Proteins AP Biology clockwise: Rubisco — most important protein on the planet? Hemoglobin — a red blooded protein :-) Collagen — strings you together Growth Hormone — working hard in you right now! AP Biology 2005-2006

Proteins Most structurally & functionally diverse group of biomolecules Function: involved in almost everything enzymes structure (keratin, collagen) carriers & transport (membrane channels) receptors & binding (defense) contraction (actin & myosin) signaling (hormones) 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!!!! AP Biology

Proteins Structure: monomer = amino acids polymer = polypeptide 20 different amino acids polymer = polypeptide protein can be 1 or more polypeptide chains folded & bonded together large & complex molecules complex 3-D shape AP Biology 2005-2006

Amino acids O | H || —C— C—OH —N— R Structure: central carbon amino group carboxyl group (acid) R group (side chain) variable group confers unique chemical properties of the amino acid —N— H | —C— C—OH || O R AP Biology

Why are these nonpolar & hydrophobic? Nonpolar amino acids nonpolar & hydrophobic Why are these nonpolar & hydrophobic? AP Biology 2005-2006

Why are these polar & hydrophillic? Polar amino acids polar or charged & hydrophilic Why are these polar & hydrophillic? AP Biology 2005-2006

AP Biology 2005-2006

AP Biology 2005-2006

Sulfur containing amino acids Disulfide bridges cysteines form cross links AP Biology 2005-2006

Building proteins Peptide bonds: dehydration synthesis linking NH2 of 1 amino acid to COOH of another C–N bond 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 AP Biology 2005-2006

Building proteins Polypeptide chains N-terminal = NH2 end C-terminal = COOH end repeated sequence (N-C-C) is the polypeptide backbone grow in one direction AP Biology 2005-2006

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 AP Biology collagen 2005-2006

Protein structure & function function depends on structure all starts with the order of amino acids what determines that order of amino acids? Lysozyme Lysozyme protects us from the ever-present danger of bacterial infection. It is a small enzyme that attacks the protective cell walls of bacteria. Bacteria build a tough skin of carbohydrate chains, interlocked by short peptide strands, that braces their delicate membrane against the cell's high osmotic pressure. Lysozyme breaks these carbohydrate chains, destroying the structural integrity of the cell wall. The bacteria burst under their own internal pressure. Glycolytic enzymes Glucose powers cells throughout your body. Glucose is a convenient fuel molecule because it is stable and soluble, so it is easy to transport through the blood from places where it is stored to places where it is needed. Glucose is packed with chemical energy, ready for the taking. In a test tube, you can burn glucose, forming carbon dioxide and water and a lot of light and heat. Our cells also burn glucose, but they do it in many small, well-controlled steps, so that they can capture the energy in more useable forms, such as ATP (adenosine triphosphate). These ten enzymes control those small steps in the process of extracting energy from glucose. Glycolysis (sugar-breaking) is the first process in the cellular combustion of glucose. Glycolysis is endlessly fascinating. In these ten enzymes, you can find examples of many of the important molecular processes that animate our cells. They have been perfected by evolution to perform their diverse chemical tasks quickly and efficiently--adding, removing, and shifting atoms without making mistakes. The pathway is carefully regulated, so that glucose is only broken down when energy is needed Point out the active sites on each glycolytic enzym lysozyme: enzyme in tears & mucus that kills bacteria the 10 glycolytic enzymes used to breakdown glucose to make ATP AP Biology 2005-2006

Primary (1°) structure Order of amino acids in chain amino acid sequence determined by DNA slight change in amino acid sequence can affect protein’s structure & it’s function even just one amino acid change can make all the difference! Sickle cell anemia: 1 DNA letter changes 1 amino acid = serious disease Hemoglobin mutation: bends red blood cells out of shape & they clog your veins. AP Biology 2005-2006

Sickle cell anemia glutamic acid is acidic & polar valine is non-polar = tries to “hide” from water of cell by sticking to another hemoglobin molecules. AP Biology

Secondary (2°) structure “Local folding” Folding along short sections of polypeptide interaction between adjacent amino acids -helix -pleated sheet It’s a helix or B sheet within a single region. Can have both in one protein but a specific region is one or another AP Biology 2005-2006

Secondary (2°) structure The Alpha Helix AP Biology

Beta-Pleated Sheets

Representations of Protein Secondary Structure lysozyme

Tertiary (3°) structure “Whole molecule folding” determined by interactions between R groups hydrophobic interactions effect of water in cell anchored by disulfide bridges (H & ionic bonds) How the whole thing holds together AP Biology

Quaternary (4°) structure Joins together more than 1 polypeptide chain only then is it a functional protein collagen = skin & tendons Structure equals function wonderfully illustrated by proteins Collagen is just like rope -- enables your skin to be strong and flexible. hemoglobin AP Biology

Protein structure (review) R groups hydrophobic interactions, disulfide bridges 3° multiple polypeptides hydrophobic interactions sequence determines structure and… structure determines function. Change the sequence & that changes the structure which changes the function. 1° aa sequence peptide bonds 2° determined by DNA R groups H bonds 4° AP Biology 2005-2006

Chaperonin proteins Guide protein folding provide shelter for folding polypeptides keep the new protein segregated from cytoplasmic influences AP Biology 2005-2006

Protein models Protein structure visualized by X-ray crystallography extrapolating from amino acid sequence computer modelling lysozyme AP Biology

Denature a protein Disrupt 3° structure pH  salt temperature unravel or denature protein disrupts H bonds, ionic bonds & disulfide bridges Some proteins can return to their functional shape after denaturation, many cannot Example: Eggs: Cooking an egg permanently denatures the proteins. AP Biology 2005-2006

Let’s build some Insulin! AP Biology

The insulin protein has two chains, with a total of 53 amino acids AP Biology

The two chains are connected by disulfide bridges from cysteine molecules After you link together the primary sequence through dehydration synthesis, you can join the cysteines together!

Each side of the room will build an insulin molecule The abbreviations for the 20 amino acids are found in the table 

The amino acids are color coded by side group: non-polar, polar, acidic, and basic

Water molecules need to be removed by dehydration synthesis Join the amino acids together, then work on the cysteines (part of tertiary structure)

Ribosome Animations of Protein Synthesis Real Time Slo-mo Older – Gumby-Like Shows secondary structure of ribosome in action

Bonus Question (1st group to answer gets candy) Some of the 20 amino acids are missing from insulin – name them all!