Atoms, Molecules, and Chemistry

What are atoms?

1. Atoms are the fundamental units of matter.

2. They are composed of smaller parts:

a. Nucleus

i. Protons (positively charged)

ii. Neutrons (have no charge)

b. Electrons

The different components of atoms determine the type and “behavior” ofthe elements…

Atoms, Molecules, and Chemistry

Atoms, Molecules, and Chemistry

Atoms, Molecules, and Chemistry

What are molecules?

The smallest unit of a substance made up of two or more atoms bound to each other.

Molecules can form by both ionic as well as covalent bonds…

Atoms, Molecules, and Chemistry

In case of ionic bonds, atoms first eitherloose or gain an electron, and becomeeither positively or negatively charged.

Note that only certain types of atoms can dothis. The ability of an atom to becomepositively or negatively charged (i.e. becomean ion), as well as the level of the charge,depends on the characteristics of the atoms,particularly the number of electrons on theirouter shells…

Once ions are formed, positive and negativecharges attract, creating individual molecules.

In case of molecules formed by ionic bonds,many of these molecules can also come together to form more organized crystal structures / salts…

Ionic Bonds:

Atoms, Molecules, and Chemistry

Covalent Bonds:In case of covalent bonds, atoms share electronson their outermost shells/orbits. This creates a physically more stable condition.

Again, the ability to form covalent bonds, the numberof the bonds, etc., depends on various characteristicsof the atoms.

Remember that covalent bonds are very strong…

Atoms, Molecules, and ChemistryWater is a very special molecule, important to all biological systems.

Water is a polar molecule (part of the molecule is slightly positively chargedand the other side is slightly negativelycharged.

This polarity allows for formationof weak bonds between water (andother charged) molecules… these bonds are referred to as hydrogen bonds.

The polarity and ability to formhydrogen bonds gives water somevery special characteristics, many of which are essential for maintaininglife on earth as we know it…

Atoms, Molecules, and ChemistryWater…

Water can be a great solvent for both salts and certain biological molecules…How do you think this works?

Water as solvent of salts Water as solvent for organic molecules

Atoms, Molecules, and ChemistryWater…

The hydrogen bonds formed by water molecules also give water a certain “stickiness” (very scientific eh?)… we therefore say that water has high cohesion.Cohesion on the surface of the water creates surface tension (resistance to being broken).

These characteristics allow water to be carried to the top of trees, or for some organismsto float, swim, or “walk” on water.

Atoms, Molecules, and ChemistryWater…

The hydrogen bonding also allows for water to remain liquid on earth…

Without hydrogen bonding, water (molecular weight 18), would freeze at-100 degrees C, and would boil at –80 degrees C (instead of 0 and 100 degrees).

A similar molecule (methane, molecular weight 16) freezes at –183 degrees C, Boils at –162 degrees C.

This simple characteristic allows for life on earth as we know it!!

A lot more to water… take marine bio and we’ll talk more about it there!!!

Biological Molecules

Typically, we think of biological molecules as carbon based, organic molecules.

Carbon is very important, as it can form single, double, or triple covalent bondswith a number of other atoms, creating large, complex, yet stable structures.

In Biology 3, we will discuss four major groups of biological molecules:

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic acids

Biological MoleculesCarbohydrates

Carbohydrates – small, water-soluble sugars, capable of making chains of sugar molecules. Can form monosaccharides, disaccharides, or polysaccharides.

Generally take on the approximate molecular formula: (CH2O)n

Note however that there are exceptions to this…

Function: 1. Energy source / storage(remember that biological bonds have energy that organisms can break down and use)

2. Structural

(this is particularly the case in plants)

Biological MoleculesCarbohydrates

Two sugar molecules can bond to each other by a dehydration process, thus creating a disaccharide… glucose and fructose for example can join each otherAnd form sucrose…

Biological MoleculesCarbohydrates

Larger number of sugar molecules can join each other to form large polysaccharides such as starch….

Biological MoleculesCarbohydrates

Carbohydrates can be very important at the structural level… particularly in case of plants.

Biological MoleculesLipids

2 major characteristics of lipids:

1. Lipids have large region of just hydrogen and carbon (no oxygen)

2. They are very hydrophobic and insoluble in water (because of 1)

Major functions of lipids:

1. Energy storage

2. Water-proofing

3. Cellular membranes

4. hormones

Biological MoleculesLipids

Different types of Lipids:

1. Oils, fats, and waxesJust contain C, H, O and are very hydrophobic

2. Phospholipids*like oils, but also contain phosphorous and nitrogen…*very important in forming cellular membranes…

*have hydrophilic and hydrophobic parts…

3. Steroids form fused rings… many work as hormones, some are involved in regulating fluidity of cellular membranes…

Biological MoleculesProteins

Proteins are made up of chains of amino acids. There are 20 common amino acids, each with their own characteristics… the total number of amino acids, as well as the type of amino acids determine the protein form and function.

Some examples of amino acids:

Biological MoleculesProteins

All amino acids have a carboxyl group and an amino group. Amino acids join each Other by a dehydration process involving these two groups.

Chains of amino acids form peptides. Some of the larger peptides may functionas proteins. (i.e. all proteins are peptides, but not all peptides are proteins…)

Biological MoleculesProteins

Protein Functions:

1. Structure2. Movement3. Defense4. Storage5. Signals6. catalysts

Function is however dependent on structure!

Biological MoleculesProteins – relationship between structure and function

Primary structure –The sequence of the amino acids

Secondary structure -Formation of helixes and sheetsby the chain of amino acids

Tertiary structure – Folding of the molecule basedon hydrophobic, hydrophilic, and other interactions.

Quaternary structure –Binding and interacting of different peptide/protein units to form one functional unit

All these combine to determine the form and functionof the protein… these same characteristics may also beinvolved in regulating the protein function

Biological MoleculesNucleic Acids

Nucleic acids are made up of individual or chains of nucleotides.

Nucleotides are typically made up of 1. A five carbon sugar group (ribose or deoxyribose)2. A phosphate group3. A nitrogen containing base

Biological MoleculesNucleic Acids

Nucleic acids include: DNA and RNA, as well as intracellular messengers, energy carriers, and coenzymes

Biological MoleculesReview

Table 3-2 from text.Page 40.