Biochemistry Concept 1 Analyzing and the chemistry of

Biochemistry Concept 1: Analyzing and the chemistry of life (Ch 2, 3, 4, 5) Let’s go back a few steps…

The Chemical Context of Life (Ch 2) l l The three subatomic particles and their significance. The types of bonds (covalent: nonpolar and polar, ionic, Hydrogen, Van der Waals interations) how they form, and their relative strengths.

Back to the basics… l All matter is made of particles (air, plants, your pen, you… etc…)

Back to the basics… l l All matter is made of particles A particle could be: l Atoms (made of protons, neutrons, and electrons)

Back to the basics… l l All matter is made of particles A particle could be: l l Atoms (made of protons, neutrons, and electrons) Ions (atoms or groups or atoms that have electrons added or taken away… charged + or -)

Back to the basics… l l All matter is made of particles A particle could be: l l l Atoms (made of protons, neutrons, and electrons) Ions (atoms or groups or atoms that have electrons added or taken away… charged + or -) Molecules (of atoms bonded together covalently)

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l Atoms want ‘full outer shells of electrons’ to be stable

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l l Atoms want ‘full outer shells of electrons’ to be stable The strongest type of bond is an intramolecular (within molecules) bond formed by a shared pair of electrons

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l l Atoms want ‘full outer shells of electrons’ to be stable The strongest type of bond is an intramolecular (between molecules) bond formed by a shared pair of electrons l COVALENT BOND

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l l Atoms want ‘full outer shells of electrons’ to be stable Another way for atoms to stabilize is by transferring electrons from one atom to another, forming ions (charged particles) and the intermolecular attraction between charged particles

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l l Atoms want ‘full outer shells of electrons’ to be stable Another way for atoms to stabilize is by transferring electrons from one atom to another, forming ions (charged particles) and the intermolecular attraction between charged particles l IONIC BOND

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l l In some molecules, the shared pair of electrons in covalent bonds are pulled to one side by a strongly positive nucleus This leaves one end of the molecule slightly negative and the other slightly positive

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l l In some molecules, the shared pair of electrons in covalent bonds are pulled to one side by a strongly positive nucleus This leaves one end of the molecule slightly negative and the other slightly positive POLAR MOLECULE Ex: WATER

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l With water, it is SO POLAR that weak intermolecular bonds form between the slightly negative end of one water molecule and the slightly positive end of another water molecule

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l l With water, it is SO POLAR that weak intermolecular bonds form between the slightly negative end of one water molecule and the slightly positive end of another water molecule HYDROGEN BONDS

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l l HYDROGEN BONDS It is the hydrogen bonding between polar water molecules that gives water its special properties

Types of Bonding l What IS ‘bonding’? l It’s all about electrons! l l HYDROGEN BONDS It is the hydrogen bonding between polar water molecules that gives water its special properties § § Solvent Temperature regulator Lubricant Involvement in chemical reactions

Types of Bonding l What IS ‘bonding’? l l It’s all about electrons! Let’s recap: l l l COVALENT BONDS: intramolecular, strong IONIC BONDS: intermolecular HYDROGEN BONDS: intermolecular, relatively weak

Polar vs Nonpolar

Polar vs Nonpolar l Polar molecules l l Do not share their covalent bonds equally and are slightly negative at one end and slightly positive at the other (though neutral overall) Nonpolar molecules l do not have one end more charged than the other (and neutral overall)

Polar vs Nonpolar l Polar molecules do not mix with nonpolar molecules (ex: water and oil)

Polar vs Nonpolar l Polar molecules do not mix with nonpolar molecules (ex: water and oil) l l Polar and ionic substances are known as hydrophilic (water loving) Nonpolar substances are known as hydrophobic (water fearing)

Polar vs Nonpolar l Hydrophobic and hydrophilic interactions are important: l in the cell membrane phospholipid bilayer

Polar vs Nonpolar l Hydrophobic and hydrophilic interactions are important l In the tertiary structure of proteins

Water and the Fitness of the Environment (Ch 3) l l The importance of hydrogen bonds to the properties of water. Four unique properties of water and how each contributes to life on Earth. How to interpret the p. H scale. The importance of buffers in biological systems.

Bryson p. 270 -272

The importance of hydrogen bonds to the properties of water. l Polar!

Four unique properties of water and how each contributes to life on Earth. l Cohesion l l l Temperature Regulator l l Ex: sweat Insulation l l Adhesion Transpiration By ice Solvent

Four unique properties of water and how each contributes to life on Earth.

How to interpret the p. H scale

The importance of buffers in biological systems.

Carbon and the Molecular Diversity of Life (Ch 4) l The properties of carbon that make it so important.

Carbon – The atom of Life! l What a beautiful thing! l The four electrons in the outer orbital want to form covalent bonds with electrons of other elements

Carbon – The atom of Life! l What a beautiful thing! l Carbon needs 4 covalent bonds to ‘feel satisfied’ (to complete its electron shell)

Carbon – The atom of Life! l What a beautiful thing! l Instead of drawing the electrons all the time, we draw sticks to represent a shared electron pair (covalent bond)

Carbon – The atom of Life! l What a beautiful thing! l The four covalent bonds can be arranged in singles, doubles, or triples

Carbon – The atom of Life! l What a beautiful thing! l Other important atoms: l l Carbon (C) : needs 4 bonds Nitrogen (N): needs 3 bonds Oxygen (O): needs 2 bonds Hydrogen (H): needs 1 bond

Carbon – The atom of Life! l What a beautiful thing! l If arranged in single bonds, the carbon molecule can be straight. l l Ex: saturated fatty acid If arranged in double bonds, the carbon molecule must be bent. l Ex: Unsaturated fatty acid

Carbon – The atom of Life! l What a beautiful thing! l Functional Groups

Carbon – The atom of Life! l What a beautiful thing! l Functional Groups: can you find the alcohol, and carboxylic acids?

Carbon – The atom of Life! l What a beautiful thing! l Reactions: dehydration synthesis and hydrolysis

Carbon and the Molecular Diversity of Life l The properties of carbon that make it so important. l l Can form, large, complex, diverse molecules, including isomers! Various functional groups allow for diverse properties

Next Class: The Structure and Function of Macromolecules To prepare: l Read Holtzclaw p 38 -42 l Campbell l Examine at figures from Chapter 5 Read “Exploring Protein Structure” Pg. 82 -83 Read “Inquiry 5. 25” p. 86

The Structure and Function of Macromolecules (Ch 5) l l l The role of dehydration synthesis in the formation of organic compounds and hydrolysis in the digestion of organic compounds. How to recognize the four biologically important organic compounds (carbohydrates, lipids, proteins, and nucleic acids) by their structural formulas. The cellular functions of all four organic compounds. The four structural levels of proteins and how changes to any level can affect the protein. How proteins reach their final shape (conformation), the denaturing impact that heat and p. H can have on a protein structure, and how these changes may affect the organism.

OK, so now what questions do you have about: l Carbohydrates l l Lipids l l Glycerol, fatty acids (unsaturated, saturated), neutral fats, phospholipids, steroids Proteins l l Monosaccharides (glucose), disacchariades (maltose), polysaccharides (glycogen, starch, cellulose) Amino acids, dipeptides, tripeptides, polypeptides, levels of structural organization (primary, secondary, tertiary, quaternary) Nucleic Acids l Nucleotides, phosphate-sugar-base, deoxyribose, adenine, thymine, uracil, guanine, cytosine, DNA, RNA, ATP