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Proteins Multipurpose molecules AP Biology 2006-2007 Proteins AP Biology *^@% I look good! Proteins! AP Biology PROTEINS Elements •Carbon •Hydrogen •Oxygen •Nitrogen •sometimes Sulfur Monomer Amino Acid NH2 There are 20 different Other variable groups determine properties. AP Biology COOH amino acids found in nature. Some of which we cannot synthesize and must be eaten, Essential Amino Acids. PROTEINS Muscles Cell receptors Most hormones Enzymes Antibodies AP Biology PROTEINS • structure • cell communication • control chemical reaction rates • fight diseases AP Biology Proteins Most structurally & functionally diverse group of biomolecules Function: involved in almost everything AP Biology enzymes (pepsin, polymerase, etc.) structure (keratin, collagen) carriers & transport (membrane channels) receptors & binding (defense: antibodies) contraction (actin & myosin) signaling (hormones: insulin) storage (bean seed proteins) Proteins 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 hemoglobin AP Biology Rubisco growth hormones Amino acids Structure: central carbon amino group carboxyl group (acid) R group (side chain) variable group confers unique chemical properties of the amino acid AP Biology H O H | || —C— C—OH —N— | H R Nonpolar amino acids nonpolar & hydrophobic Why are these nonpolar & hydrophobic? AP Biology Polar amino acids polar or charged & hydrophilic AP Biology Why are these polar & hydrophillic? Ionizing in cellular waters AP Biology H+ donors Ionizing in cellular waters AP Biology H+ acceptors Sulfur containing amino acids Form disulfide bridges cross links betweens sulfurs in amino acids H-S – S-H You wondered why perms smelled like rotten eggs? AP Biology Building proteins Peptide bonds linking NH2 of one amino acid to COOH of another C–N bond dehydration synthesis AP Biology peptide bond Building proteins Polypeptide chains N-terminus = NH2 end C-terminus = COOH end repeated sequence (N-C-C) is the polypeptide backbone can only grow in one direction AP Biology Protein structure & function Function depends on structure 3-D structure twisted, folded, coiled into unique shape pepsin hemoglobin AP Biology collagen Primary (1°) structure Order of amino acids in chain amino acid sequence determined by gene (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! AP Biology lysozyme: enzyme in tears & mucus that kills bacteria Sickle cell anemia AP Biology Secondary (2°) structure “Local folding” folding along short sections of polypeptide interaction between adjacent amino acids H bonds between R groups -helix -pleated sheet AP Biology 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) AP Biology Tertiary structure results from interactions of side chains on amino acids. AP Biology Quaternary (4°) structure More than one polypeptide chain joined together only then is it a functional protein hydrophobic interactions collagen = skin & tendons AP Biology hemoglobin Protein structure (review) R groups hydrophobic interactions, disulfide bridges, van der Waals, hydrogen bonds 3° multiple polypeptides hydrophobic interactions 1° aa sequence peptide bonds determined by DNA AP Biology 2° R groups H bonds 4° Form Fits Function H A R E Protein Structure Give and example of each Globular AP Biology Fibrous Fibrous Protein: keratin AP Biology Alpha helix held by hbonds allows for stretching by breaking bonds (example wool) Beta sheets held by hbonds, resist pulling (example silk) Prions Killer: viruses, bacteria, fungi, protists….Proteins can cause a disease? AP Biology 2006-2007 What can cause rapidly progressive dementia, leading to memory loss, personality changes and hallucinations accompanied by physical problems such as speech impairment, jerky movements, balance and coordination dysfunction, changes in gait, rigid posture, and seizures? Creutzfeld-Jacob Syndrome in humans and Bovine Spongiform Encephalitis in cows. Mad Cow disease Bovine Spongiform Encephalopathy is a fatal, neurodegenerative disease in cattle, that causes a spongy degeneration in the brain and spinal cord. BSE has a long incubation period, about 4 years, usually affecting adult cattle at a peak age onset of four to five years, all breeds being equally susceptible Caused by feeding cattle remains of other cattle in the form of meat and bone meal. Spread to humans by consumption of contaminated meat. YUCK! Prion: It’s all about shape! The infectious agent in BSE is believed to be a specific type of misfolded protein called a prion. carry an allele which causes previously normal protein molecules to contort by themselves from an alpha helical arrangement to a beta pleated sheet This results in protein aggregates, which then form dense plaque fibers, leading to the microscopic appearance of "holes" in the brain, degeneration of physical and mental abilities, and ultimately death. Mad Human disease?? Cannibalism has also been implicated as a transmission mechanism for abnormal prions, causing the disease known as kuru, found primarily among women and children of the Fore tribe in Papua New Guinea. The women and children ceremonially ate the brains of the deceased and contracted Creutzfeldt-Jakob Syndrome from infected brain tissue. AP Biology Denature a protein Unfolding a protein disrupt 3° structure pH salt temperature In Biology, size doesn’t matter, SHAPE matters! unravels or denatures protein disrupts H bonds, ionic bonds & disulfide bridges destroys functionality Some proteins can return to their functional shape after denaturation, many cannot AP Biology Chaperonin proteins Guide protein folding AP Biology provide shelter for folding polypeptides keep the new protein segregated from cytoplasmic influences Protein models Protein structure visualized by X-ray crystallography extrapolating from amino acid sequence computer modeling lysozyme AP Biology Can 2 polypeptides have same amino acid sequence but different conformations? How? Various pH or temps would change H-bond Presence or absence of cofactors/coenzymes Collagen is in fibrous tissue of bone and blood vessels Vitamin C is coenzyme for proper folding Lack of vitamin C blocks modification of R-group causing scurvy! AP Biology Of course some people use extra collagen for cosmetic reasons! But it can go wrong Very wrong! Better keep eating lots of limes! AP Biology CATALYST CATALYST A ______________ is a chemical that ____________ SPEEDS UP chemical reactions WITHOUT being __________ CHANGED by that reaction. AP Biology ENZYMES are protein catalysts Enzymes decrease the activation energy AP Biology -Enzymes are reused many times before the body gets rid of them. How does it work? Variety of mechanisms to lower activation energy & speed up reaction synthesis active site orients substrates in correct position for reaction enzyme brings substrate closer together digestion active site binds substrate & puts stress on bonds that must be broken, making it easier to separate molecules AP Biology There are Most enzyme names end in –ase! OODLES of Enzymes!! Each ENZYME is specific to its SUBSTRATE. AP Biology Enzyme Vocab Enzyme: a protein catalyst that speeds up chemical reactions without being changed by that reaction. Active Site: groove/depression where binds Substrate: the molecule the enzyme is working on. Product: the molecule created by the enzyme. NOTE* enzymes can JOIN molecules or SPLIT them!! AP Biology Enzyme lock and key What determines active site? The folding of the polypeptide chains AP Biology Enzyme Activity Called the enzymesubstrate complex AP Biology Enzyme Action… again AP Biology Induced fit model: Active site is not rigid More accurate model of enzyme action AP Biology 3-D structure of enzyme fits substrate substrate binding cause enzyme to change shape leading to a tighter fit “conformational change” bring chemical groups in position to catalyze reaction Compounds which help enzymes Fe in Activators hemoglobin cofactors non-protein, small inorganic compounds & ions Mg, K, Ca, Zn, Fe, Cu bound within enzyme molecule coenzymes non-protein, organic molecules bind temporarily or permanently to enzyme near active site AP Biology many vitamins NAD (niacin; B3) FAD (riboflavin; B2) Coenzyme A Mg in chlorophyll Cooperativity Substrate acts as an activator substrate causes conformational change in enzyme induced fit favors binding of substrate at 2nd site makes enzyme more active & effective hemoglobin Hemoglobin 4 polypeptide chains can bind 4 O2; 1st O2 binds now easier for other O2 to bind AP3Biology Factors affecting Enzymes: TEMPERATURE & pH •too HIGH of a temperature or change in pH will denature enzymes • too LOW of a temperature will ONLY SLOW DOWN their function…NOT denature them! Denature: Extreme conditions can cause enzymes to denature, or change shape. Normal Denatured Based on what you know about enzyme function, how does this change of shape impact how enzymes work? Factors affecting Enzymes: 3.CONCENTRATION 1. IfOkay….now thereifare 10there pizzas to20 deliver and ONE delivery 4. 2. What there are 10 are pizzas pizzas to be and delivered 10 delivery (you 3.How What if there are 10 pizzas to be delivered and does this scenario relate to enzyme and guy…how fastthe do you get are your pizza (assuming you people? are last again) Can and delivery there people 5 delivery work any people faster? 10 deliveryconcentration? people? substrate are last on the list)? working? Factors affecting enzyme function Enzyme concentration as enzyme = reaction rate more enzymes = more frequently collide with substrate reaction rate levels off reaction rate substrate becomes limiting factor not all enzyme molecules can find substrate AP Biology enzyme concentration Factors affecting enzyme function Salt concentration changes in salinity adds or removes cations (+) & anions (–) disrupts bonds, disrupts 3D shape disrupts attractions between charged amino acids affect 2° & 3° structure denatures protein enzymes intolerant of extreme salinity Dead Sea is called dead for a reason! AP Biology Compounds which regulate enzymes Inhibitors molecules that reduce enzyme activity competitive inhibition noncompetitive inhibition irreversible inhibition feedback inhibition AP Biology Competitive Inhibitor Inhibitor & substrate “compete” for active site penicillin blocks enzyme bacteria use to build cell walls disulfiram (Antabuse) treats chronic alcoholism blocks enzyme that breaks down alcohol severe hangover & vomiting 5-10 minutes after drinking Overcome by increasing substrate concentration AP Biology saturate solution with substrate so it out-competes inhibitor for active site on enzyme Non-Competitive Inhibitor Inhibitor binds to site other than active site allosteric inhibitor binds to allosteric site causes enzyme to change shape conformational change active site is no longer functional binding site keeps enzyme inactive some anti-cancer drugs inhibit enzymes involved in DNA synthesis stop DNA production stop division of more cancer cells cyanide poisoning irreversible inhibitor of Cytochrome C, an enzyme in cellular respiration stops production of ATP AP Biology Allosteric Control: Second binding site causes change in enzyme’s active site, so no longer binds to intended substrate. AP Biology Irreversible inhibition Inhibitor permanently binds to enzyme competitor permanently binds to active site allosteric permanently binds to allosteric site permanently changes shape of enzyme nerve gas, sarin, many insecticides (malathion, parathion…) cholinesterase inhibitors AP Biology doesn’t breakdown the neurotransmitter, acetylcholine AP Biology Metabolic pathways ABCDEFG 5 6 enzyme enzyme enzyme enzyme enzyme enzyme enzyme 1 2 3 4 Chemical reactions of life are organized in pathways AP Biology divide chemical reaction into many small steps artifact of evolution efficiency intermediate branching points control = regulation Feedback Inhibition Regulation & coordination of production product is used by next step in pathway final product is inhibitor of earlier step allosteric inhibitor of earlier enzyme feedback inhibition no unnecessary accumulation of product ABCDEFG 1 2 3 4 5 6 X enzyme enzyme enzyme enzyme enzyme enzyme AP Biology allosteric inhibitor of enzyme 1 Efficiency Organized groups of enzymes enzymes are embedded in membrane and arranged sequentially Link endergonic & exergonic reactions Whoa! All that going on in those little mitochondria! AP Biology Packaging Enzymes (for convenience) is an Emergent Property, which one? “Life is organized along a hierarchy of structure.”