Macromolecules AP Biology 2012-2013

Big Ideas 2 Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain homeostasis.

Molecules of Life 4 main classes of large biological molecules Carbohydrates Lipids Proteins Nucleic Acids Very large molecules called macromolecules macro = giant Ex. Some proteins are over 100,000 daltons

Polymers are built from Monomers 3 classes of molecules are polymers Carbohydrates, nucleic acids, and proteins They are made of many similar or identical components called monomer.

Synthesis of polymers Covalent bonds are formed between two molecules by a dehydration reaction-removal of water When the bonds form there is a loss of a water molecule The cell must expend energy to carry out dehydration synthesis Occurs only with the help of enzymes

Dehydration removes a water molecule, forming a new bond LE 5-2a Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond Longer polymer Dehydration reaction in the synthesis of a polymer

Breakdown of Polymers Polymers are broken down by hydrolysis Addition of water food, which is in the form of macromolecules, is digested with the aid of hydrolysis Monomers are absorbed in the bloodstream Hydrolysis of polymers is catalyzed by enzymes

Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer

Diversity of Polymers Diversity of macromolecules is vast Variation exists between siblings Greater variation between unrelated individuals Even greater between species

Carbohydrates Simple or single sugars- monosaccharides Double sugars – disaccharides Macromolecules are polysaccharides

Sugars Chemical formula is a multiple of – CH20 Contains a carbonyl group and a hydroxyl group Sugar can be an aldose (aldehyde sugar) or a ketose (ketone sugar) Can be categorized by the size of the carbon skeleton.

Triose sugars (C3H6O3) (C5H10O5) Hexose sugars (C5H12O6) LE 5-3 Triose sugars (C3H6O3) Pentose sugars (C5H10O5) Hexose sugars (C5H12O6) Aldoses Glyceraldehyde Ribose Glucose Galactose Ketoses Dihydroxyacetone Ribulose Fructose

Glucose is the most common monosaccharide Forms rings in aqueous solutions Cell extract energy stored in glucose through cellular respiration. Fructose is structural isomer of glucose Sugars and their carbon skeletons provide raw materials for other organic molecules.

LE 5-4 Linear and ring forms Abbreviated ring structure

Disaccharides Two monosaccharides joined by glycosidic linkgage (covalent bond through dehydration reaction) Maltose = two glucose molecules Sucrose= glucose + fructose Plants use sucrose for carbohydrate transport from roots to leaves Lactose = glucose + galactose

Dehydration reaction in the synthesis of maltose Glucose Glucose LE 5-5 Dehydration reaction in the synthesis of maltose 1–4 glycosidic linkage Glucose Glucose Maltose Dehydration reaction in the synthesis of sucrose 1–2 glycosidic linkage Glucose Fructose Sucrose

Polysaccharides Polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages. Function is determined by sugar monomers and the position of its glycosidic linkages.

Storage Polysaccharides Starch – consist of all glucose monomers Joined by 1-4 linkage (#1 C to #4 C) The bond’s angles make the polymer helical Plants can store surplus glucose in starch Starch represents energy Animals have enzymes that can hydrolyze plant starch Glycogen – animals store this polymer if glucose Humans store glycogen in the liver and muscle cells. Hydrolysis release glucose when sugar is in demand Glycogen stores are depleted in about a day.

Starch: a plant polysaccharide Glycogen: an animal polysaccharide LE 5-6 Chloroplast Starch Mitochondria Glycogen granules 0.5 µm 1 µm Amylose Amylopectin Glycogen Starch: a plant polysaccharide Glycogen: an animal polysaccharide

Structural polysaccharides Cellulose- polymer of glucose Component of cell walls Most abundant organic compound Two different ring structures for glucose Alpha ring Beta ring Starch uses alpha configuration Cellulose use beta configuration Straight, never branched

a and b glucose ring structures LE 5-7a a Glucose b Glucose a and b glucose ring structures

Starch: 1–4 linkage of a glucose monomers. LE 5-7b Starch: 1–4 linkage of a glucose monomers.

Cellulose: 1–4 linkage of b glucose monomers. LE 5-7c Cellulose: 1–4 linkage of b glucose monomers.

Cellulose microfibrils in a plant cell wall LE 5-8 Cellulose microfibrils in a plant cell wall Cell walls Microfibril 0.5 µm Plant cells Cellulose molecules b Glucose monomer

Enzymes in animals that hydrolyze alpha linkages in starch and unable to hydrolyze beta linkages. Cellulose in our food passes through the digestive system and is eliminated. Cellulose scrapes the wall of the digestive tract stimulates the lining to secrete mucus- helps the passage of food.

Figure 5-09

Chitin Used by arthropods to build exoskeletons leathery becomes hard when encrusted with Calcium carbonate Also found in fungi Similar to cellulose except the glucose has a nitrogen-containing arm.

LE 5-10 The structure of chitin. Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

Lipids Not polymers Include fats, phospholipids, and steroids. Consists of glycerol and fatty acids 3 fatty acid molecules joined to glycerol by ester linkage ( bond between hydroxyl group and carboxyl group) Also called a triaclglycerol or triglceride

Dehydration reaction in the synthesis of a fat LE 5-11 Fatty acid (palmitic acid) Dehydration reaction in the synthesis of a fat Ester linkage Fat molecule (triacylglycerol)

Saturated vs. unsaturated Fatty acids vary in length and the number and location of double bonds Saturated fat contains the maximum of hydrogen atoms with no double bonds Unsaturated fat – contains one or more double bonds

Saturated fat and fatty acid. LE 5-12 Stearic acid Saturated fat and fatty acid. Oleic acid cis double bond causes bending Unsaturated fat and fatty acid.

Animal fats are saturated fats and are solid at room temperature. Plant fats are generally unsaturated usually liquid at room temperature. Hydrogenated vegetable oils means that fat has been converted to saturated fat Diets high in saturated fats is a key factor in cardiovascular disease- atherosclerosis- deposits of plaque within the walls of blood vessels

Function of fats Storage of energy Stores 2X as much energy polysaccharide Provides animals with compact reservoir of fuel Adipose cells stock long-term reserves for mammals and humans. Provides cushions for organs Insulation in the body

Phospholipids Two fatty acids and phosphate group attached to a glycerol Hydrophobic tail and hydrophilic head Self-assemble into a double-layered aggregates or bilayer.

LE 5-13b Hydrophilic head Hydrophobic tails Phospholipid symbol

LE 5-14 WATER Hydrophilic head Hydrophobic tails WATER

Steroids Consist of 4 fused rings Vary by functional groups Cholesterol –component of animal membranes Many hormones are steroids

Figure 5-15

Proteins 50% of the dry mass of most cells Functions Speed chemical reactions Roles in structural support Storage Transport Cellular communications Movement and Defense against foreign substances

Polypeptides Polymers of amino acids are called polypeptides Amino acids contain carboxyl and amino groups R group or the side chains varies R group determines the characteristic of the amino acid

Nonpolar polar Electrically charged

Amino Acid Polymers Amino acids are join covalently by a dehydration reaction The bond is called a peptide bond Polypeptide is a polymer of many amino acids linked by peptide bonds.

Protein Conformation and Function A functioning protein is not just a polypeptide chain but one or more polypeptides twisted, folded and coiled into a molecule of unique shape. The amino acid sequence determines what the 3-D conformation will take.

LE 5-19 Groove A ribbon model Groove A space-filling model

A proteins conformation determines how it works The function often depends on the ability to recognize and bind to some other molecule

Levels of Protein Structure Primary Structure – unique sequence of amino acids Secondary Structure- alpha helix or beta pleated sheet Tertiary Structure- overall shape resulting from the interactions between the side (R groups) chains Quaternary Structure- the number of polypeptide subunits

Levels of Protein Structure

Primary Structure The unique sequence of amino acids Like the order of letters in a very long word Not random it is determined by inherited genetic information

LE 5-20a Amino end Amino acid subunits Carboxyl end

Secondary Structure Segments of polypeptide chains that have repeated coiled or folded sections Coils and folds are the result of hydrogen bonds of repeating constituents of the polypeptide backbone Alpha helix coil held together by H bonds Beta pleated sheet bonds between parallel polypeptide backbones

LE 5-20b b pleated sheet Amino acid subunits  helix

Tertiary Structure Overall shape of a polypeptide resulting from the interactions between the side chains (R groups) of the amino acids Nonpolar side chains end up in a cluster at the proteins core. van der Waal forces hold them together Ionic bonds stabilize the structure Disulfide bridges reinforce the conformation

LE 5-20d Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond

Quaternary Structure Some proteins consist of two or more polypeptide chains aggregated together

Polypeptide chain b Chains Iron Heme a Chains Hemoglobin LE 5-20e Polypeptide chain b Chains Iron Heme a Chains Hemoglobin Polypeptide chain Collagen

Sickle- Cell Disease Change in the primary sequence of the hemoglobin protein Abnormal hemoglobin crystallizes, deforming the shape of the red blood cell. Abnormal shaped red blood cells clog tiny blood vessels- stopping blood flow.

Red blood cell shape Normal cells are full of individual hemoglobin LE 5-21a 10 µm 10 µm Red blood cell shape Normal cells are full of individual hemoglobin molecules, each carrying oxygen. Red blood cell shape Fibers of abnormal hemoglobin deform cell into sickle shape.

Sickle-cell hemoglobin Primary structure Primary structure 1 2 3 4 5 6 LE 5-21b Normal hemoglobin Sickle-cell hemoglobin Primary structure Val His Leu Thr Pro Glu Glu Primary structure Val His Leu Thr Pro Val Glu 1 2 3 4 5 6 7 1 2 3 4 5 6 7 Exposed hydrophobic region Secondary and tertiary structures Secondary and tertiary structures b subunit b subunit a a   Quaternary structure Normal hemoglobin (top view) Quaternary structure Sickle-cell hemoglobin a   a Function Molecules do not associate with one another; each carries oxygen. Function Molecules interact with one another to crystallize into a fiber; capacity to carry oxygen is greatly reduced.

Protein Environment Conformation dependent on physical and chemical environment Alteration of pH, salt concentration, temperature, or other aspects can cause a protein to lose its native conformation The change is called denaturation

Chaperonins Chaperone proteins that help in the proper folding of other proteins Keep new polypeptides segregated in the cytoplasmic environment.

The cap attaches, causing the cylinder to change LE 5-23b Correctly folded protein Polypeptide Steps of Chaperonin Action: The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. An unfolded poly- peptide enters the cylinder from one end.

Nucleic Acids The amino acid sequence of a polypeptide is determined by a unit of inheritance called a gene Genes consists of DNA Two types of Nucleic Acids- DNA & RNA.

DNA Provides direction for its own replication Directs RNA synthesis And with RNA directs protein synthesis Genetic material inherit from parents

RNA Messenger RNA carries the genetic instructions Ribosomes (RNA) the sites of protein synthesis.

LE 5-25 DNA Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA Movement of mRNA into cytoplasm via nuclear pore Ribosome Synthesis of protein Amino acids Polypeptide

Structure of Nucleic Acids Nucleic Acids are polymers of monomers called nucleotides Nucleotide consist of 3 parts 5- carbon sugar Nitrogenous base Phosphate group

Nitrogenous base Phosphate group Pentose sugar LE 5-26a 5¢ end Nucleoside Nitrogenous base Phosphate group Pentose sugar Nucleotide 3¢ end Polynucleotide, or nucleic acid

Nucleotides Two classes of nitrogen bases Five carbon sugar Pyrimidines Single six ring carbon skeleton with a nitrogen atom Include cytosine, thymine, and uracil. Purines Six ring fused to a five ring carbon skeleton Larger than pyrimidines Include adenine and guanine. Five carbon sugar Ribose in RNA Deoxyribose in DNA

LE 5-26b Nitrogenous bases Pyrimidines Cytosine C Thymine (in DNA) T Uracil (in RNA) U Purines Adenine A Guanine G Pentose sugars Deoxyribose (in DNA) Ribose (in RNA) Nucleoside components

Polymerization of Nucleotides Nucleotides are linked together covalently through phosphodiester linkages between the –OH group on the 3’ carbon of one nucleotide to the phosphate on the 5’ carbon of the next. DNA strand has directionality from 5’ to 3’

The Double Helix DNA consists of two polynucleotides that spiral around each other forming a double helix. The two strands run in opposite directions are antiparallel. The two strands are held together by hydrogen bonds and by van der Waals interactions between stacked bases.

Base Pairing A (adenine) always pairs with T (thymine) G (guanine) always pairs with C (cytosine) 5’- AGGTCCG-3’ is complementary to 3’-TCCAGGC-5’

5¢ end 3¢ end Sugar-phosphate backbone Base pair (joined by LE 5-27 5¢ end 3¢ end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 5¢ end New strands 3¢ end 5¢ end 5¢ end 3¢ end

Molecular comparisons of DNA and Proteins DNA carries heritable information in the form of genes Genes and proteins document the hereditary background of an organism Siblings have similarity in DNA and proteins Molecular comparisons DNA between species show evolutionary relationships