The Chemistry of Life:

• Text: BJ Chap 2, AP Chap 5

• Reading Assignments– BJ Chap 2 pp 38 – 69, AP pp129 - 166

• Homework Assignment– Chap 2 Review Questions pp 40-41

2A. Basic Chemistry (BJ – pp 38 -54, AP pp 129 – 143)

• BJ: 2A1 – Matter (AP p 129)• Matter – anything that occupies space and has mass. In ordinarily chemical reactions

matter can neither be created or destroyed, so it is said to conserve.

• Energy - Energy is the quality or dimension that describes the amount of work that can be performed by a force, an attribute of objects and systems that is subject to a conservation law. Different forms of energy include kinetic, potential, thermal, gravitational, sound, light, elastic, and electromagnetic energy. The forms of energy are often named after a related force.

• Any form of energy can be transformed into another form, but the total energy always remains the same. This principle, the conservation of energy.

• Chemical energy is that part of the energy in a substance that can be released by a chemical reaction.

• For non-nuclear related reactions, matter and energy can be thought of as different having following three own conservation laws. But with Einstein’s theory of relativity showing the equivalence of matter and energy through the relationship of E = mc2, we now often refer to the conservation of matter and energy or mass and energy.

Element and Atoms – (AP pp 129-134)

• An element: is a pure substance that cannot be broken down into simpler substance by ordinary chemical means.– Pure substance that from form one type of atom that is defined by its

atomic number; that is, by the number of protons in its nucleus. The term is also used to refer to a pure chemical substance composed of atoms with the same number of protons.

– There are 92 - 94 naturally occurring elements and several manmade elements

– As of 2007 117 elements have been observed as of 2007, 94 occur naturally on Earth New elements are discovered from time to time through artificial nuclear reactions.

– All chemical matter consists of these elements– Elements with atomic numbers greater than 82 (i.e,. bismuth and those

above), are inherently unstable and undergo radioactive decay. In addition, elements 43 and 61 (technetium and promethium) have no stable isotopes, and also decay.

Types of Elements• -- Monatomic• -- Diatomic• -- Polyatomic • Element Symbols - - Most common See

periodic Chart. Must know the most common.• -- H, He, O, C, Na, Cl, N, • to life: • Most abundant in human body O, C, H, N, Ca

–P, K, S, Cl, Na, Mg, Cu, F, Fe, I, Zn

Atoms• An atom: the smallest component of an element having the chemical properties of

the element• Periodic Table: The periodic table (BJ p 39 not in AP) of the chemical elements or just

the periodic table is a table of all the element based upon the atomic number of the element

– Atomic– number – number of protons of an atom or ion – also number of electrons of a neutral atom - always a who number usually in the upper left corner of element on table . It is the atomic number or number of protons that determines the number of valence electrons that in turn determines the chemical properties of an atom. So the type of atom is defined by the number of protons.

– Atomic Mass- the mass of an atom expressed in atomic mass units. The atomic mass of an atom may be considered to be the total mass of protons, neutrons and electrons in a single atom

– Average Atomic Mass (weight): - the average mass of an atom and it isotopes expressed in atomic mass units. This is the number on the periodic table.

– Series – the line of element in increasing atomic number– Groups – the column of elements that group element with same valence or outer electrons.– Valence electrons: outer shell electrons– Rule of the octave (eights): The shells of an atom want 8 electrons (except inner) most shell

– s- which only needs 2.

Bohr or planetary atomic model

• Show picture of Bohr model (BJ p 40, AP p 130.

Division of Matter• Matter• Mixtures Pure Substances• Heterogeneous Homogeneous

Elements• Compounds• Elements and Their Symbols –

see periodic table

Chemical Bonds:• Sharing or “borrowing” outer shell – valence – electrons.• Follow rule of the octave• S - , P 8, D 8 and so on• Ionic bonds – borrowing electrons – not really consider a bond, but

an ionic attraction’note – electron with proton is intra-molecular interactions

• Intermolecular interaction - • Example Na+ Cl- • Covalent Bonds - sharing of electrons – true bond – very strong

bonds • Intermolecular bond• Single Bond• Double Bond• Triple Bond

Vader Walls Bonds• Vader Walls – Hydrogen Bonds –

weak interactions – not a true bonds cases by

• permanent dipole–permanent dipole forces

• permanent dipole–induced dipole forces

• induced dipole-induced dipole

Molecules and Chemical Compounds (AP p 134 – 136)

• Single atoms Monatomic: In physics and chemistry, monatomic is a combination of the words "mono" and "atomic," and means "single atom." It is usually applied to gases: a monatomic gas is one in which atoms are not bound to each other.

• At standard temperature and pressure (STP), all of the noble gases are monatomic. These are helium, neon, argon, krypton, xenon and radon. The heavier noble gases can form compounds, but the lighter ones are unreactive. All elements will be monatomic in the gas phase at sufficiently high temperatures.

• Molecules: Molecules are formed when atoms linked together (AP 134 – 135)• Diatomic molecules are molecules composed only of two atoms, of either the same

or different chemical elements. The prefix di- means two in Greek. Common diatomic molecules are hydrogen, nitrogen, oxygen, and carbon monoxide. Most elements aside from the noble gases form diatomic molecules when heated, but high temperatures - sometimes thousands of degrees - are often required.

• Chemical compound: a substance consisting of two or more elements chemically-bonded together in a fixed proportion by mass. The basic unit (smallest unit that has these properties) of a compound is the molecule.

Chemical Symbols and Formulas of Compounds

• -- Use of subscript - goes with prior symbol

• -- Use of coefficient - in front of atom or compound

Chemical and Physical Properties and changes (AP p 136 – 137)

• -- Physical properties can be observed or measured without changing the composition of matter. Physical properties are used to observe and describe matter. Physical properties include: appearance, texture, color, odor, melting point, boiling point, density, solubility, polarity, and many others.

• -- Chemical properties of matter describes its "potential" to undergo some chemical change or reaction by virtue of its composition. What elements, electrons, and bonding are present to give the potential for chemical change. It is quite difficult to define a chemical property without using the word "change". Eventually you should be able to look at the formula of a compound and state some chemical property.

Chemical and Physical Changes

• -- Physical changes occur when objects undergo a change that does not change their chemical nature. A physical change involves a change in physical properties. Physical properties can be observed without changing the type of matter. Physical changes are reversible. Examples of physical properties include: texture, shape, size, color, odor, volume, mass, weight, and density.

• -- Chemical changes are the changes in a substance through chemical reactions. The chemical reactants form a new product with equal mass.

• The following can indicate that a chemical change took place, although this evidence is not conclusive:

– * Change of color (e.g., rusting of iron causes a change in color from silver to reddish-brown).

– * Change in temperature or energy, such as the production (exothermic) or loss (endothermic) of heat.

– * Change of form (burning paper) (this change is difficult to reverse).– * An unexpected change in color– * Light, heat, or sound is given off.– * gasses formed, often appearing as bubbles.– * Formation of precipitate (insoluble particles).– * The decomposition of organic matter (rotting food)

• For example, placing a pot of water on a hot stove element causes a change in temperature and gas to be released (water vapor) but a chemical change did not take place. It was simply a physical change / change of state. An example could be a log that is burning.

• A chemical reaction produces new substances by changing the way in which atoms look. In a chemical reaction old bonds are broken and new bonds are formed between different atoms. This breaking and forming of bonds takes place when particles of the original materials collide with one another. An example of a chemical change is fireworks.

2A2 Energy (BJ 43)• Energy: the ability to perform work (move something

over a distance) ability to do work - to cause motion (create a force and act over a distance)

• Forms or Energy Different forms of energy include kinetic, potential, thermal, gravitational, sound, light, elastic, and electromagnetic energy. The forms of energy are often named after a related force.

• Transformation of Energy Any form of energy can be transformed into another form, but the total energy always remains the same. This principle, the conservation of energy.

Thermodynamics:• Zeroth law of thermodynamics: If two thermodynamic systems are each in thermal equilibrium

with a third, then they are in thermal equilibrium with each other.

• First law of thermodynamics: Law of energy conservation - first law of thermodynamics. Energy can neither be created or destroyed, but can transformed from one form of energy to the other.

• Law of conservation of mass-energy (E=mc2) - Matter is very concentrated energy - consistent with scripture?

• Second Law of Thermodynamics: The second law of thermodynamics is an expression of the universal law of increasing entropy, stating that the entropy of an isolated system which is not in equilibrium will tend to increase over time, approaching a maximum value at equilibrium.

• There are many versions of the second law, but they all have the same effect, which is to explain the phenomenon of irreversibility in nature.

• Third law of thermodynamics: Heat flows (conducts) from Hot to Cold As temperature approaches absolute zero, the entropy of a system approaches a constant.

• Combined law of thermodynamics: a mathematical summation of the first law of thermodynamics and the second law of thermodynamics subsumed into a single concise mathematical statement as shown below:

• dU - TdS + pdV <= 0

• Here, U is internal energy, T is temperature, S is entropy, p is pressure, and V is volume. In theoretical structure in addition to the obvious inclusion of the first two laws, the combined law incorporates the implications of the zeroth law, via temperature T, and the third law, through its use of free energy as related to the calculation of chemical affinities near absolute zero.

Energy, Heat, Temperature

• Energy - Ability to do work (displace) cause movement (Force)• Heat: Thermal energy in transit Kinetic Energy - Energy of motion,

consists of both potential and kinetic energy or the total energy of the molecules.

• Temperature - Average KE of motions • Kinetic Energy – energy by virtue of motion (1/2mv2)• Kinetic Molecular Energy –KE of moving molecules (BJ: p 44)• Thermal Energy - All motion (KE) straight, vibration, rotation• Potential Energy - Energy by virtue OF position.• Potential Energy of a Molecule - Energy by virtue of position Page

45.

The Measurement of Energy

• Energy - SI Joule F x ds = n - meter = ma meter = m m2/s2

• Erg - cgs = dyne - cm

• - British - BTU

• - Calorie - amount of energy to raise one gram of water 1 degree C– -- Food calorie is actually a Kilocalorie

Temperature Scales

• Celsius – based upon freezing and boiling point of water (0 and 100 C)

• Kelvin - Based upon absolute scale 0 K = no energy K = 273 + C)

• Fahrenheit – Based on normal temperature range humans experience (in UK) 0 coldest – 100 warmest C = 5/9 (F-32) F = (9/5C)+32

States of Matter (AP p 138)

• Solids, Liquid, Gas, Plasma and Ne very low Bose-Einstein condensate)

• - Progressively Higher energy states

• - Plasma

• -New Bose-Einstein condensate - at close to absolute 0 matter acts as one large atom

• Change of States– Melting - Freezing (water T = 0 C for both)– Evaporation – Condensation – Sublimation - Deposition

Types of reactions• -- Exothermic - gives off energy A + B -> C + D + energy

• -- Endothermic -- Absorbs energy A + B + energy -> C + D

• Catalyst (AP 145): Catalysis is the process in which the rate of a chemical reaction is either increased or decreased by means of a chemical substance known as a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. The catalyst may participate in multiple chemical transformations. Catalysts that speed the reaction are called positive catalysts. Catalysts that slow down the reaction are called negative catalysts or inhibitors. Substances that increase the activity of catalysts are called promoters and substances that deactivate catalysts are called catalytic poisons.

• Enzymes: Enzymes are biomolecules (organic molecules) that catalyze (i.e., increase the rates of) chemical reactions. Nearly all known enzymes are proteins. However, certain RNA molecules can be effective biocatalysts too. These RNA molecules have come to be known as ribozymes. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. (see BJ pp56-57)

BJ 2 (p 47) A-3 Solutions (AP p138)

• Solution: a homogeneous mixture of one or more substances with another substance

• Solute: A substance that dissolved in another substance, usually the component of a solution present in the lesser amount.

• Solvent: A solvent is a liquid or gas that dissolves a solid, liquid, or gaseous solute, resulting in a solution

• Concentration: In chemistry, concentration is the measure of how much of a given substance there is mixed with another substance. This can apply to any sort of chemical mixture, but most frequently the concept is limited to homogeneous solutions, where it refers to the amount of solute in the solvent.

• Concentration Gradient (BJ p50): A gradient is a measurement of how much something changes as you move from one region to another. So a concentration gradient is a measurement of how the concentration of something changes from one place to another.

• http://www.mit.edu/~kardar/teaching/projects/chemotaxis(AndreaSchmidt)/gradients.htm

Diffusion – BJ p51 AP 140• Diffusion – BJ p51 AP 140: the process by which molecules

spread from areas of high concentration, to areas of low concentration.

• Diffusion Pressure: The concentration gradient will create a force that can be expressed as energy per unit volume (E/V) or pressure (F/A).

• Osmosis – BJ p52 AP 141: Osmosis is a selective diffusion process driven by the internal energy of the solvent molecules.

• Semi-Permermeable Membrane: A semi-permeable membrane, also termed a selectively-permeable membrane, a partially-permeable membrane or a differentially-permeable membrane, is a membrane that will allow certain molecules or ions to pass through it by diffusion and occasionally specialized "facilitated diffusion."

Acids, Bases Buffers (BJ: pp 53-54)

• There is actually no completely unique definition of an acid ion bases. But the following is the most basic and useful for biology

• Acid: Any substances that give up a proton (H+) when dissolved

• Base; Any substance that give up a hydroxyl ion OH- when dissolved

• Ph: a measure of the acidity or basicity of a solution. It is defined as a relative measure (from 0 – 14) of the activity of dissolved hydrogen ions (H+). The lower the number the more acidic. The higher the number the more basic. 0 – 6.9 is acid, 7 is neutral and 7.1 – 14 is basic.

• Buffer: any substance that will combine with an H+ or OH- (whichever is in excess) to maintain proper Ph

• Acid Base reaction: This is when an acid and base reactive to neutralize each other. The general formula is

• Acid + Base ỵ→ Salt + water example HCL + NaOH =>→ NaCl + H2O

BJ 2B Organic Chemistry AP p 146 - 161

• Inorganic versus Organic Chemistry

• Inorganic Chemistry: Inorganic chemistry is the branch of chemistry concerned with the properties and behavior of inorganic compounds. This field covers all chemical compounds except the myriad organic compounds (compounds containing C-H bonds), which are the subjects of organic chemistry. The distinction between the two disciplines is far from absolute, and there is much overlap, most importantly in the sub-discipline of organometallic chemistry.

• Organic Chemistry: Organic chemistry is a discipline within chemistry which involves the scientific study of the structure, properties, composition, reactions, and preparation (by synthesis or by other means) of chemical compounds that contain carbon. These compounds may contain any number of other elements, including hydrogen, nitrogen, oxygen, the halogens as well as phosphorus, silicon and sulfur.

• Vitalism: chemistry alone and that life is in some part self-determining.

2B-1 Organic Compounds

• An organic compound is any member of a large class of chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of compounds such as carbonates, simple oxides of carbon and cyanides, as well as the allotropes of carbon, are considered inorganic. The division between "organic" and "inorganic" carbon compounds while "useful in organizing the vast subject of chemistry...is somewhat arbitrary"

• Carbon Bonds: Carbon has four valence bonds, giving it the greatest possible covalent bonding potential. Because of the unique bonding properties of carbon, there are millions of different organic chemicals. Each one has unique properties. There are organic chemicals that make up your hair, your skin, even your fingernails. All life as we know it is made up of organic compounds. Carbon (C) appears in the 2nd row of the periodic table and has atomic number of 6. Given our discussion of electron shells it is easy to see that carbon has 4 electrons in its valence shell. Since carbon needs 8 electrons to fill its valence shell, it forms 4 bonds with other atoms (each bond consisting of one of carbon's electrons and one of the bonding atom's). Every valence electron participates in bonding, thus a carbon atom's bonds will be distributed evenly over the atom's surface. These bonds form a tetrahedron, as illustrated below:

An organic molecule (hydrocarbon) is formed when carbon bonds to hydrogen. The simplest hydrocarbon consists of 4 hydrogen atoms bonded to a carbon atom (called methane):

• Carbon Backbone: Chain or ring of carbon that forms the basis for the rest of the atoms.

• Functional Groups: In organic chemistry, functional groups are specific groups of atoms within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction(s) regardless of the size of the molecule it is a part of. However, its relative reactivity can be modified by nearby functional groups. (see p56 for table of functional groups)

2B -2 Carbohydrates and Lipids

• Biomolecules: A biomolecule is any organic molecule that is produced by a living organism, including large polymeric molecules such as proteins, polysaccharides (carbohydrates), and nucleic acids as well as small molecules such as primary metabolites, secondary metabolites, and natural products.

• As organic molecules, biomolecules consist primarily of carbon and hydrogen, nitrogen, and oxygen, and, to a smaller extent, phosphorus and sulfur. Other elements sometimes are incorporated but are much less common.

• A diverse range of biomolecules exist, including:

* Small molecules:

• o Lipid, phospholipid, glycolipid, sterol, glycerolipid

• o Vitamin

• o Hormone, neurotransmitter

• o Carbohydrate, sugar

•

* Monomers:

• o Amino acids

• o Nucleotides

• o Monosaccharides

* Polymers:

• o Peptides, oligopeptides, polypeptides, proteins

• o Nucleic acids, i.e. DNA, RNA

• o Oligosaccharides, polysaccharides (including cellulose)

• o Lignin

Carbohydrates

• Carbohydrates [α] or saccharides[β] are the most abundant of the four major classes of biomolecules of . , lipids, carbohydrates (saccharides), proteins, and nucleic acids.

• the four major chemical groupings of carbohydrates are: monosaccharide, disaccharide, oligosaccharide, and polysaccharide.

• They fill numerous roles in living things, such as the storage and transport of energy (eg: starch, glycogen) and structural components (eg: cellulose in plants and chitin). Additionally, carbohydrates and their derivatives play major roles in the working process of the immune system, fertilization, pathogenesis, blood clotting, and development.

• Carbohydrates make up most of the organic matter on Earth because of their extensive roles in all forms of life. First, carbohydrates serve as energy stores, fuels, and metabolic intermediates. Second, ribose and deoxyribose sugars form part of the structural framework of RNA and DNA. Third, polysaccharides are structural elements in the cell walls of bacteria and plants. In fact, cellulose, the main constituent of plant cell walls, is one of the most abundant organic compounds in the biosphere. Fourth, carbohydrates are linked to many proteins and lipids, where they play key roles in mediating interactions between cells and interactions between cells and other elements in the cellular environment.

• Chemically, carbohydrates are simple organic compounds that are aldehydes or ketones with many hydroxyl groups added, usually one on each carbon atom that is not part of the aldehyde or ketone functional group. The basic carbohydrate units are called monosaccharides; examples are glucose, galactose, and fructose. The general stoichiometric formula of an unmodified monosaccharide is (C·H2O)n, where n is any number of three or greater; however, not all carbohydrates conform to this precise stoichiometric definition (eg: uronic acids, deoxy-sugars such as fucose), nor are all chemicals that do conform to this definition automatically classified as carbohydrates.[2]

Monosaccharides• Monosaccharides The basic carbohydrate units– examples:

glucose, galactose, and fructose - can be linked together into what are called polysaccharides (or oligosaccharides) in a large variety of ways. Many carbohydrates contain one or more modified monosaccharide units that have had one or more groups replaced or removed. For example, deoxyribose, a component of DNA, is a modified version of ribose; chitin is composed of repeating units of N-acetylglucosamine, a nitrogen-containing form of glucose.

• While the scientific nomenclature of carbohydrates is complex, the names of carbohydrates very often end in the suffix -ose. Glycoinformatics is the specialized field of study that deals with the specific and unique bioinformatics of carbohydrates.

• Glucose – example of monosaccharide

Disaccharides

• A disaccharide is the carbohydrate formed when two monosaccharides undergo a condensation reaction (dehydration synthesis) which involves the elimination of a small molecule, such as water, from the functional groups only. Like monosaccharides, disaccharides also dissolve in water, taste sweet and are called sugars.[1]

• 'Disaccharide' is one of the four chemical groupings of carbohydrates (monosaccharide, disaccharide, oligosaccharide, and polysaccharide).

Example of a disaccharides

Lactose Sucrose

Oligosaccharide

• Oligosaccharide is a saccharide polymer containing a small number (typically three to ten of component sugars, also known as simple sugars. The name is derived from the Greek word oligos, meaning "a few", and from the Latin/Greek word sacchar which means "sugar". Oligosaccharides can have many functions for example, they are commonly found on the plasma membrane of animal cells where they can play a role in cell-cell recognition.

• They are generally found either O- or N-linked to compatible amino acid side chains in proteins or to lipid moieties

Polysaccharides • Polysaccharides are polymeric carbohydrate structures, formed of repeating units

(either mono- or di-saccharides) joined together by glycosidic bonds. These structures are often linear, but may contain various degrees of branching. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure, these macromolecules can have distinct properties from their monosaccharide building blocks. They may be amorphous or even insoluble in water.

• When all the monosaccharides in a polysaccharide are the same type the polysaccharide is called a homopolysaccharide, but when more than one type of monosaccharide is present they are called heteropolysaccharides.

• Examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose and chitin.

• Polysaccharides have a general formula of Cx(H2O)y where x is usually a large number between 200 and 2500. Considering that the repeating units in the polymer backbone are often six-carbon monosaccharides, the general formula can also be represented as (C6H10O5)n where 40≤n≤3000

Starch• Starch: Starch or amylum is a polysaccharide carbohydrate

consisting of a large number of glucose units joined together by glycosidic bonds. Starch is produced by all green plants as an energy store and is a major food source for humans.

• Pure starch is a white, tasteless and odorless powder that is insoluble in cold water or alcohol. It consists of two types of molecules: the linear and helical amylose and the branched amylopectin. Depending on the plant, starch generally contains 20 to 25% amylose and 75 to 80% amylopectin. Glycogen, the glucose store of animals, is a more branched version of amylopectin.

• Starch can be used as a thickening, stiffening or gluing agent when dissolved in warm water, giving wheatpaste.

Glycogen • Glycogen is the molecule which functions as the secondary short term

energy storage in animal cells. It is made primarily by the liver and the muscles, but can also be made by glycogenesis within the brain and stomach. Glycogen is the analogue of starch, a less branched glucose polymer in plants, and is commonly referred to as animal starch, having a similar structure to amylopectin. Glycogen is found in the form of granules in the cytosol in many cell types, and plays an important role in the glucose cycle. Glycogen forms an energy reserve that can be quickly mobilized to meet a sudden need for glucose, but one that is less compact than the energy reserves of triglycerides (fat). In the liver hepatocytes, glycogen can compose up to 8% of the fresh weight (100–120 g in an adult) soon after a meal. Only the glycogen stored in the liver can be made accessible to other organs. In the muscles, glycogen is found in a much lower concentration (1% to 2% of the muscle mass), but the total amount exceeds that in the liver. However the amount of glycogen stored in the body , especially within the red blood cells liver & muscles, mostly depends on physical training, basal metabolic rate and eating habits . Small amounts of glycogen are found in the kidneys, and even smaller amounts in certain glial cells in the brain and white blood cells. The uterus also stores glycogen during pregnancy to nourish the embryo.

Cellulose• Cellulose is an organic compound with the formula

(C6H10O5)Template:Chem/dispAAA, a polysaccharide consisting of a linear chain of several hundred to over ten thousand β(1→4) linked D-glucose units.

• Cellulose is the structural component of the primary cell wall of green plants, many forms of algae and the oomycetes. Some species of bacteria secrete it to form biofilms. Cellulose is the most common organic compound on Earth. About 33 percent of all plant matter is cellulose (the cellulose content of cotton is 90 percent and that of wood is 50 percent).

• For industrial use, cellulose is mainly obtained from wood pulp and cotton. It is mainly used to produce cardboard and paper; to a smaller extent it is converted into a wide variety of derivative products such as cellophane and rayon. Converting cellulose from energy crops into biofuels such as cellulosic ethanol is under investigation as an alternative fuel source.

• Some animals, particularly ruminants and termites, can digest cellulose with the help of symbiotic micro-organisms that live in their guts. Cellulose is not digestible by humans and is often referred to as 'dietary fiber' or 'roughage', acting as a hydrophilic bulking agent for feces.

Chitin

• Chitin (C8H13O5N)n (pronounced /ˈkaɪtɨn/) is a long-chain polymer of a N-acetylglucosamine, a derivative of glucose, and is found in many places throughout the natural world. It is the main component of the cell walls of fungi, the exoskeletons of arthropods, such as crustaceans (e.g. crabs, lobsters and shrimps) and insects, including ants, beetles and butterflies, the radula of mollusks and the beaks of cephalopods, including squid and octopuses. Chitin has also proven useful for several medical and industrial purposes. Chitin is a biological substance which may be compared to the polysaccharide cellulose and to the protein keratin. Although keratin is a protein, and not a carbohydrate like chitin, both keratin and chitin have similar structural functions.

Lipids

• Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and others. The main biological functions of lipids include energy storage, as structural components of cell membranes, and as important signaling molecules.

• Lipids may be broadly defined as hydrophobic or amphiphilic small molecules; the amphiphilic nature of some lipids allows them to form structures such as vesicles, liposomes, or membranes in an aqueous environment. Biological lipids originate entirely or in part from two distinct types of biochemical subunits or "building blocks": ketoacyl and isoprene groups. Using this approach, lipids may be divided into eight categories: fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, saccharolipids and polyketides (derived from condensation of ketoacyl subunits); and sterol lipids and prenol lipids (derived from condensation of isoprene subunits).

• Although the term lipid is sometimes used as a synonym for fats, fats are a subgroup of lipids called triglycerides. Lipids also encompass molecules such as fatty acids and their derivatives (including tri-, di-, and monoglycerides and phospholipids), as well as other sterol-containing metabolites such as cholesterol. Although humans and other mammals use various biosynthetic pathways to both break down and synthesize lipids, some essential lipids cannot be made this way and must be obtained from the diet.

Fatty acid • Fatty acid is a carboxylic acid often with a long unbranched aliphatic tail (chain),

which is either saturated or unsaturated. Carboxylic acids as short as butyric acid (4 carbon atoms) are considered to be fatty acids, whereas fatty acids derived from natural fats and oils may be assumed to have at least eight carbon atoms, caprylic acid (octanoic acid), for example. Most of the natural fatty acids have an even number of carbon atoms, because their biosynthesis involves acetyl-CoA, a coenzyme carrying a two-carbon-atom group (see fatty acid synthesis).

• Fatty acids are produced by the hydrolysis of the ester linkages in a fat or biological oil (both of which are triglycerides), with the removal of glycerol. See oleochemicals.

• Fatty acids are aliphatic monocarboxylic acids derived from, or contained in esterified form in an animal or vegetable fat, oil, or wax. Natural fatty acids commonly have a chain of four to 28 carbons (usually unbranched and even numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids. This would include acetic acid, which is not usually considered a fatty acid because it is so short that the triglyceride triacetin made from it is substantially miscible with water and is thus not a lipid.

Hydrophilic: • Hydrophile, from the Greek (hydros) "water" and φιλια (philia) "friendship," refers to a

physical property of a molecule that can transiently bond with water (H2O) through hydrogen bonding. This is thermodynamically favorable, and makes these molecules soluble not only in water, but also in other polar solvents. There are hydrophilic and hydrophobic parts of the cell membrane.

• A hydrophilic molecule or portion of a molecule is one that is typically charge-polarized and capable of hydrogen bonding, enabling it to dissolve more readily in water than in oil or other hydrophobic solvents. A hydrophilic is made up of alcohol and fatty acyl chains. Hydrophilic and hydrophobic molecules are also known as polar molecules and nonpolar molecules, respectively. Some hydrophilic substances do not dissolve. This type of mixture is called a colloid. Soap has a hydrophilic head and a hydrophobic tail, which allows it to dissolve in both waters and oils, therefore allowing the soap to clean a surface.

• An approximate rule of thumb for hydrophilicity of organic compounds is that solubility of a molecule in water is more than 1 mass % if there is at least one neutral hydrophile group per 5 carbons, or at least one electrically charged hydrophile group per 7 carbons.

Hydrophobic: • hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear

phobos) refers to the physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water.

•

• Hydrophobic molecules tend to be non-polar and thus prefer other neutral molecules and nonpolar solvents. Hydrophobic molecules in water often cluster together forming micelles. Water on hydrophobic surfaces will exhibit a high contact angle.

• Examples of hydrophobic molecules include the alkanes, oils, fats, and greasy substances in general. Hydrophobic materials are used for oil removal from water, the management of oil spills, and chemical separation processes to remove non-polar from polar compounds.

• Hydrophobic is often used interchangeably with lipophilic, "fat loving." However, the two terms are not synonymous. While hydrophobic substances are usually lipophilic, there are exceptions—such as the silicones and fluorocarbons.

Triglyceride • Triglyceride (help·info) (more properly known as Triacylglycerol.ogg triacylglycerol

(help·info), TAG or triacylglyceride) is a glyceride in which the glycerol is esterified with three fatty acids. It is the main constituent of vegetable oil and animal fats.

• Triglycerides are the chemical form in which most fat exists in food as well as in the body. They're also present in blood plasma and, in association with cholesterol, form the plasma lipids.

• Triglycerides in plasma are derived from fats eaten in foods or made in the body from other energy sources like carbohydrates. Calories ingested in a meal and not used immediately by tissues are converted to triglycerides and transported to fat cells to be stored. Hormones regulate the release of triglycerides from fat tissue so they meet the body's needs for energy between meals.

• Excess triglycerides in plasma is called hypertriglyceridemia. It's linked to the occurrence of coronary artery disease in some people. Elevated triglycerides may be a consequence of other disease, such as untreated diabetes mellitus. Like cholesterol, increases in triglyceride levels can be detected by plasma measurements. These measurements should be made after an overnight food and alcohol fast.

Saturates versus Unsaturated:

• An unsaturated fat is a fat or fatty acid in which there are one or more double bonds in the fatty acid chain. A fat molecule is monounsaturated if it contains one double bond, and polyunsaturated if it contains more than one double bond. Where double bonds are formed, hydrogen atoms are eliminated. Thus, a saturated fat is "saturated" with hydrogen atoms. In cellular metabolism hydrogen-carbon bonds are broken down – or oxidized – to produce energy, thus an unsaturated fat molecule contains somewhat less energy (i.e fewer calories) than a comparable sized saturated fat. The greater the degree of unsaturation in a fatty acid (ie, the more double bonds in the fatty acid), the more vulnerable it is to lipid peroxidation (rancidity). Antioxidants can protect unsaturated fat from lipid peroxidation. Unsaturated fats also have a more enlarged shape than saturated fats.[citation needed]

Phospholipids

• Phospholipids are a class of lipids and are a major component of all cell membranes. Most phospholipids contain a diglyceride, a phosphate group, and a simple organic molecule such as choline; one exception to this rule is sphingomyelin, which is derived from sphingosine instead of glycerol. They are a type of molecule. They form a lipid bilayer within a cell membrane.

Sterols

• Sterols are an important class of organic molecules. They occur naturally in plants, animals and fungi, with the most familiar type of animal sterol being cholesterol, which has been shown to contribute to high blood pressure and heart disease. Within the past decade, interest in plant sterols as a dietary supplement has increased, due to studies showing that they can contribute to lower cholesterol levels.

2B-3 Proteins and Nuclear Acids (p62)

• Proteins (also known as polypeptides) are organic compounds made of amino acids arranged in a linear chain. The amino acids in a polymer chain are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids, however in certain organisms the genetic code can include selenocysteine — and in certain archaea — pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alter the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Proteins can also work together to achieve a particular function, and they often associate to form stable complexes.

• Amino Acids: amino acid is a molecule containing both amine and carboxyl functional groups. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula H2NCHRCOOH, where R is an organic substituent. In the alpha amino acids, the amino and carboxylate groups are attached to the same carbon, which is called the α–carbon. The various alpha amino acids differ in which side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in glycine through a methyl group in alanine to a large heterocyclic group in tryptophan.

• Amino acids are critical to life, and have a variety of roles in metabolism. One particularly important function is as the building blocks of proteins, which are linear chains of amino acids. Amino acids are also important in many other biological molecules, such as forming parts of coenzymes, as in S-adenosylmethionine, or as precursors for the biosynthesis of molecules such as heme. Due to this central role in biochemistry, amino acids are very important in nutrition.

• The amino acids are commonly used in food technology and industry. For example, monosodium glutamate is a common flavor enhancer that gives foods the taste called umami. Beyond the amino acids that are found in all forms of life, amino acids are also used in industry, with the production of biodegradable plastics, drugs and chiral catalysts being particularly important applications.

Peptides: • Peptides are short polymers formed from the linking, in a defined order, of α-amino acids. The

link between one amino acid residue and the next is known as an amide bond or a peptide bond.

• Proteins are polypeptide molecules (or consist of multiple polypeptide subunits). The distinction is that peptides are short and polypeptides/proteins are long. There are several different conventions to determine these, all of which have caveats and nuances.

• Four levels of a Protein structure and Peptide to functioning protein – (BJ p 63-64)

• Nucleic Acids: A nucleic acid is a macromolecule composed of chains of monomeric nucleotides. In biochemistry these molecules carry genetic information or form structures within cells. The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nucleic acids are universal in living things, as they are found in all cells and viruses. Nucleic acids were first discovered by Friedrich Miescher in 1871.

• Artificial nucleic acids include peptide nucleic acid (PNA), Morpholino and locked nucleic acid (LNA), as well as glycol nucleic acid (GNA) and threose nucleic acid (TNA). Each of these is distinguished from naturally-occurring DNA or RNA by changes to the backbone of the molecule.

DNA: • DNA: Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in

the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints or a recipe, or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

• DNA – Structure: Chemically, DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are therefore anti-parallel. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called transcription.

• Within cells, DNA is organized into X-shaped structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in the mitochondria (animals and plants) and chloroplasts (plants only). Prokaryotes (bacteria and archaea) however, store their DNA in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

Nucleotides

• Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. Additionally, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy (adenosine triphosphate and guanosine triphosphate), participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into important cofactors of enzymatic reactions (coenzyme A, flavin adenine dinucleotide, flavin mononucleotide, and nicotinamide adenine dinucleotide phosphate).

DNA – Replication: • DNA – Replication: Cell division is essential for an organism to grow, but when a cell divides it must replicate the

DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for DNA replication. Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, different mechanisms are used to copy the antiparallel strands of the double helix. In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.

• DNA replication, the basis for biological inheritance, is a fundamental process occurring in all living organisms to copy their DNA. This process is "semiconservative" in that each strand of the original double-stranded DNA molecule serves as template for the reproduction of the complementary strand. Hence, following DNA replication, two identical DNA molecules have been produced from a single double-stranded DNA molecule. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.

• In a cell, DNA replication begins at specific locations in the genome, called "origins". Unwinding of DNA at the origin, and synthesis of new strands, forms a replication fork. In addition to DNA polymerase, the enzyme that synthesizes the new DNA by adding nucleotides matched to the template strand, a number of other proteins are associated with the fork and assist in the initiation and continuation of DNA synthesis.

• DNA replication can also be performed in vitro (outside a cell). DNA polymerases, isolated from cells, and artificial DNA primers are used to initiate DNA synthesis at known sequences in a template molecule. The polymerase chain reaction (PCR), a common laboratory technique, employs such artificial synthesis in a cyclic manner to amplify a specific target DNA fragment from a pool of DNA.

RNA• RNA: Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of

nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-stranded; RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom); and RNA has the base uracil rather than thymine that is present in DNA.

• RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. RNA is central to the synthesis of proteins. Here, a type of RNA called messenger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. There are many RNAs with other roles – in particular regulating which genes are expressed, but also as the genomes of most viruses.

• Transcription is the synthesis of RNA under the direction of DNA. RNA synthesis, or transcription, is the process of transcribing DNA nucleotide sequence information into RNA sequence information. Both nucleic acid sequences use complementary language, and the information is simply transcribed, or copied, from one molecule to the other. DNA sequence is enzymatically copied by RNA polymerase to produce a complementary nucleotide RNA strand, called messenger RNA (mRNA), because it carries a genetic message from the DNA to the protein-synthesizing machinery of the cell. One significant difference between RNA and DNA sequence is the presence of U, or uracil in RNA instead of the T, or thymine of DNA. In the case of protein-encoding DNA, transcription is the first step that usually leads to the expression of the genes, by the production of the mRNA intermediate, which is a faithful transcript of the gene's protein-building instruction. The stretch of DNA that is transcribed into an RNA molecule is called a transcription unit. A DNA transcription unit that is translated into protein contains sequences that direct and regulate protein synthesis in addition to coding the sequence that is translated into protein. The regulatory sequence that is before (upstream (-), towards the 5' DNA end) the coding sequence is called 5' untranslated region (5'UTR), and sequence found following (downstream (+), towards the 3' DNA end) the coding sequence is called 3' untranslated region (3'UTR). Transcription has some proofreading mechanisms, but they are fewer and less effective than the controls for copying DNA; therefore, transcription has a lower copying fidelity than DNA replication.

RNA replication• As in DNA replication, RNA is synthesized in the 5' → 3' direction (from the

point of view of the growing RNA transcript). Only one of the two DNA strands is transcribed. This strand is called the template strand, because it provides the template for ordering the sequence of nucleotides in an RNA transcript. The other strand is called the coding strand, because its sequence is the same as the newly created RNA transcript (except for uracil being substituted for thymine). The DNA template strand is read 3' → 5' by RNA polymerase and the new RNA strand is synthesized in the 5'→ 3' direction.

•

• A polymerase binds to the 3' end of a gene (promoter) on the DNA template strand and travels toward the 5' end.

•

• Transcription is divided into 5 stages: pre-initiation, initiation, promoter clearance, elongation and termination.

Photosynthesis – see AP p 144

• Photosynthesis[α] is a process that converts carbon dioxide into organic compounds, especially sugars, using the energy from sunlight.Photosynthesis occurs in plants, algae, and many species of Bacteria, but not in Archaea. Photosynthetic organisms are called photoautotrophs, since it allows them to create their own food. In plants, algae and cyanobacteria photosynthesis uses carbon dioxide and water, releasing oxygen as a waste product. Photosynthesis is vital for life on Earth. As well as maintaining the normal level of oxygen in the atmosphere, nearly all life either depends on it directly as a source of energy, or indirectly as the ultimate source of the energy in their food.The amount of energy trapped by photosynthesis is immense, approximately 100 terawatts: which is about six times larger than the power consumption of human civilization.As well as energy, photosynthesis is also the source of the carbon in all the organic compounds within organisms' bodies. In all, photosynthetic organisms convert around 100,000,000,000 tonnes of carbon into biomass per year.

• Although photosynthesis can occur in different ways in different species, some features are always the same. For example, the process always begins when energy from light is absorbed by proteins called photosynthetic reaction centers that contain chlorophylls. In plants, these proteins are held inside organelles called chloroplasts, while in bacteria they are embedded in the plasma membrane. Some of the light energy gathered by chlorophylls is stored in the form of adenosine triphosphate (ATP). The rest of the energy is used to remove electrons from a substance such as water. These electrons are then used in the reactions that turn carbon dioxide into organic compounds. In plants, algae and cyanobacteria this is done by a sequence of reactions called the Calvin cycle, but different sets of reactions are found in some bacteria, such as the reverse Krebs cycle in Chlorobium. Many photosynthetic organisms have adaptations that concentrate or store carbon dioxide. This helps reduce a wasteful process called photorespiration that can consume part of the sugar produced during photosynthesis.