BIOL 420 BIOCHEMISTRYbyada D. Son

Bio 420 BIOCHEMISTRYAll the following power point presentations and the text were taken from the text books:Concepts in Biochemistry (3rd edition), by R. Boyer, and Lehninger Principles of Biochemistry (5th edition), by D.L. Nelson and M.M. Cox.Copyright 2006 by John Wiley & Sons, Inc. and 2005 by W.H. Freeman and Company.

OutlineWhat is BiochemistryHistory of BiochemistryElements in BiomoleculesBiological MacromoleculesOrganels Cells and OrganismsProperties of WaterWeak acids, bases and buffer systems

What is Biochemistry

Biochemistry = Biology + ChemistryExplains reactions necessary for LifeLife :able to extract energy from molecules called nutrientsdisplay the attributes of growth, differentiation, and reproductionability to respond to changes in their environmentsBiochemistry uses the interactions between molecules to explain LifeBiochemistry can be organized into three primary areas

Structural and functional biochemistry focuses initially on discovering the chemical structures and three-dimensional arrangements of biomolecules, those chemicals that are found in living matter. To describe biological processes, one must have a knowledge of the molecular structures of the participating biomolecules, which then often leads to an understanding of the function or purpose of the cellular molecules.Informational biochemistry defines the language(s) for storing biological data and for transmitting that data in cells and organisms. This area includes molecular genetics, which describes the molecular processes in heredity and expression of genetic information and also processes that communicate molecular signals to regulate cellular activities (i.e., hormone action). An organism is indeed a complex, information-processing system.

3. Bioenergetics describes the flow of energy in living organisms and how it may be transferred from one process to another.

How organisms use biochemical reactions and biomolecules to transfer energy between different type of events will be pivotal in our understanding of life processes.

The transfer of energy usually means the transformation of one type of energy to another. For example, the foods that we eat contain potential molecular energy that is used to maintain body temperature, regulate the flow of ions in nerve transmission, and to provide energy for the contraction of muscle.

A running person uses energyDerived from metabolism ofcarbohydrates, fats, and proteins.

WHY SHOULD WE STUDY BIOCHEMISTRY?To understand fundamentals of LifeHow food is digested? How is this providing cellular energy? How does a brain cell store information? Research in biochemistry is providing answers to these and other important questions.To understand medicine, health, nutrition, and the environmentDesign and develop new compounds to improve Life

WHY SHOULD WE STUDY BIOCHEMISTRY?Learning biochemical principles is not just important for those who will become biochemists and use the concepts daily. Many aspects of everyday life are related directly to the subject matter of biochemistry.Biochemical studies lead us to a fundamental understanding of life. All of us have a natural curiosity about how our bodies work. How is food is digested to provide cellular energy? How does a brain cell store mathematical and chemical formulas? Research in biochemistry is providing answers to these and other important questions.Biochemistry has a profound impact on our understanding of medicine, health, nutrition, and the environment. Results from biochemical studies have already led to a molecular understanding of diseases such as diabetes, cystic fibrosis, hypercholesterolemia, and some forms of cancer. Recombinant DNA technology and its ability to probe chromosomal regions for genetic mutations will play a major role in the diagnosis and treatment of diseases (gene therapy). The study of enzymes (biological catalysts) and metabolism provides a foundation for the rational design of drugs and for the detailed understanding of nutrition.

3. Biotechnology, the application of biological materials such as cells and macromolecules to technically useful operations, will also advance from biochemical studies. Already enzymes are used in the pharmaceutical industry to synthesize complex drugs. Various strains of microorganisms have been selected and altered for producing therapeutic proteins, for manufacturing fuel alcohol from corn and other plant materials, for cleaning up oil and other toxic spills, and for mining metals from natural ores.

Fifteen to twenty billion years ago, the universe arose as a cataclysmic eruption of hot, energy-rich subatomic particles. Within seconds, the simplest elements (hydrogen and helium) were formed. As the universe expanded and cooled, material condensed under the influence of gravity to form stars. Some stars became enormous and then exploded as supernovae, releasing the energy needed to fuse simpler atomic nuclei into the more complex elements. Thus were produced, over billions of years, the Earth itself and the chemical elements found on the Earth today. About four billion years ago, life arosesimple microorganisms with the ability to extract energy from organic compounds or from sunlight, which they used to make a vast array of more complex biomolecules from the simple elements and compounds on the Earths surface.Biochemistry asks how the remarkable properties of living organisms arise from the thousands of different lifeless biomolecules. When these molecules are isolated and examined individually, they conform to all the physical and chemical laws that describe the behavior of inanimate matteras do all the processes occurring in living organisms. The study of biochemistry shows how the collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws that govern the nonliving universe.

History of Biochemistry

The Road to Modern BiochemsitryTwo separate and distinct scientific events have led to our current state of biochemical knowledge.Structural characteristics of biomolecules through physical sciences Application of basic laws of physics and chemistry to explain the processes of the living cell. X-ray crystallography to study the structure of amides and peptidesThe study of cell organization and function by biologists, especially microbiologists, cell biologists, physiologists, and geneticists

The Road to Modern Biochemsitry1952 with the announcement by James Watson and Francis Crick of the double helix structure for DNA combined several disiplins together. Here the application of physics (crystallography), chemistry (structure and bonding), and biology (storage and transfer of genetic information) all came together to help solve what was the most exciting and complex biological problem at that time: the structure of the genetic material, DNA

The Road to Modern BiochemsitryThere is more than a single path from the historical beginnings to present-day biochemistry. Two separate and distinct avenues of scientific inquiry have led to our current state of biochemical knowledge. One avenue can be traced through physical sciences and emphasizes structural characteristics of biomolecules. This approach has applied the basic laws of physics and chemistry to explain the processes of the living cell. For example, Linus Pauling in the 20th century used the tool of X-ray crystallography to study the structure of amides and peptides. The other avenue traveled by the biologists, especially microbiologists, cell biologists, physiologists, and geneticists, is characterized mainly by a study of cell organization and function. The first use of the term biochemistry is unclear (perhaps around 1900); however, early scientists who considered themselves biochemist traveled on the physical sciences pathway.

The two avenues of study converged in 1952 with the announcement by James Watson and Francis Crick of the double helix structure for DNA. Here the application of physics (crystallography), chemistry (structure and bonding), and biology (storage and transfer of genetic information) all came together to help solve what was the most exciting and complex biological problem at that time: the structure of the genetic material, DNA. The growth of knowledge in biochemistry since that time has been explosive. Some of the major events are noted in the following Figure.The term molecular biology is often used to describe studies at the interface of chemistry and biology. Biochemistry and molecular biology have similar goals; however, their approaches to solving problems have been different in the past. The boundaries between biochemistry and molecular biology are rapidly disappearing and, in fact, most scientists consider the fields to be the same. Both are using the same experimental approaches and techniques of molecularbiology.Biochemistry and molecular biology are becoming indistinguishable because they seek answers to the same question: What is life?

The origins of biochemistryfrom two perspectives, the physical and the biological sciences. The dates of Nobel prizes and of selected events in the development of biochemistry are noted in the scale on the left.

James Watson (left)and Francis Crick discuss an early model of the DNA double helix.

Elements in Biomolecules

All Living Matter Contains C, H,O, N, P, and SOnly about 31 (28%) of the more than 100 naturally occurring chemical elements are essential to organisms. The four most abundant elements in living organisms, in terms of percentage of total number of atoms, are hydrogen, oxygen, nitrogen, and carbon, which together make up more than 99% of the mass of most cells. We do not understand exactly how these elements were selected by primitive life-forms during the early stages of evolutionary development.

The biochemists periodic table. Elements in red are present in bulk form in living cells are essential for life. Those in yellow are trace elements that are very likely essential. Those elements in blue are present in some organisms and may be essential.

What Decides Which ElementsTwo posibilities:Random representation of elements in biomoleculesPreference of some elements due to their charecteristicsIf the first hypothesis is true then we should observe approximately the same ratios of elements in biological organizms as we find in the universe.

Elemental composition of the universe (blue), the earths crust (pink), and the human body (purple).

What Decides Which ElementsTwo posibilities:Random representation of elements in biomoleculesPreference of some elements due to their charecteristicsIf the first hypothesis is true then we should observe approximately the same ratios of elements in biological organizms as we find in the universe. This is not the case, thus we conclude that elements were selected according to their abilities to perform certain structural functions or to provide specific reactivities

Most Abondant in Living Systems Carbon forms multiple covalent bonds with other carbon atoms as well as with other elements such a nitrogen, hydrogen, oxygen, or sulfur.

This feature allows the construction of long carbon chains and rings with the presence of reactive functional groups containing nitrogen, oxygen, and sulfur as in proteins, nucleic acids, lipids, and carbohydrates.

One of the two hypotheses may explain the selection: There was a deliberate choice because of an elements favorable characteristics or there was a random selection from the alphabet soup of elements present in the earths crust, atmosphere, and the universe. If the latter were true, then we would expect to find approximately the same ratios of elements in biological organizms as we find in the universe. Acomparison of the elemental composition of the earths crust and the universe with that of living matter which is shown in the following slide, refutes the latter hypothesis.We must conclude that elements were selected according to their abilities to perform certain structural functions or to provide specific reactivities. For exampe, carbon forms multiple covalent bonds with other carbon atoms as well as with other elements such a nitrogen, hydrogen, oxygen, or sulfur. This feature allows the construction of long carbon chains and rings with the presence of reactive functional groups containing nitrogen, oxygen, and sulfur as in proteins, nucleic acids, lipids, and carbohydrates.Elements found in the earth and atmosphere may have been tested by trial and error in living organisms during millions of years. Those elements that most effectively performed the necessary tasks and, most importantly, allowed the plant or animal to thrive were retained.

Versatility of carbon bonding. Carbon can form covalent single, double, and triple bonds (in red), particularly with other carbon atoms. Triple bonds are rare in biomolecules.

Carbon Skeletons and Functional Groups Covalently linked carbon atoms in biomolecules can form linear chains, branched chains, and cyclic structuresfunctional groups, which confer specific chemical properties can be added to these structuresMost biomolecules are derivatives of hydrocarbons, with hydrogen atoms replaced by a variety of functional groups to yield different families of organic compounds.

Covalently linked carbon atoms in biomolecules can form linear chains, branched chains, and cyclic structures. To these carbon skeletons are added groups of other atoms, called functional groups, which confer specific chemical properties on the molecule. It seems likely that the bonding versatility of carbon was a major factor in the selection of carbon compounds for the molecular machinery of cells during the origin and evolution of living organisms. No other chemical element can form molecules of such widely different sizes and shapes or with such a variety of functional groups.Most biomolecules can be regarded as derivatives of hydrocarbons, with hydrogen atoms replaced by a variety of functional groups to yield different families of organic compounds. Typical of these are alcohols, which have one or more hydroxyl groups; amines, with amino groups; aldehydes and ketones, with carbonyl groups; and carboxylic acids, with carboxyl groups.Many biomolecules are polyfunctional, containing two or more different kinds of functional groups,each with its own chemical characteristics and reactions.The chemical personality of a compound is determined by the chemistry of its functional groups and their disposition in three-dimensional space.

Several common functional groupsin a single biomolecule. Acetyl-coenzyme A (often abbreviated as acetyl-CoA) is a carrier of acetyl groups in some enzymatic reactions.Many biomolecules are polyfunctional, containing two or more different kinds of functional groups,each with its own chemical characteristics and reactions.

Cells Contain a Universal Set of Small MoleculesDissolved in the aqueous phase (cytosol) of all cells is a collection of 100 to 200 different small organic molecules (Mr ~100 to ~500) This collection of molecules includes the common amino acids, nucleotides, sugars and their phosphorylated derivatives, and a number of mono-, di-, and tricarboxylic acids.

Cells Contain a Universal Set of Small MoleculesThe molecules are polar or charged, water soluble, and present in micromolar to millimolar concentrations.

They are trapped within the cell because the plasma membrane is impermeable to themalthough specific membrane transporters can catalyze the movement of some molecules into and out of the cell or between compartments in eukaryotic cells.

Cells Contain a Universal Set of Small Molecules Dissolved in the aqueous phase (cytosol) of all cells is a collection of 100 to 200 different small organic molecules (Mr ~100 to ~500), the central metabolites in the major pathways occurring in nearly every cellthe metabolites and pathways that have been conserved throughout the course of evolution. This collection of molecules includes the common amino acids, nucleotides, sugars and their phosphorylated derivatives, and a number of mono-, di-, and tricarboxylic acids. The molecules are polar or charged, water soluble, and present in micromolar to millimolar concentrations. They are trapped within the cell because the plasma membrane is impermeable to themalthough specific membrane transporters can catalyze the movement of some molecules into and out of the cell or between compartments in eukaryotic cells.The universal occurrence of the same set of compounds in living cells is a manifestation of the universality of metabolic design, reflecting the evolutionary conservation of metabolic pathways that developed in the earliest cells.

Specific Small MoleculesThere are other small biomolecules, specific to certain types of cells or organisms. For example, vascular plants contain, in addition to the universal set, small molecules called secondary metabolites, which play a role specific to plant life. These metabolites include compounds that give plants their characteristic scents, and compounds such as morphine, quinine, nicotine, and caffeine that are valued for their physiological effects on humans but used for other purposes by plants.The entire collection of small molecules in a given cell has been called that cells metabolome, in parallel with the term genome.

Biological Macromolecules

MacromoleculesAre the Major Constituents of Cells Many biological molecules are macromoleculesProteins,Nucleic acids, Polysaccharides Triglyceridesare produced by the polymerization of relatively small compounds with molecular weights of 500 or less. The number of polymerized units can range from tens to millions. Synthesis of macromolecules is a major energy-consuming activity of cells. Macromolecules themselves may be further assembled into supramolecular complexes, forming functional units such as ribosomes.

MacromoleculesThere are four classes of macromolecules:PolysaccharidesTriglyceridesPolypeptidesNucleic acids

MacromoleculesThere are four classes of macromolecules:PolysaccharidesTriglyceridesPolypeptidesNucleic acids

PolysaccharidesCarbohydrateshave the general formula [CH2O]nwhere n is a number between 3 and 6Carbohydrates function in energy storage:short-term such as sugarsintermediate-term ex. starch for plants and glycogen for animalsas structural components in cells (cellulosein the cell wallsof plants and many protists), and chitin in the exoskeleton of insects and other arthropods

Sugarsare structurally the simplest carbohydratesThey are the structural unit which makes up the other types of carbohydratesMonosaccharidesare single sugarsImportant monosaccharides include ribose (C5H10O5), glucose (C6H12O6), and fructose

Sugars

Polysaccharides

MacromoleculesThere are four classes of macromolecules:PolysaccharidesTriglyceridesPolypeptidesNucleic acids

LipidsAre involved mainly with long-term energy storageThey are generally insoluble in polar substances such as waterfunctions of lipids include:structural components as in the case of phospholipids that are the major building block in cell membranes"messengers" (hormones) that play roles in communications within and between cells

Lipidsare composed of three fatty acids (usually) covalently bonded to a 3-carbon glycerolThe fatty acids are composed of CH2units, and are hydrophobic/not water solubleFatty acids can be saturated (meaning they have as many hydrogens bonded to their carbons as possible)or unsaturated (with one or more double bonds connecting their carbons, hence fewer hydrogens)

Lipids

MacromoleculesThere are four classes of macromolecules:PolysaccharidesTriglyceridesPolypeptidesNucleic acids

Proteinsare very important in biological systems as control and structural elementsControl functions of proteins are carried out byenzymesand proteinaceous hormonesEnzymes are chemicals that act as organic catalystsStructural proteins function in the cell membrane, muscle tissue, etc.

Amino AcidsThe building block of any protein is theamino acidhas an amino end (NH2) and a carboxyl end (COOH)In nature there is 20 amino acids commonly used for protein synthesis

Amino Acids

MacromoleculesThere are four classes of macromolecules:PolysaccharidesTriglyceridesPolypeptidesNucleic acids

Nucleic Acidsarepolymerscomposed ofmonomerunits known asnucleotidesThere are a very few different types of nucleotidesThe main functions of nucleotides are :information storage (DNA), protein synthesis (RNA), and energy transfers (ATP and NAD)consist of a sugar, a nitrogenous base, and a phosphate

Nucleic Acids

RNA StructurePhosphodiester bond

Proteins and nucleic acids are informational macromolecules: each protein and each nucleic acid has a characteristic information-rich subunit sequence.

On the other hand, some oligosaccharides, with six or more different sugars connected in branched chains, also carry information; on the outer surface of cells they serve as highly specific points of recognition in many cellular processes.

Organels Cells and Organisms

ORGANELLES, CELLS, AND ORGANISMSThe unity and diversity of organisms become apparent even at the cellular level. The smallest organisms consist of single cells and are microscopic. Larger, multicellular organisms contain many different types of cells, which vary in size, shape, and specialized function. Despite these obvious differences, all cells of the simplest and most complex organisms share certain fundamental properties, which can be seen at the biochemical level.Most cells are microscopic, invisible to the unaided eye.Animal and plant cells are typically 5 to 100 m in diameter, and many bacteria are only 1 to 2 m long. What limits the dimensions of a cell? The lower limit is probably set by the minimum number of each type of biomolecule required by the cell. The smallest cells, certain bacteria known as mycoplasmas, are 300 nm in diameter and have a volume of about 10-14 mL. A single bacterial ribosome is about 20 nm in its longest dimension, so a few ribosomes take up a substantial fraction of the volume in a mycoplasmal cell.The upper limit of cell size is probably set by the rate of diffusion of solute molecules in aqueous systems.

Viruses are an example of supramolecular assemblages (i.e., organized clusters of macromolecules). Biochemically, most viruses consist of a single DNA or RNA molecule wrapped in a protein package. Viruses cannot exist independently and are usually not considered a life-form. Instead, they are deemed parasites since they are unable to carry out metabolism or reproduction without assistance of a host cell.

Kingdoms of LifeAll living organisms fall into one of three large groups (kingdoms, or domains)

Two large groups of prokaryotes can be distinguished on biochemical grounds: archaebacteria (Greek arche-, origin) and eubacteria (again, from Greek eu, true).

Eukarya, evolved from the same branch that gave rise to the Archaea; archaebacteria are therefore more closely related to eukaryotes than to eubacteria.

All living organisms fall into one of three large groups (kingdoms, or domains) that define three branches of evolution from a common progenitor. Two large groups of prokaryotes can be distinguished on biochemical grounds: archaebacteria (Greek arche-, origin) and eubacteria (again, from Greek eu, true).Eubacteria inhabit soils, surface waters, and the tissues of other living or decaying organisms. Most of the wellstudied bacteria, including Escherichia coli, are eubacteria.The archaebacteria, more recently discovered, are less well characterized biochemically; most inhabit extreme environmentssalt lakes, hot springs, highly acidic bogs, and the ocean depths. The available evidence suggests that the archaebacteria and eubacteria diverged early in evolution and constitute two separate domains, sometimes called Archaea and Bacteria. All eukaryotic organisms, which make up the third domain,Eukarya, evolved from the same branch that gave rise to the Archaea; archaebacteria are therefore more closely related to eukaryotes than to eubacteria.

Kingdoms of Life

Phylogeny of the three domains of life. Phylogenetic relationships are often illustrated by a family tree of this type. The fewer the branch points between any two organisms, the closer is their evolutionary relationship.

Scientists have long recognized two basic classifications of organisms:

Cells with nuclear envelopes are called eukaryotes (Greek eu, true, and karyon, nucleus); those without nuclear envelopesbacterial cellsare prokaryotes (Greek pro, before).

Eukaryotic cell structure. Schematic illustrations of the two major types of eukaryotic cell: (a) a representative animal cell and (b) a representative plant cell. Plant cells are usually 10 to 100 m in diameterlarger than animal cells, which typically range from 5 to 30 m. Structures labeled in red are unique to either animal or plant cells.

Endoplasmic Reticulum

Material traffic within cellsERGolgi ApparatusTransfer vesicle

Golgi ApparatusArriving from RER or SERMoving to plasma membrane

Lysosome in action1. Foreign substance arrivesand taken in by endocytosis, 2. Isolated in a vesicle,3. Lysosome is isolated fromthe goldi body,4. Lysosome fuses with the vesicle,5. Foreign substance is digested.

Mitochondria: Power PlantPhosphate GroupsAdenineRibose

Chloroplast

The molecules, cell components, and cells that biochemists work with come in a wide range of sizes. The dimensions of biochemical objects studied in terms of length and the width or diameter; and the molecular mass, which is a measure of quantity of material in an object, as the standard, biochemical unit of molecular mass: daltons (D) or kilodaltons (kD, 1000 daltons).One dalton is equal to the mass of a hydrogen atom. The mass of a water molecule is 18 D, and hemoglobin, 64,500D (64,5 kD).

Properties of Water

PropertiesO and 2H atoms forming the water molecule are bond to each other by polar covalent bonds.This unequal sharing of the electrons results in a slightly positive and a slightly negative side of the molecule.water has a great interconnectivity of individual molecules, which is caused by the individually weak hydrogen bonds

SolutionsWater has been referred to as the universal solventLiving things are composed of atoms and molecules within aqueous solutionsSolutions are uniform mixtures of the molecules of two or more substances. The solvent is usually the substance present in the greatest amount

SolubilityThe solubility of many molecules is determined by their molecular structureThe polar covalently bonded water molecules act to exclude nonpolar moleculesThus organicmacromoleculesknown aslipids that lack polar covalent bonds will not disolve in waterThe structure of many molecules can greatly influence their solubilitySugars, such as glucose, have many hydroxyl (OH) groups, which tend to increase the solubility of the molecule.

Water has a higher melting point, boiling point, and heat of vaporization than most other common solvents. These unusual properties are a consequence of attractions between adjacent water molecules that give liquid water great internal cohesion. A look at the electron structure of the H2O molecule reveals the cause of these intermolecular attractions.Hydrogen Bonding Gives Water Its Unusual Properties

Weak interactions, called noncovalent interactions, bring together whole biomolecules for specific purposes. Four types of noncovalent interactions are important in biological systems:Van der Waals forces, ionic bonds, hydrogen bonds, and hydrophobic interactions.

Structure of the water molecule.

Hydrogen bond between two water molecules.

Hydrogen bonding in ice. In ice, each water moleculeforms the maximum of 4 hydrogen bonds, creating a regular crystal lattice. By contrast, in liquid water at room temperature and atmospheric pressure, each water molecule hydrogen-bonds with an averageof 3.4 other water molecules. This crystal lattice of ice makes it less dense than liquid water, and thus ice floats on liquid water.

Chemicals are made soluble in water by noncovalent interactions.

Dipole-dipole interactions. The carbony group of an aldehyde, ketone, or acid can be also solvated by water.Ion-dipole interactions. The positively charged sodium ion is surrounded by water molecules and the acetate ion interacts with the partially positive hydrogen atoms (dipoles) of water.

Water is a polar solvent. It readily dissolves most biomolecules, which are generally charged or polar compounds; compounds that dissolve easily in water are hydrophilic (Greek, water-loving). In contrast, nonpolar solvents such as chloroform and benzene are poor solvents for polar biomolecules but easily dissolve those that are hydrophobicnonpolar molecules such as lipids and waxes. Some significant biochemicals have dual properties; have both nonpolar and ionic characteristics. They are classified as amphipathic (amphi, on both sides or ends, and philic, loving).

Because hydrophobic molecules have no polar groups to interact water, they have to be surrounded by a boundary of water molecules.

Formation of a micelle from the sodium salt of a long-chain carboxylic acid such as Lauric acid or Palmitic acid. The nonpolar hydrocarbon tails of the acid arrange themselves to avoid contact with water. The negatively charged carboxyl groups interact with water by forming ion-dipole interactions.

Acidic and Basic ConditionsWater tends to disassociate into H+and OH-ionsIn this disassociation, the oxygen retains the electrons and only one of the hydrogens, becoming a negatively charged ion known as hydroxide.Pure water has the same number (or concentration) of H+as OH-ions thus is neutral Acidicsolutions have more H+ions than OH-ions.Basicsolutions have the opposite.

Titration CurvesTitrations are often recorded on titration curves, the independent variable is the volume of the titrant, while the dependent variable is the pH of the solution (which changes depending on the composition of the two solutions). The equivalence point is a significant point on the graph (the point at which all of the starting solution, usually an acid, has been neutralized by the titrant, usually a base).

A titration curve.

Almost every biological process is pH dependent; Buffers Are Mixtures of Weak Acids and Their Conjugate Bases

Buffers are aqueous systems that tend to resist changes in pH when small amounts of acid (H+) or base (OH-) are added.

**********Names of the Nobel Prize winners are underlined.***1. Elements found in bulk form and essential for life: carbon, hydrogen, oxygen, nitrogen, phosphorous, and sulfur make up about 92% of the dry weight of living things.2. Elements in trace quantities in most organisms and very likely essential for life, such as calcium, manganese, iron, and iodine.3. Trace elements that are present in some organisms and may be essential for life, such as arsenic, bromine, molybdenum, and vanadium.

****Typical of these are alcohols, which have one or more hydroxyl groups; amines, with amino groups; aldehydes and ketones, with carbonyl groups; and carboxylic acids, with carboxyl groups**********Structural hierarchy in the molecular organization of cells. In this plant cell, the nucleus is an organelle containing several types of supramolecular complexes, including chromosomes. Chromosomes consist of macromolecules of DNA and many different proteins. Each type of macromolecule is made up of simple subunitsDNA of nucleotides (deoxyribonucleotides), for example.

fructose (same formula but different structure than glucose)*A fat is solid at room temperature, while an oil is a liquid under the same conditions. The fatty acids in oils are mostly unsaturated, while those in fats are mostly saturated*a catalyst is a chemical that promotes but is not changed by a chemical reaction************Endoplasmic Reticulum (ER) a system of internal membranes within the cell, which divides the interior of the cell into compartments; on the surface of the ER, the cell manufactures carbohydrates and lipids.Part of the ER is covered with protein-making ribosomes this is called rough ER. The proteins made here, such as enzymes, are intended for export from the cell. Smooth ER does not have ribosomes on its surface, and is involved in fat metabolism and the detoxification of toxic substances (such as alcohol and drugs) found in the liver.*Lysosomes vesicles containing enzymes which break down macromolecules; they digest worn-out cell components to make way for newly formed ones and they eliminate unwanted particles the cell has taken in.Lysosomes are used in cells in 4 major ways:Perioxisomes self-assembling enzyme-rich organelles that destroy toxins and also participate in the breakdown of metabolic products.

*Golgi Apparatus composed of 5 to 20 flattened, smooth, membranous sacs that resemble a stack of pancakes. Here, certain molecules produced in the cell such as mucus, carbohydrates, glycoporteins, and insulin are concentrated and packaged into vesicles for transport.*Mitochondria a double-membrane bound organelle that extracts energy from organic molecules (food); the site of cell metabolism. The inner membrane is bent into numerous folds called cristae; the cristae separate the mitochondrion into two compartments, an inner matrix and an outer compartment.**Chloroplasts saclike organelles that contain chlorophyll, a green pigment that carries out photosynthesis. Chloroplasts contain thylakoid membranes, which contain concentrated chlorophyll. The thylakoid membranes stack up and make up stacks called grana or granum. The space between the grana is known as the stroma. Photosynthesis produces sugars which are used as an energy source for cells.*********The dipolar nature of the H2O molecule is shown in the following figure by (a) ball-and-stick and (b) space-filling models. The dashed lines in (a) represent the nonbonding orbitals.

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