Macromolecules You are what you eat!

Polymer Is a long molecule consisting of many similar building blocks called monomers Specific monomers make up each macromolecule E.g. amino acids are the monomers for proteins

The Synthesis and Breakdown of Polymers Monomers form larger molecules by condensation reactions called dehydration synthesis (a) Dehydration reaction in the synthesis of a polymer HO H 1 2 3 4 H2O Short polymer Unlinked monomer Longer polymer Dehydration removes a water molecule, forming a new bond Figure 5.2A

The Synthesis and Breakdown of Polymers Polymers can disassemble by Hydrolysis (addition of water molecules) (b) Hydrolysis of a polymer HO 1 2 3 H 4 H2O Hydrolysis adds a water molecule, breaking a bond Figure 5.2B

Carbohydrates Structure / monomer Function Examples monosaccharide energy raw materials energy storage structural compounds Examples glucose, starch, cellulose, glycogen glycosidic bond

Sugars 6 5 3 Most names for sugars end in -ose Classified by number of carbons 6C = hexose (glucose) 5C = pentose (ribose) 3C = triose (glyceraldehyde) Glyceraldehyde H OH O C OH H HO CH2OH O Glucose H OH HO O Ribose CH2OH 6 5 3

Bonding of Carbohydrates Disaccharides Consist of monosaccharides Are joined by a glycosidic linkage

Simple & complex sugars OH H HO CH2OH O Glucose Simple & complex sugars Monosaccharides simple 1 monomer sugars glucose Disaccharides 2 monomers sucrose Polysaccharides large polymers starch

Polysaccharides Polymers of sugars Function: costs little energy to build easily reversible = release energy Function: energy storage starch (plants) glycogen (animals) in liver & muscles structure cellulose (plants) chitin (arthropods & fungi) Polysaccharides are polymers of hundreds to thousands of monosaccharides

Polysaccharide diversity Molecular structure determines function in starch in cellulose isomers of glucose structure determines function…

Consists of glucose monomers Glycogen Consists of glucose monomers Is the major storage form of glucose in animals

But it tastes like hay! Who can live on this stuff?! Cellulose Most abundant organic compound on Earth herbivores have evolved a mechanism to digest cellulose most carnivores have not that’s why they eat meat to get their energy & nutrients cellulose = undigestible roughage Cross-linking between polysaccharide chains: = rigid & hard to digest The digestion of cellulose governs the life strategy of herbivores. Either you do it really well and you’re a cow or an elephant (spend a long time digesting a lot of food with a little help from some microbes & have to walk around slowly for a long time carrying a lot of food in your stomach) Or you do it inefficiently and have to supplement your diet with simple sugars, like fruit and nectar, and you’re a gorilla. But it tastes like hay! Who can live on this stuff?!

Structural polysaccharides Chitin, another important structural polysaccharide Is found in the exoskeleton of arthropods Can be used as surgical thread (a) The structure of the chitin monomer. O CH2OH OH H NH C CH3 (b) Chitin forms the exoskeleton of arthropods. This cicada is molting, shedding its old exoskeleton and emerging in adult form. (c) Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. Figure 5.10 A–C

Lipids Lipids are composed of C, H, O “Family groups” long hydrocarbon chains (H-C) “Family groups” fats phospholipids steroids Do not form polymers big molecules made of smaller subunits not a continuing chain Made of same elements as carbohydrates but very different structure/ proportions & therefore very different biological properties

dehydration synthesis Fats Structure: glycerol (3C alcohol) + fatty acid fatty acid = long HC “tail” with carboxyl (COOH) group “head” enzyme Look at structure… What makes them hydrophobic? Note functional group = carboxyl H2O dehydration synthesis

Why do humans like fatty foods? Fats store energy Long HC chain polar or non-polar? hydrophilic or hydrophobic? Function: energy storage concentrated all H-C! 2x carbohydrates cushion organs insulates body think whale blubber! What happens when you add oil to water Why is there a lot of energy stored in fats? • big molecule • lots of bonds of stored energy So why are we attracted to eating fat? Think about our ancestors on the Serengeti Plain & during the Ice Age. Was eating fat an advantage?

Saturated fats All C bonded to H No C=C double bonds long, straight chain most animal fats solid at room temp. contributes to cardiovascular disease (atherosclerosis) = plaque deposits Mostly animal fats

Unsaturated fats C=C double bonds in the fatty acids plant & fish fats vegetable oils liquid at room temperature the kinks made by double bonded C prevent the molecules from packing tightly together Mostly plant lipids Think about “natural” peanut butter: Lots of unsaturated fats Oil separates out Companies want to make their product easier to use: Stop the oil from separating Keep oil solid at room temp. Hydrogenate it = chemically alter to saturate it Affect nutrition? mono-unsaturated? poly-unsaturated?

Hydrogenation Hydrogenation adds more H and changes double bonds to single bonds

It’s just like a penguin… Phospholipids Structure: glycerol + 2 fatty acids + PO4 PO4 = negatively charged It’s just like a penguin… A head at one end & a tail at the other!

Steroids Structure: 4 fused C rings + ?? different steroids created by attaching different functional groups to rings different structure creates different function examples: cholesterol, sex hormones cholesterol

Cholesterol Important cell component animal cell membranes precursor of all other steroids including vertebrate sex hormones high levels in blood may contribute to cardiovascular disease

From Cholesterol  Sex Hormones What a big difference a few atoms can make! Same C skeleton, different functional groups

Proteins Most structurally & functionally diverse group Function: involved in almost everything enzymes (pepsin, DNA polymerase) structure (keratin, collagen) carriers & transport (hemoglobin, aquaporin) cell communication signals (insulin & other hormones) receptors defense (antibodies) movement (actin & myosin) storage (bean seed proteins) Storage: beans (seed proteins) Movement: muscle fibers Cell surface proteins: labels that ID cell as self vs. foreign Antibodies: recognize the labels ENZYMES!!!!

Proteins Structure monomer = amino acids polymer = polypeptide H2O Structure monomer = amino acids 20 different amino acids polymer = polypeptide protein can be one or more polypeptide chains folded & bonded together large & complex molecules complex 3-D shape Rubisco = 16 polypeptide chains Hemoglobin = 4 polypeptide chains (2 alpha, 2 beta) hemoglobin Rubisco growth hormones

Amino acids H O | H || —C— C—OH —N— R Structure central carbon amino group carboxyl group (acid) R group (side chain) variable group different for each amino acid confers unique chemical properties to each amino acid like 20 different letters of an alphabet can make many words (proteins) —N— H R Oh, I get it! amino = NH2 acid = COOH

Protein structure & function Function depends on structure 3-D structure twisted, folded, coiled into unique shape Hemoglobin Hemoglobin is the protein that makes blood red. It is composed of four protein chains, two alpha chains and two beta chains, each with a ring-like heme group containing an iron atom. Oxygen binds reversibly to these iron atoms and is transported through blood. Pepsin Pepsin is the first in a series of enzymes in our digestive system that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins. Collagen– Your Most Plentiful Protein About one quarter of all of the protein in your body is collagen. Collagen is a major structural protein, forming molecular cables that strengthen the tendons and vast, resilient sheets that support the skin and internal organs. Bones and teeth are made by adding mineral crystals to collagen. Collagen provides structure to our bodies, protecting and supporting the softer tissues and connecting them with the skeleton. But, in spite of its critical function in the body, collagen is a relatively simple protein. pepsin hemoglobin collagen

dehydration synthesis Building proteins Peptide bonds covalent bond between NH2 (amine) of one amino acid & COOH (carboxyl) of another C–N bond H2O dehydration synthesis free COOH group on one end is ready to form another peptide bond so they “grow” in one direction from N-terminal to C-terminal peptide bond

Protein structure 3° 1° 4° 2° R groups hydrophobic interactions disulfide bridges (H & ionic bonds) 3° multiple polypeptides hydrophobic interactions 1° sequence determines structure and… structure determines function. Change the sequence & that changes the structure which changes the function. amino acid sequence peptide bonds 4° 2° determined by DNA R groups H bonds

Sickle-Cell Disease: A Simple Change in Primary Structure Results from a single amino acid substitution in the protein hemoglobin

In Biology, size doesn’t matter, SHAPE matters! Protein denaturation Unfolding a protein conditions that disrupt H bonds, ionic bonds, disulfide bridges temperature pH salinity alter 2° & 3° structure alter 3-D shape destroys functionality some proteins can return to their functional shape after denaturation, many cannot

Nucleic Acids Function: genetic material stores information genes blueprint for building proteins DNA  RNA  proteins transfers information blueprint for new cells blueprint for next generation DNA proteins

Nucleic Acids Examples: Structure: RNA (ribonucleic acid) single helix DNA (deoxyribonucleic acid) double helix Structure: monomers = nucleotides DNA RNA

Nucleotides 3 parts nitrogen base (C-N ring) pentose sugar (5C) ribose in RNA deoxyribose in DNA phosphate (PO4) group Nitrogen base I’m the A,T,C,G or U part! Are nucleic acids charged molecules? DNA & RNA are negatively charged: Don’t cross membranes. Contain DNA within nucleus Need help transporting mRNA across nuclear envelope. Also use this property in gel electrophoresis.

The Structure of Nucleic Acids Each contains a sugar, phosphate group, and nitrogenous base The bonds are called phosphodiester bonds 3’C 5’ end 5’C 3’ end OH Figure 5.26 O

DNA Pairing Adenine pairs with Thymine (or Uracil in RNA) Guanine pairs with Cytosine Pairing is anti-parallel Ex. If 1 side is 5’-A-T-C-G-A-A-C-C-3’ the other side is 3’-T-A-G-C-T-T-G-G-5’

Nitrogenous bases Pyrimidines DNA The nitrogenous bases in DNA Form hydrogen bonds in a complementary fashion Purines ( Adenine and Guanine) bond only with pyrimidines ( cytosine, thymine and uracil) CH Uracil (in RNA) U Ribose (in RNA) Nitrogenous bases Pyrimidines C N O H NH2 HN CH3 Cytosine Thymine (in DNA) T HC NH Adenine A Guanine G Purines HOCH2 OH Pentose sugars Deoxyribose (in DNA) 4’ 5” 3’ 2’ 1’ Pyrimidines  Purines 

Synthesis of mRNA in the nucleus RNA directs protein synthesis 1 2 3 Synthesis of mRNA in the nucleus Movement of mRNA into cytoplasm via nuclear pore Synthesis of protein NUCLEUS CYTOPLASM DNA mRNA Ribosome Amino acids Polypeptide Figure 5.25

Tape Measures of Evolution Can examine familial similarities in DNA sequences Examine molecular genealogy of DNA to find similar species Ex. Humans and gorillas differ by only 1 amino acid