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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)
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…
All matter is made of particles (air, plants, your pen, you… etc…)
Back to the basics…
All matter is made of particles A particle could be:
Atoms (made of protons, neutrons, and electrons)
Back to the basics…
All matter is made of particles A particle could be:
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…
All matter is made of particles A particle could be:
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
What IS ‘bonding’? It’s all about electrons!
Atoms want ‘full outer shells of electrons’ to be stable
Types of Bonding
What IS ‘bonding’? It’s all about electrons!
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
What IS ‘bonding’? It’s all about electrons!
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 COVALENT BOND
Types of Bonding
What IS ‘bonding’? It’s all about electrons!
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
What IS ‘bonding’? It’s all about electrons!
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 IONIC BOND
Types of Bonding
What IS ‘bonding’? It’s all about electrons!
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
What IS ‘bonding’? It’s all about electrons!
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
What IS ‘bonding’? It’s all about electrons!
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
What IS ‘bonding’? It’s all about electrons!
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
What IS ‘bonding’? It’s all about electrons!
HYDROGEN BONDS It is the hydrogen bonding between polar water
molecules that gives water its special properties
Types of Bonding
What IS ‘bonding’? It’s all about electrons!
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
What IS ‘bonding’? It’s all about electrons! Let’s recap:
COVALENT BONDS: intramolecular, strong IONIC BONDS: intermolecular HYDROGEN BONDS: intermolecular, relatively weak
Polar vs Nonpolar
Polar vs Nonpolar
Polar molecules 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 do not have one end more charged than the other
(and neutral overall)
Polar vs Nonpolar
Polar molecules do not mix with nonpolar molecules (ex: water and oil)
Polar vs Nonpolar
Polar molecules do not mix with nonpolar molecules (ex: water and oil) Polar and ionic substances are known as
hydrophilic (water loving) Nonpolar substances are known as hydrophobic
(water fearing)
Polar vs Nonpolar
Hydrophobic and hydrophilic interactions are important: in the cell membrane phospholipid bilayer
Polar vs Nonpolar
Hydrophobic and hydrophilic interactions are important In the tertiary structure of proteins
Water and the Fitness of the Environment (Ch 3)
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 pH scale. The importance of buffers in biological
systems.
Bryson p. 270-272
The importance of hydrogen bonds to the properties of water.
Polar!
Four unique properties of water and how each contributes to life on Earth.
Cohesion Adhesion Transpiration
TemperatureRegulator Ex: sweat
Insulation By ice
Solvent
Four unique properties of water and how each contributes to life on Earth.
How to interpret the pH scale
The importance of buffers in biological systems.
Carbon and the Molecular Diversity of Life (Ch 4)
The properties of carbon that make it so important.
Carbon – The atom of Life!
What a beautiful thing!
The four electrons in the outer orbital want to form covalent bonds with electrons of
other elements
Carbon – The atom of Life!
What a beautiful thing!
Carbon needs 4 covalent bonds to ‘feel satisfied’ (to complete its electron shell)
Carbon – The atom of Life!
What a beautiful thing!
Carbon needs 4 covalent bonds to ‘feel satisfied’ (to complete its electron shell)
Carbon – The atom of Life!
What a beautiful thing!
Instead of drawing the electrons all the time, we draw sticks to represent a shared electron pair (covalent bond)
Carbon – The atom of Life!
What a beautiful thing!
Instead of drawing the electrons all the time, we draw sticks to represent a shared electron pair (covalent bond)
Carbon – The atom of Life!
What a beautiful thing!
The four covalent bonds can be arranged in singles, doubles, or triples
Carbon – The atom of Life!
What a beautiful thing!
The four covalent bonds can be arranged in singles, doubles, or triples
Carbon – The atom of Life!
What a beautiful thing!
Other important atoms: 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!
What a beautiful thing!
Other important atoms: 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!
What a beautiful thing! If arranged in single bonds, the carbon molecule
can be straight. Ex: saturated fatty acid
If arranged in double bonds, the carbon molecule must be bent. Ex: Unsaturated fatty acid
Carbon – The atom of Life!
What a beautiful thing! Functional Groups
Carbon – The atom of Life!
What a beautiful thing! Functional Groups: can you find the alcohol, and
carboxylic acids?
Carbon – The atom of Life!
What a beautiful thing! Reactions: dehydration synthesis and hydrolysis
Carbon and the Molecular Diversity of Life
The properties of carbon that make it so important. 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: Read Holtzclaw
p 38-42 Campbell
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) 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 pH can have on a protein structure, and how these changes may affect the organism.
OK, so now what questions do you have about: Carbohydrates
Monosaccharides (glucose), disacchariades (maltose), polysaccharides (glycogen, starch, cellulose)
Lipids Glycerol, fatty acids (unsaturated, saturated), neutral fats,
phospholipids, steroids Proteins
Amino acids, dipeptides, tripeptides, polypeptides, levels of structural organization (primary, secondary, tertiary, quaternary)
Nucleic Acids Nucleotides, phosphate-sugar-base,
deoxyribose, ribose, adenine, thymine, uracil, guanine, cytosine, DNA, RNA, ATP
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