Biochemistry Notes
Based on Campbell Biology
Topics: Chemical Context of Life | Water | Carbon | Macromolecules | Cell Structure | Endomembrane
System | Cytoskeleton | Cell Junctions | Membrane Structure and Transport
,1. Chemical Context of Life
1.1 Matter and Atoms
• Chemical: cannot be broken down chemically
• Atoms: smallest particles of an element
◦ Proton: positive charge, in nucleus
◦ Neutron: neutral, in nucleus
◦ Electron: negative charge, orbits nucleus
1.2 Organic Compounds in Life
• Organic compounds are carbon-based
• Major elements (96%): Carbon, Hydrogen, Oxygen, Nitrogen
• Trace elements (4%): Phosphorus, Sulfur, Calcium, Potassium, Sodium, Magnesium,
Chlorine
• Trace elements: found in small amounts, required only in tiny amounts
1.3 Carbon: The Backbone of Life
• Carbon can form 4 bonds, making very large and diverse molecules
• Carbon is the backbone of all organic molecules
• Isomers: molecules with the same molecular formula but different structures
◦ Structural isomers: differ in arrangement of atoms
◦ Isotopes: same element, different number of neutrons, used to trace atoms during
reactions
• Energy: ability to do work
◦ Potential energy: stored energy (e.g., food)
◦ Kinetic energy: energy of motion
1.4 Functional Groups
• Properties of a molecule depend on the groups attached to it
• Key functional groups that allow function and reaction:
◦ Hydroxyl (-OH): polar, forms hydrogen bonds
◦ Carbonyl (C=O): found in sugars and ketones
◦ Carboxyl (-COOH): acidic, donates H+
◦ Amino (-NH2): basic, accepts H+
◦ Sulfhydryl (-SH): forms disulfide bonds in proteins
◦ Phosphate (-OPO3): found in ATP and nucleic acids
◦ Methyl (-CH3): nonpolar, affects gene expression
1.5 Chemical Bonds
• Bonds determine shape, function, and properties of molecules
, • Covalent bonds: sharing of electrons
◦ Nonpolar covalent: equal sharing (e.g., H2)
◦ Polar covalent: unequal sharing due to electronegativity differences (e.g., H2O)
• Ionic bonds: complete loss or gain of electrons (e.g., NaCl)
◦ Ionic compounds dissolve in H2O
• Hydrogen bonds: attraction between partially positive H and electronegative atom (O,
N, F)
◦ Individually weak but collectively strong
◦ Important in water and DNA structure
1.6 VSEPR Shapes and Polarity
• Molecular shape determines function
• Dipole 1: linear (e.g., CO2)
• Dipole 2: bent (e.g., H2O)
• Polar molecules like water dissolve other polar molecules (like dissolves like)
• Nonpolar molecules do NOT dissolve in water
1.7 Intermolecular Forces
• Van der Waals forces: weak attractions between temporary dipoles
• London Dispersion Forces (LDF): attraction of temporarily unequal charge distribution
in any molecule
• Dipole-Dipole forces: hold polar molecules together
1.8 Chemical Reactions
• Breaking and forming bonds releases or absorbs energy
• Exothermic: releases energy, spontaneous (e.g., cellular respiration)
• Endothermic: absorbs energy, not spontaneous on its own (e.g., photosynthesis)
1.9 Electron Arrangements
• Electrons determine reactivity
• Full outer shell (octet/duet) = stable
• All elements in living organisms can participate in chemical bonds
1.10 Density
• Ice is less dense than liquid water (at 0 degrees C)
• Water expands when it freezes due to hydrogen bonding
• Does not apply above 4 degrees C
• Ice floating insulates aquatic environments below
◦ Keeps things from freezing solid, enabling aquatic life
,2. Water and Life
2.1 Properties of Water
Water makes up 70% of most living cells. Its properties are essential for life.
• Cohesion: attraction between water molecules via hydrogen bonds
◦ Creates surface tension
◦ Allows water to travel up plant stems (capillary action)
• Adhesion: attraction between water and other polar molecules
◦ Helps water climb cell walls in plants
• High Specific Heat: water resists temperature changes
◦ Takes a lot of heat to raise or lower water temperature by 1 degree C
◦ Stabilizes temperatures in organisms and climate
• Heat of Vaporization: large amount of heat needed to convert liquid water to gas
◦ Helps regulate temperature (evaporative cooling)
◦ Sweating cools the body
• Evaporative Cooling: fastest-moving molecules evaporate, cooling the surface
◦ Blood flow to skin allows heat loss through evaporation
2.2 Hydrophilic vs Hydrophobic
• Hydrophilic: charged or polar, dissolves in water
• Hydrophobic: nonpolar, does not dissolve in water
2.3 Solutions and Mixtures
• Solution: homogeneous liquid of 2 or more substances
• Solute: substance dissolved
• Solvent: substance doing the dissolving (water is universal solvent)
• For something to dissolve in water, it must have polarity or charge
2.4 pH and Buffers
• pH scale: 0-14, measures hydrogen ion (H+) concentration
• Pure water: pH 7 (neutral) -- [H+] = [OH-]
• Acids: increase H+ concentration (pH below 7)
• Bases: decrease H+ concentration (pH above 7)
• Buffers: resist changes in pH
◦ Donate or accept H+ to maintain pH
◦ Example: carbonic acid/bicarbonate buffer in blood
◦ H2CO3 is a weak acid that donates or accepts H+
,2.5 Water Transport in Plants
• Water enters roots by osmosis
• Adhesion to cell walls and cohesion to other water molecules pulls water up
• Transpiration from leaves creates negative pressure that draws water upward
◦ Roots absorb water from the ground
◦ Water moves through xylem vessels
◦ Stomata on leaves allow gas exchange and evaporation
◦ Evaporation pulls more water up from roots
2.6 Thermal Properties
• Water buffers temperature changes in organisms and climate
• High specific heat: 1 cal per gram per degree C
• Bodies of water (oceans, lakes) moderate climate nearby
, 3. Carbon and Molecular Diversity
3.1 The Backbone of Life
• Major elements: Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur
• Photosynthesis: CO2 + H2O becomes C6H12O6 (glucose)
• Carbon makes very large, diverse molecules due to its 4 bonding sites
3.2 Origin of Life
• Stanley Miller experiment: showed organic molecules could have formed from inorganic
compounds
• Organic molecules could have formed in pools on early Earth
• Benefits of organic chemistry:
◦ Versatile (can form many structures)
◦ Organic molecules could have arisen from inorganic sources
◦ Builds macromolecules
◦ Self-replicates
3.3 Major Reactions
• Condensation (dehydration synthesis): joining monomers to form polymers, releases
water
• Hydrolysis: breaking polymers into monomers, uses water
• Neutralization (Acid + Base): forms water + salt
• Redox (Oxidation-Reduction): electron transfer, common in photosynthesis and
cellular respiration
3.4 ATP (Adenosine Triphosphate)
• ATP = ADP + Pi + energy
• Energy currency of the cell
• Releases energy when phosphate bond is broken
Based on Campbell Biology
Topics: Chemical Context of Life | Water | Carbon | Macromolecules | Cell Structure | Endomembrane
System | Cytoskeleton | Cell Junctions | Membrane Structure and Transport
,1. Chemical Context of Life
1.1 Matter and Atoms
• Chemical: cannot be broken down chemically
• Atoms: smallest particles of an element
◦ Proton: positive charge, in nucleus
◦ Neutron: neutral, in nucleus
◦ Electron: negative charge, orbits nucleus
1.2 Organic Compounds in Life
• Organic compounds are carbon-based
• Major elements (96%): Carbon, Hydrogen, Oxygen, Nitrogen
• Trace elements (4%): Phosphorus, Sulfur, Calcium, Potassium, Sodium, Magnesium,
Chlorine
• Trace elements: found in small amounts, required only in tiny amounts
1.3 Carbon: The Backbone of Life
• Carbon can form 4 bonds, making very large and diverse molecules
• Carbon is the backbone of all organic molecules
• Isomers: molecules with the same molecular formula but different structures
◦ Structural isomers: differ in arrangement of atoms
◦ Isotopes: same element, different number of neutrons, used to trace atoms during
reactions
• Energy: ability to do work
◦ Potential energy: stored energy (e.g., food)
◦ Kinetic energy: energy of motion
1.4 Functional Groups
• Properties of a molecule depend on the groups attached to it
• Key functional groups that allow function and reaction:
◦ Hydroxyl (-OH): polar, forms hydrogen bonds
◦ Carbonyl (C=O): found in sugars and ketones
◦ Carboxyl (-COOH): acidic, donates H+
◦ Amino (-NH2): basic, accepts H+
◦ Sulfhydryl (-SH): forms disulfide bonds in proteins
◦ Phosphate (-OPO3): found in ATP and nucleic acids
◦ Methyl (-CH3): nonpolar, affects gene expression
1.5 Chemical Bonds
• Bonds determine shape, function, and properties of molecules
, • Covalent bonds: sharing of electrons
◦ Nonpolar covalent: equal sharing (e.g., H2)
◦ Polar covalent: unequal sharing due to electronegativity differences (e.g., H2O)
• Ionic bonds: complete loss or gain of electrons (e.g., NaCl)
◦ Ionic compounds dissolve in H2O
• Hydrogen bonds: attraction between partially positive H and electronegative atom (O,
N, F)
◦ Individually weak but collectively strong
◦ Important in water and DNA structure
1.6 VSEPR Shapes and Polarity
• Molecular shape determines function
• Dipole 1: linear (e.g., CO2)
• Dipole 2: bent (e.g., H2O)
• Polar molecules like water dissolve other polar molecules (like dissolves like)
• Nonpolar molecules do NOT dissolve in water
1.7 Intermolecular Forces
• Van der Waals forces: weak attractions between temporary dipoles
• London Dispersion Forces (LDF): attraction of temporarily unequal charge distribution
in any molecule
• Dipole-Dipole forces: hold polar molecules together
1.8 Chemical Reactions
• Breaking and forming bonds releases or absorbs energy
• Exothermic: releases energy, spontaneous (e.g., cellular respiration)
• Endothermic: absorbs energy, not spontaneous on its own (e.g., photosynthesis)
1.9 Electron Arrangements
• Electrons determine reactivity
• Full outer shell (octet/duet) = stable
• All elements in living organisms can participate in chemical bonds
1.10 Density
• Ice is less dense than liquid water (at 0 degrees C)
• Water expands when it freezes due to hydrogen bonding
• Does not apply above 4 degrees C
• Ice floating insulates aquatic environments below
◦ Keeps things from freezing solid, enabling aquatic life
,2. Water and Life
2.1 Properties of Water
Water makes up 70% of most living cells. Its properties are essential for life.
• Cohesion: attraction between water molecules via hydrogen bonds
◦ Creates surface tension
◦ Allows water to travel up plant stems (capillary action)
• Adhesion: attraction between water and other polar molecules
◦ Helps water climb cell walls in plants
• High Specific Heat: water resists temperature changes
◦ Takes a lot of heat to raise or lower water temperature by 1 degree C
◦ Stabilizes temperatures in organisms and climate
• Heat of Vaporization: large amount of heat needed to convert liquid water to gas
◦ Helps regulate temperature (evaporative cooling)
◦ Sweating cools the body
• Evaporative Cooling: fastest-moving molecules evaporate, cooling the surface
◦ Blood flow to skin allows heat loss through evaporation
2.2 Hydrophilic vs Hydrophobic
• Hydrophilic: charged or polar, dissolves in water
• Hydrophobic: nonpolar, does not dissolve in water
2.3 Solutions and Mixtures
• Solution: homogeneous liquid of 2 or more substances
• Solute: substance dissolved
• Solvent: substance doing the dissolving (water is universal solvent)
• For something to dissolve in water, it must have polarity or charge
2.4 pH and Buffers
• pH scale: 0-14, measures hydrogen ion (H+) concentration
• Pure water: pH 7 (neutral) -- [H+] = [OH-]
• Acids: increase H+ concentration (pH below 7)
• Bases: decrease H+ concentration (pH above 7)
• Buffers: resist changes in pH
◦ Donate or accept H+ to maintain pH
◦ Example: carbonic acid/bicarbonate buffer in blood
◦ H2CO3 is a weak acid that donates or accepts H+
,2.5 Water Transport in Plants
• Water enters roots by osmosis
• Adhesion to cell walls and cohesion to other water molecules pulls water up
• Transpiration from leaves creates negative pressure that draws water upward
◦ Roots absorb water from the ground
◦ Water moves through xylem vessels
◦ Stomata on leaves allow gas exchange and evaporation
◦ Evaporation pulls more water up from roots
2.6 Thermal Properties
• Water buffers temperature changes in organisms and climate
• High specific heat: 1 cal per gram per degree C
• Bodies of water (oceans, lakes) moderate climate nearby
, 3. Carbon and Molecular Diversity
3.1 The Backbone of Life
• Major elements: Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur
• Photosynthesis: CO2 + H2O becomes C6H12O6 (glucose)
• Carbon makes very large, diverse molecules due to its 4 bonding sites
3.2 Origin of Life
• Stanley Miller experiment: showed organic molecules could have formed from inorganic
compounds
• Organic molecules could have formed in pools on early Earth
• Benefits of organic chemistry:
◦ Versatile (can form many structures)
◦ Organic molecules could have arisen from inorganic sources
◦ Builds macromolecules
◦ Self-replicates
3.3 Major Reactions
• Condensation (dehydration synthesis): joining monomers to form polymers, releases
water
• Hydrolysis: breaking polymers into monomers, uses water
• Neutralization (Acid + Base): forms water + salt
• Redox (Oxidation-Reduction): electron transfer, common in photosynthesis and
cellular respiration
3.4 ATP (Adenosine Triphosphate)
• ATP = ADP + Pi + energy
• Energy currency of the cell
• Releases energy when phosphate bond is broken
