Polymer Principles

Most macromolecules are polymers

Polymer = (Poly = many; mer = part); large molecule consisting of many identical or similar subunits connected together.

Monomer = Subunit or building block molecule of a polymer

Macromolecule = (Macro = large); large organic polymer

Formation of macromolecules from smaller building block molecules represents another level in the hierarchy of biological organization.

There are four classes of macromolecules in living organisms: Carbohydrates

LipidsProteinsNucleic acids

Polymerization reactions = Chemical reactions that link two or more small molecules to form larger molecules with repeating structural units.

Condensation reactions = Polymerization reactions during which monomers are covalently linked, producing net removal of a water molecule for each covalent linkage.

Figure 5.2 The synthesis and breakdown of polymers

Polymerization Reaction Condensation or Dehydration Reaction

Requires energy, biological catalysts (enzymes)

Digestive enzymes catalyze hydrolytic reactions

Unity in life--only about 40-50 common monomersDiversity too---new properties emerge from complex arrangements of monomers into polymers

Figure 5.3 The structure and classification of some monosaccharides

3 5 6

Carbohydrates--sugars and their polymersSugars--smallest carbohydrates

Simple sugars--monomers of carbohydrates called monosaccharides (CH2O)

Major nutrients for cells e.g. glucose

Glucose can be produced by photosynthesis from CO2, H2O, and sunlight

Store energy--cellular respiration

Raw material for other organic molecules

Used as monomers for disaccharides and polysaccharides--condensation reactions

Asymmetrical carbon--enantiomers

Figure 5.4 Linear and ring forms of glucose

Figure 5.5 Examples of disaccharide synthesis

Polysaccharides = Macromolecules that are polymers of a fewhundred or thousand monosaccharides.

Are formed by linking monomers in enzyme-mediated condensationreactions

Have two important biological functions:

1) Energy storage (starch and glycogen)

2) Structural support (cellulose and chitin)

Figure 5.6 Storage polysaccharides

Starch--glucose polymer in plantsAmylose--unbranched polymerAmylopectin--branched polymer

Most animals can digest starch potato, wheat, corn, rice

Glycogen--glucose storage polysaccharide in animals

Very highly branchedStored in muscle and liver

Cells hydrolyze storage polysaccharidesas needed for for energy

Figure 5.7 Starch and cellulose structures 

Figure 5.7 Starch and cellulose structures 

Figure 5.7x Starch and cellulose molecular models

Glucose Glucose

Starch

Cellulose

Figure 5.8 The arrangement of cellulose in plant cell walls

Cellulose reinforces plant wallsHydrogen bonds

Cellulose cannot be digested by most organisms--no enzyme to break beta 1-4 linkage

Insoluble fiber, digestion

Figure 5.x1 Cellulose digestion: termite and Trichonympha

Figure 5.x2 Cellulose digestion: cow

Figure 5.10 Chitin, a structural polysaccharide: exoskeleton and surgical thread

Lipids: Diverse Hydrophobic Molecules

Lipids = Diverse group of organic compounds that are insoluble in water,but will dissolve in nonpolar solvents (e.g., ether chloroform, benzene).Important groups are fats, phospholipids, and steroids.

Fats store large amounts of energy

Fats = Macromolecules are constructed from:

Glycerol, a three-carbon alcohol

Fatty acid (carboxylic acid) = Composed of a carboxyl group atone end and an attached hydrocarbon chain (“tail”)

Figure 5.11 The synthesis and structure of a fat, or triacylglycerol

Carboxyl group has acid propertiesHydrocarbon chain, 16-18 carbonsNonpolar C-H bonds, hydrophobic

(Condensation Reaction)

(bond between hydroxyl group and a carboxyl group)

A triglyceride

Fats: hydrophobic, not water soluble variation due to fatty acid composition fatty acids can be the same or different fatty acids can vary in length fatty acids can vary in the number and location of double bonds (saturation)

Figure 5.12 Examples of saturated and unsaturated fats and fatty acids 

Saturated fats no double bonds between carbons in the tail saturated with hydrogen solid at room temp most animal fats, bacon grease, lard, butter

Unsaturated fats one or more double bonds in tail kinks the tail so cannot pack closely enough to solidify at room temp most plant fats

Artificial hydrogenation, peanut butter, margarine

Fats have many useful functions Energy storage 9 vs 4 Kcal/gram more compact fuel than carbohydrates Cushions organs e.g. kidney Insulates against heat loss

Phospholipids

Phospholipids = Compounds with molecular building blocks of glycerol, two fatty acids, a phosphate group, and usually, an additional small chemical group attached to the phosphate.

Differs from fat in that the third carbon of glycerol is joined to a negatively charged phosphate group

Can have small variable molecules (usually charged or polar) attached to phosphate

Are diverse depending upon differences in fatty acids and in phosphate attachments

Show ambivalent behavior toward water. Hydrocarbon tails are hydrophobic and the polar head (phosphate group with attachments) is hydrophilic.

Cluster in water as their hydrophobic portions turn away from water. One such cluster, a micelle, assembles so the hydrophobic tails turn toward the water-free interior and the hydrophilic phosphate heads arrange facing outward in contact with water.

Are major constituents of cell membranes. At the cell surface, phospholipids form a bilayer held together by hydrophobic interactions among the hydrocarbon tails. Phospholipids in water will spontaneously form such a bilayer.

Figure 5.13 The structure of a phospholipid

Phospholipids = Compounds with molecular building blocks of glycerol, two fatty acids, a phosphate group, and usually, an additional small chemical group attached to the phosphate.

Differs from fat in that the third carbon of glycerol is joined to a negatively charged phosphate group

Can have small variable molecules (usually charged or polar) attached to phosphate

Are diverse depending upon differences in fatty acids and in phosphate attachments

Show ambivalent behavior toward water. Hydrocarbon tails are hydrophobic and the polar head (phosphate group with attachments) is hydrophilic.

Are major constituents of cell membranes.

Phospholipid Bilayers of Cell Membranes

Steroids

Steroids = Lipids which have four fused carbon rings with various functional groups attached.

Cholesterol is an important steroid and is the precursor to many other steroids including vertebrate sex hormones and bile acids.

Is a common component of animal cell membranes.

Can contribute to atherosclerosis.

Figure 5.15 Cholesterol, a steroid    

MemebranesBile salts--absorption of fatsHDL and LDL---triglycerides, phospholipids, cholesterol, proteinLDL receptor deficiency--more deposition of cholesterol in arterial wallsHDL--aid in removal of cholesterol from tissues

Polypeptide chains = Polymers of amino acids that are arranged in a specific linear sequence, linked by peptide bondsProtein = A macromolecule consisting of one or more polypeptide chains folded and coiled into specific conformationsProteins make up 50% of the dry weight of cellsProteins vary extensively in structure, each with a unique 3-dimensional shape (conformation)Although they vary in structure and function, they are commonly made from only 20 amino acid monomers

Figure 5.17 The 20 amino acids of proteins: nonpolar

Amino acid = building blocks of proteinsAsymmetric carbon (alpha carbon) bonded to H, Carboxyl group, Amino group, variable R-group (side chain)Physical and chemical properties of the side chain determine the uniqueness of each amino acidAt normal cellular pH both the amino and carboxyl group are ionized---pH determines which ionic state predominates

Alpha carbon, asymmetric

CarboxylAmino

Side chain (R group)

Hydrophobic side chain

Figure 5.17 The 20 amino acids of proteins: polar and electrically charged

Hydrophillic side chain

Figure 5.18 Making a polypeptide chain

Peptide bond = covalent bond formed by condensation reaction

Backbone has a repeating sequence N-CC-N-CC-…

Carboxyl

Amino

Figure 5.19 Conformation of a protein, the enzyme lysozyme

Protein’s function depends on its specific conformationProtein conformation = 3-dimensional shapeNative conformation = functional conformation found under normal biological conditions

The conformation of a protein enables it to bind specifically to another moleculare.g. hormone/receptor, enzyme/substrate, antibody/antigen

Conformation is a consequence of a specific linear sequence of amino acidspolypeptide chain coils and folds spontaneously, mostly due to hydrophobic interactionsstabilized by chemical bonds and weak interactions between neighboring regions of the folded protein

The primary structure of a protein

4 levels of protein structurePrimarySecondaryTertiaryQuaternary

Primary structuresequence of amino acidsdetermined by genesslight change can have large effect on function

e.g. sickle-cell hemoglobinsequence can be determined in the lab

A single amino acid substitution in a protein causes sickle-cell disease

Sickled cells

The secondary structure of a protein

Secondary structure = regular, repeated coiling and foldingof a protein’s polypeptide backbone

Contributes to final conformation

Stabilized by H-bonds

Two major types of secondary structures

Alpha helix helical coil stabilized by H-bonds found in fibrous proteins e.g. keratin and collagen and some gobular proteins e.g. lysozyme

Beta pleated sheet a sheet of antiparallel chains folded into accordion pleats held together by H-bonds found in gobular proteins e.g. lysozyme also in fibrous proteins e.g. fibroin (silk)

Spider silk: a structural protein

Examples of interactions contributing to the tertiary structure of a protein

Tertiary structure = 3-dimensional shape due to bonding between and among side chains and to interactions between side chains and the aqueous environment

(Weak interaction)

(Weak interaction)

(Weak interaction)

Strong interaction (covalent bond)

The quaternary structure of proteins

Quaternary structure = structure that results from the interactions between several polypeptide chains

Supercoiled structure gives itstrength

Review: the four levels of protein structure

Figure 5.22 Denaturation and renaturation of a protein

Proteins can be denatured by:transfer to an organic solvent, alters hydrophobic interactionschemical agents that disrupt hydrogen bonds, ionic bonds, disulfide bridgesexcessive heat--disrupts weak interactions

Figure 5.23 A chaperonin in action

Figure 5.24 X-ray crystallography

Figure 5.25 DNA RNA protein: a diagrammatic overview of information flow in a cell

Nucleic Acids store and transmit hereditary information

Protein conformation is determined by primary structurePrimary structure is determined by genesGenes are hereditary units that consist of DNA, a type of nucleic acid

Two types of nucleic acids DNA (Deoxyribonucleic Acid) contains coded information that programs all cell activity contains directions for its own replication copied and passed from one generation to the next found primarily in the nucleus of eukaryotic cells makes up genes that contain instructions for protein synthesis via mRNA

RNA (Ribonucleic Acid) functions in the actual synthesis of proteins coded for by DNA Sites of protein synthesis are on ribosomes mRNA carries encoded genetic messages from nucleus to the cytoplams

The flow of genetic info is from DNA to RNA to protein

Figure 5.26 The components of nucleic acids

Nucleic Acid = polymer of nucleotides linked together by condensation reactionsNucleotide = building block of nucleic acid

made of: a 5 carbon sugar, phosphate group, nitrogenous baseNucleic acid polymers (polynucleotides) are nucleotides linked together by phosphodiester linkagesEach gene contains a unique sequence of nitrogenous bases which codes for a unique sequence of amino acids in a protein

Figure 5.27 The DNA double helix and its replication

Table 5.2 Polypeptide Sequence as Evidence for Evolutionary Relationships