosynthetic and requires energy, as in the photosynthetic reduction of carbon dioxide to glucose.

The Importance of Synthesis by Polymerization

- cellular structures such as ribosomes, chromosomes, flagella, and cell walls are made up of ordered arrays of linear or branched polymers that are called macromolecules. - Important macromolecules in cells include proteins, nucleic acids (both DNA and RNA), and polysaccharides such as starch, glycogen, and cellulose. Lipids are often regarded as macromolecules as well. - Macromolecules are important in both the structure and the function of cells.

Terpenes Are Formed from Isoprene

- erpenes are synthesized from the five-carbon compound isoprene and are therefore also called isoprenoids. - Isoprene and its derivatives are joined together in various combinations to produce such substances as vitamin A, a required nutrient in our bodies, and carotenoid pigments, which are involved in light harvesting in plants during photosynthesis. - Eicosanoids are important cell signaling molecules.

Exocytosis and Endocytosis

- exchange materials between the membrane-bounded compartments within the cell and the exterior of the cell. * exocytosis and endocytosis are processes involving membrane fusion events that are unique to eukaryotic cells. - In endocytosis, portions of the plasma membrane invaginate and are pinched off to form membrane-bounded vesicles containing substances that were previously on the outside of the cell. - In Exocytosis, membrane-bounded vesicles inside the cell fuse with the plasma membrane and release their contents to the outside of the cell.

glucose being disaccharides

- glucose also occurs in disaccharides which consist of two monosaccharide units linked covalently. * E.g, Maltose (malt sugar) consists of two glucose units linked together, whereas lactose (milk sugar) contains a glucose linked to a galactose and sucrose (table sugar) has a glucose linked to a fructose. - Each of these disaccharides is formed by a condensation reaction in which two monosaccharides are linked together via an oxygen atom following the elimination of water. * The resulting glycosidic bond is characteristic of linkages between sugars. - α glycosidic bond occurs when a carbon atom 1 with its hydroxyl group then its in the α configuration. (Look at image) - a β glycosidic bond because the hydroxyl group on carbon atom 1 of the galactose is in the β configuration. (Look at image) * E.g. Some people lack the enzyme needed to hydrolyze this β glycosidic bond and are considered lactose intolerant due to their difficulty in metabolizing this disaccharide.

Hierarchical Assembly Provides Advantages for the Cell

- how cellular structures are made. * First, large numbers of similar, or even identical, monomeric subunits are assembled by condensation into polymers. These polymers then aggregate spontaneously but specifically into characteristic multimeric units. The multimeric units can, in turn, give rise to still more complex structures and eventually to assemblies that are recognizable as distinctive subcellular structures. - "quality control" that can be exerted at each level of assembly. This allows defective components to be discarded at an early stage rather than being built into a more complex structure that would be more costly to reject and replace. Thus, if the wrong subunit becomes inserted into a polymer at some critical point in the chain, that particular molecule may have to be discarded - chemical simplicity * almost all structures found in cells and organisms are synthesized from about 30 small precursor molecules. Given these building blocks and the polymers that can be derived from them through just a few different kinds of condensation reactions, most of the structural complexity of life can be readily elaborated by hierarchical assembly into successively more complex structures.

Lipids

- lipids differ from the macromolecules discussed so far in this chapter because they are not formed by the kind of linear polymerization that gives rise to proteins, nucleic acids, and polysaccharides. - However, they are commonly regarded as macromolecules because of their high molecular weights and their presence in important cellular structures, particularly membranes. - the final steps in the synthesis of triglycerides, phospholipids, and other large lipid molecules involve condensation reactions similar to those used in polymer synthesis. - The distinguishing feature of lipids is their hydrophobic nature. * they are readily soluble in non-polar solvents such as chloroform or ether. * Some lipids, are amphipathic, having both a polar and a non-polar region. - Functionally, lipids play at least three main roles in cells. * Some serve as forms of energy storage * others are involved in membrane structure * others have specific biological functions, such as the transmission of chemical signals into and within the cell. - lipids have six main classes: fatty acids, triacylglycerols, phospholipids, glycolipids, steroids, and terpenes.

Examples of monomers

- monosaccharides such as the glucose present in cellulose or starch, the 20 different amino acids needed to make proteins, and nucleotides (represented as A, C, G, T, and U) that make up DNA and RNA.

Proteasome

- non membranous organelles - roughly barrel shaped with a hallow interior - when proteins are ready to be recycled, they are send to proteasomes for breakdown. * break peptide bonds to break chains into individual amino acids * tags are added to old proteins to target them for proteasomes.

Nucleic Acids

- nucleic acids are macromolecules of paramount importance to the cell because of their role in storing, transmitting, and expressing genetic information. - Nucleic acids are linear polymers of nucleotides strung together in a genetically determined order that is critical to their role as informational macromolecules. - The two major types of nucleic acids are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). * RNA contains the five-carbon sugar ribose in each of its nucleotides, whereas DNA contains the closely related sugar deoxyribose. * DNA serves primarily as the repository of genetic information, whereas RNA molecules play several different roles in expressing that information—that is, in gene regulation and protein synthesis.

The Peroxisome

- peroxisomes are not part of the endomembrane system. - their common property is both generating and degrading hydrogen peroxide (H2O2). * Hydrogen peroxide, a by-product of several normal metabolic reactions, is highly toxic to cells but can be decomposed into water and oxygen by the enzyme catalase. * Eukaryotic cells protect themselves from the detrimental effects of hydrogen peroxide by packaging peroxide-generating reactions together with catalase in a single compartment, the peroxisome. - Animal peroxisomes also play an important role in the oxidative breakdown of fatty acids, which are components of all triacylglycerols, phospholipids, and glycolipids. - The best-understood metabolic roles of peroxisomes occur in plant cells. During the germination of fat-storing seeds, specialized peroxisomes called glyoxysomes play a key role in converting stored fat into carbohydrates.

Polysaccharides

- polysaccharides are long-chain polymers of sugars and sugar derivatives. * Polysaccharides usually consist of a single kind of repeating unit. - They serve primarily in energy storage and as cellular structures rather than carrying information. * shorter polymers called oligosaccharides, when attached to proteins on the cell surface, play important roles in cellular recognition of extracellular signal molecules and of other cells. - polysaccharides include the storage polysaccharides starch and glycogen and the structural polysaccharide cellulose.

Proteins and their functions

- proteins fall into nine major classes * enzymes, serving as catalysts that greatly increase the rates of the thousands of chemical reactions on which life depends. * Structural proteins, on the other hand, provide physical support and shape to cells and organelles, giving them their characteristic appearances. * Motility proteins play key roles in the contraction and movement of cells and intracellular materials. * Regulatory proteins are responsible for control and coordination of cellular functions, ensuring that cellular activities are regulated to meet cellular needs. * Transport proteins are involved in the movement of other substances into, out of, and within the cell. * Signaling proteins mediate communication between cells in an organism, and receptor proteins enable cells to respond to chemical stimuli from their environment. * defensive proteins provide protection against disease, and storage proteins serve as reservoirs of amino acids.

Where Did the First Cells Come From?

- researchers currently believe that the appearance of what we now consider cells involved four phases: (1) abiotic (nonliving) synthesis of simple organic compounds such as amino acids and nitrogenous bases (2) abiotic polymerization of these monomers into macromolecules such as proteins or nucleic acids (3) emergence of a macromolecule capable of both storing genetic information and replication (4) encapsulation of this first "living" molecule within a simple membrane to form the first primitive cell.

Ribosomes Synthesize Proteins in the Cytoplasm

- ribosomes are the site of protein synthesis. * Ribosomes are far more numerous than most other intracellular structures. - Ribosomes are found in all cells, but bacteria, archaea, and eukaryotes differ from each other in ribosome size and in the number and kinds of ribosomal protein and rRNA molecules - A ribosome consists of two subunits differing in size, shape, and composition * Each ribosome is made up of a large subunit and a small subunit that join together when they attach to a messenger RNA and begin to make a protein.

Examples of self assembly

- ribosomes contain both RNA and proteins, and can be remade from the individual molecular components by self-assembly. - The phospholipids that make up membranes can self-assemble into a bilayer when mixed with water, because the hydrophobic hydrocarbon tails do not interact with water but instead associate with each other. - The Tobacco Mosaic Virus * A virus is a complex of proteins and nucleic acid, either DNA or RNA. A virus is not itself alive; but it can invade and infect a specific living host cell, take over the synthetic machinery of this cell, and use the host cell to produce more virus components. When the components—viral nucleic acid and viral proteins—are synthesized, these macromolecules spontaneously assemble into the mature virus particles. - what the image illustrates: Parts (a) through (d) show how the TMV virion will assemble spontaneously from a mixture of its coat protein and RNA constituents. All the information needed for proper assembly is contained in the proteins and RNA themselves, and no energy input is required.

Self-Assembly Has Limits

- some assembly systems appear to depend on information supplied by a preexisting structure. In such cases, the ultimate structure arises not by assembling the components into a new structure but rather by ordering the components into an existing structure. * E.g. Cell walls and cell membranes

Tertiary Structure

- tertiary structure depends almost entirely on interactions between the various R groups, regardless of where along the primary sequence they happen to be. - Tertiary structure therefore reflects the non repetitive and unique aspect of each polypeptide because it depends not on the CO and NH groups common to all of the amino acids in the chain but instead on the very feature that makes each amino acid distinctive—its R group. - Tertiary structure is neither repetitive nor readily predictable; it involves competing interactions between side groups with different properties. * Oppositely charged R groups can form ionic bonds, whereas similarly charged groups will repel each other. - As a result, the polypeptide chain will be folded, coiled, and twisted into its native conformation—the most stable three-dimensional structure for that particular sequence of amino acids. - proteins can be divided into two categories: fibrous proteins and globular proteins. * Fibrous proteins have extensive secondary structure (either α helix or β sheet) throughout the molecule, giving them a highly ordered, repetitive structure. - E.g silk, hair and wool * The polypeptide chain of a globular protein is often folded locally into regions with α-helical or β-sheet structures, and these regions of secondary structure are themselves folded on one another to give the protein its compact, globular shape. - globular protein has its own unique tertiary structure, made up of secondary structural elements (helices and sheets) folded in a specific way that is especially suited to the particular functional role of that protein.

The Cytoskeleton Provides Structure to the Cytoplasm

- the cytoskeleton is an internal framework that gives a cell its distinctive shape and high level of internal organization. - Its elaborate array of fibers forms a highly structured yet dynamic matrix that helps establish and maintain cell shape. - the cytoskeleton plays an important role in cell movement and cell division. - In eukaryotic cells, the cytoskeleton serves as a framework for positioning and actively moving organelles and macromolecules within the cytosol. - The three major structural elements of the cytoskeleton—microtubules, microfilaments, and intermediate filaments. - Microtubules: * roughly globular can rapidly assemble and disassemble, into long filaments. * involved in cell structure and support * make spindle fibers so critical to mitosis and meiosis * make most of the structures of flagella and cilia. - Microfilaments: * composed of actin proteins * assembly and disassembly rapidly * provide structure and support * critical in protein based muscle contraction

Many Proteins Spontaneously Fold into Their Biologically Functional State

- the immediate product of amino acid polymerization is actually not a protein but a polypeptide. To become a functional protein, one or more such linear polypeptide chains must coil and fold in a precise, predetermined manner to assume the unique three-dimensional structure, or conformation, necessary for biological activity. - disruption, or unfolding, can be achieved by raising the temperature, by making the pH of the solution highly acidic or highly alkaline, or by adding certain chemical agents such as urea or any of several alcohols. * called denaturation because it results in the loss of the natural three-dimensional structure of the protein—and the loss of its function as well. In the case of an enzyme, denaturation results in the loss of catalytic activity. * When the denatured polypeptide is returned to conditions in which the native conformation is stable, the polypeptide may undergo renaturation, the return to its correct three- dimensional conformation.

Molecular Chaperones Assist the Assembly of Some Proteins

- the interactions that drive protein folding may need to be assisted and controlled by proteins known as molecular chaperones to reduce the probability of the formation of incorrect structures having no biological activity. * Molecular chaperones are proteins that facilitate the correct folding of proteins and assembly of protein-containing structures but are not themselves components of the assembled structures. * they bind to specific regions that are exposed only in the early stages of assembly, thereby inhibiting unproductive assembly pathways that would lead to incorrect structures.

Polarity

- the presence of any oxygen or sulfur atoms bound to carbon or hydrogen results in a polar bond due to unequal sharing of electrons. - This is because oxygen and sulfur have higher electronegativity, or affinity for electrons, than carbon and hydrogen. - water (H2O) is polar thus, it has a higher solubility and chemical reactivity than nonpolar C—C or C—H bonds, in which electrons are equally shared.

Primary Structure

- the primary structure of a protein is a formal designation for the amino acid sequence * simply specifying the order in which its amino acids appear from one end of the molecule to the other. * amino acid sequences are always written from the N-terminus to the C-terminus of the polypeptide, which is also the direction in which the polypeptide is synthesized. * the primary structure of a protein is the result of the order of nucleotides in the DNA of the gene. * Although protein denaturation by heating unfolds a polypeptide and eliminates all but the primary structure, the information in the primary sequence specifies these higher levels of structure, and often the protein can refold into its native conformation.

The Importance of Self-Assembly

- the principle of molecular self-assembly, states that the information required to specify the spontaneous folding of macromolecules and the interactions of these macromolecules to form more complex structures is inherent in the polymers themselves; without further input of energy and information.

Bacteria, Archaea, and Eukaryotes Differ from Each Other in Many Ways

- unique sets of properties distinguish each of the three domains of life. * a eukaryotic cell has a true, membrane-bounded nucleus, bacterial and archaeal cells do not. - the genetic information (the DNA) of a bacterial or archaeal cell is folded into a compact structure within the cytoplasm known as the nucleoid. - within a eukaryotic cell most of the genetic information is localized to the nucleus. * bacterial (and archaeal) cells generally do not contain internal membranes; most of their cellular functions occur either in the cytoplasm or on the plasma membrane. - However, nearly all eukaryotic cells make extensive use of internal membranes to compartmentalize specific functions and often contain numerous organelles. * Bacterial DNA is usually present in the cell as a single, circular molecule, or chromosome, associated with relatively few proteins. - However, eukaryotic DNA exists in the cell as multiple linear molecules that are intricately complexed with large amounts of proteins known as histones. * Bacterial and archaeal cells merely replicate their chromosomes and divide by a relatively simple process called binary fission, with one replicated DNA molecule and half of the cytoplasm going to each daughter cell. - However, in eukaryotic cells, chromosomes are distributed equally to daughter cells by the more complex process of mitosis, followed by cytokinesis, the division of the cytoplasm. * Eukaryotic cells tend to transcribe genetic information in the nucleus into large RNA molecules and depend on later processing and transport processes to deliver mature messenger RNA (mRNA) molecules to the cytoplasm for protein synthesis. - While bacteria transcribe very specific segments of genetic information into RNA messages, and often a single mRNA molecule contains the information to produce several polypeptides. - Peptidoglycan cell wall is unique to bacterias, * archaea cell wall is more protein based

Viroids Are Small, Circular RNA Molecules That Can Cause Plant Diseases.

- viroids are found in some plant cells represent. - Viroids are small, circular RNA molecules, and they are the smallest known infectious agents. * the RNA molecules do not code for any protein, and are replicated in the host cell. - Viroids do not occur in free form but can be transmitted from one plant cell to another when the surfaces of adjacent cells are damaged and there is no membrane barrier to prevent RNA molecules from crossing.

The importance of Water

- water is the universal solvent in biological systems. - Water is the single most abundant component of cells and organisms.

I- cell disease

Figure a). Normal trafficking of lysosomal enzymes depends on addition of mannose to hydrolases in the rough ER. Mannose is then phosphorylated to mannose-6-phosphate (mannose-6-P) in the Golgi. Mannose-6-P-tagged enzymes move through the Golgi, eventually fuse with endosomes, and are ultimately incorporated into lysosomes. Note that many other aspects of endosomal trafficking are omitted from this diagram for clarity. Figure b). In cells of I-cell patients, the enzyme in the Golgi that adds a phosphoryl group to mannose is absent, so the enzymes are misrouted to the plasma membrane. Ultimately, lysosomes become swollen in such cells.

Mitochondria and Chloroplasts Provide Energy for the Cell

Mitochondrion: - The mitochondrion is found in most eukaryotic cells and is the site of aerobic respiration. - Most eukaryotic cells contain hundreds of mitochondria, and each is surrounded by two membranes, designated the inner and outer mitochondrial membranes. * The inner membrane encloses the mitochondrial matrix, a semifluid material that fills the mitochondria. * It is within the mitochondrion that the enzymes and intermediates involved in such important metabolic processes as the citric acid cycle and ATP generation are found. (Specifically within the matrix) - Oxidation of sugars and other cellular "fuel" molecules to carbon dioxide in mitochondria extracts energy from food molecules and conserves it as adenosine triphosphate (ATP). * Inter-membrane space accumulation of H+ in this space establishes a gradient. A gradient has potential energy that drive ATP synthesis. - cristae (singular: crista) are infoldings of the inner mitochondrial membrane. Folding allows more area for essential proteins * E.g. citric acid cycle and all proteins of ETC Chloroplast: - The chloroplast is the site for photosynthesis in plants and algae - chloroplasts are surrounded by both an inner and an outer membrane. * Inside the chloroplast there is a third membrane system consisting of flattened sacs called thylakoids and the tubular membranes (stroma thylakoids) that interconnect them. * Thylakoids are stacked together to form the grana (singular: granum) that characterize most chloroplasts. - Located within this organelle are most of the enzymes, intermediates, and light-absorbing pigments needed for photosynthesis. - Reactions involved in the conversion of carbon dioxide to sugar molecules occur within the semifluid stroma that fills the interior of the chloroplast.

Protein Structure Depends on Amino Acid Sequence and Interactions

The overall shape and structure of a protein are usually described in terms of four hierarchical levels of organization, each building on the previous one: the primary, secondary, tertiary, and quaternary structures