Chemistry of Life Flashcards
I. Basic Chemistry
Elements:
Four main elements in living things:
Carbon (C): Found in carbohydrates, lipids, proteins, and nucleic acids.
Hydrogen (H): Found in carbohydrates, lipids, proteins, and nucleic acids.
Oxygen (O): Found in carbohydrates, lipids, proteins, and nucleic acids.
Nitrogen (N): Found in proteins and nucleic acids.
Other important elements:
Phosphorus (P): Found in nucleic acids.
Sulfur (S): Found in proteins.
Calcium (Ca): Important for bones and muscle movement.
Sodium (Na) & Potassium (K): Important for nerve function and muscle movement.
Trace elements:
Iron (Fe): Found in hemoglobin.
Iodine (I): Found in thyroid hormones.
Basic Chemistry Terms:
Matter: Anything that has mass and takes up space.
Element: A substance that cannot be broken down into other substances by chemical reactions.
Atom: The smallest unit of matter that retains the chemical properties of an element.
Subatomic particles: Protons, neutrons, and electrons.
Atomic Mass: The total mass of an atom (protons + neutrons).
Atomic Number: The number of protons in an atom's nucleus.
Valence electrons: Electrons in the outermost shell, involved in bonding.
Isotopes:
Different number of neutrons.
Radioactive isotopes: Nucleus is unstable and decays over time, giving off particles and energy.
Uses in science:
Radiometric dating of fossils.
Radioactive tracers (e.g., PET scan).
Chemical Bonds:
Intramolecular bonds: Bonds within a molecule or compound (stronger).
Examples: Covalent, ionic.
Intermolecular bonds: Bonds between molecules (weaker).
Examples: Hydrogen bond, Van der Waals.
Types of Chemical Bonds:
Covalent bond: Two atoms share electrons.
Nonpolar: Electrons shared equally.
Polar: Electrons shared unequally.
Ionic bond: Electrons transferred from one atom to another, creating charged ions that attract each other.
Hydrogen bond: Formed when a partial positive hydrogen atom of a molecule is attracted to the partial negative atom of a second molecule (typically nitrogen or oxygen).
Van der Waals: Instantaneous dipole-dipole attraction between temporarily partial positive and partial negative atoms of nonpolar molecules due to electron movement (e.g., gecko wall walking).
The pH Scale:
pH: Measure of the hydrogen ion concentration, defined as -log[H^+] and ranges from 0-14.
[H^+] > [OH^-] = Acid
[H^+] = [OH^-] = Neutral
[H^+] < [OH^-] = Base
Acids and Bases:
Water Dissociation: H_2O \rightleftharpoons H^+ + OH^-
Pure Water: [H^+] = 10^{-7} M and [OH^-] = 10^{-7} M
Hydrogen and hydroxide ions are very reactive; when their concentrations are equal, the solution is neutral.
Acids and bases affect this balance.
pH of Living Things:
The internal pH of most living cells is close to 7.
pH of human blood: 7.4
A person cannot survive more than a few minutes if blood pH drops to 7 or rises to 7.8.
Buffers in our fluids keep our pH relatively constant (help maintain homeostasis).
pH Buffers:
Buffers: Substances that minimize changes in the concentrations of H^+ and OH^- in a solution.
Donate H^+ when [H^+] falls.
Absorb H^+ when [H^+] rises.
Blood Buffer: Carbonic Acid/Bicarbonate Buffering System
CO2 + H2O \rightleftharpoons H2CO3 \rightleftharpoons HCO_3^- + H^+
Adding H^+ shifts the reaction to the left to absorb the excess H^+.
Adding OH^- shifts the reaction to the right to replenish H^+.
II. Properties of Water
Hydrogen Bond:
A chemical bond formed when the partial positive hydrogen of a molecule is attracted to the partial negative atom of a 2nd molecule (typically N or O).
Cohesion:
The binding together of like molecules, often by hydrogen bonds (e.g. water).
Gives water high surface tension, high specific heat, and high heat of vaporization.
Surface Tension:
A measure of how difficult it is to stretch or break the surface of a liquid.
Specific Heat:
The amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1°C.
Heat: Total amount of kinetic energy of molecules.
Temperature: Intensity of heat due to avg. kinetic energy of molecules.
Water has a high specific heat (1 cal/g/°C) and therefore resists change.
Reason why climate near oceans and large lakes is often more moderate than that of the climate further inland
The high specific heat of water tends to stabilize ocean temperatures, creating a favorable environment for marine life.
Heat of Vaporization:
Quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to gaseous state.
Hydrogen bonding between water molecules leads to high heat of vaporization.
Evaporative cooling: Evaporating water from sweat or panting requires a relatively high amount of heat, so evaporation of water significantly cools the surface because the hottest molecules are evaporating.
Advantage: Terrestrial organisms pant/sweat to cool their bodies to maintain temperature.
Ice Floats:
Solid water is less dense than liquid water due to the crystalline structure that is formed by the hydrogen bonding.
Water freezes when there is not enough energy to break its hydrogen bonds.
Only the top of the lake freezes since ice doesn’t sink.
Water is most dense at 4°C.
Differences in Water Density in Spring & Fall leads to Lake Turnover:
Benefits of Water Turnover:
Brings nitrogen and phosphorus from the bottom of the lake to the surface where phytoplankton need it to grow.
Brings oxygen from the surface to the bottom of the lake, so the animals living throughout the lake can perform cell respiration to sustain life functions.
Adhesion:
The attraction between different kinds of molecules.
e.g., water molecules hydrogen bond with different polar molecules, water molecules act as a solvent and bind and dissolve ionic compounds.
Solution:
A homogeneous mixture of two or more substances.
Solvent:
The dissolving agent of a solution.
Solute:
The substance dissolved.
Aqueous Solution:
A solution where water is the solvent.
Hydrophilic:
Any substance that is attracted to water and therefore dissolves in water (i.e., ionic or polar substances).
Hydrophobic:
Any substance repelled by water (i.e., nonionic, nonpolar substances).
Why is Water Essential for Life?:
Water must be in a liquid form to allow for transport of chemicals into and out of cells. Water vapor and water ice do not have nearly the same ability to transfer substances as liquid water does.
Many proteins act as enzymes within cells and require liquid water for proper function (allows them to fold properly).
Water has an extremely large liquid range. Pure water freezes at 0°C (32°F) and boils at 100°C (212°F), permitting life to survive in climate and weather changes.
The high specific heat of water tends to stabilize ocean temperatures, creating a favorable environment for marine life.
Unlike almost all other molecules, water floats when it freezes. This insulates the water below, which remains liquid and supports life
“Universal” Solvent - dissolves many substances (ionic & polar)
Water’s properties allow for cell membranes to form from phospholipids.
Water’s high heat of vaporization allows terrestrial organisms to pant/sweat to maintain temperature
III. Diversity of Biological Molecules
Organic Chemistry:
Organic Molecules - Contains carbon, hydrogen bonds
Inorganic Molecules - Don’t contain carbon, hydrogen bonds
Organic Chemistry: The study of organic compounds; carbon compounds are the backbone of biological molecules.
Carbon:
4 valence electrons, allowing it to form 4 covalent bonds.
Chemical shorthand: Anywhere two points meet represents a carbon atom; atoms not listed on structure are assumed to be hydrogens.
Carbon Chains:
Form the skeletons of most organic molecules, varying in length and shape.
Hydrocarbon: Carbon & hydrogen only, nonpolar, hydrophobic, lots of energy released when bonds are broken (e.g., petroleum).
Isomer:
Molecules with the same molecular formula but different structures and properties; isomers will function differently.
Three types:
Structural
Geometric
Enantiomers (optical)
Structural Isomer:
Differ in the covalent arrangement of their atoms (e.g., C4H10).
Geometric Isomer:
Same covalent partnerships but differ in their spatial arrangements.
cis – substituents (anything but a H) are on the same side.
trans – substituents are on opposing sides (across from another).
Enantiomer (optical) Isomer:
Mirror images of each other; the two forms cannot be superimposed.
L (left-handed), D (right-handed).
Macromolecules:
Large molecule formed by the joining of small molecules
Monomer:
Small molecular unit that is the building block of a larger molecule
Polymer:
Long chain of small molecular units (monomers) connected together.
Building Polymers:
Dehydration Synthesis (condensation reaction): The process used to build polymers where a water molecule is removed.
Breaking Polymers:
Hydrolysis: The process used to break down a polymer where water is added.
Macromolecule Chart:
Macromolecule
Monomer
Polymer
Main Elements
Carbohydrate
monosaccharide
polysaccharide
CHO
Lipid
no true monomer unit
N/A
CHO (sometimes P)
Protein
Amino Acid (A.A.)
Polypeptide
CHON (sometimes S)
Nucleic Acid
Nucleotide
Polynucleotide
CHONP
Functional Groups:
Chemically reactive groups of atoms within an organic molecule.
IV. Carbohydrates
Carbohydrates:
Source of energy - 4 kcal/g.
C:H:O ratio = 1:2:1 (e.g., Glucose C6H{12}O_6).
Hydrophilic - dissolves in water.
Monomer Unit: monosaccharide
Polymer Unit: polysaccharide
Monosaccharide:
One sugar unit.
Three main examples: Glucose, Galactose, Fructose.
Disaccharide:
2 sugar units bonded together via dehydration synthesis.
Glycosidic Linkage (α or β): Covalent bond between 2 sugars.
Examples:
glucose + glucose → maltose + H_2O
glucose + fructose → sucrose + H_2O
glucose + galactose → lactose + H_2O
Carbohydrate Hydrolysis:
Your small intestine can only absorb monomers.
Disaccharides and Polysaccharides are broken down (hydrolyzed) into monomer units by enzymes in your digestive tract.
Examples:
Maltose → glucose & glucose (Lactase)
Sucrose → glucose & fructose (Maltase)
Lactose → glucose & galactose (Sucrase)
Polysaccharide:
Few hundred to a few thousand monomer sugar units connected in a chain by glycosidic linkages formed via dehydration synthesis.
Types: Starch, Glycogen, Cellulose, Chitin.
Polysaccharide: Starch
Energy storage in plants.
Polymer of glucose.
Two types:
Amylose:
unbranched: α-1,4 linkages
Amylopectin:
Branched form
α- 1,4 linkages & α- 1,6 linkages (branch point)
Polysaccharide: Glycogen
Short-term energy storage in animals.
Stored in skeletal muscle & liver.
Polymer of glucose.
More branched than starch.
α- 1,4 linkages & α- 1,6 linkages (branch point).
Polysaccharide: Cellulose
Structural component of plants cell walls.
Animals can’t digest it (fiber) due to lack of the enzyme cellulase.
Polymer of glucose.
Unbranched: β-1,4 linkages.
Herbivorous Animals:
Need symbiotic relationships with bacteria to breakdown cellulose since animals lack the cellulase enzyme.
Location of symbiotic microbes in digestive tracts differ based on herbivore:
Large cecum (hind-gut fermenter) e.g. rabbits, horses, etc.
Ruminant digestion (foregut fermenter) e.g. cows, goats, deer etc.
Polysaccharide: Chitin
Structural component of exoskeletons and fungal cell walls.
Contains Nitrogen.
Unbranched: β-1,4 linkages.
V. Lipids
Lipids:
Group of biological macromolecules with a major hydrocarbon component, mostly nonpolar, and therefore hydrophobic.
Functions:
Long-term energy storage (9 kcal/gram).
Structural component of cell membrane.
Some act as hormones (Cortisol, testosterone, Estrogen).
Three main families of lipids:
Steroids
Fats (Triglycerides)
Phospholipids
Steroids:
Typically have a core structure of four fused carbon rings.
Examples: Cholesterol, many hormones, and vitamins.
Lipoproteins:
carries cholesterol & other lipids through the bloodstream
consists of a phospholipid shell with the fatty acid tails facing inside and the phosphate head groups on the outside.
*The protein component determines the role of the lipoprotein
*Two major kinds of lipoproteins carries lipids throughout your bloodstream: - High density lipoproteins (HDL) - Low density lipoproteins (LDL)
Cholesterol Transport:
LDL cholesterol is sometimes called bad cholesterol.
Transports cholesterol from the liver to tissues that incorporate it into cell membranes.
High LDL cholesterol leads to a buildup of cholesterol in arteries, increasing your chance of getting heart disease.
HDL cholesterol is sometimes called good cholesterol.
HDL carries cholesterol from other parts of your body back to your liver. The liver removes the cholesterol from your body.
The higher your HDL cholesterol level, the lower your chance of getting heart disease
Fats and Fatty Acids:
Function: Long term energy storage (9 kcal/gram).
A fat, also known as a triglyceride, is a glycerol linked to three fatty acids.
Fatty acids can be either saturated or unsaturated.
Saturated and Unsaturated Fatty Acids:
Saturated fats:
No double bonds in the hydrocarbon chain are “saturated” with hydrogens and are very linear.
e.g., animal fats (solid).
Unsaturated fats:
Fats that have a double bond are called unsaturated and have “bends” in the hydrocarbon chain.
e.g., plant oils (liquid).
Unsaturated fats can be either monounsaturated (as shown) or polyunsaturated (more than one double bond).
Unsaturated fats are generally healthier than saturated fats.
Unsaturated fats raise HDL and lower LDL levels.
Saturated fats raise both.
Trans Fats:
Come from adding hydrogen to vegetable oil (unsaturated fats) through a process called partial hydrogenation.
Foods with less than 0.5 grams of trans fat per serving can label the food as trans fat free.
Trans fats are more solid than oils. Solid at room temperature but will melt in the mouth.
Trans fats increase the shelf life of foods.
Increase your