1 Basic Chemistry Chapter 2 BIOL1000 Dr. Mohamad H. Termos
2 Chapter 2 Objectives Following this chapter, you should be able to describe: - Atoms, molecules, and ions - Composition and properties - Types of bonds - Molecular interactions - Organic molecules - Carbohydrates, lipids, proteins, nucleic acids
3 Humans are large collections of tissues and organ systems Organ systems are large collections of cells Cells are large collections of organelles and molecules Molecules are small to large collections of elements whose atoms are held together by chemical bonds Atoms are made up of subatomic particles: an atomic nucleus with neutrons and protons and a surrounding cloud of electrons.
4 Introduction and Generalities The body is made up of atoms, ions, and molecules. Carbohydrates, proteins, lipids and nucleic acids are large molecules. What is an element? It is a simple form of matter, a substance that cannot be broken down into two or more different substances Matter: anything that has a mass and occupies space Compound: formed by atoms of 2 or more elements.
5 Atoms The atom is a unit of matter that forms all chemical substances. Atoms are made up from 3 subatomic particles: - Proton: positively charged, inside nucleus, has mass - Neutron: no charge, inside nucleus, has mass - Electron: negatively charged, orbits nucleus, no mass
6 Atoms Atomic number - The number of protons in the atom. - Every element has a different number of protons. - We can identify atoms by this number Atomic weight - It is equal to number of protons + the number of neutrons.
7 The major elements found in the body are circled
8 Atomic composition of the Body Major elements in the human body: - Carbon, Oxygen, Hydrogen, Nitrogen (accounts for 99.3% of total atoms) Essential mineral elements of human body: - Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, Magnesium (accounts for 0.7%)
9 Atomic composition of Body Trace Elements: - 13 trace elements - Essential for normal growth and function - Accounts for less than 0.01%
10 Molecule - 2 or more atoms bonded together - Bonds can be ionic, covalent, and metallic bonds. - Most common type of bond is covalent bond - Orientation of bonds determines molecular shape which, in turn determines function Molecules
11 Here, we can see a methane molecule. Notice how each of the 4 hydrogen atoms is covalently bonded ( sharing electrons with) to a carbon atom.
12 Here you can see the molecular structures of various molecules.
13 Ions - An ion is an atom which has gained or lost electrons - Ions are charged atoms - Cations: are positively charged ions, where atoms have lost electrons, example: Na + - Anions: are negatively charged ions, where atoms have gained electrons, example: Cl -
14 Ions Some common ions encountered in the body are included in this table
15 isotopes Contains the same number of protons but different number of neutrons. Examples:
16 Chemical Bonds Interactions between atoms: - Chemical interaction: interaction between 2 or more atoms that occurs as a result of activity between electrons in their outermost shells
17 Ionic Bond Formed by transfer of electrons Example: NaCl Na atom: 11 protons and 11 electrons. Loses an electron 11 protons, 10 electrons = positive charge Cl atom: 17 protons and 17 electrons. Gains an electron 17 protons, 18 electrons = negative charge.
19 Covalent bond Formed by sharing of one or more pairs of electrons between atoms. Examples: CO 2, H 2 O - Polar covalent bond: unequal sharing of electrons; example: water (H 2 O). Relative positive and negative charges in molecule. - Non-polar covalent bond: equal sharing of electrons; example: CO 2
20 Example of Covalent bond, formation of H 2
21 Formation of hydrogen bond between two water molecules (H 2 O)
22 Hydrogen Bonds - Most important polar covalent bond interaction - Created when two highly polar molecules align their opposing partial charges. - Because opposing charges attract each other, a hydrogen bond is created.
23 Water is the most common molecule in the body, and contains hydrogen bonds: in each water molecule, the shared electrons spend more time close to the larger oxygen atom, making that area slightly negative compared to the area near the hydrogen atoms.
24 Water is the universal solvent. Yet not everything can dissolve in water though. Solubility is determined by molecular properties: - hydrophilic: molecules with polar groups that readily dissolve in water (COOH/NH2/OH) - Hydrophobic: electrically neutral bonds are not attracted to water, thus insoluble (C-H) - Amphipathic: molecules that have polar region at one end and non-polar at other.
25 Properties of Water Water molecules are cohesive and adhesive. Cohesion is the ability of water molecules to cling to each other due to hydrogen bonding. Adhesion is the ability of water molecules to cling to other polar surfaces. Adhesion is due to water s polarity. Cohesion and adhesion account for water transport in plants as well as transport in blood vessels. 25
26 Properties of Water Ice is less dense than liquid water. At temperatures below 4 C, hydrogen bonds between water molecules become more rigid but also more open. Water expands as it reaches 0 C and freezes. Ice floats on liquid water. Acts as an insulator on top of a frozen body of water 26
27 Chemical reactions - Synthesis reaction: formation of a new chemical bond: A+B AB. This is also called dehydration reaction or anabolic reaction. - Decomposition reaction: breaking of a chemical bond: AB A+B. This is also called hydrolysis reaction or catabolic reaction. - Exchange reaction: AB +CD AD +CB
28 - Organic compounds: contain carbon to carbon bond or carbon to hydrogen bond. Example: carbohydrates, proteins, lipids, and nucleic acids. - Inorganic compounds: do not contain Carbon to carbon or carbon to hydrogen bond. Example: water, oxygen, carbon dioxide, electrolytes
29 Electrolytes - Acid: a molecule that releases H+ in solution, thereby increasing acidity. Example: HCl and acetic acid - Base: a substance that accepts H+ ions, thereby decreasing the acidity of a solution. Examples: NaOH, NH3. - Acidity is measured in units of ph (quantitative method), and by litmus paper that changes color according to the degree of acidity or alkalinity (qualitative method). - Buffer: is a substance that can be added to a solution to prevent drastic change in ph - Salt: is a compound that results from any chemical interaction of an acid and a base (i.e. neutralization reaction).
30 NeutralpH Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. pure water, tears H Acidic 14 Basic OH 30
32 Carbohydrates - Provide cells with energy - 1% of body weight - Composed of C,H,O in a ratio of C n H 2n O n - OH groups make carbohydrates water soluble.
33 Carbohydrates - Monosaccharide: One 6-carbon sugar molecule. Example: glucose (most useful), galactose, and fructose (in fruits) - Disaccharide: Two monos linked together. Example: sucrose (table sugar). - Polysaccharide: Many saccharide molecules linked together. Example: Glycogen (in meat), cellulose (in plant cell walls), and starch (in vegetables and grains).
34 Lipids - Nonpolar, hydrophobic (water-insoluble) compounds. - ~15% of body weight - Composed of C, H and O - Energy source - Structural role - Form integral parts of cell membranes
35 Lipids Subclasses of lipids: 1- Fatty acids 2- Triglycerides (most abundant) 3- Phospholipids (hydrophilic, hydrophobic, lipid bi-layer) 4- Steroids (involved in many structural and functional roles)
36 Proteins - Composed of C,H,N,O - Account for ~17% of body weight - Are large macromolecules with amino acid subunits - 20 different amino acids linked by peptide bonds. - Structural conformation determines functional properties
37 Levels of Protein Structure - Primary structure - Secondary structure - Tertiary structure - Quaternary structure
38 Primary protein structure is determined by the amino acid sequence.
39 Secondary and tertiary structures - Make up the 3D shape of molecule
40 Quaternary structure - Different protein chains bind together and act as one functional unit - To the right is a 3D cartoon of hemoglobin.
41 Nucleic Acids - store, express, and transmit genetic information - ~2% of body weight - Classes: 1- DNA (Deoxyribonucleic acid): stores genetic information 2- RNA (Ribonucleic acid): plays role in protein synthesis
42 Nucleic Acids - Long polymers of nucleotides - Nucleotides have 3 parts: 1- Phosphate group, 2- Sugar, 3- Base
43 Nucleic acids are hooked together between the sugar and the phosphate group, creating a sugar-phosphate backbone.
44 Comparison between DNA and RNA
45 Metabolism All the chemical reactions that occur in body cells Catabolism: - Releases energy - Breaks down molecules Anabolism - Requires energy - Builds up molecules Adenosine triphosphate (ATP) - Ribose: a pentose sugar - Adenine - 3 phosphate subunits
46 Chapter 2 conclusions In this lecture, we have learned about the smallest units, the atoms, and linked them up into large biological molecules. These biological molecules include lipids, carbohydrates, proteins, and nucleic acids. These biological molecules are the basis for all kind of life, and we will revisit these molecules often in future lectures.
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