• Chemical building blocks – The smallest chemical unit of matter is the atom.

• Many kinds of atoms exist – Matter composed of one kind of atom is an element.

• Each element has specific properties that distinguish it from other elements. Carbon (C), Oxygen (O) and nitrogen (N) are elements. – Atoms combine chemically in various ways. • When two or more atoms combine they form a molecule.

– N 2 , O 2 , H 2 (gases) • When two or more elements combine the molecule is called a compound.

– CO 2 , H 2 O – Living things consist of atoms of relatively few elements, principally carbon, hydrogen, oxygen, and nitrogen.

The Structure of Atoms See table 2.1: Atoms are made up of protons, neutrons, and electrons.

The atomic mass of one proton or one neutron = 1 The electrical charge of a proton is positive, an electron is negative and a neutron is neutral (no charge).

The atomic number = the number of protons and is always the same for any particular element.

Nucleus

• Atomic number = number of protons, and determines the chemical behavior of the element • Number of neutrons can vary and have no charge. ( 12 C, carbon has 6 protons and 6 neutrons.) They contribute to the stability of the nucleus – too many or too few and it may disintegrate by radioactive decay. These are isotopes. – Ex. 14 C has 6 protons and 8 neutrons and is unstable.

• Atomic weight = number of protons plus neutrons – Ex. 14 C has an atomic weight of 14

Protons and electrons are oppositely charged and are attracted to each other. Electrons are in constant , rapid motion, forming an electron cloud around the nucleus. Electrons with the least amount of energy are near the nucleus. The inner shell holds 2 electrons. Electrons with higher energy levels are in the outer shells. These hold 8 electrons.

Figure 2.5

Atoms with outer shells that are not full tend to react with other atoms. If the outer shell is almost full or almost empty they tend to gain or lose electrons, become ions, and form ionic bonds.

Positively charged ions are called cations and negatively charged ions are called anions.

almost empty almost full Fig. 2-2

Many compounds, especially carbon compounds, are held together by covalent bonds. The atoms do not give up their electrons, instead they share them. A single bond results from the sharing of one electron each – two electrons total A double bond results from the sharing of two electrons by each atom – four electrons total Notice that this sharing creates a full outer shell and makes for happy atoms.

Covalent bonds are stable and are important in molecules that form biological structures.

Fig. 2-3

Catabolic(digestive)

pathways break down large molecules into smaller ones and release

energy

. Breaks covalent bonds.

Anabolic (biosynthetic,

) pathways use

energy

to synthesize larger molecules from monomers. Makes covalent bonds.

These two pathways together =

metabolism

exergonic, release energy endergonic, require energy

Sharing in covalent bond formation can be unequal (polar). Large atoms like oxygen have large nuclei with powerful positive charges. These nuclei tend to pull the electrons so that they spend more time around the large nuclei (0), leaving the molecule with a partial negative charge in that area and a partially positive charge around the smaller nuclei (H).

These molecules are polar.

The weak attraction between these partial charges is called a hydrogen bond.

Water is a polar compound and many of it’s important qualities is due to it’s polarity and it’s ability to form hydrogen bonds between water molecules and between water and other molecules and ions.

checklist page 33 Fig. 2-4

Water is essential to life. Water has several properties that make it important to living things. Because water is a polar compound and forms hydrogen bonds.

1.

2.

3.

Water is a good solvent or dissolving medium for many polar molecules and for ions. Molecules that are polar and “like” water are called hydrophilic.

Water forms thin layers because it has a high surface tension and forms a thin film of water to cover membranes etc and keep them moist.

Water has a high specific heat, and can absorb large quantities of heat without changing temperature – this is very important to living things which are composed mostly of water.

Fig. 2-5 4. Water provides the medium for most chemical reactions and even takes part in many.

Synthesis Anabolism Endergonic Requires energy Breakdown Catabolism Energonic Releases energy

• A mixture consists of two or more substances that are combined in any proportion but are not chemically bound.

• A solution is a mixture of two or more substances in which the molecules are evenly distributed and ordinarily will not separate out upon sitting.

– The medium in which the substances are dissolved is the solvent – water in most living systems – The substance dissolved in the solvent is the solute – atoms, ions, molecules – in living cells, glucose, carbon dioxide, oxygen, ions....

• Colloids are mixtures in which the particles are too large to form true solutions. The inside of a cell (cytoplasm) is a colloidal dispersion.

An acid is a hydrogen ion donor (H+) – a proton donor. A base is a proton acceptor or an OH- donor. In solution an acid donates a proton to the solution. Water is the neutral solvent - pH7. pH is a measure of the concentration of hydrogen ions. The higher the concentration of H+, the lower the pH, the stronger the acid and the weaker the base. The lower the H+ concentration the higher the pH, the stronger the base is and the weaker the acid is. Most microbes grow best near neutral pH. Some, however, grow in extreme pH environments.

Fig. 2-7

• Organic chemistry is the study of compounds that contain carbon. The study of the chemical reactions that occur in living systems is biochemistry.

• The ability of carbon atoms to form covalent bonds and to link up in long chains makes an infinite number of possible organic compounds.

• The simplest carbon compounds are hydrocarbons, chains of carbon atoms with hydrogen atoms covalently bound

Carbon chains can have other atoms attached, often oxygen and/or nitrogen.

These often form functional groups - the part of a molecule that reacts chemically.

Fig. 2-8 In addition to these oxygen-containing functional groups, -NH 2 is found in proteins, the amino group in amino acids.

Oxidation is the removal of hydrogen (or electrons) or the addition of oxygen. Reduction is the removal of oxygen or the addition of hydrogen or electrons. Burning is oxidation. The more reduced a molecule, the more energy it has.

The Major Complex Organic Molecules That Make up a Living Cell Carbohydrates Lipids

Carbohydrates are the main source of energy for most living things. They also have several other important function. Monosaccharides like glucose are the building blocks of disaccharides and larger more complex polysaccharides (Table 2.4).

When monosaccharides have the same molecular formula but different structures they are isomers.

Fig. 2-9

Three ways of representing the glucose molecule. In solution the straight chain is rarely found. The actual three-dimensional structure is more complex than any of these representations, dependent on the angles and lengths of the covalent bonds. Fig. 2-10

Monosaccharides are important components of DNA and RNA. DNA contains deoxyribose, a reduced form of ribose which is found in RNA.

Glycerol is a component of fats. Mannitol is a sugar alcohol used in diagnostic tests for certain microbes. Some monosaccharides are broken down, oxidized, by cells for energy (glucose).

Fig. 2-11

Fig. 2-12 Disaccharides are formed when two monosaccharides are covalently bonded to each other by the removal of water and formation of a glycosidic bond.

Polysaccharides are formed when many monosaccharides are joined by glycosidic bonds. Many polysaccharides are found in the cell membrane and are important for cell-cell recognition. Starch/glycogen is an energy storage molecule for plants/animals. Cellulose is a structural component of cell walls and is not digested by animals, see box page 38.

LIPIDS Lipids include fats, phospholipds and steroids. They are insoluble in water (hydrophobic) and make up the cell membrane (phospholipids). Lipids contain more energy than carbohydrates and are used by cells for long term storage of energy (triacylglycerol).

Fig. 2-13

Fatty acids can be saturated (with hydrogen) or unsaturated (have double bonds). Single C—C bonds are flexible, leaving saturated fatty acids flexible and allowing them to move together closely. Saturated fatty acids are solid at room temperature. Double bonds are not flexible. This results in a “kink” in unsaturated fatty acids and keeps them from lying close together. Unsaturated fatty acids are liquid at room temperature.

made saturated.

Trans fatty acids are hydrogenated,

Phospholipids are found in all cell membranes. They have a polar hydrophilic head and hydrophobic non-polar tail. These properties are important in forming the cell membrane.

Fig. 2-14

Steroids have a four-ring structure and include cholesterol (found in cell membranes of animal cells and in mycoplasmas), steroid hormones (testesterone), and vitamin D.

Fig. 2-15

Proteins are composed of amino acid building blocks and are diverse in structure (shape) and function. Amino acids have an amino group and an acid group bound to a central carbon. This central carbon forms 4 single bonds. One with the amino group, one with the carboxylic acid, one with hydrogen, and the last with a variety of different chemical groups (R group).

Acid group Amino group Fig. 2-16

Each amino acid has a unique R group. Some are polar, some nonpolar, others are charged. These different functional groups give each amino acid different chemical characteristics.

A protein is a polymer of amino acids joined by

peptide bonds

- covalent bonds that link an amino group from one amino acid to a carboxylic acid group of another amino acid.

Fig. 2-17

Proteins (strings of amino acids) have several levels of structure. The primary sturcture is the string (sequence) of amino acids. Remember each amino acid has a distinct R group and therefore distinct chemical characteristics. These characteristics determine the secondary structure. Some sequences of amino acids lead to a pattern of hydrogen bonding that forms an alpha helix which coils like a telephone cord..

Fig. 2-18

Further bending and folding due to hydrogen bond and other interactions between amino acid R groups result in the unique tertiary structure of a particular protein. When this shape is irregular or “round” it is called globular. Hemoglobin is composed of 4 subunits that are globular.

1 2 3

Quaternary structure is formed by the association of several polypeptide chains. All of these structures are determined by the amino acid sequence - the sequence of R chemical groups.

Fig. 2-19

4

Like the globular type of proteins, fibrous proteins have a primary amino acid sequence that dictates a helical secondary structure. These helices form long, often very strong ropelike quaternary structures like found in keratin fibers of the skin.

Disruption of the hydrogen bonds that maintain these shapes (

denaturation

) by changes in pH (acidic or basic environments) or by changes in temperature - leads to the inability of the protein to do its job. Sterilization and disinfection to kill microbes use high temperatures and chemicals to denature the proteins that microbes need to survive. Remember, a protein’s shape is necessary for it’s function.

• Proteins have many functions in cells. Two important include maintenance of structure (structural proteins) and catalysts for the many chemical reactions that take place in the cell (enzymes). There are also proteins important in mobility, in cell-cell recognition, and cell-cell communication.

Enzymes speed up reactions up to 1000X by reducing the energy needed and holding the substrates in the necessary orientation.

The enzyme’s shape is necessary for it’s function. Denaturation inactivates enzymes.

Each enzyme is very specific for the substrate it binds and the reaction it catalyzes. Enzymes are not changed by the reaction.

Nucleotides and nucleic acids.

Nucleotides store energy needed for chemical reactions (like those of the enzymes we just talked about) in

high-energy bonds

. They also are the building blocks of nucleic acids, which store information that directs protein synthesis - DNA and RNA.

Nucleotides are made up of a nitrogenous base, a five-carbon sugar, and one or more phosphate groups.

Fig. 2-20

ATP

(adenosine triphosphate) is the immediate source of energy for most activities of living cells. Removal of the third phosphate releases energy used for chemical reactions.

Enzymes control the release of energy in these high energy bonds. This is important for cellular metabolism.

Nucleic acids consist of long polymers of nucleotides (polynucleotides) which form a backbone of alternating sugar and phosphate groups with the nitrogenous bases attached. The sequence of the different bases stores information for the building of proteins.

Fig. 2-11

Ribo

nucleic acid (RNA) contains the sugar ribose and is single stranded (except for a few viruses).

DNA (

deoxyribo

nucleic acid) contains deoxyribose and forms a ladder structure that twists into a helix. Each organism’s DNA is passed to new generations and determines all the heritable characteristsics of a living organisms..

RNA and DNA contain nitrogenous bases. RNA contains uracil instead of thymine. There are double ring purine bases and single ring pyrimidine bases. In DNA, these bases

hydrogen bond

to each other - A with T and G with C -

complimentary base pairing.

Fig. 2-22

Complimentary base pairing

is very important for the function of DNA. The sequence of nucleotides is a code that contains information that determines what proteins an organisms will make. Changing a nucleotide can change a protein’s amino acid sequence and therefore it’s shape. Changing a protein’s shape can alter it’s ability to function.

Complimentary base pairing between DNA and RNA allows RNA to transfer this code to the sites where proteins are made. See checklist on page 47 and do self quiz.