Organic Molecules Biochemistry
Dec 28, 2015
Organic MoleculesBiochemistry
Organic Molecule
• Is a hydrocarbon• Carbon bonds to
hydrogen• Simplest hydrocarbon
is when 4 hydrogen atoms bond to one carbon (methane)
• CH4
A Little Less Simple• Carbon binds to other
carbon atoms• This is the uniqueness
of carbon: it can bind to itself
• Ethane is C2H6
A Little More Less Simple
• Carbon likes to form long chains
• Pentane: 5 carbons• C5H12
A Little More Complicated
• Branched chains• Isohexane• C6H14
A Lot More Complicated
• Form rings• C6H12
• Cyclohexane
Even More Complicated
• Carbon-Carbon single bonds
• Carbon-Carbon double bonds
• Carbon-Carbon triple bonds
• As you increase the number of bonds between carbons, the number of hydrogen atoms decreases
How many single vs double bonds?
• Determines saturated or unsaturated
• Have special names• Saturated has only
single bonds—every carbon is bonded singly to another carbon and hydrogen occupies every other spotThese are Alkanes
Alkenes
• Unsaturated• Contain one or more
double bonds between carbon atoms
• Not EVERY possible spot is occupied by a hydrogen
Alkynes
• Contain a triple bond• Fewer hydrogen atoms
Ethyne
Living Things
• Simple hydrocarbons not common in living organisms
• They form the building blocks of more complex organic molecules that make up living organisms
Four CategoriesBased on function
• Carbohydrates
• Lipids
• Proteins
• Nucleic Acids
All four have in common…
• Carbon backbone
• Other atoms, usually H,O,N,P,and/or S
• These atoms form functional groups, which we can recognize
• These groups replace the H that would be in a typical hydrocarbon
In common…
• all form by dehydration synthesis
• This means single units (monomers) join together; water is removed to join them
• No polymers in lipids• Enzyme catalyzed
Dehydration Synthesis
Functional groups give characteristics
• Attaching the functional groups to the carbon backbone gives the chemical characteristics of the organic molecule
• Methane gas vs. methanol liquid
Methanol
Functional groups
• Formaldehyde has a strong odor, highly reactive
• Formic Acid, only slightly different—why an acid?
Hydrocarbons
• Only have H attached to carbon backbone
• Do not break easily• Very stable
CarbohydratesSugars and Starches
#1 Energy Source (quick)
Characteristic of Carbohydrates
• A 2 to 1 ratios of Hydrogen to Oxygen
• C6H12O6
• The basic monomer (or building block) is the monosaccharide
Building Chains
• Two monosaccharides is a disaccharide
• Many is a polysaccharide
• A few is an oligosaccharide
• The simple chains are sugars
• The longer chains are starches
Starches
Sugars
• Consists of three or more C atoms with either an aldehyde or a ketone group
• And at least 2 OH groups
• Formed by dehydration synthesis
Simple Sugars
• Like to form ring formations
• Glucose, galactose, fructose all have the same molecular formula
• Different arrangements
Starch: the main polysaccharide
• Other polysaccharides include glycogen (storage in animals)
• Cellulose (plant material
• Pectin (plant material)• Starch (storage in
plants)
Lipids
Characteristics
• Do not dissolve in water
• Hydrophobic
• Greasy or oily
• Energy Storage
• Structural components (esp membranes)
• Cannot polymerize
Energy Efficient
• Number one method of energy storage
• Long term• Can store twice as
much energy as carbohydrates
• Due to high number of C-H bonds—very energy efficient
Common Types
• Triglycerides: one glycerol and three fatty acids (70 types)
• Fat is solid at room temperature (saturated)
• Oils are liquid (unsaturated)
Saturated vs Unsaturated
• Saturated: contains a H at every possible location on the fatty acids
• Unsaturated: contains one or more double bonds
Saturated
Phospholipids
• Split personality
• A glycerol and two fatty acids
• A phosphate group takes the place of the third fatty acid
• Glycerol is hydrophobic
• Phosphate is hydrophyllic
Phospholipids
Phospholipids
Sterols (Steroids)
• No fatty acid tails• All have backbone of
4 fused carbon rings with functional groups
• Hormones and cholesterol are in this group
Testosterone
Waxes
• Fatty acids linked to a long chain with alcohol
• Hydrophobic• Waterproof covering
for insects, leaves, skin on fruit
Proteins
Proteins
• Most diverse group• Many functions• Shape determines
function• Functions include:
structural, hormones, enzymes
• Monomer is the amino acid
Each amino acid has
• One carbon with 4 groups attached
• The 4 groups are: amine group NH2
• Carboxyl group COOH
• Hydrogen• R group—varies with
each amino acid
Amino Acids
• The R group is what gives each amino acid its physical and chemical properties
• It does this by shape and the fact that the R group can be polar or nonpolar; acidic or basic
Making protein chains
• The more amino acids in the chain, the more complex the protein
• The amine group from one joins to the carboxyl end of the other
• This is known as a peptide bond
Protein Structure
Proteins have a 3D shape
Four factors contribute to the shape: primary structure, secondary structure, tertiary structure, and quaternary structure
Primary Structure
• This is the amino acid sequence.
• There are 20 different amino acids
• Which ones, and in what order, determines the primary structure
Secondary Structure
• Strand folds or coils• Caused by hydrogen
bonds between non adjacent amino acids
Tertiary Structure
• Actual 3D shape• Bends and loops into a
glob as R groups react with other R groups
Quaternary Structure
• Two or more polypeptide chains have joined together by numerous weak hydrogen bonds and/or covalent bonds between R groups