The Molecules of Life Chapter 2

The Molecules of Life Chapter 2

Core concepts 1.The atom is the fundamental unit of matter. 2.Atoms can combine to form molecules linked by chemical bonds. 3.Water is essential for life. 4.Carbon is the backbone of organic molecules. 5.Organic molecules include proteins, nucleic acids, carbohydrates, and lipids, each of which is built from simpler units. 6.Life likely originated on Earth through a set of chemical reactions that gave rise to the molecules of life.

2.1 PROPERTIES OF ATOMS THE ATOM IS THE FUNDAMENTAL UNIT OF MATTER Living organisms are structurally and functionally very diverse These differences are due to the molecules that build them Inspite of the diversity of molecules and their functions The chemistry of life is based on a few types of molecules, these molecules are made up of just a few elements

What are elements? Elements: Pure substances that can not be broken down further. Contain only one type of unique atom Elements known today 118 Natural Elements 94 Artificially created Elements 24 Element is indicated by its symbol, For example, Carbon (C), Hydrogen (H), Helium (He)

Nucleus (6 protons + 6 neutrons) e e Carbon Atom e e Electron + + + + + + + Proton Neutron e e e Carbon atom

2.1 PROPERTIES OF ATOMS Elements are composed of atoms. Atoms consist of protons, neutrons, and electrons. Protons are part of atomic nucleus and are positively charged particles Neutrons are part of atomic nucleus and do not have any electrical charge Electrons move around the nucleus and are negatively charged particles Protons and Neutrons together form the atomic nucleus

CARBON ATOM The number of protons is the atomic number and specifies the atom as a particular element. Atomic number = Number of Protons (given in periodic table) For example, an atom with 6 protons is always a carbon atom. The number of protons and neutrons determine the atomic mass. Atomic mass = Mass of (Protons + Neutrons) Mass number = Number of(protons + Neutrons) Therefore, Number of neutrons = Mass number Atomic number

CARBON ATOM Isotopes are atoms of the same elements that have same number of protons and different numbers of neutrons. For example, carbon has three isotopes: 6 protons and 6 neutrons, atomic mass 12 (99%) 6 protons and 7 neutrons, atomic mass 13 (1%) 6 protons and 8 neutrons, atomic mass 14 (very small fraction) Typically, an atom will have the same number of protons and electrons. However, an atom that has lost an electron would be a positively charged ion and One that has gained an electron would be a negatively charged ion.

ORBITALS AND SHELLS

CARBON ATOM Electrons move around the nucleus within orbitals defined regions of space where an electron is most of the time. The maximum number of electrons in any orbital is two. Atoms with more than two electrons have multiple orbitals, differing in size, shape, and distance from the nucleus. Orbitals exist in different energy levels, or shells. The first shell contains one spherical orbital. The second shell has four orbitals. The first shell can contain up to two electrons. The second shell can contain up to 8 electrons.

CARBON ATOM For example, carbon has six electrons. Two electrons occupy the first orbital in the first shell. The remaining four electrons are distributed among the four possible orbitals in the second shell, with no more than two electrons in each orbital.

PERIODIC TABLE

READING THE PERIODIC TABLE The periodic table of elements organizes all chemical elements in terms of their chemical properties. Note here the order of increasing atomic number.

READING THE PERIODIC TABLE Elements in the same horizontal row have the same number of shells and therefore have the same number of types of orbitals. Across a row, electrons fill the outermost shell until a full complement of eight electrons is reached. Here, you can see the filling of the shells for the elements in the second row of the periodic table. The number of electrons in the outermost shell determines in large part how elements behave and interact with other elements.

READING THE PERIODIC TABLE Vertical columns are called groups, or families. Members of a group have the same number of electrons in their outermost shell. For example, carbon and lead have the same number of electrons in their outmost shell.

2.2 MOLECULES AND CHEMICAL BONDS Atoms can combine with one another to form molecules, held together by chemical bonds. The ability of atoms to form molecules explains how a few type of elements can make many different molecules that can perform different functions.

Types of chemical bonds, 1) Covalent 2) Polar covalent 3) Hydrogen 4) Ionic CHEMICAL BONDS

1) COVALENT BOND A covalent bond is formed when two atoms share electrons. The sharing of electrons occurs in the outermost orbitals of the atoms. The electrons found in the outermost orbitals of an atom are called the valence electrons. A molecule is formed when two atoms share their valence electrons with each other. Here, two hydrogen atoms, each with one electron, combine to form hydrogen gas.

MOLECULE STABILITY Molecules tend to be the stable when they share electrons, to completely occupy the outermost shell. One carbon atom with four valence electrons combines with four hydrogens, each with one valence electron, to fill the outer orbital with eight electrons. Nitrogen has five valence electrons and combines with three hydrogens to form ammonia, filling the outer shell with eight electrons. Oxygen, with six valence electrons, combines with two hydrogens to form water and fill the outer shell with eight electrons.

2) POLAR COVALENT BOND Polar covalent bond is characterized by unequal sharing of electrons. In water, the electrons are more likely to be located near the oxygen atom than the hydrogen atoms. This is due to the property known as electronegativity the ability of an atom to attract electrons. Oxygen is more electronegative than hydrogen and attracts electrons more than does hydrogen. In a molecule of water, Oxygen has a slight negative charge while the, two hydrogen atoms have a slight positive charge.

NON-POLAR COVALENT BOND A covalent bond between atoms that have the same or nearly the same electronegativity is a nonpolar covalent bond. The electrons are shared equally H H H H Hydrogen gas, H 2 Methane, CH 4 H C H

3) HYDROGEN BONDS A hydrogen bond is an interaction of a hydrogen atom and an electronegative atom. For example, hydrogen atoms in water are covalently bound to one oxygen atom and are attracted to and interact with an oxygen atom of another water molecule. Hydrogen bonds are depicted by the dashed lines. than help Hydrogen bonds are weaker covalent bonds, but they do stabilize biological molecules.

4) IONIC BOND Ionic bonds are formed due to transfer of electrons between two oppositely charged ions. For example, NaCl. The difference in electronegativity between these two atoms is very large. The chlorine atom has such high electronegativity that it steals an electron from the sodium atom. This results in a negative charge on the chlorine atom and a positive charge on the sodium atom. When added to water, the two ions are pulled apart and become surrounded by water molecules and therefore dissolve in water. Once the water evaporates, the two ions join together and precipitate, forming salt crystals.

4) IONIC BOND

A CHEMICAL REACTION Chemical reactions are the breaking and forming of chemical bonds. Two molecules of hydrogen gas and one molecule of oxygen can react to form two molecules of water. In this reaction, the numbers of each type of atom are conserved, but their arrangement is different.

2.3 WATER: THE MEDIUM OF LIFE Water is the medium of life. When looking for life on other planets in the 1990s, NASA s strategy was to look for water. Water naturally exists in three physical states of matter: solid, liquid, and gas. All life depends on water. What makes water so special? Its properties (functions) because of its structure.

WATER CHEMISTRY Properties 1) Polar molecule 2) Good solvent 3) ph 7 Structure

WATER CHEMISTRY We saw earlier that water is a polar molecule with a partial positive charge at the hydrogens and a partial negative charge at the oxygen. Water is a versatile solvent due to its polarity, Solvent a dissolving agent of a solution Solute a substance that is dissolved Aqueous solution is one in which water is a solvent Molecules are classified based on how they react with water: hydrophilic if they are water-loving and hydrophobic if they are not.

WATER CHEMISTRY The ph of a solution measures the proton concentration by the following formula ph = log [H + ] In an acidic solution, [H + ] is greater than [OH - ], and ph < 7 An acid releases [H + ] In a neutral solution, [H + ] = [OH - ] =10-7 M In a basic solution, [H + ] is less than [OH - ], and ph > 7 A base releases [OH - ]

WATER CHEMISTRY For a neutral aqueous solution, [H + ] is 10 7 = [OH ] 10 7 [H + ] [OH ] = 10 14 ph = ( 7) = 7 ph of solutions can range from 0 to 14, Pure water has a ph of 7, which is also the ph of most of our cells.

HYDROGEN BONDING IN WATER (LIQUID AND SOLID) Water is characterized by extensive hydrogen bonding. When water freezes, it expands and becomes less dense. This is unusual because most solids are typically more dense than their liquid counterparts. The water molecules when frozen form a highly ordered, open, and hexagonal structure. As a result, it floats. Water is able to resist temperature change more than other substances because in order for its temperature to increase, hydrogen bonds must first break. This property is important for living organisms because water resists temperature variations that would otherwise result from the numerous biochemical reactions taking place within them.

HYDROGEN BONDING IN WATER (LIQUID AND SOLID) Collectively, hydrogen bonds hold water molecules together, a phenomenon called cohesion Cohesion helps the transport of water against gravity in plants Cohesion also results in Surface tension, which is a measure of the difficulty of breaking the surface of a liquid. Adhesion is an attraction between different substances, for example, between water and plant cell walls

HYDROGEN BONDING IN WATER (LIQUID AND SOLID)

CARBON: LIFE S CHEMICAL BACKBONE Human cells consists of mostly water, but after the removal of water, the cell s dry mass is represented in this graph. The four major elements are carbon, oxygen, hydrogen, and nitrogen, making up 94% of the dry mass. Carbon is 47% of that dry mass and is unique because it has the ability to combine with a wide variety of molecules. Molecules that contain carbon are called organic molecules.

CARBON & COVALENT BONDS A carbon atom behaves as if it has four unpaired electrons, forming a tetrahedron. In methane, each of the four valence electrons of carbon shares a new molecular orbital with the electron of one of the hydrogen atoms forming four covalent bonds. Each of these bonds can rotate freely about its axis. All of these bonding properties of carbon contribute importantly to the structural diversity of carbon-based molecules.

DIVERSITY IN CARBON-CONTAINING MOLECULES Carbon atoms can also link with one another to form long chains that can be branched or form a ring structure. (a)two carbon atoms have connected by a covalent bond. (b) Multiple carbons have joined to form a chain or a ring structure.

CARBON DOUBLE BONDS Adjacent carbons can also share two pairs of electrons, forming a double bond between them. The double bond is shorter than a single bond and is not free to rotate, so two carbon atoms connected by a double bond are in the same plane. Double bonds can be found in chains and ring structures as well.

ISOMERS Are molecules with same molecular formula but different structures and hence different properties (functions) Butane (C 4 H 10 ) vs Isobutane (C 4 H 10 ) Three types of isomers are: a)structural b) Geometric c) Enantiomers

ISOMERS The arrangement of atoms is also important. Two molecules with the same chemical formula may arrange differently to produce different structures and, in turn, molecules with different functions, making carbon very diverse.

CARBON-BASED MOLECULES AND THEIR BUILDING BLOCKS 1. Proteins (amino acids) 2. Nucleic acids (nucleotides) 3. Carbohydrates (sugars) 4. Lipids (fatty acids) Cellular processes depend on a few classes of carbon-based molecules: proteins, nucleic acids, carbohydrates, and lipids.

AMINO ACID The general structure of an amino acid: A central carbon atom (alpha carbon) covalently linked to four groups: -Carboxyl (COOH) -Amino (HN 2 ) -Hydrogen (H) -R group (side chain) The R group is what distinguishes one amino acid from another.

PROTEIN When amino acids are linked together in a chain, they form a protein. The carbon of the carboxyl group of one amino acid is linked to the nitrogen in the adjacent amino acid by a covalent peptide bond. The carbon atom releases an oxygen atom, and the nitrogen is losing two hydrogen atoms to form a molecule of water.

NUCLEOTIDES Nucleotides are composed of three components: 1.A 5-carbon sugar (ribose or deoxyribose) 2.A base containing nitrogen 3.And one or more phosphate groups Note that the sugars only differ by the OH group or H group at the 2 carbon.

THE BASES IN NUCLEIC ACIDS The bases in nucleic acids are a) single-ring pyrimidines (T, C, U) b) double-ring purines (A, G).

THE BOND IN THE NUCLEIC ACIDS Adjacent pairs of nucleotides are joined together by phosphodiester bonds. The phosphate group of one nucleotide is joined to the sugar unit in another nucleotide. The formation of this bond also results in the loss of a water molecule.

STRUCTURE OF DNA DNA consists of two strands of nucleotides twisted around each other in the form of a double helix. The sugar phosphate backbones wrap around the outside and the bases form complementary basepairing A-T, G-C. The base pairing in the middle results from hydrogen bonding between the bases.

CARBOHYDRATES (C 6 H 12 O 6 ) Carbohydrates are composed of C, H, and O. The simplest carbohydrates are saccharides and can be linear or cyclic and contain five or six carbons. Sugars containing an aldehyde group are aldose sugars, and those containing a ketone group are called a ketose sugars. The three sugars here each have 6 carbons, 12 hydrogens, and 6 oxygens but differ in their arrangements of the atoms. They are isomers.

NAMING SUGARS Monosaccharides One sugar Disaccharides Two sugars linked together Polysaccharides Many sugars linked together Complex carbohydrates Long, branched chains of monosaccharides

CYCLIC MONOSACCHARIDES Virtually all monosaccharides in cells are in ring form. To form a ring, the carbon in the aldehyde of a ketone group forms a covalent bond with the oxygen of the hydroxyl group carried by another carbon in the same molecule.

GLYCOSIDIC BONDS Monosaccharides are attached to one another by covalent bonds called glycosidic bonds. Again, the formation of these bonds involves the loss of a water molecule.

LIPIDS Lipids are defined by a property all are hydrophobic. Fatty Acids Phospholipids They share a property and not a structure. Lipids are a diverse group of chemicals; Steroids 1) Fats 2) Steroids 3) Phospholipids

LIPIDS 1) Fats are composed of a glycerol backbone attached to three fattyacids (long chains of carbons). 2) Steroids, like cholesterol here, are composed of many carbon atoms bonded to form rings. 3) Phospholipids are composed of a glycerol backbone, two fatty-acid chains, and a phosphate-containing head group.

1) TRIGLYCEROLS(FATS) Triacylglycerols (fats) are lipids used for energy storage. They can contain different types of fatty acid, but all are hydrophobic and form oil droplets inside the cell. By excluding water molecules, a large number can be packed into a small volume, making triacylglycerol a very efficient form of energy storage.

SATURATED VS. UNSATURATED Fatty acids are hydrocarbon attached to carboxyl group. Fatty acids that do not contain double bonds are saturated saturated with hydrogen atoms. Fatty acids with carbon-carbon double bonds are unsaturated.

VAN der WAALS FORCES Hydrocarbon chains of fatty acids contain no polar covalent bonds, and are uncharged. The constant motion of electrons leads to regions of slight charges, and these charges are attracted to or repelled by neighboring molecules. These forces are weaker than hydrogen bonds, but many act together to stabilize molecules. Length of hydrocarbon chains increases these forces. Kinks caused by unsaturated (double-bonded) carbons reduce tightness, causing a lower melting point.

2) STEROIDS Steroids like cholesterol are a component of animal cell membrane. They are composed of 20 carbon atoms bonded to form four fused rings and are hydrophobic. Cholesterol is the precursor for the synthesis of steroid hormones such as estrogen and testosterone.

HYDROPHOBIC HYDROPHILI C 3) PHOSPHOLIPIDS Polar head group Choline Phosphate Phospholipids are a major component of the cell membrane. Consist of: 1 Glycerol 2 Fatty acids and 1 Phosphate Fatty acid chains Glycerol backbone Thus, they have hydrophobic and hydrophilic groups in the same molecule.

COULD THESE BUILDING BLOCKS HAVE BEEN GENERATED ON EARLY EARTH? In 1953, Stanley Miller performed an experiment using gases thought to be present in early earth (water vapor, methane, ammonia, and hydrogen gas). He built an apparatus that would simulate early Earth and used a spark to simulate lightning within the apparatus. This caused a red substance to develop within the walls of the flask, and upon analysis of the substance, there were about 20 different amino acids present.

HOW DID BUILDING BLOCKS FORM MACROMOLECULES? Clay minerals that form from volcanic rocks can bind nucleotides on their surfaces. The clays provide a surface that places nucleotides in proximity to one another, making it possible for them to join to form chains or simple strands of nucleic acid. In an experiment, Leslie Orgel placed a short nucleic-acid sequence into a reaction vessel and then added individual chemically modified nucleotides. The nucleotides spontaneously joined into a polymer, forming the sequence complementary to the nucleic acid already present. This experiment showed that nucleic acids can be synthesized experimentally from nucleotide building blocks.