Macromolecules and Carbon

Building Blocks of Life

2007-2008

AP Biology

AP Biology

Why study Carbon?

• All of life is built on carbon.
• A molecule associated with life containing carbon.
• Cells
• ~72% H₂O
• ~25% carbon compounds
• carbohydrates
• lipids
• proteins
• nucleic acids
• ~3% salts
• Na, Cl, K…
• The major elements of life are C, H, O, N, S, and P. CHNOPS

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Carbon: Life’s Element

• Organic molecules consisting of only carbon and hydrogen.
• Carbon is unparalleled in its ability to form molecules that are large, complex, and diverse. Why?
• It has 4 valence electrons
• It can form up to 4 covalent bonds
• These can be single, double, or triple covalent bonds
• It can form large molecules
• These molecules can be chains, ring-shaped, or branched

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• Monomers: Repeating units that serve as building blocks of a polymer.

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• Polymer: A long molecule consisting of many similar of identical building blocks linked by covalent bonds. Like a train consists of a chain of train cars.

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Isomers

• Molecules with same molecular formula but different structures (shapes)
• different chemical properties
• different biological functions

6 carbons

6 carbons

6 carbons

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Bonds and Chemical Formula

C2H6

Single Bonds

C2 H4

Double covalent bonds

C2 H2

Triple Covalent bonds

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Form affects function

• Structural differences create important functional significance
• amino acid alanine
• L-alanine used in proteins
• but not D-alanine
• medicines
• L-version active
• but not D-version
• sometimes with�tragic results…

stereoisomers

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Form affects function

• Thalidomide
• prescribed to pregnant women in 50s & 60s
• reduced morning sickness, but…
• stereoisomer caused severe birth defects

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Macromolecules

• Smaller organic molecules join together to form larger molecules
• Macromolecules: Large molecules which are important in the complexity of life.
• 4 major classes of �macromolecules:
• carbohydrates
• lipids
• proteins
• nucleic acids

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Carbohydrates

• Carbohydrates include both simple sugars (glucose, fructose, galactose) and polymers such as starch made from these and other subunits.
• All carbohydrates exist in a ratio of 1 Carbon:2 Hydrogen: 1 Oxygen or CH2O
• Have 3 categories: Monosaccarides, disaccharides, and polysaccharides.
• Monosaccarides are single simple sugars such as glucose, fructose, galactose
• Disaccarides are 2 single sugars bonded together: glucose + Fructose= sucrose
• Polysaccarides include many monosaccharides bonded together=starches, cellulose.

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Monosaccharides

• The least complicated carbohydrates.
• The monomers of carbohydrates. Ex: glucose
• The three most common are glucose, galactose, fructose. Each has the same chemical formula (C₆H₁₂O₆).

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Disaccharides

-Maltose: Glucose + Glucose

-Sucrose (Table Sugar): Glucose + Fructose

-Lactose(Milk Sugar): Glucose + Galactose

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----Chemical formula for Maltose, Sucrose, and Lactose:

C₁₂H₂₂O₁₁

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Polysaccharides and Polymers

• The most complex carbohydrates which are made up of long chains of monosaccharides (glucose-like units). Starch, cellulose, and glycogen are examples. They differ because of how the subunits are bonded together.
• Two functions of Polysaccharides are energy storage and structural support.
• Energy Storage polysaccharides
• Starch is a storage polysaccharide found in plants (Example: potatoes)
• Glycogen is a storage polysaccharide found in animals, vertebrate muscle cells, and liver cells.
• Structural support polysaccharides
• Cellulose is a major component of plant cell walls
• Chitin is found in the exoskeleton of arthropods, such as lobsters and insects, and the cell walls of fungi. It gives cockroaches their “crunch”.

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Hydrolysis vs Dehydration Synthesis

• Hydrolysis occurs when water is added to split large molecules.

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• Dehydration reactions create polymers from monomers. Two monomers are joined by removing one molecule of water

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How to break down a polymer

• Digestion
• use H₂O to breakdown polymers
• reverse of dehydration synthesis
• cleave off one monomer at a time
• H₂O is split into H⁺ and OH^–
• H⁺ & OH^– attach to ends
• requires enzymes
• releases energy

Breaking up�is hard to do!

Hydrolysis

C₁₂H₂₂O₁₁ + H₂0 🡪 C₆H₁₂O₆ + C₆H₁₂O₆

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Polymers

• Long molecules built by linking repeating building blocks in a chain
• monomers
• building blocks
• repeated small units
• covalent bonds
• Polysaccharides, Proteins, Nucleic Acids

each use monomers. Lipids do NOT.

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Dehydration synthesis

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How to build a polymer

• Dehydration Synthesis
• joins monomers by “taking” H₂O out
• one monomer donates OH^–
• other monomer donates H⁺
• together these form H₂O
• requires energy & enzymes

Dehydration synthesis

Condensation reaction

You gotta� be open to�“bonding”!

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Lipids

• A group of organic compounds that include fats, oils, waxes, and related substances. Made of Carbon, hydrogen, and oxygen. There is no definite ratio of hydrogen to oxygen atoms like in carbohydrates. Simple lipids are the most common and are made up of three fatty acid molecules (C_nH2_nCOOH) and one glycerol molecule (C₃H₈O₃). They are held together with chemical bonds

(Alcohol)

C₁₆H₃₂O₂

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Saturated Fats vs Unsaturated Fats vs Trans Fats

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Hydrocarbons can grow

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Lipids are Hydrophobic.

• Fats (also called triglycerides): made of a glycerol molecule and 3 fatty acid molecules
• Fatty Acids: hydrocarbon chains of variable lengths. These chains are nonpolar and therefore hydrophobic.
• Saturated fatty acids: No double bonds between carbons, pack solidly at room temperature, produced by animals. Examples: butter and lard
• Unsaturated fatty acids: have some C=C (carbon double bonds); tend to be liquid at room temp. produced by plants. Examples: corn oil and olive oil

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Function of lipids: �

-Energy Storage. Fats store twice as many calories/gram as carbohydrates!

-Protection of vital organs and insulation. In humans and other mammals, fat is stored in adipose (fat) cells.

-Phospholipids make up cell membranes. They:

-have hydrophilic (polar) head that includes a phosphate group.

-have two fatty acid tails, which are hydrophobic.

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Steroids as an example of lipids

• Made of four rings that are fused together.
• -Cholesterol is a steroid. It is a common component of cell membranes
• -Estrogen and testosterone are steroid hormones
•  

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Proteins

• Made of amino acids bonded together. They can be very large and complex. They play a wide variety of roles in the cell.
• Some are structural, others are hormones, enzymes, or pigments.
• They are made off carbon, hydrogen, oxygen, and nitrogen; some contain sulfur. They are bonded by dehydration synthesis. Bonds between amino acids are called peptide bonds. Meat, beans, eggs, nuts, and milk contain a lot of proteins.

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Protein Structure:

• Amino Acids: Contain a central carbon bonded to a carboxyl group (COOH) at one end, an amino group (NH2) at the other end, a hydrogen atom, and an R group (variable group or side chain)
• Peptide Bonds: link amino acids together. They are formed by dehydration synthesis between the amino and carboxyl groups of adjacent monomers.

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4 Levels of Protein Structure

• Primary Structure
• Secondary Structure
• Tertiary Structure
• Quaternary Structure

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Primary Structure

Primary Structure is the unique sequence of which amino acids are joined.

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Secondary Structure

Secondary Structure: one of two three-dimensional shapes that are the result of hydrogen bonding between members of the polypeptide backbone (not the amino acid side chains) 

Alpha helix: a coiled shape much like a slinky

Beta pleated sheet: is like an accordion shape

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Tertiary Structure

• Tertiary Structure: a complex globular shape due to interactions between the side chains (R groups), such as hydrophobic interactions, van der waals interactions, hydrogen bonds, and disulfide bridges. Example: enzymes.

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Quaternary Structure

• Quaternary Structure: refers to the association of two or more polypeptide chains into one large protein. Hemoglobin is a globular protein with quaternary structure because it is composed of four chains.

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Protein shape affects function

• When a protein does not fold properly, its function is changed. This can be a result of a single amino acid substitution, such as that seen in abnormal hemoglobin typical of sickle-cell disease. The key must be shaped correctly to open the lock.
• A protein is denatured when it loses its shape and ability to function due to heat, a change in pH, or some other disturbance. Keep in mind: change in shape, change in function!

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Enzymes (Specialized Proteins)

• Enzymes act as catalysts in living cells. A catalyst increases the rate of a chemical reaction, allowing it to proceed rapidly when it would otherwise occur very slowly.
• Enzymes lower the activation energy needed for a reaction to occur. Each enzyme has an optimum range of temperature and pH at which is operates most efficiently.
• Without enzymes in our cells, reactions would take too long and cells would die.
• Cofactors are nonprotein molecules that assist enzymes.
• Coenzymes are organic cofactors that usually function to donate or accept some component of a reaction, often electrons. Some vitamins are coenzymes or components of coenzymes.
• Inorganic cofactors are often metal ions, like Fe and Mg.

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Nucleic Acids

• DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are the two nucleic acids. Their monomers are nucleotides.
• Nucleotides are made up of three parts
• -Nitrogenous base (adenine, thymine, cytosine, and guanine in DNA, adenine, uracil, cytosine, and guanine in RNA)
• -Pentose (5 carbon) sugar: deoxyribose in DNA, ribose in RNA
• -Phosphate group

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Nucleic Acids (Two Types: DNA and RNA)�

• DNA is the molecule of heredity
• -Double Stranded helix
• -Nucleotides consist of adenine, thymine, cytosine, and guanine
• -Adenine always binds with thymine, cytosine always binds with guanine
• RNA is
• -Single stranded.
• -Nucleotides consist of adenine, uracil, cytosine, and guanine
• -3 forms of RNA
• -mRNA-Carries DNA code to ribosomes
• -rRNA-Assembles proteins
• -tRNA-Transfers amino acids to ribosomes

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Functional groups

• Functional groups attached to the carbon skeleton have diverse properties. The behavior of organic molecules is dependent ono the identity of their functional groups. Functional groups include Hydroxyl-OH, Carboxyl -COOH, Carbonyl CO, Amino NH2, Phosphate PO3, Sulfhydryl -SH, and Methyl -CH3.
• Parts of organic molecules that are involved in chemical reactions
• give organic molecules distinctive properties

 hydroxyl  amino

 carbonyl  sulfhydryl

 carboxyl  phosphate

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Functional Groups cont.

• Affect reactivity
• makes hydrocarbons hydrophilic
• increase solubility in water
• It is recommended that you know the following functional groups by sight and not the particular details of each.

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Amino

• -NH₂
• N attached to 2 H
• compounds with NH₂ = amines
• amino acids
• NH₂ acts as base
• ammonia picks up H⁺ from solution

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Carboxyl

• –COOH
• C double bonded to O & single bonded to OH group
• compounds with COOH = acids
• fatty acids
• amino acids

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Carbonyl

• C=O
• O double bonded to C
• if C=O at end molecule = aldehyde
• if C=O in middle of molecule = ketone

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Hydroxyl

• –OH
• organic compounds with OH = alcohols
• names typically end in -ol
• ethanol

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Phosphate

• –PO₄
• P bound to 4 O
• connects to C through an O
• lots of O = lots of negative charge
• highly reactive
• transfers energy between organic molecules
• ATP, GTP, etc.

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Sulfhydryl

• –SH
• S bonded to H
• compounds with SH = thiols
• SH groups stabilize the structure of proteins

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