Presentation on theme: "Chapter 3-2 & 3-3 Biochemistry"— Presentation transcript:
1 Chapter 3-2 & 3-3 Biochemistry Carbon CompoundsOrganic compounds,Molecules of LifeMacromoleculesWhy do they matter? Because what goes on at this small scale which I might add has an entirely different set of rules from the large scale, has a huge impact. And with so many billions of atoms having to be in the right place in the right time it’s a miracle we manage to keep this bucket of bolts together. We’ll start small and work our way up.
2 ObjectivesDefine organic compound, name 3 elements commonly found in organic compoundsExplain why carbon forms so many different compoundsDefine functional group and explain its significanceCompare condensation reaction with hydrolysisDefine monosaccharide, disaccharide, polysaccharide & discuss their significanceRelate the sequence of amino acids to the structure of proteins.Relate the structure of lipids to their functionsList 2 essential functions of nucleic acids
3 Structural IsomersMolecular formulae are identical, but the structures and chemical properties are differentEthanol: Flammable; colorless; found in alcoholic beveragesEthyl ether is an anesthetic, and starting fluid for diesel enginesYou can get the most information from the structural, but it takes up space.
4 Metabolism All the chemical reactions of the body Catabolism Anabolism energy releasing (exergonic) decomposition reactionsAnabolismenergy releasing (endergonic) synthesis reactions
5 Organic Molecules Carbon compounds and functional groups carbohydrates lipidsproteinsnucleotides and nucleic acids
6 Organic Molecules: Carbon Bonds readily with other carbon atoms, hydrogen, oxygen, nitrogen, sulfurneeds 4 more valence electronsCan form rings or long carbon chains that serve as the backbone for organic moleculesWhat is it about carbon that makes it such a good element of compounds found in living things? What alternatives might there be? It’s shape, ability to bond to four things. It can make these great polymer’s that organize and store energy easily. Silicon: So there’s theory that Silicon based life exists
7 Functional Groups Groups of atoms attach to carbon backbone Determine the properties of organic molecules
8 Monomers and Polymers Monomers Polymers Polymerization subunits of macromoleculesDNA has 4 different monomers (nucleotides)proteins have 20 different monomers (amino acids)Polymersseries of monomers bonded togetherPolymerizationthe bonding of monomers together to form a polymercaused by a reaction called dehydration synthesisRemember your prefixes: Mono = 1, Poly = many What are some example words? Monotheism, Polytheism,
9 Dehydration Synthesis Monomers bond together to form a polymer (synthesis), with the removal of a water molecule (dehydration)
10 HydrolysisSplitting a polymer (lysis) by the addition of a water molecule (hydro)Digestion consists of hydrolysis reactionsThis reaction is thermodynamically irreversible, so the body uses it in many of its metabolic pathways, Its great for breaking up proteins.
11 Organic Molecules: Carbohydrates Hydrophilic organic moleculeGeneral formula(CH2O)n , n = number of carbon atomsfor glucose, n = 6, so formula is C6H12O6Names of carbohydratesword root sacchar- or the suffix -ose often usedmonosaccharide or glucoseThey’ll often going to end in OSE
12 Monosaccharides Three major monosaccharides Simplest carbohydrates General formula is C6H12O6structural isomersThree major monosaccharidesglucose, galactose and fructosemainly produced by digestion of complex carbohydrates
13 Disaccharides Pairs of monosaccharides Three major disaccharides sucroseglucose + fructoselactoseglucose + galactosemaltoseglucose + glucoseWhen fruits are frozen just a little the water comes out of them as ice leaving behind more of the sugar making them sweeter.
14 Polysaccharides Starch, cellulose and glycogen long chains of glucose form these polysaccharidesStarch produced by plants is digested by amylaseCellulose gives structure to plants, fiber to our dietCellulose is great because it is the most abundant biomolecule on the planet. Its in every blade of grass, and tree. And we can’t eat it. Certain microorganisms can, some animals like cows and termites have made a home for these microorganisms in their gut so they can eat grass. Imagine if you were the bioengineer who figured out how to enable people to get their energy from yard grass or trees, you’d solve world hunger.
15 PolysaccharidesGlycogen is an energy storage polysaccharide produced by animalsLiver cells synthesize glycogen after a meal to maintain blood glucose levelsWhen you have diabetes you can’t process this glycogen correctly. The assembly line backs up, the liver might get too much, and the blood too little.
16 Carbohydrate Functions Source of energyConjugated carbohydratesglycolipidsexternal surface of cell membraneglycoproteinsmucus of respiratory and digestive tractsproteoglycanscarbohydrate component dominantcell adhesion, gelatinous filler of tissues (eye) and lubricates joints
17 Organic Molecules: Lipids Hydrophobic organic moleculeLess oxidized than carbohydrates, have more calories per gramFive primary typesfatty acidstriglyceridesphospholipidseicosanoidssteroids
18 Fatty AcidsChain of usually 4 to 24 carbon atomsCarboxyl (acid) group on one end and a methyl group on the otherPolymers of two-carbon acetyl groups
19 Fatty AcidsSaturated fatty acid - carbon atoms saturated with hydrogenUnsaturated fatty acid - contains C=C bonds that could bond more hydrogen
20 Triglyceride Synthesis (1) Three fatty acids bonded to glycerol by dehydration synthesis
21 Triglyceride Synthesis (2) Triglycerides called neutral fatsfatty acids bond with their carboxyl ends, therefore no longer acidic
22 Triglycerides Hydrolysis of fats occurs by lipase enzyme Triglycerides at room temperatureliquid called oils, often polyunsaturated fats from plantssolid called fat, saturated fats from animalsFunction - energy storagealso insulation and shock absorption for organs
23 CholesterolAll steroids have this 4 ringed structure with variations in the functional groups and location of double bondsThe name originates from the Greek chole- (bile) and stereos (solid), as researchers first identified cholesterol in solid form in gallstones.
24 The good, the bad, and the cholesterol LDL: “Bad” cholesterolLow-density LipoproteinBuilds up as plaques in arteries. Causing Heart Attacks Hydrogenated oils & trans fatty acids are sourcesHDL: “Good” cholesterolHigh-density LipoproteinRemoves LDL cholesterol back to the liver
25 Phospholipids Amphiphilic character Hydrophobic “tails” similar to neutral fats with two fatty acids attached to glycerolHydrophilic “head” differs from neutral fat with the third fatty acid replaced with a phosphate group attached to other functional groups
27 Steroids Cholesterol other steroids derive from cholesterol cortisol, progesterone, estrogens, testosterone and bile acidsrequired for proper nervous system function and is an important component of cell membranesproduced only by animals85% naturally produced by our bodyonly 15% derived from our diet
29 Organic Molecules: Proteins Polymer of amino acids20 amino acidsidentical except for -R group attached to central carbonamino acid properties determined by -R groupThe amino acids in a protein determine its structure and function
30 Amino Acids Nonpolar -R groups are hydrophobic Polar -R groups are hydrophilicProteins contain many amino acids and are often amphiphilic
31 Peptides A polymer of 2 or more amino acids Named for the number of amino acids they containdipeptides have 2, tripeptides have 3oligopeptides have fewer than 10 to 15polypeptides have more than 15proteins have more than 100Dehydration synthesis creates a peptide bond that joins amino acids
33 Protein Structure Secondary structure Tertiary structure Primary structuredetermined by amino acid sequence (as the sequence of letters of our alphabet make up different words)Secondary structureα helix (coiled), β-pleated sheet (folded) shapes held together by hydrogen bonds between nearby groupsTertiary structureinteraction of large segments to each other and surrounding waterQuaternary structuretwo or more separate polypeptide chains interacting
38 Sickle Cell Caused by one different ammino acid in hemoglobin Genetic Pain in jointsNo cure at presentStrangely Sickle Cell raises resistance to Malaria
39 Protein Conformation and Denaturation Conformation - overall 3-D shape is crucial to functionimportant property of proteins is the ability to change their conformationopening and closing of cell membrane poresDenaturationdrastic conformational change that destroys protein functionas occurs with extreme heat or pHoften permanent
40 Protein Functions Structure Communication Membrane Transport Catalysis collagen, keratinCommunicationsome hormones, cell receptorsligand - molecule that reversibly binds to a proteinMembrane Transportform channels, carriers (for solute across membranes)Catalysisenzymes are proteinsRollie FingersRollie Fingers
41 Protein Functions 2 Recognition and protection Movement Cell adhesion glycoprotein antigens, antibodies and clotting proteinsMovementmuscle contractionCell adhesionproteins bind cells together
42 Enzymes Function as catalysts promote rapid reaction ratesSubstrate - the substance an enzyme acts uponNaming Conventionenzymes now named for their substrate with -ase as the suffixamylase enzyme digests starch (amylose)Lower activation energyenergy needed to get reaction started is loweredenzymes facilitate molecular interaction
44 Enzyme Structure and Action Active sitesarea on enzyme that attracts and binds a substrateEnzyme-substrate complextemporarily changes a substrates conformation, promoting reactions to occurReusability of enzymesenzymes are unchanged by reactions and repeat processEnzyme-substrate specificityactive site is specific for a particular substrateEffects of temperature and pHchange reaction rate by altering enzyme shapeoptimum: temp = body temp, pH = location of enzyme
46 Cofactors and Coenzymes nonprotein partners, (like iron, copper, zinc, magnesium or calcium ions) may bind to an enzyme and change its shape, creating an active sitemany enzymes cannot function without cofactorsCoenzymesorganic cofactors usually derive from water-soluble vitaminspantothenic acid in coenzyme A (required for synthesis of triglycerides and ATP), niacin in NAD+ and riboflavin (B2) in FAD (transfer electrons as H)
47 Coenzyme Action NAD+ involved in ATP synthesis transfers electrons and energyreview redox reactions next
48 Oxidation - Reduction Reactions molecule releases electrons and energy, often on hydrogen atomsReduction (negative e- reduces charge)molecule accepts electrons, gains chemical energy (E)AH NAD+ A NADHhigh E low E low E high Ereduced oxidized oxidized reducedstate state state state
49 Metabolic Pathways Chain of reactions, each catalyzed by an enzyme A B C DA is initial reactant, B+C are intermediates and D is the end product, , represent enzymesRegulation of metabolic pathwaysactivation or deactivation of the enzymes in a pathway regulates that pathwayend product D may inhibit or enzymescofactors
50 Organic Molecules: Nucleotides 3 principle componentsnitrogenous basesingle or double carbon-nitrogen ringsugar (monosaccharide)one or more phosphate groupsATP containsadenineribose3 phosphate groupsATP is the universal energy carrying molecule
51 ATPHigh energy bondssecond and third phosphate groups are attached by high energy covalent bondsphosphate groups are negatively charged and naturally repel each otherATPases hydrolyze the 3rd high energy phosphate bond of ATP producing ADP + Pi + energyKinases (phosphokinases)enzymes that phosphorylate (add the Pi released from ATP to) other enzymes or molecules to activate them
54 ATP Production - Glycolysis splits one 6 carbon glucose into two 3 carbon pyruvic acid moleculesyield 2 net ATP’s
55 ATP Production - Anaerobic Fermentation If no oxygen is available pyruvic acid is converted to lactic acid (build up causes muscle soreness)No ATP producedAllows glycolysis to start over (regenerates NAD+)
56 ATP Production - Aerobic Respiration If oxygen is available pyruvic acid is efficiently consumedyielding 36 more ATP molecules (from the original glucose)Aerobic respiration occurs in mitochondrion
58 Other Nucleotides Guanosine triphosphate (GTP) may donate a phosphate group (Pi) to other molecules or to ADPCyclic adenosine monophosphate (cAMP)formed after removal of both high energy Pi’safter chemical signal (first messenger) binds to cell surface, it triggers the conversion of ATP to cAMP (second messenger) to activate effects inside cellNucleic acids are polymers of nucleotides
60 Nucleic Acids DNA (deoxyribonucleic acid) RNA (ribonucleic acid) 100 million to 1 billion nucleotides longcontains the genetic code forcell division, sexual reproduction, the instructions for protein synthesisRNA (ribonucleic acid)3 forms of RNA range from 70 to 10,000 nucleotides longcarries out instructions given by DNAsynthesizes the proteins coded for by DNA
61 1. What is an organic compound? Carbon covalently bonded to carbon and other elements2. What property allows carbon compounds to exist in a number of forms?A carbon atom has 4 valence electrons so it can form 4 bonds with other atoms
62 Define functional group and give an example. Clusters of atoms that influence the moiety of the molecules they make up.4. How does a polymer form?Condensation reactions between monomers
63 5. How does a polymer break down? Hydrolysis6. Comparing the different forms of carbon in a substance allows you to tell how old it is. Is this more useful for organic substances or inorganic substances?
64 Define monosaccharide, disaccharide, polysaccharide Describe the structure of amino acids and proteinsExplain the relationship between an enzyme and its substrate
65 How are the ends of phospholipids different? Name 2 types of nucleic acids and describe their substancesHigh temperatures or changes can weaken bonds between different parts of a protein changing its shape. How might this change the effectiveness of an enzyme?